Download Consulta: repository:"17" Registros recuperados: 3.453 Máximo de

Consulta: repository:"17"
Registros recuperados: 3.453
Máximo de registros impressos: 2500
Data/hora: 09/06/2017 09:15:10
1. MIRIAM Identifiers and Resources / 2. Existing Identifier Schemes
Provedor de dados: 17
Autores: Nick Juty; Camille Laibe; Nicolas Le Novere.
(1) An overview of the MIRIAM identifier scheme is presented, together with a description of the supporting tools and resources
which allow its use as a robust cross-referencing framework.
(2) An overview of existing identifier schemes
within the life sciences is presented, describing the status of each scheme, the prerequisites that a user must meet to use them, and
their limitations.
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6154/version/1
*100 Semi-supercentenarians and older as a proposed sample set for the Archon Genomics X PRIZE
Validation Protocol*
Provedor de dados: 17
Autores: Thomas Perls; Nir Barzilai.
The
"Archon
Genomics
X
PRIZE
Validation
Protocol":http://precedings.nature.com/documents/5731/version/1 has been posted in part to solicit comments from the
scientific community. Here, we suggest 100 subjects age >=105 years as the source of DNAs for the
competition.

Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5756/version/1
11-amino-5-N-methyl-7-fluorine- quindoline derivatives: The Potential Anti-angiogenic Agents
Targeting G-quadruplex Structure in Vascular Endothelial Cell Growth Factor
Provedor de dados: 17
Autores: Tian-miao Ou; Yu-jing Lu; Xiao-dong Wang; Zeng-yun An; Yan-ping Li; Zhi-shu Huang; Lian-quan Gu.
Vascular endothelial growth factor (VEGF), a pluripotent cytokine and angiogenic growth factor, plays crucial roles in embryonic
development and tumour progression, and is over-expressed in many types of cancer and generally associated with tumour
progression and survival rate. The polypurine/polypyrimide sequence located upstream (-89 to -43) of the promoter region of the
human VEGF gene that can form specific G-quadruplex structures and raise the possibility for transcriptional control of the VEGF
gene by G-quadruplex ligands. In the present study, we investigated the interaction between the 5-N-methyl-7-fluorine-quindoline
derivatives (11-amino-5-N-methyl-7-fluorine- quindoline derivatives) and the G-rich sequence in VEGF's promoter
and the...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2008
URL: http://precedings.nature.com/documents/1946/version/1
11[beta]-hydroxysteroid dehydrogenase-type 2 evolved from an ancestral 17[beta]-hydroxysteroid
dehydrogenase-type 2
Provedor de dados: 17
Autores: Michael E. Baker.
11[beta]-hydroxysteroid dehydrogenase type-2 (11[beta]-HSD2) regulates the local concentration of cortisol that can activate the
glucocorticoid receptor and mineralocorticoid receptor, as well as the concentration of 11-keto-testosterone, the active androgen in
fish. Similarly, 17[beta]-HSD2 regulates the levels of testosterone and estradiol that activate the androgen receptor and estrogen
receptor, respectively. Interestingly, although human 11[beta]-HSD2 and 17[beta]-HSD2 act at different positions on different
steroids, these enzymes are paralogs. Despite the physiological importance of 11[beta]-HSD2 and 17[beta]-HSD2, details of
their origins and divergence from a common ancestor are not known. An opportunity to understand their evolution is...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4649/version/1
12x coverage 454/Sanger Hybrid Assembly of Cucumber (Cucumis sativus L. cv.Borszczagovski)
genome - the most efficient way to begin post genomic era
Provedor de dados: 17
Autores: Rafał Wóycicki; Justyna Witkowicz; Magdalena Pawełkowicz; Ewa Siedlecka;
Wojciech Gutman; Wojciech Pląder; Anna Seroczyńska; Mieczysław Śmiech;
Katarzyna Niemirowicz-Szczytt; Stanisław Karpiński; Stefan Malepszy; Zbigniew Przybecki.
New sequencing technologies make it possible to achieve genome sequence fast and cheap. Since the assembly step of such next
generation reads is still not well standardized it is the most cumbersome part of sequencing projects. 
We
present here approaches undertaken on the way to the draft assembly the cucumber (Cucumis sativus L. cv. Borszczagowski)
genome done with the use of 8x unpaired and 4x paired (3 Kbp) pyrosequenced 454 XLR Titanium reads, together BAC library
ends fragments (12,7x physical coverage). Two different assembly approaches, namely Celera and Celera/Arachne were finally
used. The Celera result was 15’196 contigs of 197 Mbp length and N50 27’086 bp and
4’157 scaffolds of 224 Mbp length...
Tipo: Poster
Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5466/version/1
14-3-3ζ is Amplified, Overexpressed and Possesses Oncogenic Activities in Head and
Neck Squamous Cell Carcinoma
Provedor de dados: 17
Autores: Mauting Lin; Carl D. Morrison; Susie Jones; Nehad Mohamed; Jason Bacher; Christoph Plass.
Gene amplification, a common mechanism for oncogene activation in cancers, has been used in the discovery of novel oncogenes.
DNA amplification is frequently observed in head and neck squamous cell carcinomas (HNSCCs) where numerous amplification
events and potential oncogenes have already been reported. Recently, we applied restriction landmark genome scanning (RLGS)
to study gene amplifications in HNSCC and located novel amplified and uncharacterized regions in primary tumor samples. DNA
amplification on 8q22.3, the location of 14-3-3[zeta] (YWHAZ, KCIP-1) is found in 30-40% HNSCC cases. Data obtained from
fluorescent in-situ hybridization (FISH) and immunohistochemistry on HNSCC tissue microarrays confirmed frequent low-level
14-3-3[zeta] copy number...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2008
URL: http://precedings.nature.com/documents/1953/version/1
16S rRNA based identification of _Aeromonas sp. kumar_ by constructing phylogenetic tree and
identification of regulatory elements from the harmful Red Tide bloom, Gulf of Mannar
Provedor de dados: 17
Autores: P. Kumar; C. M. Ramakritinan; A. K. Kumaraguru.
A bacterial strain, designated _Aeromonas sp. kumar_, was isolated from a water sample collected from Red tide Bloom occurred
in the region of Gulf of Mannar region, Puthumadam Coast, India and the strain was identified using 16S rRNA based
identification. During the sample collection, microbiology analysis was done to study the morphology of the bacteria. Pure culture
of strain was maintained through out the study. DNA was isolated and sequenced using 16S rRNA primers. A length of 1452
nucleotide was sequenced and was put in public data base for obtaining accession number. The sequence was studied using
MEGA 4, to estimate the evolutionary distances and to construct the Phylogenetic tree. Along with that Regulatory elements and
Transcription factors were...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3898/version/1
17 years of integrated research, monitoring, and management of HWA and hemlock ecosystems at
Delaware Water Gap National Recreation Area
Provedor de dados: 17
Autores: Richard Evans.
Delaware Water Gap National Recreation Area (“the park”) covers 28,000 ha along the Delaware
River in Pennsylvania and New Jersey. Eastern hemlock forests cover 2,200 ha (8%) of the park, and are often associated with
trout streams and scenic waterfalls. Activities like trout fishing, bird watching, and hiking are concentrated in hemlock forests, and
many of these areas are officially designated as “Outstanding Natural Features” having
“high intrinsic or unique values.” In 1989 hemlock woolly adelgid (HWA) was detected in the park,
and since 1993 the park has conducted a program to address the threats that hemlock woolly adelgid and hemlock decline poses to
park resources. This program...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/5520/version/1
1st INCF Workshop on Genetic Animal Models for Brain Diseases
Provedor de dados: 17
Autores: Olaf Riess; Holm Graessner.
The INCF Secretariat organized a workshop to focus on the “role of neuroinformatics in the processes of building,
evaluating, and using genetic animal models for brain diseases” in Stockholm, December 13–14,
2009. Eight scientists specialized in the fields of neuroinformatics, database, ontologies, and brain disease participated together
with two representatives of the National Institutes of Health and the European Union, as well as three observers of the national
INCF nodes of Norway, Poland, and the United Kingdom.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5909/version/1
1st INCF Workshop on Global Portal Services for Neuroscience
Provedor de dados: 17
Autores: Jaap van Pelt; Gordon Shepherd.
The goal of this meeting was to map out existing portal services for neuroscience, identify their features and future plans, and
outline opportunities for synergistic developments. The workshop discussed alternative formats of future global and integrated
portal services.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1779/version/1
1st INCF Workshop on Needs for Training in Neuroinformatics
Provedor de dados: 17
Autores: David Willshaw.
The INCF workshop on Needs for Training in Neuroinformatics was organized by the INCF National Node of the UK. The scope
of the workshop was to provide as overview of the current state of neuroinformatics training and recommendations for future
provision of training. The report presents a summary of the workshop discussions and recommendations to the INCF.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2563/version/1
1st INCF Workshop on Neuroanatomical Nomenclature and Taxonomy
Provedor de dados: 17
Autores: Mihail Bota; Larry Swanson.
The goal of this workshop was to agree on a general strategy for developing a systematic, useful, and scientifically appropriate
framework for neuroanatomical nomenclature. The workshop focused on general principles that will serve as a basis for future
decisions on implementation strategies. The report discusses the problems arising from the use of different parcellation schemes
and use of different terminologies and highlights the need of a universal vocabulary for describing the structural organization of
the nervous system. Workshop participants encourage the creation of an International Coordinating Committee for
Neuroanatomical Nomenclature and propose short- and long-term goals for such a committee.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/1780/version/1
1st INCF Workshop on NeuroImaging Database Integration
Provedor de dados: 17
Autores: Lars Forsberg; Per Roland.
The goal of this meeting was to map existing neuroimaging databases, particularly databases containing primary data, and to
identify mechanisms that could facilitate integrated use of such databases, including possible fusion of databases. The report
provides an overview of existing neuroimaging databases that were discussed during the workshop and examines the feasibility of
database federations. The report includes several recommendations for future developments.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/1781/version/1
1st INCF Workshop on Sustainability of Neuroscience Databases
Provedor de dados: 17
Autores: Jack Van Horn; Jaap van Pelt.
The goal of the workshop was to discuss issues related to the sustainability of neuroscience databases, identify problems and
propose solutions, and formulate recommendations to the INCF. The report summarizes the discussions of invited participants
from the neuroinformatics community as well as from other disciplines where sustainability issues have already been approached.
The recommendations for the INCF involve rating, ranking, and supporting database sustainability.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/1983/version/1
2011 German Escherichia coli O104:H4 outbreak: Alignment-free whole-genome phylogeny by
feature frequency profiles
Provedor de dados: 17
Autores: Man Kit Cheung; Lei Li; Wenyan Nong; Hoi Shan Kwan.
Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is
particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we
constructed a whole-genome phylogeny of 10 isolates from the current German E. coli outbreak against 30 existing E. coli
genomes as well as that of a historical EHEC isolate using the alignment-free feature frequency profile method. Our results
revealed a high similarity among E. coli isolates from the current outbreak and the historical EHEC being the most closely related
isolate sequenced thus far.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6109/version/2
2011 German Escherichia coli outbreak: Alignment-free whole-genome phylogeny by feature
frequency profiles
Provedor de dados: 17
Autores: Man Kit Cheung; Lei LI; Wenyan Nong; Hoi Shan Kwan.
Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is
particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we
constructed a whole-genome phylogeny of 9 E.coli isolates from the 2011 German outbreak against existing E. coli genomes
using the alignment-free feature frequency profile method. In addition, we looked for gene elements that distinguish the outbreak
group from the other E. coli strains and possibly accounted for the emergence of the outbreak isolates using the distinguishing
feature analysis.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6109/version/1
2011 German Escherichia coli outbreak: Prophage analysis of close-assembled TY2482 against 55989
using PHAST
Provedor de dados: 17
Autores: Man Kit Cheung; Lei LI; Wenyan Nong; Hoi Shan Kwan.
Using the Hiseq data of the German E. coli outbreak isolate TY2482, preliminary prophage analyses have been performed by
some researchers previously. With the closed assembly of the same isolate being available, another round of analysis might help
in resolving questions that remain unclear due to the incompleteness of the dataset.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6110/version/1
21 Tesla Micro-MRI of Rat Skin
Provedor de dados: 17
Autores: Rakesh Sharma; Suniket Fulzele; Kiran Shetty; Mandeep Sachdeva; Bruce R. Locke.
*Aim:* A rapid ultra high resolution ex vivo MRI imaging method was evaluated to visualize rat skin structure. The main
objectives were:1.qualitative assessment of viable epidermis, hair, oil and fat-rich skin features by multi-contrast
approach;2.achievement of spatial resolution up to 15 microns; 3.comparison of skin histology with MRI skin features obtained by
21 Tesla magnetic resonance imaging (MRI) imager. 

*Introduction:* The ultrawide
bore 900 MHz magnet has high resolution NMR magnet has a central field of 21.1 T. The high resolution MRI technique has
potential for both quantitative and non-invasive morphological evaluation at micrometer level. The MRI signal was sensitive to
water protons and glycolipid...
Tipo: Poster
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2639/version/1
21 Tesla MRI Microimaging of Rat Heart by Superparamagnetic Antimyoglobin Bound
Nanoparticles
Provedor de dados: 17
Autores: Rakesh Sharma.
Superparamagnetic iron-oxide bound antimyoglobin (SPIOM) characteristics were analyzed at different pH. After injecting
SPIOM in heart, ex vivo magnetic resonance microimaging (MRM) technique was used to visualize microvasculature of rat heart
including cardiac arteries, veins, cordate tendons attached with valves.
The measurement accuracy of ventricles, aorta,
vasculature and dimensions of cordate tendons were close to coregistered histology measurements.
Tipo: Poster
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/2643/version/2
21 Tesla MRI Microimaging of Rat Heart by Superparamagnetic Antimyoglobin Bound
Nanoparticles
Provedor de dados: 17
Autores: Rakesh Sharma.
Superparamagnetic iron-oxide bound antimyoglobin (SPIOM) characteristics were analyzed at different pH. After injecting
SPIOM in heart, ex vivo magnetic resonance microimaging (MRM) technique was used to visualize microvasculature of rat heart
including cardiac arteries, veins, cordate tendons attached with valves.
The measurement accuracy of ventricles, aorta,
vasculature and dimensions of cordate tendons were close to coregistered histology measurements.
Tipo: Poster
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2643/version/1
21 Tesla MRI Microscopy of Mice Kidney, Heart and Skin: Quantitation of MRI Visible Features
Provedor de dados: 17
Autores: S Sharma; Rakesh Sharma.
Excised mice kidney, heart and skin MRI visible features were quantitated using ex vivo 21 Tesla MRI microimager. The fast
MRI acquisition protocols of FLASH, gradient echo flow compensated (GEFC) techniques were used to visualize
microvasculature of mice kidney, mice heart including cardiac arteries, veins, cordate tendons and mice skin epidermis with hair
follicle features.
Tipo: Presentation
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3484/version/1
21 Tesla Rat Heart Magnetic Resonance Microimaging by Paramagnetic Anti-Troponin Bound
Polyethylene Based Iron-Oxide Nanoparticles and Image Processing
Provedor de dados: 17
Autores: Rakesh Sharma.
21T MR microimaging with the first use of troponin nanoparticles enhances the visualization of cardiac muscle fibers and offers
technical advancement for the future. Diffusion weighting offers fiber tracking and functional analysis. Image processing offers
heart
probabilistic
atlas
and
maps.

http://www.ismrm.org/10/program/ELECTRONICPOSTERS.htm
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6650/version/1
26Al/10Be Age of Peking Man
Provedor de dados: 17
Autores: Guanjun Shen; Xing Gao; Bin Gao; Darryl Granger.
The chronological position of Peking Man, or Homo erectus pekinensis, has long been pursued, but has remained problematic due
to lack of a suitable dating method^1-7^. Here we report cosmogenic ^26^Al/ ^10^Be burial dating of quartz sediments and
artifacts from the lower strata of Zhoukoudian Locality 1 where the remains of early members of the Peking Man family were
discovered. This study marks the first radioisotopic dating of any early hominin site in China beyond the range of mass
spectrometric U-series dating. The weighted mean of six meaningful measurements, 0.75 +/-; 0.09 (0.11) Ma (million years),
provides the best age estimate for lower cultural Layers ^7-10^. Together with previously reported U-series^3^ and
paleomagnetic^4^ data, as well as...
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2275/version/1
3D computer modeling in micropalaeontology – Late Paleozoic conodonts and
foraminifers as example
Provedor de dados: 17
Autores: Andrey V. Zhuravlev; Yadviga A. Vevel.
Three-dimension modeling of fossils is one of the branches of computer using in palaeontology. The branch has wide perspectives
but it is hardly developed, especially in micropalaeontology. Proposed method of 3D modelling of microfossils demands no
unique and expansive equipment and can be realized practically in any palaeontological laboratory. Lower accuracy of the models
developed is not critical for most the fields of their utilization: for teaching purposes, construction of illustrated databases and
virtual atlases, and for the display of microfossils to a general audience.
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1632/version/1
3D model of amphioxus steroid receptor complexed with estradiol
Provedor de dados: 17
Autores: Michael E. Baker; David J. Chang.
The origins of signaling by vertebrate steroids are not fully understood.
An important advance was the report that an
estrogen-binding steroid receptor [SR] is present in amphioxus, a basal chordate with a similar body plan as vertebrates. To
investigate the evolution of estrogen binding to steroid receptors, we constructed a 3D model of amphioxus SR complexed with
estradiol. This 3D model indicates that although the SR is activated by estradiol, some interactions between estradiol and human
ER[alpha] are not conserved in the SR, which can explain the low affinity of estradiol for the SR. These differences between the
SR and ER[alpha] in the steroid-binding domain are sufficient to suggest that another steroid is the physiological regulator of the
SR....
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3316/version/1
3D model of lamprey estrogen receptor with estradiol and 15[alpha]-hydroxy-estradiol
Provedor de dados: 17
Autores: Michael E. Baker; David J. Chang; Charlie Chandsawangbhuwana.
Lamprey, a basal vertebrate, contains orthologs of the estrogen receptor (ER), progesterone receptor and corticoid receptor. A
perplexing property of lamprey is that 15[alpha]-hydroxy-steroids are active steroids. For example, 15[alpha]-hydroxy-estradiol
[15[alpha]-OH-E2] is the estrogen, instead of estradiol (E2). To investigate how 15[alpha]-OH-E2 binds lamprey ER, we
constructed a 3D model of the lamprey ER with E2 and 15[alpha]-OH-E2. Our 3D model shows that S[delta] on Met-409 can
form a hydrogen bond with the 15[alpha]-hydroxyl on 15[alpha]-OH-E2. In human ER[alpha], the corresponding residue Ile-424
has a van der Waals contact with 15[alpha]-OH-E2. BLAST analysis of GenBank indicates that among vertebrate ERs, only
lamprey ER contains a...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2768/version/1
3D models of lamprey corticoid receptor complexed with 11-deoxycortisol and deoxycorticosterone
Provedor de dados: 17
Autores: Michael E. Baker; Kayla Y. Uh; Paiyuam Asnaashari.
The serum of Atlantic sea lamprey, a basal vertebrate, contains two corticosteroids, 11-deoxycortisol and deoxycorticosterone.
Only 11-deoxycortisol has high affinity [Kd~3 nM] for the corticoid receptor [CR] in lamprey gill cytosol. To investigate the
binding of 11-deoxycortisol to the CR, we constructed 3D models of lamprey CR complexed with 11-deoxycortisol and
deoxycorticosterone.
These 3D models reveal that Leu-220 and Met-299 in lamprey CR have contacts with the
17[alpha]-hydroxyl on 11-deoxycortisol. Lamprey CR is the ancestor of the mineralocorticoid receptor [MR] and glucocorticoid
receptor [GR]. Unlike human MR and human GR, the 3D model of lamprey CR finds a van der Waals contact between Cys-227
in helix 3 and Met-264 in helix 5. Mutant...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6216/version/1
3D Structure Development of Chikungunya Virus and its Structural Characterization –
an In silico approach
Provedor de dados: 17
Autores: Anuraj Nayarisseri; Mukesh Yadav; Dowlathabad Muralidhara Rao; Sonam Kukreja; Sheaza Ahmed; Pooja Singh.
The 3 Dimensional structure of a protein is an expedient for structure based drug design and identifying the conformational
epitopes that are foremost for designing the vaccines. Chikungunya (CHIKV) is a heat sensitive RNA virus which causes a viral
disease which is transmitted in humans by human-mosquito-human transmission. Disease mostly found in the tropic and
subtropical countries mainly in South India and in few other Asian countries. The primary transmission agents of Chikungunya
Virus are yellow fever mosquito (_Aedes aegypti_) and forest day mosquito (_Aedes albopictus_). The forest day mosquito bites
during day time and hence day time mosquito bite is the main reason for transmission. The main distinctive of the disease is a
fever along with an...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5143/version/1
3DScape: three dimensional visualization plug-in for Cytoscape
Provedor de dados: 17
Autores: Qi Wang.
3DScape is the first plug-in which enables three-
dimensional network visualization in Cytoscape. The extra
dimension is useful in accommodating, visualizing, and distinguishing larger networks with multiple crossing
connections.
Special features in 3DScape include 3D layout algorithms, mapping onto 3D models and
animation effects on a series of expression data. 3DScape is available at http://www.rendware.com
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6094/version/1
9aaTAD Prediction result (2006)
Provedor de dados: 17
Autores: Martin Piskacek.
Recently reported, 9aaTAD transcription factors p53, VP16, MLL/ALL, E2A, HSF1, NF-IL6, NFAT1 and NF-kB interact directly
with the general coactivator CBP/p300 aside from already referred TAF9. All four domains of CBP/p300 - KIX, TAZ1, TAZ2 and
IBiD provide multiple interactions with 9aaTADs, e.g. p53. Annotation of predicted 9aa TAD using Pattern search ScanProsite on
ExPASy and relevant experimental data are listed.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3984/version/1
9aaTADs mimic DNA to interact with a pseudo-DNA Binding Domain KIX of Med15 (Molecular
Chameleons)
Provedor de dados: 17
Autores: martin piskacek.
The KIX-domain of Gal11/MED15 was shown to interact with short transactivation domain of Pdr1 and Oaf1 (12 and 9 amino
acids respectively) annotated to 9aaTAD family. Reported NMR data revealed a surprising sequence similarity of KIX domain
and basic-leucine zipper (bZIP).
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3939/version/1
A Bacterial Enzyme Catalyzing Double Reduction of a β,δ-Diketo Ester with
Unprecedented Stereoselectivity
Provedor de dados: 17
Autores: Xuri Wu; Nan Liu; Yunmian He; Yijun Chen.
Various ketoreductases exclusively participate in all common biological events, and they are a class of important biocatalysts for
the production of chiral alcohols. While many types of ketoreductase have been extensively studied and their functions, properties
and utilities have been well known, the capability of stereoselectively reducing two carbonyl groups in the same diketohexanoate
ester molecule to form a dihydroxy product by a single ketoreductase has not been evidently characterized. Here we show that a
unique and novel enzyme, diketoreductase, was cloned from Acinetobacter baylyi, heterogeneously expressed in _Escherichia
coli_ and purified to homogeneity. The diketoreductase is up to 78% homologous to bacterial 3-hydroxyacyl coenzyme-A...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/1697/version/1
A Bacterial Enzyme Catalyzing Double Reduction of a β,δ-Diketo Ester with
Unprecedented Stereoselectivity
Provedor de dados: 17
Autores: Xuri Wu; Nan Liu; Yunmian He; Yijun Chen.
Various ketoreductases exclusively participate in all common biological events, and they are a class of important biocatalysts for
the production of chiral alcohols. While many types of ketoreductase have been extensively studied and their functions, properties
and utilities have been well known, the capability of stereoselectively reducing two carbonyl groups in the same diketohexanoate
ester molecule to form a dihydroxy product by a single ketoreductase has not been evidently characterized. Here we show that a
unique and novel enzyme, diketoreductase, was cloned from Acinetobacter baylyi, heterogeneously expressed in _Escherichia
coli_ and purified to homogeneity. The diketoreductase is up to 78% homologous to bacterial 3-hydroxyacyl coenzyme-A...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/1697/version/2
A Bayesian Framework for Parameter Estimation in Dynamical Models with Applications to
Forecasting
Provedor de dados: 17
Autores: Flávio Codeço Coelho; Claudia T. Codeço.
Mathematical models in Biology are powerful tools for the study and exploration of complex dynamics. Nevertheless, bringing
theoretical results to an agreement with experimental observations involves acknowledging a great deal of uncertainty intrinsic to
our theoretical representation of a real system.
Proper handling of such uncertainties, is key to the successful
usage of models to predict experimental or field observations. This problem has been addressed over the years by
many tools for model calibration an parameter estimation. In this article we present a general framework for uncertainty analysis
and parameter estimation which is designed to handle uncertainties associated with the modeling of dynamic biological systems...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4044/version/1
A Bayesian Hierarchical Model to Derive Novel Gene Networks from Gene Ontology Fingerprints
Provedor de dados: 17
Autores: Tingting Qin; Lam Tsoi; Andrew Lawson; Jim Zheng.
We developed a Bayesian hierarchical model to identify gene networks based on the similarity score generated from comparing
the gene ontology fingerprints of gene pairs. Genes in this network were assumed to have similar biological functions that can be
indicated by their ontology fingerprints. Our results indicate that different pathways show consistent score threshold that allow us
to distinguish biological relevant gene—gene connections in the network.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3511/version/1
A bestiary of non-linear functions for growth analysis
Provedor de dados: 17
Autores: C. E. Timothy Paine; Toby Marthews; Deborah Vogt; Drew Purves; Mark Rees; Andy Hector; Lindsay Turnbull.
Plant growth is an essential ecological process, integrating across scales from physiology to community dynamics. Predicting the
growth of plants is essential to understand a wide range of ecological issues, including competition, plant-herbivore interactions
and ecosystem functioning.
A challenge in modeling plant growth is that growth rates almost universally
decrease with increasing size, for a variety of reasons. Traditional analyses of growth are hampered by the need to remain within
the structures of linear models, which handle this slowing poorly. We demonstrate the implementation of a variety of non-linear
models that are more appropriate for modeling plant growth than are the traditional, linear,...
Tipo: Presentation
Palavras-chave: Ecology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5257/version/1
A Biomimetic Model of the Outer Plexiform Layer by Incorporating Memristive Devices
Provedor de dados: 17
Autores: Andras Gelencser; Themistoklis Prodromakis; Christofer Toumazou; Tamas Roska.
In this paper we present a biorealistic model for the first part of the early vision processing by incorporating memristive
nanodevices. The architecture of the proposed network is based on the organisation and functioning of the outer plexiform layer
(OPL) in the vertebrate retina. We demonstrate that memristive devices are indeed a valuable building block for neuromorphic
architectures, as their highly non-linear and adaptive response could be exploited for establishing ultra-dense networks with
similar dynamics to their biological counterparts. We particularly show that hexagonal memristive grids can be employed for
faithfully emulating the smoothing-effect occurring at the OPL for enhancing the dynamic range of the system. In addition, we
employ a...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6664/version/1
A bizarre Jurassic maniraptoran from China with elongate ribbon-like feathers
Provedor de dados: 17
Autores: Fucheng Zhang; Zhonghe Zhou; Xing Xu; Xiaolin Wang; Corwin Sullivan.
Recent coelurosaurian discoveries have greatly enriched our knowledge of the dinosaur-bird transition, but all reported taxa close
to this transition are from relatively well-known coelurosaurian groups^1-3^. Here we report a new basal avialan, Epidexipteryx
hui gen. et sp. nov., from the Middle-Late Jurassic of Inner Mongolia, China. This new species is characterized by an unexpected
combination of characters seen in several different theropod groups, particularly the Oviraptorosauria. Phylogenetic analysis
shows it to be the sister taxon to Epidendrosaurus^4,5^, forming a new clade at the base of Avialae^6^. Epidexipteryx also
possesses two pairs of elongate ribbon-like tail feathers (ETFs), and its limbs lack contour feathers for flight. This finding...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2326/version/1
A call for disruptive innovation in science publishing with a new open data-sharing platform for the
life sciences
Provedor de dados: 17
Autores: Donald C. Cooper.
“A disruptive innovation is an innovation that helps create a new market and value network, and eventually goes on
to disrupt an existing market and value network (over a few years or decades), displacing an earlier technology. The term is used
in business and technology literature to describe innovations that improve a product or service in ways that the market does not
expect.”
-Wikipedia
On
April
3rd,
2012
Nature
Precedings,
Nature
Publishing
Group’s experiment in free pre-print publishing was shut down and no longer accepts submissions. According to the
Nature Precedings website it was created in 2007 as “a place for researchers to share documents, including
presentations, posters, white...
Tipo: Manuscript
Palavras-chave: Biotechnology; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7151/version/1
A Case For Killing Humpback Whales?
Provedor de dados: 17
Autores: Nicholas J. Gales; Phillip J. Clapham; C. Scott Baker.
During the austral summer of 2007/08, hunting of Southern Hemisphere (SH) humpback whales will recommence after almost
half a century of protection. The stated rationale for this hunt, by the Government of Japan (GoJ), is to gather important scientific
information for use in management. If the scientific need were defensible, and the proponents had accommodated reasonable
conservation concerns, then criticisms of the hunt would be limited to philosophical issues. This is not the case. The
program’s research objectives are unlikely to be achieved by lethal methods and do not address the principal
research needs for SH humpback whales identified by the International Whaling Commission (IWC).
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/1313/version/1
A century of warfare shoots holes in anti-Caulerpa campaign
Provedor de dados: 17
Autores: John R. M. Chisholm; Pavel P. Povinec; Valerie Briet; Janine Gastaud; Jean M. Jaubert; Sang-Han Lee; Isabelle
Levy-Palomo; Manuel Marchioretti; Audrey Minghelli-Roman.
Effort to have all varieties of the marine alga Caulerpa taxifolia listed as noxious weeds hinges on the argument that the
alga's proliferation in the Mediterranean Sea is a cause and not a consequence of environmental degradation. Until
now, the occurrence of two populations in a pristine part of the northern Mediterranean near the island of Porquerolles has upheld
this claim. Here we show that the alga's development at Porquerolles is indeed a consequence of environmental
degradation caused by military weapons' impacts on seagrass beds during the last century. The available data show
that substratum enrichment plays a key role in fostering development of Caulerpa, irrespective of whether this results directly
from pollution or...
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/1240/version/1
A common subcortical oscillatory network contributes to recovery after spinal cord injury
Provedor de dados: 17
Autores: Yukio Nishimura; Yosuke Morichika; Tadashi Isa.
Recent studies in monkeys showed that when the direct cortico-motoneuronal connection was transected at mid-cervical segments,
remaining, indirect cortico-motoneuronal pathways compensated for finger dexterity within one to three months. To elucidate the
changes in dynamic properties of neural circuits during the recovery, we investigated the cortico-muscular and inter-muscular
couplings of activities throughout the recovery course. Activities of antagonist muscle pairs showed co-activation during the
second postoperative week, and oscillated coherently at frequencies of 30-46 Hz (gamma-band) by one month postoperatively.
Such gamma-band inter-muscular coherence was not observed preoperatively, but became prominent and distributed widely over
proximal and...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1937/version/1
A community of biocurators
Provedor de dados: 17
Autores: Pascale Gaudet.
Biocuration is a difficult mission: biological data is highly heterogeneous, and there are few areas where guidelines for data
preservation and exchange exist. This has hampered the speed, quantity and diversity of data possible to capture. Hence, a major
challenge for the biocuration community is to explore innovative ways to capture, represent and display information. It is also
essential to increase the involvement of researchers, publishers and funding agencies in this process. I will discuss the work of the
International Society for Biocuration to build a community of biocurators to achieve these goals.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5134/version/1
A comparative analysis of 21 literature search engines
Provedor de dados: 17
Autores: Kshitish K. Acharya; Greta Kasliwal; Haritha Haridas.
With increasing number of bibliographic software, scientists and health professionals either make a subjective choice of tool(s)
that could suit their needs or face a challenge of analyzing multiple features of a plethora of search programs. There is an urgent
need for a thorough comparative analysis of the available bio-literature scanning tools, from the user’s perspective.
We report results of the first time semi-quantitative comparison of 21 programs, which can search published (partial or full text)
documents in life science areas. The observations can assist life science researchers and medical professionals to make an
informed selection among the programs, depending on their search objectives. 
Some of the important...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2101/version/1
A comparative assessment of octanol-water partitioning and distribution constant estimation methods
for perfluoroalkyl carboxylates and sulfonates
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
New experimental data is available in the literature regarding the octanol-water distribution behavior of representative straight
chain perfluoroalkyl carboxylate (PFCA) and sulfonate (PFSA) congeners. The current study provides the first investigation into
the predictive ability of various software programs for estimating the corresponding octanol-water partitioning (log P) and
distribution (log D) constants of PFCAs and PFSAs. Wide predictive variation was found within and between the various
methods. Several programs were able to accurately estimate the log P/D fragmental contributions of a -CF~2~- group for PFCAs,
as well as the associated Gibbs free energies for partitioning into octanol from water due to the hydrophobic character of the...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3282/version/2
A comparative assessment of octanol-water partitioning and distribution constant estimation methods
for perfluoroalkyl carboxylates and sulfonates
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
New experimental data is available in the literature regarding the octanol-water distribution behavior of representative straight
chain perfluoroalkyl carboxylate (PFCA) and sulfonate (PFSA) congeners. The current study provides the first investigation into
the predictive ability of various software programs for estimating the corresponding octanol-water partitioning (log P) and
distribution (log D) constants of PFCAs and PFSAs. Wide predictive variation was found within and between the various
methods. Several programs were able to accurately estimate the log P/D fragmental contributions of a -CF~2~- group for PFCAs,
as well as the associated Gibbs free energies for partitioning into octanol from water due to the hydrophobic character of the...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3282/version/1
A Comparative Study of the Magnitude, Frequency and Distribution of Intense Rainfall in the United
Kingdom
Provedor de dados: 17
Autores: John C. Rodda; Max A. Little; Harvey J. E. Rodda; Patrick E. McSharry.
During the 1960s, a study was made of the magnitude, frequency and distribution of intense rainfall over the UK, employing data
from more than 120 daily-read rain gauges covering the period 1911 to 1960. Using the same methodology, that study was
recently updated utilizing data for the period 1961 to 2006 for the same gauges, or from those nearby. This paper describes the
techniques applied to ensure consistency of data and statistical modelling. It presents a comparison of patterns of extreme rainfalls
for the two periods and discusses the changes that have taken place. Most noticeably, increases up to 20% have occurred in the
north west of the country and in parts of East Anglia. There have also been changes in other areas, including decreases of the...
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3847/version/1
A comparative study on the production of ethanol from lignocellulosic biomass by chemical and
biological method
Provedor de dados: 17
Autores: Shaheed SM; Rohit JP; Madhan R; Selvakumar K.
Ethanol derived from non-edible biomass is renewable and a clean source of energy. It is independent of the food industry and it is
economically feasible. The first generation biofuel or bioethanol is still not a very convenient source of energy as it prominently
depends on the availability of grains. The main objective of this work is to develop an industrious efficient process to produce
ethanol from lignocellulosic biomasses like wood and leaf in a lab scale. Two processes were compared. The first process
involved an alkaline pre-treatment of the powdered biomass followed by dilute acid hydrolysis. The second process involved an
alkaline treatment followed by direct hydrolysis of the biomass by use of a fungal species obtained from rotting wood....
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/6579/version/1
A conceptual framework for the evolutionary selection of biologically
'essential' elements
Provedor de dados: 17
Autores: Mark Conyers.
Standard texts dutifully list 16 essential elements for plant growth, yet the literature indicates that the boundary between essential
and nonessential nutrients for plants is not always clear. When animals and 'lower' organisms are
considered, the team of 16 is considerably expanded and the notion of essentiality is blurred. Why are some elements more
important than others to plants and to organisms in general? Here I propose three criteria by which elements might have been
selected in the development of organisms: low atomic weight, at least modest abundance, and ease of assembly into complex
structures. Assembly of the structural elements C, N, S, P, and O is based on valency and ionic potential. The selection of
monovalent elements...
Tipo: Manuscript
Palavras-chave: Earth & Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3223/version/1
A condition of cooperation. Games on network
Provedor de dados: 17
Autores: Tomohiko Konno.
Natural selection is often regarded as a result of severe competition. Defect seems beneficial for a single individual in many
cases.However, cooperation is observed in many levels of biological systems ranging from single cells to animals, including
human society. We have yet known that in unstructured populations, evolution favors defectors over cooperators. On the other
hand, there have been much interest on evolutionary games^1,2^ on structured population and on graphs^3-16^. Structures of
biological systems and societies of animals can be taken as networks. They discover that network structures determine results of
the games. Together with the recent interest of complex networks^17,18^, many researchers investigate real network structures.
Recently...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3028/version/1
A coordinated phosphorylation cascade initiated by MSK1 directs RAR alpha recruitment to target
gene promoters
Provedor de dados: 17
Autores: Nathalie Bruck; Dominique Vitoux; Christine Ferry; Vanessa Duong; Annie Bauer; Hughes de The; Cecile
Rochette-Egly.
The nuclear retinoic acid (RA) receptor alpha (RARα) is a transcriptional transregulator that controls the expression
of specific gene subsets through binding at response elements and dynamic interactions with coregulators, which are coordinated
by the ligand. Here, we highlighted a novel paradigm in which the transcription of RARα-target genes is controlled
by phosphorylation cascades initiated by the rapid RA activation of the p38MAPK/MSK1 pathway. We demonstrate that MSK1
phosphorylates RARα at S369 located in the Ligand Binding Domain, allowing the binding of TFIIH and thereby
phosphorylation of the N-terminal domain at S77 by cdk7/cyclin H. MSK1 also phosphorylates Histone H3 at S10. Finally, the
phosphorylation cascade...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2107/version/1
A Critical Evaluation of Clinical Trials in Cancer and Pharmacogenomics
Provedor de dados: 17
Autores: I. C. Baianu.
A critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view
to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer
trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell
genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is
rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and
computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Immunology;
Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7052/version/1
A Database for TSSs of Human MicroRNAs
Provedor de dados: 17
Autores: Malay Bhattacharyya; Sanghamitra Bandyopadhyay.
MicroRNAs (miRNAs) are small endogeneous non-coding RNAs of about 22nt length. These short RNAs regulate the expression
of mRNAs by hybridizing with their 3'-UTRs or by translational repression. They have been shown to take crucial
roles in many biological processes. Many of the current studies are focused over how mature miRNAs regulate mRNAs, even
though there is very limited knowledge about their transcriptional loci. Primary miRNAs (pri-miRs) are first transcribed from the
DNA, followed by the formation of precursor miRNA (pre-miR) by endonucleases activity, which finally produces mature
miRNAs. Unfortunately, the identification of the loci of pri-miRs, and the associated information about transcription start sites
(TSSs) and promoters is...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6832/version/1
A database of naturally occurring human urinary peptides and proteins for use in clinical
applications
Provedor de dados: 17
Autores: Petra Zürbig; Joshua Coon; Hartwig Bauer; Georg Behrens; Mohammed Dakna; Anna Dominiczak; Stephane
Decramer; Jochen Ehrich; Danilo Fliser; Moritz Frommberger; Arnold Ganser; Mark Giolami; Igor Golovko; David Good;
Wilfried Gwinner; Marion Haubitz; Stefan Herget-Rosenthal; Holger Jahn; George Jerums; Bruce Julian; Markus Kellmann;
Volker Kliem; Walter Kolch; Andrzej Krolewski; Mario Luppi; Ziad Massy; Michael Melter; Christian Neusüss; Jan
Novak; Karlheinz Peter; Kasper Rossing; Harald Rupprecht; Joost Schanstra; Eric Schiffer; Jens-Uwe Stolzenburg; Lise Tarnow;
Dan Theodorescu; Visith Thongboonkerd; Raymond Vanholder; Eva Weissinger; Harald Mischak; Philippe Schmitt-Kopplin.
Owing to its availability, ease of collection and correlation with (patho-) physiology, urine is an attractive source for clinical
proteomics. However, the lack of comparable datasets from large cohorts has greatly hindered development in this field. Here we
report the establishment of a high resolution proteome database of naturally occurring human urinary peptides and proteins ranging from 800-17,000 Da - from over 3,600 individual samples using capillary electrophoresis coupled to mass spectrometry,
yielding an average of 1,500 peptides per sample. All processed data were deposited in an SQL database, currently containing
5,010 relevant unique urinary peptides that serve as classifiers for diagnosis and monitoring of diseases, including kidney and...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2007
URL: http://precedings.nature.com/documents/1219/version/1
A database of orthologous exons in primates for comparative analysis of RNA-seq data
Provedor de dados: 17
Autores: Ran Blekhman.
RNA-seq technology facilitates the study of gene expression at the level of individual exons and transcripts. Moreover, RNA-seq
enables unbiased comparative analysis of expression levels across species. Such analyses typically start by mapping sequenced
reads to the appropriate reference genome before comparing expression levels across species. However, this comparison requires
prior knowledge of orthology at the exon level. With this in mind, I constructed a database of orthologous exons across three
primate species (human, chimpanzee, and rhesus macaque). The database facilitates cross-species comparative analysis of exonand transcript-level regulation. A web application allowing for an easy database query: http://giladlab.uchicago.edu/orthoExon/
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7054/version/1
A decline in pollinator dependent vegetable crop productivity in India indicates pollination limitation
and consequent agro-economic crises.
Provedor de dados: 17
Autores: Parthiba Basu; Ritam Bhattacharya; Pietro Ianetta.
Approximately 70% of the tropical crop species depend on pollinators for optimum yields (Roubik, 1995, Klein 2007). The
economic value of such pollinated crops to India is $726 million and India is the world's second largest vegetable
producer (Sidhu, 2005). This status has been underpinned by large-scale changes in land-use and pesticide dependency (Fazal,
2000; Shaw & Satish, 2007). A method (c.f. Aizen et al. 2008) that partitions crops into categories depending on their
relative pollinator dependence (Index of pollinator dependence, DI) was applied to analysis of vegetable yields for India over 45
years (1963-2008) using FAO data. This has revealed that since 1993, relative yields of crop production has either flattened or
declined,...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6044/version/1
A Discrete State Model for Kinesin-1 with Rate Constants Modulated by Neck Linker Tension
Provedor de dados: 17
Autores: Steven J. Koch; Lawrence J. Herskowitz.
Kinesin-1 is a homodimeric molecular motor protein that uses ATP and a hand-over-hand motion to transport cargo along
microtubules. How kinesin converts chemical energy into directed motion is a question that has been actively studied since its
discovery. Even at the most coarse-grained level of chemical kinetics, understanding is still lacking. Minimal kinetic models are
often developed to both explain kinesin’s hand-over-hand forward-stepping behavior and to infer important kinetic
rate constants from experimental data. These minimal models are often limited to a handful of two-headed states on a core cycle
and have been essential for the current level of understanding. However, it is not always clear how to evolve these core-cycle
models to...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5038/version/1
A Draft Sequence of the Puerto Rican Parrot Genome (Amazona vittata) – a Genome
Project funded by a Local Community Effort
Provedor de dados: 17
Autores: Taras K. Oleksyk.
The genome of the Puerto Rican parrot (Amazona vittata) has been sequenced and assembled in an international collaboration
supported by many individual donations from the people of Puerto Rico. This is a critically endangered endemic bird, the only
surviving native parrot species in the territory of the United States, and the first parrot belonging to the large genus Amazona to
have its genome sequenced and assembled. A genome of one A. vittata female was sequenced resulting in a total of almost 42.5
billion nucleotide bases equivalent to 26.89X average coverage depth. After filtering out the short fragments (<500bp),
the assembly resulted in 259,423 short fragment library contigs, half of them (N50) of at least 6,983 bp in length, with a...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6552/version/1
A Drosophila systems model of withdrawal from chronic pentylenetetrazole relevant in
post-epileptogenesis
Provedor de dados: 17
Autores: Priyanka Singh; Farhan Mohammad; Abhay Sharma.
Rodent kindling induced by pentylenetetrazole (PTZ) is an established model of epileptogenesis and antiepileptic drug (AED)
testing. Recently, a Drosophila systems model has been described in which chronic PTZ causes a decreased climbing speed in
adult males on 7th day. Some AEDs ameliorate development of this locomotor deficit. Time-series of microarray expression
profiles of heads of flies treated with PTZ has been found to resemble transcriptomic alterations associated with epileptogenesis.
In the fly model, withdrawal from seven day long PTZ treatment causes an increased climbing speed on 7th consequent day. Here,
we present a systems model of the post-PTZ withdrawal regime. Unlike AED-untreated individuals, flies treated with any of the
five AEDs...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3447/version/1
A dynamical model of genetic networks describes cell differentiation
Provedor de dados: 17
Autores: Roberto Serra; Villani Marco; Alessia Barbieri.
Cell differentiation is a complex phenomenon whereby a stem cell becomes progressively more specialized and eventually gives
rise to a specific cell type. Differentiation can be either stochastic or, when appropriate signals are present, it can be driven to take
a specific route. Induced pluripotency has also been recently obtained by overexpressing some genes in a differentiated cell. Here
we show that a stochastic dynamical model of genetic networks can satisfactorily describe all these important features of
differentiation, and others. The model is based on the emergent properties of generic genetic networks, it does not refer to specific
control circuits and it can therefore hold for a wide class of lineages. The model points to a peculiar role of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4741/version/1
A few remarks on the relationship between visuo-spatial attention deficits and dyslexia
Provedor de dados: 17
Autores: John Skoyles; Bernt C. Skottun.
Dyslexia and attentional problems are often comorbid. This raises the question whether reading deficits might etiologically follow
from attentional difficulties, a hypothesis that has been proposed in regard to visuo-spatial attention deficits. This visuo-spatial
attention deficit hypothesis would predict that attention deficits should be specific to dyslexia. However, it is here estimated that
at the population level there are more non-dyslexic individuals than dyslexic individuals with visuo-spatial attention deficits. The
reason for this is that in the overall population level there are far more individuals without dyslexia than with dyslexia. Thus, a
relatively modest percentage presence of attention problems in the non-dyslexic population can result...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5525/version/1
A Formal Ontology of Sequences
Provedor de dados: 17
Autores: Robert Hoehndorf; Janet Kelso; Heinrich Herre.
The Sequence Ontology is an OBO Foundry ontology that provides categories of sequences and sequence features that are applied
to the annotation of genomes. To facilitate interoperability with other domain ontologies and to provide a foundation for
automated inference, we provide here an axiom system for the Sequence and Junction categories in first- and second-order
predicate logics.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3537/version/1
A Framework for BioCuration Workflows (part II)
Provedor de dados: 17
Autores: Martin Krallinger.
This is the second part of the talk ‘A Framework for BioCuration Workflows’, given by Martin
Krallinger from the Spanish National Cancer Research Centre at the 'Text Mining for the BioCuration
Workflow' workshop. The first part was held by Gully APC Burns (USC Information Sciences Institute, USA). This
presentation covered some of the main general tasks often shared by existing literature biocuration workflows: Identification of
relevant articles, identification and normalization of the actual bio-entities, the extraction of the annotation event and the
identification of some evidential support (e.g. experimental evidence). Some of the important aspects, bottlenecks and potential
text mining approaches were briefly...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3126/version/1
A Fresh Look at Energy, Materials, and Labor in Agriculture
Provedor de dados: 17
Autores: Aaron W. Baum; Tadeusz Patzek; Martin Bender; Steve Renich; Wes Jackson.
An understanding of agriculture's energy, material, and labor requirements is essential for achieving economic and
ecological sustainability, and for assessing the effectiveness of relevant policy decisions (biofuel subsidies, regulations, labeling,
etc.). Previous studies of energy, materials, and labor use in farming have been based on either unverified voluntary reporting or
test plots, rather than on the high-resolution measurements of mass and energy flows. Here we present a recursive analysis of 1.25
million data points describing in unprecedented detail the resource transactions on a 60 ha farm functioning for over 6 years. This
analysis highlights the importance of accounting for all types of materials, as well as capital equipment,...
Tipo: Manuscript
Palavras-chave: Ecology; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4291/version/1
A functional dissociation of conflict processing within anterior cingulate cortex
Provedor de dados: 17
Autores: Chobok Kim; James Kroger; Jeounghoon Kim.
Goal-directed behavior requires cognitive control to regulate neural processing when conflict is encountered. The dorsal anterior
cingulate cortex (dACC) has been associated with detecting response conflict during conflict tasks. However, recent findings have
indicated not only that two distinct subregions of dACC are involved in conflict processing but also that the conflict occurs at both
perceptual and response levels. We clarified a functional dissociation of the caudal dACC (cdACC) and the rostral dACC
(rdACC) in responding to different sources of conflict. The cdACC was selectively engaged in perceptual conflict whereas the
rdACC was more active in response conflict. Further, the dorsolateral prefrontal cortex (DLPFC) was coactivated not with
cdACC...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2505/version/1
A G4MP2 theoretical study on the gas phase enthalpies of formation for various polycyclic aromatic
hydrocarbons (PAHs) and other C~10~ through C~20~ unsaturated hydrocarbons
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas phase enthalpies of formation at 298.15 and 1 atm (Δ~f~H~(g),298K~) were calculated using the atomization
approach at the G4MP2 composite method level of theory for 86 polyaromatic hydrocarbons (PAHs) and other C~10~ through
C~20~ unsaturated hydrocarbons. Where available, good agreement with prior experimental data and/or high level theoretical
estimates was obtained. Linear regressions between semiempirical MNDO, MNDO-d, AM1, PM3, RM1, and PM6 estimated
Δ~f~H~(g),298K~ and the corresponding G4MP2 values were employed to obtain G4MP2 corrected semiempirical
Δ~f~H~(g),298K~ for a suite of 156 C~11~ through C~42~ unsaturated hydrocarbons and PAHs.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6450/version/1
A G4/W1BD theoretical study into the gas phase enthalpies of formation for potential high energy
materials
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Enthalpies of formation (Δ~f~H~(g)~) at 298.15 K and 0 K were calculated for various potential high energy
materials (HEMs) using the high-level Gaussian-4 (G4) and W1BD methods with the atomization approach. Where prior high
level estimates are available in the literature, the G4 and W1BD Δ~f~H~(g)~ are in good agreement. The results
presented herein represent the highest level calculations performed to date on this suite of HEMs. These G4/W1BD enthalpies of
formation should provide utility among the research community as a benchmark set of values against which to assess future
experimental and/or theoretical data.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6461/version/1
A general model of continuous character evolution
Provedor de dados: 17
Autores: Carl Boettiger.
I present a general model for continuous character evolution, review some of the common challenges that emerge in such complex
methods and review strategies for handling them.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6080/version/1
A generic approach for representing complex structures in biological models
Provedor de dados: 17
Autores: Robert I. Muetzelfeldt.
Increasingly, the biological modelling community is looking for ways of handling complex and possibly dynamic structures in
their models.
On the one hand, the pathway-modelling groups (SBML and CellML) seek to move up levels of organisation,
while on the other hand the "Virtual X" communities (where X is some organism or organ) need to
represent the organisational structure within their object of study.
SBML
Level
3
'comp',
To date, various approaches have been proposed, such as the
'spatial',
'array'
and
'dyn' extension packages, and domain-specific elements in languages such as NeuroML, but there is no
generic approach intended to be adopted by the various...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5188/version/1
A Genome-Wide Analysis Reveals Significant Overlap of Transcription and DNA Repair in
Stationary Phase Yeast
Provedor de dados: 17
Autores: Aviv de Morgan; Leonid Brodsky; Yefim Ronin; Eviatar Nevo; Abraham Korol; Yechezkel Kashi.
The association between transcription and DNA repair is acknowledged as a player in the generation of mutations in a
non-random fashion in prokaryotes and eukaryotes. Previous studies demonstrated that the transcription complex is capable of
directing DNA repair to sites of transcription. This process is especially important to growth-arrested cells, in which many DNA
repair capacities are diminished; it may also lead to mutations preferentially in transcribed genes. Using microarray analysis of
growth-arrested yeast cultures, we demonstrated on a genomic scale, the co-localization of a DNA-turnover marker, indicative of
DNA-repair-associated DNA synthesis, with genes persistently transcribed during stationary phase. This may serve as a clue
regarding the...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1543/version/1
A global assessment of deep-sea basalt sites for carbon sequestration
Provedor de dados: 17
Autores: David Goldberg; Angela L. Slagle.
In recent years, the debate over the most effective means to stabilize greenhouse gas concentrations in the atmosphere has
endorsed multiple approaches and a variety of technologies. Assuring secure storage of anthropogenic carbon dioxide is one of
our most pressing global scientific challenges that may contribute to achieving a stable solution over the next several decades.
Geological sequestration by injection into deep-sea basalt formations provides unique and significant advantages over other
potential storage options, including: (a) vast reservoir capacities with high porosity and permeability, sufficient to accommodate
centuries-long U.S. production of fossil fuel CO~2~ at locations within a few hundreds of kilometers of populated areas; (b)
chemical...
Tipo: Poster
Palavras-chave: Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2640/version/1
A Handy Script to Implement Genetic Models in R
Provedor de dados: 17
Autores: Wei Zhang.
Genome-wide associations between genotypic and phenotypic data often assume certain genetic models. A handy script in R was
written to implement three commonly used genetic models: additive, dominant and recessive models. This script can be easily
inserted into more complicated programs to facilitate high-throughput association studies.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1537/version/2
A Handy Script to Implement Genetic Models in R
Provedor de dados: 17
Autores: Wei Zhang.
Genome-wide associations between genotypic and phenotypic data often assume certain genetic models. A handy script in R was
written to implement three commonly used genetic models: additive, dominant and recessive models. This script can be easily
inserted into more complicated programs to facilitate high-throughput association studies.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1537/version/1
A hydrometric analysis of the Moose Jaw River near Burdick (05JE006): Temporal trends and
frequency analyses for mean, minimum, and maximum flows
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
A hydrometric analysis over the available historical record (1973-2010) was conducted for the Moose Jaw River station near
Burdick in south-central Saskatchewan, Canada. Frequency analyses on mean monthly, average annual, monthly
minimum/maximum, and annual minimum flows generally yielded poor fits, and problems with negative flow predictions for
mid- to long-term return periods regardless of distribution type. The annual maximum streamflow time series is reasonably
well-described by linear and log Pearson Type III distributions, although both distribution types underestimate extreme maximum
flows. Mann-Kendall linear time series analysis on mean monthly and annual streamflows reveals no trend in annual water yields,
nor in mean monthly flows between March...
Tipo: Poster
Palavras-chave: Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6697/version/1
A Hyperstable Miniprotein: Additive Effects of D- and L-Ala Substitutions
Provedor de dados: 17
Autores: D. V. Williams; Bipasha Barua; Niels H. Andersen.
The effects of alanine substitutions in each helical segment of the structure, and Gly to D-Ala mutations at sites where glycines
have positive phi angles in the Trp-cage miniprotein are reported. The effects of the stabilizing mutation were additive, yielding a
20-residue construct (Tm = 83^o^C). Gly to L-Ala substitutions were uniformly destabilizing ([DELTA][DELTA]G~F~
> 11 kJ/mol): the preference for a D-Ala can be as large as 16 kJ/mol. Glycine to D-Ala mutations are validated as a
strategy for the design of hyperstable miniprotein scaffolds suitable for stereospecific pharmacophore display.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/2074/version/1
A Hypothetic Mechanism of Ordering and Shaping Cells within Discrete Regions
Provedor de dados: 17
Autores: Yaroslav Strokovskyy.
We propose a hypothetic mechanism of ordering and shaping cells during _C. elegans_ embryogenesis. The mechanism is based
on the assumption that during each round of division of cells, daughter cells acquire electric charges from its mother cells (charge
conservation law is taken into account). Between the acts of division, the total electric field, generated by a system of charged
cells, change relative positions of the charged cells within the region. In one’s turn, the positions of the charged
cells determine the pattern of the electrostatic field. A mathematical model of such self-consistent mechanism is developed. The
process of developing the sixteen-cell structure starting with one cell is simulated. The results correspond to the known...
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4277/version/1
A Latent Variable Approach to Multivariate Quantitative Trait Loci
Provedor de dados: 17
Autores: Bob O'Hara; Päivi Komulainen; Outi Savolainen; Mikko J. Sillanpää.
A novel approach based on latent variable modelling is presented for the analysis of multivariate quantitative and qualitative trait
loci. The approach is general in the sense that it enables the joint analysis of many kinds of quantitative and qualitative traits
(including count data and censored traits) in a single modelling framework. In the framework, the observations are modelled as
functions of latent variables, which are then affected by quantitative trait loci. Separating the analysis in this way means that
measurement errors in the phenotypic observations can be included easily in the model, providing robust inferences. The
performance of the method is illustrated using two real multivariate datasets, from barley and Scots pine.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4137/version/1
A Lateralized Brain Network for Visuo-Spatial Attention
Provedor de dados: 17
Autores: Michel Thiebaut de Schotten; Flavio Dell'Acqua; Stephanie Forkel; Andrew Simmons; Francesco Vergani;
Declan G.M. Murphy; Marco Catani.
Looking for a friend in the crowd, avoiding a sudden danger or contemplating a work of art are some examples of actions based
on the efficiency of our visuo-spatial attention system. The specialization of the right brain hemisphere for visuo-spatial attention
is a characteristic of most humans, but its anatomical basis remains largely unknown. Our study is the first to report in humans the
existence of a bilateral parieto-frontal network whose hemispheric lateralization predicts the degree of specialization of the right
hemisphere for visuo-spatial attention. Our results also suggest that this specialization is associated with an unbalanced speed of
visuo-spatial processing between the two hemispheres. This lateralization may be predictive of visuo-spatial...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5549/version/1
A Linguistic Approach to Aligning Representations of Human Anatomy and Radiology
Provedor de dados: 17
Autores: Pinar Wennerberg; Manuel Möller; Sonja Zillner.
To realize applications such as semantic medical image search different domain ontologies are necessary that provide
complementary knowledge about human anatomy and radiology. Consequently, integration of these different but nevertheless
related types of medical knowledge from disparate domain ontologies becomes necessary. Ontology alignment is one way to
achieve this objective. Our approach for aligning medical ontologies has three aspects: (a) linguistic-based, (b) corpus-based, and
(c) dialogue-based. We briefly report on the linguistic alignment (i.e. the first aspect) using an ontology on human anatomy and a
terminology on radiology.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3521/version/2
A Linguistic Approach to Aligning Representations of Human Anatomy and Radiology
Provedor de dados: 17
Autores: Pinar Wennerberg; Manuel Möller; Sonja Zillner.
To realize applications such as semantic medical image search different domain ontologies are necessary that provide
complementary knowledge about human anatomy and radiology. Consequently, integration of these different but nevertheless
related types of medical knowledge from disparate domain ontologies becomes necessary. Ontology alignment is one way to
achieve this objective. Our approach for aligning medical ontologies has three aspects: (a) linguistic-based, (b) corpus-based, and
(c) dialogue-based. We briefly report on the linguistic alignment (i.e. the first aspect) using an ontology on human anatomy and a
terminology on radiology
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3521/version/1
A Linked Data Approach to Help Identify Therapeutic Targets for Cancer
Provedor de dados: 17
Autores: Helena Deus.
Cancer is still one of the leading causes of death in the developed world. To address this problem, the US National Institutes of
Health (NIH) has launched The Cancer Genome Atlas (TCGA), a large scale systematic approach to characterize tumor samples
from 20 cancer types and approximately 10,000 donor patients by using multiple high-throughput approaches.


Multidisciplinary projects such as TCGA and related projects across Europe aim at
identifying cancer “driver” mutations to be used as therapeutic targets or diagnostic tests. Extracting
and aggregating the knowledge necessary to identify such mutations remains a challenge primarily due to the need to reliably
integrate the experimental datasets...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6169/version/1
A logistic regression model for microalbuminuria prediction in overweight male population
Provedor de dados: 17
Autores: BaoDe Chen; WeiYi Xu; Chen Yu; ZhenYun Ni; XueFen Li; DaWei Cui.
Background: Obesity promotes progression to microalbuminuria and increases the risk of chronic kidney disease. Current
protocols
of
screening
microalbuminuria
are
not
recommended
for
the
overweight
or
obese.

Design and Methods: A cross-sectional study was conducted. The relationship
between metabolic risk factors and microalbuminuria was investigated. A regression model based on metabolic risk factors was
developed
and
evaluated
for
predicting
microalbuminuria
in
the
overweight
or
obese.

Results: The prevalence of MA reached up to 17.6% in Chinese overweight
men. Obesity, hypertension, hyperglycemia and hyperuricemia were the important risk factors for microalbuminuria in the
overweight....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5372/version/1
A Long-Term Analysis of the Moose Jaw Climate Station (4015322/4015320): Temporal Trends and
Frequency Analyses for Temperatures, Precipitation, and Wind Speed
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
A long-term analysis of temporal trends and frequency analyses for temperatures (1913-2010), precipitation (1909-2010), and
wind speed (1954-1996) was conducted on the Moose Jaw climate station in south-central Saskatchewan, Canada. Average annual
and springtime temperatures are increasing over time, as are daily mean temperatures during March. Mean daily maximum
temperatures are increasing on an annual basis and during the spring period, whereas mean daily minimum temperatures are
increasing during February, March, August, and September, as well as on an annual basis and during spring and summer. There
are significant positive time trends for growing degree days base 8C (GDD~8~) and 10C (GDD~10~). Rainfall has been
increasing during March as well as...
Tipo: Poster
Palavras-chave: Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6703/version/1
A Mathematical Model of a Neuron with Synapses based on Physiology
Provedor de dados: 17
Autores: Xiaolin Zhang.
The neuron, when considered as a signal processing device, itsinputs are the frequency of pulses received at the synapses, and its
output is the frequency of action potentials generated- in essence, a neuron is a pulse frequency signal processing device. In
comparison, electrical devices use either digital or analog signals for communication or processing, and the mathematics behind
these subjects is well understood. However, in regards to pulse frequency processing devices, there has not yet been a clear and
persuasive mathematical model to describe the functions of neurons. It goes without saying that such a model is very important,
not only for understanding neuron and neural system behavior, but also for undeveloped potential applications in industry....
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1703/version/1
A memoryless, stochastic mechanism of timing of phases of behavior by a neural network controller
Provedor de dados: 17
Autores: Saaniya Contractor; Nataliya Kozlova; Vladimir Brezina.
For a sensorimotor network to generate adaptive behavior in the environment, the phases of the behavior must be appropriately
timed. When the behavior is driven simply by the sensory stimuli from the environment, these can supply the timing. But when
the behavior is driven by an internal "goal" that ignores and perhaps even opposes the immediate sensory
stimuli, the timing must be generated internally by the network. We have modeled a realistic behavioral scenario that requires
such internal timing.

When the sea slug Aplysia feeds, it incrementally ingests long
strips of seaweed, driven by ingestive stimuli emanating from the seaweed. But if, having ingested a strip, the animal fails to
break the...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2817/version/1
A Meta-analysis of Studies on Plant Growth Rate and Allocation to Roots and Shoots
Provedor de dados: 17
Autores: Daniel R. Taub.
I performed a meta-analysis of studies examining the relationships among nutrient availability, plant growth rate and allocation to
roots vs. shoots. Species characteristic of high fertility habits grew faster than species characteristic of less fertile habitats. While
species were highly plastic in root/shoot ratio, there was a strong correlation in root/shoot across fertility levels when plants were
grown across fertility gradients. This suggests that the proportional mass allocation to roots is a consistent characteristic of
individual species relative to other species. There was no consistent relationship between allocation to roots and either growth rate
or the fertility of habitats that species typically are found in.
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/185/version/1
A Meteorite Ablation Debris: Testing and Analysis
Provedor de dados: 17
Autores: Saheeb Ahmed Kayani.
In this research report, X-ray diffraction (XRD) and X-ray fluorescence (XRF) spectrometry have been used to determine the
mineralogical and elemental composition of a stone sample recovered from a location near village Lehri in district Jhelum,
Pakistan. The test data is compared with previous findings (as reported in literature and included in references) to identify this
sample stone as part of a prehistoric meteorite ablation debris.
Further to this, carbon content of a specimen
of the meteorite debris has been determined through combustion analysis. This carbon abundance has been compared with carbon
wt% value of a certain type of meteorites to establish the origin and nature of the parent body of this particular meteorite debris.
Tipo: Manuscript
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5450/version/1
A Micropropagation, Molecular and Physiochemical Analysis of Canola Brassica napus L. From
Seeds
Provedor de dados: 17
Autores: Israr Khan; Muhammad Shuaib; Sikandar Khan; Muhammad Amir Zia; Haji Akbar.
Canola is important for its oil, anticarcinogenic phytochemicals and low saturated fat content and has wide scope for further
improvement through genetic transformations. Micropropagation is the practice of rapidly multiplying stock plant material to
produce a large number of disease free progeny plants, using modern asceptic plant tissue culture methods and also to conserve
germ plasm. A combination of auxin and cytikinin and a shock on growth regulator free medium is used for micropropagation.
Molecular and physiochemical analysis done to know variation in seeds protein content and electric conductivity.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Molecular Cell Biology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4781/version/2
A model explaining some bryozoan colonies
Provedor de dados: 17
Autores: Dawid Mazurek.
Although the colonialism surely developed independently in Graptolithoidea and Bryozoa, both groups share similar patterns of
astogeny. One of the common features is the presence of morphological gradients. Many attempts at its explanation were made for
more than a half of the century. This paper discusses a new model of the late astogeny in some bryozoan colonies, showing a
cyclic reappearance of secondary zones of astogenetic change and astogenetic repetition that cannot be explained by the single
morphogen gradient theory.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1585/version/1
A modelling study of beta-amyloid induced change in hippocampal theta rhythm
Provedor de dados: 17
Autores: Xin Zou; Damien Coyle; KongFatt Wong-Lin; Liam Maguire.
Many dementia cases, such as Alzheimer’s disease (AD), are characterized by an increase in low frequency field
potential oscillations. However, a definitive understanding of the effects of the beta-Amyloid peptide, which is a main marker of
AD, on the low frequency theta rhythm (4-7Hz) is still unavailable. In this work, we investigate the neural mechanisms associated
with beta-Amyloid toxicity using a conductance-based neuronal network model of the hippocampus CA1 region. We simulate the
effects of beta-Amyloid on the A-type fast inactivating K+ channel by modulating the maximum conductance of the current in
pyramidal
cells,
denoted
by
gA.
Our
simulation
results
demonstrate
that
as
gA
decreases
(through
A[beta]
blockage), the...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6004/version/1
A Modular Semantic Annotation Framework: CellML Metadata Specifications 2.0
Provedor de dados: 17
Autores: Michael T. Cooling.
In the last decade or so, model encoding efforts such as CellML and SBML have greatly facilitated model availability. But, as the
complexity of models increases, the utility of these models can vary. The addition of semantic information is crucial to
transforming mathematical models from esoteric to informative resources. 

We have
developed a metadata specification framework to better enable the annotation of CellML models with metadata. The framework
consists of a core specification describing, in general terms, how annotations should be attached using RDF/XML, and satellite
specifications covering several domains of immediate interest, using elements from the Dublin Core, FOAF (Friend-Of-A-Friend),
BIBO (Bibliographic...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6391/version/1
A multiple-instance scoring method to predict tissue-specific cis-regulatory motifs and regions
Provedor de dados: 17
Autores: Jin Gu.
Transcription is the central process of gene regulation. In higher eukaryotes, the transcription of a gene is usually regulated by
multiple cis-regulatory regions (CRRs). In different tissues, different transcription factors bind to their cis-regulatory motifs in
these CRRs to drive tissue-specific expression patterns of their target genes. By combining the genome-wide gene expression data
with the genomic sequence data, we proposed multiple-instance scoring (MIS) method to predict the tissue-specific motifs and the
corresponding CRRs. The method is mainly based on the assumption that only a subset of CRRs of the expressed gene should
function in the studied tissue. By testing on the simulated datasets and the fly muscle dataset, MIS can identify true...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4038/version/1
A network-based signaling mechanism of cancer development and progression
Provedor de dados: 17
Autores: Edwin Wang.
We conducted a comprehensive analysis of a manually curated human signaling network containing 1634 nodes and 5089
signaling regulatory relations by integrating cancer-associated genetically and epigenetically altered genes. We find that cancer
mutating genes are enriched in positive signaling regulatory loops, whereas the cancer-associated methylating genes are enriched
in negative signaling regulatory loops. We further characterized an overall picture of the cancer-signaling architectural and
functional organization. From the network, we extracted an oncogene-signaling map, which contains 326 nodes, 892 links and the
interconnections of mutated and methylated genes. The map can be decomposed into 12 topological regions or
oncogene-signaling blocks,...
Tipo: Presentation
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2238/version/1
A neural model for the visual tuning properties of action-selective neurons
Provedor de dados: 17
Autores: Martin A. Giese; Vittorio Caggiano; Falk Fleischer.
SUMMARY: The recognition of actions of conspecifics is crucial for survival and social interaction. Most current models on the
recognition of transitive (goal-directed) actions rely on the hypothesized role of internal motor simulations for action recognition.
However, these models do not specify how visual information can be processed by cortical mechanisms in order to be compared
with such motor representations. This raises the question how such visual processing might be accomplished, and in how far
motor processing is critical in order to account for the visual properties of action-selective neurons.
We
present a neural model for the visual processing of transient actions that is consistent with physiological data and that
accomplishes...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5862/version/1
A new approach to generating research-quality data through citizen science: The USA National
Phenology Monitoring System
Provedor de dados: 17
Autores: Ellen G. Denny; Abraham J. Miller-Rushing; Brian P. Haggerty; Lisa Benton; Theresa M. Crimmins; Mark Losleben;
Andrew D. Richardson; Alyssa Rosemartin; Mark D. Schwartz; Kathryn A. Thomas; Jake F. Weltzin; Bruce E. Wilson.
Phenology is one of the most sensitive biological responses to climate change, and recent changes in phenology have the potential
to shake up ecosystems. In some cases, it appears they already are. Thus, for ecological reasons it is critical that we improve our
understanding of species’ phenologies and how these phenologies are responding to recent, rapid climate change.
Phenological events like flowering and bird migrations are easy to observe, culturally important, and, at a fundamental level,
naturally inspire human curiosity— thus providing an excellent opportunity to engage citizen scientists. The USA
National Phenology Network has recently initiated a national effort to encourage people at different levels of...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3695/version/1
A new approach to generating research-quality phenology data: The USA National Phenology
Monitoring System
Provedor de dados: 17
Autores: Ellen G. Denny; Abraham J. Miller-Rushing; Brian P. Haggerty; Bruce E. Wilson; Jake F. Weltzin; the rest of the
USA-NPN Protocol Development Team.
The USA National Phenology Network (www.usanpn.org) has recently initiated a national effort to encourage people at different
levels of expertise—from backyard naturalists to professional scientists—to observe phenology and
contribute to a national database that will be used to greatly improve our understanding of spatio-temporal variation in phenology
and associated phenological responses to climate change. Many phenological observation protocols identify specific
single dates at which individual phenological events are observed, but the scientific usefulness of long-term
phenological observations can be improved with a more carefully structured protocol. At the USA-NPN we have developed a new
approach that...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/3695/version/2
A new approach to the spatio-temporal pattern identification in neuronal multi-electrode registrations
Provedor de dados: 17
Autores: Federico Esposti; Jacopo Lamanna; Maria Gabriella Signorini.
A lot of methods were created in last decade for the spatio-temporal analysis of multi-electrode array (MEA) neuronal data sets.
All these methods were implemented starting from a channel to channel analysis, with a great computational effort and onerous
spatial pattern recognition task. 
Our idea is to approach the MEA data collection from a different point of
view, i.e. considering all channels simultaneously. We transform the 2D plus time MEA signal in a mono-dimensional plus time
signal and elaborate it as a normal 1D signal, using the Space-Amplitude Transform method. 
This
geometrical transformation is completely invertible and allows to employ very fast processing algorithms. 

Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1306/version/1
A New Behavior of Nuclei during Mitosis of Lilium Hybrids
Provedor de dados: 17
Autores: Zheng Sixiang; Liu Feihu; Zhang Chaojun; Chen Zhilin; Ma Yuhua; Meng Pinghong; Zhao Yan.
Mitosis is nuclear division plus cytokinesis,and produces two identical daughter cells during prophase, prometaphase, metaphase,
anaphase, and telophase. However, a new nucleus behavior in interspecific hybrid progenies of Lilium was observed in our
experiment. Very unusual behaviors of nuclei surprisingly presented during the mitosis, such as sprouting or germination,
tube-like elongation, penetrating cell membrane into a neighbor cell, the top of nuclei tube expanding, intruding and splitting of
the tube-like nucleus, and micronucleus formation, and so on. Furthermore, the tetrad of meiosis was founded in mitosis of
root.

Routine of the unusual nucleus behaviors observed in our experiment may be
summarized as nucleus...
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4631/version/1
A new dynamic property of human consciousness
Provedor de dados: 17
Autores: UnCheol Lee; Seunghwan Kim; Gyu-Jeong Noh; Byung-Moon Choi.
As pointed out by William James, "the consciousness is a dynamic process, not a thing" , during which
short term integration is succeeded by another differentiated neural state through the continual interplay between the environment,
the body, and the brain itself. Thus, the dynamic structure underlying successive states of the brain is important for understanding
human consciousness as a process. In order to investigate the dynamic property of human consciousness, we developed a new
method to reconstruct a state space from electroencephalogram(EEG), in which a trajectory, reflecting states of consciousness, is
constructed based on the global information integration of the brain. EEGs were obtained from 14 subjects received an
intravenous...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1244/version/1
A new functional role for lateral inhibition in the striatum: Pavlovian conditioning
Provedor de dados: 17
Autores: Patrick Connor; Thomas Trappenberg.
The striatum has long been implicated in reinforcement learning and has been suggested by several neurophysiological studies as
the substrate for encoding the reward value of stimuli. Reward prediction error (RPE) has been used in several basal ganglia
models as the underlying learning signal, which leads to Pavlovian conditioning abilities that can be simulated by the
Rescorla-Wagner model.

Lateral inhibition between striatal projection neurons was
once thought to have a winner-take-all function, useful in selecting between possible actions. However, it has been noted that the
necessary reciprocal connections for this interpretation are too few, and the relative strength of these synaptic connections is weak.
Still,...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5986/version/1
A New General Allometric Biomass Model
Provedor de dados: 17
Autores: Wei Sheng Zeng; Shou Zheng Tang.
To implement monitoring and assessment of national forest biomass, it is becoming the trend to develop generalized single-tree
biomass models suitable for large scale forest biomass estimation. Considering that the theoretical biomass allometric model
developed by West et al. [1,2] was statistically different from the empirical one, the two parameters in the most commonly used
biomass equation M=aDb were analyzed in this paper. Firstly, based on the knowledge of geometry, the theoretical value of
parameter b was deduced, i.e., b=7/3(≈2.33), and the comparison with many empirical studies conducted throughout
the globe indicated that the theoretical parameter could describe soundly the average allometric relationship between aboveground
biomass M...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6704/version/1
A New General Allometric Biomass Model
Provedor de dados: 17
Autores: Wei Sheng Zeng; Shou Zheng Tang.
To implement monitoring and assessment of national forest biomass, it is becoming the trend to develop generalized single-tree
biomass models suitable for large scale forest biomass estimation. Considering that the theoretical biomass allometric model
developed by West et al. [1,2] was statistically different from the empirical one, the two parameters in the most commonly used
biomass equation M=aDb were analyzed in this paper. Firstly, based on the knowledge of geometry, the theoretical value of
parameter b was deduced, i.e., b=7/3(~2.33), and the comparison with many empirical studies conducted throughout the globe
indicated that the theoretical parameter could describe soundly the average allometric relationship between aboveground biomass
M and D...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6704/version/2
A new mathematical model for radiation cell killing mechanism: Target cumulating model
Provedor de dados: 17
Autores: Zhao Liang; Wu Shixiu; Xie Congyin; Zhang Li.
There are numerous mathematical or statistical models have been given out for radiation cell killing mechanism. Unfortunately,
none of the model could explain the mechanism perfectly. The more advanced model for it is still necessary to be researched.
Following common assumption, a new theoretical model named "target cumulating" model is induced from
the molecular and particle physics level. The result of theoretical calculation gives the equation of cell survival rate corresponding
to delivered dose and other sensitivity parameters. In addition to fit the cell survival curve well, the new model showed advantages
with comparing to previous models. Also, the new model predicts or explains some phenomenon that had been observed in...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/2880/version/1
A New Method for Characterization of Natural Zeolites and Organic Nanostructure using Atomic
Force Microscopy
Provedor de dados: 17
Autores: Domenico P. R. O. F. Fuoco.
In order to study and develop an economic solution to environmental pollution in water, a wide variety of materials were
investigated. Natural zeolites emerge from that research as the best in class of this category. Zeolites are natural materials
relatively abundant and non biodegradable, economic and good to perform processes of environmental remediation. This paper
contains a full description of a new method to characterize superficial properties of natural zeolites of exotic provenience
(Caribbean Islets) with atomic force microscopy (AFM). AFM works with the optical microscope simplicity and the high
resolution typical of a transmission electron microscope (TEM). Structural information of mesoporous material is obtained using
scanning and transmission...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2012
URL: http://precedings.nature.com/documents/6828/version/1
A new multicompartmental reaction-diffusion modeling method links transient membrane
attachment of E. coli MinE to E-ring formation
Provedor de dados: 17
Autores: Satya N. V. Arjunan; Masaru Tomita.
Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm
and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo
method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and
the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus,
cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and
reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the
localization...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3845/version/1
A new outlook towards kidney injuries
Provedor de dados: 17
Autores: Mahesh Satwekar; Abhijeet Satwekar.
Acute and chronic progression of injury to the kidney leads to the failure of the renal system and has become an increasingly
important cause of morbidity and mortality. Present diagnosis detects the condition only after irreversible loss of 70 percent of
kidney function. Current research is focused only on the clinical manifestations after the kidney injuries and not towards the exact
cause of the condition. Here we propose a new outlook- that there is an involvement of a pathogen in the pathogenesis of kidney
injuries. Basis for our proposal is given by the similarity of the pathogenesis events occurring between a classical example of
hepatitis and kidney injuries. Furthermore, literature regarding the role of early kidney injury biomarkers in innate...
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology; Microbiology.
Ano: 2012
URL: http://precedings.nature.com/documents/7021/version/1
A new phylogenetic comparative method: detecting niches and transitions with continuous characters
Provedor de dados: 17
Autores: Carl Boettiger.
Traditional information criteria approaches can lead to misleading model choice in comparative phylogenetics. I present examples
of these weaknesses using a classic data set on Anoles lizards. I describe a more robust comparison by likelihood ratio. I then
discuss a new class of models to capture the transition process between evolutionary regimes.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4615/version/1
A new potential radiosensitizer: ammonium persulfate modified WCNTs
Provedor de dados: 17
Autores: Jian-She Yang; Bo-Zhang Yu; Wen-Xin Li.
Radiotherapy plays a very important role in cancer treatment. Radiosensitizers have been widely used to enhance the
radiosensitivity of cancer cells at given radiations. Here we fabricate multi-walled carbon nanotubes with ammonium persulfate,
and get very short samples with 30-50 nanometer length. Cell viability assay show that f-WCNTs induce cell death significantly.
We hypothesize that free radicals originated from hydroxyl and carbonyl groups on the surface of f-WCNTs lead cell damage.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry.
Ano: 2007
URL: http://precedings.nature.com/documents/1421/version/1
A normalization technique for next generation sequencing experiments
Provedor de dados: 17
Autores: Günter Klambauer; Karin Schwarzbauer; Andreas Mayr; Sepp Hochreiter.
Next generation sequencing (NGS) are these days one of the key technologies in biology. NGS' cost effectiveness and
capability of finding the smallest variations in the genome makes them increasingly popular. For studies aiming at genome
assembly, differences in read count statistics do not affect the outcome. However, these differences bias the outcome if the goal is
to identify structural DNA characteristics like copy number variations (CNVs). Thus a normalization step must removed such
random read count variations subsequently read counts from different experiments are comparable. Especially after normalization
the commonly used assumption of Poisson read count distribution in windows on the chromosomes is more justified. Strong
deviations of...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4710/version/1
A normalization technique for next generation sequencing experiments
Provedor de dados: 17
Autores: Günter Klambauer; Karin Schwarzbauer; Andreas Mayr; Sepp Hochreiter.
Next generation sequencing (NGS) are these days one of the key technologies in biology. NGS' cost effectiveness and
capability of finding the smallest variations in the genome makes them increasingly popular. For studies aiming at genome
assembly, differences in read count statistics do not affect the outcome. However, these differences bias the outcome if the goal is
to identify structural DNA characteristics like copy number variations (CNVs). Thus a normalization step must removed such
random read count variations subsequently read counts from different experiments are comparable. Especially after normalization
the commonly used assumption of Poisson read count distribution in windows on the chromosomes is more justified. Strong
deviations of...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4710/version/2
A Note on Measures of Single Timeseries Activity in Resting-State fMRI Studies
Provedor de dados: 17
Autores: Xi-Nian Zuo.
In statistics, signal processing and mathematical finance, a time series is a sequence of data points, measured typically at
successive times spaced at uniform time intervals. Here, I only focus on the discrete time series. The motivation of writing this
methodology note is to clarify the relationship between the measures to quantify activity of an observed timeseries. Particularly,
focus one several measures used in recently emerged field of resting-state fMRI studies. Although all these measures have been
extensively developed in EEG or other timeseries studies, many researchers focusing on various applications in or new comers to
this new field need to know existed measures and the relationships among these measures.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4379/version/1
A Note On The Denisova Cave mtDNA Sequence
Provedor de dados: 17
Autores: Niccolo Caldararo; Michael Guthrie.
The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern
humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was
found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one
introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the
sequences for other published samples and Neanderthals from the same perspective.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5360/version/2
A Note On The Denisova Cave mtDNA Sequence
Provedor de dados: 17
Autores: Niccolo Caldararo; Michael Guthrie.
The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern
humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was
found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one
introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the
sequences for other published samples and Neanderthals from the same perspective.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/5360/version/4
A Note On The Denisova Cave mtDNA Sequence
Provedor de dados: 17
Autores: Niccolo Caldararo; Michael Guthrie.
The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern
humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was
found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one
introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the
sequences for other published samples and Neanderthals from the same perspective.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5360/version/3
A Note On The Denisova Cave mtDNA Sequence
Provedor de dados: 17
Autores: Niccolo Caldararo.
The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern
humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was
found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one
introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the
sequences for other published samples and Neanderthals from the same perspective.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5360/version/1
A novel alveolar Krebs cycle-triggered CO2 sensing mechanism regulates regional pulmonary
ventilation.
Provedor de dados: 17
Autores: Rainer Kiefmann; Paula Keller; Oliver Tritt; Kai Heckel; Sascha Tank; Martina Kiefmann; Leoni Schulte-Uentrop;
Alwin Goetz.
Pulmonary perfusion disorders provoke atelectasis in order to minimize ventilation/perfusion mismatch. However, the underlying
mechanisms remain unknown. Because intraalveolar CO2 concentration ([CO2]iA) declines as a consequence of poor pulmonary
perfusion we postulated the existence a novel alveolar CO2-sensing mechanism which adapts the ventilation to perfusion.
Real-time fluorescence imaging of rat lungs revealed that low [CO2]iA decreased cytosolic and increased mitochondrial Ca2+ in
alveolar epithelial cells (AEC), leading to reduction of surfactant secretion and alveolar ventilation. Mitochondrial inhibition by
ruthenium red or rotenone blocked the hypocapnia-induced responses. In cultured Type 2 AEC hypocapnia decreased cytosolic
Ca2+ independently...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6185/version/1
A novel apparatus/protocol designed for optogenetic manipulation and recording of individual
neurons during a motivation and working memory task in the rodent
Provedor de dados: 17
Autores: Samuel Dolzani; Donald C. Cooper.
Innovative molecular tools allow neuroscientists to study neural circuitry associated with specific behaviors. Consequently,
behavioral methods must be developed to interface with these new molecular tools in order for neuroscientists to identify the
causal elements underlying behavior and decision-making processes. Here we present an apparatus and protocol for a novel
Go/No-Go behavioral paradigm to study the brain attention and motivation/reward circuitry in awake, head-restrained rodents.
This experimental setup allows: (1) Painless and stable restraint of the head and body; (2) Rapid acquisition to simple or complex
operant tasks; (3) Repeated electrophysiological single and multiple unit recordings during ongoing behavior; (4) Pharmacological
and...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7152/version/1
A novel class of endogenous shRNAs in human cells
Provedor de dados: 17
Autores: Tongjun Gu; James Q. Yin; Yanwei Xu; ZhengHua Dai; Zhengge Qiu; Shenzhong Feng; Xiang Yi; Ling Jiang; Hongjie
Zhang.
Until now it is still not clear how many types and amounts of small RNAs (sRNAs) exist in humans. Here we report the
identification of 1258 distinct sRNAs derived from intronic regions of protein-coding genes in human with a new approach. These
endogenous short hairpin RNAs (shRNAs) appear to be similar to exogenous shRNAs in structure, have a broad distribution in the
stem length, and function as microRNAs (miRNAs), small interfering RNAs (siRNA) and/or piwi-interacting RNAs (piRNAs).
Except for a few shRNAs, the majority of shRNAs are not phylogenetically conserved. They are differentially expressed in
different cells and at diverse developmental stages. Overall, their expression levels are lower than miRNAs', but can
be detected by quantitative...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/1531/version/1
A novel _Drosophila_ post-genomic CNS drug discovery model detects tetraethylammonium chloride
with therapeutic potential
Provedor de dados: 17
Autores: Priyanka Singh; Farhan Mohammad*; Abhay Sharma.
A _Drosophila_ behavioral and transcriptomic model of locomotor plasticity induced by chronic pentylenetetrazole (PTZ) has
recently been developed. In this model, two of the five antiepileptic drugs (AEDs) tested, sodium valproate (NaVP) and
levetiracetam (LEV), not ethosuximide (ETH), gabapentin (GBP) and vigabatrin (VGB), ameliorate development of chronic PTZ
induced locomotor alteration. Transcriptomic effect of the AEDs and PTZ in fly head has been described. Here, we analyze
microarray expression profile of heads of flies treated with the convulsants tetraethylammonium chloride (TEA) and pilocarpine
hydrochloride (PILO). Strikingly, microarray clustering placed TEA, not PILO, with LEV and NaVP in one group that was
distinct from the other one...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3418/version/1
A novel Drosophila transcriptomic and behavioral model detects potassium chloride with therapeutic
potential
Provedor de dados: 17
Autores: Farhan Mohammad; Priyanka Singh; Abhay Sharma.
In a newly described _Drosophila_ model, two of the five antiepileptic drugs (AEDs) tested, sodium valproate (NaVP) and
levetiracetam (LEV), not ethosuximide (ETH), gabapentin (GBP) and vigabatrin (VGB), ameliorate development of chronic
pentylenetetrazole (PTZ) induced locomotor alteration. To further characterize the model, we analyze here the microarray
expression profile of heads of flies treated with depolarizing compound potassium chloride (KCl). Surprisingly, microarray
clustering showed unexpected similarity among KCl, LEV and NaVP. Further, like the two effective AEDs in the fly model, KCl
regulated genes overrepresented ribosomal pathway. Interestingly, KCl also ameliorated development of locomotor deficit in the
chronic PTZ model. Both...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3429/version/1
A novel mathematical tool for generating highly conserved protein domain via different organismal
genomic landscapes
Provedor de dados: 17
Autores: Arunava Goswami; Pabitra Pal Choudhury; Rajneesh Singh; Sk. Sarif Hassan.
Darwinian evolution hypothesizes that a short stretch of DNA was first constructed and then it expanded to give rise to a long
strand. This long strand then produced a mix of exons, introns and repetitive DNA sequence. The order of production of above
three kinds of DNA sequence is unknown. Reshuffling of stretches of DNA like above within organisms has given rise to different
chromosomes. Till date it is not known how this process is governed. In this paper we show that starting with a sixteen base-pair
human olfactory DNA sequence one can form a highly conserved protein domain. Once this domain is formed repetitive DNA
sequences of a particular kind starts generating which signifies that this particular conserved protein domain will be unique in
nature....
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4850/version/1
A Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for
Composition Improvements- (v.4)
Provedor de dados: 17
Autores: Valentin Prisecaru; I. C. Baianu.
Amino acid NIR calibrations were developed in our Physical Chemistry of Foods Laboratory of the University of Illinois at
Urbana for three selected amino acid groups that include essential amino acids for identified soybean accessions. Conventional
“wet chemistry” analytical methods are time-consuming and costly. As a result, soybean breeders
and researchers have an imperative need to utilize faster and less expensive methods. NIR Spectroscopy is a rapid and inexpensive
method for composition analysis for academia and industry. Recent advancements in instrumentation design, such as the
application of the Diode Array (DA) technique and the Fourier Transform (FT) IR and NIR techniques, have significantly
improved overall instrument...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell
Biology; Bioinformatics; Earth & Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6231/version/4
A novel predicted calcium-regulated kinase family implicated in neurological disorders
Provedor de dados: 17
Autores: Małgorzata Dudkiewicz; Anna Lenart; Krzysztof Pawłowski.
Protein kinases are essential effectors of cellular signaling. Surprisingly, using bioinformatics tools, we predicted protein kinase
structure and function for proteins of unknown function (FAM69 family) coded by five related human genes and their Metazoan
homologues. Analysis of three-dimensional structure models and conservation of the classic catalytic motifs of protein kinases in
four of human FAM69 proteins suggests they might have retained catalytic phosphotransferase activity. The FAM69 genes,
FAM69A, FAM69B, FAM69C, C3ORF58 and CXORF36, are by large uncharacterized molecularly, yet linked to several
neurological disorders in genetics studies. An EF-hand Ca2+-binding domain in FAM69A and FAM69B proteins, inserted within
the structure of the kinase...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7015/version/1
A novel regulator of the p53-mediated mitochondrial apoptotic pathway
Provedor de dados: 17
Autores: Bo Young Ahn; Diane Trinh; Laura Zajchowski; Sung-Woo Kim.
The p53 tumor suppressor protein induces apoptosis in response to genotoxic and environmental stress. Recent studies have
revealed the existence of a transcription-independent mitochondrial p53 apoptosis pathway, however the mechanism regulating
p53 translocation to mitochondria and subsequent initiation of apoptosis was not known. Here, we show that Tid1, also known as
mtHsp40 or Dnaja3, interacts with p53 and directs its translocation to mitochondria in cells exposed to hypoxia. Overexpression
of Tid1 in tumor cells promoted mitochondrial localization of both wildtype and mutant forms of p53 and was able to restore the
pro-apoptotic activity of mutant p53 proteins that were otherwise unable to induce apoptosis. Tid1's mitochondrial
signal...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1892/version/1
A novel strategy for the targeted analysis of protein and peptide metabolites
Provedor de dados: 17
Autores: Nicholas A. Williamson; Charles Reilly; Chor-Teck Tan; Sri-Harsha Ramarathinam; Alun Jones; Christie L. Hunter;
Francis R. Rooney; Anthony W. Purcell.
The detection and quantitation of exogenously administered biological macromolecules (e.g. vaccines, peptide and protein
therapeutics) and their metabolites is frequently complicated by the presence of a complex endogenous mixture of closely related
compounds. We describe a method that incorporates stable isotope labeling of the compound of interest allowing the selective
screening of the intact molecule and all metabolites using a modified precursor ion scan. This method involves monitoring the low
molecular weight fragment ions produced during MS/MS that distinguish isotopically labelled material from related endogenous
compounds. All isotopically labelled substances can be selected using this scanning technique for further analysis whilst other...
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3812/version/1
A novel superior factor widely controlling the rice grain quality
Provedor de dados: 17
Autores: Kao-Chih She; Hiroaki Kusano; Kazuyoshi Koizumi; Hiromoto Yamakawa; Makoto Hakata; Tomohiro Imamura;
Masato Fukuda; Natsuka Naito; Yumi Tsurumaki; Ken'ichiro Matsumoto; Mari Kudoh; Eiko Itoh; Shoshi Kikuchi;
Naoki Kishimoto; Junshi Yazaki; Tsuyu Ando; Masahiro Yano; Takashi Aoyama; Tadamasa Sasaki; Hikaru Satoh; Hiroaki
Shimada.
Synthesis of storage starch and protein accumulation is the main action of endosperm organogenesis in term of the economic
importance of rice. This event is strongly disturbed by abiotic stresses such as high temperature; thus, the upcoming global
warming will cause a crisis with a great impact on food production^1,2^. The enzymes for the protein storage and starch synthesis
pathway should work in concert to carry out the organogenesis of rice endosperm^3-5^, but the regulatory mechanism is largely
unknown. Here we show that a novel regulatory factor, named OsCEO1, acts as the conductor of endosperm organogenesis during
the rice grain filling stage. The physiological properties of _floury-endosperm-2_ (_flo2_) mutants showed many similarities to
symptoms...
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3283/version/1
A novel therapeutic strategy for pancreatic neoplasia using a novel RNAi platform targeting PDX-1
Provedor de dados: 17
Autores: Shi-He Liu; Donald Rao; John Nemunaitis; Neil Senzer; David Dawson; Marie-Claude Gingras; Zhaohui Wang;
Richard Gibbs; Michael Norman; Nancy Templeton; Francesco DeMayo; Kelly Stehling; William Fisher; Charles Brunicardi.
Bi-functional shRNA (bi-shRNA), a novel RNA interference (RNAi) effector platform targeting PDX-1 utilizing a systemic
DOTAP-Cholesterol delivery vehicle, was studied in three mouse models of progressive pancreatic neoplasia. Species-specific
bi-functional PDX-1 shRNA (bi-shRNAPDX-1) lipoplexes inhibited insulin expression and secretion while also substantially
inhibiting proliferation of mouse and human cell lines via disruption of cell cycle proteins in vitro. Three cycles of either
bi-shRNA<sup>mousePDX-1</sup>
or
shRNA<sup>mousePDX-1</sup> lipoplexes administered intravenously prevented
death from hyperinsulinemia and hypoglycemia in a lethal insulinoma mouse model. Three cycles of...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics & Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6047/version/1
A Novel Thermodynamic Method For Quantifying Ligand-Receptor Interactions: The IC (1/3)
Standard Vs IC (50)
Provedor de dados: 17
Autores: Dr Sudarsan Prasad.
A method based on the Concentration Derivative Product (CDP) is proposed to analyze the thermodynamics of Drug-Receptor
interactions. CDP is defined as the product of the fractional inhibition f and it’s concentration derivative. Assuming
Michaelis-Menten kinetics, it is shown that for a number of drug-receptor systems (HIV protease, ACE, HMG-CoA, Opioid
receptor inhibitors, etc.) f max = 0.333, irrespective of the nature of bonding interactions and Ki.
The CDP max = [4 / ( 27 Ki )
], and gives a measure of the drug potency directly. CDP also gives thermodynamic information about the ratio of the gradients of
the inhibitor chemical potential in the free and bound states.
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6006/version/1
A Paradigm for Biology's Next Revolution
Provedor de dados: 17
Autores: Fredric D. R. Young.
A recent essay on biology's next revolution described attributes of a future theory of biology that would replace post
hoc modeling with an interplay between quantitative prediction and experimental test, more characteristic of the physical
sciences1. The article suggested that flux from the environment whether it be energy, chemicals metabolites, or genes is a defining
characteristic of life. The essay also suggests that an interdisciplinary approach to collective phenomena centered on statistical
mechanics and dynamical systems theory will be required to make use of this perspective. Over the last 30 years we have
developed an approach to drug discovery and translational research that is based on a paradigm for complex systems modeling
that fits...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/1770/version/1
A periodic pattern of SNPs in the human genome
Provedor de dados: 17
Autores: Bo Eskerod Madsen; Palle Villesen; Carsten Wiuf.
By surveying all validated SNPs in the human genome we have found that SNPs positioned 1, 2, 4, 6 or 8 bp apart are more
frequent than SNPs 3, 5, 7 or 9 bp apart. This holds even when we correct for nucleotide frequencies and site dependencies in
nucleotide usage in the genome. The observed pattern is not restricted to any of the genomic regions that might give sequencing or
alignment errors; i.e. transposable elements (SINE, LINE and LTR), tandem repeats and large duplicated regions. However we
can define periodic DNA, which virtually capture the entire pattern. Periodic DNA is defined as small DNA sequences (16.9 bp
average length) with a high degree of periodicity in nucleotide usage. Periodic DNA is widely distributed in the genome,
underrepresented in...
Tipo: Poster
Palavras-chave: Genetics & Genomics.
Ano: 2007
URL: http://precedings.nature.com/documents/435/version/1
A Physiological Role for Amyloid Beta Protein: Enhancement of Learning and Memory
Provedor de dados: 17
Autores: John Morley; Susan Farr; William Banks; Steven N. Johnson; Kelvin A. Yamada; Lin Xu.
Amyloid beta protein (A[beta]) is well recognized as having a significant role in the pathogenesis of Alzheimer's
disease (AD). The reason for the presence of A[beta] and its physiological role in non-disease states is not clear. In these studies,
low doses of A[beta] enhanced memory retention in two memory tasks and enhanced acetylcholine production in the
hippocampus _in vivo_. We then tested whether endogenous A[beta] has a role in learning and memory in young, cognitively
intact mice by blocking endogenous A[beta] in healthy 2-month-old CD-1 mice. Blocking A[beta] with antibody to A[beta] or
DFFVG (which blocks A[beta] binding) or decreasing A[beta] expression with an antisense directed at the A[beta] precursor APP
all resulted in impaired...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2119/version/1
A PI3K-mediated negative feedback regulates Drosophila motor neuron excitability
Provedor de dados: 17
Autores: Eric Howlett; Curtis C. J. Lin; William Lavery; Michael Stern.
Negative feedback can act as a homeostatic mechanism to maintain neuronal activity at a particular specified value. At the
Drosophila neuromuscular junction, a mutation in the type II metabotropic glutamate receptor gene (mGluRA) increased motor
neuron excitability by disrupting an autocrine, glutamate-mediated negative feedback. We show that mGluRA mutations increase
neuronal excitability by preventing PI3 kinase (PI3K) activation and consequently hyperactivating the transcription factor Foxo.
Furthermore, glutamate application increases levels of phospho-Akt, a product of PI3K signaling, within motor nerve terminals in
an mGluRA-dependent manner. In humans, PI3K and type II mGluRs are implicated in epilepsy, neurofibromatosis, autism,
schizophrenia and...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1767/version/1
A population-based study of glutathione-S-transferase M1, T1 and P1 genotypes
Provedor de dados: 17
Autores: Monika Sivoňová; Iveta Waczulíková; Dušan Dobrota;
Tatiana Matáková; Jozef Hatok; Peter Račay; Ján Kliment.
A retrospective study on healthy, unrelated subjects was conducted in order to estimate population glutathione-S-transferases
(GST) genotype frequencies in Slovak population of men and compare our results with already published data (GSEC project)^1^.
A further aim of the study was to evaluate frequencies of the _GST_ polymorphisms also in patients with prostate cancer in order
to compare the evaluated proportions with those found in the control subjects. Analysis for the _GST_ gene polymorphisms was
performed by PCR and PCR-RFLP. We found that the proportions are not significantly different from those estimated in a
European multicentre study or from the results published by another group in Slovakia. We found significantly increased
age-standardized...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics & Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2559/version/1
A Possible Solution to the Etiological Paradox that Ties Anti-Social Personality Disorder to Major
Depression
Provedor de dados: 17
Autores: Alvaro Machado Dias.
Abstract. Antisocial personality disorder (ASPD) is a pervasive condition among youngsters around the globe, which has
particular pungency in countries where the socioeconomic context favors delinquency. Several behavioral genetics studies have
linked the disorder to the presence of copies of a polymorphic variation of the MAO-A gene that leads to enzymatic hypofunction.
An emerging tendency in this literature is to also associate it to the presence of short variations of the 5-HTTLPR polymorphism,
which is well-known for its possible role in the vulnerability to major depression of individuals that were exposed to early-life
stress. The current paper argues that the association of these findings introduce a theoretical problem that is not trivial...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6308/version/1
A potential cyanobacterial ancestor of Viridiplantae chloroplasts
Provedor de dados: 17
Autores: Wriddhiman Ghosh; Prabir Haldar; Sabyasachi Bhattacharya; Jaideb Chatterjee; Prosenjit Pyne; Masrure Alam.
The theory envisaging the origin of plastids from endosymbiotic cyanobacteria is well-established but it is difficult to explain the
evolution (spread) of plastids in phylogenetically diverse plant groups. It is widely believed that primordial endosymbiosis
occurred in the last common ancestor of all algae^1^, which then diverged into the three primary photosynthetic eukaryotic
lineages, viz. the Rhodophyta (red algae), Glaucocystophyta (cyanelle-containing algae) and Viridiplantae (green algae plus all
land plants)^2^. Members of these three groups invariably have double membrane-bound plastids^3^, a property that endorses the
primary endosymbiotic origin of the organelles. On the other hand, the three or four membrane-bound plastids of the
evolutionary...
Tipo: Manuscript
Palavras-chave: Microbiology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6607/version/1
A potential diagnostic biomarker: Proteasome LMP2/b1i-differential expression in human uterus
neoplasm
Provedor de dados: 17
Autores: Takuma Hayashi; Akiko Horiuchi; Hiroyuki Aburatani; Nobuo Yaegashi; Susumu Tonegawa; Ikuo Konishi.
Uterine leiomyosarcoma (ULMS) develops more often in the muscle tissue layer of the uterine body than in the uterine cervix.
The development of gynecologic tumors is often correlated with female hormone secretion; however, the development of uterine
ULMS is not substantially correlated with hormonal conditions, and the risk factors are not yet known. Importantly, a
diagnostic-biomarker which distinguishes malignant ULMS from benign tumor leiomyoma (LMA) is yet to be established.
Accordingly, it is necessary to analyze risk factors associated with uterine ULMS, to establish a treatment method. Proteasome
low-molecular mass polypeptide 2(LMP2)/b1i-deficient mice spontaneously develop uterine LMS, with a disease prevalence of
~40% by 14 months of age. We...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2012
URL: http://precedings.nature.com/documents/7082/version/1
A potential role for Dkk-1 in the pathogenesis of osteosarcoma predicts novel diagnostic and
treatment strategies.
Provedor de dados: 17
Autores: Carl Gregory; Narae Lee; Angela Smolarz; Scott Olson; Odile David; Jacob Reiser; Robert Kutner; Najat Daw; Darwin
Prockop; Edwin Horwitz.
Canonical Wnt signaling is an osteo-inductive signal that promotes bone repair through acceleration of osteogenic differentiation
by progenitors. Dkk-1 is a secreted inhibitor of canonical Wnt signaling and thus inhibits osteogenesis. To examine a potential
osteo-inhibitory role of Dkk-1 in osteosarcoma (OS), we measured serum Dkk-1 in pediatric patients with OS (median age, 13.4
years) and found it to be significantly elevated. We also found that Dkk-1 was maximally expressed by the OS cells at the tumor
periphery and _in vitro_ Dkk-1 and RANKL are co-expressed by rapidly proliferating OS cells. Both Dkk-1 and conditioned
media from OS cells reduces osteogenesis by human mesenchymal cells and by immuno-depletion of Dkk-1, or by adding a
GSK3[beta]...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer.
Ano: 2007
URL: http://precedings.nature.com/documents/130/version/1
A prelude report on molecular docking of HER2 protein towards comprehending anti-cancer
properties of saponins from Solanum tuberosum
Provedor de dados: 17
Autores: Puneet K. Singh; Pratyoosh Shukla.
Saponins are extensively known for many biological activities e.g. antimicrobial, anti-palatability, anti-cancer and hemolytic. As
cancer cells have a more cholesterol-like compound in their membrane structure the saponins bind cholesterol due to their natural
affinity to bind cancer cell membrane. This prevents them from entering the body through the intestinal tract, where they have the
ability to attach themselves to vital organs and grow. This study reports the effective use of lower dose saponins like immunotoxin
so that they can inhibit the proliferation of cancerous pancreatic cells. The investigation of pancreatic cancer metabolic pathway it
was found that proteins 3H3B produced by genes HER-2 are involved in the enhancement of this type of cancer....
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7147/version/1
A probabilistic model of plasmid replication regulation by a combination of handcuffing, iteron
number and dimerization of RepA protein.
Provedor de dados: 17
Autores: Milind Watve; Gauri Tendulkar; Ketaki Ghate.
Plasmids are small circular DNA molecules in bacteria which replicate sharing the replication machinery with the bacterial
chromosome. Since plasmids are much smaller than the chromosome, unless their replication is tightly regulated, their copy
numbers can escalate quickly. A number of mechanisms of plasmid replication regulation are known in P1 plasmid of E. coli.
Mechanisms such as autorepression of the replication initiator protein (RepA) and its dimerization are unable to explain copy
number regulation by themselves. The number of RepA binding sites (iterons) is inversely related to copy numbers. Handcuffing
of plasmids by RepA dimer is believed to be the main mechanism of arresting replication. We show here with a probabilistic
model that for the...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5421/version/1
A Proposal of Genomic Analytical Workflow in a Bacterial Pathogen Outbreak Investigation
Provedor de dados: 17
Autores: Hoi Shan Kwan; Chun Hang Au; Chi Keung Cheng; Man Kit Cheung; Qianli Huang; Lei Li; Wenyan Nong; Man Chun
Wong.
The German Escherichia coli O104:H4 outbreak causing Hemolytic Uremic Syndrome (HUS) started in early May 2011.
Conventional typing methods including serotyping, multi-locus sequence typing (MLST) and pulse-field gel electrophoresis
(PFGE) seemed to yield only limited information about the causative agent. The advantages of the Genome sequencing approach
are apparent compared to conventional methods. Genome sequencing and analyses with an appropriate workflow would be the
new paradigm in bacterial outbreak investigation.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/6663/version/1
A Quality Evaluation Framework for Bio-Ontologies
Provedor de dados: 17
Autores: Jesualdo Tomas Fernandez-Breis; Mikel Egaña Aranguren; Robert Stevens.
Over the past few years the number of bio-ontologies has rapidly increased. The evaluation of ontologies has long been a
problematic issue. The growing number of ontologies makes the need for a strategy for evaluating quality more urgent. We
propose a framework for evaluating the quality of bio-ontologies. This framework is inspired by a well-known software quality
standard, which has been adapted to the needs of ontology evaluation. An example of how to use the framework, comparing two
versions of the Open Biomedical Ontologies' Cell Type Ontology, is included as an illustration.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3479/version/1
A Quality Evaluation Framework for Bio-Ontologies
Provedor de dados: 17
Autores: Jesualdo Tomas Fernandez-Breis; Mikel Egaña Aranguren; Robert Stevens.
Over the past few years the number of bio-ontologies has rapidly increased. The evaluation of ontologies has long been a
problematic issue. The growing number of ontologies makes the need for a strategy for evaluating quality more urgent. We
propose a framework for evaluating the quality of bio-ontologies. This framework is inspired by a well-known software quality
standard, which has been adapted to the needs of ontology evaluation. An example of how to use the framework, comparing two
versions of the Open Biomedical Ontologies' Cell Type Ontology, is included as an illustration.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3478/version/1
A Quantitative Approach to Investigating the Hypothesis of Prokaryotic Intron Loss
Provedor de dados: 17
Autores: Robert M. Sinclair.
Using a novel method, we show that ordered triplets of motifs usually associated with spliceosomal intron recognition are
underrepresented in the protein coding sequence of complete Thermotogae, archaeal and bacterial genomes. The
underrepresentation observed does not extend to the noncoding strand, suggesting that the cause of the asymmetry is related to
mRNA rather than DNA. Our data do not suggest that the underrepresentation is due to gene transfer from eukaryotes. We
speculate that one possible explanation for these observations is that the protein coding sequence of Thermotogae, Archaea and
Bacteria was at some time in the past subjected to selection against certain motifs appearing in an order which might initiate
splicing in environments harboring...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5770/version/1
A quantitative model for efficient construction of lentiviral vectors with a unique clone site
Provedor de dados: 17
Autores: Gang Zhang; Anurag Tandon.
Lentiviral vectors (LVs) were a powerful tool for transgene expression in vivo and in vitro. However, the construction of LVs is
of low efficiency, due to the large sizes and lack of proper clone sites. Therefore, it is critical to develop efficient strategies for
cloning LVs. Here, we reported a combinatorial strategy to efficiently construct LVs using EGFP, hPlk2 wild type (WT) and
mutant genes as inserts. Firstly, site-directed mutagenesis (SDM) was performed to create BamH I site for the inserts; secondly,
pWPI LV was dephosphorylated after BamH I digestion; finally, the amounts and ratios of the insert and vector DNA were
optimized to increase monomeric ligation. Our results showed that the total percentage of positive clones was approximately...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2012
URL: http://precedings.nature.com/documents/6876/version/1
A Quantitative Model for Human Olfactory Receptors
Provedor de dados: 17
Autores: Sk. Sarif Hassan; Pabitra Pal Choudhury; Aritra Bose.
A wide variety of chemicals having distinct odors are smelled by humans. Odor perception initiates in the nose, where it is
detected by a large family of olfactory receptors (ORs). Based on divergence of evolutionary model a sequence of human ORs
database has been proposed by D. Lancet et al (2000, 2006). It is quite impossible to infer whether a given sequence of
nucleotides is a human OR or not, without any biological experimental validation. In our perspective, a proper quantitative
understanding of these ORs is required to justify or nullify whether a given sequence is a human OR or not. In this paper, all
human OR sequences have been quantified, and a set of clusters have been made using the quantitative results based on two
different metrics. Using...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6967/version/1
A Quantitative Model for Human Olfactory Receptors
Provedor de dados: 17
Autores: Sk. Sarif Hassan; Pabitra Pal Choudhury; Aritra Bose.
A wide variety of chemicals having distinct odors are smelled by humans. Odor perception initiates in the nose, where it is
detected by a large family of olfactory receptors (ORs). Based on divergence of evolutionary model, a sequence of human ORs
database has been proposed by D. Lancet et al (2000, 2006). It is quite impossible to infer whether a given sequence of
nucleotides is a human OR or not, without any biological experimental validation. In our perspective, a proper quantitative
understanding of these ORs is required to justify or nullify whether a given sequence is a human OR or not. In this paper, all
human OR sequences have been quantified, and a set of clusters have been made using the quantitative results based on two
different metrics. Using...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6967/version/2
A quick trip through openness, freedom and transparency
Provedor de dados: 17
Autores: Konrad U. Foerstner.
This talk aims to give scientists an introduction to the concepts of openness, freedom and transparency and their applications (not
only) for science. It covers the topics of open source, open formats, Creative Commons, open access, and open
science/knowledge. A video of the talk is available on the author's website.

Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1225/version/1
A randomised controlled trial of an intervention to promote early presentation of breast cancer in
older women: effect on breast cancer awareness
Provedor de dados: 17
Autores: Louise Linsell; Lindsay J. L. Forbes; Marcia Kapari; Caroline Burgess; Lynne Omar; Lorraine Tucker; Amanda
J. Ramirez.
There is virtually no evidence for the effectiveness of interventions to promote early presentation in breast cancer. We tested the
efficacy of an intervention to equip older women with the knowledge, skills, confidence and motivation to detect symptoms and
seek help promptly, with the aim of promoting early presentation with breast cancer symptoms. We randomised 867 women aged
67 to 70 attending for their final routine appointment on the UK NHS Breast Screening Programme to receive: a scripted
ten-minute interaction with a radiographer plus a booklet; a booklet alone; or usual care. The primary outcome was whether or not
a woman was breast cancer aware based on knowledge of breast cancer symptoms and age-related risk; and reported breast
checking. At one...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3816/version/1
A Rate Distortion approach to protein symmetry
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry breaking argument is applied to the problem of protein folding, via a Rate Distortion analysis of the
relation between genome coding and the final condensation of the protein molten globule. In the 'energy'
picture, the average distortion between codon message and protein structure, under constraints driven by evolutionary selection,
serves as a temperature analog, so that low values limit the possible distribution of protein forms, producing the canonical folding
funnel. A dual 'developmental' perspective sees the rate distortion function itself as the temperature
analog, and permits incorporation of chaperons or toxic exposures as catalysts, driving the system to different possible outcomes
or...
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4280/version/2
A Rate Distortion approach to protein symmetry
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry breaking argument is applied to the problem of protein form, via a Rate Distortion analysis of the
relation between genome coding and the final condensation of the protein 'molten globule'. The Rate
Distortion Function, under coding constraints, serves as a temperature analog, so that low values act to drive proteins to simple
symmetries. The Rate Distortion Function itself is significantly constrained by the availability of metabolic free energy. This work
extends Tlusty's (2007) elegant exploration of the evolution of the genetic code, suggesting that rate distortion
considerations may play a critical role across a broad spectrum of molecular expressions of evolutionary process.
Tipo: Manuscript
Palavras-chave: Chemistry; Developmental Biology; Genetics & Genomics; Molecular Cell Biology; Bioinformatics; Earth
& Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4280/version/1
A Reaction Route Approach to Flux Balance Analysis
Provedor de dados: 17
Autores: Ilie Fishtik.
Background: Flux balance and network-based pathway analyses are theoretical tools aimed to find optimal steady state flux
distributions in a metabolic network subject to additional constraints on the rates of the reaction steps. Although these methods are
mathematically accurate, there are several physicochemical and computational aspects that are questionable and misleading. In
particular, it is well known that the flux balance analysis may result in multiple flux distributions for the same objective function.


Results: The flux balance and network-based pathway analyses are reformulated in
terms of reaction routes (RRs), a theoretical framework that has been developed by Horiuti over 50 years ago. Not only does the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2788/version/1
A reassessment of the Carnot cycle and the concept of entropy
Provedor de dados: 17
Autores: Sosale Chandrasekhar.
It is argued that the Carnot cycle is a highly inaccurate representation of a steam engine, and that the net work obtained in its
operation would be zero. This conclusion is also supported by an elementary mathematical approach, which re-examines the work
done in the four individual steps of the cycle. An important consequence of this is that the concept of entropy, originally proposed
on the basis of the Carnot theorem, may not be a fundamentally valid thermodynamic quantity. Also, the experimental approach
generally adopted in the determination of entropy is questionable, and the importance of increasing randomness in natural
processes not universally valid. In fact, a more viable basis, at least vis-à-vis chemical reactions, appears to be the...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1852/version/1
A Report of the Mosquito Host Range of Pythium guiyangense Su
Provedor de dados: 17
Autores: Xiaoqing Su.
Mosquito causes problems in both disease transmission and disturbance to people's daily life. The controlling methods
used now are mainly application of chemical pesticides which result in serious harm to environment. Biological control of the pest
is one of the ideal ways. But, lack of suitable agent makes it difficult to extend this technique in wider scope. _Pythium
guiyangense_ Su is a newly found fungal pathogen of mosquitoes and is promising for practical use. Here we summarize a list of
mosquitoes that can be infected by the fungus so far, which shows the potential significance of the application of the fungus in the
future.
Tipo: Manuscript
Palavras-chave: Microbiology; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1875/version/1
A review of journal policies for sharing research data
Provedor de dados: 17
Autores: Heather A. Piwowar; Wendy W. Chapman.
*Background:* Sharing data is a tenet of science, yet commonplace in only a few subdisciplines. Recognizing that a data
sharing culture is unlikely to be achieved without policy guidance, some funders and journals have begun to request and require
that investigators share their primary datasets with other researchers. The purpose of this study is to understand the current state
of data sharing policies within journals, the features of journals which are associated with the strength of their data sharing
policies, and whether the strength of data sharing policies impact the observed prevalence of data sharing.


*Methods:* We investigated these relationships with respect to gene expression
microarray data in the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1700/version/1
A Roadmap of Cancer Systems Biology
Provedor de dados: 17
Autores: Edwin Wang.
What is cancer systems biology? Why should we conduct systems biology research in cancer? What is the relationships between
systems biology and personalized medicine? How do we conduct cancer systems biology research? This paper illustrates
strategies, procedures and computational techniques for the study of cancer systems biology by focusing on network
reconstruction, network analysis and modeling. Finally, certain challenges and hurdles in cancer systems biology will also be
discussed.
Tipo: Manuscript
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4322/version/1
A Roadmap of Cancer Systems Biology
Provedor de dados: 17
Autores: Edwin Wang.
What is cancer systems biology? Why should we conduct systems biology research in cancer? What is the relationships between
systems biology and personalized medicine? How do we conduct cancer systems biology research? This paper illustrates
strategies, procedures and computational techniques for the study of cancer systems biology by focusing on network
reconstruction, network analysis and modeling. Finally, certain challenges and hurdles in cancer systems biology will also be
discussed.
Tipo: Manuscript
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4322/version/2
A schistosome [beta] subunit remodels inactivation of a calcium channel _via_ an N-terminal
polyacidic motif
Provedor de dados: 17
Autores: Vicenta Salvador-Recatala; Robert M. Greenberg.
The beta subunit of high voltage-activated Ca (Cav) channels targets the pore forming [alpha]~1~ subunit to the plasma
membrane and defines the biophysical phenotype of the Cav channel complex. Cav channel inactivation following activation and
opening is tightly regulated and is an essential property that not only prevents excessive entry of Ca^2+^ into the cell but may also
have functions in signal transduction. The [beta] subunit modulates Ca^2+^-dependent and voltage-dependent components of Cav
channel inactivation via its interaction with the I-II linker of the [alpha]~1~ subunit. Here, using Cav2.3 and whole-cell
patch-clamp, we show that a [beta] subunit from the human parasite _Schistosoma mansoni_ ([beta]~Sm~) accelerates
inactivation via a unique,...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4230/version/1
A science metrics based citation for tagging the biomedical researchers
Provedor de dados: 17
Autores: Adeilton Brandao.
With the thousands of scientific papers being produced every month, picking an authors name, associate it to a research field and
right evaluate his or her performance is in most of times a cumbersome task. I am proposing here that science indexes as h-index,
g-index, total citations and published papers could be added to biomedical bibliographic citation in order to create a unique
identifier for a given researcher.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/794/version/1
A Secret of Hypnosis: A Dynamic Rubber Hand Illusion
Provedor de dados: 17
Autores: Tomohisa Asai; Eriko Sugimori; Yoshihiko Tanno.
Presenting a suggestion of heaviness to a person in a hypnotic trance (e.g., "your arm is getting heavier and
heavier") tends to result in a corresponding change in the person's body position (e.g., the arm lowers).
This phenomenon may be a result of activation of the mirror neuron system, which leads the subject to anticipate actual weight on
the arm. The mirror system underlies people's ability to sense, in the absence of actual sensory input, experiences of
other people. Perhaps this system allows the same anticipatory experience regarding non-human objects. In this study, we showed
participants a picture of a rubber hand holding what appeared to be a lightweight rubber ball. In reality, the ball was weighted
with...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2276/version/1
A Semantic Model for Federated Queries Over a Normalized Corpus
Provedor de dados: 17
Autores: Samuel Croset.
We present here a model implemented in OWL which improves information retrieval and data integration of the corpus. The
model is populated with entities from CALBC and some simple queries over it are presented.

Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5823/version/1
A Semantic Model for Federated Queries Over a Normalized Corpus
Provedor de dados: 17
Autores: Samuel Croset; Christoph Grabmüller; Dietrich Rebholz-Schuhmann.
We present here a model implemented in OWL which improves information retrieval and data integration of the corpus. The
model is populated with entities from CALBC and some simple queries over it are presented.

Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5823/version/2
A sensorimotor area (NIf) is required for the production of learned vocalizations
Provedor de dados: 17
Autores: Sharon M. H. Gobes; Bence P. Ölveczky.
Sensory feedback is essential for the acquisition of complex motor behaviors, including birdsong. In zebra finches, auditory
feedback is relayed to the descending motor pathway primarily through the nucleus interfacialis nidopalii (NIf). NIf projects to
HVC - a premotor region essential for song, which projects to RA, a motor cortex analogue brain area that drives muscle activity
required for vocalizations. NIf is also essential for ‘sleep replay’, a recapitulation of song-related
neural dynamics in the motor pathway during sleep. Despite being one of the major inputs to the song control pathway, there is no
known role for NIf in the production of zebra finch song. To address this, we reversibly inactivated NIf using TTX or Muscimol...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5856/version/1
A set of ontologies to drive tools for the control of vector-borne diseases
Provedor de dados: 17
Autores: Pantelis Topalis; Emmanuel Dialynas; Elvira Mitraka; Elena Deliyanni; Inga Siden-Kiamos; Christos Louis.
We are developing a set of ontologies that deal with vector-borne diseases and the arthropod vectors that transmit them. For
practical reasons (application priorities), we initiated this project with an ontology of insecticide resistance followed by a series of
ontologies that describe malaria as well as physiological processes of mosquitoes that are relevant to, and involved in, disease
transmission. These will be expanded to encompass other vector-borne diseases as well as non-mosquito vectors. The aim of the
whole undertaking, which is worked out in the frame of the international IDO (Infectious Disease Ontology) project, is to provide
the community with a set of ontological tools that can be used both in the development of specific databases and, most...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3464/version/1
A similarity criterion for forest growth curves
Provedor de dados: 17
Autores: Georgii A. Alexandrov; Georgy S. Golitsyn.
Comparison of forest growth curves has led many to the conclusion that there is a similarity between forest stands growing in
different conditions. Here we treat the same subject from the viewpoint of similarity theory. Our goal is to form a dimensionless
ratio of biophysical entities that could parameterize the diversity of forest growth curves. (Such ratios are called similarity
criteria.) Pursuing this goal, we focus on the analogy between tree crown growth and atomic explosion. A blast wave is formed
when the rate of energy release is much higher than the rate of energy dissipation. The difference between the rates of energy
release and dissipation is the essence of this phenomenon. The essential feature of crown growth is the difference between the...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6561/version/1
A simple clustering of the BioModels database using semanticSBML
Provedor de dados: 17
Autores: Falko Krause; Wolfram Liebermeister.
The BioModels database contains biochemical network models in SBML format, in which the biochemical meaning of elements is
specified by MIRIAM-compliant RDF annotations. We used these annotations to define a similarity measure for models, scoring
the overlap of the biochemical systems described. Based on this score, we used two-way clustering to detect groups of similar
models and groups of co-occuring model elements. To recognize and compare biochemical elements, we used routines from the
software semanticSBML. A Python script extracts all MIRIAM annotations (regardless of their qualifiers) using the
semanticSBML annotation classes. The result is a matrix in which the rows represent the models (e.g. BioModel 001), while the
columns represent specific...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3444/version/1
A Simple Nested Simulation for SED-ML
Provedor de dados: 17
Autores: Frank T. Bergmann.
This document describes a simple nested Simulation Experiment for SED-ML [1] that is easy to implement and will help to
broaden what SED-ML is able to encode.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4257/version/1
A Simple, Rapid Method for Extracting Large Plasmid DNA from Bacteria
Provedor de dados: 17
Autores: Spencer D. Heringa; Jonathan D. Monroe; James B. Herrick.
We are studying the lateral transfer of transmissible antibiotic resistance plasmids among stream bacteria impacted by fecal runoff
from poultry and cattle. Such plasmids are typically large (ca. 40 – 100 kb) and occur in low copy numbers in the
cell and have therefore typically been difficult to isolate and therefore to study. Traditional protocols, based upon variations of the
standard alkaline-lysis method, are long (ca. 1 1/2 to 2 days) and difficult. Commercial kits designed for the isolation of Baterial
Artificial Chromosomes (BACs) can be used and are an improvement; however, these are expensive and still require hours of
sustained effort. We have adapted a method published by Rondon et al. (1999), originally designed for the isolation of...
Tipo: Poster
Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology.
Ano: 2007
URL: http://precedings.nature.com/documents/1249/version/1
A simulation study on different STDP models concerning localized gamma oscillations
Provedor de dados: 17
Autores: Florian Hauser; Andreas Knoblauch; Günther Palm.
Gamma oscillations are a prominent feature in experimental as well as theoretical descriptions of brain activity. One of the
network models which has the capability to generate such oscillations is what we call a local cell assembly (CA), i.e. a group of
neighboring neurons which are strongly interconnected in an excitatory manner. Postulated by experimenters and extensively used
in theoretical studies, these local networks seem to be a good candidate for investigating the impact of biological constraints given
by models of spike-timing-dependent plasticity (STDP) on local gamma oscillating structures in the mammalian brain. Therefore
we fitted a two-compartment neuron model with AMPA- and NMDA-receptor mediated synaptic currents to desired...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5802/version/1
A snake of a different color: physiological color change in Arizona black rattlesnakes
Provedor de dados: 17
Autores: Melissa Amarello; Jeffrey J. Smith.
Coloration may serve a variety of behavioral (e.g., crypsis, communication) and physiological (e.g., thermoregulation, protection)
functions for terrestrial ectotherms. However, optimal coloration for a given function may vary over environments (spatial or
temporal) or conflict with other functions. Physiological color change (rapid change due to movement of pigment granules
within chromatophores) may be an adaptation to resolve conflicting selective pressures on coloration. The proximate factors
related to physiological color change are well known in many animals, but few studies have investigated the ecological or
evolutionary implications of this behavior. Here, we present alternative hypotheses for physiological color change and discuss
biotic and...
Tipo: Poster
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6711/version/1
A sorites paradox in the conventional definition of amount of substance
Provedor de dados: 17
Autores: Nigel Wheatley.
The conventional definition of amount of substance _n_ is as a quantity proportional to number of entities _N_. This implies that n
is discrete for small _N_ while _n_ is considered to be continuous at the macroscopic scale, leading to a sorites paradox. A
practical criterion is proposed for distinguishing between amount of substance and number of entities, and the implications for the
conventional definition of amount of substance are discussed.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/5568/version/1
A stable backbone for the fungi
Provedor de dados: 17
Autores: Ingo Ebersberger; Matthias Gube; Sascha Strauss; Anne Kupczok; Martin Eckart; Kerstin Voigt; Erika Kothe; Arndt
von Haeseler.
Fungi are abundant in the biosphere. They have fascinated mankind as far as written history goes and have considerably
influenced our culture. In biotechnology, cell biology, genetics, and life sciences in general fungi constitute relevant model
organisms. Once the phylogenetic relationships of fungi are stably resolved individual results from fungal research can be
combined into a holistic picture of biology. However, and despite recent progress, the backbone of the fungal phylogeny is not yet
fully resolved. Especially the early evolutionary history of fungi and the order or below-order relationships within the
ascomycetes remain uncertain. Here we present the first phylogenomic study for a eukaryotic kingdom that merges all publicly
available fungal...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2901/version/1
A stem-cell ageing hypothesis on the origin of Parkinson's disease
Provedor de dados: 17
Autores: André X. C. N. Valente; Jorge Sousa; Tiago Outeiro; Lino Ferreira.
A transcriptome-wide blood expression dataset of Parkinson’s disease (PD) patients and controls was analyzed
under the hypothesis-rich mathematical framework. The analysis pointed towards differential expression in blood cells in many of
the processes known or predicted to be disrupted in PD. We suggest that circulating blood cells in PD patients can be in a
full-blown PD-expression state. We put forward the hypothesis that sporadic PD can originate as a case of hematopoietic stem
cell/differentiation process expression program defect and suggest this research direction deserves further investigation.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4263/version/2
A stem-cell ageing hypothesis on the origin of Parkinson's disease
Provedor de dados: 17
Autores: André Valente; Jorge Sousa; Tiago Outeiro; Lino Ferreira.
A transcriptome-wide blood expression dataset of Parkinson’s disease (PD) patients and controls was analyzed
under the hypothesis-rich mathematical framework. The analysis pointed towards differential expression in blood cells in many of
the processes known or predicted to be disrupted in PD. We suggest that circulating blood cells in PD patients can be in a
full-blown PD-expression state. We put forward the hypothesis that sporadic PD can originate as a case of hematopoietic stem
cell/differentiation process expression program defect and suggest this research direction deserves further investigation.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4263/version/1
A Study of prevalence of malnutrition in government School children in the field area of Azad nagar
Bangalore, India
Provedor de dados: 17
Autores: Izhar Hasan.
Malnutrition is a problem at varying proportions in developing countries, and anthropometry is a simple tool to assess its
magnitude in children. This study was aimed at identifying the prevalence of malnutrition among 500 children of govt schols of
Azad Nagar, bangalore south Asia. The value of using various field based formulae and of various anthropometric indicators used
for classification of malnutrition was also studied. The study was focused on children aged 8-14 years studying in class 1st to 8th
in govt schools. Anthropometric data and eating practices of children were collected with the help of a pretested questionnaire and
food intake diary. Selected anthropometric measurements were taken using standard techniques. Their Body Mass Index (B.M.I)...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5009/version/1
A Study of the Mechanism of Action of Zervamicin IIB Peptide Antibiotic by Molecular Dynamics
Simulation
Provedor de dados: 17
Autores: Konstantin Shaitan; Olga V. Levtsova; Vladimir Makarov; Mikhail P. Kirpichnikov.
We model mechanism of action of a channel-forming peptide antibiotic, zervamicin IIB, by molecular dynamics (MD) simulation.
Interaction of this peptide with neutral and negatively charged lipid bilayers is investigated. It is found that charge of membrane
surface influences the orientation of zervamicin IIB molecule, that may in turn effect its permeation into the membrane. On this
basis we propose modifications to ZrvIIB structure that may increase its affinity towards the prokaryotic cellular membrane.
Zervamicin IIB transmembrane channels are modeled as bundles consisting of 4, 5 and 6 individual peptide monomers. Our
results suggest that four monomers don’t form a stable water-filled ion channel. Thus the channel with the least
number of...
Tipo: Manuscript
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3624/version/1
A Study on the Origin of Peroxisomes: Possibility of Actinobacteria Symbiosis
Provedor de dados: 17
Autores: Duhita Narendra; Saruhashi Satoshi; Hamada Kazuo; Miyata Daisuke; Horiike Tokumasa; Shinozawa Takao.
Withdrawn
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/1866/version/2
A Study on the Origin of Peroxisomes: Possibility of Actinobacteria Symbiosis
Provedor de dados: 17
Autores: Duhita Narendra; Saruhashi Satoshi; Hamada Kazuo; Miyata Daisuke; Horiike Tokumasa; Shinozawa Takao.
The origin of peroxisomes as having developed from the endoplasmic reticulum (ER) was proposed on the basis of the similarity
between some peroxisomal proteins and ER proteins, and the localization of some peroxisomal proteins on the ER. To study the
evolutionary distance between peroxisomes and ER and Prokaryotes, we carried out a phylogenetic analysis of CDC48 (cell
division control 48) and its homologs, including ER-localized CDC48, CDC48 homologs in Prokaryotes and
peroxisome-localized PEX1 and PEX6. A similarity search analysis of peroxisomal protein sequences to prokaryotic protein
sequences using BLAST at several thresholds (E-values) was also done. We propose Actinobacteria symbiosis for the origin of
peroxisomes based on the following evidence:...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1866/version/1
A subset of co-expressed genes in Slug-based cancer mesenchymal transition signature remains
coexpressed in normal samples in a tissue-specific manner
Provedor de dados: 17
Autores: Weiyi Cheng; Dimitris Anastassiou.
A recently identified gene expression signature of EMT markers containing the transcription factor Slug was found present in
samples from many publicly available cancer gene expression datasets of multiple cancer types except leukemia. We also found
many of these genes co-expressed in human cancer xenografted cells, but not in mouse stroma cells, suggesting that the signature
is largely produced by cancer cells undergoing some type of EMT. Here we report that a partial signature consisting of a subset of
the co-expressed genes of the full signature, including at least Slug (SNAI2), collagens COL1A1, COL1A2, COL3A1, COL6A3
and genes DCN and LUM, is also present in leukemia, in which case it is also strongly associated with the chemokine CXCL12
(aka SDF1)....
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics & Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6813/version/1
A Systematic Approach to Identifying Protein-Ligand Binding Profiles on a Proteome Scale
Provedor de dados: 17
Autores: Li Xie; Nancy Buchmeier; Lei Xie; Philip Bourne.
Identification of protein-ligand interaction networks on a proteome scale is crucial to address a wide range of biological problems
such as correlating molecular functions to physiological processes and designing safe and efficient therapeutics. We have
developed a novel computational strategy to identify ligand binding profiles of proteins across gene families and applied it to
predicting protein functions, elucidating molecular mechanisms of drug adverse effects, and repositioning safe pharmaceuticals to
treat different diseases.
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2207/version/1
A system-level neural model of the
rats
brain mechanisms underlying
instrumental devaluation in
Provedor de dados: 17
Autores: Francesco Mannella; Marco Mirolli; Gianluca Baldassarre.
Goal-directed behaviours are defined by the presence of two kinds of effect on instrumental learning. First, degrading the
contingencies between produced actions and desired outcomes diminishes the number of instrumental responses; second,
devaluing a reward results in a lower production of instrumental actions to obtain it. We present a computational model of the
neural processes underlying instrumental devaluation in rats. The model reproduces the interaction between the basolateral
complex of the amygdala (BLA) and the limbic, associative and somatosensory striato-cortical loops. Firing-rate units are used to
abstract the activity features of neural populations. Learning is reproduced through the use of dopamine-dependent simple and
differential hebbian...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5849/version/1
A Systems Biology Approach to the Evolution of Codon Use Pattern
Provedor de dados: 17
Autores: Ines Thiele; Ronan M. T. Fleming; Richard Que; Aarash Bordbar; Bernhard O. Palsson.
The genetic code is redundant as amino acids are encoded by synonymous codons that are unequally used.This codon usage bias
(CUB) affects gene expression and cellular functions yet the underlying mechanisms have not been elucidated. We used a
sequence-specific, stoichiometric model of metabolism and macromolecular synthesis for Escherichia coli K12 MG1655 to test
the effect of randomly changed CUB on growth maximization under various environmental conditions. Amongst CUB mutant
strains, we identified reduced growth phenotypes, which were caused by tRNA supply shortage. We propose, supported by
computations and bibliomic data, that expansion of tRNA gene content or tRNA reading is a mechanism to respond to changes in
CUB. Our systems biology modelling...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6312/version/1
A Systems Biology Approach towards Deciphering the Unfolded Protein Response in
Huntington's Disease
Provedor de dados: 17
Autores: Kameshwar R. Ayasolla; Ravi K. R. Kalathur; Matthias E. Futschik.
Although the disease causing gene huntingtin has been known for some time, the exact cause of neuronal cell death during
_Huntington's disease_ (HD) remains unknown. One potential mechanism contributing to the massive loss of neurons
in HD brains might be the _Unfolded Protein Response_ (UPR) which is activated by accumulation of misfolded proteins in the
endoplasmic reticulum (ER). As an adaptive response, UPR upregulates transcription of chaperones, temporarily attenuating new
translation and activates protein degradation via the proteasome. However, at high levels of ER stress, UPR signalling can
contribute to neuronal apoptosis.

Our primary aims include (a) construction of the
UPR signalling network, (b)...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7078/version/1
A Target Restricted Assembly Method (TRAM) for Phylogenomics
Provedor de dados: 17
Autores: Kevin P. Johnson; Kimberly K. O. Walden; Hugh M. Robertson.
While next generation sequencing technology can produce sequences covering the entire genome, assembly and annotation are
still prohibitive steps for many phylogenomics applications. Here we describe a method of Target Restricted Assembly (TRAM)
of a single lane of Illumina sequences for genes of relevance to phylogeny reconstruction, i.e. single copy protein-coding genes.
This method has the potential to produce a data set of hundreds of genes using only one Illumina lane per taxon.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4612/version/1
A Targeted Therapeutic Rescues Botulinum Toxin-A Poisoned Neurons
Provedor de dados: 17
Autores: Prabhati Ray; Bal Ram Singh; Radharaman Ray; Peng Zhang; Dan Li; James Keller; Michael Adler.
Botulinum neurotoxin (BoNT), a Category A biothreat agent, is the most potent poison known to mankind. Currently no antidote
is available to rescue poisoned synapses. BoNT acts specifically by blocking neurotransmission primarily at peripheral
nerve-muscle junctions causing severe flaccid muscle paralysis, which is fatal if proper medical care is not provided. The
neurotoxin acts by specifically entering the presynaptic nerve endings where it interferes with the biochemical machinery involved
in the process of neurotransmitter release, i.e., neuroexocytosis. Most serotypes of BoNT are known to remain active for weeks to
months after entering the nerves, but BoNT/A is the most potent and long lasting in causing muscle paralysis. An effective
medical...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2149/version/1
A test of _psbK-psbI_ and _atpF-atpH_ as potential plant DNA barcodes using the flora of the Kruger
National Park (South Africa) as a model system
Provedor de dados: 17
Autores: Renaud R. Y. Lahaye; Vincent Savolainen; Sylvie Duthoit; Olivier Maurin; Michelle van der Bank.
A DNA barcode consists of a standardized short sequence of DNA (400-800bp) used to identify the taxonomic species a small
organic fragment belongs to. Even though it has been easy to discriminate animal species by using the mitochondrial gene _cox1_,
this is still difficult for plants seeing that the mitochondrial genome is not variable enough on the species level. During the Second
International Barcode of Life Conference in Tapei (September 2007), different plastid regions were proposed as potential plant
DNA barcodes, such as _atpF-atpH_ and _psbK-psbI_, but no consensus on which region to use was reached during the meeting.
The largest plant DNA barcoding study to date proposed _matK_ as the best candidate and suggested that in combination with...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1896/version/1
A theory for the tissue specificity of BRCA1/2 related and other hereditary cancers
Provedor de dados: 17
Autores: Bernard Friedenson.
Women who inherit a defective BRCA1 or BRCA2 gene have risks for breast and ovarian cancer that are so high and seem so
selective that many mutation carriers choose to have prophylactic surgery.
There has been much conjecture to explain such
apparently striking tissue specificity. All these suggestions share the assumption that some disabled function of normal tumor
suppressor genes leads to a tissue specific cancer response. Here the idea is proposed and tested that major determinants of
where BRCA1/2 hereditary cancers occur are related to tissue specificity of the cancer pathogen, the agent that causes chronic
inflammation or the carcinogen. The target tissue may have receptors for the pathogen, become selectively exposed to an
inflammatory process...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics & Genomics; Immunology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4881/version/1
A Therapeutically Relevant Difference in Leukemia and Normal Stem Cell Self Renewal
Provedor de dados: 17
Autores: Soledad Negrotto; Zhenbo Hu; Kevin A. Link; Kwok Peng Ng; Juraj Bodo; Hien Duong; Andrew Schade; Eric Hsi;
Daniel Lindner; Jaroslaw Maciejewski; James Mulloy; Yogen Saunthararajah.
Abnormal self-renewal and differentiation are defining features of acute myeloid leukemia (AML).
Using models of
hematopoiesis, we show that persistent self-renewal that ignores differentiation signals can be produced through two distinct
pathways. One pathway prevents repression of stem cell genes, producing daughter cells that resemble parental stem cells
despite differentiation inducing lineage-specifying factor or cytokines. Runx1 deficiency, a frequent abnormality in AML,
demonstrates the second pathway, which allows cytokine/lineage-specifying factor mediated repression of stem cell genes but
impairs subsequent activation of differentiation genes that terminate transit-amplification, producing self-renewal in daughter cells
that do not resemble...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3044/version/1
A Thoracic Mechanism of Mild Traumatic Brain Injury Due to Blast Pressure Waves
Provedor de dados: 17
Autores: Amy Courtney; Michael Courtney.
The mechanisms by which blast pressure waves cause mild to moderate traumatic brain injury (mTBI) are an open question.
Possibilities include acceleration of the head, direct passage of the blast wave via the cranium, and propagation of the blast wave
to the brain via a thoracic mechanism. The hypothesis that the blast pressure wave reaches the brain via a thoracic mechanism is
considered in light of ballistic and blast pressure wave research. Ballistic pressure waves, caused by penetrating ballistic
projectiles or ballistic impacts to body armor, can only reach the brain via an internal mechanism and have been shown to cause
cerebral effects. Similar effects have been documented when a blast pressure wave has been applied to the whole body or focused
on...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2169/version/1
A Three dimesional stochastic spatio-temporal model of cell spreading
Provedor de dados: 17
Autores: Yuguang P. Xiong; Padmini Rangamani; Benjamin Dubin-Thaler; Michael Sheetz; Ravi Iyengar.
Cell motility is important for many physiological processes and the underlying
biochemical reactions
motility have been well-characterized. Mathematical models, using
the biochemical reactions and focused
on different types of spreading behavior have been
constructed and analyzed. In this study, we build on
these previous models to develop a
three-dimensional stochastic model of isotropic spreading of mammalian
fibroblasts. The model is composed of three actin remodeling reactions that occur stochastically in space and time and are
regulated by membrane resistance forces. Numerical simulations indicate that the model qualitatively captures the experimentally
observed isotropic cell...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/62/version/1
A three-dimensional stochastic spatio-temporal model of cell spreading
Provedor de dados: 17
Autores: Yuguang P. Xiong; Padmini Rangamani; Benjamin Dubin-Thaler; Michael Sheetz; Ravi Iyengar.
Cell motility is important for many physiological processes and the underlying
biochemical reactions
motility have been well characterized. Mathematical models, using
the biochemical reactions and focused
on different types of spreading behavior have been
constructed and analyzed. In this study, we build on
these previous models to develop a
three-dimensional stochastic model of isotropic spreading of mammalian
fibroblasts. The model is composed of three actin remodeling reactions that occur stochastically in space and time and are
regulated by membrane resistance forces. Numerical simulations indicate that the model qualitatively captures the experimentally
observed isotropic cell...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/62/version/2
A Tobacco Homolog of DCN1 is Involved in Cellular Reprogramming and in Developmental
Transitions
Provedor de dados: 17
Autores: Julia Hosp; Alexandra Ribarits; Katarzyna Szaszka; Yongfeng Jin; Alisher Tashpulatov; Marina Baumann; Tatiana
Resch; Christina Friedmann; Elisabeth Ankele; Viktor Voronin; Klaus Palme; Alisher Touraev; Erwin Heberle-Bors.
Plant proteomes show remarkable plasticity in reaction to environmental challenges and during developmental transitions. Some
of this adaptability comes from ubiquitin-mediated protein destruction regulated by cullin-RING E3 ubiquitin ligases (CRLs).
CRLs are activated through modification of the cullin subunit with the ubiquitin-like protein RUB/NEDD8 by an E3 ligase called
defective in cullin neddylation 1 (DCN1). Here we show that tobacco DCN1 binds ubiquitin and RUB/NEDD8, and associates
with cullin. When knocked down by RNAi, tobacco pollen formation stopped and zygotic embryogenesis was blocked around the
globular stage. Additionally, we found that RNAi of DCN1 inhibited the stress-triggered reprogramming of cultured microspores
from their intrinsic...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics & Genomics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5728/version/1
A transgenic rat model for reducing adult neurogenesis.
Provedor de dados: 17
Autores: Jason S. Snyder; Laura Grigereit; Michelle Brewer; Jim Pickel; Heather A. Cameron.
The function of adult neurogenesis remains unclear. While many tools for manipulating neurogenesis have been developed for
mice, there are fewer tools for rats. Radiological and chemical strategies have been used to inhibit adult neurogenesis in rats but
these methods may also have undesired side effects. Since rats have a larger brain and can perform complex behaviors, it would
be useful to have additional rat models for studying neurogenesis. To address this gap we therefore developed a transgenic
GFAP-TK rat in which adult neurogenesis can be specifically inhibited. Preliminary results suggest that, as in mice, reduced adult
neurogenesis leads to anhedonia.
Tipo: Poster
Palavras-chave: Genetics & Genomics; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6592/version/1
A Unified Approach for Representing Structurally-Complex Models in SBML Level 3
Provedor de dados: 17
Autores: Robert Muetzelfeldt.
The aim of this document is to explore a unified approach to handling several of the proposed extensions to the SBML Level 3
Core specification.
The approach is illustrated with reference to Simile, a modelling environment which appears to have most of
the capabilities of the various SBML Level 3 package proposals which deal with model structure.
Simile
(http://www.simulistics.com) is a visual modelling environment for continuous systems modelling which includes the ability to
handle complex disaggregation of model structure, by allowing the modeller to specify classes of object and the relationships
between them.

The note is organised around the 6 packages listed on the SBML Level
3 Proposals web page...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4372/version/1
A unified mechanistic model of niche, neutrality and violation of the competitive exclusion principle
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
The origin of species richness is one of the most widely discussed questions in ecology. The absence of unified mechanistic model
of competition makes difficult our deep understanding of this subject. Here we show such a two-species competition model that
unifies (i) a mechanistic niche model, (ii) a mechanistic neutral (null) model and (iii) a mechanistic violation of the competitive
exclusion principle. Our model is an individual-based cellular automaton. We demonstrate how two trophically identical and
aggressively propagating species can stably coexist in one stable homogeneous habitat without any trade-offs in spite of their 10%
difference in fitness. Competitive exclusion occurs if the fitness difference is significant (approximately more than 30%)....
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7089/version/1
A Unifying Scenario on the Origin and Evolution of Cellular and Viral Domains
Provedor de dados: 17
Autores: Claudiu I. Bandea.
The cellular theory on the nature of life has been one of the first major advancements in biology. Viruses, however, are the most
abundant life forms, and their exclusion from mainstream biology and the Tree of Life (TOL) is a major paradox in biology. This
article presents a broad, unifying scenario on the origin and evolution of cellular and viral domains that challenges the
conventional views about the history of life and supports a TOL that includes viruses. Co-evolution of viruses and their host cells
has led to some of the most remarkable developments and transitions in the evolution of life, including the origin of non-coding
DNA as a genomic protective device against viral insertion damage. However, one of the major fundamental evolutionary...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Immunology; Microbiology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3888/version/1
A unique avenue to control drug resistant pathogens: Experimental evidences
Provedor de dados: 17
Autores: Sribir Sen.
Drug resistant bacterial pathogens are increasing in the environment due to multiple reasons. If any drug resistant pathogen grows
in a host, the host will face death treat because there is no way to resist their growth in the host system. Eventuality is death in
almost all cases. Reports on the mechanisms of drug resistance in bacteria are many. However, there is no solution for these cases.
The present work is providing an important understanding to fight against drug resistant pathogens and that can be used in
gastrointestinal diseases.
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/4934/version/1
A Universal Carrier Test for the Long Tail of Mendelian Disease
Provedor de dados: 17
Autores: Balaji S. Srinivasan; Jason Flannick; A. Scott Patterson; Christopher C. Chang; Tuan Pham; Sharon Young; Amit
Kaushal; James J. Lee; Pasquale Patrizio; Eric A. Evans.
*Background:* 

Mendelian disorders are individually rare but collectively common,
forming a "long tail" of genetic disease. More than 20 million people worldwide suffer from a disease in
this long tail before the age of 25, with minorities and developing countries at highest risk and with the number of carriers far in
excess of this figure. Importantly, the Jewish community’s campaign for universal Tay-Sachs screening shows that
these incurable diseases can nevertheless be prevented if carrier status is known before conception. A single highly-accurate assay
for the long tail of Mendelian disease would allow us to scale this successful campaign up to the general population, thereby
improving...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4192/version/1
A visual sense of number
Provedor de dados: 17
Autores: David Burr; John Ross.
Evidence exists for a non-verbal capacity to apprehend number, in humans^1^ (including infants^2,3^) and in other
primates^4-6^. Here we show that perceived numerosity is susceptible to adaptation, along with primary visual properties of a
scene like colour, contrast, size and speed. Apparent numerosity was decreased by adapting to large numbers of dots and increased
by adapting to small numbers, the effect depended entirely on the numerosity of the adapter, not on contrast, size, orientation or
pixel density, and occurred with very low adapter contrasts. We suggest that numerosity is also an independent primary visual
property, not reducible to others like spatial frequency or density of texture^7^.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1353/version/1
A war-prone tribe migrated out of Africa to populate the world.
Provedor de dados: 17
Autores: Eduardo Moreno.
Of the tribal hunter gatherers still in existence today, some lead lives of great violence, whereas other groups live in societies with
no warfare and very little murder^1,2,3,4,5^. Here I find that hunter gatherers that belong to mitochondrial haplotypes L0, L1 and
L2 do not have a culture of ritualized fights. In contrast to this, almost all L3 derived hunter gatherers have a more belligerent
culture that includes ritualized fights such as wrestling, stick fights or headhunting expeditions. This appears to be independent of
their environment, because ritualized fights occur in all climates, from the tropics to the arctic. There is also a correlation between
mitochondrial haplotypes and warfare propensity or the use of murder and suicide to resolve...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics & Genomics; Earth & Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4303/version/1
AAD-2004, a potent spin trapping molecule and microsomal prostaglandin E synthase-1 inhibitor,
shows safety and efficacy in a mouse model of ALS
Provedor de dados: 17
Autores: Jin Shin; Young Lee; Jae Lee; Yong Lee; Woong Cho; Doo Im; Jin Lee; Bok Yun; Sun Son; Sun Park; Soo Byun; Joe
Springer; Byoung Gwag.
While free radicals and inflammation constitute major routes of neuronal injury occurring in neurodegenerative diseases, neither
antioxidants nor nonsteroidal anti-inflammatory drugs (NSAIDs) have shown significant efficacy in human clinical trials. To
explore the possibility that concurrent blockade of free radicals and PGE2-mediated inflammation might constitute a safe and
effective
therapeutic
approach
to
certain
neurodegenerative
diseases,
we
have
developed
2-hydroxy-5-[2-(4-trifluoromethylphenyl)-ethylaminobezoic acid (AAD-2004) as a derivative of aspirin. AAD-2004 completely
removed free radicals at 50 nM as a potent spin trapping molecule and inhibited microsomal prostaglandin E synthase-1
(mPGES-1) with an IC50 of 230 nM. Oral administration of...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5237/version/1
ABC for ancestral inference
Provedor de dados: 17
Autores: Richard Wilkinson; Simon Tavare.
ABC for ancestral inference
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5963/version/1
ABC for Temporally Sampled Genetic Data
Provedor de dados: 17
Autores: Mark A. Beaumont.
ABC for Temporally Sampled Genetic Data
Tipo: Presentation
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5953/version/1
ABC Methods for Bayesian Model Choice
Provedor de dados: 17
Autores: Christian P. Robert.
Approximate Bayesian computation (ABC), also known as likelihood-free methods, have become a standard tool for the analysis
of complex models, primarily in population genetics but also for complex financial models. The development of new ABC
methodology is undergoing a rapid increase in the past years, as shown by multiple publications, conferences and even software.
While one valid interpretation of ABC based estimation is connected with nonparametrics, the setting is quite different for model
choice issues. We examined in Grelaud et al. (2009, Bayesian Analysis) the use of ABC for Bayesian model choice in the specific
of Gaussian random fields (GRF), relying on a sufficient property only enjoyed by GRFs to show that the approach was
legitimate. Despite...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5961/version/1
ABC SMC for parameter estimation and model selection with applications in systems biology
Provedor de dados: 17
Autores: Tina Toni.
Approximate Bayesian Computation (ABC) methods can be used in situations where the evaluation of the likelihood is
computationally prohibitive. They are thus ideally suited for analyzing the complex dynamical models encountered in systems
biology, where knowledge of the full (approximate) posterior is often essential.

This
talk gives an overview of an ABC algorithm based on Sequential Monte Carlo (ABC SMC). Different uses of the algorithm will
be presented, depending on the application question of interest. The first is the general parameter estimation framework, where the
interest lies in estimating the posterior parameter distribution from available experimental data. In the second context we ask
whether the model can...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5964/version/1
Ablation of smooth muscle myosin heavy chain SM2 increases smooth muscle contractility and results
in postnatal death in mice
Provedor de dados: 17
Autores: Mei Chi; Yingbi Zhou; Srikanth Vedamoorthyrao; Gopal Babu; Muthu Periasamy.
The smooth muscle myosin heavy chains (SMHC) are motor proteins powering smooth muscle contraction. Alternate splicing of
SHMC gene at the C-terminus produces SM1, and SM2 myosin isoforms; SM2 (200 kDa) contains a unique 9-amino-acid
sequence at the carboxyl terminus, whereas SM1 (204 kDa) has a 43 amino acid non-helical tail region. To date the functional
difference between C-terminal isoforms has not been established; therefore, we used an exon-specific gene targeting strategy and
generated a mouse model specifically deficient in SM2. Deletion of exon-41 of the SMHC gene resulted in a complete loss of
SM2 in homozygous (_SM2^-/-^_) mice, accompanied by a concomitant down-regulation of SM1 in bladders. While
heterozygous (_SM2^+/-^_) mice appeared normal...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics & Genomics; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1643/version/1
ABO and Rh Blood Group Distribution Among Kunbis (Maratha) population of Amravati District,
Maharashtra
Provedor de dados: 17
Autores: NANDKISHOR E. WARGHAT; NAVIN R. SHARMA; MUMTAZ M. BAIG; A. R. Yadav; S. H. Sharma; G. S.
Pachalore.
The present study reports the distribution of ABO and Rh blood groups among the Kunbis (Maratha) population of Amravati
district. The phenotypic frequency of blood group B is observed highest (33.06) percent, O (31.04), A (27.02) and AB is lowest
(08.33) percent. The phenotypic frequency of Rh negative is (04.26) percent. TheKunbis (Maratha) population shows close
genetic relationship with the Gujratis.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4868/version/1
Aboveground Net Primary Productivity in Grazed and Ungrazed pastures: Grazing Optimisation
Hypothesis or Local Extinction of Vegetation Species
Provedor de dados: 17
Autores: Silvanus G. Otieno; Jesse T. Njoka; Truman P. Young; Stephen M. Mureithi; Robinson K. Ngugi.
The controversy that has surrounded herbivory studies in the last few decades prompted our investigation to establish the extent to
which herbivore optimisation hypothesis or compensatory growth evidence is real. We used the traditional movable cage method
to collect primary productivity data on herbage, functional groups and key individual grass species in various controlled large
herbivore treatments in an east African savanna. The herbivore treatments in triplicate blocks included cattle, wild herbivores with
and without mega herbivores and combinations of cattle and wild herbivores also with and without mega herbivores. The findings
revealed that at herbage level, most grazed treatments (four out of five) had higher productivity than the ungrazed...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3452/version/1
Absence of historical temporal trends in monthly, seasonal, and annual streamflows for the Okanagan
and Similkameen Rivers in south-central British Columbia, Canada
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Potential historical temporal trends in monthly, seasonal, and annual mean, minimum, and maximum streamflows and date of the
spring freshet runoff peak were investigated for the Okanagan and Similkameen Rivers in south-central British Columbia, Canada.
There appears to be no compelling evidence that streamflow patterns in the Okanagan and Similkameen Rivers have changed over
the available hydrometric record, nor does there appear to be evidence that future changes in streamflow patterns are imminent or
likely.
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6584/version/1
Absolute Aqueous Redox Potentials ( via a new link between aqueous and gaseous properties)
Provedor de dados: 17
Autores: Raji Heyrovska.
The new finding here, that the conventional standard potentials (based on S.H.E.) are linearly dependent on ionization potentials,
has yielded the absolute values of aqueous standard potentials.
Tipo: Presentation
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3395/version/1
Absolute Potentials of Standard Reference Electrodes at 25 C
Provedor de dados: 17
Autores: Raji Heyrovska.
Aqueous standard redox potentials are conventionally referred to that of the standard hydrogen electrode (SHE) as zero (IUPAC
definition), in the absence of the knowledge of its absolute value. Recently, the author obtained its value (4.20 V) from a newly
found linear dependence of redox potentials on ionization potentials. This has enabled now to express the potentials of standard
reference electrodes in terms of the absolute values.
Tipo: Presentation
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4354/version/1
Abundance and Composition of Zooplankton (Copepoda, Cladocera, Rotifera) in Lake Taal: Potential
Impact of Intensive Size-Selective Predation by the Freshwater Sardine, Sardinella tawilis (Herre
1927)
Provedor de dados: 17
Autores: Rey Donne Papa; Roberto Pagulayan; Alicia Ely Pagulayan.
Zooplankton are considered to be important members of the lake ecosystem. The abundance and composition of which are due to
several factors, for example, the impact of intensive size-selective predation by planktivorous fishes residing in the lake. In this
study, the abundance and composition of zooplankton found in the vicinity of Isla Napayun - a known fishing ground of the
freshwater sardine, Sardinella tawilis (Herre 1927) was analyzed using samples taken from vertical plankton tows from the 10 and
20 m depths in 2 sampling sites from the said area. These were then compared with the stomach contents of S. tawilis taken
during the same period. Results show that there were 4 genera of Copepoda, 4 genera of Cladocera and 2 genera of Rotifera
found in...
Tipo: Presentation
Palavras-chave: Ecology; Earth & Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/684/version/1
Abundance of intrinsic disorder in SV-IV, a multifunctional androgen-dependent protein secreted
from rat seminal vesicle
Provedor de dados: 17
Autores: Silvia Vilasi; Raffaele Ragone.
The potent immunomodulatory, anti-inflammatory and procoagulant properties of the
protein no. 4 secreted
from the rat seminal vesicle epithelium (SV-IV) have been
previously found to be modulated by a
supramolecular monomer-trimer equilibrium.
More structural details that integrate experimental data into a
predictive
framework
have
fold-recognition
strategies
recently
were
not
been
reported.
successful
in
Unfortunately,
creating
a
homology
theoretical
modelling
model
of
and
the
structural
organization of SV-IV. It was inferred that the global structure of SV-IV is not
similar
to any protein of known three-dimensional structure. Reversing...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1394/version/1
ACAT1, Cav-1, and PrP expression in brains and skin fibroblasts from Sarda breed sheep with
scrapie-resistant and scrapie-susceptible genotype.
Provedor de dados: 17
Autores: Alessandra Pani; Marirosa Putzolu; Claudia Mulas; Cristina D. Orrù; Claudia Abete; Claudia Norfo; M.
Dolores Cannas; Sergio Laconi; Paolo La Colla; Sandra Dessì.
Scrapie is an infective ovine neurodegenerative disease; the only identified component of the infectious agent being an aberrant
isoform (PrPSc) of the cellular prion protein (PrPC). So far, no means for ante-mortem diagnosis are available for Scrapie as well
as for any other mammal Transmissible Spongiform Encephalopaties. We recently found a strong relationship between cell
susceptibility to scrapie-infection and intracellular cholesterol homeostasis alterations. In brain tissues as well as in ex vivo
cultures of skin fibroblasts and PBMCs from healthy and scrapie-affected sheep carrying a scrapie-susceptible (ARQ/ARQ)
genotype, the levels of cholesterol esters were consistently higher than in tissues and cultures derived from animals with a...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1211/version/1
ACBD: Database for Ascidian Chemical Genomics
Provedor de dados: 17
Autores: Yuichiro Hira; Jun Terai; Mitsuru Nakamura; Etsu Tashiro; Masaya Imoto; Kotaro Oka; Kohji Hotta.
Chemical biology approach enables us to understand the complex biological systems,using small molecules such as a specific
activator or inhibitor of protein, a hormone-likeinducer, or a neurotransmitter etc. When such approach is performed
genome-widely, that research is especially called "chemical genomics". We are planning to make a new
start of chemical genomics using one of chordate model animal, ascidian. As a first step, we constructed a database called ACBD
(Ascidians Chemical Biology Database).

First, we reviewed and annotated past
articles which describe the uses of small chemicals in the field of ascidians biology. In ACBD, chemical information and effects
on ascidian are manually extracted...
Tipo: Poster
Palavras-chave: Developmental Biology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5087/version/2
ACBD: Database for Ascidian Chemical Genomics
Provedor de dados: 17
Autores: Yuichiro Hira; Jun Terai; Masaya Imoto; Etsu Tashiro; Kohji Hotta.
Chemical biology approach enables us to understand the complex biological systems, using small molecules such as a specific
activator or inhibitor of protein, a hormone-like inducer, or a neurotransmitter. When such approach is performed genome-widely,
that research is especially called "chemical genomics". We are planning to make a new start of chemical
genomics using one of chordate model animal, ascidian. As a first step, we constructed a database called ACBD (Ascidians
Chemical Biology Database). 

 First, we reviewed and annotated past articles which
describe the uses of small chemicals in the field of ascidians biology. In ACBD, chemical information and effects on ascidian are
manually extracted...
Tipo: Poster
Palavras-chave: Developmental Biology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/5087/version/1
Accelerated Macromolecular Solution Structure Recovery
Provedor de dados: 17
Autores: Petrus Zwart; Haiguang Liu.
Small Angle X-ray Scattering (SAXS) is a standard technique for the determination of low-resolution shapes of macromolecules
and their complexes, adding important insights in understanding biological function. We present a novel and computationally
efficient method for shape reconstruction from SAXS data. High-quality molecular shapes are calculated in less than two minutes,
providing real-time feedback during SAXS experiments.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6521/version/1
Accounting for molecular stochasticity in systematic revisions: species limits and phylogeny of
Paroaria
Provedor de dados: 17
Autores: Liliana M. Dávalos; Ana L. Porzecanski.
Different frameworks have been proposed for using molecular data in systematic revisions, but there is ongoing debate on their
applicability, merits and shortcomings. In this paper we examine the fit between morphological and molecular data in the
systematic revision of Paroaria, a group of conspicuous songbirds endemic to South America. We delimited species based on
examination of > 600 specimens, and developed distance-gap, and distance- and character-based coalescent
simulations to test species limits with molecular data. The morphological and molecular data collected were then analyzed using
parsimony, maximum likelihood, and Bayesian phylogenetics. The simulations were better at evaluating the new species limits
than using genetic distances....
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3357/version/1
Accumulation of Neural Activity in the Posterior Insula Encodes the Passage of Time
Provedor de dados: 17
Autores: Marc Wittmann; Alan N. Simmons; Jennifer L. Aron; Martin P. Paulus.
The experience of time, i.e. the estimation of duration, is fundamental for perception and behavior and, therefore, essential for the
survival of the individual organism. Over the last decades, neuroimaging, neurophysiological and clinical neuropsychological
studies have pointed to many different brain areas involved in the processing of time. However, the core neural substrates and the
processes accounting for the encoding of duration, which could form a timekeeping mechanism (essentially, a neural clock), are
still unknown. Here we present evidence of neurophysiological activity in circumscribed areas of the human brain that is involved
in the encoding of duration. Time-activity curves of neural activation derived from event-related functional magnetic...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2062/version/1
Accuracy of computational solvation free energies for neutral and ionic compounds: Dependence on
level of theory and solvent model
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas to aqueous phase standard state (1 atm to 1 mol/L; 298.15 K) free energies of solvation ([DELTA]G^o^~solv~) were
calculated for a range of neutral and ionic inorganic and organic compounds using various levels and combinations of
Hartree-Fock and density functional theory (DFT) and composite methods (CBS-Q//B3, G4MP2, and G4) with the IEFPCM-UFF,
CPCM, and SMD solvation models in Gaussian 09 (G09). For a subset of highly polar and generally polyfunctional neutral
organic compounds previously identified as problematic for prior solvation models, we find significantly reduced
[DELTA]G^o^~solv~ errors using the revised solvent models in G09. The use of composite methods for these compounds also
substantially reduces their apparent [DELTA]G^o^~solv~...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4864/version/1
Accurate estimation of homologue-specific DNA concentration-ratios in cancer samples allows
long-range haplotyping
Provedor de dados: 17
Autores: Scott L. Carter; Matthew Meyerson; Gad Getz.
Interpretation of allelic copy measurements at polymorphic markers in cancer samples presents distinctive challenges and
opportunities. Due to frequent gross chromosomal alterations occurring in cancer (aneuploidy), many genomic regions are present
at homologous-allele imbalance. Within such regions, the unequal contribution of alleles at heterozygous markers allows for direct
phasing of the haplotype derived from each individual parent. In addition, genome-wide estimates of homologue specific copyratios (HSCRs) are important for interpretation of the cancer genome in terms of fixed integral copy-numbers. We describe
HAPSEG, a probabilistic method to interpret bi- allelic marker data in cancer samples. HAPSEG operates by partitioning the
genome into...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6494/version/1
Accurate modeling of confounding variation in eQTL studies leads to a great increase in power to
detect trans-regulatory effects
Provedor de dados: 17
Autores: Nicolo Fusi; Oliver Stegle; Neil Lawrence.
Expression quantitative trait loci (eQTL) studies are an integral tool to investigate the genetic component of gene expression
variation. A major challenge in the analysis of such studies are hidden confounding factors, such as unobserved covariates or
unknown environmental influences. These factors can induce a pronounced artifactual correlation structure in the expression
profiles,
which
may
create
spurious
false
associations
or
mask
real
genetic
association
signals.


Here, we report PANAMA (Probabilistic ANAlysis of genoMic dAta), a novel
probabilistic model to account for confounding factors within an
eQTL analysis. In contrast to previous
methods, PANAMA learns hidden factors jointly with the...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5995/version/1
Accurate Reconstruction of Molecular Phylogenies for Proteins Using Codon and Amino Acid Unified
Sequence Alignments (CAUSA)
Provedor de dados: 17
Autores: Xiaolong Wang; Yu Fu; Yue Zhao; Qi Wang; Chandra Sekhar Pedamallu; Shuang-yong Xu; Yingbo Niu;
Jingjie Hu.
Based on molecular clock hypothesis, and neutral theory of molecular evolution, molecular phylogenies have been widely used
for inferring evolutionary history of organisms and individual genes. Traditionally, alignments and phylogeny trees of proteins
and their coding DNA sequences are constructed separately, thus often different conclusions were drawn. Here we present a new
strategy for sequence alignment and phylogenetic tree reconstruction, codon and amino acid unified sequence alignment
(CAUSA), which aligns DNA and protein sequences and draw phylogenetic trees in a unified manner. We demonstrated that
CAUSA improves both the accuracy of multiple sequence alignments and phylogenetic trees by solving a variety of molecular
evolutionary problems in...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6730/version/1
Accurate telemonitoring of Parkinson’s disease progression by non-invasive speech tests
Provedor de dados: 17
Autores: Athanasios Tsanas; Max A. Little; Patrick E. McSharry; Lorraine O. Ramig.
Tracking Parkinson's disease (PD) symptom progression often uses the Unified Parkinson’s Disease
Rating Scale (UPDRS), which requires the patient's presence in clinic, and time-consuming physical examinations by
trained medical staff. Thus, symptom monitoring is costly and logistically inconvenient for patient and clinical staff alike, also
hindering recruitment for future large-scale clinical trials. Here, for the first time, we demonstrate rapid, remote replication of
UPDRS assessment with clinically useful accuracy (about 7.5 UPDRS points difference from the clinicians’
estimates), using only simple, self-administered, and non-invasive speech tests. We characterize speech with signal processing
algorithms,...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3920/version/1
Acknowledging contributions to online expert assistance
Provedor de dados: 17
Autores: Andra Waagmeester; Gareth Palidwor; Pawel Szczesny; Istvan Albert; Mary Mangan; Chris Miller; Simon Cockell;
Pierre Lindenbaum; Daniel A. M. M. Silvestre; Giovanni Marco Dall’Olio; Chris Miller.
We present a poster which contains a sequence of a question, answers to this question and comments regarding acknowledging
content on BioStar. Biostar.stackexchange.com is a website where questions about Bioinformatics can be asked and answered.
Users can also comment on both the questions and the answers. The site is modelled after www.stackoverflow.com (see
description
from
Joel
Spolsky),
a
comparable
site
for
programmers.



Users find the site valuable both for answers to questions they have and as a
reference. Since the content can also be viewed without registration the site likely reaches a larger audience. For instance, BioStar
questions are often referenced on Twitter and FriendFeed. This leads to...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6043/version/1
Acknowledging contributions to online expert assistance
Provedor de dados: 17
Autores: Andra Waagmeester; Gareth Palidwor; Pawel Szczesny; Istvan Albert; Mary Mangan; Chris Miller; Simon Cockell;
Pierre Lindenbaum; Daniel A. M. M. Silvestre; Giovanni Marco Dall’Olio; Chris Evelo.
We present a poster which contains a sequence of a question, answers to this question and comments regarding acknowledging
content on BioStar. Biostar.stackexchange.com is a website where questions about Bioinformatics can be asked and answered.
Users can also comment on both the questions and the answers. The site is modelled after www.stackoverflow.com (see
description from Joel Spolsky), a comparable site for programmers.
 
Users find the
site valuable both for answers to questions they have and as a reference. Since the content can also be viewed without registration
the site likely reaches a larger audience. For instance, BioStar questions are often referenced on Twitter and FriendFeed. This
leads to the question of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6041/version/1
Activation of an Estrogen/ Estrogen Receptor Signaling by BIG3 Through Its Inhibitory Effect on
Nuclear Transport of PHB2/REA in Breast Cancer
Provedor de dados: 17
Autores: Jung-Won Kim; Miki Akiyama; Jae-Hyun Park; Meng-Lay Lin; Arata Shimo; Tomomi Ueki; Yataro Daigo; Tatsuhiko
Tsunoda; Toshihiko Nishidate; Yusuke Nakamura; Toyomasa Katagiri.
Breast cancer is known to be a hormone-dependent disease, and estrogens through an interaction with estrogen receptor (ER)
enhance the proliferative and metastatic activity of breast tumor cells. Here we show a critical role of transactivation of BIG3,
brefeldin A-inhibited guanine nucleotide-exchange protein 3, in activation of the estrogen/ER signaling in breast cancer cells.
Knocking-down of BIG3 expression with small-interfering RNA (siRNA) drastically suppressed the growth of breast cancer cells.
Subsequent co-immunoprecipitation and immunoblotting assays revealed an interaction of BIG3 with prohibitin 2/repressor of
estrogen receptor activity (PHB2/REA). When BIG3 was absent, stimulation of estradiol caused the translocation of PHB2/REA
to the...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics & Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/2834/version/1
Activation of Ras-ERK pathway by Fgf8 and its downregulation by Sprouty2 for the isthmus
organizing activity
Provedor de dados: 17
Autores: Asuka Suzuki-Hirano; Tatsuya Sato; Harukazu Nakamura.
In the previous studies, we showed that strong Fgf8 signaling activates the Ras-ERK pathway to induce cerebellum. Here, we
show importance of negative regulation of this pathway. 'Prolonged' activation of ERK by misexpression
of _Fgf8b_ and dominant-negative _Sprouty2_ (_dnSprouty2_) did not change the fate of the mesencephalic alar plate.
Downregulation of ERK activity using a MEK inhibitor, U0126, or by tetracycline dependent Tet-off system after co-expression
of _Fgf8b_ and _dnSprouty2_, forced the mesencephalic alar plate to differentiate into cerebellum. We then paid attention to
Mkp3. After misexpression of _dnMkp3_ and _Fgf8b_, slight downregulation of ERK activity occurred, which may be due to
Sprouty2, and the mesencephalon...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2089/version/1
Activation of TRF3 Transcription Factor by Small Interfering RNAs
Provedor de dados: 17
Autores: Stephan Persengiev.
RNA interference (RNAi) is a conserved biological response to double-stranded RNAs that results in posttranscriptional silencing
of target gene expression. Double-stranded processed RNAs of 21-23 nt were found to affect in a non-specific manner a number
of signaling and transcription pathways, including interferon and PKR cascades. We report here that siRNAs induce the
expression of general transcription factor TRF3, which can trigger an interferon response in mammalian cells.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1206/version/1
Activity of Exoenzymes in Treated Wastewater Irrigated Soils
Provedor de dados: 17
Autores: Elisabeth Jüschke; Bernd Marschner.
The reuse of reclaimed wastewater for irrigation of agricultural fields greatly influences the activity of soil microorganisms
through the input of organic compounds. Due to the production of exoenzymes by microorganisms for the decomposition of
substrates it can be assumed that the irrigation with treated wastewater (TWW) has a strong influence on the soil enzyme pool. In
this study the activity of ten exoenzymes, which catalyses processes in C, N and P nutrient cycles, were determined in 3 different
soils in 0-10, 10-20, 20-30, 30-50, 50-70 and 70-100 cm soil depth. The soils were used for agriculture and irrigated with
reclaimed wastewater reused after a secondary treatment step. Additionally a control after freshwater irrigation was studied. Due
to the...
Tipo: Presentation
Palavras-chave: Ecology; Microbiology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6278/version/1
Acute Toxicity of Perfluorooctane Sulfonic Acid on Early Life Stages of Daphnia Magna, Siriella
Armata, Paracentrotus Lividus Sea Urchin, and Turbot (Scophthalmus Maximus L.).
Provedor de dados: 17
Autores: Lazhar Mhadhbi; Sara Pérez Fernandez; Diego Real Conde; Moncef Boumaiza; Ricardo Beiras.
Perfluorooctane sulfonate (PFOS) is a persistent organic pollutant whose potential toxicity is causing great concern. In the present
study, we used two crustaceans (_Daphnia magna_, _Siriella armata_), echinoid embryos (_Paracentrotus lividus_) and turbot
(_Scophthalmus maximus L._) embryos and larvae to investigate the acute toxicity of this compound. The marine species _S.
armata_ exhibited greater sensitivity than the freshwater species _D. magna_. In the 48-h acute toxicity test the median lethal
concentration was 10.96 mg/L for _S. armata_ and 87.46 mg/L for _D. magna_. In the 96h toxicity test, turbot showed the lowest
EC50 (0.155 mgL-1), whilst the EC50 for _S. armata_ was 7.92 mgL-1 which was approximately three times lower than that for
sea urchin...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Ecology; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4657/version/1
Adapting natural resource management to climate change on the Olympic Peninsula
Provedor de dados: 17
Autores: Jessica Halofsky; David L. Peterson.
Climate change presents a major challenge to natural resource managers both because of the magnitude of potential effects of
climate change on ecosystem structure, process, and function, and because of the uncertainty associated with those potential
ecological effects. Concrete ways to adapt to climate change are needed to help natural resource managers take the first steps to
incorporate climate change into management and take advantage of opportunities to balance the negative effects of climate
change. We initiated a climate change adaptation case study at Olympic National Forest and Olympic National Park to determine
how to adapt management of federal lands on the Olympic Peninsula to climate change. As a part of the case study process, we
conducted a...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5239/version/1
Adaptive evolution and then what?
Provedor de dados: 17
Autores: Richard Svanbäck; Mario Pineda-Krch; Michael Doebeli.
Traits determining ecological interactions and dynamics are generally subject to natural selection. That genetically based
individual variation in ecological traits can influence population dynamics has interested population biologist from various
perspectives. Population ecologists recognized the need to incorporate individual variation in models of population regulation,
while evolutionary biologists wish to understand genetic and evolutionary dynamics, e.g. of life history traits, in density-regulated
populations. But how does adaptation in ecological traits affect population dynamics? In this project we investigated how
ecological dynamics changes as a consequence of adaptive evolution in ecological traits using an individual-based predator-prey
model.
Tipo: Poster
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/57/version/1
Adding automated data analysis and biological evaluation to affyanalysisQC
Provedor de dados: 17
Autores: Anwesha Dutta.
Almost every cell in the body contains a full set of chromosomes and identical genes. However, only a fraction of these genes are
turned on, at any given time and it is this subset of genes that are expressed, which confers unique properties to each cell type.
Gene expression is the term used to describe the transcription of the information contained within the DNA into messenger RNA
(mRNA) molecules that are then translated into proteins which perform most of the critical functions of cells.


Gene expression is a highly complex and tightly regulated process that allows a cell
to respond dynamically both to environmental stimuli and to its own changing needs. This mechanism acts as both an on/off
switch to control which...
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5969/version/1
Adenovirus-mediated transfer of siRNA against survivin enhances the radiosensitivity of human
non-small cell lung cancer cells
Provedor de dados: 17
Autores: Cheng-Ta Yang; Jhy-Ming Li; Hsu-Huei Weng; Ya-Chin Li; Miao-Fen Chen.
Expression of survivin has been reported to be correlated with shorter survival in patients with non-small cell lung cancer
(NSCLC), and overexpression of survivin may lead to radioresistance in various human cancers. In this study, we inhibited
survivin expression by using an adenoviral vector (AdsiSurvivin)-mediated RNAi to elucidate the combined effect of
survivin-targeting gene therapy and radiotherapy on the NSCLC cells. Our data revealed that AdsiSurvivin exerted survivin gene
silencing, induced apoptosis, and significantly attenuated the growth potential in NSCLC cells within 72 hours after infection. The
combined treatment modalities with AdsiSurvivin infection and radiation were significantly more potent on cell-growth inhibition
than monotherapy....
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2589/version/1
Adherence to cancer screenings: Is the telephone survey a good method of investigation?
Provedor de dados: 17
Autores: Alessandro Cucchi; Mauro Bergamini.
*INTRODUCTION* - In order to define subjective variables, the methodology on the assessment of the women participation to
screening programs to prevent cervical cancer is presented.
*MATERIALS AND METHODS* - The study
was conducted using a structured questionnaire administered by telephone to a sample of women invited to screening, regardless
of their real participation to the Pap test. The phone calls were made within 2 days prior to the Pap test session. The questionnaire
contained 12 closed questions.	
*RESULTS* - We contacted a total of 1206 women: a total of
1100
women
(93.70%)
received
the
invitation
letter
and
answered
to
the
questionnaire.	
*CONCLUSIONS* - The chosen procedure...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3016/version/1
ADME/Tox WEB in silico predictions of longer chain perfluoroalkyl carboxylic acid pKa values are
more accurate than other computational methods
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Perfluoroalkyl carboxylates are contaminants whose environmental fate and toxicological effects are of broad interest within the
academic, industrial, and governmental science and regulatory communities. In addition, coupled perfluoroalkyl and carboxylate
moieties are often used in medicinal chemistry as part of the drug design process. However, to date there has been a notable
absence of reliable acidity constant estimation programs for these compounds. Here we report that the ADME/Tox WEB method
for in silico pKa value predictions is more accurate than the PM6, SPARC, and COSMOtherm methods for the longer chain
perfluoroalkyl carboxylic acids, suggesting this may be a good general acidity constant estimation approach for these compounds.
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2936/version/1
Adopting Nrf2 and NF-κB from cancer: Is there any role of the duo in diabetes?
Provedor de dados: 17
Autores: Geeta Negi; Ashutosh Kumar; Shyam S. Sharma.
Oxidative stress and inflammation are two well-recognized events occurring in normal cells during cancer chemotherapy. Several
antioxidant and anti-inflammatory agents have therefore been tried as rational and effective strategies for chemoprotection.
Elaborate studies on antioxidants and anti-inflammatory agents in various experimental models of cancer revealed that these
agents act by modulating the expression and/or activity of the transcription factors nuclear factor erythroid 2-related factor 2
(Nrf2) and nuclear factor-kappa B (NF-κB). Nrf2 is considered the main sentinel of antioxidant defense as it induces
many antioxidant and phase 2 enzymes in response to stressful conditions. Likewise, NF-κB is considered as a
denominator of...
Tipo: Manuscript
Palavras-chave: Cancer; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6581/version/1
Adoption of simultaneous different strategies against different opponents enhances cooperation
Provedor de dados: 17
Autores: Lucas Wardil; Jafferson K. L. da Silva.
The emergence of cooperation has been widely studied in the context of game theory on structured populations. Usually the
individuals adopt one strategy against all their neighbors. The structure can provide reproductive success for the cooperative
strategy, at least for low values of defection tendency. Other mechanisms, such punishment, can also be responsible for
cooperation emergence. But what happens if the players adopt simultaneously different strategies against each one of their
opponents, not just a single one? Here we study this question in the prisoner dilemma scenario structured on a square lattice and
on a ring. We show that if an update rule is defined in which the players replace the strategy that furnishes the smallest payoff,
a...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3035/version/1
ADP-ribose polymer - a novel and general biomarker of human cancers of head & neck,
breast, and cervix
Provedor de dados: 17
Autores: Rennie O. Lakadong; Amal C. Kataki; Rajeshwar N. Sharan.
Background: Poly-ADP-ribosylation (PAR), a reversible post-translational modification of cellular proteins, is involved in various
cellular and molecular processes including carcinogenesis (Althaus & Richter, 1987; Jacobson & Jacobson,
1989; Poirier & Moreau, 1992; Boulikas, 1993; Sharan, 2009). ADP-ribose polymer adducts are added onto target
cellular proteins by this metabolic process. We hypothesize that a decrease in the concentration of total poly-ADP-ribose adducts
of
peripheral
blood
lymphocyte
(PBL)
proteins
strongly
correlates
with
incidence
of
human
cancer.

Methods: A novel, sensitive and convenient immunoprobe assay of poly-ADP-ribose adducts of cellular
proteins has been employed using slot blots of...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2010
URL: http://precedings.nature.com/documents/4650/version/1
Adsorption of uranium and thorium on new adsorbent prepared from Moroccan oil shale
impregnated with phosphoric acid
Provedor de dados: 17
Autores: El Hassane Khouya; Khadija Legrouri; Said Fakhi; Hassan Hannache.
Attention has been focused recently on the production of new adsorbents from Moroccan oil shale of Tarfaya (layer R3) by
chemical activation with phosphoric acid and its application in wastewaters treatment. The optimal conditions for the preparation
were searched and the tests of adsorption of uranium and thorium ions were affected. The best product was obtained by used of
the ratio of activated agent/precursor equal 3 and activation of the mixture in air at 250°C during two hours after
prepocessing at 120°C in air. Under these conditions the maximal adsorption capacity of methylene blue and specific
area (SBET) of the new adsorbent were 526 mg/g and 630 m2/g, respectively. A batch mode experiment was used to explore the
performances of...
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5098/version/1
Advanced thermodynamic and processing modelling integration for amine scrubbing in
post-combustion CO~2~ capture
Provedor de dados: 17
Autores: Niall Mac Dowell; Amparo Galindo; Claire S. Adjiman; George Jackson.
The reduction in CO~2~ emissions from anthropogenic sources has become a topic of widespread interest over the past number of
years. As the power generation sector is by far the largest stationary-point-source of CO~2~, being responsible for approximately
35% of total global CO~2~ emissions^1^ this question has special relevance for this industry. As the inclusion of carbon capture
facilities incurs a significant energy penalty on the efficiency coal-fired power-stations, there is a strong requirement for the
improvement of these systems in terms of the minimisation of operation and maintenance costs, capital costs and the
maximisation of efficiency and flexibility. This last issue has relevance for start-up times and ramp-rates. Post-combustion
capture...
Tipo: Presentation
Palavras-chave: Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2638/version/1
Advancing transcriptome platforms
Provedor de dados: 17
Autores: Shuobo Shi.
During the last decade of years, remarkable technological innovations have emerged that allow the direct or indirect determination
of the transcriptome at unprecedented scale and speed. Studies using these methods have already altered our view of the extent
and complexity of transcript profiling, which has advanced from one-gene-at-a-time to a holistic view of the genome. Here, we
outline the major technical advances in transcriptome characterization, including the most popular used hybridization-based
platform, the well accepted tag-based sequencing platform, and the recently developed RNA-Seq (RNA sequencing) based
platform. Importantly, these next-generation technologies revolutionize assessing the entire transcriptome via the recent RNA-Seq
technology.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5894/version/1
Adverse Effects of Trichothiodystrophy DNA Repair and Transcription Gene Abnormalities on
Human Fetal Development
Provedor de dados: 17
Autores: Roxana Moslehi; Caroline Signore; James Troendle; Amiran Dzutsev; James L. Mills.
The effects of DNA repair and transcription genes in human prenatal life have never been studied. Trichothiodystrophy (TTD) is a
rare (affected frequency of 10^-6^) recessive disorder caused by mutations in genes involved in the nucleotide excision repair
(NER) pathway and in transcription. Based on our clinical observations, we conducted a genetic epidemiologic study to
investigate gestational outcomes associated with TTD. We compared pregnancies resulting in TTD-affected offspring (N=24)
with respect to abnormalities in their antenatal and neonatal periods to pregnancies resulting in their unaffected siblings (N=18),
accounting for correlation, and to population reference values. Significantly higher incidence of several severe gestational
complications...
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics & Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3582/version/1
Adversity and sex differences in social and emotional sensitivity in children; a possible mechanism for
sex differences in psychiatric disorders
Provedor de dados: 17
Autores: Jonathan Hill; Helen Sharp; Lynne Murray.
Females are superior to males on a range of tasks indexing social sensitivity, the capacity to infer others' mental states
and respond with appropriate behaviours and emotions(1-3). There are also sex differences in psychiatric disorders in children and
adolescents. Boys have higher rates of psychiatric disorders before puberty, but disorders increase markedly in girls after puberty
(4). The causes of the commonest forms of disorder, antisocial behaviour problems in boys, and depression in girls, entail altered
brain function caused by genetic variations and psychosocial adversities mainly arising in the family, and the interaction between
the two (5;6). This may be explained by sex differences in social and emotional sensitivity provided they...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4553/version/1
Aetiology and treatment of epidermal depigmentory disorder in humans
Provedor de dados: 17
Autores: S. S. Sawhney.
The epidermal depigmentary trigger in humans at post-natal level may occur with the toxification of skin organ with the
endogenously produced melanocytotoxic hydrogen peroxide and subsequent formation of hydrogen peroxide- melanolipoprotein
conjugate involving the hydrogen bonding of complementary hydroxyl and carbonyl molecular surfaces of these biosignitures
respectively. The condition is multifactorial but reversible. The structural and functional degeneration of melanocytes under the
acquired condition never occur. The molecular conjugation theory on the aetiology and line of treatment of the epidermal
depigmentary disorder (recoined as hepato-epidermal syndrome HES) has been proposed. The inherent sulfoxides of Allium cepa
have been found as the...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2012
URL: http://precedings.nature.com/documents/7025/version/1
Affordances of distractors and compatibility effects: a study with the computational model
TRoPICALS
Provedor de dados: 17
Autores: Daniele Caligiore; Anna M. Borghi; Domenico Parisi; Rob Ellis; Angelo Cangelosi; Gianluca Baldassarre.
Seeing an object activates in the brain both visual and action codes. Crucial evidence supporting this view is offered by
compatibility effect experiments (Ellis et al. (2007). J Exp Psychol: Hum Percept Perform): perception of an object can facilitate
or interfere with the execution of an action (e.g. grasping) even when the viewer has no intention of interacting with the object.
TRoPICALS (Caligiore et al. (2010). Psychol Rev) is a computational model developed to study compatibility effects. It provides
a general hypothesis about the brain mechanisms underlying compatibility effects, suggesting that the top-down bias from
prefrontal cortex (PFC), and its agreement or disagreement with the affordances of objects, plays a key role in such phenomena....
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5848/version/1
Affymetrix probes containing runs of contiguous guanines are not gene-specific
Provedor de dados: 17
Autores: Graham J. Upton; William B. Langdon; Andrew P. Harrison.
High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to
match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in the designated probe
set will provide a consistent message signifying the gene's presence. However, we demonstrate by data mining
thousands of CEL files from NCBI's GEO database that 4G-probes (defined as probes containing sequences of four or
more consecutive guanine (G) bases) do not react in the intended way. Rather, possibly due to the formation of G-quadruplexes,
most 4G-probes are correlated, irrespective of the expression of the thousands of genes for which they were separately intended. It
follows that...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1825/version/1
African wild ungulates compete with or facilitate cattle depending on season
Provedor de dados: 17
Autores: Wilfred O. Odadi; Moses Karachi; Shaukat Abdulrazak; Truman Young.
Savanna ecosystems are vital for both economic and biodiversity values. In savannas worldwide, management decisions are based
on the concept that wildlife and livestock compete for grassland resources[1-4], yet there are virtually no experimental data to
support this assumption[1]. Specifically, the critical assessment of whether or not wild ungulates alter livestock performance (e.g.,
weight gain, reproduction or survival) has rarely been carried out, although diminished performance is an essential prerequisite for
inferring competition[1]. Here we use a large-scale experiment in a semi-arid savanna in Kenya to show that wild ungulates do
depress cattle performance (weight gain) during the dry season, indicating a competitive effect, but enhance cattle...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/4828/version/1
Age and origin of enigmatic megaherbs from the subantarctic islands
Provedor de dados: 17
Autores: Steven J. Wagstaff; Ilse Breitwieser; Christopher Quinn; Motomi Ito.
Biogeographic relationships in the southern hemisphere have puzzled biologists for the last two centuries. Once joined to form the
supercontinent Gondwana, Africa, Antarctica, Australia, New Zealand and South America are widely separated by the Pacific and
Indian oceans. Sir Joseph Hooker was the first to suggest that Antarctica served as a corridor for plant migration not unlike the
land-bridges in the northern hemisphere. While the Antarctic flora was largely erased by glaciation during the Pleistocene, at least
some of these Antarctic plant communities found refuge on the subantarctic islands. Here we provide support for the hypothesis
that giant herbs persisted in the subantactic islands prior to the onset of Pleistocene glaciation, then dispersed...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1272/version/1
Ageing as a price of cooperation and complexity: Self-organization of complex systems causes the
ageing of constituent networks
Provedor de dados: 17
Autores: Huba J. M. Kiss; Ágoston Mihalik; Tibor Nánási; Bálint Őry;
Zoltán Spiró; Csaba Sőti; Peter Csermely.
The analysis of network topology and dynamics is increasingly used for the description of the structure, function and evolution of
complex systems. Here we summarize key aspects of the evolvability and robustness of the hierarchical network-set of
macromolecules, cells, organisms, and ecosystems. Listing the costs and benefits of cooperation as a necessary behaviour to build
this network hierarchy, we outline the major hypothesis of the paper: the emergence of hierarchical complexity needs cooperation
leading to the ageing of the constituent networks. Local cooperation in a stable environment may lead to over-optimization
developing an ‘always-old’ network, which ages slowly, and dies in an apoptosis-like process. Global
cooperation...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2610/version/1
Agenda of the “BioSharing workshop - Unifying Bio-Resources
Descriptors”
Provedor de dados: 17
Autores: Susanna-Assunta Sansone; Philippe Rocca-Serra; Pascale Gaudet; Dawn Field.
Organized by members of the BioSharing initiative (www.biosharing.org) and the International Society for Biocuration (ISB,
www.biocurator.org), this workshop brought together developers, curators, journal editors and researchers to discuss the growing
number
of
(closely
related
efforts)
developing
to
catalogues
of
tools,
databases,
related
data
and
publications.

The focus on the workshop was a strawman uniform system for
describing these bio-resources (www.biodbcore.org), in particular, indicating in a consistent manner which community-defined
standards
(minimal
information
checklists,
terminologies
and
exchange
formats)
(www.biosharing.org/standards).

Location: ISMB/ECCB,...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6148/version/1
they
implement
Agenda of the "BioSharing workshop - Bringing catalogues of bio-resource and
standards together"
Provedor de dados: 17
Autores: Susanna-Assunta Sansone; Philippe Rocca-Serra; Dawn Field; Pascale Gaudet.
This workshop has brought together representatives of groups developing catalogues of bio-resources and its aims were
twofold:

1. Ensure that BioSharing (www.biosharing.org), a catalogue of minimal
information checklists, terminologies and exchange formats (hereafter called standards) and policies, complements and links to
existing
catalogues
of
tools
and
databases,
and
also
to
publications
and
related
material;

2. Outline the technical implementations of the bioDBcore checklist
(www.biodbcore.org), the proposed uniform system for describing the catalogues of tools and databases, in particular, how to
ensure (bi-directional) linking to the BioSharing catalogue....
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6145/version/1
Aggregation of Single Nucleotide Polymorphisms in a Human H5N1 Clade 2.2 Hemagglutinin
Provedor de dados: 17
Autores: Henry L. Niman; Magdi D. Saad; Jeffery Tjaden; Kenneth C. Earhart; Marshall R. Monteville; Mona M. Aly; Moustafa
M. Mansour; Nasr El-Sayed; Ahmed E. Nayel; Ahmed S. Abdelghani; Hala M. Esmat; Emad M. Labib; Ehab A. Ayoub;
Abdelattar Arafa; Gregory A. Raczniak; Mensah Agyen-Frempong; William K. Ampofo; Bruce R. Boynton.
The evolution of H5N1 has attracted significant interest 1-4 due to linkages with avian 5,6 and human infections 7,8. The basic
tenets of influenza genetics 9 attribute genetic drift to replication errors caused by a polymerase complex that lacks a proof
reading function. However, recent analysis 10 of swine influenza genes identifies regions copied with absolute fidelity for more
than 25 years. In addition, polymorphism tracing of clade 2.2 H5N1 single nucleotide polymorphisms identify concurrent
acquisition 11 of the same polymorphism onto multiple genetic backgrounds in widely dispersed geographical locations. Here
we show the aggregation of regional clade 2.2 polymorphisms from Germany, Egypt, and sub-Sahara Africa onto a human
Nigerian H5N1...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics & Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/743/version/1
Aggregation of Single Nucleotide Polymorphisms in a Human H5N1 Clade 2.2 Hemagglutinin
Provedor de dados: 17
Autores: Henry L. Niman; Magdi D. Saad; Jeffery Tjaden; Kenneth C. Earhart; Marshall R. Monteville; Mona M. Aly; Moustafa
M. Mansour; Nasr El-Sayed; Ahmed E. Nayel; Ahmed S. Abdelghani; Hala M. Esmat; Emad M. Labib; Ehab A. Ayoub;
Abdelattar Arafa; Gregory A. Raczniak; Mensah Agyen-Frempong; William K. Ampofo; Bruce R. Boynton.
The rapid evolution of the H5N1 serotype of avian influenza has been explained by a mechanism involving the selection of single
nucleotide polymorphisms generated by copy errors. The recent emergence of H5N1 Clade 2.2 in fifty countries, offered a
unique opportunity to view the acquisition of new polymorphism in these evolving genomes.
We analyzed the H5N1
hemagglutinin gene from a fatal human case from Nigeria in 2007. The newly emerged polymorphisms were present in diverse
H5N1 isolates from the previous year. The aggregation of these polymorphisms from clade 2.2 sub-clades was not supported by
recent random mutations, and was most easily explained by recombination between closely related sequences.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/743/version/2
Aging as a consequence of misrepair -- A novel theory of aging
Provedor de dados: 17
Autores: Jicun Wang; Thomas Michelitsch; Arne Wunderlin; Ravi Mahadeva.
It is now increasingly realized that the underlying mechanisms which govern aging is a complex interplay of genetic regulation
and damage accumulation. Aging as a result of accumulation of ‘faults’ on cellular and molecular
levels, has been proposed in the damage (fault)-accumulation theory by Kirkwood 2006. However, this theory fails to explain
some aging phenotypes such as fibrosis and premature aging, since terms such as ‘damage’ and
‘fault’ are not specified. Therefore we introduce here a specification of the underlying mechanism of
aging and arrive at a novel theory: aging of the body is a result of the accumulation of Misrepair of tissue. It emphasizes: a) it is
Misrepair, not the...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2988/version/2
Aging as a consequence of misrepair -- A novel theory of aging
Provedor de dados: 17
Autores: Jicun Wang; Thomas Michelitsch; Arne Wunderlin; Ravi Mahadeva.
It is now increasingly realized that the underlying mechanisms which govern aging is a complex interplay of genetic regulation
and damage accumulation. Aging as a result of accumulation of ‘faults’ on cellular and molecular
levels, has been proposed in the damage (fault)-accumulation theory by Kirkwood 2006. However, this theory fails to explain
some aging phenotypes such as fibrosis and premature aging, since terms such as ‘damage’ and
‘fault’ are not specified. Therefore we introduce here a specification of the underlying mechanism
and arrive at a novel theory: aging of the body is a result of the accumulation of Misrepair of tissue. It emphasizes: a) it is
Misrepair, not the original...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2988/version/1
Aging as a consequence of misrepair -- A novel theory of aging
Provedor de dados: 17
Autores: Jicun Wang; Thomas Michelitsch; Arne Wunderlin; Ravi Mahadeva.
It is now increasingly realized that the underlying mechanisms which govern aging is a complex interplay of genetic regulation
and damage accumulation. Aging as a result of accumulation of ‘faults’ on cellular and molecular
levels, has been proposed in the damage (fault)-accumulation theory by Kirkwood 2006. However, this theory fails to explain
some aging phenotypes such as fibrosis and premature aging, since terms such as ‘damage’ and
‘fault’ are not specified. Therefore we introduce here a specification of the underlying mechanism of
aging and arrive at a novel theory: aging of the body is a result of the accumulation of Misrepair of tissue. It emphasizes: a) it is
Misrepair, not the...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2988/version/3
Aging-associated Alteration in the Cardiac MIF-AMPK Cascade in Response to Ischemic Stress
Provedor de dados: 17
Autores: Heng Ma; Jingying Wang; Erin Lane; Lin Leng; Wenkui Wang; Jun Ren; Richard Bucala; Ji Li.
An important role for a macrophage migration inhibitory factor (MIF)-AMP-activated protein kinase (AMPK) signaling pathway
in ameliorating myocardial damage following ischemia/reperfusion has been described. An aging-associated reduction in AMPK
activity may be associated with a decline in the ability of cardiac cells to activate the MIF-AMPK cascade, thereby resulting in
reduced tolerance to ischemic insults. To test this hypothesis, _in vivo_ regional ischemia was induced by occlusion of the left
anterior descending (LAD) coronary artery in young (4-6 months) and aged (24-26 months) mice. The ischemic AMPK activation
response was impaired in aged hearts compared to young ones (p<0.01). Notably, cardiac MIF expression in aged
hearts was lower...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2466/version/1
AGMAAS: a GIS integrated tool for modelling wind-borne spreading of FMD virus
Provedor de dados: 17
Autores: Judit Sábitz; Zoltán Barcza Solymosi; Norbert Solymosi.
The aim of our work was to develop a tool integrated into Quantum GIS (QGIS) that can help
the user
estimate and visualize the possible infective areas around an outbreak based on HYbrid Single-Particle Lagrangian Integrated
Trajectory (HYSPLIT) model.
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment.
Ano: 2012
URL: http://precedings.nature.com/documents/7022/version/1
Agriculture: Nanotechnology’s Green Field
Provedor de dados: 17
Autores: Siddhartha Sankar Mukhopadhyay.
Natural agricultural production functions in open system, where energy and matter are exchanged freely between geosphere
(especially pedosphere), biosphere, and atmosphere. The self regulation of biophysical processes in these spheres is crucial for
global sustainability. However, modern farming practices have stressed the system to the extent that damaged C, N, and P cycles
are threatening catastrophic consequences. High food-wastage coupled with high food price, high soil fertility zones but low crop
productivity, and highly productive irrigated farming marred with ecological disasters are examples of global paradoxes
associated with modern farming. High incidence of pesticide residues in soil and water bodies, low use efficiency of agricultural
inputs,...
Tipo: Presentation
Palavras-chave: Chemistry; Ecology; Earth & Environment.
Ano: 2012
URL: http://precedings.nature.com/documents/6900/version/1
Ajuvant effect of a Synthetic Aluminium - Magnesium Silicate on chloroquine phosphate, against
Plasmodium berghei.
Provedor de dados: 17
Autores: madike ezeibe; obianuju obianuju Okoroafor; nnenna elendu-eleke; Augustine Ngene.
Abstract effect of a synthetic Aluminium - Magnesium Silicate (AMS) on antiplasmodial activity of chloroquine was tested.
Plasmodium berghei-infected mice were treated with 7 mg/kg, 5 mg/kg and 3 mg/kg chloroquine, respectively. The two subgroups
in each experiment were treated with chloroquine alone and with chloroquine in AMS respectively. Parasitaemia (%) of the group
treated with 7 mg/kg was higher than that of the control. At 5 mg/kg, chloroquine treatment significantly reduced parasitaemia
from 3.60 to 2.46 (P =0.01). Incorporating chloroquine in AMS significantly improved its ability to reduce P. berghei parasitaemia
at 5 mgkg and at 3 mg/kg, from 2.46 0.21 to 1.57 0.25 (P = 0.01) and from 3.82 0.06 to 2.12 0.08 (P =0.01 ). It also increased...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6749/version/1
Aligning the top-level of SNOMED-CT with Basic Formal Ontology
Provedor de dados: 17
Autores: William Hogan.
Effective translational research requires automated analysis of large datasets collected by multiple researchers working at multiple
locations.
Reliable, machine interpretation of-—and reasoning with—-large datasets assembled at
different times and places by different researchers requires standard representations of data. These representations are controlled,
structured vocabularies also known as ontologies. By far, the most successful ontology is the Gene Ontology (GO), used by
bioinformatics researchers to annotate genomics data. However, to address the phenotype side of translational research will
require annotation of electronic medical record data and clinical research data with a clinical-phenotype ontology analogous to
GO....
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2373/version/1
Alignment of Linear Biochemical Pathways Using Protein Structural Classification
Provedor de dados: 17
Autores: Sridhar Hariharaputran; Thoralf Töpel; Timm Oberwahrenbrock; Ralf Hofestädt.
Metabolic, signaling and regulatory pathways form the basis of biological processes and are important for the analysis of cellular
behavior and evolution. This paper presents an approach of aligning biochemical pathways on the basis of the structure of
involved
proteins and
their
classification.
system.
SIGNALIGN
The
is
suitable
available
information is retrieved
at:
from an integrated
http://agbi.techfak.uni-bielefeld.de/signalign/index.jsp



Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1943/version/1
Allele-specific primer based identification of dimeric alpha-amylase inhibitor
Provedor de dados: 17
database
Autores: Pradeep Sharma; Pooja Sharma; Manoj Saini; S. S. Singh.
Wheat is one of the most important staple food crops cultivated over 200 mha in the range of environment throughout the world.
Wheat production must continue to increase by 2% annually, more particularly in developing world including south-east Asia.
Besides increasing the inherent productivity of wheat, it is important to minimize the losses caused to production by various
abiotic and biotic factors. Alpha–amylase inhibitors are attractive candidates for the control of seed weevils as these
insects are highly dependent on starch as the energy source. They play an important role in the carbohydrate metabolism of many
heterotrophic and autotrophic organisms. In this study, we aimed to make sequence comparison and phylogenetic relationship
among...
Tipo: Poster
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/5596/version/1
Allelic Frequency of ABO And Rh D Blood Group Among The Banjara Backward Caste of Yavatmal
District, Maharashtra , India
Provedor de dados: 17
Autores: Aravind B. Chavhan; Santosh S. Pawar; Mumtaz M. Baig.
The distribution of ABO blood groups and Rh(D) factor has been studied among the Banjara of Backward population of Yavatmal
(Maharashtra). The A, B, O and AB blood group percentage were recorded as 24.54%, 33.82%, 29.64% and 12% respectively.
The allele frequencies of O, A, B and AB groups in the combined data were found to be 0.5354, 0.2022 and 0.2624 respectively.
The distribution of Rh(D) group varies among the ABO blood groups. The Rh(D) positive allelic frequency was 0.8405 and the
Rh(D) negative incidence was recorded as 02.55% in the studied population.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/5482/version/1
Allelic Frequency of ABO And Rh D Blood Group Among The Banjara Caste Population of Akola
District, Maharashtra , India
Provedor de dados: 17
Autores: Aravind B. Chavhan.
The distribution of ABO blood groups and Rh (D) factor has been studied among the Banjara Caste population of Akola District
(Maharashtra). The O, A, B, and AB blood group percentage were recorded as 27.64%, 22.91%, 37.45% and 12% respectively.
The Rh negative incidence was recorded as 02.55%. The allele frequencies of O, A, B and AB groups in the combined data were
found to be 0.5196, 0.2880, and 0.1924 respectively and Rh (D) positive allelic frequency was 0.8405.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5771/version/1
Allergies, Asthma, and Eczema: Response to Disturbance of the Microbiota of the Newborn Gut
Provedor de dados: 17
Autores: Debra L. Wohl; William J. Curry.
*Background/Question/Methods*
The birth of a child may include routine use of antibiotics or a delivery by
cesarean section. We applaud these medical advances for their direct benefits. However, birthing practices have been shown to
disrupt the colonization of the microbial gut in newborns, which may have long term consequences on the development of a
child’s immune system resulting in atopies (i.e., asthma, allergies, and eczema). Animal models and other research
have been used to demonstrate that not only the presence, but also the community composition of the gut microbiota, is essential
for normal immune development. Furthermore, it has been established that there are differences in the intestinal microbiota of
children...
Tipo: Presentation
Palavras-chave: Ecology; Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/3685/version/1
Allergological and toxicological risk assessment of genetically modified (GM) plants - Development of
a model system
Provedor de dados: 17
Autores: Alain Steinmann; Kristin Entzian; Birgit Grümmer; Udo Meyer.
Technical advances in biotechnology lead to a rising number of genetically modified plants and derived food and feed. Therefore,
the international interest in adequate and standardized analytical methods increases to assess health risks in a rapid and low cost
manner.
To address this issue a decision support system (DSS), which will be based on baseline data and
thresholds of key parameters, is going to be established in the framework of a joint project (BioOK). Determination of the
potential allergenicity or toxicity of novel proteins caused by the genetic modification compared to near isogenic variants (NIV) is
a key issue in this context. For the development of DSS the model plant “potato” was used to
compare...
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4441/version/1
Allicin from garlic suppresses TNF-α and augments IFN-γ expressions in
monocyte cultures from patients with Vaginitis
Provedor de dados: 17
Autores: Najmul Islam; Jawed Iqbal; Nazarul Hasan; Zeeshan Fatima; Hamida Thakur; Nazia Hasan; Abbas Ali Mahdi; Tamkin
Khan; Farzana Bano; Irfan Ahmad Ansari.
Objective: We tried to explore beneficial effects of allicin- a natural antioxidant from garlic in the possible management of
vaginitis. 
Methods: Peripheral blood mononuclear cells (PBMC’s) were isolated from blood
of patients having vaginal infections as well as normal healthy subjects as per our published protocol. Monocytes
(MN’s) from above PBMC’s were adhered, rested overnight and cultured without or with varying
doses of allicin (0-500 ng/ml). Some cultures received SN50 and SN50M (100 ug/ml). After 24 hrs cultures, the cells were
harvested and the supernatants subjected to secreted TNF-α and sIFN-γ assays by ELISA.
Treated/untreated harvested cells were subjected to glutathione...
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1560/version/1
Allosteric modulation of beta1 integrin function induces lung repair in animal model of emphysema.
Provedor de dados: 17
Autores: Rehab J. Al-Jamal; Linda Wilson; Chris J. Armit; Susan McIntyre; Mark Marsden; Steven D. Shapiro; David J.
Harrison.
Emphysema is a progressive lung disease characterised by loss of lung parenchyma with associated functional changes including
decreased tissue elastance. Here we report beta1 integrin is a novel target for tissue repair and regeneration in emphysema. We
show a single dose of a monoclonal antibody against beta1 integrin induced both functional and structural reversal of
elastase-induced lung injury in vivo, and we found that similar matrix remodelling changes occurred in human lung tissue. We
also identified a potential mechanism of action as this allosteric modulation of beta1 integrin inhibited elastase-induced caspase
activation, F-actin aggregate formation and changes in cellular ATP levels. This was accompanied by maintenance of
beta1?integrin levels...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2007
URL: http://precedings.nature.com/documents/437/version/1
Alpha band oscillations track temporal orienting of attention
Provedor de dados: 17
Autores: Gustavo Rohenkohl; Anna Christina Nobre.
Introduction: Recent investigations using field-potential recordings in visual and auditory cortices have shown that oscillatory
activity in neuronal ensembles become entrained to the timing of rhythmically presented stimuli according to their modality and
location (Lakatos, Chen et al. 2007; Lakatos, Karmos et al. 2008; Lakatos, O'Connell et al. 2009). In spite of the
evidence showing the role of brain oscillations on forming predictions about forthcoming sensory events (for a review (Engel,
Fries et al. 2001), little is known about the role of such oscillations in the temporal orienting of attention (Nobre 2001; Coull and
Nobre 2008). To test the effect of temporal orienting of attention on early perceptual processing, motor selection, and...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4509/version/1
Altered cholesterol ester cycle in _ex vivo_ skin fibroblasts from Alzheimer patients
Provedor de dados: 17
Autores: Alessandra Pani; Sandra Dessi; Giacomo Diaz; Claudia Abete; Claudia Mulas; Claudia Norfo; Marirosa Putzolu; Maria
Dolores Cannas; Christina Doriana Orru; Alessandra Mocali; Pier Luigi Cocco; Paolo La Colla; Francesco Paoletti.
Recent studies in both animal and cell models of Alzheimer's disease (AD) indicated that sub-cellular cholesterol
distribution seems to regulate amyloid-beta (A[beta]) generation in the brain. In particular, cholesterol-esters (CE), rather than
total cholesterol levels, appear directly correlated with A[beta] production. Here we observed that, similarly to brain cells, skin
fibroblasts obtained from AD patients produce and accumulate more CE than skin fibroblasts from age-matched healthy controls
do. AD fibroblasts also exhibited a 2 fold increase in the expression of ACAT1, in addition to lower levels of SREBP2, nCEH,
Caveolin-1 and ABCA1 mRNA levels, all of which are involved in the CE cycle. HMGCoA-reductase and LDL-receptor mRNAs
levels did...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1602/version/1
Altered copy gene function in plants following total intron replacement in precursor RNA
Provedor de dados: 17
Autores: Drew Schwartz.
Evidence is presented for two novel genetic mechanisms: total intron replacement in transcribedprecursor RNA by multiple short
sequences and reverse transcription of the precursor RNA followedby incorporation into the genome as copy genes, some of
which have acquired an altered function.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Plant Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4307/version/1
Altruism among relatives and non-relatives
Provedor de dados: 17
Autores: Howard Rachlin; Bryan A. Jones.
The amount of their own monetary reward that undergraduate participants claimed they were willing to forgo, in order to give $75
to another person, decreased hyperbolically as social distance increased between the participant and the other person. Relatives
tended to be ranked at closer social distances than were non-relatives. However, even at the same social distance, participants
were willing to forgo significantly more money for the benefit of relatives than for the benefit of non-relatives. These results
imply that altruism is determined by factors in addition to social distance.
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1565/version/1
Aluminium - Magnesium Silicate enhances antibacterial activity of Ampicillin trihydrate, against
Salmonella gallinarum
Provedor de dados: 17
Autores: Madike Ezeibe; George Anosa; Okechi Okorie; Nnenna Elendu-Eleke; Obianuju Okoroafor; Augustine Ngene;
Ogechukwu Chikelu.
Solutions of different concentrations, of Ampicillin trihydrate (AT) and of a formulation of AT in Aluminium Magnesium Silicate
(AMS), were used for sensitivity test on Salmonella gallinarum cultures. Also, S. gallinarum-infected chicks were treated with; 10
mg / Kg (AT), 10 mg / Kg (AT in AMS), 7.5 mg / Kg ( AT), 7.5 mg /Kg (AT in AMS). Mean inhibition area, 28.39 mm produced
by AT did not vary significantly (P ) from 26.36 mm produced by AT in AMS. However, 17.5 105 Salmonella gallinarum culture
forming units per ml of bile of the untreated chicks and 3.4 105 (80.58 % reduction), 2.5 105 (85.7 % reduction) , 5.4 105 (69.2 %
reduction ) and 0.38 105 (97.8 % reduction ) of the respective treated groups, showed AMS significantly (P 0.01) improved
AT`s...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6814/version/1
Alzheimer's disease is TH17 related autoimmune disease against misfoded beta amyloid
Provedor de dados: 17
Autores: Wan-Jiung(Wan-Chung) Hu.
Alzheimer's disease is a common neurodegenerative disorder. However, its exact etiology is still unknown. There
were several mechanisms proposed such as the tau hypothesis and amyloid hypothesis. However, there is evidence challenging the
above two hypotheses. Here, I propose the immune-amyloid hypothesis as a mechanism for Alzheimer's disease. Th17
related autoimmunity contributes to the disease pathogenesis. Accumulation of misfolded beta amyloid can trigger heat shock
protein which in turn induces TH17 immunity. By microarray analysis of peripheral blood mononuclear cells, there is
up-regulation of many TH17 related molecules after Alzheimer's disease. After knowing the exact disease
pathogenesis, we can develop new...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5934/version/1
Alzheimer's disease is TH17 related autoimmune disease against misfolded beta amyloid
Provedor de dados: 17
Autores: Wan-Jiung(Wan-Chung) Hu.
Alzheimer's disease is a common neurodegenerative disorder. However, its exact etiology is still unknown. There
were several mechanisms proposed such as the tau hypothesis and amyloid hypothesis. However, there is evidence challenging the
above two hypotheses. Here, I propose the immune-amyloid hypothesis as a mechanism for Alzheimer's disease. Th17
related autoimmunity contributes to the disease pathogenesis. Accumulation of misfolded beta amyloid can trigger heat shock
protein which in turn induces TH17 immunity. By microarray analysis of peripheral blood mononuclear cells, there is
up-regulation of many TH17 related molecules after Alzheimer's disease. After knowing the exact disease
pathogenesis, we can develop new...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5934/version/2
Alzheimer's disease is TH17 related autoimmune disease against misfolded beta amyloid
Provedor de dados: 17
Autores: Wan-Jiung(Wan-Chung) Hu.
Alzheimer's disease is a common neurodegenerative disorder. However, its exact etiology is still unknown. There
were several mechanisms proposed such as the tau hypothesis and amyloid hypothesis. However, there is evidence challenging the
above two hypotheses. Here, I propose the immune-amyloid hypothesis as a mechanism for Alzheimer's disease. Th17
related autoimmunity contributes to the disease pathogenesis. Accumulation of misfolded beta amyloid can trigger heat shock
protein which in turn induces TH17 immunity. By microarray analysis of peripheral blood mononuclear cells, there is
up-regulation of many TH17 related molecules after Alzheimer's disease. After knowing the exact disease
pathogenesis, we can develop new...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5934/version/3
Ambiguous Dependence Of Minimal Plant Generation Time On Nuclear DNA Content
Provedor de dados: 17
Autores: Victor B. Ivanov.
AMBIGUOUS DEPENDENCE OF MINIMAL PLANT GENERATION TIME ON NUCLEAR DNA CONTENT Victor B.
Ivanov The minimum generation time (MGT) of plant development was suggested to depend on nuclear DNA content, which
varies in plants over wide limits1. In ephemeral species with the shortest MGT, the average C values were significantly lower than
in annual species, whereas the average C values in annual species were lower than those in perennial plants. However, nobody has
paid attention to the ratio of annual to perennial species number as a function of C values. Here I show that with increasing C the
ratio of annual to perennial species increases to C values equal to 7-8 pg (monocots) and 6-7 pg (eudicots) and then decreases and
that the fraction of annuals is abundant...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4943/version/1
Amino acid features: a missing compartment of prediction of protein function
Provedor de dados: 17
Autores: Esmaeil Ebrahimie; Mansour Ebrahimi; Mahdi Ebrahimi.
Enormous computational efforts have been carried out to predict structure and function of protein. However, nearly all of these
efforts have been focused on prediction of function based on primary nucleic acid sequence or modeling 3D structure of protein
from its nucleic acid sequence. In fact, it seems that amino acid attributes, which is an intermediate phase between DNA/RNA and
advanced protein structure, has been missed.
From 2010, we examined the possibility of precise prediction
of structural protein function based on amino acid features by improving the following three aspects of amino acid research: (1)
Increasing the number of computationally calculated amino acid features, (2) Testing different feature selection (attribute...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6693/version/1
AMIS, The Article Minimum Information Standard
Provedor de dados: 17
Autores: Delphine Dauga.
The curation process is significantly slowed down by missing information in the articles analyzed (for example, the identity of the
clones used to generate ISH probes, the precise sequences tested in reporter assays, etc..). To help authors ensure in the future that
necessary information is present in their article, we defined the Article Minimum Information Standard (AMIS) guidelines. This
standard describes for each experiment the mandatory information that should be mentioned in literature articles to facilitate the
curation process. These guidelines extend the minimal information defined by the MISFISHIE format (Deutsch at al. 2008,
_Nature Biotechnology_). This standard was deduced from the ANISEED curation pipeline (Tassy, Dauga, Daian, Sobral et al....
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5054/version/1
∆N-p63 functions as an invasion, migration, and metastasis suppressor
Provedor de dados: 17
Autores: Lakshmanane Boominathan.
The tumor suppressor p53 homologues, TA-p73, and p63 have been shown to function as tumor suppressors. However, how they
function as tumor suppressors remains elusive. Expression of p63 is controlled by two distinct promoters. Consequently, this
results in two different gene products such as TA-(transactivation domain containing NH2 terminus) p63 and
∆N-(lacks NH2 terminus) p63. It is generally thought that the TA-p63 functions as a tumor suppressor, while the
∆N-p73
functions as a
proto-oncogene.
However,
careful interpretation of the
data
concerning
∆N-p63 suggests that it could function as an invasion and metastasis/tumor suppressor in a cell context dependent
manner.
Tipo: Manuscript
Palavras-chave: Cancer; Genetics & Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/4771/version/1
∆N-p63 functions as an invasion, migration, and metastasis suppressor
Provedor de dados: 17
Autores: Lakshmanane Boominathan.
The tumor suppressor p53 homologues, TA-p73, and p63 have been shown to function as tumor suppressors. However, how they
function as tumor suppressors remains elusive. Expression of p63 is controlled by two distinct promoters. Consequently, this
results in two different gene products such as TA-(transactivation domain containing NH2 terminus) p63 and
∆N-(lacks NH2 terminus) p63. It is generally thought that the TA-p63 functions as a tumor suppressor, while the
∆N-p73
functions as a
proto-oncogene.
However,
careful interpretation of the
data
concerning
∆N-p63 suggests that it could function as an invasion and metastasis/tumor suppressor in a cell context dependent
manner.
Tipo: Manuscript
Palavras-chave: Cancer; Genetics & Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/4771/version/2
"Dark Mediators" of Proteins as Revealed by NMR in Water:
Residue-selective Anion Bindings that are Masked by Pre-existing Buffer
Provedor de dados: 17
Autores: Jianxing Song; Linlin Miao; Haina Qin.
Ions are commonly believed to impose their effects on proteins by unspecific electrostatic screening. Here, by NMR we reveal
that in water sulfate, chloride and thiocyanate are able to bind a well-folded WW domain at distinctive residues and affinities,
which is surprisingly masked by the pre-existing buffer. Our study reveals that the specific anion binding is so ubiquitous and
consequently no longer negligible in establishing "postreductionist framework" for protein biochemistry.
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Earth & Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6769/version/1
"Ribopepzymes" are probably a link from ribozymes to protein enzymes
Provedor de dados: 17
Autores: Yongjie Sheng; Dazhi Jiang; Zhen Zeng; Feng Pan; Jin Zhang.
The evolutionary relationship between RNA- and protein-based biocatalysts was key to the evolution of living systems. This
relationship is thought to have depended upon the transfer of both genetic information and catalytic function in living systems. We
investigated whether ribozymes could transfer genetic information and catalytic function at the chemical level. We identified a
family of peptides encoded by ribozymes: 13-residue peptide encoded by the hammerhead ribozyme, a 19-residue peptide
encoded by the genomic hepatitis delta virus (HDV+) ribozyme, a 25-residue peptide encoded by the antigenomic HDV (HDV-)
ribozyme, a 15-residue peptide encoded by the smallest trans-acting genomic HDV (SHDV) ribozyme, and a 22-residue peptide
encoded by an open...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1708/version/1
'Kuthiru' and 'Orkayama' – Newly
Identified Genetic Resources from Kerala, India for Salinity Tolerance in Indica Rice
Provedor de dados: 17
Autores: Vanaja Taliyil; K P. Mammootty.
Existence of genetic variability for salt tolerance within species is of paramount importance in crop improvement program.
Pokkali land race of Kerala, India is the international donor parent of most of the salinity tolerance breeding programs in rice.
Here we report two new genetic resources, ‘Kuthiru’ and ‘Orkayama’ for
salinity tolerance, from Kaipad saline tracts of Kerala. They differ in their morphological, physico-chemical characteristics and
cooking qualities. Panicles of these cultivars are long with bold grains. Duration of ‘Kuthiru’ is 110
-120 days, and that of ‘Orkayama’ is 135 -140 days. Molecular analysis revealed that the salinity
tolerance mechanism...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4561/version/1
'Magnetized' brains are slower: The cognitive effects of fMRI
Provedor de dados: 17
Autores: Jack R. Foucher; Daniel Gounot; Bich-Thuy Pham; Corinne Marrer; Andre Dufour.
MRI is generally thought to have no impact on cognition. Although safety experiments have shown that MRI is not harmful, its
finer effects have not been investigated. Because we repeatedly observed delayed response time during functional MRI (fMRI),
we designed an experiment to confirm this effect and to identify its causal factor(s), including environment, noise, static magnetic
field and/or gradient switch. Here we show that the participants had increased response times of +70 ms (up to +30%) in two
different detection tasks, with most of this effect due to the 2 Tesla static magnetic field. The latter also specifically accounted for
the longer time interval needed to detect two stimuli as occurring successively rather than simultaneously. These...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2443/version/1
An Advanced Clinical Ontology
Provedor de dados: 17
Autores: Riichiro Mizoguchi; Hiroko Kou; Jun Zhou; Kouji Kozaki; Ken Imai; Kazuhiko Ohe.
This article discusses a fundamental issues of medical ontology based on ontological theory. We focus on "anatomical
structure of organs" and "abnormal states in the human body". On the basis of the investigation,
we distinguish organ-specific types from those independent of any organ to maximize the explicitness of ontology. The next
feature of our ontology is to allow on-demand reorganization of is-a hierarchy of diseases instead of one fixed hierarchy to cope
with various viewpoints which physician might have. We also take care of the notorious issue related to conflict of is-a and part-of
relations.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3498/version/1
An Advanced Clinical Ontology
Provedor de dados: 17
Autores: Riichiro Mizoguchi; Kouji Kozaki; Hiroko Kou; Ken Imai; Kazuhiko Ohe.
This article discusses a fundamental issues of medical ontology based on ontological theory. We focus on "anatomical
structure of organs" and "abnormal states in the human body". On the basis of the investigation,
we distinguish organ-specific types from those independent of any organ to maximize the explicitness of ontology. The next
feature of our ontology is to allow on-demand reorganization of is-a hierarchy of diseases instead of one fixed hierarchy to cope
with various viewpoints which physician might have. We also take care of the notorious issue related to conflict of is-a and part-of
relations.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3506/version/1
An albumin-derived peptide scaffold capable of binding and catalysis
Provedor de dados: 17
Autores: Immacolata Luisi; Silvia Pavan; Giampaolo Fontanive; Alessandro Tossi; Fabio Benedetti; Adriano Savoini; Elisa
Maurizio; Riccardo Sgarra; Daniele Sblattero; Federico Berti.
We have identified a 101-amino-acid polypeptide derived from the sequence surrounding the IIA binding site of human albumin.
The polypeptide contains residues that make contact with ligands as warfarin in the parent protein, and eight cysteine residues to
form disulfide bridges, which stabilize the polypeptide structure. Seventy-four amino acids are located in six [alpha]-helical
regions, with the remaining amino acids forming six connecting coil/loop regions. Codon usage optimization was used to express
a GST fusion protein in E. coli in yields as high as 4 mg/l. This fusion protein retains its structural integrity and aldolase activity,
the ability to direct the stereochemical outcome of a diketone reduction, and its binding capacity to warfarin and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2012
URL: http://precedings.nature.com/documents/6894/version/1
An ancient adaptive episode of convergent molecular evolution confounds phylogenetic inference
Provedor de dados: 17
Autores: Todd A. Castoe*; A.P. Jason de Koning*; Hyun-Min Kim; Wanjun Gu; Brice P. Noonan; Zhi J. Jiang; Christopher L.
Parkinson; David D. Pollock.
Convergence can mislead phylogenetic inference by mimicking shared ancestry, but has been detected only rarely in molecular
evolution. Here, we show that significant convergence occurred in snake and agamid lizard mitochondrial genomes. Most
evidence, and most of the mitochondrial genome, supports one phylogenetic tree, but a subset of mostly amino acid-altering
mitochondrial sites strongly support a radically different phylogeny. These sites are convergent, probably selected, and overwhelm
the signal from other sites. This suggests that convergent molecular evolution can seriously mislead phylogenetics, even with
large data sets. Radical phylogenies inconsistent with previous evidence should be treated cautiously.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2123/version/1
An apparent medieval stereogram incorporating a symbol for optical illusion
Provedor de dados: 17
Autores: John L. Cisne.
Stereograms
mark
a
threshold
in
understanding
visual
perception.
Modern
study
of
stereopsis
began
with
Wheatstone's invention of the stereogram and stereoscope (~ 1832), important tools in vision research and technical
imagery ever since. Stereoscopic images formed with frieze and wallpaper patterns in illuminated Insular manuscripts such as the
Book of Durrow (~ 680 CE), Lindisfarne Gospels (~ 700-720), and Book of Kells (~ 800) show that, long before spectacle-quality
magnifying lenses (~ 1286), illuminators somehow copied multicolored, microscopically detailed designs _freehand_ with an
accuracy unsurpassed in scientific instruments until the Renaissance (but well within the power of normally sighted
humans' stereoscopic...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3994/version/1
An approach able to escape the most common problem during protein Crystallization i.e. formation of
salt crystal
Provedor de dados: 17
Autores: K. Awaneesh Singh; Patrick Celie; G. R. K. Rao; M. V. Jagannatham.
Formation and differentiation of salt crystal is a most common as well as challenging problem during protein crystallography.
Although there are some methods used for their differentiation i.e. physical manipulation, birefringence, dye absorption and run a
gel but all of them are totally depends on own perception and expertise as well as also require a good crystal (final stage crystal).
To escape this problem the screening was done with PACT, JCSG and other automated screens as everyone do. But during
optimization the additives/salts were ignored at first and optimization screen was made just based on different buffers and
precipitant. After selecting suitable buffer, the type and percentage of precipitant was optimized. We got some ugly crystals and
with...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4725/version/1
An artificial spiking synapse made of molecules and nanoparticles
Provedor de dados: 17
Autores: Fabien Alibart; Stephane Pleutin; David Guerin; Christian Gamrat; Dominique Vuillaume.
Molecule-based devices are envisioned to complement silicon devices by providing new functions or already existing functions at
a simpler process level and at a lower cost by virtue of their self-organization capabilities, moreover, they are not bound to von
Neuman architecture and this may open the way to other architectural paradigms. Here we demonstrate a device made of
conjugated molecules and metal nanoparticles (NPs) which behaves as a spiking synapse suitable for integration in neural network
architectures. We demonstrate that this device exhibits the main behavior of a biological synapse. These results open the way to
rate coding utilization of the NOMFET in perceptron and Hopfield networks. We can also envision the NOMFET as a building
block of...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3031/version/1
An assessment of organic solvent based equilibrium partitioning methods for predicting the
bioconcentration behavior of perfluorinated sulfonic acids, carboxylic acids, and sulfonamides
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
SPARC, KOWWIN, and ALOGPS octanol-water partitioning (log K~ow~) and distribution (log D) constants were calculated for
all C~1~ through C~8~ and the straight chain C~9~ through C~15~ perfluoroalkyl sulfonic acids (PFSAs) and carboxylic acids
(PFCAs). Application of five established models for estimating bioconcentration factors (BCFs) were applied to the PFSA and
PFCA log K~ow~ and log D data and compared to available field and laboratory BCF data. Wide variability was observed
between the methods for estimating log K~ow~ and log D values, ranging up to several log units for particular congeners, and
which was further compounded by additional variability introduced by the different BCF equations applied. With the exception of
n-perfluorooctanecarboxylic...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3256/version/1
An attempt to understand Barstar, Barnase and Olfactory receptor protein folding problems using
mathematical biological approach
Provedor de dados: 17
Autores: Arunava Goswami; Sk Sarif Hassan; Pabitra Pal Choudhury.
Protein folding problem as attracted structural biologists immensely (1). Till date, correlation between X-ray crystallographic and
NMR data are considered to be the best methods for determining structure of intra-cellular proteins. Generating crystals and
finding correct experimental conditions for NMR are largly a gamble and resultant data processing highly time consuming. Even
if, a large number of laboratories around the world and India make crystals of protein but majority of them fail to generate
crystallographic data less than or equal to 10A resolution with currently available instruments. This means that X-ray
crystallographic data have been generated from protein crystals with non-uniform lattices. We believe that a large portion of
(chain of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4891/version/1
An emerging protagonist: Sodium Glucose Co-transporters (SGLTs) as a burgeoning target for the
treatment of diabetes mellitus
Provedor de dados: 17
Autores: Danish Ahmed; Manju Sharma; Vikas Kumar; Pankaj S Yadav.
Contemporary therapies to rationalize the hyperglycaemia in type 2 diabetes mellitus (T2DM) generally involve insulin-dependent
mechanisms and lose their effectiveness as pancreatic b-cell function decreases to a greater extent. The kidney emerges out as a
novel and potential target to trim down the T2DM. The filtered glucose is reabsorbed principally through the sodium glucose
co-transporter-2 (SGLT2), a low affinity transport system, which is present at the luminal surface cells that cover the first segment
of proximal tubules. Competitive inhibition of SGLT2 therefore represents an innovative therapeutic strategy for the treatment of
hyperglycaemia and/or obesity in patients with type 1 or type 2 diabetes by enhancing glucose and energy loss through the...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7057/version/1
An evaluation of taxonomic name finding & next steps in Biodiversity Heritage Library
(BHL) developments
Provedor de dados: 17
Autores: Chris Freeland.
The Biodiversity Heritage Library (BHL) is an international consortium of natural history libraries that are actively scanning
scientific literature from their collections and publishing the digitized content online at http://www.biodiversitylibrary.org. The
presentation will cover updates on BHL progress thus far, including a review of the BHL portal application and services
developed for bibliographic data exchange, as well as a roadmap of features scheduled for design and development. Of interest to
taxonomists and bioinformaticians, the presentation will also cover a recently completed evaluation of taxonomic name finding
algorithms, including TaxonFinder and FAT. Discussion will include a review of successes and failures in extracting taxonomic
name...
Tipo: Presentation
Palavras-chave: Bioinformatics; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3372/version/1
An evolutionary approach to Function
Provedor de dados: 17
Autores: Phillip Lord.
The distinction between function and role is a vexed and difficult one. While the distinction appears to be useful, in practice it is
hard to apply; this can be even worse when applying this distinction to biology. In this paper, I take an evolutionary approach,
considering a series of examples, to develop and generate definitions for these concepts. I test them in practice against work
performed on the Ontology for Biomedical Investigations (OBI). Finally, I give an axiomatisation and discuss methods for
applying these definitions in practice.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3228/version/1
An exercise on developing an ontology-epistemology about schizophrenia and neuroanatomy
Provedor de dados: 17
Autores: Rodolpho Freire; Danilo Nunes Santos; Marcos Vinicius dos Santos; Paulo Eduardo Santos.
This paper describes preliminary ideas on formalizing some concepts of neuroanatomy into ontological and epistemological terms.
We envisage the application of this ontology on the assimilation of facts about medical knowledge about neuroimages from
schizophrenic patients.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3483/version/1
An experimental and modelling exploration of the host-sanction hypothesis in legume-rhizobia
mutualism
Provedor de dados: 17
Autores: Diana Marco; Juan Carbajal; Sergio Cannas; Rebeca Perez-Arnedo; Angeles Hidalgo-Perea; Jose Olivares; Jose
Ruiz-Sainz; Juan Sanjuán.
Despite the importance of mutualism as a key ecological process, its persistence in nature is difficult to explain since the existence
of exploitative, 'cheating' partners that could erode the interaction is common. By analogy with the
proposed policing strategy stabilizing intraspecific cooperation, host sanctions against non N2 fixing, cheating symbionts have
been proposed as a force stabilizing mutualism in legume-Rhizobium symbiosis. Following this proposal, penalizations would
include decreased nodular rhizobial viability and/or early nodule senescence in nodules occupied by cheating rhizobia. In this
work, we analyze the stability of Rhizobium-legume symbiosis when "cheating" strains are present, using
an...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1964/version/1
An illusion induced by an illusion -perceptual filling-in of coloured negative afterimages
Provedor de dados: 17
Autores: Adam Geremek; Kai Hamburger; Lothar Spillmann.
Visual filling-in relates to a perceptual phenomenon in which a stimulus pattern apparently undergoes dynamic changes assuming
an attribute such as colour, texture, or brightness from the surround. This perceptual completion effect has up to now been shown
only for real images. Here, we present filling-in in negative afterimages, a phenomenon not yet reported. Using coloured disk-ring
patterns for stimuli, we demonstrate that afterimage filling-in arises independently, and is not simply a replica of filling-in
observed in real images. Such filling-in does not occur when the afterimage is elicited dichoptically, suggesting its emergence
within the monocular visual pathway. In this way, our findings indicate that filling-in under certain conditions may...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3789/version/1
An innovative method for the biological control of Alternanthera philoxeroides
Provedor de dados: 17
Autores: Yusong Cao; Huiming Wang.
Biological invasion has become a serious global environmental problems and been considered as an important component of
global change^1-2^. Invasions by alien species can have an impact at several levels of ecological complexity from genes to
ecosystems^3-4^. Invasive alien species had seriously threated the biodiversity and natural ecosystems in China^5^, and caused
economic losses by more than US$7 billion every year^6^. Alternanthera philoxeroides, commonly known as Alligator weed, is
an invasive amphibious plant^7^. The effect of physical methods such as mechanical or artificial salvage, removal of A.
philoxeroides were very limited. Moreover, these measure should be carried out very carefully or would easy lead to its
rebound^8^. The mainly biological...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5267/version/1
An insight into the kinships of the fungi
Provedor de dados: 17
Autores: Riddhi Datta; Joy Sarkar; Krishnendu Acharya.
The evolutionary origin of fungi is important in determining the phylogenetic relationships between fungi, animals and plants.
However, determining the true relationship of fungi has been somewhat difficult owing to their simple morphology and presence
of convergent characters. With the advent of newer molecular techniques, analysis of conserved protein sequences, cytochrome
systems, mitochondrial and nuclear genetic material and rRNAs are being employed in elucidating
phylogenetic kinships
among the eukaryotes. These emerging evidences suggest that the derivation of the fungi from plants or algae would require more
evolutionary changes than its derivation from protozoa, the unicellular ancestor of the animals. To gain an overview of the current
state of...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7095/version/1
An Integrated IGCC-CSS Design Course for Graduate Students in Petroleum Engineering
Provedor de dados: 17
Autores: Gioia Falcone; Behnam Jafarpour; Maria Barrufet.
A new graduate course on CO2 Capture and Uses was offered for the first time at Texas A&M, Pet. Eng., in Fall 2008.

A multidisciplinary team of instructors from the Pet. Eng. & Chem. Eng. departments was
assembled to ensure the appropriate expertise.
The objective of the course is to let the students understand
the need for / potential of Carbon Capture and Storage (CCS) & Enhanced Oil Recovery (EOR).
Tipo: Presentation
Palavras-chave: Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2627/version/1
An integrated solution for rapid biosensing combining linker free binding, freeze drying and high
sensitivity ellipsometric detection
Provedor de dados: 17
Autores: Yongbai Yin; David R. McKenzie; Keith Fisher; Chuan Guo; Neil Nosworthy; Marcela M. Bilek.
A novel integrated biosensor methodology is proposed and demonstrated. The methodology utilizes a nitrogen-containing plasma
polymer to achieve linker-free binding of biorecognition molecules that allows the sensor surface to be freeze dried for long shelf
life under ambient conditions. The sensor is configured for single wavelength ellipsometric detection providing a low cost,
versatile, and rapid sensing and diagnosis platform suitable for a wide range of applications and end-users. The merits of the
methodology were demonstrated using three antigen-antibody pairs.
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2012
URL: http://precedings.nature.com/documents/6764/version/1
An intelligent liposome that may deliver drug molecules in a well controlled fashion
Provedor de dados: 17
Autores: Dumitru Popescu; Alin Gabriel Popescu.
The passage of molecules, especially large ones, through the cellular membrane is a very important problem for some
biotechnological applications, such as drug delivery. The appearance of pores in the lipid bilayer following some controlled
mechanisms may be an adequate and interesting way. Some pores, named stochastic pores, can appear due to structural and
dynamic properties of lipid bilayer, but others may be favored by mechanical tension induced by different ways. Recently, a
sequence of 30-40 pores was observed in the same vesicle, a pore at a time, which can appear in vesicles stretched by optical
induced mechanical tension. There are two very interesting biotechnological applications that require the increase of membrane
permeability: gene therapy...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2007
URL: http://precedings.nature.com/documents/1220/version/1
An offside position in football cannot be detected in zero milliseconds
Provedor de dados: 17
Autores: Francisco Belda Maruenda.
Errors when judging an offside position in football are very frequent. In the last years, several scientific papers have tried to
explain the causes for human errors. When a referee or an assistant referee misjudges an offside position, it is thought to be caused
by a human error. A human error means to carry out incorrectly an action we are physiologically qualified for. The hypothesis to
be studied in this paper is if when judging an offside position it is possible to attribute errors to humans or to the fact that human
physiology and the technical media are not capable of detecting an offside position. The offside rule has to be applied in real time,
in zero milliseconds, in the precise moment when the ball is being passed, never 1 millisecond or even 1...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3835/version/1
An Olfactory Receptor Pseudogene whose Function emerged in Humans
Provedor de dados: 17
Autores: Peter Lai; Gautam Bahl; Maryse Gremigni; Valery Matarazzo; Olivier Clot-Faybesse; Catherine Ronin; Chiquito J.
Crasto.
Human olfactory receptor, hOR17-210, is identified as a pseudogene in the human genome. Experimental data has shown
however, that the gene product of cloned hOR17-210 cDNA was able to bind an odorant-binding protein and is narrowly tuned for
excitation by cyclic ketones. Supported by experimental results, we used the bioinformatics methods of sequence analysis,
computational protein modeling and docking, to show that functionality in this receptor is retained due to sequence-structure
features not previously observed in mammalian ORs. This receptor does not possess the first two transmembrane helical domains
(of seven typically seen in GPCRs). It however, possesses an additional TM that has not been observed in other human olfactory
receptors. By...
Tipo: Manuscript
Palavras-chave: Biotechnology; Neuroscience; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1290/version/1
An Ontology for Designing Models of Epidemics
Provedor de dados: 17
Autores: Geoffrey Frank; William Wheaton; Vesselina Bakalov; Phillip Cooley; Diane Wagener.
Models of epidemics allow decision makers to explore the consequences of different interventions. The Models of Infectious
Disease Agent Study (MIDAS) project has been collecting studies, models, data supporting the models, and publications
providing historical evidence about epidemics.
An ontology has been developed for MIDAS to support the
collection, documentation, and dissemination of models. It uses relations to link taxonomies (including a subset of the infectious
disease ontology) that define the scope of its models and supporting documentation.
The ontology is used to
aid in the navigation process that is part of the user interface for identifying which studies and publications are available in the
MIDAS repository...
Tipo: Presentation
Palavras-chave: Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3555/version/1
An Ontology To Represent Knowledge On Animal Testing Alternatives
Provedor de dados: 17
Autores: Thomas Wächter; Ursula G. Sauer; Andreas Doms; Barbara Grune; Michael R. Alvers; Horst Spielmann;
Michael Schroeder.
EU Directive 86/609/EEC for the protection of laboratory animals obliges scientists to consider whether a planned animal
experiment can be replaced, reduced or refined (3Rs principle). To meet this regulatory obligation, scientists must consult the
relevant scientific literature prior to any experimental study using laboratory animals. More than 50 million potentially 3Rs
relevant documents are spread over the World Wide Web, biomedical literature and patent databases. In April 2008, the beta
version of Go3R ("www.Go3R.org":http://www.Go3R.org), the first knowledge-based semantic search
engine for alternative methods to animal experiments, was released. Go3R is free of charge and enables scientists and regulatory
authorities involved in...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3148/version/1
An Ontology-Based Framework for Clinical Research Databases
Provedor de dados: 17
Autores: Richard H. Scheuermann; Megan Kong; Carl Dahlke; David Karp.
The Ontology-Based eXtensible data model (OBX) was developed to serve as a framework for the development of a clinical
research database in the Immunology Database and Analysis Portal (ImmPort) system. OBX was designed around the logical
structure provided by the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). By using the
logical structure provided by these two well-formulated ontologies, we have found that a relatively simple, extensible data model
could be developed to represent the relatively complex domain of clinical research.
In addition, the common framework
provided by the BFO should make it straightforward to utilize OBX database data dictionaries based on reference and application
ontologies from the OBO...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3482/version/1
An open source LABVIEW platform for simulating image series of
gliding assays
fluorescent microtubules in
Provedor de dados: 17
Autores: Lawrence J. Herskowitz; Steven J. Koch.
We describe an open-source LabVIEW software platform for generating simulated images of microtubules in gliding motility
assays. We describe how the software works and how to obtain the software.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4374/version/1
An optimized energy potential can predict SH2 domain-peptide interactions
Provedor de dados: 17
Autores: Zeba Wunderlich; Leonid Mirny.
Peptide recognition modules (PRMs) are used throughout biology to mediate protein-protein interactions, and many PRMs are
members of large protein domain families. Members of these families are often quite similar to each other, but each domain
recognizes a distinct set of peptides, raising the question of how peptide recognition specificity is achieved using similar protein
domains. The analysis of individual protein complex structures often gives answers that are not easily applicable to other
members of the same PRM family. Bioinformatics-based approaches, one the other hand, may be difficult to interpret physically.
Here we integrate structural information with a large, quantitative data set of SH2-peptide interactions to study the physical
origin...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1881/version/1
An OWL-DL Ontology for Classification of Lipids
Provedor de dados: 17
Autores: Hong-Sang Low; Christopher J. O. Baker; Alexander Garcia; Markus R. Wenk.
Lipids can be systematically classified according to functional properties, structural features, biochemical origin or biological
system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership
of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at the same time semantically explicit. We
report on the reuse of existing lipid nomenclature, ontology describing chemical structure and the extension of the OWL-DL Lipid
Ontology to support the classification of lipid molecules. We applied definitions, DL-axioms, to describe lipids classes and
illustrate suitability of the ontology for the classification of Fatty Acyl lipids and Mycolic acids.
Tipo: Presentation
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3590/version/2
An OWL-DL Ontology for Classification of Lipids
Provedor de dados: 17
Autores: Hong-Sang Low; Christopher J. O. Baker; Alexander Garcia; Markus R. Wenk.
Lipids can be systematically classified according to functional properties, structural features, biochemical origin or biological
system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership
of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at the same time semantically explicit. We
report on the reuse of existing lipid nomenclature, ontology describing chemical structure and the extension of the OWL-DL Lipid
Ontology to support the classification of lipid molecules. We applied definitions, DL-axioms, to describe lipids classes and
illustrate suitability of the ontology for the classification of Fatty Acyl lipids and Mycolic acids.
Tipo: Presentation
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3590/version/1
An OWL-DL Ontology for Classification of Lipids
Provedor de dados: 17
Autores: Hong Sang Low; Christopher J. O. Baker; Alex Garcia; Markus R. Wenk.
Lipids can be systematically classified according to functional properties, structural features, biochemical origin or biological
system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership
of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at the same time semantically explicit. We
report on the reuse of existing lipid nomenclature, ontology describing chemical structure and the extension of the OWL-DL Lipid
Ontology to support the classification of lipid molecules. We applied definitions, DL-axioms, to describe lipids classes and
illustrate suitability of the ontology for the classification of Fatty Acyl lipids and Mycolic acids.
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3542/version/1
An RNA _cis_-element upstream of the HMGA1a binding site affects exon exclusion caused by
HMGA1a
Provedor de dados: 17
Autores: Kenji Ohe; Takayuki Manabe; Taiichi Katayama; Masaya Tohyama; Akila Mayeda.
In addition to its characteristics as a DNA binding transcription factor, HMGA1a is known to bind RNA, sequence specifically
and regulate aberrant splicing of the _Presenilin-2_ gene in sporadic Alzheimer’s disease^1,2^. We show here that
an RNA _cis_-element, immediately upstream the HMGA1a binding site, induces exon inclusion upon mutating a GU sequence to
CA. Psoralen mediated UV crosslinking showed U1 snRNP did not bind this sequence but oligonucleotide-mediated RNase H
digestion showed it important for U1 snRNP to recognize the authentic 5’ splice site. This sequence
(5’-AAGUAC-3’) was tested for hnRNPA1 binding and function. Coimmunoprecipitation of
endogenous HMGA1a and hnRNPA1 in HeLa nuclear extract,...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/4119/version/1
An uncultured human-associated bacterium model
Provedor de dados: 17
Autores: Jorge M. Dinis; David E. Barton; Jamsheed Ghadiri; Deepa Surendar; Kavitha Reddy; Fernando Velasquez; Carol M.
Chaffee; Wendy Lee; Helen Gavrilova; Hazel Ozuna; Samuel A. Smits; Cleber C. Ouverney.
The Bacteria Domain experienced an explosion of novel lineages identified within the last decade, especially of lineages made
entirely of uncultured members. Since numerous cultivable bacteria have been shown to be instrumental in human development,
health, and diseases, it is reasonable to speculate that strains from uncultured groups, which comprise nearly 80% of the human
gut and 68% of human oral microbial consortia, participate in similar functions. The study of human-associated uncultured
bacteria, however, has many practical limitations, such as access to patient samples, unpredictable microbial composition, and low
relative abundance, all of which challenge experimental promptness and reproducibility. We propose that uncultured bacteria
from...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/5757/version/1
Analysis and visualisation of RDF resources in Ondex
Provedor de dados: 17
Autores: Catherine Canevet; Artem Lysenko; Andrea Splendiani; Matthew Pocock; Chris Rawlings.
An increasing number of biomedical resources provide their information on the Semantic Web and this creates the basis for a
distributed knowledge base which has the potential to advance biomedical research [1]. This potential, however, cannot be
realized until researchers from the life sciences can interact with information in the Semantic Web. In particular, there is a need
for tools that provide data reduction, visualization and interactive analysis capabilities.
Ondex is a data
integration and visualization platform developed to support Systems Biology Research [2]. At its core is a data model based on
two main principles: first, all information can be represented as a graph and, second, all elements of the graph can be annotated
with...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5430/version/1
Analysis of acceptance of bacillus to various heavy metals and antibiotics
Provedor de dados: 17
Autores: Yamini Singh Sisodia; Vivek Bajpai; Deeksha Gaur; Pankaj Kumar Jain.
The present study was carried out to systematically examine the pathogenic microorganisms in sewage samples isolated from the
Shekhawati region of Rajasthan. In this survey, 26 bacterial strains were isolated and identified using biochemical and molecular
methods. Molecular identification of isolates was done by DNA isolation, PCR amplification using 16S rDNA primer and partial
sequencing of purified product after sequencing, out of 26, 10 sequences were submitted to NCBI. Out of these 10 isolates
Bacillus pumilis, Bacillus subtilis and Bacillus licheniformis were taken for further studies. There is growing awareness of the
need for development of new antimicrobial agents for the treatment of human, animal and plant diseases. Keeping this fact in
mind, we...
Tipo: Poster
Palavras-chave: Biotechnology; Microbiology; Molecular Cell Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7073/version/1
Analysis of Antarctic Ice Core Data (EPICA Dome C) with Flicker-Noise Spectroscopy
Provedor de dados: 17
Autores: Yuriy Polyakov; Jean Robert Petit; Serge Timashev.
Evolution of Earth’s climate system over the past 800,000 years represents a complex process with successions of
uneven glacial and interglacial periods. The length, amplitudes, and development of each climate cycle depend on a number of
different factors, including the orbital parameters attributed to insolation and the complex responses of the Earth system to solar
radiation primarily through the amplification by Earth’s albedo and greenhouse gas and secondarily through a
system of heat reservoirs, such as ice sheet and deep ocean, distributed throughout our planet. The purpose of this study is to
analyze the transitions related to climate cycles in Antarctic ice core data (EPICA Dome C) of deuterium composition and dust...
Tipo: Poster
Palavras-chave: Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3341/version/1
Analysis of binding properties of VP2 protein of Human parvovirus B19 through in silico molecular
docking
Provedor de dados: 17
Autores: Praneetha Amburu; Dibyabhaba Pradhan; Vani Priyadarshini; Munikumar Manne; Umamaheswari Amineni.
Human parvovirus B19, a member of the Parvoviridae family, is a pathogen associated with a wide variety of diseases. Most
commonly, it causes childhood rash erythema infectiosum, but in some cases more serious symptoms such as persistent
arthropathy, critical failures of red cell production causing transient aplastic crisis, this infection in pregnancy causes hydrops
fetalis and myocarditis. Traditional immunosuppressive therapy being unsuccessful, anti-viral therapy might be worthy of
consideration. Functional annotation would provide role of viral proteome in its survival and pathogenic mechanisms. SVMProt
functional family annotations of VP2 protein had deciphered its zinc-binding, coat protein, outer membrane, chlorophyll
biosynthesis, DNA repair and...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5289/version/1
Analysis of Cancer Omics Data In A Semantic Web Framework
Provedor de dados: 17
Autores: Matthew Holford; James P. McCusker; Kei Cheung; Michael Krauthammer.
Our work concerns the elucidation of the cancer (epi)genome, transcriptome and proteome to better understand the complex
interplay between a cancel cell's molecular state and its response to anti-cancer therapy. To study the problem, we
have previously focused on data warehousing technologies and statistical data integration. In this paper, we present recent work
on extending our analytical capabilities using Semantic Web technology. A key new component presented here is a SPARQL
endpoint to our existing data warehouse. This endpoint allows the merging of observed quantitative data with existing data from
semantic knowledge sources such as Gene Ontology (GO). We show how such variegated quantitative and functional data can
be integrated and...
Tipo: Presentation
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5391/version/1
Analysis of circadian pattern reveals tissue-specific alternative transcription in leptin signaling
pathway
Provedor de dados: 17
Autores: Andrey Ptitsyn; Jeffrey Gimble.
*Background*
It has been previously reported that most mammalian genes display a circadian oscillation in
their baseline expression. Consequently, the phase and amplitude of each component of a signal transduction cascade has
downstream consequences. 

*Results*
We report our analysis
of alternative transcripts in the leptin signaling pathway which is responsible for the systemic regulation of macronutrient storage
and energy balance. We focused on the circadian expression pattern of a critical component of the leptin signaling system,
suppressor of cytokine signaling 3 (SOCS3). On an Affymetrix GeneChip 430A2 microarray, this gene is represented by three
probe sets targeting different...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/858/version/1
Analysis of DNA structure as a 2D random walk by complex wavelet transform
Provedor de dados: 17
Autores: Eugene B. Postnikov; Alexander Y. Loskutov; Sergey A. Larionov; Evgeny V. Ryadchenko; Roman V. Kiseliov.
We propose the original method of the time-scale wavelet analysis of DNA sequence represented as a 2D walk on a complex
plane. Namely, we consider the mapping of two irreducible A − T and G − C sequences into a walk
trajectory in the plane AGTC (firstly proposed by M. Gates) as a unique complex-valued function. 

This
function is processed with the new algorithm of the continuous wavelet transform with the Morlet wavelet. This method is based
on the representation of the transform’s result as a solution of the specific Cauchy problem for the system of PDE.


As an example, we applied the described algorithm to a part of the telomer region of the 22 human
chromosome and demonstated...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1461/version/1
Analysis of DTC nutrigenetic services in Italy: state of the art, agreement to the ESHG statement and
future outlooks
Provedor de dados: 17
Autores: Vincenzo Cinque; Fabio Acquaviva; Paola Vergara; Alessandra Cianflone; Imma Castaldo; Antonella Monticelli;
Sergio Cocozza; Michele Pinelli.
Background: In both USA and Europe operate companies selling Direct-to-consumer genetic tests (DTC). These tests are offered
to healthy people aiming to identify predispositions to complex diseases and to take preventive measures. Several
DTC-nutrigenetic tests (DNTs) are available on the market. They propose the definition of a personalized diet, on the basis of the
investigated genetic variants, which would reduce the risk of developing those diseases which have been associated to specific
genetic markers. However, the risk/benefit balance of exposing unselected population to genetic testing without any medical
surveillance is far from be established. Furthermore, it lacks an accepted procedure to select which genetic markers needs to be
investigated, to...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2012
URL: http://precedings.nature.com/documents/7135/version/1
Analysis of Endocrine Disruption in Southern California Coastal Fish using an Aquatic Multi-Species
Microarray
Provedor de dados: 17
Autores: Michael E. Baker; Barbara Ruggeri; James Sprague; Colleen Eckhardt; Jennifer Lapira; Ivan Wick; Laura Soverchia;
Massimo Ubaldi; Alberta M. Polzonetti-Magni; Doris Vidal-Dorsch; Steven Bay; Joseph R. Gully; Jesus A. Reyes; Kevin M.
Kelley; Daniel Schlenk; Ellen C. Breen; Roman Šášik; Gary Hardiman.
BACKGROUND:
Endocrine disruptors include plasticizers, pesticides, detergents and pharmaceuticals.
Turbot and other
flatfish are used to characterize the presence of chemicals in the marine environment. Unfortunately, there are relatively few
genes of turbot and other flatfish in GenBank, which limits the use of molecular tools such as microarrays and qRT-PCR to study
disruption of endocrine responses in sentinel fish captured by regulatory agencies.
OBJECTIVES:
A
multi-gene cross species microarray was fabricated as a diagnostic tool to screen the effects of environmental chemicals in fish,
for which there is minimal genomic information. The array included genes that are involved in the actions of adrenal and sex
steroids, thyroid...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Genetics & Genomics; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2823/version/1
Analysis of feral pig (Sus scrofa) movement in a Hawaiian forest ecosystem using GPS satellite collars
Provedor de dados: 17
Autores: Lasha-Lynn H. Salbosa; Dr. Christopher A. Lepczyk.
The ecosystem altering impacts of feral pigs have been widely documented around the world. However, a general framework for
their control and management has been lacking, especially in island ecosystems. One reason for this lack of management is that
we have little knowledge of how pigs move through different island ecosystems, especially ones that are topographically
challenging such as Hawai‛i. With recent advances in telemetry and movement modeling, it is now becoming
practical to understand where these large introduced animals are moving and how they are using habitat. Hence, the primary goal
of this study is to understand feral pig movement in terms of terrain, slope restrictions, and distance traveled beyond a natal site,
within an...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3903/version/1
Analysis of Genetic Interaction Maps Reveals Functional Pleiotropy
Provedor de dados: 17
Autores: Shuye Pu; Karen Ronen; James Vlasblom; Jack Greenblatt; Shoshana J. Wodak.
Epistatic or genetic interactions, representing the effects of mutations on the phenotypes caused by other mutations, can be very
helpful for uncovering functional relationships between genes. Recently, the Epistasis Miniarray Profile (E-MAP) method has
emerged as a powerful approach for identifying such interactions systematically. As part of this approach, hierarchical clustering
is used to partition genes into groups on the basis of the similarity between their global interaction profiles. Here we present an
original biclustering algorithm for identifying groups of functionally related genes from E-MAP data in a manner that allows
individual genes to be assigned to more than one functional group. This enables investigation of the pleiotropic nature of...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2182/version/1
Analysis of Human Spleen Contamination
Provedor de dados: 17
Autores: Martin Kopani; Martin Weis; Jan Jakubovsky.
Besides carbon, oxygen and nitrogen, numerous other elements and their compounds are significant in the body of humans and
other animals. Accumulation of some elements and their compounds is recognized by clinical and biochemical evaluation. The
physical-chemical properties and topical characteristics of elements in tissues may play a crucial role in evaluation their effect on
human body. The ^57^Fe Mössbauer measurement was used for evaluation of iron–oxide biomagnetic
nanoparticles composition and properties. Absorption spectra of the powdered spleen recorded at 77K and 300K were measured
and subsequently analyzed. From fitted data it is possible to obtain material composition as well as discuss the mean particle size
(received from...
Tipo: Poster
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/1408/version/1
Analysis of Nebivolol hydrochloride and Valsartan in Pharmaceutical Dosage Form by High
Performance Thin Layer Chromatographic Method
Provedor de dados: 17
Autores: Shradhanjali Singh; Anil K. Singh; Shanti B. Mishra; Alok Mukerjee; Mrinalini C. Damle.
A simple, accurate and precise high performance thin layer chromatographic method has been developed for the estimation of
Valsartan and Nebivolol hydrochloride simultaneously from a tablet dosage form. The method employed silica gel 60 F254
pre-coated plates as stationary phase and a mixture of Ethyl acetate: Methanol: Ammonia (6.5:2.5:0.5 %v/v/v) as mobile phase.
Densitometric scanning was performed at 280 nm using a Camag TLC scanner 3. Beer’s law was obeyed in the
concentration range of 800ng/spot-2400ng/spot for Nebivolol hydrochloride and 200ng/spot-1000ng/spot for Valsartan. The
Retention factor for Nebivolol hydrochloride is 0.75 ± 0.04 and is 0.27 ± 0.01 for Valsartan . The method
was validated as per ICH Guidelines,...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6134/version/1
Analysis of N-Glycosylation Sites in HIV glycoprotein 160
Provedor de dados: 17
Autores: Rajendra Mandage.
HIV infection is a condition caused by the human immunodeficiency virus. The condition gradually destroys the immune system,
which makes it harder for the body to fight infections. HIV presents a complex knot for scientists to unravel. An envelope protein
of the human HIV that is encoded by the env gene contains numerous glycosylation sites. It serves as a precursor for both the
GP120 and the GP41. Here statistical investigation was done to study the sequential aspects of amino acids around the
N-glycosylated protein from HIV virus. Sequences containing N-glycosylated asparagine were selected from the uniprot database
of N-glycosylated proteins. The frequency of occurrence of amino acid residues around the glycosylated asparagine showed that
there are...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5571/version/1
Analysis of plant metabolites – the baseline-threshold principle
Provedor de dados: 17
Autores: Katja Neubauer; Jenny Bandomir; Anett Grunenberg; Andreas Müller; Udo Kragl; Kerstin Schmidt.
With the environmental risk assessment (ERA) for genetically modified plants (GMP) the identification of equivalence or
differences in the composition of ingredients of GMPs and non-GMPs has to be investigated. The strategy is based upon the idea
that traditionally cultivated crops have been used safely for many years, thus every divergence within the compounds of a GMP in
contrast
to
its
non-GMP
counterpart
could
refer
to
a
risk
and
has
to
be
further
analysed.

The BioOK company offers the opportunity to analyse very different
aspects from the ERA of GMPs in one hand. Beside toxicological analysis and the determination of environmental effects via soil
analysis, we can look into several plant metabolites to identify...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4439/version/1
Analysis of plant metabolites – the baseline-threshold principle
Provedor de dados: 17
Autores: Katja Neubauer; Jenny Bandomir; Anett Grunenberg; Andreas Müller; Udo Kragl; Kerstin Schmidt.
With the environmental risk assessment (ERA) for genetically modified plants (GMP) the identification of equivalence or
differences in the composition of ingredients of GMPs and non-GMPs has to be investigated. The strategy is based upon the idea
that traditionally cultivated crops have been used safely for many years, thus every divergence within the compounds of a GMP in
contrast
to
its
non-GMP
counterpart
could
refer
to
a
risk
and
has
to
be
further
analysed.

The BioOK company offers the opportunity to analyse very different
aspects from the ERA of GMPs in one hand. Beside toxicological analysis and the determination of environmental effects via soil
analysis, we can look into several plant metabolites to identify...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4439/version/2
Analysis of Sustainable Water Resources Management (SWRM) in Agriculture
Provedor de dados: 17
Autores: Ahmad Reza Ommani; Mohammad Chizari.
The purpose of this research was analysis Sustainable Water Resources Management (SWRM) in agriculture of Khouzestan
Province of Iran. The research method was quantitative research. Total population of experts in the study included all agricultural
extension experts (N=96) of Agricultural-Jihad Organization of Khuzestan Province, Iran. Based on frequency of respondents
about importance rate of supportive policies regarding SWRM in agriculture, 70.8% of respondents stated that encouraging
farmers for using sustainable methods had very high importance. In reference to the frequency of respondents about extension
system roles on realization of SWRM dimensions in agriculture, 52.8% of respondents stated conservation of water resources had
very high importance...
Tipo: Manuscript
Palavras-chave: Ecology; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/4046/version/1
Analyzing local image statistics via maximum-entropy constructions
Provedor de dados: 17
Autores: Jonathan D. Victor; Daniel J. Thengone; Mary M. Conte.
Because the space of signals that the visual system encounters is high-dimensional, investigations of visual processing and
perception must utilize a sampling strategy. One kind of approach begins with a class of models for input-output relations, and
then chooses a stimulus ensemble such as white noise that enables efficient determination of model parameters. A second kind of
approach begins with the explicit recognition that it is important to understand the visual system in the context of the inputs under
which it functions and evolves; this motivates the use of naturalistic stimulus ensembles. Neither approach alone is sufficient:
models built from ensembles such as white noise provide only a fair account of responses to natural scenes, and the...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5794/version/1
Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant
sister species are
Provedor de dados: 17
Autores: Shi Huang.
There exists a remarkable correlation between genetic distance as measured by protein or DNA dissimilarity and time of species
divergence as inferred from fossil records. This observation has provoked the molecular clock hypothesis. However, data
inconsistent with the hypothesis have steadily accumulated in recent years from studies of extant organisms. Here the published
DNA and protein sequences from ancient fossil specimens were examined to see if they would support the molecular clock
hypothesis. The hypothesis predicts that ancient specimens cannot be genetically more distant to an outgroup than extant sister
species are. Also, two distinct ancient specimens cannot be genetically more distant than their extant sister species are. The
findings...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1676/version/2
Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant
sister species are
Provedor de dados: 17
Autores: Shi Huang.
There exists a remarkable correlation between genetic distance and time of species divergence as inferred from fossil records.
This observation has provoked the molecular clock hypothesis. However, data inconsistent with the hypothesis have steadily
accumulated in recent years from studies on extant organisms. Here the published DNA and protein sequences from ancient
fossil specimens were examined to see if they would support the molecular clock hypothesis. The hypothesis predicts that
ancient specimens cannot be genetically more distant to an outgroup than extant sister species are. Also, two distinct ancient
specimens cannot be genetically more distant than their extant sister species are. The findings here did not support these
predictions....
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1676/version/1
Ancient Trephinations in Neolithic People - Evidence for Stone Age Neurosurgery?
Provedor de dados: 17
Autores: Juergen Piek; Gundula Lidke; Thomas Terberger.
The authors present the case of a late neolithic skull (14C dating: 1940 calBC) found 1921 at Bölkendorf, 60 km
north-easterly of Berlin. It shows a left frontal trephination (53 x 50 mm) and additionally a left temporo-occipital depressed skull
fracture (both survived). Microscopic and 3D-CT analyses strongly suggest that the trephination has been performed for medical
purposes.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1615/version/1
Androgen Receptor and Vasopressin Receptor (AVPR1a) Genetic Polymorphisms are not associated
with Marital Status or Fertility among Ariaal Men of Northern Kenya
Provedor de dados: 17
Autores: Peter B. Gray; Dan T. A. Eisenberg; Benjamin C. Campbell.
A growing body of scholarship implicates testosterone and vasopressin in male reproductive behavior, including in humans. Since
hormones exert their effects through their respective receptors, an open question has been whether genetic polymorphisms in the
androgen receptor and vasopressin 1a receptor (AVPR1a) impact human male social behavior. Here, we sought to test for
associations between polymorphisms in the coding region of the androgen receptor and promoter region of AVPR1a in relation to
marital status and fertility among pastoralist Ariaal men of northern Kenya. None of the three polymorphisms were related to
marital status (single, monogamously married, polygynously married) or fertility (number of current living children). We discuss
these null...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3208/version/1
Angiogenesis and Vasculogenesis at 7-Day of Reperfused Acute Myocardial Infarction
Provedor de dados: 17
Autores: Sheng Kang; Yue-jin Yang; Qing-zhi Wang; Yue L. I. Li; Yi Tian; Yu-tong Cheng; Wei-feng Shen.
Objectives 
This study is to investigate the angiogenesis and vasculogenesis at the first week of reperfused
acute myocardial infarction (AMI).
Methods 
16 of mini-swines (20 to 30 Kg) were
randomly assigned to the sham-operated group and the AMI group. The acute myocardial infarction and reperfusion model was
created and the pig tail catheter was performed to monitor hemodynamics before left anterior descending coronary artery (LAD)
occlusion, 90 min of LAD occlusion and 120 min of LAD reperfusion. Pathologic myocardial tissue was collected at 7-day of
LAD reperfusion and further assessed by immunochemistry, dual immunochemistry, in-situ hybridization, real-time quantitative
polymerase chain reaction and...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2066/version/1
Angiogenesis in Chronic Obstructive Pulmonary Disease
Provedor de dados: 17
Autores: Alessandro Matarese; Gaetano Santulli.
Angiogenesis is a crucial component of lung pathophysiology, not only in cancer but also in other disorders, such as chronic
obstructive pulmonary disease (COPD). In COPD angiogenesis is definitely able to control and orchestrate the progression of
airway remodeling. Herein, we provide several remarkable translational aspects of angiogenesis in COPD, exploring both basic
and clinical research in this field. Indeed, we present a number of pro- and anti-angiogenic factors, which can be also used as
potential biomarkers to monitor disease progression. 

This pre-print has subsequently
been published at http://www.unisa.it/uploads/7100/06.pdf
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7112/version/1
Angiotensinergic innervation of rat and human mesenteric resistant blood vessels
Provedor de dados: 17
Autores: Jaspal Patil; Eva Heiniger; Thomas Schaffner; Oliver Muhlemann; Hans Imboden.
In contrast to the current believe that angiotensin II (Ang II) only interacts with the sympathetic nervous system (SNS) as a
circulating hormone, we document here the existence of an endogenous renin-angiotensin system (RAS) in the sympathetic
coeliac ganglion and the angiotensinergic innervation with mesenteric resistant blood vessels. Our findings indicate that Ang II is
synthesized inside the neurons of sympathetic coeliac ganglion and may act as an endogenous neurotransmitter locally on the
mesenteric resistant blood vessels.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/354/version/1
Anhedonia in the shadow of chronic social defeat stress, or When the experimental context matters
Provedor de dados: 17
Autores: Natalia P. Bondar; Irina L. Kovalenko; Damira F. Avgustinovich; Dmitry A. Smagin; Natalia N. Kudryavtseva.
One of the core symptoms of major depression in human is anhedonia. For that reason, one of the main requirements towards
experimental depression models is that they be able to demonstrate anhedonia in animals, that have been exposed to stressful
events, and other behavioral changes attributable to a depression-like state. However, the results presented in the literature are
contradictory: sweet solution intake, which is considered as a parameter of hedonic/anhedonic behavior in animals, responds quite
differently to stressful situations in that it is either unaffected or increased or decreased. Different experimental designs used for
the study of anhedonia in male mice exposed to chronic social defeat stress were tried to understand the reasons for so...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2682/version/1
Animal emergence during Snowball Earths by thermosynthesis in submarine hydrothermal vents
Provedor de dados: 17
Autores: Anthonie W. J. Muller.
Darwin already commented on the lateness in the fossil record of the emergence of the animals, calling it a valid argument against
his theory of evolution^1^. This emergence of the animals (metazoans: multicellular animals) has therefore attracted much
attention^2-5^. Two decades ago it was reported that extensive global glaciations (Snowball Earths) preceded the
emergence^6-7^. Here we causally relate the emergence and the glaciations by invoking benthic sessile^8-11^
thermosynthesizing^12-13^ protists that gained free energy as ATP while oscillating in the thermal gradient between a submarine
hydrothermal vent^14^ and the ice-covered ocean. During a global glaciation their size increased from microscopic to
macroscopic due to the selective advantage of a...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3333/version/1
Animal emergence during Snowball Earths by thermosynthesis in submarine hydrothermal vents
Provedor de dados: 17
Autores: Anthonie W. J. Muller.
Darwin already commented on the lateness in the fossil record of the emergence of the animals, calling it a valid argument against
his theory of evolution^1^. This emergence of the animals (metazoans: multicellular animals) has therefore attracted much
attention^2-5^. Two decades ago it was reported that extensive global glaciations (Snowball Earths) preceded the
emergence^6-7^. Here we causally relate the emergence and the glaciations by invoking benthic sessile^8-11^
thermosynthesizing^12-13^ protists that gained free energy as ATP while oscillating in the thermal gradient between a submarine
hydrothermal vent^14^ and the ice-covered ocean. During a global glaciation their size increased from microscopic to
macroscopic due to the selective advantage of a...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3333/version/2
ANN Based Virtual Classification Model for Discriminating Active and Inactive Withanolide E
Analogs against Human Breast Cancer Cell Line MCF-7
Provedor de dados: 17
Autores: Om Prakash; Feroz Khan; R.S. Sangwan.
Withanolides are a group of natural C-28 steroids built on an ergostane skeleton and classified into two major groups according to
their structural skeleton: (a) compounds with a beta-oriented side chain and (b) compounds with an alpha-oriented side chain.
Withanolide E represents one of the members of the latter group. Classification of active compounds on the basis of
pharmacophore against specific cancer cell line poses a serious concern at the primary stage of virtual screening. To overcome this
problem we have developed an artificial neural network based virtual screening model for discriminating active and non-active
Withanolide-E-like derivatives or analogs against human breast cancer cell line MCF-7. In the present work, a 2D chemical
descriptors...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6616/version/1
Annotated Manhattan plots and QQ plots for GWAS using R, Revisited
Provedor de dados: 17
Autores: Stephen D. Turner.
This manuscript provides software and a tutorial for creating manhattan plots and QQ plots for genome-wide association studies
using the R statistical computing environment.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6070/version/1
Annotating Whole Genome Sequencing in COSMIC (The Catalogue of Somatic Mutations in Cancer)
Provedor de dados: 17
Autores: C Y Kok; S A Forbes; N Bindal; S Bamford; C G Cole; M Jia; D Breare; R Shepherd; A Menzies; K Leung; J Teague;
M R Stratton; P A Futreal.
"COSMIC, the Catalogue Of Somatic Mutations In Cancer":http://www.sanger.ac.uk/cosmic is designed to
store and display somatic mutation information relating to human cancers, combining detailed information on publications,
samples and mutation types. The information is curated both from the primary literature and the laboratories at the Cancer
Genome Project, Sanger Institute, UK, and then semi-automatically entered into the COSMIC database. The v47 release (May
2010) contained the curation of 9202 papers describing 116,977 mutations across 466,851 samples. In order to provide consistent
annotation of the data, COSMIC has developed a classification system for cancer histology and tissue ontology, and adapted
HGVS mutation nomenclature...
Tipo: Poster
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5106/version/1
Annotation and Curation of the Protein Data Bank
Provedor de dados: 17
Autores: Jasmine Young; RCSB PDBj PDBe Protein Data Bank.
The Protein Data Bank (PDB) is the worldwide repository for experimentally determined 3D structures of biological
macromolecules. Established in 1971 with just seven structures, it presently includes more than 56,000 entries. To maintain the
highest standards in curation and processing, the members of the worldwide Protein Data Bank (wwPDB) collaborate in data
annotation and the development of procedures, tools, and resources. Annotation-related issues, particularly those impacted by new
developments
in structural biology, are critically reviewed at in-person and virtual meetings regularly and
frequently. Comprehensive documentation of the procedures, formats, and related data dictionaries used in data annotation are
available at the wwPDB...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3379/version/1
Annotation of SBML Models Through Rule-Based Semantic Integration
Provedor de dados: 17
Autores: Allyson L. Lister; Phillip Lord; Matthew Pocock; Anil Wipat.
*Motivation:* The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive,
manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model.
Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and
with a minimum of manual effort. Here, we present a method using off-the-shelf semantic web technology which enables this
process: the heterogeneous data sources are first syntactically converted into ontologies; these are then aligned to a small domain
ontology by applying a rule base. Integrating resources in this way can accommodate multiple formats with different semantics; it
provides...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3286/version/1
Annotation-based meta-analysis of microarray experiments
Provedor de dados: 17
Autores: Jie Zheng; Junmin Liu; Elisabetta Manduchi; Christian J. Stoeckert, Jr.
We are developing software applications to perform meta-analysis of microarray experiments based on standardized experiment
annotations aiming to identify similar experiments and cluster experiments. The applications were tested on files obtained from
the ArrayExpress public repository. Annotation terms were used to compute experiment dissimilarities to find experiments related
to a query experiment. These applications may motivate efforts of bench biologists to better annotate experiments.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3569/version/1
Annual cycle of aerosol backscatter coefficient and aerosol mixed layer height above
Neuchâtel (Switzerland, 47.00°N, 6.95°E)
Provedor de dados: 17
Autores: Manoj K Srivastava; Max Frioud; Renoud Matthey; Valentin Mitev.
Due to the complexity of the direct and indirect effects of the atmospheric aerosols on the air quality and atmospheric radiation
balance, complementary methods are necessary to assess the aerosol optical properties. In this sense the backscatter lidar methods
are critical in aerosol vertical distribution study. This work presents the annual cycle of aerosol backscatter coefficient (ABC) and
aerosol mixed layer (AML) height over Neuchâtel, Switzerland (47.00 N; 6.950 E, 485 m asl). The study is performed
by a ground based backscatter lidar operating at 532 nm wavelength as part of EARLINET program of EU. Atmospheric
layering for this study is based on a classification of lower atmosphere from 1 km to 2 km above sea level (asl) and from 2 km to
5...
Tipo: Poster
Palavras-chave: Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6425/version/1
Annual population rhythm of Anopheles mosquitoes in Indian subcontinent
Provedor de dados: 17
Autores: Mohit Bhardwaj; Leena Bharadwaj; Kritika Trigunayat; Madan Mohan Trigunayat.
Several organisms show a rhythm based behavior in their life. Mosquitoes are surviving successfully since ancient time on earth
while lots of biological creatures have been extinct. Thus it is interesting to study their population load. Climatic conditions affect
mosquito population significantly so on the basis of malaria cases their population is estimated in present study in Indian
geographical scenario. In this study it was found that their annual population load show a scientific rhythm. A schematic wave
form representation is also presented here to show mosquito population load. This study will be helpful in malaria vector
eradication and health care policies. 

Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/4569/version/2
Annual population rhythm of Anopheles mosquitoes in Indian subcontinent
Provedor de dados: 17
Autores: Mohit Bhardwaj; Leena Bharadwaj; Kritika Trigunayat; Madan Mohan Trigunayat.
Several organism show a rhythm based behavior in their life. Mosquitoes are surviving successfully since ancient time on earth
while lots of biological creatures have been extinct. Thus it is interesting to study their population load. Climatic conditions affect
mosquito population significantly so on the basis of malaria cases their population is estimated in present study in Indian
geographical scenario. In this study it was found that their annual population load show a scientific rhythm. A schematic wave
form representation is also presented here to show mosquito population load. This study will be helpful in malaria vector
eradication and health care policies. 

Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/4569/version/1
Ant Species Richness Around Amravati City Maharashtra, India
Provedor de dados: 17
Autores: Aravind B. Chavhan; Santosh S. Pawar; Mumtaz M. Baig.
Ants deserve a special place in the study of ecology, including behavior, given their species richness, social habits, and high
densities, contributing to much of the animal biomes on earth (Gadagkar et.at. 1993). As ants can be studied virtually everywhere
from forest interiors below ground, right up to the kitchen, we attempted a study to assess the ant species richness in a variety of
habitats in and around Amravati city. The prime objective of this study is to prepare a partial checklist of ants of Amravati and to
compare species richness between selected study sites. Eight study sites with different levels and types of vegetation were selected
for the study.
We employed an “all out search” method for collection...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5491/version/1
AntEpiSeeker2.0: extending epistasis detection to epistasis-associated pathway inference using ant
colony optimization
Provedor de dados: 17
Autores: Yupeng Wang; Xinyu Liu; Romdhane Rekaya.
Genome-wide association studies (GWAS) have become a standard method for finding genetic variations that contribute to
common, complex diseases. Recently, it is suggested that these diseases may be caused by epistatic interactions of multiple
genetic variations. Although tens of software tools have been developed for epistasis detection, few are able to infer pathway
importance from the identified epistatic interactions. AntEpiSeeker is originally an algorithm for detecting epistatic interactions in
case-control studies, using a two-stage ant colony optimization (ACO) algorithm. We have developed AntEpiSeeker2.0, which
extends the AntEpiSeeker algorithm to inference of epistasis-associated pathways, based on a natural use of the ACO
pheromones. By looking...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6994/version/1
Anterior Olfactory Nucleus
Provedor de dados: 17
Autores: Allen Institute for Brain Science; Beth M. Solan; Lydia L. Ng; Angela L. Guillozet-Bongaarts.
This report contains a gene expression summary of the anterior olfactory nucleus (AON), derived from the Allen Brain Atlas
(ABA) in situ hybridization mouse data set. The structure's location and morphological characteristics in the mouse
brain are described using the Nissl data found in the Allen Reference Atlas. Using an established algorithm, the expression values
of the AON were compared to the values of the macro/parent-structure, in this case the olfactory areas, for the purpose of
extracting regionally selective gene expression data. The genes with the highest ranking selectivity ratios were manually curated
and verified. 50 genes were then selected and compiled for expression characterization. The experimental data for each gene may
be...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2093/version/1
Anthropogenic Renourishment Feedback on Shorebirds: a Multispecies Bayesian Perspective
Provedor de dados: 17
Autores: Matteo Convertino; Joseph Donoghue; Ma Librada Chu-Agor; Gregory Kiker; Rafael Munoz-Carpena; Richard
Fischer; Igor Linkov.
In this paper the realized niche of the Snowy Plover (Charadrius alexandrinus), a primarily resident Florida shorebird, is described
as a function of the scenopoetic and bionomic variables at the nest-, landscape-, and regional-scale. We identified some possible
geomorphological controls that influence nest-site selection and survival using data collected along the Florida Gulf coast. In
particular we focused on the effects of beach replenishment interventions on the Snowy Plover (SP), and on the migratory Piping
Plover	(PP)	(Charadrius	melodus
)	and	Red	Knot	(RK)	(Calidris	canutus ).	Additionally,
we investigated the potential differences between the SP breeding and wintering...
Tipo: Manuscript
Palavras-chave: Ecology; Earth & Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5872/version/1
Antibodies targeting Cancer stem cells, A novel pattern in Immunotherapy
Provedor de dados: 17
Autores: Sarfaraz Alam.
Antibody targeting of cancer is showing clinical and commercial success after deep research and development over the last 3
decades. They have the great potential to deliver long-term cures but a shift in thinking towards a cancer stem cell (CSC) model
for tumour development is certain to have an impact on how antibodies are selected and developed, the targets they bind to and
the drugs used in combination with them. CSCs have been identified from many human tumours and share many of the
characteristics of normal stem cells such as the ability to renew and metabolically or physically protect themselves from
xenobiotic and DNA damage. Targeting CSCs could be a strategy to improve the outcome of cancer therapy. Monoclonal
antibodies are clinically and...
Tipo: Presentation
Palavras-chave: Cancer; Immunology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5428/version/1
Antibody responses to a Cryptosporidium parvum rCP15/60 vaccine
Provedor de dados: 17
Autores: Alexandra J. Burton; Daryl V. Nydam; Gary Jones; Jennifer Zambriski; Thomas C. Linden; Graham Cox; Randy Davis;
Alicia Brown; Dwight D. Bowman.
Cryptosporidium parvum is a zoonotic apicomplexa-protozoan pathogen that causes gastroenteritis and diarrhoea in mammals
worldwide. The organism is transmitted by ingestion of oocysts, which are shed in faeces, and completes its lifecycle in a single
host.^1^ C. parvum is ubiquitous on dairy operations worldwide and is one of the leading causes of diarrhoea in calves on these
farms.^2,3^ Here, for the first time, we describe the antibody response in a large group of cows to a recombinant C. parvum
oocyst surface protein (rCP15/60) vaccine and the antibody response in calves fed rCP15/60-immune colostrum produced by these
vaccinated cows. Results of recent genotype surveys indicate that calves are the only major reservoir for C. parvum infections in...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2009
URL: http://precedings.nature.com/documents/3988/version/1
Antibody-antigen interactions: What is the required time to equilibrium?
Provedor de dados: 17
Autores: Karl Andersson; Hanna Björkelund; Magnus Malmqvist.
The use of antibodies is widespread in many areas including in-vivo and in-vitro diagnostics, quantitative analysis in research
laboratories and as therapeutic substances. Since the methods for generation of antibodies has improved and regularly results in
high-affinity interactions, the standard assays used for quantification of the interaction properties should be revisited because they
do not necessarily produce accurate results. Here we show that in several cases, the affinity determination of strongly binding
antibodies will be inherently difficult when using standard procedures, due to impractically long incubation times. Real-time
kinetic analysis is often the only realistic alternative for affinity determination.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/5218/version/1
Anticancer efficacy of phenolics based structurally related compounds and their radical scavenging
action
Provedor de dados: 17
Autores: Vijaya Dubey; Nusrat Masood; Suaib Luqman; Arvind S. Negi.
Cancer, one of the leading causes of death worldwide, is an abnormal cell proliferation that fails to respond to the normal signals.
In an effort to eradicate the growing menace of cancer, a clear understanding of fundamental biology and molecular mechanism of
carcinogenesis is essential for targeted therapies. Among the devised strategies in use for cancer treatment, the one that is of
immense interest is the development of plant based novel anticancer agents. Due to their tremendous availability, biological
activity and efficacy, the phytochemicals deemed a gibbous future in chemoprevention. In the present study, several phenolics
based structurally related compounds of steroidal and non-steroidal skeleton were synthesized and tested for their...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6644/version/1
Antidepressant suppression of REM and spindle sleep impairs hippocampus-dependent learning and
memory but fosters striatal-dependent strategies
Provedor de dados: 17
Autores: Alain Watts; Howard Gritton; Jamie Sweigart; Gina Poe.
REM sleep enhances hippocampus-dependent associative memory but has little impact on striatal-dependent procedural learning.
Antidepressant medications like desipramine (DMI) inhibit rapid-eye-movement (REM) sleep but it is little understood how
antidepressant treatments affect learning. We found that DMI strongly suppressed REM sleep in rats for several hours and
impaired reconsolidation of a familiar maze and consolidation of moved baited positions (reversal learning) in a sleep-dependent
fashion. Unexpectedly, DMI also reduced the spindle-rich transition-to-REM sleep state (TR) and spatial memory changes were
more related to TR than to REM sleep. Working memory was unaffected, but overnight reference memory was significantly
impaired and subjects...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6524/version/1
Antidiabetic, Anti-hyperlipidemic & Hepatoprotective effect of a Polyherbal Unani
formulation “Qurs Tabasheer” in STZ-diabetic wistar rats
Provedor de dados: 17
Autores: Danish Ahmed; Manju Sharma; Alok Mukerjee; Raja Kamal Kant; Vikas Kumar.
The present study was undertaken to evaluate the antihyperglycemic, antihyperlipidemic and hepatoprotective effect of a
traditional unani formulation “Qurs Tabasheer” in streptozotocin (STZ) induced diabetic wistar rats.
Up until now, no study was undertaken to appraise the efficacy of “Qurs Tabasheer” in the diabetic
rats. Qurs Tabasheer is a unani formulation restraining preparations from six various herbs namely Tukhme Khurfa (Portulaca
oleracea seed), Gule Surkh (Rosa damascena flower), Gile armani (Arminium bole), Gulnar (Punica granatum flower), Tabasheer
(Bambusa arundinasia dried exudate on node), Tukhme Kahu (Lactuca sativa Linn seed). The effect of Qurs Tabasheer was
assessed in STZ (60 mg/kg, i.p...
Tipo: Manuscript
Palavras-chave: Pharmacology; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7056/version/1
Anti-HIV therapy: pipeline approaches and future directions
Provedor de dados: 17
Autores: Lavkush Dwivedi; Mansi Shrivastava.
Human immunodeficiency virus (HIV), with about 30 million deaths and double infections (in developing countries), is an open
challenge today for global scientists. Developing safe and effective measurements against it has become the prime need of hour.
Though, putting it at health priority, various efforts like chemotherapy, vaccines and others are attempted globally over last
decade. Consequently, highly active antiretroviral therapy was introduced but fails to completely block the viral replication due to
drug resistance and various other severe side effects. The antigenic variability and lack of appropriate experimental models is the
major obstacle in the development of an ever effective treatment against HIV. However, to overcome the present hurdles...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2011
URL: http://precedings.nature.com/documents/5540/version/1
Antimicrobial activity of skin secretions isolated from Indian toad, Bufo melanostictus Schneider 1799
Provedor de dados: 17
Autores: Abhishek Dinkarnath Garg; Dattatrey V. Kanitkar; Rajshekhar V. Hippargi; Amit N. Gandhare.
Amphibians like toads have been known to secrete antimicrobial secretions outside their body into their environments, through
skin pores and parotid glands. Toad skin-secretions contain four types of compounds namely, biogenic amines, bufadienolides,
alkaloids & steroids and peptides & proteins. Bulk of research relating to amphibian antimicrobial secretions
has been done on frogs. In toads, such research has only been done in South America, Europe and China. Antimicrobial secretions
vary considerably from specie-to-specie and drastically across various biomes. This prompted us to examine and confirm presence
of antimicrobial activity (if any) in Indian Common Toad (Bufo melanostictus Schneider 1799) skin secretions since; no such...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2007
URL: http://precedings.nature.com/documents/1204/version/1
Antimicrobial and Phytochemical Analysis of Centella asiatica (L.)
Provedor de dados: 17
Autores: Ramar Perumal Samy; Vincent TK Chow.
In vitro antibacterial studies were carried out using hexane, dichloromethane and methanol extract of leaves of Centella asiatica by
disc-diffusion method against gram-positive and gram-negative bacteria. The methanol and dichloromethane extracts of leaf
showed a broad spectrum antibacterial activity. Thus the results substantiate the traditional usage of this plant as a medicine.
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6033/version/1
Antioxidant response of overwintering conifers suggest species specific strategies for coping with
excess excitation energy
Provedor de dados: 17
Autores: Kim Hughes; Amy Verhoeven; Alex Kokula.
Background/Question/Methods:
Evergreen plants, growing in seasonally cold environments, must cope with
a severe imbalance between light absorption and its utilization, as low temperatures during winter inhibit photosynthetic carbon
reduction. In such conditions photoprotective mechanisms are critical, including the leaf antioxidant systems of plants. In a
previous study examining _Taxus cuspidata_, we found significant increases in the enzyme glutathione reductase (GR) and the
metabolite glutathione (GSH) during winter, but no increases in the enzymes superoxide dismutase, ascorbate peroxidase (APX)
or the metabolite ascorbate (ASC). These results led to the hypothesis that GR and GSH serve an important role during winter
stress that was...
Tipo: Poster
Palavras-chave: Earth & Environment; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5324/version/1
Antiviral activity of (E)-cinnamaldehyde revisited with nanoscience tools
Provedor de dados: 17
Autores: Arunava Goswami; Ayesha Rahman.
Contradictory results have been reported regarding the anti-viral activity of (E)-cinnamaldehyde, a major constituent (~69%) of
cinnamon. Here we show that (E)-cinnamaldehyde alone has very low antiviral property contrary to the belief of commoners.
There are early sporadic reports in ancient medicinal practices that fine sand was used for increasing the efficacy of antiviral
drugs. Can we increase the efficacy of (E)-cinnamaldehyde marginally by using one of the major constituents of sand like silica?
Yes, when nanosilica is used as a carrier during (E)-cinnamaldehyde administration, the antiviral efficacy of the resultant cocktail
increases marginally. Therefore, (E)-cinnamaldehyde consumed for centuries in tribal therapy as well as in alternative...
Tipo: Manuscript
Palavras-chave: Biotechnology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/5043/version/1
Antiviral Effects of a Synthetic Aluminium-Magnesium Silicate on Avian Influenza Virus
Provedor de dados: 17
Autores: Madike Ezeibe; Anthony Egbuji; Obianuju Okoroafor; James Eze; Omadi Ijabo; Augustine Ngene; Ikechukwu Eze;
Joeseph Ugonabo; Mary Sanda; Ijeoma Mbuko.
Effects of a synthetic Aluminium-Magnesium Silicate (AMS) on Avian Influenza Virus (AIV) were tested. Equal amounts of
H5N1 AIV samples and of AMS were mixed, left one hour, at room temperature before centrifuging. The supernatants were
remeasured and tested for viral titre, for Mean Death Time (MDT) and Embryo Mortality Rate (EMR) of chicken eggs. Volumes
of the viral samples reduced at rate of 23.4 ± 5.48 %. Viral titres reduced significantly (P from HA, 73 ±
32.72 to 1.4 ±0.43). Also, mortality of infected embryos reduced from 100 % to 65% while MDT of those that died,
increased significantly (P = 0.001) from 76 ± 4.38 to 130 ±17.27 hours. When incubation with AMS was
repeated on portions of the same sample,...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/6509/version/1
Apellicon: a web-based tool for constructing and curating Textpresso databases.
Provedor de dados: 17
Autores: William M. Urbanski; Brian G. Condie.
As more research literature in the biological sciences is made available in electronic format, text mining systems are increasingly
being used to improve the ability of investigators to retrieve relevant information. Through the use of advanced indexing
techniques that utilize biological ontologies, semantic databases, and other formal representations of biological concepts text
mining systems have been able to effectively parse biological literature. While text mining systems are increasingly effective at
creating the linkages required to provide context-specific search results, the systems themselves are difficult to set up and use by
novice computer users due to the highly technical nature of the applications. Because most researchers in the biological...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4927/version/1
Apoptotic gene expression in neuropathic pain
Provedor de dados: 17
Autores: Dario Siniscalco; Catia Giordano; Carlo Fuccio; Livio Luongo; Annalucia Migliozzi; Francesco Rossi; Sabatino
Maione.
Pain initiated or caused by a primary lesion or dysfunction in the nervous system is defined as neuropathic pain. It results from
direct injury to nerves in the peripheral or central nervous system and is associated with several clinical symptoms. Neuropathic
pain treatment is extremely difficult, as it is a very complex disease, involving several molecular pathways. Excitatory or
inhibitory pathways controlling neuropathic pain development show altered gene expression, caused by peripheral nerve
injury.
This study used several experimental pain models to demonstrate the occurrence of programmed cell
death in the centers controlling pain induction and maintenance, such as spinal cord and pre-frontal cortex. We combined
behavioural,...
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/1549/version/1
Apotemnophilia - the Neurological Basis of a 'Psychological' Disorder
Provedor de dados: 17
Autores: Paul D. McGeoch; David J. Brang; Tao Song; Roland R. Lee; Mingxiong Huang; Vilayanur S. Ramachandran.
The question of how the human brain combines disparate sensory inputs to construct a unified body image is of longstanding
interest^1,2,3^ . We approached this subject by studying the unusual medical condition of apotemnophilia, in which otherwise
mentally normal individuals express the strong and persistent desire for the amputation of a specific healthy limb^4,5,6^ . Here we
show using functional brain imaging - magnetoencephalography (MEG) - that the condition is characterised by an absence of
activity in the right superior parietal lobule (SPL) when the affected limb is touched. When this discovery is combined with our
earlier finding of a simultaneous increase in skin conductance response (SCR) on touching the affected limb^7^ , which reflects...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2954/version/1
Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro
Provedor de dados: 17
Autores: David Tollervey; Jonathan Houseley.
Trans-splicing, the in vivo joining of two RNA molecules, is well characterized in several groups of simple organisms but was
long thought absent from fungi, plants and mammals. However, recent bioinformatic analyses of expressed sequence tag (EST)
databases suggested widespread trans-splicing in mammals^1-2^. Splicing, including the characterised trans-splicing systems,
involves conserved sequences at the splice junctions. Our analysis of a yeast non-coding RNA revealed that around 30% of the
products of reverse transcription lacked an internal region of 117 nt, suggesting that the RNA was spliced. The junction sequences
lacked canonical splice-sites but were flanked by direct repeats, and further analyses indicated that the apparent splicing actually...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4203/version/1
Application of a periodic table for the genetic code of the influenza A/H3N2 virus
Provedor de dados: 17
Autores: Susumu Morimoto.
The progress of life sciences would be greatly enhanced if biological data were available in a manner similar to the periodic table
of the elements. Currently, the mutation rules for influenza viruses remain ambiguous. In light of the threat of Avian Influenza
there is an urgent need to understand the governing principles behind influenza virus mutations. Here, the applicability of a
periodic table for the genetic code of influenza A/H3N2 virus is explored. In addition, two rules regarding single point mutations
of the hemagglutinin gene are presented. The first rule states that non-synonymous single point mutations are intimately
associated with the first or second base replacements between two congener codons of four groups (5, 6, 9, and 10) in the...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/428/version/2
Application of a periodic table for the genetic code to influenza A/H3N2 virus
Provedor de dados: 17
Autores: Susumu Morimoto.
If biologists can utilize a table to have access to biological phenomena in the manner analogous to the periodic table for chemical
elements, they may get hold of a directing post in life science. Currently the mutational rule of influenza viruses have remained
perplexed and to reveal it should be now desired when avian influenza virus has just then threatened human beings. Here I
examine the applicability of a novel periodic table for the genetic code to influenza A/H3N2 virus, while presenting two rules
regarding single point mutations of its virus hemagglutinin gene. One rule is that non-synonymous single point mutations are
intimately associated with the first or second base replacements between four groups (5, 6, 9, and 10) in the periodic table....
Tipo: Manuscript
Palavras-chave: Chemistry; Genetics & Genomics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/428/version/1
Application of space technology to the design of sustainable settlements in hot deserts:
Bioregenerative life support systems
Provedor de dados: 17
Autores: Yuriy Polyakov; Ibrahim Musaev; Sergey Polyakov.
Water scarcity in hot deserts, which cover about one-fifth of the Earth’s land area, along with rapid expansion of hot
deserts into arable lands is one of the key global environmental problems. This paper proposes and substantiates an
interdisciplinary approach to sustainable settlements in hot deserts using the accomplishments in the design of closed
bioregenerative life support systems (CBLSS) for beyond-Earth (Lunar, Martian) settlements. Extensive space technology
experience in the design of CBLSSes, which simultaneously produce food, water, nutrients, and fertilizers, process wastes, and
revitalize air, has been analyzed and systematized with application to hot deserts, which represent extreme habitats with high input
of solar energy, poor...
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3926/version/1
Application of the Sensory Contact Model for Pharmacological Studies under Simulated Clinical
Conditions
Provedor de dados: 17
Autores: Natalia N. Kudryavtseva; Damira F. Avgustinovich; Natalia P. Bondar; Michael V. Tenditnik; Irina L. Kovalenko.
The sensory contact model allows forming different psycho-pathological states (anxious depression, catalepsy, social withdrawal,
pathological aggression, cognition disturbances, anhedonia, addictive states etc.) produced by repeated agonistic interactions in
male mice and investigating the therapeutic and preventive properties of any drug as well as its efficiency under simulated clinical
conditions. This approach can be useful for a better understanding of the drugs’ action in different stages of disease
development in individuals. It is suggested that this behavioral approach and pharmacological designs may be applied for the
screening of novel psychotropic drugs. 

Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2007
URL: http://precedings.nature.com/documents/1439/version/1
Applications Of Microspectroscopy, Hyperspectral Chemical Imaging And Fluorescence Microscopy
In Chemistry, Biochemistry, Biotechnology, Molecular And Cell Biology
Provedor de dados: 17
Autores: I. C. Baianu.
Chemical imaging is a technique for the simultaneous measurement of spectra (chemical information) and images or pictures
(spatial information)^1,2^. The technique is most often applied to either solid or gel samples, and has applications in chemistry,
biology^3-8^, medicine^9,10^, pharmacy^11^ (see also for example: Chemical Imaging Without Dyeing), food science, Food
Physical Chemistry, Biotechnology^12,13^, Agriculture and industry. NIR, IR and Raman chemical imaging is also referred to as
hyperspectral, spectroscopic, spectral or multi-spectral imaging (also see micro-spectroscopy). However, other ultra-sensitive and
selective, chemical imaging techniques are also in use that involve either UV-visible or fluorescence microspectroscopy.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Molecular Cell
Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6593/version/1
Apply of Textmining Method to Study the Roles in Improving the Health by Lactoferrin, a
Multi-Functional Milk Protein
Provedor de dados: 17
Autores: Kei-ichi K. Shimazaki; Tatsuya T. Kushida; Koji K. Yamauchi; Toshihisa T. Takagi.
Lactoferrin is a metal-binding glycoprotein found in milk, blood and other exocrine secretions. This is a multi-functional protein
that exhibits many activities such as: anti-microbial, anti-viral, immunomodulatory, anti-inflammatory, anti-tumor,
anti-metastatic, cell growth-promoting, and anti-oxidant activities, as well as regulation of granulopoiesis and iron absorption, etc.
To date, a number of academic reports concerning the biological activities of lactoferrin have been published and are easily
accessible through public databases. In order to overcome the information overload associated with lactoferrin information, we
have applied the text mining method to the accumulated lactoferrin literature. To this end, we used the information extraction...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5100/version/1
Applying Biomedical Ontologies on Semantic Query Expansion
Provedor de dados: 17
Autores: Andre Bechara; Maria Luiza C. Machado; Vanessa Braganholo.
*1- Introduction*

The interpretation of a question (or information need) depends,
among other things, of a series of lexicalsemantic relations that complement and help the cognitive process of answering that
information need. Despite this fact, currently used information retrieval mechanisms take few advantages of the semantic
interpretation of users’ information needs (usually specified through keywords). In most of the cases, those
mechanisms are based on keyword matching, and thus are excessively dependant on the query and document
terms.

There are several past results showing that, in general, information retrieval
based on domain knowledge decreases the accuracy of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3550/version/1
Applying of novel subtracted method Genetically Directed Differential Subtraction Chain (GDDSC)
in plant genomes
Provedor de dados: 17
Autores: Ewa Siedlecka; Aneta Hromada-Judycka; Magdalena Pawełkowicz; Rafał
Wóycicki; Monika Rakoczy-Trojanowska; Zbigniew Przybecki.
We present a simple subtraction procedure of GDDSC as a modification of the original DSC and GDRDA methods. Genetically
Directed Differential Subtraction Chain (GDDSC) is a process by which highly related genomes are compared in order to isolate
tags carrying the polymorphisms. 
To detect specific DNA fragment (tag), we can then monitor offspring
plants for efficient molecular breeding. The GDDSC protocol was applied to isolation of new sex related clones from cucumber
plants (_Cucumis_ _sativus_ L.) and new tissue culture response clones from rye (_Secale_ _cereale_ L.). The newly identified
tags, obtained by GDDSC represent pools of candidate genes and other sequences, which could serve as potential markers for
requested traits.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics & Genomics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5465/version/1
Applying of novel subtraction method Genetically Directed Differential Subtraction Chain (GDDSC)
in plant genomes
Provedor de dados: 17
Autores: Ewa Siedlecka; Aneta Hromada-Judycka; Magdalena Pawełkowicz; Rafał
Wóycicki; Monika Rakoczy-Trojanowska; Zbigniew Przybecki.
We present a simple subtraction procedure of GDDSC as a modification of the original DSC and GDRDA methods. Genetically
Directed Differential Subtraction Chain (GDDSC) is a process by which highly related genomes are compared in order to isolate
tags carrying the polymorphisms. 
To detect specific DNA fragment (tag), we can then monitor offspring
plants for efficient molecular breeding. The GDDSC protocol was applied to isolation of new sex related clones from cucumber
plants (_Cucumis_ _sativus_ L.) and new tissue culture response clones from rye (_Secale_ _cereale_ L.). The newly identified
tags, obtained by GDDSC represent pools of candidate genes and other sequences, which could serve as potential markers for
requested traits.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics & Genomics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5465/version/2
Aptamer-based multiplexed proteomic technology for biomarker discovery
Provedor de dados: 17
Autores: Larry Gold; Deborah Ayers; Jennifer Bertino; Christopher Bock; Ashley Bock; Edward N. Brody; Jeff Carter; Virginia
Cunningham; Andrew Dalby; Bruce E. Eaton; Tim Fitzwater; Dylan Flather; Ashley Forbes; Trudi Foreman; Cate Fowler; Bharat
Gawande; Meredith Goss; Magda Gunn; Shashi Gupta; Dennis Halladay; Jim Heil; Joe Heilig; Brian Hicke; Gregory Husar;
Nebojsa Janjic; Thale Jarvis; Susan Jennings; Evaldas Katilius; Tracy R. Keeney; Nancy Kim; Terese Kaske; Tad Koch; Stephan
Kraemer; Luke Kroiss; Ngan Le; Daniel Levine; Wes Lindsey; Bridget Lollo; Wes Mayfield; Mike Mehan; Robert Mehler;
Michele Nelson; Sally K. Nelson; Dan Nieuwlandt; Malti Nikrad; Urs Ochsner; Rachel M. Ostroff; Matt Otis; Thomas Parker;
Steve Pietrasiewicz; Dan Resnicow; John Rohloff; Glenn Sanders; Sarah Sattin; Dan Schneider; Britta Singer; Martin Stanton;
Alana Sterkel; Alex Stewart; Suzanne Stratford; Jonathan D. Vaught; Mike Vrkljan; Jeffrey J. Walker; Mike Watrobka; Sheela
Waugh; Allison Weiss; Sheri Wilcox; Alexey Wolfson; Steve Wolk; Chi Zhang; Dom Zichi.
Interrogation of the human proteome in a highly multiplexed and efficient manner remains a coveted and challenging goal in
biology. We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring
thousands of proteins from small sample volumes (15 [mu]L of serum or plasma). Our current assay allows us to measure ~800
proteins with very low limits of detection (1 pM average), 7 logs of overall dynamic range, and 5% average coefficient of
variation. This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which
greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected.
Proteins in complex...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4538/version/1
Aqueous Electrolyte Ionization over Extreme Ranges as Simple Fundamental Relation with Density
and Believed Universal; Sodium Chloride Ionization from 0^o^ to 1000^o^C and to 1000 MPa (10000
Atm.)
Provedor de dados: 17
Autores: William L. Marshall.
The chemical nature of aqueous electrolyte ionization is illustrated by a simple relationship with water as a reactant believed to
correlate ionization of aqueous sodium chloride approaching infinite dilution over the entire range of temperature and pressure [0
to 1000^o^C; 0.1 to 1000 MPa (10000 Atm)]. The derived equation accurately and smoothly describes the ionization constant of
sodium chloride [_K_(NaCl)] in both water and water strongly diluted by inert solvent. Effects of water density on ionization are
quantitatively and simply described that oppose conventional theory that ionization is a function only of dielectric constant, and
theorists should apply this simplicity with density in understanding aqueous electrolyte ionization. There appears...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2476/version/1
Aqueous phase hydration and hydrate acidity of perfluoroalkyl and n:2 fluorotelomer aldehydes
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Perfluoroalkyl aldehydes (PFAlds) and n:2 fluorotelomer aldehydes (FTAlds) are degradation products of precursor compounds
that include fluorotelomer alcohols, iodides, acrylates, phosphate esters, and other derivatives, as well as hydrofluorocarbons and
hydrochlorofluorocarbons. The SPARC software program and comparative density functional theory (DFT) calculations were
used to investigate the aqueous phase hydration equilibrium constants (K~hyd~) of PFAlds and FTAlds. DFT studies suggest that
all PFAlds will be dominantly present as the hydrated form in aqueous solution. While SPARC correctly estimates the K~hyd~ for
the C~1~ PFAld, it appears to incorrectly predict a large decline in K~hyd~ (particularly between C~1~ and C~2~) with
increasing...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4520/version/1
Aqueous synthesis of CdTe quantum dot as biological fluorescent probe for monitoring methyl
parathion by fluoro-immunosensor
Provedor de dados: 17
Autores: Raghuraj Chouhan; Aaydha Vinayaka; Munna Thakur.
Bioconjugation of quantum dots (QDs) provide high resolution in biological fluorescent labelling as a result of physical and
optical properties of QDs. This intrinsic property of QDs can be made use of for sensitive detection of target analytes including
food and environmental monitoring. In this investigation, we report the bioconjugation of thiol stabilized CdTe QD for the
sensitive detection of methyl parathion (MP) at picogram level. The specificity in the analysis was attributed by highly specific
competitive immunological reactions between free MP and CdTe QD bioconjugated MP (MP-BSA-CdTe) for immobilized
anti-MP IgY antibodies in a simple flow injection system. We also report the possible resonance energy transfer phenomenon as a
result of...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3451/version/1
Arbuscular mycorrhizal fungus spores host bacteria and their biofilm efficient in nutrient
biodynamics and soil-borne plant pathogen suppression
Provedor de dados: 17
Autores: Andre Cruz; Takaaki Ishii.
The combination of bacteria and arbuscular mycorrhizal fungi (AMF) would be ideal for nutrient biodvnamics in soils and
protection from soil-borne plant pathogens (SBPP). During the process of plant colonization AMF interact with bacteria where
spores cytoplasm and hvphae provide specific niches for certain populations of bacteria. The clarification of the relationship
AMF-bacteria has great potential for sustainable agriculture. The currently research aimed to isolate and characterize bacteria.
Which we have designated most probable endobacteria (MPE) from an AMF spore. Three bacterial strains were taken from about
500 spores by using a 200 µm diameter hvpodermic needle. These bacteria were identified by DNA and morphological
methods. Antagonism...
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/5544/version/1
Archaebacterial Whole-Genome Duplication and Origin of Eukaryots
Provedor de dados: 17
Autores: Milanko Stupar.
Division of the ancestral prokaryotic pragenome into two circular double-stranded DNA molecules by genetic recombination, is a
base for the future separate evolution of the nuclear and mitochondrial gene compartment. This suggests monophyletic origin of
both mitochondrion and nucleus. Presumed organism which genome undergoes genetic recombination has to be searched among
an aerobic, oxygen non-producing archaeon with no rigid cell wall, but a plasma membrane. Plastids evolve from an aerobic,
oxygen producing proto-eukaryot, after mitoplastide genome duplication and subsequent functional segregation.In this proposal
origin of eukaryots occur by a three-step mechanism. First, replication fork pauses and collapses generating a breakage in the
genome of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2302/version/1
Archon Genomics X PRIZE Validation Protocol
Provedor de dados: 17
Autores: Larry Kedes; Granger Sutton; Edison Liu; Victor Jongeneel.
This document is a collective assembly of techniques designed to test the quality and accuracy of 100 whole human genome
sequences resulting from the $10 Million Archon Genomics X PRIZE (AGXP) competition. The purpose of this article is to enlist
constructive criticism from the genomic and genetic community on the outlined approaches. The intent for the final version of this
Validation Protocol is to become a useful standard by which to gauge the capabilities of whole genome sequencing technologies
that emerge even after 2012.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5731/version/1
Are endocannabinoid type 1 receptor gene (CNR1) polymorphisms associated with obesity and
metabolic syndrome in postmenopausal Polish women?
Provedor de dados: 17
Autores: Katarzyna Dunajska; Felicja Lwow; Diana Jedrzejuk; Andrzej Milewicz; Urszula Tworowska-Bardzinska; Lukasz
Laczmanski.
Objective: The aim of this study was to determine whether genetic variation at the cannabinoid receptor-1 (CNR1) locus could
have an effect on adiposity, fat distribution and obesity-related metabolic disorders in Polish postmenopausal women.Design and
Subjects: The A3813G, G1422A and A4895G single nucleotide polymorphisms of CNR1 were genotyped in 348 randomly
selected postmenopausal women aged 50-60 years recruited from the Wroclaw city population. Measurements: CNR1 genotypes,
anthropometric measures (BMI, WC, body fat distribution by DEXA) and metabolic parameters (glucose, lipid profile, insulin
FIRI) were determined.Results: The 3813G allele was not significantly associated with higher body mass, BMI, WC, total fat, or
fat percentage, but was...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3946/version/1
Are men evolutionarily wired to love the "Easy" buttons?
Provedor de dados: 17
Autores: Irina Trofimova.
Men's drive for group control and power appears to be an evolutionary inheritance, but it is females, and not males,
who developed better abilities for prolonged control and group interaction while males have higher rates of ADHD and autism.
This contradictory allocation of sex-related abilities describes the observable behavior, but not the internal meaning attribution
leading to the motivation of men and women. Our study in Canada, China and Russia shows that men estimate power- and
status-related concepts in significantly more positive terms than women, but give significantly more negative estimations to
work-related and reality-related concepts. Men also have a consistent tendency to estimate concepts as less real (even...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5562/version/1
Are plants with anti-cancer activity resistant to crown gall? : A test of hypothesis
Provedor de dados: 17
Autores: R Srirama; BT. Ramesha; G. Ravikanth; R. Uma Shaanker; KN Ganeshaiah.
The Crown gall tumour assay (CGTA) is one of several bench top bioassays recommended for the rapid screening of plants with
anti-cancer activity. The rationale for the use of the bioassay is that the tumorogenic mechanism initiated in plant tissues by
_Agrobacterium tumefaciens_ is in many ways similar to that of animals. Several plant species with anti-cancer activity have
already been discovered using this bioassay. However till date no explicit test of an association between anti-cancer activity of
plants and their resistance to crown gall formation has been demonstrated. Demonstration of an association could have exploratory
potential when searching for plants with anti-cancer activity. In this paper, we determined whether or not a statistically...
Tipo: Manuscript
Palavras-chave: Cancer; Pharmacology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1456/version/1
Area Postrema
Provedor de dados: 17
Autores: Allen Institute for Brain Science; Katie J. Glattfelder; Lydia L. Ng; John A. Morris.
This report contains a gene expression summary of the area postrema (AP), derived from the "Allen Brain
Atlas":http://www.brain-map.org/welcome.do;jsessionid=EDE40ADC940845D169DE378ADC9B71BD
(ABA)
in-situ hybridization (ISH) mouse data set. The structure’s location and morphological characteristics in the mouse
brain
are
described
using
the
Nissl
data
found
in
the
"Allen
Reference
Atlas":http://www.brain-map.org/mouse/atlas/coronal/legend.html. Using an established algorithm, the expression
values of the AP were compared to the values of the macro/parent-structure, in this case the medulla, for the purpose of extracting
regionally specific gene expression data. The highest ranking ratios were then manually...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2053/version/1
Argudas: arguing with gene expression information
Provedor de dados: 17
Autores: Kenneth McLeod.
In situ hybridization gene expression information helps biologists identify where a gene is expressed. However, the databases that
republish the experimental information are often both incomplete and inconsistent. This presentation examines a system, Argudas,
designed to help tackle these issues. Argudas is an evolution of an existing system, and so that system is reviewed as a means of
both explaining and justifying the behavior of Argudas. Throughout the discussion of Argudas a number of issues will be raised
including the appropriateness of argumentation in biology and the challenges faced when integrating apparently similar online
biological databases.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5394/version/1
ARHI (DIRAS 3), an Imprinted Tumor Suppressor Gene, Binds to Importins, and Blocks Nuclear
Translocation of Stat3
Provedor de dados: 17
Autores: Shaoyi Huang; In Soon Chang; Wenbo Lin; Robert Luo; Zhen Lu; Yiling Lu; Ke Zhang; Warren Liao; Tao Tao; Robert
Bast, Jr.; Xiaomin Chen; Yinhua Yu.
ARHI (DIRAS3) is an imprinted tumor suppressor gene whose expression is lost in the majority of breast and ovarian cancers.
Unlike its homologs Ras and Rap, ARHI functions as a tumor suppressor. Our previous study showed that ARHI can interact with
transcription activator Stat3 and inhibit its nuclear translocation in human breast and ovarian cancer cells. To identify proteins that
interact with ARHI in nuclear translocation, we have performed proteomic analysis and identified several importins that can
associate with ARHI. To further explore this novel finding, we have purified 10 GST-importin fusion proteins (importin 7, 8, 13,
b1, a1, a3, a5, a6, a7 as well as mutant a1). Using a GST-pull down assay, we found that ARHI can bind strongly to most...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2392/version/1
ArrayMining.net: a web-server for integrative microarray and gene set analysis
Provedor de dados: 17
Autores: Enrico Glaab; Jonathan M. Garibaldi; Natalio Krasnogor.
DNA microarray experiments provide a means to understand cancer and genetic diseases on a molecular level, improve diagnosis
and identify new drug targets. However, choosing appropriate data processing methods and parameters is a difficult and
time-consuming task, particularly for researchers without prior experience in this field. 
We present
*ArrayMining.net*, a free web-service for automatic microarray analysis to address these issues. ArrayMining.net covers several
major areas in statistical microarray analysis - Feature Selection, Clustering, Prediction, Gene Set and Network Analysis providing access to several algorithms for each of these tasks based on a single, easy-to-use interface.
Tipo: Poster
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5552/version/1
Arrhenius' theory of partial dissociation and hydration of electrolytes in solutions
replaces existing activity concepts
Provedor de dados: 17
Autores: Raji Heyrovska.
The author shows that Arrhenius's theory of partial electrolytic dissociation was immaturely displaced about eight
decades ago by the empirical concept of ionic activities and the assumption of complete dissociation of electrolytes at all
concentrations. The latter brought the theory of electrolytes over the next decades into a complicated state without any physical
significance. Therefore, the author started a systematic investigation of the available data and could completely restore the original
theory of partial dissociation. Now solution properties can be easily understood and quantitatively explained in terms of absolute
concentrations and volumes of ions and ion pairs and hydration.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6416/version/2
Artificial Antigen Presenting Cells With Preclustered anti-CD28/-CD3/-LFA-1 Monoclonal Antibodies
Are Highly Effective To Induce The Ex-Vivo Expansion Of Functional Human Antitumor T Cells
Provedor de dados: 17
Autores: Roberta Zappasodi; Massimo Di Nicola; Carmelo Carlo-Stella; Roberta Mortarini; Alessandra Molla; Claudia Vegetti;
Lorena Passoni; Salvatore Albani; Andrea Anichini; Alessandro M. Gianni.
Effective adoptive T cell therapy requires the _ex vivo_ generation of functional T lymphocytes with a long lifespan _in vivo_.
We evaluated _in vitro_ T cell expansion by artificial antigen presenting cells (aAPC) generated with activating (human
anti-CD3), co-stimulating (human anti-CD28) and adhesion (human anti-LFA-1) monoclonal antibodies pre-clustered in
microdomains (MDs) held by a liposome scaffold. The co-localization of T cell ligands in MDs and the targeting of an adhesion
protein, increasing the efficiency of immunological synapse formations, represent the novelties of our system. These aAPCs
allowed increased expansion of polyclonal CD4^+^ and CD8^+^ T cells and of tumor antigen-specific CD8^+^ T cells compared
to anti-CD28- and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Immunology.
Ano: 2007
URL: http://precedings.nature.com/documents/1250/version/1
Artificial Neural Network
Provedor de dados: 17
Autores: Smrita Singh.
In the postgenomic era, computational methods are being used in diverse areas like drug discovery, robotics, weather forecasting
etc. Computational methods are incorporated with various programmes that are further instructed with complex algorithms based
on different logistic approaches. Artificial neural network is one of them to be utilized in various molecular dynamics and
simulation studies. Therefore, it is essential to understand the basic logic while programming in order to troubleshoot the
computational methods.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6623/version/1
Artificial Photosynthesis Would Unify the Electricity-Carbohydrate-Hydrogen Cycle for
Sustainability
Provedor de dados: 17
Autores: Yi-Heng Percival Zhang.
Sustainable development requires balanced integration of four basic human needs – air (O2/CO2), water, food, and
energy. To solve key challenges, such as CO2 fixation, electricity storage, food production, transportation fuel production,
water conservation or maintaining an ecosystem for space travel, we wish to suggest the electricity-carbohydrate-hydrogen
(ECHo) cycle, where electricity is a universal energy carrier, hydrogen is a clean electricity carrier, and carbohydrate is a
high-energy density hydrogen (14.8 H2 mass% or 11-14 MJ electricity output/kg)carrier plus a food and feed source. Each
element of this cycle can be converted to the other reversibly & efficiently depending on resource availability, needs,
and costs. In...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Ecology; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4167/version/1
Assemblage-structuring force of species interactions varies spatially and temporally: Co-occurrence
analysis of canopy arthropod distributions
Provedor de dados: 17
Autores: Matthew K. Lau; Laura E. Hagenauer; Thomas G. Whitham.
*Background/Question/Methods* Understanding how interactions amongst species contribute to their distribution is central to
community ecology. However, it is not understood how these processes may change under different environmental conditions. In
this study, we present evidence that suggests interactions amongst canopy arthropods contribute to assemblage structure,
depending on both the sampling time and location. We sampled canopy arthropod species abundances on individual trees in three
adjacent, monospecific stands of Populus fremontii (Fremont cottonwood), which differ in planting year (2000, 2002, 2005). We
then conducted null-model based co-occurrence analysis using the freely available software EcoSim (Kesey-Bear and Acquired
Intelligence, Inc.)...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3600/version/1
Assembling the Tree of Life in Europe (AToLE)
Provedor de dados: 17
Autores: Olaf R. P. Bininda-Emonds; Wieslaw Bogdanowicz; Thomas Borsch; Frederic Delsuc; Alexandre Hassanin; Ulf
Jondelius; Gitte Petersen; Susanne S. Renner; Vincent Savolainen; Ole Seberg; Erik Smets; Alfried Vogler.
A network of scientists under the umbrella of 'Assembling the Tree of Life in Europe (AToLE)' seeks
funding under the FP7-Theme: Cooperation - Environment (including Climate Change and Biodiversity Conservation)
programme of the European Commission.

Tipo: Presentation
Palavras-chave: Genetics & Genomics; Earth & Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2891/version/1
Assessing functional novelty of PSI structures via structure-function analysis of large and diverse
superfamilies
Provedor de dados: 17
Autores: Benoit H. Dessailly; Oliver C. Redfern; Christine A. Orengo.
The structural genomics initiatives have had as one of their aims to improve our understanding of protein function by providing
representative structures for many structurally uncharacterised protein families. As suggested by the recent assessment of the
Protein Structure Initiative (Structural Genomics Initiative, funded by the NIH), doubts have arisen as to whether Structural
Genomics as initially planned were really beneficial to our understanding of biological issues, and in particular of protein
function.
A few protein domain superfamilies have been shown to account for unexpectedly large numbers
of proteins encoded in fully sequenced genomes. These large superfamilies are generally very diverse, spanning a wide range of
functions,...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2214/version/1
Assessing performance of conservation-based Best Management Practices: Coarse vs. fine-scale
analysis
Provedor de dados: 17
Autores: Denise A. Piechnik; Sarah C. Goslee; Tamie L. Veith.
Background/Questions/Methods
Animal agriculture in the Spring Creek watershed of central Pennsylvania
contributes sediment to the stream and ultimately to the Chesapeake Bay. Best Management Practices (BMPs) such as stream
bank buffers are intended to intercept sediment moving from heavy-use areas toward the stream. The placement of BMPs on a
farm is generally based on untested assumptions about flow paths. Most often, a straight-line distance from the heavy-use area to
the stream is assumed to be correct. Our objective was to compare the straight-line path to hydrologic flow paths calculated from
fine-, medium- and coarse-grained Digital Elevation Models (DEMs; 1m, 10m, 30m) for 471 mapped heavy-use points within
100m of the stream. The...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5248/version/1
Assessing the conservation value of farmland ponds: Use of predictive techniques to identify
surrogare groups
Provedor de dados: 17
Autores: Margherita Gioria.
Background/Question/Methods. Ponds are among the most diverse and yet threatened components of freshwater biodiversity. The
conservation of ponds would greatly benefit from the identification of surrogate taxa in preliminary assessments aimed at
detecting ponds of potentially high biodiversity value. Vascular plants and water beetles have often been used in pond
conservation assessments. To evaluate whether wetland plants are a suitable surrogate group to evaluate pond biodiversity, we
used plant, beetle, and environmental data collected from 54 ponds located in two farmed regions in Ireland. Specifically, we
aimed at assessing cross-taxon congruence between water beetles and plants; quantifying and comparing the capacity of
vegetation data and...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5214/version/1
Assessing the Genotypic Differences for Seed Set and Seed Abortion in Tomato Genotypes
Provedor de dados: 17
Autores: Chalapathy K. Reddy; Ganeshaiah Narayana; Uma Shaanker.
Tomato (_Lycopersicon esculentum_ Mill.) is one of the most popular fruit vegetable around the world. Seed abortion where in
only a small proportion of ovules in an ovary develops into matured seeds, is a wide spread phenomenon in multi-ovulated
species. In agriculturally important crops such as chickpea, groundnut, Brassica, pigeon pea and field bean seed abortion
substantially reduces their productivity. Tomato genotypes exhibited seed abortion where in only some proportion of ovules
developed into matured seeds. Seed abortion in tomato cultivars would increase the cost of hybrid seed production. In this study,
we have analyzed 19 genotypes for number of ovules, seed set and seed abortion. Tomato genotypes differed significantly for
number of ovules per...
Tipo: Manuscript
Palavras-chave: Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3183/version/1
Assessment Of Response To Heart Failure Therapy: Ventricular Volume Changes Versus Shape
Changes
Provedor de dados: 17
Autores: Srilakshmi Adhyapak; V.Rao Parachuri.
The prolate ellipsoid left ventricular geometry is crucial for its unique contraction and relaxation patterns. Perturbations in optimal
cardiac function preceding overt heart failure ensue when this ellipsoid shape assumes a more spherical configuration. This stage
of spherical configuration, prior to overt dilatation, is when therapy should be intensified. The dynamic shape changes during the
cardiac cycle of systole and diastole in valvular regurgitations when ventricular volumes are within normal range have proved that
shape changes are clearly dissociated from volume changes in the early stages. In the scenario of advanced heart failure, several
therapeutic interventions have been tried with variable success. These therapies aim at decreasing the...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6707/version/1
Assisting natural forest regeneration in Northern Ethiopia: one intervention is not enough
Provedor de dados: 17
Autores: Raf Aerts; Eva November; Martin Hermy; Jozef Deckers; Mitiku Haile; Bart Muys.
Management strategies aimed at rehabilitating degraded and cleared forests often rely on temporary or permanent exclusion of
herbivores (wild animals, livestock or both). But in many cases, this simple management technique is not sufficient to induce
ecosystem restoration: many negative effects keep the ecosystem in a suboptimal, low biomass state. The presence of such stable
states
requires
restoration
measures
to
act
on
multiple
stress
factors
simultaneously.

Compensating for all limiting factors is neither practically nor
economically feasible. But detailed knowledge about the autoecology of tree species – i.e. their site requirements,
regeneration strategies and recruitment dynamics – may be...
Tipo: Presentation
Palavras-chave: Earth & Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/2437/version/2
Assisting natural forest regeneration in Northern Ethiopia: one measure is not enough
Provedor de dados: 17
Autores: Raf Aerts; Eva November; Martin Hermy; Jozef Deckers; Mitiku Haile; Bart Muys.
Management strategies aimed at rehabilitating degraded and cleared forests often rely on temporary or permanent exclusion of
herbivores (wild animals, livestock or both). But in many cases, this simple management technique is not sufficient to induce
ecosystem restoration: many negative effects keep the ecosystem in a suboptimal, low biomass state. The presence of such stable
states
requires
restoration
measures
to
act
on
multiple
stress
factors
simultaneously.

Compensating for all limiting factors is neither practically nor
economically feasible. But detailed knowledge about the autoecology of tree species – i.e. their site requirements,
regeneration strategies and recruitment dynamics – may be...
Tipo: Presentation
Palavras-chave: Earth & Environment; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2437/version/1
Association Analysis Techniques for Discovering Functional Modules from Microarray Data
Provedor de dados: 17
Autores: Gaurav Pandey; Gowtham Atluri; Michael Steinbach; Vipin Kumar.
An application of great interest in microarray data analysis is the identification of a group of genes that show very similar patterns
of expression in a data set, and are expected to represent groups of genes that perform common/similar functions, also known as
functional modules. Although clustering offers a natural solution to this problem, it suffers from the limitation that it uses all the
conditions to compare two genes, whereas only a subset of them may be relevant. Association analysis offers an alternative route
for finding such groups of genes that may be co-expressed only over a subset of the experimental conditions used to prepare the
data set. The techniques in this field attempt to find groups of data objects that contain coherent values...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2184/version/1
Association of autoimmune diseases to allele 2 of the 3' immuno-globulines HS1.2
enhancer bearing an NF-κB binding site.
Provedor de dados: 17
Autores: Domenico D. Frezza; Elisa Gremese; Vincenzo Giambra; Claudia Mattioli; Barbara Tolusso; Silvia Bosello; Maria
DeSantis; Barbara Birshtein; Gianfranco Ferraccioli.
We identified allele *2 in the HS1.2 enhancer of the Igh 3' regulatory region (3'RR-1) as a risk factor for
systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) and systemic sclerosis (SSc) (scleroderma). An
NF-κB binding site specific to allele *2 may contribute to the association of this allele with chronic inflammatory
autoimmune diseases.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/4102/version/1
Assortative human pair-bonding for partner ancestry and allelic variation of the dopamine receptor
D4 (DRD4) gene
Provedor de dados: 17
Autores: Dan T. A. Eisenberg; Coren L. Apicella; Benjamin C. Campbell; Anna Dreber; Justin R. Garcia; J. Koji Lum.
The 7R allele of the dopamine receptor D4 gene has been associated with attention-deficit hyperactivity disorder and risk taking.
On the cross-population scale, 7R allele frequencies have been shown to be higher in populations with more of a history of
long-term migrations. It has also been shown that the 7R allele is associated with individuals having multiple-ancestries. Here we
conduct a replication of this latter finding with two independent samples. Measures of subjects’ ancestry are used to
examine past reproductive bonds. The individuals’ history of inter-racial/ancestral dating and their feelings about
this are also assessed. Tentative support for an association between multiple ancestries and the 7R allele were found. These...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Neuroscience; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2660/version/1
Astrobiological Perspectives on Consciousness
Provedor de dados: 17
Autores: Rodrick Wallace.
The Stanley Miller experiment suggests that amino acid-based life is ubiquitous in our universe, although its varieties are not
likely to have followed the particular, highly contingent and path-dependent, trajectory found on Earth. Are many of these life
forms likely to be conscious in ways that we would recognize? Almost certainly. Will many conscious entities develop high order
technology? Less likely. If so, will we be able to communicate with them? Only on a basic level, and only with profound
difficulty. The argument is straightforward.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5286/version/1
Asymmetric development of Cotyledons of Tomato Embryo: Testing the prediction of
Self-Organization
Provedor de dados: 17
Autores: Chalapathy Reddy.
Developmental biologists have long strived to understand how organisms acquire shape and form. The architecture of the mature
plant is established during embryogenesis. They have learned much about how gene expression controls the specification of cell
type and about how cells interact with one another to coordinate such specific decisions. Far less is known about autocatalytic
feedback flow of resource molecules regulating a plant and its parts, shape and form. Indeed, it has even been proposed that the
development of shape is not under genetic control but rather is determined by physical forces. Asymmetric development of sinks
that depend on common resource pool has been viewed as a consequence of autocatalytic feedback process of flow of resource
units...
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2989/version/1
Asynchronous Rhythm of Steroidogenic Factor 1 and Period Homolog 2 mRNA Expression in Mouse
Y1 Adrenocorticol Tumor Cells
Provedor de dados: 17
Autores: Kenji Ohe; Kouichirou Sonoda; Makoto Akashi; Koichi Oba; Masatoshi Nomura; Taijiro Okabe; Koichi Node; Ryoichi
Takayanagi; Hajime Nawata; Toshihiko Yanase.
The relationship between the expression of Steroidogenic factor 1 (Sf1) and the circadian-related gene, period homolog 2 (Per2),
in the adrenal cortex is still unknown. We show here that in Y1 adrenocortical tumor cells, expression of steroidogenic-related
genes such as P450scc mRNA and Sf1 mRNA were asynchronous with Per2 mRNA. SF1 promoter analyses showed that the
E-box element functions in a rhythmic pattern. Rhythmic expression of Upstream factor 1 mRNA, correlated well with Sf1
mRNA expression. We propose that tumorigenesis of adrenocortical lesions cause disruption of synchronous expression of
steroidogenic-related and circadian-related genes.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4523/version/1
Atlases of Minnesota Water Sustainability: Creation from Models, Analytical Methods, and Database
of Watershed Characteristics
Provedor de dados: 17
Autores: John Nieber; Roman Kanivetsky; Heidi Peterson; Francisco Lahoud; David Mulla; Boris Shmagin.
Confident assessment of the numbers of regional water balance and water resources for Atlases of MN Water Sustainability
(AMNWS) has to be based on the best science, advanced knowledge and modern technology. Creating a watershed characteristic
database is the first and most significant step in the analysis of time spatial distributions of Minnesota’s water
balance components. The database spatially associates hydrologic data (annual discharge, monthly proportion, and yield) with
topographical, soil and vadoze zone, ecological and hydrogeological conditions and properties. USGS stream flow data for 129
gauging stations surrounding MN was manipulated within ArcGIS. Characteristics of the 129 watersheds (drainage areas
100-10000 square miles) were...
Tipo: Presentation
Palavras-chave: Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2378/version/1
Atmospheric hypoxia limits selection for large body size in insects
Provedor de dados: 17
Autores: C Jaco Klok; Jon Harrison.
Recent geological models indicate a marked increase in atmospheric oxygen partial pressure (aPO~2~) to 32 kPa in the
Permo-Carboniferous (approx. 300 million years ago), subsequently falling to 13 kPa in the Triassic^1^.These aPO~2~ changes
have been hypothesized to cause multiple major evolutionary events^2^ including the appearance and subsequent extinction of
giant insects and other taxa^3, 4^. Patterns of increasing tracheal investment in larger insects support this hypothesis^5^, as do
observations of positive relationships between aPO~2~ and body size in single- or multi-generational experiments with
_Drosophila melanogaster_ and other insects^6^. Large species likely result from many generations of selection for large body
size driven by predation,...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1831/version/1
Atomic and molecular structures of positronium, dipositronium and positronium hydride
Provedor de dados: 17
Autores: Raji Heyrovska.
The three positron based chemical entities, analogous to hydrogen atom, hydrogen molecule and hydride, are drawing increasing
attention in the literature. While a lot is known about the binding energies, not much is known about the radii of the atoms and
ions and bond lengths and structures of these exotic entities. This article brings for the first time exact values of these structural
properties which are comparable with known data. It is hoped that the results will be of help for a better understanding and further
development of the chemistry and physics of these exotic compounds and of their possible role as intermediates in chemical and
interfacial processes.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6290/version/1
Atomic Structures of Molecules Based on Additivity of Atomic and/or Ionic Radii
Provedor de dados: 17
Autores: Raji Heyrovska; Sara Narayan.
The authors have shown in recent years that interatomic and interionic distances are sums of the radii of the adjacent atoms and/or
ions. Many examples will be provided and it will be shown how the experimental bond lengths agree with the radii sums. The
examples include inorganic compounds like alkali halides, metal hydrides, graphene, etc., organic like aliphatic and aromatic
compounds and biochemical like nucleic acids, amino acids, caffeine-related compounds and vitamins.
Tipo: Poster
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3292/version/1
Attention induces dynamic changes in coherence between monkey area V1 and V4
Provedor de dados: 17
Autores: Iris Grothe; Simon D. Neitzel; Sunita Mandon; Andreas K. Kreiter.
Neurons receive a vast number of synaptic inputs at the same time. To successfully process a relevant piece of information, a
neuron needs to select relevant, while suppressing irrelevant signals. In order to dynamically route a meaningful set of signals
through processing pathways, neurons need to have a fast and flexible mechanism to change their effective connectivity. Here, we
hypothesize
that
attention
changes
effective
connectivity
by
modulating
the
synchrony
between
neuronal
populations.
We investigated whether attention dynamically changes effective connectivity between area V4
neurons and their V1 input. Single unit activity, multi unit activity and local field potentials (LFP) were recorded simultaneously
from macaque...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5884/version/1
Attentional control and engagement with digital technology
Provedor de dados: 17
Autores: Tracy Alloway; Ross Alloway.
Multiple demands comprise the efficiency of attentional control. There is abundant evidence that when an individual attempts two
or more attentionally demanding activities at the same time, the allocation of attention to the tasks is limited and performance
suffers as a result. Yet, recent technological innovations require many individuals to manage multiple digital technologies
simultaneously or to switch attentional control between tasks. The ability to multitask with various digital technologies involves
dividing attention, switching between tasks, and keeping track of multiple strands of information in working memory.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5603/version/1
Auditory cortex mediates the perceptual effects of acoustic temporal expectation
Provedor de dados: 17
Autores: Santiago Jaramillo; Anthony M. Zador.
When events occur at predictable instants, anticipation improves performance. Knowledge of event timing modulates motor
circuits, improving response speed. By contrast, the neuronal mechanisms underlying changes in sensory perception due to
expectation are not well understood. We have developed a novel behavioral paradigm for rats in which we manipulated
expectations about sound timing.
Valid expectations improved both the speed and the accuracy of subjects'
performance, indicating not only improved motor preparedness but also enhanced perception. Single neuron recordings in
primary auditory cortex revealed enhanced representation of sounds during periods of heightened expectation. Furthermore, we
found that activity in auditory cortex was...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5139/version/1
Autism-associated SNPs in the clock genes _npas2_, _per1_ and the homeobox gene _en2_ alter DNA
sequences that show characteristics of microRNA genes.
Provedor de dados: 17
Autores: Brad Nicholas; Michael J. Owen; Dawn C. Wimpory; Thomas Caspari.
Intronic single nucleotide polymorphisms (SNPs) in the clock genes _npas2_ and _per1_ and the homeobox gene _en2_ are
reported to be associated with autism. This bioinformatics analysis of the intronic regions which contain the autism-associated
SNPs rs1861972 and rs1861973 in _en2_, rs1811399 in _npas2_, and rs885747 in _per1_, shows that these regions encode RNA
transcripts with predicted structural characteristics of microRNAs. These microRNA-like structures are disrupted _in silico_ by
the presence of the autism enriched alleles of rs1861972, rs1861973, rs1811399 and rs885747 specifically, as compared with the
minor alleles of these SNPs. The predicted gene targets of these microRNA-like structures include genes reported to be implicated
in autism...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2366/version/1
Automated Annotation-Based Bio-Ontology Alignment with Structural Validation
Provedor de dados: 17
Autores: Cliff Joslyn; Bob Baddeley; Judith Blake; Carol Bult; Mary Dolan; Rick Riensche; Karin Rodland; Antonio Sanfilippo;
Amanda White.
We outline the structure of an automated process to both align multiple bio-ontologies in terms of their genomic co-annotations,
and then to measure the structural quality of that alignment. We illustrate the method with a genomic analysis of 70 genes
implicated in lung disease against the Gene Ontology.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3518/version/1
Automated ocular artifact removal: comparing regression and component-based methods
Provedor de dados: 17
Autores: Alois Schloegl; Andreas Ziehe; Klaus-Robert Müller.
Objective: The aim is to compare various fully automated methods for reducing ocular artifacts from EEG
recordings.
Methods: Seven automated methods including regression, six component-based methods for
reducing ocular artifacts have been applied to 36 data sets from two different labs. The influence of various noise sources is
analyzed and the ratio between corrected and uncorrected EEG spectra, has been used to quantify the distortion.

Results: The results show that not only regression but also component-based methods are vulnerable to
over- or under-compensation and can cause significant distortion of EEG. Despite common belief, component-based methods did
not demonstrate an advantage over the simple regression method....
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3446/version/1
Automatic protein clustering as a basis of automatic annotation
Provedor de dados: 17
Autores: Naoki Sato.
Development of new generation sequencers enabled genome sequencing feasible for every organism in a laboratory. A typical
data flow of de novo seuqencing includes (1) assembly of sequence reads, (2) estimation of open reading frames, (3) annotation of
proteins, and (4) finding RNA genes. The annotation is normally performed by BLASTP searches against several different
databases. However, it is usually hard to find a plausible annotation by just looking at the results of BLASTP
searches.

Here I propose a potentially automatic method of annotation that exploits
automatic protein clustering using the software GCLUST, which estimates proper similarity threshold for each list of homologs
using ‘entropy-optimized...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5086/version/1
Automatisation in UniProtKB / Swiss-Prot Annotation: New Rules and Tools
Provedor de dados: 17
Autores: The HAPMAP Team; The PROSITE Team; Edouard de Castro; Alan Bridge; UniProt Consortium.
The development of next generation sequencing technologies promises a massive increase in the rate of submission of new protein
sequences to sequence databases such as the Universal Protein Resource Knowledge Base, UniProtKB. At UniProtKB/Swiss-Prot
we propose to meet this challenge by continuing to expand and develop systems for the automatic propagation of existing
annotation to newly submitted protein sequences. These developments will promote the standardization of ortholog annotation
both across and within kingdoms and significantly enhance our ability to accurately annotate new protein sequences which are
being produced at an ever increasing rate.

Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3215/version/1
Autosegregation of enzyme loci Me1 and Gpi2 in agamospermous progenies of triploid sugarbeet
plants
Provedor de dados: 17
Autores: Evgenii Levites; Svetlana Kirikovich.
Ratios of malic-enzyme (ME1) and glucosephosphate isomerase (GPI2) phenotypic classes were studied in agamospermous
progenies of triploid sugar beet plants. It was shown that the ratio of enzymes phenotypic classes quite well accords with the
calculations based on the supposition about reduplication of chromosome sites carrying alleles of enzyme loci accompanied by a
loss of excessive allelic copies in the first cell division under embryogenesis. Polyteny – conditioned allelic dose
increase leads to the occurrence of alleles – absent in the initial parent – at a certain frequency in the
developing progeny. The notions of “meiotic autosegregation” and “mitotic
autosegregation”...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/5464/version/1
Aven and Survivin Expression in Egyptian Acute Leukemia and Their Relation to Apoptosis
Provedor de dados: 17
Autores: Magda Assem; Thorraya Abedel- ALhameid; Gihan A-Basset; Amany M. Hilal; Mahmoud Kamel; Iman Khalil; Nahla
Alsharkawey; Ayman Metwally.
Background: Several anti apoptotic signals have been recently identified. Aven and Survivin are broadly expressed and are
conserved in mammalian species. Patients and Methods: 39 AML and 25 ALL were tested. Aven and Survivin expression were
detected by RT-PCR. DNA fragmentation was carried out daily after treatment..Results: Survivin was expressed (P=0.06) more in
AML (74%) than in ALL (52%). While, Aven was equally expressed in both leukemias. Patients were categorized into 3 groups
based on DNA fragmentation. Absence of Aven significantly (p‹0.001) contributed to DNA fragmentation,but
Survivin did not contribute as much. None of the concordant both positive Survivin and Aven were in group III (the good 5 day
fragmentation, (P< 0.001)....
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3771/version/1
Averaging Transformations of Synaptic Potentials on Networks
Provedor de dados: 17
Autores: Hamid Reza Noori.
The problem of the transformation of microscopic information to the macroscopic level is an intriguing challenge in
computational neuroscience, but also of general mathematical importance. Here, a phenomenological mathematical model is
introduced that simulates the internal information processing of brain compartments. Synaptic potentials are integrated over small
number of realistically coupled neurons to obtain macroscopic quantities. The striatal complex, an important part of the basal
ganglia circuit in the brain for regulating motor activity, has been investigated as an example for the validation of the model.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3348/version/1
Azadirachta indica induced suppression of Mycobacterium tuberculosis secreted proteins in human
monocyte
Provedor de dados: 17
Autores: Jawed Iqbal; Ajay Kumar; Najmul Islam.
The H37Rv strain of MTB was grown in modified Sauton’s medium till mid-log phase. Peripheral blood
mononuclear cells (PBMC) were isolated by density gradient sedimentation on Ficoll-Paque separation medium. Adherent
monocytes obtained from PBMC’s were infected with H37Rv for 90 min. in the ratio of 1:1 (1 bug: 1 cell).
Thereafter, after washing, infected cells were co-cultured with varying doses of neem extract for 24 hrs, and harvested
subsequently. Modulation of secreted TNF-[alpha], iNOS and MTB Ag85 complex expressions in culture supernatants was
estimated by ELISA.
We report the high basal expression of secreted tumor necrosis factor-[alpha]
(TNF-[alpha]), inducible nitric oxide synthase (iNOS) and MTB Ag85...
Tipo: Poster
Palavras-chave: Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1562/version/1
B6 deficient feeding or homocysteic acid induces the earlier Alzheimer's pathological
change in normal C57BL male mice
Provedor de dados: 17
Autores: Tohru Hasegawa; Nobuyuki Mikoda; Masashi Kitazawa; Frank LaFerla.
It is the first report that the earlier Alzheimer's pathological changes can be induced in normal C57BL mice, by B6
deficient feeding for 3 month, and this pathological changes were completely inhibited by anti-homocysteic acid antibody.
According to Koch's postulate, if a pathogen of Alzheimer's disease is administrated to the normal animal,
we would observe the Alzheimer's pathology in the normal animal. We actually have observed this pathology in
normal C57BL male mice.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2764/version/1
Backup machinery of yeast transcriptional regulatory network
Provedor de dados: 17
Autores: Dhriti Sengupta; Sudip Kundu.
Several studies have suggested the existence of backup machinery of transcriptional regulatory networks (TRNs). Here, we have
quantified the backup machinery of yeast gene's TRNs under five different conditions in terms of alternate paths and
have revealed that a statistically significant (p<0.0001) stronger backup is maintained for endogenous processes
(ENPs) than exogenous processes (EXPs). A number of biologically important genes (SUC2, MF(ALPHA)2, CLN2 etc) are
observed that maintain a higher backup. Hub and random transcription factor (TF) knockouts in TRNs have showed ENPs are
more robust to deletion than EXPs. While higher average connectivity of TFs in EXPs than ENPs can't explain the
higher robustness in ENPs, we have...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/1791/version/1
Bacteria have transient influences on marine corrosion of steel
Provedor de dados: 17
Autores: Robert E. Melchers; Robert Jeffrey.
The contribution of bacteria to the corrosion mass loss and to pitting of mild steel was observed over 2.5 years using parallel
streams of unpolluted natural (biotic) and nominally sterilized (abiotic) Pacific Ocean coastal seawater. As also observed by
others, in artificial laboratory exposures, corrosion mass loss within the first few days of exposure was much greater in the biotic
stream. However, after only about 10 days the difference in mass losses were gradually reduced and were very similar up to about
one year of exposure. Thereafter, the corrosion loss in the biotic stream again became more severe. Pitting corrosion in the biotic
stream was more severe from the very first exposure throughout the 2.5 years. Corrosion in both seawater streams...
Tipo: Manuscript
Palavras-chave: Chemistry; Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/5767/version/1
Bacterial Capnine Blocks Transcription of Human Antimicrobial Peptides
Provedor de dados: 17
Autores: Trevor G. Marshall.
The US CDC believes that 65% of all infections in developed countries may be caused by pathogens in biofilms. Electron
Microscopy has shown that these bacterial communities can evade phagocytosis, and persist in the cytoplasm of monocytes,
macrophages, lymphocytes and neutrophils. Three decades ago, Wirostko _et al._ found such intraphagocytic communities in
Crohn’s disease, Juvenile Rheumatoid Arthritis and Sarcoidosis. However, the mechanism(s) by which such
persistent bacteria could evade the immune system have remained elusive. Recently, 16S RNA from species of gliding bacteria
never thought to be able to survive _in vivo_, have been found in surgically removed biofilms. This study set out to identify
whether the genomes of these gliding...
Tipo: Poster
Palavras-chave: Immunology; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/164/version/1
Bacteriophages as a model for studying carbon regulation in aquatic system
Provedor de dados: 17
Autores: Swapnil G. Sanmukh; Waman N. Paunikar; Sandhya Swaminathan; Satish K. Lokhande.
The interconversion of carbon in organic, inorganic and refractory carbon is still beyond the grasp of present environmentalists.
The bacteria and their phages, being the most abundant constituents of the aquatic environment, represent an ideal model for
studing carbon regulation in the aquatic system. The refractory dissolved organic carbon (DOC), a recently coined terminology
from the microbe-driven conversion of bioavailable organic carbon into difficult-to-digest refractory DOC by microbial carbon
pump (MCP), is suggested to have the potential to revolutionize our view of carbon sequestration. It is estimated that about 95%
of organic carbon is in the form of refractory DOC, which is the largest pool of organic matter in the ocean. The refractory DOC...
Tipo: Manuscript
Palavras-chave: Ecology; Earth & Environment.
Ano: 2012
URL: http://precedings.nature.com/documents/6770/version/1
Balancing noise and plasticity in gene expression
Provedor de dados: 17
Autores: Djordje Bajic; Juan F. Poyatos.
Coupling the control of expression stochasticity (noise) with the capacity to expression change (plasticity) can constrain gene
function and limit adaptation. Which factors contribute then to modulate this coupling? Transcription re-initiation is generally
associated with coupling and this is commonly related to strong chromatin regulation. We alternatively show how strong
regulation can however lead to plasticity uncorrelated to noise. The character of the regulation is also relevant, with plastic but
noiseless genes usually subjected to broad expression activation whereas plastic and noisy genes experience targeted repression.
This differential action is similarly noticed in how histones influence these genes. In contrast, we find that translational...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6729/version/1
Ball Milling as a Tool Towards Solubility Problems in Synthesis – Simple and
Solvent-free Preparation of K[B(CN)4]
Provedor de dados: 17
Autores: Roland Pawelke.
A simple ball milling route to the tetrayanoborate anion is presented: The K[B(CN)4] synthesis is one fine example, how a
synthesis problem based on solubility may be solved by a ball milling approach. The solid state 13C- and 11B-MAS-NMR spectra
have been recorded.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6258/version/1
Barlow-Hall in vitro Evolution Protocol
Provedor de dados: 17
Autores: Barry G. Hall; Miriam Barlow.
The Barlow-Hall method for in vitro evolution is a simple alternative to methods such as DNA shuffling and is particularly
applicable to predicting the evolution of target genes in nature. This detailed protocol includes the procedure itself and, as
Appendices, describes particularly effective protocols for electroporation and for preparation of electrocompetent cells.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1772/version/1
Basic emotions: Differences in time sequence and functional imaging with low resolution brain
electrical tomography (LORETA)
Provedor de dados: 17
Autores: Tommaso Costa; Manuella Crini.
The aim of the present study is to investigate the relationship between the time course of brain activation during the observation of
pictures depicting scenes associated with the four basic emotion of happiness, sadness, fear and disgust. Twenty-nine right-handed
volunteers (17 male, 12 female; mean age 24.6 years) took part in the study. To study the time course of the affective processing
the low resolution brain electromagnetic tomography (LORETA) has been used. Each emotional condition has shown specific
activation patterns in different brain regions, changing over time. Our findings are in good agreement with other brain-imaging
studies (PET/fMRI) but with the advantage to investigate the temporal evolution of the emotional process in the millisecond...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5566/version/1
BBSRC Data Sharing Policy
Provedor de dados: 17
Autores: Amanda Collis; David McAllister; Michael Ball.
BBSRC recognizes the importance of contributing to the growing international efforts in data sharing. BBSRC is committed to
getting the best value for the funds we invest and believes that making research data more readily available will reinforce open
scientific inquiry and stimulate new investigations and analyses. BBSRC supports the view that data sharing should be led by the
scientific community and driven by scientific need. It should also be cost effective and the data shared should be of the highest
quality. Members of the community are expected and encouraged to practice and promote data sharing, determine standards and
best practice, and create a scientific culture in which data sharing is embedded.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics & Genomics; Immunology; Microbiology; Molecular
Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Plant Biology; Evolutionary Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6015/version/1
Beautifying Data in the Real World
Provedor de dados: 17
Autores: Jean-Claude Bradley; Rajarshi Guha; Andrew Lang; Pierre Lindenbaum; Cameron Neylon; Antony Williams; Egon
Willighagen.
This chapter from the O'Reilly book "Beautiful Data" describes the use of Open Notebook
Science to crowdsource solubility data. The use of GoogleDocs, wikis, ChemSpider, RDF, the Chemistry Development Kit and
Second Life is described.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4918/version/1
Behavioral and Psychiatric Genetics: Learning from History
Provedor de dados: 17
Autores: Kenneth Schaffner.
Behavioral and Psychiatric Genetics (BPG) offers great promise for clarifying the causes of both normal behaviors as well as
psychiatric disorders, and in the latter case serving as a more rational basis for treatments. But the field has also generated serious
social concerns about individual and ethnic stereotyping of intelligence and violent behaviors. This short talk identifies some of
these themes from the 1970s, 80s, and 90s, and reviews recent shifts about the directions BPG is taking in the first decade of the
twenty-first century. I cover the collapse of simple molecular gene-behavior models in the 1990s, and the rise of
gene-environment interaction paradigms, as well as the increasing role of neuroscience in BPG in the present decade. I close by...
Tipo: Presentation
Palavras-chave: Genetics & Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2621/version/1
Behavioral Genetics and Equality
Provedor de dados: 17
Autores: Dan Brock.
I will explore the implications of findings in behavioral genetics for two conceptions of equality: equality of opportunity and the
equal moral worth of persons. New findings in behavioral genetics showing that behavioral traits, and the variance in behavioral
traits, have some genetic underpinnings would not seem in themselves to threaten either of these notions of equality--we have long
known that there is significant variation in these traits across persons and have assumed that some significant portion of that
variation has genetic sources. I believe it is the uncertain and probably distant prospect of genetic interventions to enhance some
behavioral traits, which could greatly increase the range and inequality of those traits in humans, that may seem...
Tipo: Presentation
Palavras-chave: Genetics & Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2566/version/1
Behavioral origins of metabolic syndrome disorders
Provedor de dados: 17
Autores: Milind Watve; Maithili Jog; Prajakta Belsare.
The metabolic syndrome disorders (MSD) including type 2 diabetes, hypertension, hypercholesterolemia, atherosclerosis and
cardiovascular disease are known to be triggered by lifestyle change. We state and support a hypothesis here that changes in
behavior rather than changes in diet and metabolism are central to MSD. We provide and discuss evidence in support of the
following sequence of arguments. (i) Diet, thriftiness and obesity centered paradigm is inadequate to explain most of the
physiological and immunological changes associated with metabolic syndrome disorders (MSD). (ii) Comparative studies show
that relative obesity rather than absolute obesity is strongly associated with various parameters of MSD and further perception of
calories without...
Tipo: Presentation
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4833/version/1
Benchmarking the SPARC software program for estimating solubilities of naphthalene and
anthracene in organic solvents
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
The SPARC software program was benchmarked for calculating the solubilities of two representative polyaromatic hydrocarbons
(PAHs), naphthalene and anthracene, in a range of organic solvents at various temperatures. Although SPARC was able to
reasonably approximate the solubilities of naphthalene in some organic solvents, gross errors were obtained for other solvents. For
anthracene, poor prediction performance was observed in all solvents considered. Overall, the results suggest that SPARC is
currently not suitable for accurately predicting the solubilities of representative PAHs relevant for the petroleum sector in various
organic solvents.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6648/version/1
Benchmarking triple stores with biological data
Provedor de dados: 17
Autores: Vladimir Mironov.
We have compared the performance of five non-commercial triple stores, Virtuoso-open source, Jena SDB, Jena TDB,
SWIFT-OWLIM and 4Store. We examined three performance aspects: the query execution time, scalability and run-to-run
reproducibility. The queries we chose addressed different ontological or biological topics, and we obtained evidence that
individual store performance was quite query specific. We identified three groups of queries displaying similar behavior across the
different stores: 1) relatively short response time, 2) moderate response time and 3) relatively long response time. OWLIM proved
to be a winner in the first group, 4Store in the second, and Virtuoso in the third. Our benchmarking showed Virtuoso to be a very
balanced performer...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5417/version/1
Beneficial role of allicin from garlic in cervical cancer
Provedor de dados: 17
Autores: Irfan Ahmad Ansari; Najmul Islam.
Introduction: Cervical cancer remains a global health concern for females. Thus, in order to control cervical cancer, attempts are
being made by researchers globally to somehow induce programmed cell death in the said cancerous cells. Wide spectrums of
molecules are being probed for its ability to induce apoptosis in cervical cancer cells. Focus has now shifted in exploring natural
compounds having antioxidant and anti-inflammatory molecules that may induce apoptosis in cancerous cells. Thus, we have
employed allicin from garlic- a natural antioxidant, to probe the above in the present study.
Objective: To
probe whether or not allicin from garlic, a natural antioxidant, induces apoptosis in monocytes from patients with cervical...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1561/version/1
Berberine induces caspase-independent cell death in colon tumor cells through activation of
apoptosis-inducing factor
Provedor de dados: 17
Autores: Lihong Wang; Liping Liu; Yan Shi; Hamwei Cao; Rupesh Chaturvedi; Tianhui Hu; Keith Wilson; D. Brent Polk; Fang
Yan.
Berberine, an isoquinoline alkaloid derived from plants, is a traditional medicine for treating bacterial diarrhea and intestinal
parasite infections. Although berberine has recently been shown to suppress growth of several tumor cell lines, information
regarding the effect of berberine on colon tumor growth is limited. Here, we investigated the mechanisms underlying the effects of
berberine on regulating the fate of colon tumor cells, specifically the immorto Min mouse colonic epithelial (IMCE) cells carrying
the Apcmin mutation, and of normal colon epithelial cells, namely young adult mouse colon (YAMC) epithelial cells. Berberine
decreased colon tumor colony formation in agar, and induced cell death and LDH release in a time- and
concentration-dependent...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2011
URL: http://precedings.nature.com/documents/6438/version/1
Best practices for building interoperable systems for translational research
Provedor de dados: 17
Autores: Warren Kibbe.
Research databases, clinical systems, and lab systems all have different standards, formats and drivers for data capture, operation,
analysis and integration. For interdisciplinary nutritional researchers, however, there is a dependence on all of these areas and
technologies. While building and integrating these systems can be difficult, using agile practices including short iterations, testing
and continuous integration methods, and close engagement with all stakeholders to create useful systems for translational
research. Interoperability also requires good data standards, including the use of structured data dictionaries and existing data
standards such as HL7, UMLS, LOINC, ICD, and OBO foundry ontologies.
Tipo: Presentation
Palavras-chave: Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5197/version/1
Betaine aldehyde dehydrogenase (BADH) from Hordeum vulgare- an in-silico study
Provedor de dados: 17
Autores: Kaushal Kumar Bhati; Vijay Kumar Singh.
Glycine Betaine is a quaternary amino compound that accumulates in stress conditions, mainly abiotic stresses like drought and
salinity & synthesized
catalyzed
by
Choline
by
the
two-step
monooxygenase
and
oxidation
Betaine
of
choline
via
aldehyde dehydrogenase
the intermediate
betaine
aldehyde,
(BADH).
The
sequence analysis of key enzymes of Glycine betaine biosynthesis i.e. BADH was carried out using various online proteomic tools
available on Expasy and EBL, and then homologous modeling of this enzyme was performed using automated mode
SWISS-MODEL & GENO 3D and models were analyzed on QMEAN. This was an attempt to find the possible
model of BADH, because no physical model of BADH is yet available on...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6360/version/1
Better Analysis, Better Acceptance ‐Take up the Challenge of Publishing in
Bioinformatics
Provedor de dados: 17
Autores: Malay Bhattacharyya.
This presentation teaches the novice in bioinformatics research to publish quality analysis in good venues.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7124/version/1
Bevacizumab-induced tumor calcifications can be elicited in glioblastoma microspheroid culture and
represent massive calcium accumulation death (MCAD) of tumor endothelial cells
Provedor de dados: 17
Autores: Larry Weiseenthal; Summer Williamson; Cindy Brunschwiler; Constance Rueff-Weisenthal.
Bähr and colleagues reported that 22 of 36 glioblastoma patients treated with bevacizumab showed tumor
calcifications on 8 week post therapy follow up with MRI. Early tumor calcification strongly predicted for response, time to
progression, and overall survival. The authors didn’t understand the mechanism, but speculated that it was vascular
in nature. At the 13th International Anti-Angiogenic Symposium (2011), we presented our discovery of the phenomenon of
massive calcium accumulation death, wherein MCAD occurred in endothelial cells (tumor, circulating, and HUVEC), in response
to VEGF depletion by bevacizumab and other putative anti-angiogenic agents, but not in response to non-specific cytotoxins. In
subsequent work, we have...
Tipo: Poster
Palavras-chave: Cancer.
Ano: 2012
URL: http://precedings.nature.com/documents/7069/version/1
Beyond Spike Timing Theory – Thermodynamics of Neuronal Computation
Provedor de dados: 17
Autores: Dorian Aur; Mandar S. Jog.
This paper highlights ionic fluxes as information carriers in neurons. The theoretical framework regarding information transfer is
presented as changes in the thermodynamic entropy that underlie specific computations determined by ionic flow. The removal or
accumulation of information is analyzed in terms of ionic mass transfer related with changes in Shannon information entropy.
Specifically, information transfer occurs during an action potential (AP) via the voltage gated ion channels in membranes and the
same physical mechanism can be extended to various types of synapses. Since sequential APs from a selected neuron are not
alike, then every spike may transfer slightly different amounts of information during their occurrence. The average efficiency in...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1254/version/1
Beyond Structure: KiSAO and TEDDY -- Two Ontologies Addressing Pragmatical and Dynamical
Aspects of Computational Models in Systems Biology
Provedor de dados: 17
Autores: Dagmar Köhn; Nicolas Le Novère; Christian Knüpfer.
Computational models are becoming more and more the central scientific paradigm for understanding the complexity of living
systems. With the increasing number and size of these models there is a growing need for model reuse and exchange.
Furthermore, detailed models are not manageable without computer support. There are efforts to formalise the mathematical
structure of models (e.g. SBML) and to standardise the kinetic and biological meaning of model components (e.g. SBO, GO,
UniProt). However, formalising only the structure of computational models is not sufficient to easily exchange and reuse models
and to achieve full computer support for modelling. We also need to formalise the pragmatical and dynamical aspects of...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3137/version/1
Beyond the fuzzy lock-and-key: spontaneous symmetry shifts and glycan/lectin logic gates
Provedor de dados: 17
Autores: Rodrick Wallace.
Changes in the molecular topology of glycan/lectin interaction may explain observed reaction punctuation driven by experimental
gradients in reactant concentration. Adoption of a 'biological renormalization' perspective from statistical
physics for the analysis of such phase transitions suggests, in marked contrast to conventional physical systems, a broad spectrum
of possible universality class behaviors. This spectrum may, in typical perverse biological manner, be of central scientific interest.
Generalization, via formalism abducted from coevolutionary theory, suggests that glycan/lectin molecular switches instantiate
logic gates that may be as sophisticated as those characterizing basic neural process, if on a different scale.
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology; Microbiology; Molecular Cell Biology; Pharmacology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6849/version/1
BFO/DOLCE Primitive Relation Comparison
Provedor de dados: 17
Autores: A. Patrice Seyed.
This paper examines the primitive relations (dependence, quality, and constitution) of the BFO and DOLCE upper ontologies,
employed in developing domain ontologies of the biomedical sciences. The strengths in both upper ontologies are examined,
which sets a framework for developing a common upper ontology that utilizes the assets of both.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3481/version/1
BHL, The Biodiversity Heritage Library: An Expanding International Collaboration
Provedor de dados: 17
Autores: Constance Rinaldo; Catherine Norton.
*Background/Question/Methods*
The
Biodiversity
Heritage
Library
(BHL;
"http://www.biodiversitylibrary.org/":http://www.biodiversitylibrary.org/), one of the cornerstones of the
Encyclopedia of Life (eol.org), now contains nearly 13 million digitized pages of 12,000 titles comprised of 32,000 volumes of
the published literature of biodiversity held in the collections of major natural history libraries. The BHL has made this literature
available for open access and responsible use as a part of a global “biodiversity commons.” The BHL
partnership is working with the global taxonomic community, publishers, organizations such as JSTOR and BIOONE, and the
Internet Archive, to ensure that the biodiversity...
Tipo: Poster
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3620/version/1
Bias Correction in Logarithmic Regression and Comparison with Weighted Regression for Nonlinear
Models
Provedor de dados: 17
Autores: Wei Sheng Zeng; Shou Zheng Tang.
Non-linear models with heteroscedasticity are commonly used in ecological and forestry modeling, and logarithmic regression and
weighted regression are usually employed to estimate the parameters. Using the single-tree biomass data of three large samples,
the bias correction in logarithmic regression for non-linear models was studied and comparison between logarithmic regression
and weighted regression was discussed in this paper. Firstly, the imminent cause producing bias in logarithmic regression was
analyzed, and a new correction factor was presented with which three commonly used bias correction factors were examined
together, and the results showed that the correction factors presented here and derived by Baskerville (1972) should be
recommended,...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6708/version/1
Bias in culture-independent assessments of microbial biodiversity in the global ocean
Provedor de dados: 17
Autores: Ben B. Temperton; Anna Oliver; Dawn Field; Bela Tiwari; Martin Muhling; Ian Joint; Jack Gilbert.
On the basis of 16S rRNA gene sequencing, the SAR11 clade of marine bacteria has almost universal distribution, being detected
as abundant sequences in all marine provinces. Yet SAR11 sequences are rarely detected in fosmid libraries, suggesting that the
widespread abundance may be an artefact of PCR cloning and that SAR 11 has a relatively low abundance. Here the relative
abundance of SAR11 is explored in both a fosmid library and a metagenomic sequence data set from the same biological
community taken from fjord surface water from Bergen, Norway. Pyrosequenced data and 16S clone data confirmed an 11-15%
relative abundance of SAR11 within the community. In contrast not a single SAR11 fosmid was identified in a pooled shotgun
sequenced data set of 100...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics & Genomics; Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/2818/version/1
Biased amino acid composition in warm-blooded animals
Provedor de dados: 17
Autores: Guang-Zhong Wang; Martin J. Lercher.
Among eubacteria and archeabacteria, amino acid composition is correlated with habitat temperatures. In particular, species living
at high temperatures have proteins enriched in the amino acids E-R-K and depleted in D-N-Q-T-S-H-A. Here, we show that this
bias is a proteome-wide effect in prokaryotes, and that the same trend is observed in fully sequenced mammals and chicken
compared to cold-blooded vertebrates (Reptilia, Amphibia and fish). Thus, warm-blooded vertebrates likely experienced
genome-wide weak positive selection on amino acid composition to increase protein thermostability.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2974/version/1
Binding Pattern Determination Of Class of Antifungal Drugs
Provedor de dados: 17
Autores: Arpit Tandon; A Naqvi; Nitin Chitranshi; Siddharth Sinha.
Crystal Structure of cytochrome p450 2B4 has 476 amino acids, through docking approach we have attempted to explain the
specificity of CYP2B4, total 28 imidazole drug were used for the studies as antifungal drugs in which bound bifonazole
(reference) shows the binding energy of -8.67 kcal/mol .Compound Miconazole shows the minimum binding energy of -10.45
kcal/mol. The 2B4-bifonazole structure identified 10 residues (ALA 298, GLY 299, GLU 301, THR 302, ILE 363, VAL 292)
within 6.5 Å of the active site of bifonazole. GLU 301, THR 302 are also located in 6.5 Å of the bound
ligand in 2B4 structure. Due to the presence of the multiple binding substrates in cytochrome p450, it acts as the major target of
many drugs in xenobiotic...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4314/version/1
Binge and Emotional Eating in obese subjects seeking weight loss treatment
Provedor de dados: 17
Autores: Valdo Ricca; Giovanni Castellini; Carolina Lo Sauro; Claudia Ravaldi; Francesco Lapi; Edoardo Mannucci; Carlo
Maria Rotella; Carlo Faravelli.
Objective: Binge Eating Disorder (BED) is highly prevalent among individuals seeking weight loss treatment. Considering the
possible trigger factors for BED, different studies focused on the role of emotional eating. The present study compared threshold,
subthreshold BED, and subjects without BED in a population of overweight/obese individuals seeking weight loss treatment,
considering the anamnesis, the eating disorder specific and general psychopathology, the organic and psychiatric comorbidity, the
emotional eating as a trigger factor for binge eating, and the quality of life. Design: cross-sectional survey.Subjects: Four hundred
thirty eight overweight subjects seeking weight loss treatment have been enrolled in the study. Measurements: Subjects have...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2125/version/1
BiNoM Cytoscape Plugin for constructing, querying and analyzing biological networks, using systems
biology standards
Provedor de dados: 17
Autores: Andrei Zinovyev.
BiNoM is a Cytoscape plugin which allows to read, analyze and convert biological networks represented in various systems
biology standards.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5120/version/1
Bio2RDF: Convert, Provide And Reuse.
Provedor de dados: 17
Autores: Marc-Alexandre Nolin; Jacques Corbeil; Luc Lamontagne; Michel Dumontier.
The Bio2RDF project uses open-source Semantic Web technologies to provide interlinked life science data in order to maximize
productivity and facilitate biological knowledge discovery. Using both syntactic and semantic data integration techniques,
Bio2RDF
puts
into
practice
a
simple
methodology
to
generate
and
seamlessly
integrate
machine-interpretable data that can be powerfully interrogated with SPARQL-based queries to answer sophisticated
questions.

At its core, database records are converted into a set of statements or
so-called triples that are captured together as a named graph annotated with provenance. The records and the entities they are
about are provided with a Uniform Resource Identifier...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5060/version/1
BioBrick Promoter Measurement Kit Instruction Sheets
Provedor de dados: 17
Autores: Jason Kelly.
Instructions for inserting a test promoter into the measurement kit plasmid for characterization as well as instructions for
measuring the activity of the test promoter in Standard Promoter Units (SPUs). These instructions were distributed to the teams
participating in the International Genetically Engineered Machines competition (iGEM).
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2028/version/1
BioCatalogue: A Curated Web Service Registry For The Life Science Community
Provedor de dados: 17
Autores: Carole A. Goble; Khalid Belhajjame; Franck Tanoh; Jiten Bhagat; Katy Wolstencroft; Robert Stevens; Eric
Nzuobontane; Hamish McWilliam; Thomas Laurent; Rodrigo Lopez.
Web Services have gained a momentum as a means for packaging existing data and computational resources in a form that is
amenable for use and composition by third party applications. The life science community is certainly among the first adopters of
Web Services. For example, "Taverna":http://www.mygrid.org.uk, a workflow workbench that is popular
within the life science community, provides access to over 3500 thousands web services that can be composed by scientists for
constructing and enacting their _in silico_ experiments. However, one of the main issues that hinders the wide adoption and use of
Web Services is the difficulty in locating the “appropriate” Web Service, i.e., the Web Service that
performs the...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3132/version/1
Biochemical Composition of Normal Urine
Provedor de dados: 17
Autores: Atif Baig.
The urine composition defines the quality of homeostasis of the body. Learning about the normal urine composition is very
important to compare it with the suspended and non suspended particles in urine in different pathologies.
Tipo: Presentation
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6595/version/1
Bio-Communication of Bacteria and its Evolutionary Interrelations to Natural Genome Editing
Competences of Viruses
Provedor de dados: 17
Autores: Guenther Witzany.
Communicative competences enable bacteria to develop, organise and coordinate rich social life with a great variety of behavioral
patterns even in which they organise themselves like multicellular organisms. They have existed for almost four billion years and
still survive, being part of the most dramatic changes in evolutionary history such as DNA invention, cellular life, invention of
nearly all protein types, partial constitution of eukaryotic cells, vertical colonisation of all eukaryotes, high adaptability through
horizontal gene transfer and co-operative multispecies colonisation of all ecological niches. Recent research demonstrates that
these bacterial competences derive from the aptitude of viruses for natural genome editing....
Tipo: Manuscript
Palavras-chave: Ecology; Genetics & Genomics; Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1738/version/1
Bio-Communication of Bacteria and its Evolutionary Interrelations to Natural Genome Editing
Competences of Viruses
Provedor de dados: 17
Autores: Guenther Witzany.
Communicative competences enable bacteria to develop, organise and coordinate rich social life with a great variety of behavioral
patterns even in which they organise themselves like multicellular organisms. They have existed for almost four billion years and
still survive, being part of the most dramatic changes in evolutionary history such as DNA invention, cellular life, invention of
nearly all protein types, partial constitution of eukaryotic cells, vertical colonisation of all eukaryotes, high adaptability through
horizontal gene transfer and co-operative multispecies colonisation of all ecological niches. Recent research demonstrates that
these bacterial competences derive from the aptitude of viruses for natural genome editing....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1738/version/2
Biocommunication of Fungal Organisms
Provedor de dados: 17
Autores: Guenther Witzany.
The development and growth of fungal organisms depend on successful communication processes (a) within the organism and
between organisms, (b) with the same or related species and (c) with non-related organisms. In order to generate an appropriate
response behaviour, fungal organisms must also be able to (d) correctly interpret meaningful information from the abiotic
environment. However, these communication and interpretation processes can also fail. In such cases the overall results can
induce
disease-causing
and
even
lethal
consequences
for
the
organism.


	This review will not enrich the knowledge of specialists in fungal
research, but will demonstrate to a broader readership the different levels of fungal...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics & Genomics; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/1883/version/1
Bio-communication of Plants
Provedor de dados: 17
Autores: Guenther Witzany.
Plants communicate with a great variety of symbiotic partners, above and below ground. Constant monitoring of signals of biotic
origin as well as abiotic environmental influences allows plants to generate appropriate response behavior. These communication
processes are primarily sign-mediated interactions and not simply an exchange of information. They involve active coordination
and active organization of a great variety of different behavioural patterns – mediated by signs.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Molecular Cell Biology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1429/version/1
Bioconversion of eugenol into food flavouring agent vanillin
Provedor de dados: 17
Autores: Suaib Luqman; Sudeep Tandon; Alok Somvanshi; Suchita Srivastava; Mahendra P. Darokar; Suman P. S.
Khanuja.
Microorganisms have the ability to chemically modify a wide variety of organic compounds by a process referred to as biological
or microbial transformation, or in general, bioconversion. The microbial cells and their catalytic machinery (enzymes) accept a
wide array of complex molecules as substrates, yielding products with unparallel chiral (enantio-), positional (region-) and
chemical (chemo-) selectivity through various biochemical reactions. The present study was formulated on the objective of the
conversion of abundantly available phytomolecules eugenol into vanillin, a compound of industrial importance, using
microorganisms Aspergillus flavus, Aspergillus niger and Pseudomonas aeruginosa. These microbes were found to be capable of
converting eugenol...
Tipo: Poster
Palavras-chave: Biotechnology; Microbiology; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6926/version/1
Biocuration Workflow Catalogue
Provedor de dados: 17
Autores: Gully Burns; Martin Krallinger; Kevin Cohen; Cathy Wu; Lynette Hirschman.
As the first phase of a knowledge engineering study of biocuration workflows, we performed a preliminary task-modeling
exercise on seven separate bioinformatics systems. This involved constructing UML activity diagrams from detailed interviews
with curators in order to understand the organization of the process the biocurators used to populate their system. The objective of
this work was to identify common patterns within the workflows where we might apply text mining methods to accelerate
curation. We compiled a number of workflows in a common format but were largely unable to consolidate these structures into a
formal structure that facilitated comparison across workflows. We presented this work as a slideshow and publish this account of
the catalog as...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3250/version/1
bioDBcore: overview of the checklist and steps towards implementation
Provedor de dados: 17
Autores: Pascale Gaudet ([email protected]); Philippe Rocca-Serra ([email protected]).
Members of the International Society for Biocuration (ISB, biocurator.org) and the BioSharing (biosharing.org) initiative work
together to develop and implement BioDBcore (biodbcore.org), a community-defined, uniform system for describing the core
attributes of biological databases, in particular, indicating in a consistent manner which community-defined standards (minimal
information checklists, terminologies and exchange formats) they implement. The BioSharing catalogue offers this
“one-stop shop” for those seeking information about the standards and data sharing
policies.

This presentation illustrates the rational for BioDBcore(P Gaudet) and the
progresses for its implementation (P Rocca-Serra),...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6167/version/1
Biodegradable Luminescent Silicon Quantum Dots for Two Photon Imaging Applications
Provedor de dados: 17
Autores: Chen-An Tien; Folarin Erogbogbo; Ching-Wen Chang; Priscilla Adjei-Baffour; Wing-Chueng Law; Mark T.
Swihart.
Cadmium- and lead-based quantum dots are normally coated for biological applications, because their degradation may result in
the release of toxic heavy metal ions. Here, we synthesize silicon quantum dots that are expected to biodegrade to non-toxic
products. A chitosan coating is used to render the silicon quantum dots stable in storage conditions and biodegradable at
physiological conditions. The applications of these particles are demonstrated in cellular imaging with single and two-photon
excitation. These results open the door for a new generation of silicon quantum dots that may have a wide variety of applications
derived from the flexibility of chitosan.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry.
Ano: 2012
URL: http://precedings.nature.com/documents/7012/version/1
Biodiesel: Freedom from Dependence on Fossil Fuels?
Provedor de dados: 17
Autores: B. Anjan Kumar Prusty; Rachna Chandra; P. A. Azeez.
In view of the depleting oil reserves and exponential rise in petroleum prices, the search for alternative sources of fuel is very
timely and important. The present paper addresses the underlying issues in biodiesel production from biomaterials and sustainable
production and supply of first-generation biofuels, especially the one from jatropha. The agencies and research institutions
involved in the production of biofuels and the national and international efforts made in this regard are discussed here. There is
also a dire need of a step towards large-scale production and supply of second-generation biofuels, although in infant stage, to
strengthen the world economy in general and Indian economy in particular. However, the production of biofuels are likely...
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2658/version/1
Biodiversity Conservation Of The Irtysh River
Provedor de dados: 17
Autores: Yevgeniy Kulikov; Olga Kirichenko.
One of the basic principles of environmental protection is the conservation of biological diversity of natural objects. In addressing
this issue plays an important role the Red Book of Kazakh-stan, which is one of the main effective instruments for the
preservation and restoration of rare and declining in numbers and endangered species. Red Books are the main weapon of
environmental education tool for the inventory of rare and endangered species, scientifically sound foundation for their protection.
Studies of fish that are listed and recommended for inclusion in the Red Book, is a priority and is evidenced not only on the state
of study of the securities and small fish species, but also to demonstrate the quality of protection and conservation of...
Tipo: Manuscript
Palavras-chave: Ecology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5687/version/1
Biodiversity informatics: the challenge of linking data and the role of shared identifiers
Provedor de dados: 17
Autores: Roderic Page.
A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have
relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have
limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research
means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the
use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different
databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1760/version/1
Biodiversity is a cauliflower under the sunlight
Provedor de dados: 17
Autores: Roberto Gatti Cazzolla.
For a long time ecologists have questioned the variations of biodiversity across the latitudinal gradient. Recently it has emerged
that the changes in [beta]-diversity are caused simply by changes in the sizes of species pools. I combined the species pool size
and the fractal nature of ecosystems to clarify some general patterns of this gradient. Considering temperature, humidity and NPP
as the main variables of an ecosystem niche and as the axis of the polygon in the Cartesian plane, it is possible to build fractal
hypervolumes, whose the fractal dimension rises up to three, moving towards the equator. It follows that the best figure that
graphically synthesizes the evolutionary forces that fit this ecosystem hypervolume is the fractal cauliflower.
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6917/version/1
Biodiversity Quality: a paradigm for biodiversity
Provedor de dados: 17
Autores: Alan Feest; Timothy Aldred; Katrin Jedamzik.
The internationally accepted definition of biodiversity creates difficulty in measuring difference and change. The authors suggest
that well-sampled data can be used to generate a range of numerical indices reflecting species group characteristics/functionality
(Species Richness, Simposons Index, Population Density, Biomass and Species Conservation Value) that can be viewed in
combination to create a picture of biodiversity quality. This overall approach has considerable advantages over the currently
accepted Convention on biological Diversity definition based on the "variability" of genes, species and
ecosystems, since the numerical expression of the indices allows the probability of difference between biodiversity quality trends
and...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3205/version/1
Biodiversity shapes tree species aggregations in tropical forests
Provedor de dados: 17
Autores: Shan-Huah Wu; Wei-Chun Chao; Chang-Fu Hsieh.
Spatial patterns of conspecific trees are considered as the consequences of biological interactions and environmental influences.
They also reflect species interactions in plant communities. However, biological attributes are often neglected while deliberating
the factors shaping species distributions. As rising attentions are paid to spatial patterns of tropical forest trees, we noticed that
seven Center of Tropical Forest Sites and four Forest Dynamic Plots in Asia and America have presented analogously high
proportions of species with aggregated conspecific individuals coincidently. This phenomenon is distinctive and repudiates
fundamental ecology hypotheses which suggested dispersed distributions of conspecific tropical trees due to intensive density...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1670/version/1
BioenergyProduction From Plant Biomass: Bioethanol From Concept To Reality
Provedor de dados: 17
Autores: Israr Khan; Muhammad Waheed Akhtar.
Natural energy reserves like petrol and diesel etc are depleting. As such, it is of paramount importance to find alternative fuels.
Solar energy is trapped as biomass in plants. Biomass provide an excellent reserve for trapping solar energy on field. Complex
enzymatic machinery comprising of hydrolytic reactions and consolidated bioprocessing is needed to make viable bioenergy,
mostly biofuels like bioethanol for locomotives, industries and general use in the future.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6286/version/1
Biogeographic relationships among deep-sea hydrothermal vent faunas at global scale
Provedor de dados: 17
Autores: Charleyne Bachraty; Pierre Legendre; Daniel Desbruyères.
The discovery of deep-sea hydrothermal vent fauna, kilometers deep in the oceans, is a great achievement of 20th-century marine
biology. The deep-sea hydrothermal food web does not directly depend on the sun energy. Vent communities rely primarily on
trophic associations between chemoautotrophic bacteria and consumers. A small number of endemic taxa are adapted to this
highly toxic environment distributed along ridge crests. Where they appeared and how they dispersed is among the important
questions ecologists must answer. Here, by statistical analysis of the most comprehensive data base ever assembled about
deep-sea hydrothermal fauna, we delineate six major hydrothermal provinces in the World Ocean, then we identify five significant
dispersal flows...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1823/version/1
bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics
Provedor de dados: 17
Autores: Roderic Page.
Linking together the data of interest to biodiversity researchers (including specimen records, images, taxonomic names, and DNA
sequences) requires services that can mint, resolve, and discover globally unique identifiers (including, but not limited to, DOIs,
HTTP URIs, and LSIDs). bioGUID implements a range of services, the core ones being an OpenURL resolver for bibliographic
resources, and a LSID resolver. The LSID resolver supports Linked Data-friendly resolution using HTTP 303 redirects and
content negotiation. Additional services include journal ISSN look-up, author name matching, and a tool to monitor the status of
biodiversity data providers. bioGUID is available at "http://bioguid.info/":http://bioguid.info/. Source code
is...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3079/version/1
Bioinformatic approaches for the genetic and phenotypic characterization of a Saccharomyces
cerevisiae wine yeast collection
Provedor de dados: 17
Autores: Ricardo Franco-Duarte; Lan Umek; Blaz Zupan; Dorit Schuller.
The objective of the present study was to compare genetic and phenotypic variation of 103 Saccharomyces cerevisiae strains
isolated from winemaking environments. We used bioinformatics approaches to identify genetically similary strains with specific
phenotypes and to estimate a strain's biotechnological potential. 
A S. cerevisiae collection,
comprising 440 strains that were obtained from winemaking environments in Portugal has been constituted during the last years.
All strains were genetically characterized by a set of eleven highly polymorphic microsatellites and showed unique allelic
combinations. Using neural networks, a subset of 103 genetically most diverse strains was chosen for phenotypic analysis, that
included growth...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2288/version/1
Bioinformatics analysis of homologies between pathogen antigens, autoantigens and the CFTR cystic
fibrosis protein: A role for immunoadsorption therapy?
Provedor de dados: 17
Autores: Christopher Carter.
The cystic fibrosis CFTR chloride channel is involved in pathogen entry into epithelial cells, and provides the glutathione and
hypochlorous acid necessary for bactericidal and viricidal actions. CFTR mutations block these effects, diminishing pathogen
defence and allowing pathogen accumulation in the extracellular space, where antibody encounter is likely. The pathogen antigens
observed in cystic fibrosis (including P. Aeruginosa, S.Aureus and S.Maltophilia proteins) are homologous to the autoantigens
reported in cystic fibrosis and all are homologous to the CFTR protein itself. Antibodies to pathogens and autoantigens may also
target the CFTR protein, acting as antagonists, further compromising its function. The tripartite relationship between pathogen...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5352/version/1
Bioinformatics Approach for Functional Glycomics
Provedor de dados: 17
Autores: James C. Paulson.
Presentation in the Human Glycomics Proteomics Disease Initiative (HGPI) session.
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/15/version/1
Bioinformatics for Human Proteomics: Current State and Future Status
Provedor de dados: 17
Autores: Amos Bairoch.
We are entering a new era in the exploration of the human proteome.
Advances in technologies are allowing
researchers to map with a much
better resolution and improved accuracy this very complex universe.
Such
an exploration also requires a compendium of adequate bioinformatics
tools,
data repositories and knowledge resources. We are going to describe
what are the state of the art in term of
data and knowledge resources for
human proteins: from repositories of proteomics data such as
PRIDE,
PeptideAtlas
or
Peptidome,
databases
such
as
SRMAtlas
and
HPA
and
knowledgebase such as UniProtKB/Swiss-Prot....
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5050/version/1
Biological Activities of Extracts from Sumac (Rhus spp.): A Review
Provedor de dados: 17
Autores: Sierra Rayne; Giuseppe Mazza.
Sumac is the common name for a genus (Rhus) that contains over 250 individual species of flowering plants in the family
Anacardiaceae. These plants are found in temperate and tropical regions worldwide, often grow in areas of marginal agricultural
capacity, and have a long history of use by indigenous peoples for medicinal and other uses. The research efforts on sumac
extracts to date indicate a promising potential for this plant family to provide renewable bioproducts with the following reported
desirable bioactivities: antifibrogenic, antifungal, antiinflammatory, antimalarial, antimicrobial, antimutagenic, antioxidant,
antithrombin, antitumorigenic, antiviral, cytotoxic, hypoglycaemic, and leukopenic. As well, the bioactive components can be
extracted...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/631/version/1
Biological networks and epistasis in genome-wide association studies
Provedor de dados: 17
Autores: Mathieu Emily; Leif Schauser; Thomas Mailund; Mikkel H. Schierup.
Over the last few years, technological improvements have made possible the genotyping of hundreds of thousands of SNPs,
enabling whole-genome association studies. The first genome-wide association studies have recently been completed to detect
causal variant for complex traits. Although increasing evidence suggests that interaction between loci, such as epistasis between
two loci, should be considered, most of these studies proceed by considering each SNP independently. One reason for this choice
is that looking at all pairs of SNPs increases dramatically the number of tests (approximatively 50 billions of tests for a 300,000
SNPs data set) that faces with computational limitation and strong multiple testing correction.
We proposed
to...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/466/version/1
Biological resource catalog: NIF and NeuroLex
Provedor de dados: 17
Autores: Anita E. Bandrowski.
In the digital age one can find data and teaching materials on the web, however data and materials of a high quality are not always
ranked very high on commercial search engines that look at the number of other sites that link to a page rather than the quality of
the information. Additionally, many such materials are maintained within databases that are inaccessible to search technology. To
solve these problems, the Neuroscience Information Framework (NIF: http://www.neuinfo.org) was created to aid the
neuroscience community to discover useful digital resources, such as academic databases, and it has also developed a large digital
catalog of resources that are related to neuroscience.
NIF has developed a “resource...
Tipo: Presentation
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6238/version/1
Biological robotics and nanorobotred cells: Characterization and applications
Provedor de dados: 17
Autores: Rakesh Sharma; Soonjo Kwon; Ching J. Chen.
In human body, nanorobot-like red blood cells get exposed to human body fluids and many physico-chemical changes inside
while these nanorobots (fullerene structure coated hemoglobin embedded iron inorganic elements) remain safe and perform killer
action against bacteria or virus. We propose this killer action as ‘nanorobot driven nanomedical
treatment’ to combat a bacterial or viral infection. The red cells also act as imaging agent due to oxygen binding
character. Our experiments were focused on the application of nanorobot (red cells) to make them immune resistant against
viruses and making them as useful contrast agents in magnetic resonance imaging use based on their behavior in nanomagnetic
fields. It consists of an injection of...
Tipo: Presentation
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/4262/version/1
Biological taxonomy and ontology development: scope and limitations
Provedor de dados: 17
Autores: Nico M. Franz; David M. Thau.
The prospects of integrating full-blown biological taxonomies into an ontological reasoning framework are reviewed. We contrast
the common usage of a static 'snapshot' hierarchy in ontological representations of taxonomy with a more
realistic situation that involves dynamic, piece-meal revisions of particular taxonomic groups and requires alignment with relevant
preceding perspectives. Taxonomic practice is characterized by a range of phenomena that are orthogonal to the logical semantic
background from which ontological entities and relationships originate, and therefore pose special challenges to ontological
representation and reasoning. Among these phenomena are: (1) the notion that there is a single phylogenetic hierarchy in nature...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4593/version/1
Bioluminescence emission of the firefly
Provedor de dados: 17
Autores: Anurup Gohain Barua; Simanta Hazarika; Nayanmoni Saikia; Gaurangadhar Baruah.
We have recorded _in vivo_ emission and time-resolved spectra of the firefly species _Pyrophorus noctilucus_. The emission
spectrum shows the FWHM value for this particular species to be 55 nm, which is significantly smaller than the half widths
reported till now. The time-resolved spectrum reveals that a flash, of duration about a hundred milliseconds, is in fact composed
of a number of microsecond pulses. This result suggests that the speed of the enzyme-catalyzed chemiluminescence reaction in the
firefly for the emission of light is much greater than is believed to be.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/1351/version/1
Bioluminescence emissions of firefly _Luciola praeusta_ Kiesenwetter 1874 (Coleoptera : Lampyridae
: Luciolinae)
Provedor de dados: 17
Autores: Anurup Gohain Barua; Simanta Hazarika; Nayanmoni Saikia; Gauranga Dhar Baruah.
_In vivo_ emission and time-resolved spectra of firefly _Luciola praeusta_ Kiesenwetter 1874 (Coleoptera : Lampyridae :
Luciolinae) have been recorded. The emission spectrum shows the FWHM value for this particular species to be 55 nm, which is
significantly narrower than the _in vivo_ half widths reported till now. The time-resolved spectrum reveals that a flash, of
duration about a hundred milliseconds, is in fact composed of a number of microsecond pulses. This result suggests that the speed
of the enzyme-catalysed chemiluminescence reaction in the firefly for the emission of light is much faster than is believed to be.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1351/version/2
BioMed Central - open data guidance for authors
Provedor de dados: 17
Autores: Naomi Attar.
All research articles published by BioMed Central are open access. In keeping with the spirit of open access publishing, we aim to
maximize the availability of data associated with these articles.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6234/version/1
Biomedical Resource Ontology
Provedor de dados: 17
Autores: Trish Whetzel.
none
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6354/version/1
Biomimetic assemblage of nucleobase 5-fluorouracil into nano-size three-dimensional particles
Provedor de dados: 17
Autores: Arun Chauhan; Swaleha Zubair; Qamar Zia; Saba Tufail; Asif Sherwani; Mohammad Sajid; Mohammad Owais.
Biomimetic nano-assembly formation offers a convenient and bio friendly approach to fabricate complex structures from simple
components with sub-nanometer precision. Recently, extract from cells of microorganism/plant origin have emerged as a simple
and viable route for the synthesis of metal and inorganic material nano-particles. In the present study, we have extended biological
synthesis of nano-particles to organic molecules, namely the anticancer agent, 5-fluorouracil (5-FU) using Aloe vera leaf extract.
The formation of 5-FU nano- particles was assessed by UV, FT-IR and fluorescence spectroscopic techniques. Transmission
electron microscopy and atomic force microscopic techniques confirmed nano-size of the synthesized particles. Importantly, the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6182/version/1
BioModels Database: curation and annotation
Provedor de dados: 17
Autores: Michael Schubert; Ishan Ajmera; Vijayalakshmi Chelliah; Lukas Endler; Nicolas Rodriguez; Camille Laibe; Nicolas Le
Novère.
The BioModels Database is a freely accessible online resource for storing, viewing, retrieving, and analyzing published,
peer-reviewed quantitative models of biological processes.

In this poster we provide
an overview of its capabilities, as well as the curation and annotation process with two use cases concerning blood coagulation
and glucose homeostasis.
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6361/version/1
BioModels Database: Next generation model repository
Provedor de dados: 17
Autores: Camille Laibe; Michael Hoehl.
Public
announce
that
the
software
system
running
BioModels
Database
("http://www.ebi.ac.uk/biomodels/":http://www.ebi.ac.uk/biomodels/) will evolve from open source to a
community developed project.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5127/version/1
BioPax and SBML output from Reactome: where we are, where we are heading
Provedor de dados: 17
Autores: David Croft.
Reactome is a free, open-source, open access, pathway database. Currently, Reactome has over 5000 human proteins, involved in
over 4000 manually curated reactions. Additionally, it has nearly 30,000 reactions inferred by orthology projection from human
to 20 other model organisms. Facilities exist for exporting single pathways or the entire database to either BioPax or SBML.
SBML generation now uses libSBML, ensuring syntactic correctness, and has adopted MIRIAM URIs for references to external
databases. For the future, we anticipate that users will be able to submit a list of species to Reactome and obtain as an output
customized BioPax or SBML, based on reactions extracted from Reactome.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6376/version/1
Biopax and Semantics
Provedor de dados: 17
Autores: Ismael Navas-Delgado; Maria Jesús García-Godoy; Maria del Mar
Roldán-García; José F. Aldana-Montes.
Biopax community is producing sets of data in RDF files, but most of them are not available through query interfaces. The
publication of SPARQL endpoints is feasible with current sets of data, but the use of reasoning in these interfaces is unfeasible in
many cases. The use of large scale reasoners is a need to take advantage of these data sets.
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6320/version/1
BioPAX: next steps for Semantic Web / CV workgroup
Provedor de dados: 17
Autores: Andrea Splendiani.
Outline of the next steps which will be proposed as actions in the Semantic Web/ Linking/ CV workgroup of
BioPAX.
One main focus will be to clean the RDF representation and adopt some basic relations, in order to
address use cases in data-integration, pathway analysis and simple ontology/pathway integration.

Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4968/version/1
BioPAX Support in CellDesigner
Provedor de dados: 17
Autores: Anushya Muruganujan; Huaiyu Mi.
BioPAX is a pathway data exchange language that is widely used by pathway database resources. Here we describe a mechanism
that allows users to curate pathway data in diagrams using CellDesigner, a pathway graphical editing tool, and save the pathway
data in BioPAX format. We used this mechanism to create BioPAX files for all 165 pathways from the PANTHER database. In
addition, we are also working on graphically visualizing BioPAX data by importing them into CellDesigner.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5679/version/1
Bio::Phylo - Phyloinformatic Analysis Using Perl
Provedor de dados: 17
Autores: Rutger Vos.
Recent years have seen the emergence of the field of phyloinformatics. In the course of a phyloinformatic analysis, data and
metadata are generated, transformed, filtered, analyzed and summarized before they can be interpreted to answer meaningful
biological questions. Based on first principles of good science such steps should be reproducible; and, in practice, analysis steps
often need to be redone by the researcher multiple times anyway and are too error-prone, tedious and time-consuming to do by
hand. Hence, phyloinformatic analyses benefit from increased automation. 

The
Bio::Phylo toolkit promotes this by giving easy access to phylogenetic data objects (trees, taxa, character state matrices) read from
a variety of...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4601/version/1
Biophysical Effects Of Ion Concenteration On The Affinity Between Nanopore, OmpF Lumen and
Passing Nucleotide
Provedor de dados: 17
Autores: Saeid Hadi; Hamid Mobasheri.
OmpF an outer-membrane porin channel of _E. Coli_ posses beta-barrel structure, whose conductivity and gating phenomena are
affected by changes in pH, salt concentration and so on. The distribution of amino acids in OmpF induces a non homologous
electric potential in channel lumen. The intrinsic charge distribution caused be amino acid may be affected by lipid bilayer, extra
and intra cellular ion concentration, and other physico-chemical condition of environment including, pH, temperature,
polyelectrolytes etc. Nucleotides are considered as one of most important metabolite in the cell that have pass through membrane
whenever necessary. The experimental study of translocation of such a molecules through channels have provided invaluable
information...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5101/version/1
Biophysical Mechanisms Supporting Conscious Perception: Prospects for an Artificial Astrocyte
Provedor de dados: 17
Autores: Alfredo Pereira Jr.
In perceptual processes, signals carrying information about a stimulus are transmitted through multiple processing lines to
populations of receptive neurons and thalamocortical circuits, leading to the formation of a spatial ensemble of local field
potentials. This paper addresses the problem of how the brain integrates patterns embodied in local fields to (re)construct the
stimulus in a conscious episode. Four examples of human perception are given to illustrate the requirements of the integrative
process. Considering the strategic position of astrocytes, mediating somatic signals carried by blood flow and information carried
by the neuronal network, as well as their intrinsic information processing capabilities, these cells are in an adequate condition...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6484/version/1
Biophysical visual virtual reality in retinotopic visual areas
Provedor de dados: 17
Autores: István Bókkon; Jack Tuszynski; Vahid Salari.
Previously, we have pointed out that biophoton production can be a controlled process that originates from regulated redox/radical
reactions. Our biophoton experiments support the notion that various visual related phenomena such as discrete retinal noise,
retinal phosphenes as well as negative afterimages are due to biophotons. We have also suggested a new model, stating that the
brain is able to create biophysical pictures in retinotopic visual areas via redox regulated biophotons of synchronized neurons.
According to our interpretation, visualization (imagery) is a special kind of representation i.e., visual imagery requires peculiar
inherent biophysical processes. Our idea of biophysical visual virtual reality in retinotopic areas may be a possible...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6051/version/1
BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse
Provedor de dados: 17
Autores: Patricia L. Whetzel; Nigam H. Shah; Natalya F. Noy; Benjamin Dai; Michael Dorf; Nicholas Griffith; Clement Jonquet;
Cherie Youn; Adrien Coulet; Chris Callendar; Daniel L. Rubin; Barry Smith; Margaret-Anne Storey; Christopher G. Chute; Mark
A. Musen.
BioPortal ("http://bioportal.bioontology.org":http://bioportal.bioontology.org) is an open repository of
biomedical ontologies that provides programmatic and web-based access to ontologies developed in OBO, OWL,
Protégé frames, and RDF. Features include browsing, searching, and visualization of ontologies. Searching
of integrated data resources is also possible through ontology-based indexing of biomedical resources with BioPortal ontologies.


Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3868/version/1
Bio-resources for sharing: which communities and what specific needs
Provedor de dados: 17
Autores: Andres Metspalu.
Biobanks are an important source to obtain samples and data for research purposes for a wide array of communities. In fact,
sharing of bio-resources and data is an integral part of a biobank's role. For an effective partnership a list of
requirements or needs have to be met, assuring quality of the resources shared as well as quality of the collaboration in general.
Tracking and documenting bio-resource sharing and collaborations of a biobank can be seen as one indicator of the
"impact" a biobank has to the field. As an example, the practice of the Estonian Genome Center of the
University of Tartu is presented.
Tipo: Presentation
Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5659/version/1
BioSharing Overview
Provedor de dados: 17
Autores: Susanna-Assunta Sansone; Dawn Field; Annapaola Santarsiero; Eamonn Maguire; Philippe Rocca-Serra; Chris Taylor;
Lee Harland; The BioSharing Communities.
Download this poster providing an overview of the BioSharing effort.
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5936/version/1
BioSharing: Standards, Policies and Communication in Bioscience
Provedor de dados: 17
Autores: Dawn Field; Susanna-Assunta Sansone; Philippe Rocca-Serra.
BioSharing works at the global level to build stable linkages between journals, funders, implementing data sharing policies, and
well-constituted standardization efforts in the biosciences domain, to expedite the communication and the production of an
integrated standards-based framework for the capture and sharing of high-throughput genomics and functional genomic bioscience
data.
Tipo: Presentation
Palavras-chave: Biotechnology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6436/version/1
BioSharing - standards, policies and communication in bioscience
Provedor de dados: 17
Autores: Susanna-Assunta Sansone.
Research communities, funding agencies, and journals participate in the development of reporting standards for the bioscience
domain to ensure that shared experiments are reported with enough information to be comprehensible and (in principle)
reproducible, compared or integrated (Field, Sansone et al., Science, 2009). Similar trends exist in both the regulatory arena and
commercial
science.

Proliferation
of
standards
is
a
positive
sign
of
stakeholders’ engagement, but how much do we know about these standards? Which ones are mature and stable
enough
to
use
or
recommend?
Which
tools
and
databases
implement
which
standard?
Etc...

The BioSharing catalogue (www.biosharing.org)...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6153/version/1
BioSilicoSystems - A Multipronged Approach Towards Analysis and Representation of Biological
Data (PhD Thesis)
Provedor de dados: 17
Autores: Sridhar Hariharaputran.
The rising field of integrative bioinformatics provides the vital methods to integrate, manage and also to analyze the diverse data
and allows gaining new and deeper insights and a clear understanding of the intricate biological systems. The difficulty is not only
to facilitate the study of heterogeneous data within the biological context, but it also more fundamental, how to represent and
make the available knowledge accessible. Moreover, adding valuable information and functions that persuade the user to discover
the interesting relations hidden within the data is, in itself, a great challenge. Also, the cumulative information can provide greater
biological insight than is possible with individual information sources. Furthermore, the rapidly growing...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5164/version/1
Biospheric context of Siberian development
Provedor de dados: 17
Autores: Georgii A. Alexandrov; Gen Inoue; Tsuneo Matsunaga.
Productivity of ecosystems surrounding a city is important for supporting its activities in a sustainable way. The total terrestrial
net primary production (NPP) shows biosphere potential to supply primary food energy source for all non-autotrophic species
including humans. Humans appropriate approximately 20% of NPP, in average. Even in the relatively well-populated regions of
Siberia, NPP per capita exceeds the average level by several times suggesting the window of opportunity for achieving sustainable
development. (3 pages, 1086 words, 2 maps)

Tipo: Manuscript
Palavras-chave: Ecology; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2478/version/1
Biospheric context of Siberian development
Provedor de dados: 17
Autores: Georgii A. Alexandrov; Gen Inoue; Tsuneo Matsunaga.
Recent publications on human appropriation of Net Primary Production (NPP) raise the question of how much of the
biosphere’s productivity we can appropriate in a sustainable way. This article brings the issue into the context of
Siberian development. In contrast to many other regions of the world, the population density in Siberia is still very low as
compared to the NPP supplied by regional ecosystems. Hence, it is not too late to raise the question on how much of the NPP
supplied by Siberian ecosystems we can appropriate in a sustainable way.
Tipo: Manuscript
Palavras-chave: Ecology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/2478/version/2
Biostratigraphic Study of the Gurpi Formation Based on Planktonic Foraminifera In Lar Area
(Kuh-e-kurdeh Section)
Provedor de dados: 17
Autores: Meysam Shafiee Ardestani; Ebrahim Ghasemi-Nejad; Ali Mandanizadeh.
The study of planktonic foraminifera of the Gurpi formations at Lar area (Kuh-e-kurdeh section) enables me to find the most
standard biozones defined in mediterranean regions, especially Tethysian domain. Five biozones were determined. Biozones I
(Globotruncanita elevata zone) and II (Globotruncana ventricosa zone) and III (Radotruncana calcarata zone) indicate the Early
Campanian and Middle and Late Campanian, respectively. Biozones IV (Globotruncanita stuarti zone) and V (Gansserina gansseri
zone) suggest the Early and Middle Maastrichtian, respectively. In the Late Maastrichtian, due to decreasing in water depth at the
study
area,
Abathomphalus
mayaroensis
recognised.


Tipo: Manuscript
zone
defined
in
Tethysian
domain
was
not
Palavras-chave: Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2947/version/1
Biostratigraphy and assigning the paleosalinity by using Echinocorys and Planktonic foraminifera at
Upper Maastrichtian, in Jorband section, Central Alborz, Iran
Provedor de dados: 17
Autores: Masood Asgharian Rostami; Behnaz Balmaki; Meysam Shafiee Ardestani; Esmail Kohansal.
Jorband section is located in the north slope of central Alborz, and 28 Km south of Noor. It has been sampled and index fossilic
groups of planktonic foraminifera and echinoids were studied in order to assign the paleosalinity and biozonation in central
Alborz. The planktonic foraminiferal biozones identified within the Upper maastrichtian sequence of the Jorband section are three
zones of Contustruncana contusa, Planoglobulina brazoensis, and Racemiguembelina fructicosa. The salinity changes were also
searched in this section. In three layers in Jorband section examination echinocorys genus and is drawn as a diagram which in
middle of the section, the salinity mounts is fewer than the beginning and top of the section.
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3699/version/1
Biostratigraphy of the Danian/Selandian transition: A case study from Kamestan anticline section,
northwest of Izeh city in Khuzestan province, Southern Iran
Provedor de dados: 17
Autores: Nasrin Hadavandkhani; Abbas Sadeghi.
The planktonic foraminifera turnover across the Danian-Selandian boundary (early to late Paleocene, ~60 Ma) has been studied in
the Kamestan anticline section. The studied interval span planktonic foraminifera zones P2-P3. In this section Danian-Selandian
boundary is located in Pabedeh – Gurpi Formations transition. Here, the boundary of Pabeh and Gurpi Formations is
a transitional one and identified by with color change of from grey shale to purple shale of Gurpi Formation to Pabdeh Formation
.


Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4338/version/1
Biostratigraphy of the Ruteh Formation at Harijan section (Central Alborz) northern Iran using
foraminifera and conodont
Provedor de dados: 17
Autores: Bahaoddin Hamdi; Abbas Sadeghi; Ebrahim Kohansa; Meysam Shafiee Ardestani; Behnaz Balmak.
In order to study the fossil contents of the Ruteh Formation for biostratigraphical purposes, the 200 meters thick section was
sampled at Harijan section, Central Alborz. The sequence is mainly made up of limestone and shale's. The lower
contact of the formation with Dorud Formation is disconform while the upper contact with under learing Dorud Formation is
disconformable with overling Nesen Formation is as well as disconformable. Fifty four species belonging to 27 genera
(foraminifera and conodonts) were identified and three biozones were differentiated. These are formation: 1- _Schubertella
giraudi_- _Codonofusiella distincta_ Assemblage Zone, 2- _Cribrigenerina sumatruna_- _Langella ocarina_ Assemblage Zone, 3_Sweetognathus whitei_ Biozone....
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3376/version/1
Biotransformation of artemisinin mediated through fungal strains for obtaining derivatives with novel
activities
Provedor de dados: 17
Autores: Suchita Srivastava; Suaib Luqman; Atiya Fatima; Mahendra P. Darokar; Arvind S. Negi; J K. Kumar; Karuna
Shanker; Chandan S. Chanotiya; Sudeep Tandon; Suman P. S. Khanuja.
Artemisinin, a sesquiterpene lactone, is the active antimalarial constituent of Artemisia annua. Several fungal strains
Saccharomyces cerevisiae, Aspergillus flavus, Aspergillus niger and Picchia pastoris were used to biotransform artemisinin.
Among these strains, A. flavus was the only microorganism capable of transforming artemisinin to deoxyartemisinin in higher
yields than the previous reports. The structure of deoxyartemisinin was elucidated by spectroscopy. Deoxyartemisinin showed
antibacterial activity against Staphylococcus aureus, S. epidermidis and S. mutans at a minimum inhibitory concentration (MIC)
of 1 mg/mL compared to artemisinin whose MIC was >2 mg/mL.
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Microbiology; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6925/version/1
Bird pollination of Canary Island endemic plants
Provedor de dados: 17
Autores: Jeff Ollerton; Louise Cranmer; Ralph Stelzer; Steve Sullivan; Lars Chittka.
The Canary Islands are home to a guild of endemic, threatened bird pollinated plants. Previous work has suggested that these
plants evolved floral traits as adaptations to pollination by flower specialist sunbirds, but subsequently they appear to be have
co-opted passerine birds as sub-optimal pollinators. To test this idea we carried out a quantitative study of the pollination biology
of three of the bird pollinated plants, Canarina canariensis (Campanulaceae), Isoplexis canariensis (Veronicaceae) and Lotus
berthelotii (Fabaceae), on the island of Tenerife. Using colour vision models, we predicted the detectability of flowers to bird
and bee pollinators. We measured pollinator visitation rates, nectar standing crops, as well as seed set and pollen...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1977/version/1
Bird surveys for REDD+: avian communities indicate forest degradation in a Peruvian coffee
landscape
Provedor de dados: 17
Autores: Raf Aerts; Sarah Spranghers; Bruno Verbist; Luc Lens; Cagan Sekercioglu.
Shade coffee cultivation in the Peruvian Andes assists in reducing emissions from deforestation because it avoids conversion to
non-forest land uses such as coca and sun grown coffee farming. REDD+ is a potential finance mechanism which may provide
incentives for local coffee cooperatives to maintain high shade tree cover. REDD+ has potential multiple benefits other than
carbon sequestration, including the conservation of biodiversity. When monitoring for REDD+, surveys of bird biodiversity may
prove to be particularly valuable: apart from their high intrinsic value and their value as essential ecosystem service providers,
birds inhabiting forest habitats are extremely sensitive to forest loss and forest degradation and are therefore potential useful...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6589/version/1
Birth Control Does Not Significantly Alter Women’s Preferences for Variants of
Men’s Voices
Provedor de dados: 17
Autores: Jason W. J. W. W. Whitaker; Ryan R. S. Setten; Ulv U. A. Ankerstjerne.
Research shows that women‘s preferences for masculine voices (low pitch) vary as a function of the menstrual
cycle, becoming positively augmented around ovulation. The proximate cause catalyzing this effect is attributed to fluctuating
estrogen levels. Thus, the introduction of hormonally based birth control has been to shown to have a dampening effect in
experiments researching women‘s preference of dimorphic secondary sexual characteristics. However, this
dampening effect has not yet been explored in respect to women‘s preferences for masculine voice types. This
experiment sought, first, to investigate the effect of birth control on subjects off and on birth control; and, second, to replicate past
findings:...
Tipo: Poster
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5895/version/1
Body Fat is Associated with Decreased Endocrine and Cognitive Resilience to Acute Emotional Stress
Provedor de dados: 17
Autores: Lilianne R. Mujica-Parodi; Rudolph Renelique; Marcus K. Taylor.
*Objective:* Cortisol is elevated both in individuals with increased emotional stress as well as with higher percentages of body
fat. Cortisol is also known to affect cognitive performance, particularly spatial processing, selective attention, and working
memory. We hypothesized that increased body fat might therefore be associated with decreased performance on a spatial
processing task, in response to an acute real-world stressor. 

*Design:* We tested two
separate samples of subjects undergoing their first (tandem) skydive. In the first sample (N=78), subjects were tested for salivary
cortisol and state-anxiety (Spielberger State Anxiety Scale) during the plane's fifteen-minute ascent to altitude in
immediate...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2072/version/1
Body-specific representations of action word meanings in right and left handers
Provedor de dados: 17
Autores: Daniel Casasanto.
If understanding action words involves mentally simulating our own actions, then the neurocognitive representation of word
meanings must differ for people with different kinds of bodies, who perform actions in systematically different ways. In a test of
the _Body-Specificity Hypothesis_, right- and left-handers were compared on two motor-meaning congruity tasks. Double
dissociations in both action execution and recognition memory results showed that right and left handers form body-specific
representations of words for manual actions.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1321/version/1
Bogoch Replikins Pandemic Prevention: Increase of Strain-Specific Influenza Genomic Replikin
Counts, Having Predicted Outbreaks and their Location Seven Times Consecutively, Up to Two Years
in Advance, Provides Time for Prevention of Pandemics
Provedor de dados: 17
Autores: Samuel
Bogoch; Elenore S. Bogoch.
Earlier studies have shown that the increased concentration of a new class of virus genomic peptides, Replikins, precedes and
predicts virus outbreaks. We now find that the area in the genome of the highest concentration of Replikins, and the country in
which this peak exists in scout viruses, have permitted in the past five years seven consecutive accurate predictions of the
geographic localization of coming outbreaks, including those now realized in Mexico for H1N1, and in Cambodia for H5N1.
Real-time Replikin analysis of the evolution of the virus genome identified both mutations and structural reorganization of the
hemagglutinin and p B1 genes over several years before each outbreak. This information, together with the specific Replikin
sequences so...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6952/version/1
Bottom-up and top-down effects on algal community dynamics in an aridland river: the Middle Rio
Grande, New Mexico
Provedor de dados: 17
Autores: Ayesha S. Burdett; Rebecca J. Bixby.
Background/Question/Methods

In this study, we examined interactive effects of
nutrient availability, river flow and food web structure on algal growth and species composition in the Middle Rio Grande, New
Mexico. Algal community dynamics can be affected by both bottom-up and top-down factors. Algal production may be limited by
low levels of nutrients or low light availability. Conversely, production is expected to increase when nutrient levels are high and
light availability is not limited. Top-down factors such as grazing by invertebrates can also alter periphyton growth and
community composition. Generally, a reduction in grazers results in periphyton biomass increases and shifts in growth forms (to
more upright...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3664/version/1
BRAGOMAP - a new Perl script for high throughoutput blast results analysis including GO and
MapMan automatic annotations
Provedor de dados: 17
Autores: Rafal Woycicki; Wojciech Gutman; Zbigniew Przybecki.
Analyzing of sequences similarities is the first and most important method used to find out the function of unknown nucleotides.
Searching of homologs should be done carefully not to loose any important ones. Having thousands of results from various
long-read sequencing projects (ie. differentially expressed tags, genomic polymorphons or BAC ends), the by-hand ability to
retrieve interesting (to our goal) similarities in hundreds of Blast results decreases rapidly. Decreasing the number of retrieved
sequences by giving more stringency in e-value threshold or displaying less results could lead to false deductions. Functional
genomics, proteomics and metabolomics could give us answers to the role of nucleotide sequences. It makes the need to annotate
as much...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3900/version/1
Brain, language, and handedness: a family affair
Provedor de dados: 17
Autores: Bernard Mazoyer; Gregory Simon; Fabrice Crivello; Laure Zago; Laurent Petit; Emmanuel Mellet; Nathalie
Tzourio-Mazoyer.
The left planum temporale is a marker of left hemisphere language specialization. We investigated the effect of individual
handedness and familial sinistrality on left planum temporale surface area and found the size is reduced in proportion with the
number of left-handed immediate family members and is lowest when one's mother is left-handed. This reduction is
independent of an individual's handedness or sex and has no counterpart in the right hemisphere.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2982/version/1
BrainGrab: Capturing Curator Expertise as Reusable Annotation Rules
Provedor de dados: 17
Autores: Daniel H. Haft; Malay K. Basu; Roland A. Richter.
Experienced biocurators can outperform automated systems on specific genes once they determine which pieces of evidence
should drive annotation, and which annotations should be spread. The annotation logic may weigh both homology evidence
(BLAST matches or HMM hits) and non-homology evidence (neighboring genes, metabolic context, taxonomic group).
Unfortunately, the expertise developed to annotate each gene is short-lived, and is mostly lost if the logic driving the annotation is
not captured. We report the development of BrainGrab, an interface added to the MANATEE manual annotation tool for
prokaryotic genomes. The curator can specify evidence scenarios that should always lead to equivalent annotation for similar
genes in similar contexts, and thus...
Tipo: Presentation
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3313/version/1
Breast Cancer Associated Metastasis is Significantly Increased in a Model of Autoimmune Arthritis
Provedor de dados: 17
Autores: Lopamudra Das Roy; Latha Pathangey; Teresa Tinder; Pinku Mukherjee.
Chronic inflammation is known to play a role in cancer initiation, promotion,and metastasis. However, the mechanism by which
inflammation promotes metastasis is still unclear. We evaluated if chronic inflammation induced by autoimmune arthritis may
contribute to increased breast cancer-associated metastasis. We report a three-fold increase in lung metastasis and a significant
increase in the incidence of bone metastasis in the pro-arthritic mice compared to control mice. The metastatic breast tumors in
turn augment the severity of arthritis resulting in a vicious cycle that increases both bone destruction and metastasis. Enhanced
neutrophilic and granulocytic infiltration in lungs and bone of the pro-arthritic mice and subsequent increase in circulating...
Tipo: Manuscript
Palavras-chave: Cancer; Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/2632/version/1
Breeding biology of pond heron in Kerala, South India
Provedor de dados: 17
Autores: K Seedikkoya; PA Azeez; EA Abdul Shukkur.
Regular intensive investigations to locate nesting colonies were carried out early monsoon of 1999 up to 2002. For detailed study
a few breeding colonies were selected. The nesting trees, nest characteristics, eggs characteristics, incubation, hatching and
hatchlings were investigated.

Altogether 17 plant species were used for nesting. Nest
materials were collected from 24 plant species for building nest. The mean maximum size of the nest material used was 29.05 cm
and the mean minimum size was 13.46 cm. The clutch size varied from 2-5 and clutches of three were very common. The
maximum and minimum length and breadth of eggs were 48.0 x 32.0 and 33.3 x 24.1 respectively. The weight of eggs varied
between 17.8 and 11.2 gm....
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2558/version/1
Breeding ecology and conservation of Brown booby in Gorgona Island, eastern tropical Pacific Ocean
Provedor de dados: 17
Autores: Andres Ospina-Alvarez.
Breeding ecology and reproductive traits of Brown Booby _Sula leucogaster_ etesiaca in Gorgona Natural National Park,
Colombia, were studied. Adults morphometrics, eggs dimensions, chicks growth and nesting site characteristics, were examined at
three different locations in the park. As with other subspecies, Brown Booby in Gorgona presents inverted sexual dimorphism,
with adult females being lengthier, wider and heavier than adult males. Breeding of S. l. etesiaca results in eggs from the first
deposition bigger in weight and dimensions than eggs from the second or third deposition. Growth of brown boobies chicks fit to a
natural log equation: bodymass(g) = 0.8773 ln(days) + 3.3895. A variety of spawning aggregations was found, and their
relationship with...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5620/version/1
BridgeDb: standardized access to gene, protein and metabolite identifier mapping services
Provedor de dados: 17
Autores: Martijn P. van Iersel; Alexander R. Pico; Thomas Kelder; Jianjiong Gao; Isaac Ho; Kristina Hanspers; Bruce R.
Conklin; Chris T. A. Evelo.
Many interesting problems in bioinformatics require integration of data from various sources. For example when combining
microarray data with a pathway database, or merging co-citation networks with protein-protein interaction networks. Invariably
this leads to an identifier mapping problem, where different datasets are annotated with identifiers that are related, but originate
from different databases.

Solutions for the identifier mapping problem exist, such as
Biomart, Synergizer, Cronos, PICR, HMS and many more. This creates an opportunity for bioinformatics tool developers. Tools
can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This
approach...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5023/version/1
Bridging the gap between social tagging and semantic annotation: E.D. the Entity Describer
Provedor de dados: 17
Autores: Benjamin M. Good; Edward A. Kawas; Mark D. Wilkinson.
Semantic annotation enables the development of efficient computational methods for analyzing and interacting with information,
thus maximizing its value.
With the already substantial and constantly expanding data generation capacity of the life sciences as
well as the concomitant increase in the knowledge distributed in scientific articles, new ways to produce semantic annotations of
this information are crucial. While automated techniques certainly facilitate the process, manual annotation remains the gold
standard in most domains. In this manuscript, we describe a prototype mass-collaborative semantic annotation system that, by
distributing the annotation workload across the broad community of biomedical researchers, may help to produce the volume of...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/945/version/2
Bridging the gap between social tagging and semantic annotation: E.D. the Entity Describer
Provedor de dados: 17
Autores: Benjamin M. Good; Edward A. Kawas; Mark D. Wilkinson.
Semantic annotation enables the development of efficient computational methods for analyzing and interacting with information,
thus maximizing its value.
With the already substantial and constantly expanding data generation capacity of the life sciences as
well as the concomitant increase in the knowledge distributed in scientific articles, new ways to produce semantic annotations of
this information are crucial. While automated techniques certainly facilitate the process, manual annotation remains the gold
standard in most domains. In this manuscript, we describe a prototype mass-collaborative semantic annotation system that, by
distributing the annotation workload across the broad community of biomedical researchers, may help to produce the volume of...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/945/version/1
Bridging the Gaps between Fundamental, Preclinical and Clinical Research: Report from a Global
HIV Vaccine Enterprise Working Group
Provedor de dados: 17
Autores: Lawrence Corey; Brigitte Autran; Louis Picker; the Working Group convened by the Global HIV Vaccine
Enterprise.
The Global HIV Vaccine Enterprise (the Enterprise) convened a two-day workshop on 17-18 September 2009, at the Enterprise
offices in New York; to discuss approaches to bridging the gaps between fundamental,preclinical and clinical HIV vaccine
research. The topic of this Working Group originated from discussions of the Enterprise Science Committee,which proposed that
more effective collaboration between these three areas of HIV vaccine research is needed in order to accelerate the pace of
scientific progress in the field. Because the meeting took place before the release of the RV144 trial results held in Thailand, the
conclusions reached during the meeting were further discussed during consultations at scientific conferences and at a joint
meeting of the...
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4799/version/1
Bridging the Gaps between Fundamental, Preclinical and Clinical Research: Report from a Global
HIV Vaccine Enterprise Working Group
Provedor de dados: 17
Autores: Lawrence Corey; Brigitte Autran; Louis Picker; the Working Group convened by the Global HIV Vaccine
Enterprise.
The Global HIV Vaccine Enterprise (the Enterprise) convened a two-day workshop on 17-18 September 2009, at the Enterprise
offices in New York; to discuss approaches to bridging the gaps between fundamental,preclinical and clinical HIV vaccine
research. The topic of this Working Group originated from discussions of the Enterprise Science Committee,which proposed that
more effective collaboration between these three areas of HIV vaccine research is needed in order to accelerate the pace of
scientific progress in the field. Because the meeting took place before the release of the RV144 trial results held in Thailand, the
conclusions reached during the meeting were further discussed during consultations at scientific conferences and at a joint
meeting of the...
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4799/version/2
BRIF and Variant Databases
Provedor de dados: 17
Autores: Raymond Dalgleish.
Databases of sequence variation in human genes (LSDBs) are an important resource for biology and medicine. Currently, the
measurement of importance is not as objective as it might be and the establishment of impact factors would be of benefit to those
who curate LSDBs. Specific issues relating to such databases are discussed.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5586/version/1
BRIF Workshop Introduction
Provedor de dados: 17
Autores: Anne Cambon-Thomsen.
This presentation aims at introducing the place of BRIF in the landscape of data sharing, the BRIF concept, a presentation of the
working group, the ongoing debates and the workshop objectives.
Tipo: Presentation
Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5658/version/1
BRIF Workshop Minutes
Provedor de dados: 17
Autores: Laurence Mabile.
This document is a detailed summary of the presentations and discussions from the BRIF (Bioresource Impact Factor) workshop,
held in Toulouse on 17-18 january 2011.


Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5879/version/1
BRIF workshop working group.
Provedor de dados: 17
Autores: Laurence Mabile.
Number of attendees, geographical origin of the group, skills and areas represented, tools developed to help the BRIF progress.
Tipo: Presentation
Palavras-chave: Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5582/version/1
Bringing Text Miners and Biologists Closer Together
Provedor de dados: 17
Autores: Anália Lourenço; Sónia Carneiro; Rafael Carreira; Miguel Rocha; Isabel Rocha;
Eugénio C. Ferreira.
The boosting of Biomedical Text Mining (BioTM) research in the last few years has led the way for finally bridging out the gap
between text miners and biologists. Beyond the development of enhanced entity recognisers and the construction of relationship
extraction systems, now, more than ever, it is the time for applying available tools to real-world scenarios. Moreover, it is crucial
to develop end-user tools that can assist biologists in their research activities. Such tools should be able to emulate biologist
conventional curation, recurring to the same knowledge bases and making the same assumptions that biologists usually do,
whereas delivering automated capabilities. The search and selection of PubMed articles, the construction of dictionaries from...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3188/version/1
Broadening Pfam Protein Sequence Annotations
Provedor de dados: 17
Autores: Jaina Mistry; Penny Cogghill; Sean Eddy; Rob Finn; John Tate; Alex Bateman.
Pfam is a database of conserved protein families or domains commonly used for genome annotation and sequence classification. It
comprises two parts: (1) Pfam-A families, which are fully annotated and consist of a representative seed alignment, HMMs, and a
full alignment comprising all sequences that score above the curated threshold; (2) Pfam-B families, which are automatically
generated clusters of domains not matched by Pfam-A but that often indicate conserved sequence regions. Pfam release 23.0
predicts at least one Pfam-A domain on 74% of the sequences in UniProtKB, and predicts either a Pfam-A or Pfam-B domain on
93% of the sequences in UniProtKB.

With the ever increasing rate of deposition of
new proteins of all...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3194/version/1
Building and Using Geospatial Ontology in the BioCaster Surveillance System
Provedor de dados: 17
Autores: Son Doan; Quoc-Hung Ngo; Ai Kawazoe; Nigel Collier.
This abstract presents an approach to building a geospatial ontology from Wikipedia and using it in BioCaster, a system for
detecting and tracking infectious disease outbreaks from online news. Motivated by the need to interpret the geospatial dynamics
of events we built a database containing the names of countries and major cities from Wikipedia. We started by automatically
extracting country and dependent territory names and sub-country (subdivision and dependent area) names in the form of ISO
3166-1 and ISO 3166-2, respectively. Then, we re-created the part-whole relation between countries and sub-countries by
verifying links from countries to their sub-countries. Verification was done by manual checking. The building process is
semi-automatically...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2110/version/1
Building Block and Building Rule: Dual Descriptor Method for Biological Sequence Analysis
Provedor de dados: 17
Autores: Bin-Guang Ma.
The emergence of “Systems Biology” in recent years highlights the systematic viewpoint of
bio-system modeling. Building on such a background, Dual Descriptor Method, a generic methodology for biological sequence
analysis is proposed. From a systematic perspective, Dual Descriptor is defined as a two element set of Composition Weight Map
and Position Weight Function which aim at reflecting the composition and permutation information of a sequence. An alternate
training algorithm is provided to get an optimum description of the building patterns of the sequences. In this paper, dual
descriptor method has been applied to the analysis of two typical problems of molecular biology: gene identification and the
prediction of protein function....
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2223/version/1
Building conceptual spaces for exploring and linking biomedical resources
Provedor de dados: 17
Autores: Rafael Berlanga; Voctoria Nebot; Ernesto Jimenez-Ruiz.
The establishment of links between data (e.g., patient records) and Web resources (e.g., literature) and the proper visualization of
such discovered knowledge is still a challenge in most Life Science domains (e.g., biomedicine). In this paper we present our
contribution to the community in the form of an infrastructure to annotate information resources, to discover relationships among
them, and to represent and visualize the new discovered knowledge. Furthermore, we have also implemented a Web-based
prototype tool which integrates the proposed infrastructure.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5381/version/1
Bumblebees gain fitness through learning
Provedor de dados: 17
Autores: Nigel E. Raine; Lars Chittka.
Despite the widespread assumption that the learning abilities of animals are adapted to the particular environments in which they
operate, the quantitative effects of learning performance on fitness remain virtually unknown. Here we evaluate the learning
performance of bumblebees (_Bombus terrestris_) from multiple colonies in an ecologically relevant associative learning task
under laboratory conditions, before testing the foraging performance of the same colonies under the field conditions. We
demonstrate that variation in learning speed among bumblebee colonies is directly correlated with foraging performance, a robust
fitness measure, under natural conditions. Colonies vary in learning speed by a factor of nearly 5, with the slowest learning
colonies...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/1298/version/1
Bumblebees under the midnight sun - Monitoring circadian rhythms of bumblebees under continuous
daylight, using radio frequency identification (RFID)
Provedor de dados: 17
Autores: Ralph J. Stelzer; Lars Chittka.
Circadian rhythms enable organisms to anticipate and to prepare for predictable changes in their environment. Most previous
studies on circadian rhythms focused on solitary animals. However, in social insects, the colony as a superorganism has a foraging
rhythm aligned to the patterns of resource availability. Within this colony rhythm, the activity patterns of individuals are
embedded. In temperate regions bumblebee foragers show strong circadian rhythms that adjust their foraging activity to the
changing light conditions in the course of the day. But what about circadian foraging patterns under continuous daylight? One
would assume that the colony as a whole extends its foraging activity over the whole 24 hours of a day under such light conditions
to...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1719/version/1
Bystander B cells rapidly acquire antigen receptors from activated B cells by membrane transfer: a
novel mechanism for enhancing specific antigen presentation
Provedor de dados: 17
Autores: Ben J. C. Quah; Vaughan P. Barlow; Virginia McPhun; Klaus
I. Matthaei; Mark D. Hulett; Christopher
R.
Parish.
The B cell antigen receptor (BCR) efficiently facilitates the capture and processing of a specific antigen for presentation on MHC
class II molecules to antigen specific CD4+ T cells (1). Despite this, the majority of B cells are only thought to play a limited role
in CD4+ T cell activation since BCRs are clonotypically expressed. Here we show, however, that activated B cells can, both in
vitro and in vivo, rapidly donate their BCR to bystander B cells, a process that is mediated by direct membrane transfer between
adjacent B cells and is amplified by the interaction of the BCR with specific antigen. This results in a dramatic expansion in the
number of antigen-binding B cells in vivo, with the transferred BCR endowing recipient B cells with the ability to...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2007
URL: http://precedings.nature.com/documents/1207/version/1
CA2 Pyramidal Layer
Provedor de dados: 17
Autores: Allen Institute for Brain Science; Rachel A. Dalley; Lydia L. Ng; Angela L. Guillozet-Bongaarts.
This report contains a gene expression summary of the CA2 pyramidal cell layer (CA2sp), derived from the Allen Brain Atlas
(ABA) in situ hybridization mouse data set. The structure's location and morphological characteristics in the mouse
brain are described using the Nissl data found in the Allen Reference Atlas. Using an established algorithm, the expression values
of the CA2sp were compared to the values of the macro/parent-structure, in this case the pyramidal layer of
Ammon’s Horn, for the purpose of extracting regionally selective gene expression data. The genes with the highest
ranking selectivity ratios were manually curated and verified. 50 genes were then selected and compiled for expression
characterization. The experimental...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2096/version/1
Calming down the seas: the near collapse of an Atlantic coastal fishery
Provedor de dados: 17
Autores: Pablo Pita; Juan Freire.
For years now the estimates of the consequences of overfishing for marine ecosystems have differed greatly within the scientific
community^1^. The use of commercial catch statistics to estimate tendencies has been much criticised^2^, but alternative
information sources with long time series are rare. Here we employ the historic archive (1953-2007) of the recreational
spearfishery in Galicia (NW Spain), which does not have the problems common to other fishery registers, to estimate long-term
changes in coastal ecosystems. Using generalized additive regression models (GAM) we estimated decreases of around 83% in the
abundances of coastal fish over the last 50 years. In the same period the average body size decreased by 36%. In addition, the
relative catch...
Tipo: Manuscript
Palavras-chave: Ecology; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4529/version/1
Caloric restriction causes symmetric cell division and delays aging in Escherichia coli
Provedor de dados: 17
Autores: Milind G. Watve; Samit Watve; Prajakta Belsare; Uttara Lele; Snehal Bari; Sarika Karande.
Aging is one of the most intriguing processes of biology and despite decades of research, many aspects of aging are poorly
understood. Aging is known to occur in bacteria and yeast that divide with morphological asymmetry. Morphologically
symmetrically dividing bacteria such as _Escherichia coli_ were assumed not to age until they were shown to divide with
functional asymmetry leading to aging and death of some of the cells even in exponentially growing cultures. In asymmetrically
dividing _E. coli_ the newly synthesized components are presumed to occupy one pole so that after division one of the daughter
cells receives newly synthesized components whereas the other retains the older components. Mathematical models predicted that
at the population level,...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/2071/version/1
Calorific values and ash contents of different organs of Masson pine (Pinus massoniana) in southern
China
Provedor de dados: 17
Autores: Wei Sheng Zeng; Shou Zheng Tang; Qian Hui Xiao.
Calorific values of plants are important indices for evaluating and reflecting material cycle and energy conversion in forest
ecosystems. Based on the data of Masson Pine (Pinus massoniana) in southern China, the calorific values (CVs) and ash contents
(ACs) of different plant organs were analyzed systematically using hypothesis test and regression analysis in this paper. The
results show: (i) the CVs and ACs of different plant organs are almost significantly different, and the order by AFCV (ash-free
calorific value) from the largest to the smallest is foliage (23.55 kJ/g), branches (22.25 kJ/g), stem bark (21.71 kJ/g), root (21.52
kJ/g) and stem wood (21.35 kJ/g); and the order by AC is foliage (2.35%), stem bark (1.44%), root (1.42%), branches (1.08%)...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2012
URL: http://precedings.nature.com/documents/6750/version/1
Can ABC be Used for Model Selection?
Provedor de dados: 17
Autores: Xavier Didelot; Rich Everitt; Adam Johansen; Dan Lawson.
Over the past ten years, Approximate Bayesian Computation (ABC) has become hugely popular to estimate the parameters of a
model when the likelihood function cannot be computed in a reasonable amount of time. ABC can in principle be used also to
perform Bayesian model comparison, but this raises the
question of which summary statistic should be used for such
applications. Here we present a general method for constructing a summary statistic that is sufficient for the model choice
problem. We apply this construction to models from the exponential family. Unfortunately, in more complex models, our
construct often results in statistics with too high dimensionality to use in ABC. We therefore discuss the possibility of applying
ABC with non-sufficient...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5955/version/1
Can bacteria adapt to starvation-free environment?
Provedor de dados: 17
Autores: Kei Kitahara.
Bacteria will experience starvation-free environment if infinite nutrition is supplied continuously for a long period. In this study,
an evolutionary experiment was performed for 118 days where bacteria adapted to starvation-free environment and reduced their
doubling time. It is anticipated that this finding will help to select bacterial strains that can grow more rapidly in rich media.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7017/version/1
Can global models reproduce the current increase in Western United States Wildfires and project a
reliable future trend?
Provedor de dados: 17
Autores: Dominique Bachelet; Dave Conklin; Brendan Rogers; Maureen McGlinchy; Jim Lenihan; Ron Neilson; Ray Drapek.
Background/Question/Methods:
Wildfires in the western U.S. are generally thought to have increased since
the 1980s. Many factors have contributed to this increase such as fire suppression, livestock grazing, and urban sprawl. Fires have
also been associated with variations in sea surface temperatures and described by indices such as El Niño Southern
Oscillation (ENSO), the Pacific Decadal Oscillation (PDO), and the Atlantic Multidecadal Oscillation (AMO). Recent analyses
have also shown that we may have entered a new fire regime starting with a climate shift in 1998 and are currently entering years
of combined long-term warm AMO phase with cool ENSO and PDO phases usually associated with increased drought-induced
fires in the...
Tipo: Presentation
Palavras-chave: Ecology; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3618/version/1
Can Hawaiian carnivorous caterpillars attack invasive ants or vice versa?
Provedor de dados: 17
Autores: Shinji Sugiura.
The Hawaiian Islands have allowed insects to evolve unique habits, because the islands are isolated and originally lacked
predators, such as ants and wasps. Ambush carnivorous caterpillars (_Eupithecia_ spp.; Lepidoptera: Geometridae) provide a
remarkable example of a feeding behaviour unique to the Hawaiian Islands. Their prey includes various arthropods species.
_Eupithecia_ larvae even attack predatory arthropods such as parasitoids. However, it is unclear whether _Eupithecia_ can attack
ants. Here, I examined whether _Eupithecia orichloris_ can attack the invasive ant _Pheidole megacephala_ under laboratory
conditions. _Eupithecia orichloris_ could successfully attack the minor worker of _P. megacephala_. However, the major worker
of _P. megacephala_...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5374/version/1
Can one invasion lead to another? Niche space and the future of Southwestern U.S. riparian zones
Provedor de dados: 17
Autores: Lindsay Reynolds; David Cooper.
Background/Question/Methods: Invasive species are increasingly problematic world-wide. Scientists working to understand why
invasive species are successful must first understand the processes of invasion. Invasion facilitation and empty niche exploitation
are key processes that have not been well-studied in species rich ecosystems such as riparian areas. In the southwestern United
States (U.S.) two prominent invaders of riparian habitats are the exotic woody plant species tamarisk (Tamarix ramosissima, T.
chinensis, and their hybrids) and Russian olive (Eleagnus angustifolia). These plants were introduced by humans throughout the
southwest around 1900. Both tamarisk and Russian olive have invaded the ephemeral stream system in Canyon de Chelly
National...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3842/version/1
Can Plant-Made Copper Chaperones Heal Early Alzheimer’s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; Jürgen Horst.
Commercially available medicinal plant extracts such as Ginkgo biloba leaf extract show no consistent pattern of clinical benefit
for people with dementia or cognitive impairment, and have been suggested to be toxic to cells at higher doses. However,
medicinal plants may contain other more efficient bioactive molecules apart from the well-known flavonoids and terpenoids.
Therapeutic recombinant proteins, plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba
leaves, may establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ
systems of younger Alzheimer patients (> 50 years). Medications developed from plant-made copper chaperone
proteins may delay progression...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/9
Can Plant-Made Copper Chaperones Heal Early Alzheimer’s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; Jürgen Horst.
Commercially available medicinal plant extracts such as Ginkgo biloba leaf extract show no consistent pattern of clinical benefit
for people with dementia or cognitive impairment, and have been suggested to be toxic to cells at higher doses. However,
medicinal plants may contain other more efficient bioactive molecules apart from the well-known flavonoids and terpenoids.
Therapeutic recombinant plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba leaves may
establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ systems of
younger Alzheimer patients (> 50 years). Medications developed from plant-made copper chaperone proteins may
delay progression during early...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/2
Can Plant-Made Copper Chaperones Heal Early Alzheimer’s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; Jürgen Horst.
Commercially available medicinal plant extracts such as Ginkgo biloba leaf extract show no consistent pattern of clinical benefit
for people with dementia or cognitive impairment, and have been suggested to be toxic to cells at higher doses. However,
medicinal plants may contain other more efficient bioactive molecules apart from the well-known flavonoids and terpenoids.
Therapeutic recombinant plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba leaves may
establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ systems of
younger Alzheimer patients (> 50 years). Medications developed from plant-made copper chaperone proteins may
delay progression during early...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/4
Can Plant-Made Copper Chaperones Heal Early Alzheimer’s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; Jürgen Horst.
Commercially available medicinal plant extracts such as Ginkgo biloba leaf extract show no consistent pattern of clinical benefit
for people with dementia or cognitive impairment, and have been suggested to be toxic to cells at higher doses. However,
medicinal plants may contain other more efficient bioactive molecules apart from the well-known flavonoids and terpenoids.
Therapeutic recombinant plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba leaves may
establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ systems of
younger Alzheimer patients (> 50 years). Medications developed from plant-made copper chaperone proteins may
delay progression during early...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/5
Can Plant-Made Copper Chaperones Heal Early Alzheimer’s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; Jürgen Horst.
Therapeutic recombinant plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba leaves may
establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ systems of
younger Alzheimer patients (> 50 years). Medications developed from plant-made copper chaperone proteins may
delay progression during early disease stages or even be a basis for a possible causal treatment of preclinical stages of
Alzheimer’s disease by restoring cellular function of the CCS-SOD-1 mechanism and by preventing formation of
Aβ plaques, a major putative factor involved in Alzheimer’s disease pathogenesis.
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/1
Can Plant-Made Copper Chaperones Heal Early Alzheimer’s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; Jürgen Horst.
Commercially available medicinal plant extracts such as Ginkgo biloba leaf extract show no consistent pattern of clinical benefit
for people with dementia or cognitive impairment, and have been suggested to be toxic to cells at higher doses. However,
medicinal plants may contain other more efficient bioactive molecules apart from the well-known flavonoids and terpenoids.
Therapeutic recombinant proteins, plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba
leaves, may establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ
systems of younger Alzheimer patients (> 50 years). Medications developed from plant-made copper chaperone
proteins may delay progression...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/6
Can Plant-Made Copper Chaperones Heal Early Alzheimer’s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; Jürgen Horst.
Commercially available medicinal plant extracts such as Ginkgo biloba leaf extract show no consistent pattern of clinical benefit
for people with dementia or cognitive impairment, and have been suggested to be toxic to cells at higher doses. However,
medicinal plants may contain other more efficient bioactive molecules apart from the well-known flavonoids and terpenoids.
Therapeutic recombinant plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba leaves may
establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ systems of
younger Alzheimer patients (> 50 years). Medications developed from plant-made copper chaperone proteins may
delay progression during early...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/3
Can Plant-Made Copper Chaperones Heal Early Alzheimer’s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; Jürgen Horst.
Commercially available medicinal plant extracts such as Ginkgo biloba leaf extract show no consistent pattern of clinical benefit
for people with dementia or cognitive impairment, and have been suggested to be toxic to cells at higher doses. However,
medicinal plants may contain other more efficient bioactive molecules apart from the well-known flavonoids and terpenoids.
Therapeutic recombinant proteins, plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba
leaves, may establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ
systems of younger Alzheimer patients (> 50 years). Medications developed from plant-made copper chaperone
proteins may delay progression...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/7
Can Plant-Made Copper Chaperones Heal Early Alzheimer’s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; Jürgen Horst.
Commercially available medicinal plant extracts such as Ginkgo biloba leaf extract show no consistent pattern of clinical benefit
for people with dementia or cognitive impairment, and have been suggested to be toxic to cells at higher doses. However,
medicinal plants may contain other more efficient bioactive molecules apart from the well-known flavonoids and terpenoids.
Therapeutic recombinant proteins, plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba
leaves, may establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ
systems of younger Alzheimer patients (> 50 years). Medications developed from plant-made copper chaperone
proteins may delay progression...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/8
Can the nutrient dynamics of a northern hardwood forest explain variation in its trophic structure?
Provedor de dados: 17
Autores: Erik E. Stange; Matthew P. Ayres.
Background/Question/Methods: A time series of Lepidoptera larvae (caterpillar) abundance and biomass in the northern hardwood
forests of central New Hampshire, USA, shows large interannual fluctuations in aggregated caterpillar biomass (52-fold variation
in mg caterpillars/ 8000 leaves) that were spatially correlated across a regional landscape. Primary production of these mature
forests has not varied over this period, and many hundreds of Lepidoptera species share comparatively few host plants. Therefore,
interannual changes in nutritional quality of even one host plant species may be capable of generating correlated population
dynamics for many species in the Lepidoptera community. We tested the hypothesis that variation in soil nutrient availability...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3859/version/1
Can Vision Exist Without Somatosensation?
Provedor de dados: 17
Autores: Manivannan Muniyandi; Pawan Kumar Suresh.
The interconnection between vision and somatosensation is already well-established and is further supplemented by the
evolutionary link between eyes and photoreceptors, and the functional connection between photosensation and thermoreception.
However, our analysis hypothesizes a possibility that vision is not just linked to somatosensation, but may not exist without
somatosensation. Surprisingly, our photoreceptor itself needs somatosensory proteins for its functioning, and our entire visual
pathway depends on somatosensory cues for its functioning.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3436/version/1
Can we detect changes in high-latitude soil respiration over decadal time scales?
Provedor de dados: 17
Autores: Ben Bond-Lamberty; Allison Thomson.
Soil respiration (RS), the soil surface CO~2~ flux, is the second-largest terrestrial carbon flux, but because of its high variability
and the inaccessibility of the soil medium it remains one of the least well-constrained parts of the terrestrial carbon cycle. If the
carbon stored in high-latitude ecosystems is being mobilized by climate changes (whether by increasing temperature, changing
precipitation, altered disturbance regimes, etc.) we may be able to detect RS changes in the now forty-year record of RS chamber
measurements. We searched the published literature and found 194 RS observations from 1964 to 2008 at high latitudes, and
paired their known measurement locations with a global climate data set spanning the time period. Linear regression was...
Tipo: Presentation
Palavras-chave: Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/4093/version/1
caNanoLab – A Tool To Benefit Biomedical Nanomaterials Research
Provedor de dados: 17
Autores: Michal Lijowski.
The
cancer
Nanotechnology
Laboratory
Web
portal
("http://cananolab.nci.nih.gov/caNanoLab/welcome.do":http://cananolab.nci.nih.gov/caNanoLab/welcome.
do) is designed to promote sharing of nanomedicine data and to provide support for the annotation of nanoparticles with
information about their composition, function, and characterization. The project is a part of NCI cancer Biomedical Informatics
Grid (caBIG®), and includes a collaboration among the NCI Center for Biomedical Informatics and Information
Technology (CBIIT), the NCI Nanotechnology Characterization Laboratory (NCL), and the NCI Alliance for
Nanotechnology.

Currently,
caNanolab
contains
nanomaterial
data
of
765
"public"...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5175/version/1
Cancer and the social induction of aging
Provedor de dados: 17
Autores: Rodrick Wallace; Deborah Wallace.
Age has long been known as the primary population 'risk factor' for cancer. We suggest that the observed
disparities in hormonal cancers by ethnicity, gender, and other indices of social structure and power relationships, imply a
differential aging by psychosocial and environmental exposures, in the context of cross-generational epigenetic heritage. A
relatively simple model of malignancy regulation illuminates the cellular root of induced aging, and explains the decline in cancer
rate with extreme old age via telomere shortening. We find that the multifactorial determinants of the disorder cannot be
effectively addressed by 'small molecule' interventions at the individual level, but must involve
comprehensive prevention...
Tipo: Manuscript
Palavras-chave: Cancer; Immunology; Pharmacology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6146/version/1
Cancer Biology Data Curation at the Mouse Tumor Biology Database (MTB)
Provedor de dados: 17
Autores: Debra M. Krupke; Dale A. Begley; Steven B. Neuhauser; Joel E. Richardson; John P. Sundberg; Carol J. Bult; Janan T.
Eppig.
Many advances in the field of cancer biology have been made using mouse models of human cancer. The Mouse Tumor Biology
(MTB, "http://tumor.informatics.jax.org":http://tumor.informatics.jax.org) database provides web-based
access to data on spontaneous and induced tumors from genetically defined mice (inbred, hybrid, mutant, and genetically
engineered strains of mice). These data include standardized tumor names and classifications, pathology reports and images,
mouse genetics, genomic and cytogenetic changes occurring in the tumor, strain names, tumor frequency and latency, and
literature citations.

Although primary source for the data represented in MTB is
peer-reviewed scientific literature an...
Tipo: Poster
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3245/version/1
Cancer chemopreventive action of α-(-)-bisabolol, a sesquiterpene alcohol involves
inhibition of cathepsin D and ornithine decarboxylase via tramping nitric oxide
Provedor de dados: 17
Autores: Suchita Srivastava; Suaib Luqman.
Terpenoids, traditionally used for cosmetic and medicinal purposes, are currently being explored as cancer chemopreventive as
well as chemotherapeutic agent in clinical trials. α-(-)-bisabolol, a naturally occurring monocyclic sesquiterpene
alcohol is a major component of essential oil of chamomile (Matricaria recutita L., Chamomilla recutita L., Matricaria
chamomilla; Family Asteraceae). As substantiated previously, α-(-)-bisabolol is known to have antimicrobial,
anti-irritant, anti-inflammatory and anti-allergic properties. It also affects cell viability and growth of various human and murine
cell lines by either inducing apoptosis or suppressing Akt activation or down regulating expression of some genes implicated in
carcinogenesis....
Tipo: Poster
Palavras-chave: Cancer; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6902/version/1
Cancer Clinical Trials Optimization and Pharmacogenomics
Provedor de dados: 17
Autores: I. C. Baianu.
A critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view
to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer
trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell
genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is
rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and
computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics & Genomics; Immunology; Molecular Cell Biology;
Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7046/version/1
Cancer invasion associated gene expression signature is present in differentially expressed genes in the
reprogramming of fibroblasts into stem cells
Provedor de dados: 17
Autores: Wei-yi Cheng; Hoon Kim; Jessica Kandel; Dimitris Anastassiou.
Tumors become invasive by penetrating adjacent connective tissue, but the underlying biological mechanisms remain obscure. We
recently identified a precise gene expression signature of fibroblastic origin associated with cancer invasion, the first step of the
metastatic cascade. The signature contains many coordinately overexpressed genes, prominent among which are COL11A1,
THBS2 and INHBA. Here we show that there is a striking similarity between the set of expressed genes in this
metastasis-associated fibroblastic (MAF) signature and the set of genes that are downregulated when fibroblasts are
reprogrammed to induced pluripotent stem cells (iPSCs). Because it is known that fibroblast reprogramming involves a
mesenchymal epithelial transition (MET), the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5924/version/1
Cancer is a side effect of evolution of viruses and bacteria
Provedor de dados: 17
Autores: Valentin Mitin.
Any human organism is home to viruses and bacteria. However, viruses (as well as other intracellular parasites) are interested in
continuous division of the host cells. Unlimited division of the host cells means unlimited expansion of the living space and
possibility for unlimited multiplication of viral particles. For this, human Cell Cycle Regulation System has to be affected in such
a way to induce unlimited division of host cells. The present work describes oncogenome`s model of cancer development,
according to which, in order to stimulate cell division, viruses affect a gene (or several genes) during transduction of a signal for
cell division from growth factor to cyclin/CDK system. At the same time, controlling gene (p53, RB etc.) function and a...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2011
URL: http://precedings.nature.com/documents/6322/version/1
Capsaicin protects neuromuscular junctions from the inhibitory effects of botulinum neurotoxin A
Provedor de dados: 17
Autores: Baskaran Thyagarajan; Carmen Garcia; Joseph Potian; Natalia Krivitskaya; Kormakur Hognason; Joseph McArdle.
Within 24 hrs after injecting botulinum neurotoxin A (BoNT/A) into the hindlimb, mice lost the toe spread reflex and developed
progressive muscle weakness. At the same time, the compound muscle action potential amplitude decreased. Injection of
capsaicin before BoNT/A significantly reduced these affects and protected the muscle twitch tension of the Extensor digitorum
longus (EDL) nerve muscle preparation. Acute in vitro exposure of isolated nerve muscle preparations, as well as Neuro 2a cells,
to capsaicin prevented uptake of Alexa 647 BoNT/A. Motor nerve endings as well as Neuro 2a cells express the capsaicin
receptor, a transient receptor potential channel of the vanilloid family (TRPV1). Capsaicin as well as disruption of clathrin coated
pits (CCPs)...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2717/version/1
Capturing lost research
Provedor de dados: 17
Autores: Rebecca Lawrence.
A very significant proportion of valuable research conducted is lost, either after presentation at a meeting or even at the stage of
the creation of the initial dataset; _F1000 Posters_ and _F1000 Research_ aim to capture this valuable information.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6175/version/1
Capturing Protein Sequence Data: UniProt Knowledgebase (UniProtKB) submissions and Journal
Scanning
Provedor de dados: 17
Autores: Paul Browne; Ruth Eberhardt.
Most sequences in UniprotKB are derived from the translation of nucleotide sequence, but we also add sequences obtained
through direct sequencing of peptides by Edman degradation and tandem mass spectrometry. This allows us to capture protein
sequences for which no nucleotide sequence is available, and can also confirm that a predicted protein exists and elucidate the
post-translational processing it undergoes. Scientists submit protein sequences to UniProtKB via the web-based submission tool
"SPIN":http://www.ebi.ac.uk/swissprot/Submissions/spin. Curators use a range of sequence analysis tools
to check the submission and frequently discuss the sequence and supporting evidence with the submitter. Submitted entries can be
kept confidential...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3120/version/1
Carbon Dioxide Splitting: A Summary of the Peer-Reviewed Scientific Literature
Provedor de dados: 17
Autores: Sierra Rayne.
Increasing concentrations of carbon dioxide (CO2) in the atmosphere have stimulated significant global research and development
efforts regarding the reduction in CO2 emissions from all point and non-point sources. In addition to technologies that do not use
carbon feedstocks or which capture and "permanently" store CO2 (i.e., sequestration), there is considerable
worldwide interest among the academic, industrial, and government communities regarding methods for dissociating waste stream
carbon dioxide molecules into their constituent carbon and oxygen ("CO2 splitting") atoms as a final
"end-of-pipe" treatment option. The splitting of carbon dioxide has also been actively discussed and
researched in the...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1741/version/1
Carbon Finance Schemes - Incentives for Forest and Agroforestry Systems
Provedor de dados: 17
Autores: Christina Seeberg-Elverfeldt; Stefan Schwarze; Manfred Zeller.
Deforestation contributes a quarter of all anthropogenic greenhouse gas emissions. On the island of Sulawesi in the vicinity of the
Lore Lindu National Park, smallholders contribute to deforestation processes with their agricultural practices, specifically with
cocoa plantations. This study assesses the impact of carbon sequestration payments for forest management systems on the
prevailing land use systems. Additionally, the level of incentives which induces farmers to adopt sustainable agroforestry practices
is determined. We show that low carbon credit prices have a small impact on household income. However, with rising prices, the
poorest households can realise an increase of 18 percent. The majority of the households have an incentive to adopt the more...
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2504/version/1
Carbon Storage: Integrating Experiments & Modelling to Quantify Trapping Capacity
& Efficiency in the Subsurface
Provedor de dados: 17
Autores: Christopher H. Pentland; Saleh Al-Mansoori; Stefan Iglauer; Ran Qi; Branko Bijeljic; Tara LaForce; Martin J. Blunt.
This is a fundamental study of trapping of non-wetting fluids in porous media. When injecting CO~2~ into an aquifer for carbon
storage, the non-wetting phase (CO~2~) is trapped due to capillary forces. This process is investigated in the laboratory for
analogue fluids. 

We then design an injection strategy to maximise CO~2~ storage
capacity and efficiency on the field scale - incorporating experimental and pore scale modelling results. A streamline based
simulator is modified for this purpose.
Tipo: Poster
Palavras-chave: Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2626/version/1
Carbon-driven Chemical Interactions between Alumina and Iron: A possible reaction pathway in
Earth's interior
Provedor de dados: 17
Autores: Rita Khanna; Mohammad Ikram-ul Haq; Veena Sahajwalla.
Seismological and geochemical observations have revealed a complex structure for the earth's core-mantle boundary
(CMB) region, with lateral and chemical heterogeneities. The presence of higher than expected concentrations of siderophile
elements (Ni, Co, Pt etc) in the earth's mantle, iron enrichment of the lower mantle relative to the upper mantle, and a
possible carbon flux from the core suggest the possibility of continual long-term exchange of materials between the core and the
mantle. The chemical interactions of molten iron with complex mantle oxides and diffusion have been postulated as key
mechanisms. A number of studies have been carried out on the reduction reactions taking into account the extreme conditions of...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2336/version/1
Cardiovascular Gene Ontology Annotation Initiative
Provedor de dados: 17
Autores: Varsha K. Khodiyar; Daniel G. Barrell; Peter Scambler; Mike Hubank; Rolf Apweiler; Philippa J. Talmud; Ruth C.
Lovering.
Gene Ontology (GO) provides a controlled vocabulary, which is used by several groups around the world to provide functional
annotation
to
proteins
across
a
wide
range
of
species
("www.geneontology.org":http://www.geneontology.org). The BHF-UCL team is funded by the British
Heath Foundation to supply GO annotation specifically for human proteins involved in cardiovascular (CV) processes. This is
the first time that a physiological process-centered approach has been used for human protein GO annotation. Experienced GO
curators from the BHF-UCL team work alongside the bench scientists from the CV genetics group at University College London.
By working in a CV dedicated environment the GO curators are able to build up their expertise in...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3135/version/1
CARE1, a TY3-gypsy long terminal repeat retrotransposon in the food legume chickpea (Cicer
arietinum L)
Provedor de dados: 17
Autores: Manoj D. R. Rajput; Kailash C. Upadhyaya.
We report a novel Ty3-gypsy long terminal repeat retrotransposon CARE1 (_Cicer arietinum_ retro-element 1) in chickpea. This
5920-bp AT-rich (63%) element carries 723-bp 5' and 897-bp 3' LTRs respectively flanking an internal
region of 4300-bp. The LTRs of CARE1 show 93.9% nucleotide identity to each other and have 4-bp (ACTA) terminal inverted
repeats. A 17-bp potential tRNAmet primer binding site downstream to 5' LTR and a 13-bp polypurine tract upstream
to 3' LTR have been identified. The order of domains (Gag-proteinase-reverse transcriptase-RNaseH-integrase) in the
deduced amino acid sequence and phylogenetic tree constructed using reverse transcriptase sequences places CARE1 in the gypsy
group of retrotransposons....
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/819/version/1
Carrier cell-mediated cell lysis of squamous cell carcinoma by squamous cell carcinoma antigen 1
promoter-driven oncolytic adenovirus
Provedor de dados: 17
Autores: Katsuyuki Hamada; Ting Zhang; Junzo Desaki; Koh-ichi Nakashiro; Hiroshi Ito; Kenzaburo Tani; Yoshiyuki Koyama;
Hiroyuki Hamakawa.
The squamous cell carcinoma antigen (SCCA) serves as a serological marker for squamous cell carcinomas. Molecular cloning of
the SCCA genomic region has revealed the presence of two tandemly arrayed genes, SCCA1 and SCCA2. We examined the
promoter activity of the 5'-flanking proximal region of the SCCA1 gene. Deletion analysis of SCCA1 promoter
identified a 175-bp core promoter region and an enhancer region at -525 to -475 bp upstream of the transcription start site. The
transcriptional activity of the SCCA1 promoter was up-regulated in squamous cell carcinoma cells, compared with normal
keratinocyte, normal non-keratinocyte and adenocarcinoma cells. Five tandem repeats of enhancer increased SCCA1 promoter
activity by 4-fold. Oncolytic adenovirus...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3213/version/1
Cartographic scale effect on channel slopes and stream power calculations
Provedor de dados: 17
Autores: Adalto Gonçalves Lima.
The channel slope is important in determining the stream power. In some research situations the slope is measured by
topographical maps that, depending on the scale, can provide differentiated values. The objective of the research here reported
was to delineate the implications of the inter-scales differences of channel slopes on the stream power calculation. Slopes of a
small river, with a mixed bedrock–alluvial bed, located in a basaltic plateau in south Brazil, were examined. The
measured slopes were compared at 1:50,000 and 1:10,000 scales. In the field, the bankfull geometry was surveyed in ten cross
sections, for discharge calculation. The slopes measured by maps were used to determine the discharge, using the
Gauckler–Manning...
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/1359/version/1
CASIMIR & ENFIN
Provedor de dados: 17
Autores: John Hancock.
I review the development of draft database registries in the CASIMIR and ENFIN projects and the development of the CASIMIR
Database Description Framework.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6158/version/1
Category of Metabolic-Replication Systems in Biology and Medicine
Provedor de dados: 17
Autores: I. C. Baianu.
Metabolic-repair models, or (M,R)-systems were introduced in Relational Biology by Robert Rosen. Subsequently, Rosen
represented such (M,R)-systems (or simply MRs)in terms of categories of sets, deliberately selected without any structure other
than the discrete topology of sets. Theoreticians of life's origins postulated that Life on Earth has begun with the
simplest possible organism, called the primordial. Mathematicians interested in biology attempted to answer this important
question of the minimal living organism by defining the functional relations that would have made life possible in such a minimal
system- a grandad and grandma of all living organisms on Earth.
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Neuroscience; Bioinformatics; Earth & Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7045/version/1
Cationic State Distributions over Chlorophyll Pairs in Photosystem I and II
Provedor de dados: 17
Autores: Keisuke Saito; Hiroshi Ishikita.
Photosystem I (PSI) and II (PSII) possess chlorophyll pairs P~A~/P~B~ and P~D1~/P~D2~, respectively. These chlorophylls are
the primary electron donors in the light-induced electron transfer. After the electron transfer, the radical cation remains on these
chlorophyll pairs, forming [P~A~/P~B~]^·+^ and [P~D1~/P~D2~]^·+^. The positive charge distributions
over the two chlorophylls were reported to be 10/90-50/50 for P~A~^·+^/P~B~^·+^ [1,2] and 70/30-80/20
for P~D1~^·+^/P~D2~^·+^ [3,4]. To clarify the origin of the distributions, we calculated ratios of
P~A~^·+^/P~B~^·+^
and
P~D1~^·+^/P~D2~^·+^
with
a
quantum
mechanical/molecular mechanical (QM/MM) approach and the...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6486/version/1
Cattle Egrets and dry fish business in coastal areas
Provedor de dados: 17
Autores: Kotta Seedikkoya; PA Azeez.
Cattle Egret is one of the common wetland birds in India known for its efficiency to make use of human interfered habitats. The
present study is an attempt to document maggots of houseflies and calliphorids in the coastal sun drying fish yards and the role of
the species in containing the vector species. The number of flies and maggots were found related with the visit of cattle egrets,
demonstrating the importance of the species in controlling the vectors.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/2752/version/2
Cattle Egrets and dry fish business in coastal areas
Provedor de dados: 17
Autores: Kotta Seedikkoya; PA Azeezpa.
Cattle Egret is one of the common wetland birds in India known for its efficiency to make use of human interfered habitats. The
present study is an attempt to document maggots of houseflies and calliphorids in the coastal sun drying fish yards and the role of
the species in containing the vector species. The number of flies and maggots were found related with the visit of cattle egrets,
demonstrating the importance of the species in controlling the vectors.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/2752/version/1
Causal Stability Ranking
Provedor de dados: 17
Autores: Daniel J. Stekhoven; Lars Hennig; Gardar Sveinbjörnsson; Izabel Moraes; Marloes H. Maathuis; Peter
Bühlmann.
Genotypic causes of a phenotypic trait are typically determined via randomized controlled intervention experiments. Such
experiments are often prohibitive with respect to durations and costs. We therefore consider inferring stable rankings of genes,
according to their causal effects on a phenotype, from observational data only. Our method allows for efficient design and
prioritization of future experiments, and due to its generality it is useable for a broad spectrum of applications.
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/6716/version/1
Caveat Emptor: The Meaning of Perception and Integration in Speech Perception
Provedor de dados: 17
Autores: Dominic Massaro.
A recent letter^1^ claimed integration of auditory and tactile information in speech perception. Although I have been an advocate
of multisensory integration, neither perception nor integration was sufficiently formalized, operationalized, and tested to support
this claim.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/4016/version/1
_Cavernularia malabarica_ Fowler, 1894 from the Bay coast of Visakhapatnam, Andhra Pradesh
Provedor de dados: 17
Autores: Veena Shettigar; Kaladharan P.
Many initiatives have come up to investigate the fauna around India. Due to accidental sighting and dislocation caused due to
fishing and forming a part of the trash brought ashore is how the organisms are located. During regular sampling carried out from
Mangamaripeta fish landing centre of Visakhapatnam, delicate shallow-water sea pens were collected and investigated. No
previous records are available pertaining to the presence of these animals from this area and the species have not been identified
from these waters. This report identifies and describes the species as _Cavernularia malabarica_ Fowler, 1894 for the first time
from these waters.
Tipo: Manuscript
Palavras-chave: Ecology; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4952/version/1
CD14 Modulates PI3K/AKT/p38-MAPK Licensing of Negative Regulators of TLR Signaling to
Restrain Chronic Inflammation
Provedor de dados: 17
Autores: Bikash Sahay; Rebeca L. Patsey; Nicole Whatley; Sasmita Nayak; Christian H. Eggers; Justin D. Radolf; Timothy J.
Sellati.
Current thinking emphasizes the primacy of CD14 in facilitating TLR recognition of microbes to initiate proinflammatory
signaling events and the importance of p38-MAPK in augmenting such responses. Herein, this paradigm is challenged by
demonstrating that recognition of _Borrelia burgdorferi_ not only triggers an inflammatory response in the absence of CD14, but
one that is uncontrolled as a consequence of impaired PI3K/AKT/p38-MAPK signaling and negative regulation of TLR2. CD14
deficiency results in hyperphosphorylation of AKT and reduced activation of p38. Such aberrant signaling leads to decreased
negative regulation by SOCS1, SOCS3, and CIS thereby engendering a more severe and persistent inflammatory response to _B.
burgdorferi_. Perturbation of this...
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/2005/version/1
CDAO-Store: A New Vision in Data Integration
Provedor de dados: 17
Autores: Brandon Chisham; Trung Le; Enrico Pontelli; Tran Son; Ben Wright.
The Comparative Data Analysis Ontology (CDAO) 1 is an ontology developed, as part of the EvoInfo2 and EvoIO3 groups
supported by NESCent4, to provide semantics to the descriptions of data and transformations commonly found in the domain of
phylogenetic inference. The core concepts of the ontology enables the description of phylogenetic 
trees and
associated character data matrices. 

Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4585/version/2
CDAO-Store: A New Vision in Data Integration
Provedor de dados: 17
Autores: Brandon Chisham; Trung Le; Enrico Pontelli; Tran Son; Ben Wright.
The Comparative Data Analysis Ontology (CDAO) is an ontology developed, as part of the EvoInfo and EvoIO groups
supported by NESCent, to provide semantics to the descriptions of data and transformations commonly found in the domain of
phylogenetic inference. The core concepts of the ontology enables the description of phylogenetic trees and associated character
data matrices. 

CDAO-store is a repository providing a rich set of API’s
for querying and visualizing phyloinformatics data. It is a triple-store encoding data as RDF triples constructed according to the
CDAO concept vocabulary. CDAO-store provides three classes of services: a service for importing data in CDAO format, a
PhyloWS interface supporting an...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4586/version/1
CDAO-Store: A New Vision in Data Integration
Provedor de dados: 17
Autores: Brandon Chisham; Trung Le; Enrico Pontelli; Tran Son; Ben Wright.
The Comparative Data Analysis Ontology (CDAO) 1 is an ontology developed, as part of the EvoInfo2 and EvoIO3 groups
supported by NESCent4, to provide semantics to the descriptions of data and transformations commonly found in the domain of
phylogenetic inference. The core concepts of the ontology enables the description of phylogenetic 
trees and
associated character data matrices. 

Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4585/version/1
CDK2 and CKI targeting can significantly lower the cellular senescence bar - reveals a mathematical
model of G1/S checkpoint pathway
Provedor de dados: 17
Autores: Hong Ling; Sandhya Samarasinghe; Don Kulasiri.
Cellular senescence, a mechanism employed by cells for thwarting proliferation, has shown to play an important role in protecting
cells against cancer development in recent experimental observations, indicating that a deeper understanding of the cellular
senescence pathway can help exploit its capacity for more effective cancer treatment. Furthermore, some experimental evidence
points out that inhibition of CDK2 or Skp2 can be the critical trigger for cellular senescence. However, no mathematical model
has been developed to highlight cellular senescence until now. In this study, we first implement a mathematical model of G1/S
transition involving the DNA-damage pathway to highlight cellular senescence by lowering the critical trigger- CDK2. For this,
we...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4950/version/1
Cell Adhesion: A surprising cohesive force
Provedor de dados: 17
Autores: Hugues H. Vasseur.
When an experimentalist or a biological mechanism applies an external force onto a cell chemically sticking to its substrate, a
reacting "suction" force, due to the slow penetration of the surrounding fluid between the cell and the
substrate, opposes to the dissociation. This force can overcome other known adhesive forces when the process is sufficiently
violent (typically 10^5^ pN). Its maximal contribution to the total adhesive energy of the cell can then be estimated to 2 10^-3^
J/m2. The physical origin of this effect is quite simple, and it may be compared with that leaning a
"suction-cup" against a bathroom wall. We address the consequences of this effect on (i) the separation
energy, (ii) the motion of the fluid...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1416/version/1
Cell Proteomic Footprint
Provedor de dados: 17
Autores: Petr Lokhov; Elena Balashova; Maxim Dashtiev.
The authentication of mammalian cell cultures and their subpopulations are of tremendous demand in biotechnology and cell
therapy. However, current techniques are either not efficient or can be very complex and expensive. Here we report a simple and
straightforward approach for authentication of biological cells and their subpopulations with high speed, high throughput, low
sample
cost,
and
high
sensitivity.
We
discovered
that
cell
cultures
treated
with
protease
at
soft,
“non-killing” conditions release fragments of cell surface proteins, which composition is a strong
characteristic of the cells. Mass spectrometric analysis of the released fragments allows a direct comparison of the produced mass
spectrum with the mass spectrum of...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2091/version/1
Cell-free Embryonic Stem Cell Extract-mediated Derivation of Multi-potent Stem Cells from NIH3T3
Fibroblasts for Functional and Anatomical Ischemic Tissue Repair
Provedor de dados: 17
Autores: Johnson Rajasingh; Hiromichi Hamada; Evelyn Bord; Tina Thorne; Ilona Goukassian; Erin Lambers; Prasanna
Krishnamurthy; Gangjian Qin; Karen Schlauch; Kenneth M. Rosen; Deepali Ahluwalia; Yan Zhu; Douglas W. Losordo; Raj
Kishore.
The oocyte-independent generation of multipotent stem cells is one of the goals in regenerative medicine. We report that upon
exposure to mouse ES cell (ESC) extracts, reversibly permeabilized NIH3T3 cells undergo de-differentiation followed by
stimulus-induced re-differentiation into multiple lineage cell types. Genome-wide expression profiling revealed significant
differences between NIH3T3 and ESC-extract treated NIH3T3 cells including re-activation of ESC specific transcripts.
Epigenetically, ESC extracts induced CpG de-methylation of Oct4 promoter, hyper-acetylation of histones 3 and 4 and decreased
lysine 9 (K-9) dimethylation of histone 3. In mouse models of surgically-induced hind limb ischemia (HLI) or acute myocardial
infarction (AMI)...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2007
URL: http://precedings.nature.com/documents/1208/version/1
CellML 1.1 modularity
Provedor de dados: 17
Autores: Poul Nielsen.
CellML 1.1 is an open XML-based language designed to store and exchange computer-based mathematical models. It has a
simple facility to import existing models in order to create new models. The import facility encourages the development of
hierarchical models and model reuse through the creation of well-curated model components in public model repositories. This
presentation describes some of the features of CellML 1.1 and best practices for taking advantage of these features.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5005/version/1
CellML + [CMISS | OpenCMISS]
Provedor de dados: 17
Autores: David P. Nickerson.
A brief introduction and comparison to the usage of CellML models in CMISS and OpenCMISS.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5896/version/1
CellML: current status and future directions
Provedor de dados: 17
Autores: David Nickerson.
An overview of the current status of the CellML project and some ideas on where things are heading.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6417/version/1
Cellular delivery of antibodies: effective targeted subcellular imaging and new therapeutic tool
Provedor de dados: 17
Autores: Marzia Massignani; Irene Canton; Nisa Patikarnmonthon; Nicholas J. Warren; Steven P. Armes; Andrew L. Lewis;
Giuseppe Battaglia.
It is already more than a century since the pioneering work of the Nobel Laureate Ehrlich gave birth to the side chain theory1,
which helped to define antibodies and their ability to target specific biological sites. However, the use of antibodies is still
restricted to the extracellular space due to the lack of a suitable delivery vehicle for the efficient transport of antibodies into live
cells without inducing toxicity. In this work, we report the efficient encapsulation and delivery of antibodies into live cells with no
significant loss of cell viability or any deleterious affect on the cell metabolic activity. This delivery system is based on
poly(2-(methacryloyloxy)ethyl phosphorylcholine)-block-(2-(diisopropylamino)ethyl methacrylate), (PMPC-PDPA),...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Immunology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4427/version/1
Cerebellar Cortex, Purkinje Cell Layer
Provedor de dados: 17
Autores: Allen Institute for Brain Science; Emily M. Wright; Lydia L. Ng; Angela L. Guillozet-Bongaarts.
This report contains a summary of expression patterns for genes that are enriched in the Purkinje cell layer (CBXpu) of the
cerebellum. All data is derived from the Allen Brain Atlas (ABA) in situ hybridization mouse project. The structure's
location and morphological characteristics in the mouse brain are described using the Nissl data found in the Allen Reference
Atlas. Using an established algorithm, the expression values of the CBXpu were compared to the values of its larger parent
structure, in this case the cerebellar cortex, for the purpose of extracting regionally selective gene expression data. The highest
ranking genes were manually curated and verified. 50 genes were then selected and compiled for expression analysis. The
experimental...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2200/version/1
Cerebral and Spinal Modulation of Pain by Emotions
Provedor de dados: 17
Autores: Mathieu Roy; Mathieu Piche; Jen-I Chen; Isabelle Peretz; Pierre Rainville.
Emotions have powerful effects on pain perception. However, the brain mechanisms underlying these effects remain largely
unknown. In this study, we combined functional cerebral imaging with psychophysiological methods to explore the neural
mechanisms implicated in the emotional modulation of spinal nociceptive responses (RIII-reflex) and pain perception in healthy
participants. Emotions induced by pleasant or unpleasant pictures modulated the responses to painful electrical stimulations in the
right insula, paracentral lobule, parahippocampal gyrii, thalamus and amygdala. Right insula activation covaried with the
modulation of pain perception, consistent with a role of this structure in the integration of pain signals with the ongoing emotion.
In contrast,...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2885/version/1
Cerebral malaria admissions in Papua New Guinea may show inter-annual cyclicity: An example of
about a 1.5-year cycle for malaria incidence in Burundi
Provedor de dados: 17
Autores: Borislav D. Dimitrov; Penka A. Atanassova.
Best available descriptions of malaria incidence and mortality dynamics are important to better plan and evaluate the
implementation of programs to monitor (e.g., remote sensing) and control the disease, especially in endemic zones. This was
stressed recently by Cibulskis et al (2007) in the view of completeness of monthly reporting for cerebral malaria admissions in
Papua New Guinea (latitude 6 degree S, 1987-1996). Notably, regardless of the rate of its completeness, the temporal dynamics of
admissions was preserved over the years, however, neither raw data nor results on further analyses about eventual inter-annual
cyclic components (periods T>1 year) were provided despite obvious graphical patterns for such a specific time
structure...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/1769/version/1
Cervical Cancer-Associated Human Papillomavirus 16 E7 Oncoprotein Inhibits Induction of
Anti-Cancer Immunity by a CD4+ T Cell Dependent Mechanism
Provedor de dados: 17
Autores: Marion E. G. Brunck; Xiao Song Liu; Jie Zhong; Germain J. Fernando.
Attempts to develop therapeutic vaccines against cervical cancer have been proven difficult. One of the major causes of the failure
is due to the use of the wrong mouse models based on transplantable tumours in testing the efficacy of vaccines. Now that a
transgenic epithelial mouse model has been developed to closely mimic cervical cancer, the mechanisms needed to eliminate this
type of cancer could be studied. The E7 oncoprotein of Human Papillomavirus (HPV) is the most expressed HPV protein in
cervical cancers and its continuous production is essential to maintain the cancerous state and therefore the obvious target in the
development of vaccines. Skin grafts expressing the HPV 16 E7 protein (E7 autografts) are not spontaneously rejected from an
MHC...
Tipo: Manuscript
Palavras-chave: Cancer; Immunology.
Ano: 2009
URL: http://precedings.nature.com/documents/3405/version/1
CFP and YFP photostabilities are differentially affected by common mounting fluids
Provedor de dados: 17
Autores: Johannes A. Schmid.
The use of spectrally distinct variants of green fluorescent protein (GFP) such as cyan or yellow mutants (CFP and YFP,
respectively) is very common in all different fields of life sciences, e.g. for marking and tracing of specific proteins or cells or to
determine protein interactions. In the later case, the quantum physical phenomenon of fluorescence resonance energy transfer
(FRET) is visualized by specific microscopy techniques. When we applied a commonly used FRET microscopy technique - the
increase in CFP-fluorescence after bleaching of YFP, we noticed that it worked well for live cells, but that most of the
FRET-signal was lost in fixed cells mounted in commercial microscopy mounting fluids. Subsequently, we could show that CFP
bleached much faster...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4517/version/1
Challenges in modeling disturbances' effects on terrestrial carbon cycling
Provedor de dados: 17
Autores: Ben Bond-Lamberty.
Ecosystem disturbance presents modelers with a number of problems, of which the disturbance event itself may be the least
problematic. First, most ecosystem models depend on reaching a steady state before the main computation begins; this
already-tricky initial value problem is complicated by disturbances during spinup, which may prevent steady state from being
reached. Second, vegetation dynamics becomes more important in disturbed ecosystems, with nutrient cycling, albedo, and
evapotranspiration all changing markedly. Succession is handled crudely (or not at all) by many large-scale models, however.
Third, disturbances tend to export the carbon--and its climate forcing potential--from the system under study, complicating and
expanding the scope of the...
Tipo: Presentation
Palavras-chave: Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/4095/version/1
Challenges in Whole-Genome Annotation of Pyrosequenced Fungal Genomes
Provedor de dados: 17
Autores: Alan Kuo; Igor Grigoriev.
Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to
the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the
new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which
complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of
ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454 sequenced fungal genome
that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) _Aspergillus carbonarius_
belongs to the _Aspergillus_...
Tipo: Presentation
Palavras-chave: Genetics & Genomics; Bioinformatics; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3191/version/1
Challenging or Reinforcing Social Prejudice?
Provedor de dados: 17
Autores: Helen Longino.
Behavior genetics holds out the hope of unbiased study of the biological bases of human behavior. Without more rigorous
reflection on behavioral concepts, however, behavior genetics will succeed only in reinforcing social biases. This point is
illustrated
with
reference
to
studies
on
aggression,
sexual
orientation,
and
gender
differences.

To watch Professor Longino's presentation, please see the
"Google
Video
posting":http://video.google.com/videoplay?docid=-3926548921438712173&hl=en.
Tipo: Presentation
Palavras-chave: Genetics & Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2567/version/1
Changes in Antioxidant Enzymes Activity and Oxidative Damage in Four Argania spinosa Ecotypes
Under Water Stress Conditions
Provedor de dados: 17
Autores: Abdelghani Chakhchar; Abderrahim Ferradous; Mouna
Lamaoui; Said Wahbi; Cherkaoui El Modafar.
_Argania spinosa_ L. Skell, a tree endemic of Morocco, grows in semiarid and arid areas. Biochemical response to drought in four
ecotypes of the _A. spinosa_ was compared. Choice of ecotypes was based on evident differences in geographical features in
south-west Morocco: two coastal ecotypes (Essaouira and Agadir) and two paralittorale ecotypes (Aoulouz and Lakhssas). Lipid
peroxidation (malonyldialdehyde (MDA)), content of endogenous hydrogen peroxide (H2O2) and antioxidant enzyme system
(Catalase (CAT), Ascorbate peroxidase (APX), Total peroxidase (POD) and Polyphenoloxidase (PPO) were measured in control
(100% relative humidity (RH) at field capacity (FC)) and water-stressed plants (50 and 25% RH at FC). For all ecotypes, drought
stress significantly...
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6189/version/1
Changes in Cholesterol Metabolism in Peripheral Cells of Alzheimer Disease Patients and Their
Relatives
Provedor de dados: 17
Autores: Alessandra Pani; Paolo La Colla; Claudia Abete; Claudia Mulas; Marirosa Putzolu; Claudia Norfo; Sergio Laconi; Anna
Borgia; Christina Zaru; Manuela Palmas; Paolo F. Putzu; Alessandra Mocali; Francesco Paoletti; Sandra Dessi.
Background. Previous epidemiological and experimental studies indicated cholesterol as a central player in Alzheimer disease
(AD). Here, we utilized skin fibroblasts and PBMC as possible ex vivo models for the study of dysfunctions of cholesterol
homeostasis which may be related to AD development. 
Methods. We analyzed cholesterol homeostasis
using colorimetric, thin layer chromatography (TLC), and histologic technique in ex vivo cultures of skin fibroblasts and PBMCs
from patients with probable AD and their first-degree relatives. Additionally, healthy age-matched individuals served as controls.

Findings. As compared to controls, skin fibroblasts and PBMCs from AD patients, displayed an evident
alteration of cholesterol...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1246/version/1
Changes in enzyme activities and in the functional diversity of actinomycetes due to long term
agricultural management
Provedor de dados: 17
Autores: Jessica L. M. Gutknecht; Elke Schulz; Venukumar Vemula; Jana Schmidt; Gabi Henning; Jackie Rose; Yvonne
Eckstein; Mika Tarkka.
Long-term agricultural management alters soil organic matter, nutrient status, and potentially the decomposer community. We
measured the abundance and activity of cellulose, chitin, and protease degrading bacteria, and total soil extra-cellular enzyme
activity for cellulose (β-glucosidase), chitinase (N-acetyl-glucosaminidase), xylosidase, and phosphatase activity. By
combining these methods, we could determine how bacterial decomposer abundance and function were altered by long-term
management, and how the bacterial decomposer community relates to overall soil enzyme activity. We also measured microbial
total fungal and bacterial biomass, soil organic carbon pools, and extractable nitrogen for supplementary comparisons. Soil
samples were taken...
Tipo: Poster
Palavras-chave: Ecology; Microbiology; Earth & Environment.
Ano: 2012
URL: http://precedings.nature.com/documents/6792/version/1
Changes in Fitness, physical activity, fatness, and screen time: A longitudinal study in children and
adolescents
Provedor de dados: 17
Autores: Luisa Aires; Lars Bo Andersen; Denisa Mendonça; Clarice Martins; Gustavo Silva; Maria Paula Santos; Jose
Ribeiro; Jorge Mota.
*_Objective:_* To analyze whether changes in Physical Activity Index (PAI), sedentary time (ST; TV and PC use), and Body
Mass Index (BMI) made a significant contribution to longitudinal changes in Physical Fitness (PF) of children and adolescents.
Additionally,
we
analyzed
interaction
between
baseline
fitness
level
and
changes
in
fitness.


*_Methods:_* This is a three years longitudinal study of 345 high school students
aged 11-19 years. Students were invited to perform tests from Fitnessgram battery for strength (curl-ups, push-up), and
Cardiorespiratory fitness (20m-shuttle run). PAI and ST were evaluated using a standard questionnaire. Standardized scores of
physical fitness tests were summed (ZPF). Changes over time,...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3004/version/1
Changes in Scholarly Communication and the Potential Impact on Biocuration
Provedor de dados: 17
Autores: Philip Bourne.
Open access in particular and changes in on-line scholarship have the potential to impact biocuration which often involves
translating information currently read in papers to knowledge that is found in a variety of biological resources. The implication of
these changes in scholarly communication to the biocuration process will be discussed with references to our work and that of
others.

Tipo: Presentation
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3229/version/1
Changes in Simpson’s Diversity Index in Microcosms Impacted with Monosodium
Methane Arsenate
Provedor de dados: 17
Autores: Peter A. Kish; Nelson W. Daniel.
The objective of our studies is to analyze environmental impacts of Monosodium Methane Arsenate, MSMA, on aquatic habitats
using the Aqua-Terra microcosm system. MSMA was applied at environmentally relevant(recommended) doses to microcosms to
determine the change in biodiversity and the bio-concentration of arsenic in the aquatic plants (_Elodea Sp._) used in the
microcosms as an oxygen source. The microcosms are filled with unfiltered pond water and the diversity of each microcosm was
determined before application of the herbicide. After population stabilization, the herbicide is applied to the terrestrial portion of
the microcosm. The herbicide is watered into the microcosm by allowing the herbicide to be filtered by soil into the aquatic
portion of...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3663/version/1
Changes in temperature-moisture covariance could increase soil carbon loss
Provedor de dados: 17
Autores: Asko S. Noormets; Michael Gavazzi; Sara Strickland; Ge Sun; Jiquan Chen; John King; Steve G. McNulty.
Soils store about 1.5x10^16 g of carbon (C), about as much as terrestrial vegetation and atmosphere combined 1. The complex
interplay between factors that regulate C release from soil through respiration is not completely understood, but could potentially
exert strong influence on global radiation balance and climate change2. Respiration exerts strong effect on the spatial
heterogeneity of terrestrial C cycle 3 and its temporal variation remains more poorly understood compared to gross ecosystem
production (GEP) 4. This variation can analytically be attributed to changes in environmental factors, but forecasting individual
deviations remains a challenge 4. Here we propose that deviations of the typical covariance pattern of primary environmental
drivers...
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/290/version/1
Changing the Culture of “Ding”: Education, Legislation and Research on
Concussive Brain Injury in Youth Athletics
Provedor de dados: 17
Autores: Claire D. Overturf; Donald C. Cooper.
The number of emergency department visits concerning sport related TBI in youth increased 57% from 2001 to 2009 and while a
fraction of that increase may be attributed to injuries that were once missed now being identified due to greater general awareness,
the fact remains that there are nearly 200,000 children every year who suffer sport related concussion or other TBI serious enough
to prompt a visit to the ED. 40% of sports related concussions involve children between the ages of 8 and 13, and in this group the
rate of concussion doubled between 1997 and 2007. The risk of concussion is highest in football and there are nearly 67,000
diagnosed concussions in high school football every year. In other sports that males and females play, such as basketball,...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/7076/version/1
Characteristics of oligonucleotide frequencies across genomes: Conservation versus variation, strand
symmetry, and evolutionary implications
Provedor de dados: 17
Autores: Shang-Hong Zhang; Ya-Zhi Huang.
One of the objectives of evolutionary genomics is to reveal the genetic information contained in the primordial genome (called the
primary genetic information in this paper, with the primordial genome defined here as the most primitive nucleic acid genome for
earth’s life) by searching for primitive traits or relics remained in modern genomes. As the shorter a sequence is, the
less probable it would be modified during genome evolution. For that reason, some characteristics of very short nucleotide
sequences would have considerable chances to persist during billions of years of evolution. Consequently, conservation of certain
genomic features of mononucleotides, dinucleotides, and higher-order oligonucleotides across various genomes may exist;...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2146/version/1
Characteristics of Staphylococcus aureus infections to consider in designing an effective vaccine.
Provedor de dados: 17
Autores: Francisco Romero-Pastrana; Pablo Hernández-Jáuregui; Beatriz E. Baca.
_Staphylococcus aureus_ is a very versatile and adaptable microorganism. It can potentially infect virtually any host tissue. Given
the appropriate conditions it can become a life-threatening pathogen, or a commensal colonizer of the nose. Extensive antibiotic
use for infection control facilitated the rise of antibiotic resistance, stressing the need for alternate forms of control. Vaccine
efforts in other pathogens have proved successful, but so far _S. aureus_ candidate vaccines have not been as effective. Here we
review _S. aureus_ factors involved in pathogenesis that could help develop a successful vaccine, like host nasal colonization and
immune evasion factors. An effective multicomponent vaccine could incorporate antigenic fragments from several...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4598/version/1
Characteristics of Uremic Cardiomyopathy with Reversible Systolic Dysfunction
Provedor de dados: 17
Autores: Srilakshmi Adhyapak; Shamanna Iyengar.
Background: There exists a sub group of patients with uremic cardiomyopathy who experience resolution of heart failure
following hemodialysis. It has been hypothesized that these patients are fluid overloaded, and following hemodialysis, show
improvements in cardiac geometry and function. We wanted to study their clinical, biochemical and echocardiographic features to
define any other additional characteristics.

Aim: To define characteristics of
reversible systolic dysfunction.

Methods: We studied 72 patients with chronic kidney
disease on hemodialysis of whom 52 presented with congestive heart failure, over a period of 190 days. We studied their
echocardiographic profile and blood...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3199/version/1
Characterization And Rejuvenation Of Local Ecorace Sukinda In Odhisa State
Provedor de dados: 17
Autores: Alok Sahay; Subrat Satpathy; Shashikant Sharan.
An experiment of outdoor rearing was conducted with the available Sukinda (TV) stock of BSM&TC, Sundargarh
(SG), CTSSS, Lakha (CTS) and CTR&TI, Ranchi. The objective of this activity is to utilize economic wild life,
conserving the associated environment for sustainable rural and tribal development (Raffi and Ramanujam, 2001; Gill and Lal,
2002; Mahapatra, 2009).

The crop performance of SG showed highest cocoon yield
i.e., 83 cocoons / dfl in 1st crop followed by 80 cocoons / dfl in 3rd crop and 42 cocoons / dfl during 2nd crop. Yellow coloured
cocoons dominated (94-96%) the population in all the three crops. The cocoon weight, Shell weight and Silk Ratio were (9.72g,
1.07g&11 %) in 1st...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6210/version/1
Characterization of a pig skeletal muscle microarray to study pork quality: the GenmascqChip 15K
Provedor de dados: 17
Autores: Marie Damon; Frédéric Herault; Annie Vincent; Pascale Le Roy; Pierre Cherel.
Pork quality is highly variable and availability of relevant predictors of fresh meat quality at slaughter is critical to optimize
carcass use and improve its valuation. High throughput gene expression studies have been widely used to describe biological
mechanisms underlying variation of several traits but data are scarce regarding their use as tools for development of biomarkers.
The GENMASCQ (GENomics enabled Marker Assisted Selection and Certification of Quality in Pork products ) research
program was set up to select, using high-throughput gene expression screening, markers of the biological variation mostly
appropriate to describe, and ultimately forecast, the sensory quality of an important meat product, accounting for nearly 40 % of
meat protein...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5730/version/1
Characterization of Fut10 and Fut11, Putative Alpha-1-3/4 Fucosyltransferase Genes Important for
Vertebrate Development
Provedor de dados: 17
Autores: Santosh K. Patnaik.
Two new, putative alpha-1-3/4 fucosyltransferases ([alpha]1-3/4 Fuc-Ts), Fuc-TX and Fuc-TXI, were identified in the vertebrate
genome and transcriptome sequence databases through sequence homology-based queries. These proteins have a significant
sequence similarity to only [alpha]1-3/4 Fuc-Ts, and possess peptide motifs that are evolutionarily conserved among the known
vertebrate [alpha]1-3/4 Fuc-Ts. However, Fuc-TX and Fuc-TXI lack the HH[R/W][D/E] sequence that determines the specificity
for type 1 or 2 substrates among the known vertebrate enzymes, and Fuc-TXI proteins do not possess a transmembrane domain.
The Fut10 and Fut11 genes that encode these proteins are expressed ubiquitously in the adult mouse and in the mouse embryo
throughout development....
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/141/version/1
Characterizing genetic diversity and creating novel gene pools in rice for trait dissection and gene
function discovery
Provedor de dados: 17
Autores: Ramil Mauleon; Kenneth McNally; Hei Leung; Richard Bruskiewich; Ruaraidh Sackville-Hamilton.
Rice diversity is the foundation for rice improvement programs. At IRRI, over 100,000 rice accessions are deposited, and
intelligent use of this diversity can not only help solve current production problems but also create future production opportunities
and tackle climate change challenges. To fully explore and utilize rice diversity, two ingredients are needed: 1 - the genetic
blueprints of diverse rice accessions in use, 2 - plant populations with recombined genotypes allowing expression of phenotypic
variation and discovery of new genes/QTLs for use in breeding programs. Sequencing of the genomes & obtaining
SNP genotypes of many rice accessions is feasible due to decreasing cost of advanced DNA sequencing technologies. Coupled
with the...
Tipo: Presentation
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5114/version/1
Charting the NF-kB pathway interactome map
Provedor de dados: 17
Autores: Paolo Tieri; Alberto Termanini; Elena Bellavista; Stefano Salvioli; Claudio Franceschi.
One of the phenomena observed in human aging is the progressive increase of a systemic inflammatory state, a condition referred
to as “inflammaging”, negatively correlated with longevity. The five components of the Nuclear
Factor kB (NF-kB) family are prominent mediators of inflammation. Several different signaling pathways activated by very
diverse stimuli converge on NF-kB, resulting in a regulatory system characterized by high complexity. It is increasingly
recognized that the number of components that impinges upon phenotypic outcomes of signal transduction pathways may be
higher than those taken into consideration from canonical pathway representations. Scope of this analysis is to provide a wider,
systemic picture of such...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Immunology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5266/version/1
ChEBI – an Open-access Chemistry Resource for the Life Sciences:Facilities
for On-line Submission and Curation
Provedor de dados: 17
Autores: Marcus Ennis; Nico Adams; Adriano Dekker; Paula de Matos; Janna Hastings; Kenneth Haug; Duncan Hull; Zara
Josephs; Gareth Owen; Steve Turner; Christoph Steinbeck.
ChEBI (Chemical Entities of Biological Interest) is a database of ‘small’ molecular entities structured
around a chemical ontology. It contains almost 600,000 entries, of which approximately 20,000 have been manually curated, as
well as entries for groups (parts of molecular entities) and classes of entities. It provides a wide range of information such as
chemical nomenclature, structures and related chemical values, and establishes interrelationships between entities in the ontology,
in terms of both structure and role. ChEBI places a strong focus on quality, with exceptional efforts being applied to upholding
IUPAC nomenclature recommendations and best IUPAC practices when drawing chemical structures....
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5089/version/1
ChEBI, an Open-access Chemistry Resource for the Life Sciences: Facilities for On-line Submission
and Curation
Provedor de dados: 17
Autores: Marcus Ennis.
ChEBI (Chemical Entities of Biological Interest) is a database of ‘small’ molecular entities structured
around a chemical ontology. It contains almost 600,000 entries, of which approximately 20,000 have been manually curated, as
well as entries for groups (parts of molecular entities) and classes of entities. It provides a wide range of information such as
chemical nomenclature, structures and related chemical values, and establishes interrelationships between entities in the ontology,
in terms of both structure and role. ChEBI places a strong focus on quality, with exceptional efforts being applied to upholding
IUPAC nomenclature recommendations and best IUPAC practices when drawing chemical structures....
Tipo: Presentation
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5091/version/1
Check Your Data Freedom: A Taxonomy to Assess Life Science Database Openness
Provedor de dados: 17
Autores: Melanie Dulong de Rosnay.
Molecular biology data are subject to terms of use that vary widely between databases and curating institutions. This research
presents a taxonomy of contractual and technical restrictions applicable to databases in life science. It builds upon research led by
Science Commons demonstrating why open data and the freedom to integrate facilitates innovation and how this openness can be
achieved. The taxonomy describes technical and legal restrictions applicable to life science databases, and its metadata have been
used to assess terms of use of databases hosted by Life Science Resource Name (LSRN) Schema. While a few public domain
policies are standardized, most terms of use are not harmonized, difficult to understand and impose controls that prevent others...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/2083/version/1
ChemAxiom – An Ontological Framework for Chemistry in Science
Provedor de dados: 17
Autores: Nico Adams; Edward O. Cannon; Peter Murray-Rust.
We present ChemAxiom as the first ontological framework for chemistry in science. ChemAxiom enables discourse about
chemical objects in a computable language and is useful for the management of chemical concepts and data, the retrospective
typing of resources, the identification of ambiguity and supports chemical text mining.
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3714/version/1
ChemCloud: Chemical e-Science Information Cloud
Provedor de dados: 17
Autores: Alexandru Todor; Adrian Paschke; Stephan Heineke.
Our Chemical e-Science Information Cloud (ChemCloud) – a Semantic Web based eScience infrastructure
– integrates and automates a multitude of databases, tools and services in the domain of chemistry, pharmacy and
bio-chemistry available at the Fachinformationszentrum Chemie (FIZ Chemie), at the Freie Universitaet Berlin (FUB), and on the
public Web. Based on the approach of the W3C Linked Open Data initiative and the W3C Semantic Web technologies for
ontologies and rules it semantically links and integrates knowledge from our W3C HCLS knowledge base hosted at the FUB, our
multi-domain knowledge base DBpedia (Deutschland) implemented at FUB, which is extracted from Wikipedia (De) providing a
public semantic resource for chemistry, and...
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5642/version/1
Chemical Physics of Phonons & Superconductivity: A Heuristic Approach
Provedor de dados: 17
Autores: Michael J. Bucknum.
Several lines of thought are pursued in an attempt to further clarify the role played by phonons in the theory of superconductivity.
The central results of BCS theory are examined in the context of anharmonicity in the phonon motion and the role that
Badger's rule of spectroscopy can play in simplifying and making more chemically intuitive the nature of the
mechanism of superconductivity.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1586/version/2
Chemical Physics of Phonons & Superconductivity: A Heuristic Approach
Provedor de dados: 17
Autores: Michael J. Bucknum.
Several lines of thought are pursued in an attempt to further clarify the role played by phonons in the theory of superconductivity.
The central results of BCS theory are examined in the context of anharmonicity in the phonon motion and the role that
Badger's rule of spectroscopy can play in simplifying and making more chemically intuitive the nature of the
mechanism of superconductivity.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1586/version/1
Chemical Profiles of Essential Oils and Non-Polar Extractables from Sumac (Rhus spp.)
Provedor de dados: 17
Autores: Sierra Rayne.
Sumac is the common name for a genus (Rhus) with >250 individual species of flowering plants in the family
Anacardiaceae. These plants are globally distributed in temperate and tropical regions and can grow on marginal lands, making
them strong candidates for renewable bioproduct sources. Despite the extensive historical use of some members of Rhus spp. for
tannins and other commercial phenolics, little is known about the non-phenolic components of extracts and essentials oils. The
current review highlights opportunities available to extend these limited prior studies to other sumac species, and for obtaining
value-added compounds to complement already established phenolic extractions in these commercial plant species. To date, a
number of...
Tipo: Manuscript
Palavras-chave: Chemistry; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5926/version/1
Chemical Topology of Crystalline Matter
Provedor de dados: 17
Autores: Michael J. Bucknum.
This work is intended as a review and extension of the seminal work in chemical topology developed by the crystallographer A.F.
Wells in the 20th century.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1587/version/1
Chemical Topology of Crystalline Matter and the Transcendental Numbers ϕ , e and
π
Provedor de dados: 17
Autores: Michael J. Bucknum; Eduardo A. Castro.
This work is intended as a review and extension of the seminal work in chemical topology developed by the crystallographer A.F.
Wells in the 20th century.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/1587/version/3
Chemical Topology of Crystalline Matter and the Transcendental Numbers ϕ , e and
π
Provedor de dados: 17
Autores: Michael J. Bucknum; Eduardo A. Castro.
This work is intended as a review and extension of the seminal work in chemical topology developed by the crystallographer A.F.
Wells in the 20th century.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1587/version/2
Chemistry Crowdsourcing and Open Notebook Science
Provedor de dados: 17
Autores: Jean-Claude Bradley; Kevin Owens; Antony Williams.
This is a pre-proposal written for the NSF program
CDI (Cyber-Enabled Discovery and Innovation) in Jan
2008.

The current system of dissemination of scientific data and knowledge is far less
efficient than it needs to be to facilitate improved collaborative science, especially considering current publication vehicles and
infrastructure. There is a growing movement promoting more Open Science with the belief that a more transparent scientific
process can perform far more effectively.
The logical extension of this concept is full transparency - exposing a
researcher's complete record of progress to the public in near real time. Not only will such a process enable ongoing
data sharing it also provides an...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1505/version/1
Chemopreventive potential of natural products isolated from a alchornea glandulosa, pterogyne
nitens and its semisynthetic analogs
Provedor de dados: 17
Autores: Mauro C. C. Morais; Laura E. Marler; Suaib Luqman; Tamara P. Kondratyuk; Maicon S. Petronio; Luis O.
Regasini; Dulce H. S. Silva; Vanderlan S. Bolzani; Christiane P. Soares; John M. Pezzuto.
INTRODUCTION: Chemoprevention involves the use of natural or synthetic substances to reduce the risk of developing cancer.
Gallic acid was found to possess several pharmacological activities, such as anti-oxidant and anti-inflammatory. Guanidine
alkaloids
display
a
broad
spectrum
of
biological
activities
and
its
cytotoxic
effect
were
well
investigated.
OBJECTIVES: The present study evaluated the chemopreventive potential of natural products
and its semi-synthetic analogs using quinone reductase (QR) induction, aromatase inhibition and the suppression of
NFκB activity, which are well established strategies for screening compounds to cancer chemoprevention.

METHODS: Gallic acid was isolated from Alchornea...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6923/version/1
Chemotherapy effects on brain glucose metabolism at rest
Provedor de dados: 17
Autores: Bruno Baudino; Federico D'Agata; Giancarlo Castellano; Paola Caroppo; Simona Cauda; Antonella Parente;
Matteo Manfredi; Elisabetta Geda; Laura Orsi; Franco Cauda; Lorys Castelli; Katiuscia Sacco; Rita Ardito; Riccardo Torta;
Gianni Bisi.
Background: A growing number of studies reports that chemotherapy may impair brain functions inducing cognitive changes
which can persist in a subset of cancer survivors. 
Aims: To investigate the neural basis of the
chemotherapy-induced neurobehavioral changes by means of metabolic imaging and voxel-based statistical parametric mapping
analyses.
Methods: We studied the resting brain [18]FDG-PET/CT images of 43 adult cancer patients with
solid (n=12, 28%) or hematologic malignancies (n=31, 72%); 12 patients were studied prior to chemotherapy (No chemotherapy)
while treated patients were divided into two matched subgroups: Early High (<9 months after chemotherapy,
>6 chemotherapy cycles, n=10), and Late...
Tipo: Manuscript
Palavras-chave: Cancer; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5637/version/1
ChemTextMiner: An open source tool kit for mining medical literature abstracts
Provedor de dados: 17
Autores: Muthukumarasamy Karthikeyan; Yogesh Pandit; Deepak Pandit; Ganesh Nainaru; Sunil Nalwade; Renu Vyas;
Esha Jain.
Text mining involves recognizing patterns from a wealth of information hidden latent in unstructured text and deducing explicit
relationships among data entities by using data mining tools. Text mining of Biomedical literature is essential for building
biological network connecting genes, proteins, drugs, therapeutic categories, side effects etc. related to diseases of interest. We
present an approach for textmining biomedical literature mostly in terms of not so obvious hidden relationships and build
biological network applied for the textmining of important human diseases like MTB, Malaria, Alzheimer and Diabetes. The
methods, tools and data used for building biological networks using a distributed computing environment previously used for
ChemXtreme[1]...
Tipo: Poster
Palavras-chave: Chemistry; Developmental Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6435/version/1
China is on the track tackling Enteromorpha spp forming green tide
Provedor de dados: 17
Autores: Naihao Ye; Zhimeng Zhuang; Xianshi Jin; Qingyin Wang; Xiaowen Zhang; Demao Li; Hongxia Wang; Yuze Mao;
Zengjie Jiang; Bin Li; Zhixin Xue.
Green tide management is supposed to be a long term fight rather than an episode during the 29th Olympic Games for China,
since it has been gaining in scale and frequency during the past 3 decades in both marine and estuary environment all over the
world. A number of rapid-responding studies including oceanographic comprehensive surveys along the coastline have been
conducted during the bloom and post-bloom periods in 2008 by Chinese marine scientists. The preliminary results are as below:
(1) phylogenetic analysis indicates that the bloom forming alga forms a clade with representatives of the green seaweed
Enteromorpha linza, though, the alga has been identified as E. proliera by means of morphological; (2) the present data suggest
that the bloom was...
Tipo: Manuscript
Palavras-chave: Ecology; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2352/version/1
ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription
factor oncogenes
Provedor de dados: 17
Autores: Adam A. Margolin; Teresa Palomero; Pavel Sumazin; Andrea Califano; Adolfo Ferrando; Gustavo A. Stolovitzky.
ChIP-on-chip has emerged as a powerful tool to dissect the complex network of regulatory interactions between transcription
factors and their targets. However, most ChIP-on-chip analysis methods use conservative approaches aimed to minimize
false-positive transcription factor targets. We present a model with improved sensitivity in detecting binding events from
ChIP-on-chip data. Biochemically validated analysis in human T-cells reveals that three transcription factor oncogenes, NOTCH1,
MYC, and HES1, bind one order of magnitude more promoters than previously thought. Gene expression profiling upon
NOTCH1 inhibition shows broad-scale functional regulation across the entire range of predicted target genes, establishing a closer
link between occupancy and...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1364/version/1
ChlamyCyc - a comprehensive database and web-portal centered on _Chlamydomonas reinhardtii_
Provedor de dados: 17
Autores: Jan-Ole Christian; Patrick May; Stefan Kempa; Dirk Walther.
*Background* - The unicellular green alga _Chlamydomonas reinhardtii_ is an important eukaryotic model organism for the
study of photosynthesis and growth, as well as flagella development and other cellular processes. In the era of high-throughput
technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using
computational methods and database resources to provide comprehensive information about the whole cellular system of a single
organism.
*Results* - In the framework of the German Systems Biology initiative GoFORSYS a
pathway/genome database and web-portal for _Chlamydomonas reinhardtii_ (ChlamyCyc) was established, which currently
features about 270 metabolic pathways...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3108/version/1
Chlorinated Diphenyl Ethers in Sediments, Biota, and the Water Column from Coastal British
Columbia, Canada
Provedor de dados: 17
Autores: Sierra Rayne; Ikonomou G. Michael; Chris Garrett.
Polychlorinated diphenyl ethers (PCDEs) are impurities in technical chlorophenol mixtures, are used as dielectric fluids in
capacitors and as herbicides, antiseptics, food preservatives, and papers and textiles, and can be formed through the chlorination of
organics in water and wastewater streams. Samples from semipermeable membrane devices (SPMDs), sediments, English sole,
mussels, and Dungeness crab were collected from urban/industrial and remote sites along the marine coast of British Columbia
and analyzed by congener-specific GC-MS analysis for mono- through deca-substituted PCDEs. Higher concentrations in biota
and sediments were observed near urban/industrial areas, with evidence for food-chain biomagnification within major harbours.
Correlations...
Tipo: Presentation
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/690/version/1
Chloroplast and Cell Imaging at Submicron Resolution by Two-Photon Excitation
Provedor de dados: 17
Autores: I C. Baianu.
Novel, two-photon NIR excitation fluorescence correlation microspectroscopy tests and preliminary results were presented in this
article with submicron resolution for concentrated suspensions of functional cells and chloroplast membranes. Related
developments of these technique involve applications of Fluorescence Cross-Correlation Spectroscopy (FCCS) detection to
monitoring: 
DNA- telomerase interactions, DNA hybridization kinetics, ligand-receptor interactions, and
HIV-HBV testing. 

Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics & Genomics; Immunology; Molecular Cell Biology;
Bioinformatics; Plant Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7116/version/1
Choice reveals that rats are majoritarily resilient to cocaine addiction
Provedor de dados: 17
Autores: Lauriane Cantin; Magalie Lenoir; Sarah Dubreucq; Fushia Serre; Caroline Vouillac; Serge H. Ahmed.
Assessing the relative reward value of cocaine and how it changes with repeated use represents a long-standing goal in addiction
research. Surprisingly, recent experimental research in rats – the most frequently used animal model in the field
– suggests that the reward value of cocaine may in fact be relatively weak at least in the majority of individuals.
Here, we provide strong additional evidence that confirms and extends the validity and generality of this research. Specifically, we
demonstrate that no matter how heavy is past cocaine self-administration, most rats value cocaine poorly and readily decide to quit
when offered the opportunity of making a different choice (i.e., drinking water sweetened with saccharin, an otherwise...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3738/version/1
Cholesterol Esterification During Differentiation by Hexamethylene Bisacetamide of Friend
Virus-Induced Erythrokeukemia
Provedor de dados: 17
Autores: Maria F. Mulas; Antonella Mandas; Claudia Abete; Sandra Dessi; Mario Pani; Rosa Manconi; Alessandra Mocali;
Francesco Paoletti.
Cholesterol is an essential constituent of all mammalian cell membranes, and its availability is therefore a prerequisite for cellular
growth and other functions. Several lines of evidence are now indicating an association between alterations of cholesterol
homeostasis and cell cycle progression in cancer cells. However, the role of cholesterol in cell differentiation is still largely
unknown. To begin to address this issue, in this study we examined changes in cholesterol metabolism and in the mRNA levels of
proteins involved in cholesterol import and esterification (multi-drug resistance, MDR-3) and acylCoA:cholesterol acyltransferase
(ACAT) and cholesterol export (caveolin-1) in Friend virus-induced erythroleukemia cells (MELC), in the absence or in the...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5155/version/1
Cholinergic innervation is necessary to shift reward timing activity in rodent visual cortex
Provedor de dados: 17
Autores: Emma Roach; Marshall Hussain Shuler.
While the biological analogue of prediction error has been well characterized in the midbrain dopaminergic system, the possibility
of other neuromodulatory systems acting as global reinforcers is a topic of much debate. Reward timing, the phenomenon by
which
single
unit
responses
in
primary
visual
cortex
(V1)
reflect
an
operantly
learned
stimulus‐reward interval, offers a tractable preparation to investigate reinforcement learning in vivo: theoretical
work suggests that reward timing results from the interaction of stimulus‐evoked recurrent network activity and a
global reinforcement signal that indicates the time of
received reward. We hypothesized that this signal is
conveyed by cholinergic neurons...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5813/version/1
Chopped Arms & Big Macs: ERP Correlates of Viewing and Imagining Aversive and Food
Photos
Provedor de dados: 17
Autores: Amy Comeau; Wei-Hsien Yeh; Alfonso Abizaid; Kim Hellemans; Amedeo D'Angiulli.
OBJECTIVES
We investigated the Event-Related Potential (ERP) correlates of perceived and imagined
food photos and their relation to the perception and imagery of unpleasant emotional photos. Our aim was to determine whether
similar or different patterns of neural activity were associated with viewing and imagining food photos versus emotional photos.


METHODS 
Nine volunteers with prescreened normal mood
and anxiety levels wore a 32 channel Cap with embedded electrodes (10/20 international system) connected to a high-density
low-noise Neuroscan EEG system. Participants were tested during two different blocks: a hunger block (containing 25 neutral and
food photos) and an emotional block...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4576/version/1
Chorionic Structures in Maternal Blood
Provedor de dados: 17
Autores: Nilo Pereira Luz.
Chorionic villi are the exchange structures of the placenta where human fetuses receive oxygen and nutrients from maternal blood,
this article reports an improvement of a published method to recover them from the blood of pregnant, women, quotes their
number and illustrates their size and trypsin impregnation. The reasons to explain the presence of chorionic structures and villi in
the circulating maternal blood, the possible significance of their existence in maternal blood and the mechanisms to remove them
are discussed. Their size and trypsin impregnation are illustrated. This paper discusses the significance of the presence of such
allogeneic structures in the circulating blood of pregnant women and presents a brief discussion on the role of trypsin...
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1393/version/1
Chromium uptake by Fenugreek
Provedor de dados: 17
Autores: Xanthate D S; Murthy Ch V R; Rajan S C S; Sekhar D M R.
Fenugreek (Trigonella foenum- graecum) is both herb (leaves) and a spice (seed) belonging to the family Fabaceae. Fenugreek
leaves and seeds are used in the cuisine of India. Fenugreek also has medicinal value. Fenugreek seeds are known to reduce serum
glucose and improve glucose tolerance and hence are prescribed to diabetic patients. In the recent past supplemental Chromium is
being prescribed to diabetic patients to activate (increased- insulin binding, insulin receptor number, insulin receptor
phosphorylation) insulin. Plants can uptake substantial quantities of toxic metals from contaminated soils if these soils are well
ameliorated. 

It is then probable that the medicinal efficacy of Fenugreek in the case
of...
Tipo: Manuscript
Palavras-chave: Pharmacology; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6762/version/1
Chromobacterium violaceum ATCC12472: Multi-drug and ethidium bromide resistant
Provedor de dados: 17
Autores: Cristiana G. O. Dal'Molin; Regina V. Antônio; Luismar M. Porto.
_Chromobacterium violaceum_ is an opportunistic human pathogen causing a range of gastric infections and occasionally
septicemia. This Gram-negative bacillus is a common inhabitant of soil and water in tropical and subtropical areas of the world.
Infection occurs after contamination of damaged skin exposed to soil or environmental water. Alternatively, systemic infection
can follow the aspiration or ingestion of contaminated water. The major features of infections by _C. violaceum_ are, in generally,
rapid clinical course, multiple visceral abscesses, and high mortality. Genomic data on the type strain ATCC 12472 has provided a
comprehensive basis for detailed studies of pathogenicity, virulence and drug resistance genes. In this study, the susceptibility...
Tipo: Manuscript
Palavras-chave: Microbiology; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3366/version/1
Chromosomal mutational algebra: a new algebra to manipulate chromosomal mutation
Provedor de dados: 17
Autores: Dipankar Mazumdar.
This study leads to a new algebra. An algebra is defined on the common mechanisms of chromosomal mutation. The algebra
(_S^[PSI](C)_^, ~*~, ', [DELTA], _D_) is constructed for a given _C_ and [PSI]. This algebra represents the most
common chromosomal mutational mechanisms. This can lead to a new way to manipulate chromosomal mutation with higher
structures of abstract mathematics. The first proposal of the algebra was reported in Mazumdar _et al._, 2007.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3874/version/1
Chronic cocaine enhances release of neuroprotective amino acid taurine: a microdialysis study
Provedor de dados: 17
Autores: Elena Yablonski-Alter; Mervan Agovic; Eleonora Gashi; Theodore Lidsky; Eitan Freedman; Shailesh Banerjee.
Cocaine inhibits high-affinity neurotransmitter uptake at the presynaptic nerve terminals to increase synaptic levels of dopamine,
norepinephrine and serotonin^1^. This increase of synaptic dopamine may cause neurotoxicity^2,3^. At least two different
mechanisms have been proposed for the development of dopamine-related neurotoxicity: 1) dopamine produces a free radical that
may induce cell toxicity^2,3^ and 2) dopamine reduces glutamate transport at its presynaptic sites to increase synaptic levels of
this amino acid^4^ and augments glutamate transmission by activating dopamine D1 receptors in different areas of the brain^5-7^.
Increase in glutamatergic transmission mediated by the activation on N-methyl dextro-aspartate (NMDA) receptors has been
shown to...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2319/version/1
Chronic hyperplastic anemia as an independent risk factor for atherosclerotic lesions: a lesson from
thalassemia intermedia
Provedor de dados: 17
Autores: Maria Eliana Lai; Stefania Vacquer; Maria Paola Carta; Alessandra
Angius; Antonella
Spiga; Pier Luigi
Cocco; Fabrizio
Mandas; Sandra Dessi.
Introduction. Cardiovascular involvement represents a well-known complication and the primary cause of mortality, both in
transfusion-dependent beta thalassemia major (β-TM) and in transfusion-independent beta thalassemia intermedia
(β-TI). In β-TM, heart iron overload is considered the main cause of this complication. This is likely due
to poor adherence to iron-chelating therapy, resulting in the inability of the body to efficiently remove iron excess derived from
transfused red blood cell breakdown. Different clinical pictures may instead be evoked in cardiovascular involvement occurring in
β-TI; however, until now, no factor has emerged as the major one responsible for these complications....
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4169/version/1
Chronic Morbilliviral Encephalitis in a Young Striped Dolphin from Italy
Provedor de dados: 17
Autores: Giovanni Di Guardo; Cristiano Cocumelli; Francesco Scholl; Cristina Esmeralda Di Francesco; Roberto Speranza;
Massimiliano Pennelli; Claudia Eleni.
A young male striped dolphin (Stenella coeruleoalba) found stranded in November 2009 was affected by a chronic
non-suppurative encephalitis, with prominent mononuclear cell perivascular cuffs, neuronal degeneration, microgliosis,
neuronophagia and occasional presence of multinucleate syncytia. Immunohistochemical and biomolecular investigations for
Morbillivirus were positive exclusively from the brain, but not from the cerebellum nor from any other tissue, with morbilliviral
antigen being detected in neurons and astrocytes. A low neutralizing antibody titer (1:10) against Morbillivirus (CDV) was also
found, with no simultaneous presence of anti-Brucella antibodies.
The main reason why the present case
appears to be of interest is provided...
Tipo: Manuscript
Palavras-chave: Microbiology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4912/version/1
Chronic thoracic hemisection spinal cord injury in adult rats induces a progressive decline in
transmission from uninjured fibers to lumbar motoneurons
Provedor de dados: 17
Autores: Victor L. Arvanian; Lisa Schnell; Li Lou; Roobeh Golshani; Arsen Hunanyan; Arko Ghosh; Damien D. Pearse; John
K. Robinson; Martin E. Schwab; James W. Fawcett; Lorne M. Mendell.
Although most spinal cord injuries are anatomically incomplete, only limited functional recovery has been observed in people and
rats with partial lesions. To address why surviving fibers cannot mediate more complete recovery, we evaluated the physiological
and anatomical status of spared fibers after unilateral hemisection (HX) of thoracic spinal cord in adult rats. We made intracellular
and extracellular recordings at L5 (below HX) in response to electrical stimulation of contralateral white matter above (T6) and
below (L1) HX. Responses from T6 displayed reduced amplitude, increased latency and elevated stimulus threshold in the fibers
across from HX, beginning 1-2 weeks after HX. Ultrastructural analysis revealed demyelination of intact axons...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2165/version/1
Chronobiology of Epilepsy
Provedor de dados: 17
Autores: Sachin S. Talathi; Dong-Uk Hwang; William Ditto; Mark Spano; Hector Sepulveda; Tom Mareci; Paul Carney.
A fine balance between neuronal excitation and inhibition governs the physiological state of the brain. It has been hypothesized
that when this balance is lost as a result of excessive excitation or reduced inhibition, pathological states such as epilepsy emerge.
Decades of investigation have shown this to be true in vitro. However, in vivo evidence of the emerging imbalance during the
"latent period" between the initiation of injury and the expression of the first spontaneous behavioral
seizure has not been demonstrated. Here, we provide the first demonstration of this emerging imbalance between excitation and
inhibition in vivo by employing long term, high temporal resolution, and continuous local field recordings from microelectrode...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1679/version/1
CIPRO 2.5: Ciona intestinalis Protein integrated database with large-scale omics data, bioinformatic
analyses and curated annotation, with ability for user rating and comments
Provedor de dados: 17
Autores: Toshinori Endo; Keisuke Ueno; Kouki Yonezawa; Katsuhiko Mineta; Kohji Hotta; Yutaka Satou; Lixy Yamada; Michio
Ogasawara; Hiroki Takahashi; Ayako Nakajima; Mia Nakachi; Mamoru Nomura; Junko Yaguchi; Alu Konno; Sasakura
Yasunori; Akiyasu C. Yoshizawa; Hisaaki Taniguchi; Chisato Yamasaki; Miho Sera; Tadashi Imanishi; Kazuo Inaba.
CIPRO database is an integrated protein database for a tunicate species Ciona intestinalis that belongs to the Urochordata.
Although the CIPRO database deals with proteomic and transcriptomic data of a single species, the animal is considered unique in
the evolutionary tree, representing a possible origin of the vertebrates and is a good model for understanding chordate evolution,
including that of humans. Furthermore, C. intestinalis has been one of the favorites of developmental biologists; there exists a
huge amount of accumulated knowledge on its development and morphology, in addition to the recent genome sequence and gene
expression data. The CIPRO database is aimed at not only collecting published data, but also presenting unique information,...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5435/version/1
Ciproxifan, an H~3~ Receptor Antagonist, Improves Learning and Memory in the APP Mouse Model
of Alzheimer's Disease
Provedor de dados: 17
Autores: Mark E. Bardgett; Natasha N. Davis; Molly S. Griffith.
Mice that express the mutant form of the human amyloid precursor gene associated with early-onset familial
Alzheimer's disease demonstrate memory deficits and amyloid plaques. We show here that ciproxifan, a prototypical
antagonist of H~3~-type histamine receptors, alleviates two types of learning and memory impairments in such mice. These data
support the idea that modulation of H~3~ receptors represents a viable therapeutic strategy in the treatment of
Alzheimer's disease.
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/4041/version/1
Circadian Preference and Sexual Selection: A Novel Evolutionary Approach
Provedor de dados: 17
Autores: Davide Piffer.
Human sleep patterns differ across age groups and between males and females, and their association with age and gender suggest
that they might have been the target of sexual selection during human evolutionary history. In this study, I will test the hypothesis
that a phase-delayed circadian phase is a sexually selected trait in humans. A short version of the Horne and Ostberg questionnaire
and a questionnaire on sexual behaviour were administered to 134 males and 140 females. A significant negative relationship was
found between the MEQ score and the number of sexual partners among males, with evening types reporting more sexual partners
than morning types. No significant relationship between females MEQ and number of sexual partners was found. Findings...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/2964/version/2
Circadian Preference and Sexual Selection: A Novel Evolutionary Approach
Provedor de dados: 17
Autores: Davide Piffer.
Human sleep patterns differ across age groups and between males and females, and their association with age and gender suggest
that they might have been the target of sexual selection during human evolutionary history. In this study, I will test the hypothesis
that a phase-delayed circadian phase is a sexually selected trait in humans. A short version of the Horne and Ostberg questionnaire
and a questionnaire on sexual behaviour were administered to 134 males and 140 females. A significant negative relationship was
found between the MEQ score and the number of sexual partners among males, with evening types reporting more sexual partners
than morning types. No significant relationship between females MEQ and number of sexual partners was found. Findings...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2964/version/1
Circadian rhythmic kinase CK2α phosphorylates BMAL1 to regulate the mammalian
clock
Provedor de dados: 17
Autores: Teruya Tamaru; Jun Hirayama; Yasushi Isojima; Katsuya Nagai; Shigemi Norioka; Ken Takamatsu; Paolo
Sassone-Corsi.
Clock proteins govern circadian physiology and their function is regulated by a variety of signaling pathways. Here, we show that
p45^PFK^, a previously reported circadian rhythmic kinase, corresponds to CK2[alpha]. Rhythmic phosphorylation of the core
clock protein BMAL1 by CK2[alpha] occurs in the suprachiasmatic nuclei (SCN), the mammalian central pacemaker. Circadian
BMAL1 phosphorylation controls its nucleocytoplasmic localization. Gene silencing for CK2[alpha] and BMAL1 mutagenesis of
a highly conserved CK2 phosphorylation site (Ser 90) result in impaired BMAL1 accumulation in the nucleus and subsequent
disruption of clock function. These findings reveal that circadian rhythmic kinase CK2 is an essential regulator of the mammalian
circadian system.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1702/version/1
Circulating Neutrophils from Trauma Patients Induce Apoptosis Through Dephosphorylation of
Epithelial Cell Caspase-8
Provedor de dados: 17
Autores: Songhui Jia; Jean Parodo; Emmanuel Battisti-Charbonney; Jennifer Tsang; Sangyang Jia; Ori D. Rotstein; Andras
Kapus; John C. Marshall.
Activated neutrophils can cause oxidant-mediated bystander injury to host cells. This injury has previously been ascribed to the
direct effects of oxidants on membrane phospholipids. We show here that oxidants released by neutrophils activated in vivo in
survivors of multiple trauma or in vitro by exposure to bacterial lipopolysaccharide (LPS) can also promote the apoptotic death of
epithelial cells, through the SHP-1-mediated dephosphorylation of epithelial cell caspase-8. Neutrophils from a cohort of patients
who sustained serious injury induced the apoptotic death of cultured epithelial cells in a manner that was dependent on the activity
of the NADPH oxidase and the generation of neutrophil-derived reactive oxygen intermediates. Caspase-8 is...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2011
URL: http://precedings.nature.com/documents/6393/version/1
Citizen Science in Disaster and Conflict Resilience
Provedor de dados: 17
Autores: Keith G Tidball; Marianne Krasny.
*Background/Question/Methods*

Within
the
disaster
and
conflict
response
communities, concern about lack of effectiveness of outside responses has led to a debate about the role of local people in
developing the capacity to prepare for a crisis and to respond after calamity has struck. Pelling (2007) points out the potential for
participatory disaster risk assessment to build local capacity and for generating knowledge that, along with more expert-driven
data collection, is used to identify and reduce the risk of disaster. Similarly, Weinstein and Tidball (2007) and Tidball et al. (2008)
present an alternative model for post-crisis intervention based on local assets, including ongoing attempts of communities to
manage...
Tipo: Presentation
Palavras-chave: Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5200/version/1
City rats: From rat behaviour to human spatial cognition in urban environments
Provedor de dados: 17
Autores: David Eilam; Juval Portugali; Osnat Yaski.
The structure and shape of an urban environment influence our ability to find our way about in the city^1-2^. Indeed, urban
designers who face the challenge of planning environments that facilitate wayfinding^3^, have a consequent need to understand
the relations between the urban environment and spatial cognition^4^. Previous studies have suggested that certain qualities of
city elements, such as a distinct contrast with the background (e.g. The Eiffel Tower in Paris), or a clear morphology (e.g. the grid
layout of Manhattan's streets) affect spatial behaviour and cognition^1,5-7^. However, only a few empirical studies
have examined the relations between the urban environment and spatial cognition. Here we suggest that testing rats in...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4759/version/1
ClassTAL
Provedor de dados: 17
Autores: Federico D'Agata.
This is the description of a Matlab script (classTAL.m) that automatically classifies BrainVoyager .voi maps with afni, MRIStudio
white matter and fcon1000 Intrinsic Connectivity Networks brain atlas. The script saves many useful output files (tables, figures
and .voi).
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6142/version/2
ClassTAL
Provedor de dados: 17
Autores: Federico D'Agata.
This is the description of a Matlab script (classTAL.m) that automatically classifies BrainVoyager .voi maps with afni brain atlas.
The script saves many useful output files.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6142/version/1
Clays: Colloidal Properties in Nanodomain
Provedor de dados: 17
Autores: Siddhartha S. Mukhopadhyay.
The ever-growing application of clays in nanotechnology rests on fundamental principles of colloid chemistry. They make soils as
nature’s great electrostatic chemical reactor. Highly anisotropic and often irregular particle shape, broad particle
size distribution, different types of charges within the unit cells, heterogeneity of layer charges, pronounced CEC, dis-articulation
and flexibility of layers, and different modes of aggregation make clays different from other colloidal materials. Their inseparable
association with the genesis of life on Earth and evolutionary diversification of Neoproterozoic life is a safety-belt of
nanotechnology. 

Nanotechnology promises to be the greatest technological...
Tipo: Presentation
Palavras-chave: Chemistry; Ecology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5807/version/1
Clean Coal and Spirulina maxima (Cyanobacteria) Production through Alkaline-Seawater
Provedor de dados: 17
Autores: Md. Abu Affan; Dae-Won Lee; Heung-Sik Park; Jae-Hoon Noh; Soo-Jin Heo; Chulhong Oh; Seon-Mi Jeon; Joo-Won
Son; Seung-Gyu Son; Hyi-Seung Lee; Hyeon Yong Lee; Do-Hyung Kang.
Carbon capture and storage have involved high cost and an earthquake threat. Coal in NaOH-natural seawater (NSW) can produce
clean coal, and organic carbon enriched pretreated sweater (PSWS) can be used to grow Spirulina maxima. However, with
freshwater shortage, high cost CO2 feedstock incurs S. maxima biomass production, and using PSWS should be considered as an
alternative. NaHCO3 and Na2CO3 were used to sediment Mg2+ and Ca2+ of NSW to resolve turbidity and decreasing phosphate
solubility. Here, we show that pre-combustion coal and NaOH concentration calculated by our devised formulae for any salinity
could dilute volatile matter 19.8 Kg plus CO2 116.50 to 168.89 Kg Ton^-1^ coal in NaOH-NSW by sedimentation Mg2+ and
Ca2+ of 99.91% and 32.52%,...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2012
URL: http://precedings.nature.com/documents/6930/version/1
Climate Change and Disease Simulation
Provedor de dados: 17
Autores: Somnath Jha.
Climate change has manifested differential impacts on various components of the earth system. The impact of climate change is
not merely limited to the climatic variable. Climate change has resulted in complex, unforeseen consequences in the biosphere of
earth. The silent but gradual changes arise out of varied responses of disease-causing organism to the combination of the
disease-conducive environmental variables. The change is the same for both the target hosts plant as well as the animal kingdom.
There is an urgent need to look into the changing disease dynamics and the disease pathogen genome sensitivity to the changes in
climatic variables. The long memory of genetic makeup of disease pathogen to capture, inherit and evolve or mutate the changed
or...
Tipo: Presentation
Palavras-chave: Ecology; Genetics & Genomics; Earth & Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6949/version/1
Clinical Study and Molecular Genetic Analyses of Malaysian GEFS+ Patients
Provedor de dados: 17
Autores: Emmilia Tan; Salmi Abdul Razak; Abdul Aziz Mohamed Yusoff; Jafri Malin Abdullah.
Generalized epilepsy with febrile seizure plus (GEFS+) is a familial epilepsy syndrome characterized by phenotypic and genetic
heterogeneity. Neuronal voltage gated sodium channel α-1 subunit gene, SCN1A is the most clinically relevant and
associated with GEFS+. The objective was to study the clinical presentations of GEFS+ and analyze the SCN1A gene associated
with Malaysian GEFS+ patients. Blood samples were collected from 30 unrelated GEFS+ patients and genomic DNA was
obtained using the Qiagen DNA Blood Mini Kit following the manufacturer’s instructions. The 26 exons of SCN1A
genes were analyzed by polymerase chain reaction (PCR) and denaturing high performance liquid chromatography (DHPLC). The
aberrant profile peak from DHPLC...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5393/version/1
Clinical validity assessment of a breast cancer risk model combining genetic and clinical information
Provedor de dados: 17
Autores: Matthew E. Mealiffe; Renee P. Stokowski; Brian K. Rhees; Ross L. Prentice; Mary Pettinger; David A. Hinds.
_Background:_ The extent to which common genetic variation can assist in breast cancer (BCa) risk assessment is unclear. We
assessed the addition of risk information from a panel of BCa-associated single nucleotide polymorphisms (SNPs) on risk
stratification offered by the Gail Model.

_Methods:_ We selected 7 validated SNPs
from the literature and genotyped them among white women in a nested case-control study within the Women’s
Health Initiative Clinical Trial. To model SNP risk, previously published odds ratios were combined multiplicatively. To
produce a combined clinical/genetic risk, Gail Model risk estimates were multiplied by combined SNP odds ratios. We assessed
classification performance using...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/4295/version/1
Clonal Complexes in Biomedical Ontologies
Provedor de dados: 17
Autores: Albert Goldfain; Lindsay G. Cowell; Barry Smith.
An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment
decisions. Multi-Locus Se-quence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are
used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for
bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to
clonal complexes in biomedical ontologies.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3476/version/1
Clonal origin of Epstein-Barr virus-infected T/NK-cell subpopulations in chronic active Epstein-Barr
virus infection
Provedor de dados: 17
Autores: Shouichi Ohga; Masataka Ishimura; Goichi Toshimoto; Toshihiro Miyamoto; Hidetoshi Takada; Tamami Tanaka;
Koichi Ohshima; Ken-Ichi Imadome; Yasunobu Abe; Koichi Akashi; Toshiro Hara.
Clonal expansion of Epstein-Barr virus (EBV) infected B-cells occasionally occurs in immunocompromized subjects.
EBV-infected T/natural killer (NK)-cells proliferate in patients with chronic active EBV infection (CAEBV) that is a rare
mononucleosis syndrome. It is classified into either T-cell type or NK-cell type according to the primary target of infection, while
the pathogenesis remains unclear. To search the clonal origin of EBV-infected T/NK-cells, virus distribution and clonotype were
assessed by using highly purified cell fractions obtained from 6 patients. Patient 1 had a monoclonal proliferation of EBV-infected
T-cell
receptor
Vδ2/Vγ9-expressing
cells,
and
carried
lower
copy
number
of
EBV
αβT-cells....
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4238/version/1
Cloning and expression of first gene for biodegrading microcystins by Sphingopyxis sp. USTB-05
in
Provedor de dados: 17
Autores: Hai Yan; Junfeng Wang; Jian Chen; Wei Wei; Hui Wang.
Harmful cyanobacterial blooms (HCBs) in natural waters are a growing environmental problem worldwide because microcystins
(MCs) produced by cyanobacteria are potent hepatotoxins and tumor promoters. MCs are resistant against physical and chemical
factors. Thus, biodegradation is the most efficient method for removing MCs, and a number of bacterial strains, especially genus
_Sphingomonas_, have been isolated for biodegrading MCs. Although the pathway, enzyme, and gene for biodegrading MCs by
_Sphingomonas sp._ have been widely identified recently, no gene concerned with the biodegradation of MCs has been
successfully cloned and expressed. In this study, we show that the first and most important gene of mlrA, containing 1,008 bp
nucleotides in length, in the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4846/version/1
Closed bioregenerative life support systems: Applicability to hot deserts
Provedor de dados: 17
Autores: Yuriy Polyakov; Ibrahim Musaev; Sergey Polyakov.
Water scarcity in hot deserts, which cover about one-fifth of the Earth’s land area, along with rapid expansion of hot
deserts into arable lands is one of the key global environmental problems. As hot deserts are extreme habitats characterized by the
availability of solar energy with a nearly complete absence of organic life and water, space technology achievements in designing
closed ecological systems may be applicable to the design of sustainable settlements in the deserts. This review discusses the key
space technology findings for closed biogenerative life support systems (CBLSS), which can simultaneously produce food, water,
nutrients, fertilizers, process wastes, and revitalize air, that can be applied to hot deserts. Among them are the...
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/3926/version/2
CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA
amplicon sequencing – standard operating procedure, version 1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian
Fricke.
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence
datasets:

A) Mothur – a C++-based software package used for
clustering 16S rRNA sequences into operational taxonomic units (OTUs). Mothur creates OTUs using a matrix that describes
pairwise distances between representative aligned sequences and subsequently estimates within-sample diversity (alpha
diversity);
B) The Ribosomal Database (RDP) naïve Bayesian classifier assigns each 16S
sequence
to
a
reference
taxonomy
with
associated
empirical
probabilities
frequencies;
C) Qiime – a python-based workflow package,...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5888/version/2
based
on
oligonucleotide
CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA
amplicon sequencing – standard operating procedure, version 1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian
Fricke.
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence
datasets:

A) Mothur – a C++-based software package used for
clustering 16S rRNA sequences into operational taxonomic units (OTUs). Mothur creates OTUs using a matrix that describes
pairwise distances between representative aligned sequences and subsequently estimates within-sample diversity (alpha
diversity);
B) The Ribosomal Database (RDP) naïve Bayesian classifier assigns each 16S
sequence
to
a
reference
taxonomy
with
associated
empirical
probabilities
based
on
oligonucleotide
frequencies;
C) Qiime – a python-based workflow package,...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5888/version/3
CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA
amplicon sequencing – standard operating procedure, version 1.1
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian
Fricke.
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence
datasets: 

A) Qiime – a Python-based workflow package, allowing for
sequence processing and phylogenetic analysis using different methods including the phylogenetic distance metric UniFrac,
UCLUST, PyNAST and the RDP Bayesian classifier;

B) UCHIME – a tool for rapid
identification of chimeric 16S sequence fragments; 
C) Mothur – a C++-based software
package for 16S analysis;
D) Metastats and custom R scripts used to generate additional statistical and
graphical evaluations.
 
CloVR-16S...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6287/version/1
CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA
amplicon sequencing – standard operating procedure, version 1.1
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian
Fricke.
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence
datasets: 

A) Qiime – a Python-based workflow package, allowing for
sequence processing and phylogenetic analysis using different methods including the phylogenetic distance metric UniFrac,
UCLUST, PyNAST and the RDP Bayesian classifier;

B) UCHIME – a tool for rapid
identification of chimeric 16S sequence fragments; 
C) Mothur – a C++-based software
package for 16S analysis;
D) Metastats and custom R scripts used to generate additional statistical and
graphical evaluations.
 
CloVR-16S...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6287/version/2
CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA
amplicon sequencing – standard operating procedure, version1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence
datasets:

A) Mothur [1] – a C++ - based software package used for
clustering 16SrRNA sequences into operational taxonomic units (OTUs). Mothur creates OTUs using a matrix that describes
pairwise distances between representative aligned sequences and subsequently estimates within-sample diversity (alpha
diversity);
B)The Ribosomal Database (RDP) naive Bayesian classifier [2] assigns each 16S sequence to a
reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies;
C) Qiime
[3] – a python-based workflow package,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5888/version/1
CloVR-Metagenomics: Functional and taxonomic microbial community characterization from
metagenomic whole-genome shotgun (WGS) sequences – standard operating procedure,
version 1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcom Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian
Fricke.
The CloVR-Metagenomics pipeline employs several well-known tools and protocols for the analysis of metagenomic
whole-genome shotgun (WGS) sequence datasets:

A) UCLUST – a
C++-based
software
package
for
clustering
redundant
DNA
sequences
and
removing
artificial
454
replicates;
B) BLASTX and BLASTN for functional and taxonomic assignment of sequences,
respectively;
C) Metastats and custom R scripts to generate additional statistical and graphical
evaluation.

The CloVR-Metagenomics pipeline accepts as input multiple fasta files (1
sample per file) and a corresponding tab-delimited metadata file that specifies features associated with the samples,...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5886/version/3
CloVR-Metagenomics: Functional and taxonomic microbial community characterization from
metagenomic whole-genome shotgun (WGS) sequences – standard operating procedure,
version 1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-Metagenomics pipeline employs several well-known tools and protocols for the analysis of metagenomic
whole-genome shotgun (WGS) sequence datasets:

A) UCLUST [1] – a
C++-based software package for clustering redundant DNA sequences and removing artificial 454 replicates [1];

B)
BLASTX
and
BLASTN
[2]
for
functional
and
taxonomic
assignment
of
sequences,
respectively;
C) Metastats [3] and custom R scripts to generate additional statistical and graphical
evaluation.

The CloVR-Metagenomics pipeline accepts as input multiple fasta files (1
sample per file) and a corresponding tab-delimited metadata file that specifies features associated...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5886/version/1
CloVR-Metagenomics: Functional and taxonomic microbial community characterization from
metagenomic whole-genome shotgun (WGS) sequences – standard operating procedure,
version 1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcom Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian
Fricke.
The CloVR-Metagenomics pipeline employs several well-known tools and protocols for the analysis of metagenomic
whole-genome shotgun (WGS) sequence datasets:

A) UCLUST – a
C++-based
software
package
for
clustering
redundant
DNA
sequences
and
removing
artificial
454
replicates;
B) BLASTX and BLASTN for functional and taxonomic assignment of sequences,
respectively;
C) Metastats and custom R scripts to generate additional statistical and graphical
evaluation.

The CloVR-Metagenomics pipeline accepts as input multiple fasta files (1
sample per file) and a corresponding tab-delimited metadata file that specifies features associated with the samples,...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5886/version/2
CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single
microbial genome projects – standard operating procedure, version 1.0
Provedor de dados: 17
Autores: Kevin Galens; James R. White; Cesar Arze; Malcolm Matalka; Michelle Gwinn Giglio; The CloVR Team; Samuel V.
Angiuoli; W. Florian Fricke.
The CloVR-Microbe pipeline performs the basic processing and analysis steps required for standard microbial single-genome
sequencing projects: A) Whole-genome shotgun sequence assembly; B) Identification of protein and RNA-coding genes; and C)
Functional gene annotation. B) and C) are based on the IGS Annotation Engine (http://ae.igs.umaryland.edu/), which is described
elsewhere (K Galens et al. submitted). The assembly component of CloVR-Microbe can be executed independently from the gene
identification and annotation components. Alternatively, pre-assembled sequence contigs can be used to perform gene
identifications and annotations. The pipeline input may consist of unassembled raw sequence reads from the Sanger, Roche/454
GS FLX or Illumina GAII or...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5887/version/1
CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single
microbial genome projects – standard operating procedure, version 1.0
Provedor de dados: 17
Autores: Kevin Galens; James R. White; Cesar Arze; Malcolm Matalka; Michelle Gwinn Giglio; The CloVR Team; Owen
White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-Microbe pipeline performs the basic processing and analysis steps required for standard microbial single-genome
sequencing projects: A) Whole-genome shotgun sequence assembly; B) Identification of protein and RNA-coding genes; and C)
Functional gene annotation. B) and C) are based on the IGS Annotation Engine (http://ae.igs.umaryland.edu/), which is described
elsewhere (K Galens et al. submitted). The assembly component of CloVR- Microbe can be executed independently from the gene
identification and annotation components. Alternatively, pre-assembled sequence contigs can be used to perform gene
identifications and annotations. The pipeline input may consist of unassembled raw sequence reads from the Sanger, Roche/454
GS FLX or Illumina GAII or...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5887/version/3
CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single
microbial genome projects – standard operating procedure, version 1.0
Provedor de dados: 17
Autores: Kevin Galens; James R. White; Cesar Arze; Malcolm Matalka; Michelle Gwinn Giglio; The CloVR Team; Owen
White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-Microbe pipeline performs the basic processing and analysis steps required for standard microbial single-genome
sequencing projects: A) Whole-genome shotgun sequence assembly; B) Identification of protein and RNA-coding genes; and C)
Functional gene annotation. B) and C) are based on the IGS Annotation Engine (http://ae.igs.umaryland.edu/), which is described
elsewhere (K Galens et al. submitted). The assembly component of CloVR- Microbe can be executed independently from the gene
identification and annotation components. Alternatively, pre-assembled sequence contigs can be used to perform gene
identifications and annotations. The pipeline input may consist of unassembled raw sequence reads from the Sanger, Roche/454
GS FLX or Illumina GAII or...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5887/version/2
Cluster Analysis of Breast Cancer Microarray Data
Provedor de dados: 17
Autores: Kirtan P. Dave.
High-throughput genomic technology has rapidly become a major tool for the study of breast cancer. The recent development
gene expression microarray and related technology provide to an opportunity to perform more detail profiling of the disease
However, whole-genome approaches are still relatively new and critics have been quick to highlight, non-overlapping results from
groups testing similar hypotheses. In this canopy, cluster analysis helps to reduce complex multivariate data and may be used to
devise in the development of classification systems or taxonomies by gene ontology.
Tipo: Poster
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4936/version/1
c-Myc induced changes in higher order rDNA structure accompany growth factor stimulation of
quiescent cells
Provedor de dados: 17
Autores: Chiou-Nan Shiue; Rachel G. Berkson; Anthony P. H. Wright.
Human c-Myc is believed to be a high level coordinator of protein synthesis capacity and cell growth rate, capable of activating
transcription by all three nuclear RNA Polymerases. Direct activation of rDNA transcription by c-Myc is functionally conserved
in rat cells, despite high divergence in non-coding rDNA sequences, suggesting that this coordinating role is likely to be a general
within mammals. Upon re-feeding of starved cells, c-Myc activity enhances the efficiency of RNA Polymerase I and SL1/TIF-1B
recruitment to the rDNA and rapidly induces higher order gene loop structures in rDNA chromatin that juxtapose upstream and
downstream rDNA sequences. Furthermore c-Myc induced gene-loop formation in rDNA genes occurs independently of rDNA...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2007
URL: http://precedings.nature.com/documents/1448/version/1
cn.FARMS: a probabilistic model to detect DNA copy numbers
Provedor de dados: 17
Autores: Djork-Arné Clevert; Andreas Mitterecker; Andreas Mayr; Robert Burger; An De Bondt; Marianne
Tuefferd; Willem Talloen; Hinrich Göhlmann; Sepp Hochreiter.
Motivation: Existing pre-processing methods for DNA microarrays designed to detect copy number variations (CNVs) lead to
high false discovery rates (FDRs). High FDRs misguide researchers especially in the medical context where CNVs are wrongly
associated with diseases. We propose a probabilistic latent variable model, cn.FARMS, for array-based CNV analysis which
controls the FDR without loss of sensitivity. At a DNA region, cn.FARMS constructs a model by a Bayesian maximum a
posteriori estimation where the unobserved, latent variable represents the copy number that is measured by observed genetic
markers (probes). The latent variable’s prior prefers parameters which represent the null hypothesis, (same copy
number for all samples), from which...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4712/version/1
CO2 Enhancement of Forest Productivity Constrained by Limited Nitrogen Availability
Provedor de dados: 17
Autores: Richard J. Norby; Jeffrey M. Warren; Colleen M. Iversen; Charles T. Garten; Belinda E. Medlyn; Ross E. McMurtrie.
Stimulation of terrestrial productivity by rising CO~2~ concentration is projected to reduce the airborne fraction of anthropogenic
CO~2~ emissions; coupled climate-carbon (C) cycle models, including those used in the IPCC Fourth Assessment Report (AR4),
are sensitive to this negative feedback on atmospheric CO~2~^1^. The representation of the so-called CO~2~ fertilization effect in
the 11 models used in AR4 and subsequent models^2,3^ was broadly consistent with experimental evidence from four free-air
CO~2~ enrichment (FACE) experiments, which indicated that net primary productivity (NPP) of forests was increased by 23 +/2% in response to atmospheric CO~2~ enrichment to 550 ppm^4^. Substantial uncertainty remains, however, because of the
expectation...
Tipo: Manuscript
Palavras-chave: Earth & Environment; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3747/version/1
Cocaine self-administration in the mouse: A low-cost, chronic catheter preparation
Provedor de dados: 17
Autores: Matthew B. Pomrenze; Michael V. Baratta; Brian A. Cadle; Donald C. Cooper.
Intravenous drug self-administration is the most valid animal model of human addiction because it allows volitional titration of the
drug in the blood based on an individual’s motivational state together with the pharmacokinetic properties of the
drug. Here we describe a reliable low-cost mouse self-administration catheter assembly and protocol that that can be used to
assess a variety of drugs of abuse with a variety of protocols. We describe a method for intravenous catheter fabrication that
allows for efficient and long-lasting intravenous drug delivery. The intravenous catheters remained intact and patent for several
weeks allowing us to establish stable maintenance of cocaine acquisition. This was followed by a dose response study in the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7040/version/1
Co-detection: Ultra-reliable Nanoparticle-Based Electrical Detection of Biomolecules in the Presence
of Large Background Interference
Provedor de dados: 17
Autores: Yang Liu; Evangelyn Alocilja; Shantanu Chakrabartty.
Contrary to popular belief, we report that background interference in conductimetric biochips can be exploited using a novel
"co-detection" principle to significantly improve the reliability of detecting trace quantities of
biomolecules. The technique called "co-detection" exploits the non-linear redundancy amongst
synthetically patterned biomolecular logic circuits for deciphering the presence or absence of target biomolecules in a sample. In
this paper, we demonstrate the "co-detection" principle on gold-nanoparticle based conductimetric
soft-logic circuits which uses a silver-enhancement technique for signal amplification. Using co-detection, we have been able to
measure a 1000 times improvement in...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/4389/version/1
Codonopsis pilosula twines either to the left or to the right
Provedor de dados: 17
Autores: Gonghua Lin; Fang Zhao; Eviatar Nevo; Tongzuo Zhang; Jianping Su.
We report the twining handedness of Codonopsis pilosula, which has either a left- or right-handed helix among different plants,
among different tillers within a single plant, and among different branches within a single tiller. The handedness was randomly
distributed among different plants, among the tillers within the same plants, but not among the branches within the same tillers.
Moreover, the handedness of the stems can be strongly influenced by external forces, i.e. the compulsory left and right forming
inclined to produce more left- and right-handed twining stems, respectively, and the reversing could make a left-handed stem to be
right-handed and vice versa. We also discuss the probable mechanisms these curious cases happen.
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7026/version/1
Coexistence by recruitment variation: How large is the contribution of relative nonlinearity?
Provedor de dados: 17
Autores: Chi Yuan; Peter Chesson.
*Background/Question/Methods*

Recruitment variation is believed to be an
important mechanism of species coexistence in variable environments. This mechanism, however, is a composite of two other
mechanisms: the storage effect, and relative nonlinearity. The storage effect is a formalization of the concept of temporal
environmental niche differentiation. It is well-understood theoretically and has been tested in natural systems such as forests and
annual plant communities. Relative nonlinearity results from species differences in nonlinear responses to fluctuations in
competition. Such differences arise whenever species differ in life-history traits such as mean longevity. While the storage effect
is assumed to be the...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3595/version/1
Coexistence of grazed and grazing excluded patches increases plant and invertebrate diversity in a
Mediterranean oak woodland
Provedor de dados: 17
Autores: Miguel M. N. Bugalho; Lecomte Xavier; Maria Caldeira; Merícia Gonçalves; Manuela Branco.
Grazing is a global, dominant land use affecting biodiversity and ecosystem processes. In Mediterranean ecosystems grazing is a
major ecological and evolutionary driver but, surprisingly, there is little information on the use of grazing as a tool to manage
biodiversity in these ecosystems. We conducted an experiment to assess if the coexistence of grazing and grazing-excluded
patches would increase plant and invertebrate diversity in a Mediterranean evergreen oak woodland. Plant community traits were
different between treatments. Plant and litter biomass was higher, and the proportion of bare ground was lower, in
grazing-excluded plots. Grazing affected functional diversity with legumes, invertebrate detritivores and sup sucking insects being
more...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5194/version/1
Co-expression Toggling of MicroRNAs in Alzheimer’s Brain
Provedor de dados: 17
Autores: Malay Bhattacharyya.
We present the findings on how microRNA expression profiles changes in Alzheimer's brain.
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7123/version/1
Cognitive deficits of schizophrenia: the flower workshop initiative
Provedor de dados: 17
Autores: Maria Alice Ornellas Pereira; Alfredo Pereira Jr.
Advancement of research on the neurobiology of the schizophrenic brain has revealed a complex of factors, from genetic
tendencies affecting the development of brain structure to functional impairment caused by defective molecular signaling.
Recently, the attention of psychiatrists and mental health professionals has been directed to the presence of cognitive deficits,
responsible for most of the obstacles to the social insertion of patients.The schizophrenic person has a difficulty to manage the
flux of consciousness in social interactions. We address this difficulty with the Flower Arrangement Workshop, a methodology of
Psycho-Social Rehabilitation that reduces the vulnerability of the schizophrenic in the social environment. The workshop was
offered...
Tipo: Presentation
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1497/version/1
Cognitive dimensions of predator responses to imperfect mimicry?
Provedor de dados: 17
Autores: Lars Chittka; Daniel Osorio.
Many palatable insects, for example hoverflies, deter predators by mimicking well-defended insects such as wasps. However, for
human observers, these flies often seem to be little better than caricatures of wasps – their visual appearance and
behaviour are easily distinguishable. This imperfect mimicry baffles evolutionary biologists, because one might expect natural
selection to do a more thorough job. Here we discuss two types of cognitive processes that might explain why mimics
distinguishable mimics might enjoy increased protection from predation. Speed accuracy tradeoffs in predator decision making
might give imperfect mimics sufficient time to escape, and predators under time constraint might avoid time-consuming
discriminations between...
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1258/version/1
Cognitive epidemiology of ethnic health and the CHRM2 vagal vigour hypothesis
Provedor de dados: 17
Autores: Roy A. Frye.
Ethnic populations representing areas throughout California were compared regarding cognitive ability, socioeconomic position,
and mortality. Cognition and socioeconomic position were inversely correlated with mortality. The single nucleotide
polymorphism rs8191992 in the M2 muscarinic receptor gene (CHRM2) was previously linked to IQ and modulation of vagal
tone. The CHRM2 vagal vigour hypothesis posits that variation at rs8191992 alters the binding site for a brain-expressed
microRNA (hsa-mir-383) thereby changing expression of brain M2 muscarinic receptors to cause pleiotropic effects on cognition
and vagus nerve signalling which then affects health via the vagal cholinergic anti-inflammatory pathway. This may help explain
ethnic health differences,...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Immunology; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2862/version/1
Cognitive Sciences and Child Poverty: Facts and Challenges
Provedor de dados: 17
Autores: Amedeo D'Angiulli; Sebastian Lipina.
In the context of cognitive neuroscience, the study of poverty and social gradients is a very young area of research where a core
consensus of basic results is quickly emerging. However, as any emerging scientific discipline, the approaches used are influenced
by epistemological stances inherited from other disciplines, and potentially implicit ideological systems as well. Explicitly or
inadvertently, such influences can lead this critically important new area of research to methodological and ethical foundational
challenges and to issues that are in need of debate (e.g., poverty definition criteria, lack of specificity when considering child
poverty in terms of how children experience different type of deprivations, or lack of critics regarding social...
Tipo: Presentation
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4679/version/1
Coincidence between transcriptome analyses on different microarray platforms using a parametric
framework
Provedor de dados: 17
Autores: Tomokazu Konishi; Fumikazu Konishi; Shigeru Takasaki; Kohei Inoue; Kouji Nakayama; Akihiko Konagaya.
A parametric framework for the analysis of transcriptome data is demonstrated to yield coincident results when applied to data
acquired using two different microarray platforms. Discrepancies among transcriptome studies are frequently reported, casting
doubt on the reliability of collected data. The inconsistency among observations can be largely attributed to differences among the
analytical frameworks employed for data analysis. The existing frameworks normalizes data against a standard determined from
the data to be analyzed. In the present study, a parametric framework based on a strict model for normalization is applied to data
acquired using an in-house printed chip and GeneChip. The framework is based on a common statistical characteristic of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1746/version/1
Collaborate in conservation: A method for volunteer-scientist teams to monitor plant community
composition long-term in a private old-growth forest
Provedor de dados: 17
Autores: Erin J. Fleming; Nelson F. Galvis; Bette A. Loiselle; Julia F. Nerbonne.
To date, most studies on the management of invasive species have been done in nature reserves or national parks. Few published
studies demonstrate how scientists and local communities might collaborate to develop science-based management programs in
private forests. We present an example of such collaboration. The Congregational Summer Assembly (CSA) is a mixture of
common and privately owned lots within old-growth beech-maple forest in Lower Michigan. The community is trying to conserve
the forest and, thus, is interested in ecological variables that should be considered when designing a long-term ecosystem based
management plan. 
 In this base-line study we developed methods for volunteer-scientist teams to monitor 1)
the abundance of...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/5527/version/1
Collaborative platforms for streamlining workflows in Open Science
Provedor de dados: 17
Autores: Konrad U. Förstner; Gregor Hagedorn; Claudia Koltzenburg; M. Fabiana
Kubke; Daniel Mietchen.
Despite the internet’s dynamic and collaborative nature, scientists continue to produce grant proposals, lab
notebooks, data files, conclusions etc. that stay in static formats or are not published online and therefore not always easily
accessible to the interested public. Because of limited adoption of tools that seamlessly integrate all aspects of a research project
(conception, data generation, data evaluation, peer-reviewing and publishing of conclusions), much effort is later spent on
reproducing or reformatting individual entities before they can be repurposed independently or as parts of
articles.

We
propose
that
workflows
-
performed
both
individually
and
collaboratively - could potentially become more...
Tipo: Manuscript
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6066/version/1
Collagen-bound low density lipoprotein modifies endothelial cell adhesion to type V collagen:
Implications for atherosclerosis
Provedor de dados: 17
Autores: Stefan Lorkowski; Jürgen Rauterberg; Bärbel Harrach-Ruprecht; David Troyer.
Low density lipoprotein (LDL) is retained in the extracellular matrix of the arterial wall where it is considered to be atherogenic,
but little is known about how cell adhesion to the matrix is affected by collagen-bound LDL. We tested the effect of native,
oxidized and acetylated LDL reacted with adsorbed monomeric type I, III and V collagen on endothelial cell adhesion to collagen
using a colorimetric adhesion assay. We found that none of the LDL species affected adhesion to type I and III collagen, but that
collagen-bound native and acetylated LDL enhanced attachment to type V collagen, whereas bound oxidized LDL inhibited
adhesion to this collagen. We suggest that oxidized LDL associated with type V collagen in the arterial wall would favor...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1238/version/1
Collective Animal Behavior from Bayesian Estimation and Probability Matching
Provedor de dados: 17
Autores: Alfonso Perez-Escudero; Gonzalo de Polavieja.
Animals living in groups make movement decisions that depend, among other factors, on social interactions with other group
members. Our present understanding of social rules in animal collectives is based on empirical fits to observations and we lack
first-principles approaches that allow their derivation. Here we show that patterns of collective decisions can be derived from the
basic ability of animals to make probabilistic estimations in the presence of uncertainty. We build a decision-making model with
two stages: Bayesian estimation and probabilistic matching.
In the first stage, each animal makes a Bayesian
estimation of which behavior is best to perform taking into account personal information about the environment and social...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/5939/version/1
Collective Animal Behavior from Bayesian Estimation and Probability Matching
Provedor de dados: 17
Autores: Alfonso Perez-Escudero; Gonzalo G. de Polavieja.
Animals living in groups make movement decisions that depend, among other factors, on social interactions with other group
members. Our present understanding of social rules in animal collectives is mainly based on empirical fits to observations, with
less emphasis in obtaining first-principles approaches that allow their derivation. Here we show that patterns of collective
decisions can be derived from the basic ability of animals to make probabilistic estimations in the presence of uncertainty. We
build
a
decision-making
model
with
two
stages:
Bayesian
estimation
and
probabilistic
matching.

In the first stage, each animal makes a Bayesian estimation of which
behavior is best to perform taking into account personal...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/5939/version/2
Collective cell guidance by cooperative intercellular forces
Provedor de dados: 17
Autores: Dhananjay T. Tambe; Charles C. Hardin; Jeffrey J. Fredberg; Xavier Trepat.
Cells comprising a tissue migrate as part of a collective. In order to coordinate collective multi- cellular migration, each
constituent cell integrates local information including chemical signals and mechanical stresses.	The boundary between
a constituent cell and its immediate neighbors comprises cell-cell junctions and cryptic lamellipodia, but the state of local
mechanical stress exerted at that boundary has not been accessible experimentally. As such it is not clear how collective
mechanical processes could be coordinated over length scales spanning large multi-cellular assemblies. We report here maps of
the stresses exerted within and between cells comprising a monolayer. Within the cell sheet there arise unanticipated fluctuations
of...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5405/version/1
Colored filters improve exclusion of perceptual noise in visually symptomatic dyslexics
Provedor de dados: 17
Autores: Nadia Northway; Velitchko Manahilov; William A. Simpson.
Dyslexic individuals have deficits in detecting visual stimuli embedded in high levels of perceptual noise. Here we show that
visually symptomatic dyslexics, who otherwise had elevated contrast thresholds for discriminating symbols in visual noise, had
thresholds similar to non-dyslexics when wearing colored filters. These findings provide evidence that colored filters, which
minimize the visual distortions and discomfort of dyslexics when reading, improve dyslexics' noise exclusion to
normal levels.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1729/version/1
Colour reverse learning and animal personalities: the advantage of behavioural diversity assessed
with agent-based simulations
Provedor de dados: 17
Autores: Adrian G. Dyer; Alan Dorin; Verena Reinhardt; Marcello G. P. Rosa.
Foraging bees use colour cues to help identify rewarding from unrewarding flowers, but as conditions change, bees may require
behavioural flexibility to reverse their learnt preferences. Perceptually similar colours are learnt slowly by honeybees and thus
potentially pose a difficult task to reverse-learn. Free-flying honeybees (N = 32) were trained to learn a fine colour discrimination
task that could be resolved at ca. 70% accuracy following extended differential conditioning, and were then tested for their ability
to
reverse-learn
this
visual
problem
multiple
times.
Subsequent
analyses
identified
three
different
strategies:
‘Deliberative-decisive’ bees that could, after several flower visits, decisively make a large change to...
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/7037/version/1
COMBINE - a vision
Provedor de dados: 17
Autores: Nicolas Le Novere.
A decade ago, the creation of the Systems Biology Markup Language (SBML) changed the way people exchanged, verified and
re-used models in systems biology. The robustness and versatility of this format, coupled to a wide software support, fostered the
emergence of an entire area of research centered on model processing such as encoding, annotation, merging, comparison and
integration with other datasets. Recently, new languages appeared that complement the model description, such as SED-ML to
describe the simulation experiments or SBRML to encode the numerical results. In neuroscience, other fledgling efforts cover for
instance multi-compartment neurons with NeuroML, and neuronal networks with NineML. More are needed to cover the wide
spectrum of...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5992/version/1
COMBINE and MIRIAM Registry
Provedor de dados: 17
Autores: Nicolas Le Novere.
N/A
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6152/version/1
COMBINE - What it is, what it could be
Provedor de dados: 17
Autores: Nicolas Le Novere.
The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the
development of the various community standards and formats for computational models, initially in Systems Biology and related
fields. By doing so, it is expected that the federated projects will develop a set of interoperable and non-overlapping standards
covering all the aspects of modeling in biology.

Building on the experience of mature
projects, which already have stable specifications, software support, user-base and community governance, COMBINE will help
foster or support fledging efforts aimed at filling gaps or new needs. As those efforts mature, they may become part of the core set
of COMBINE...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6332/version/1
Combining systems biology and pharmacokinetics - drug cardiotoxicity assessment
Provedor de dados: 17
Autores: Sebastian Polak.
Cardiotoxicity assessment is a compulsory element of the drug development process required by drug agencies including the FDA
and EMA. The risk of fatal ventricular arrhythmia triggered by drugs is the rationale for such requirements. Over the last two
decades prolongation of QT interval has been responsible for the withdrawal of several drugs from the market and extensive black
box labeling restrictions. Although there are a number of mechanisms by which drugs may lead to QT prolongation, inhibition of
the potassium channels encoded by the hERG gene has been a cause in many cases. Thus, it is not surprising that interaction with
the hERG channel has become a major pharmacological safety concern. It can be reliably assessed with use of in silico realized...
Tipo: Presentation
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5900/version/1
Combining Transfer of TTF-1 and Pax-8 Gene: a Potential Strategy to Promote Radioiodine Therapy
of Thyroid Carcinoma
Provedor de dados: 17
Autores: Da Mu; Rui Huang; Xiaojuan Ma; Suping Li; Anren Kuang.
Cotransfer of TTF-1 and Pax-8 gene to tumor cells, resulting in the reexpression of iodide metabolism-associated proteins, such as
sodium iodide symporter (NIS), thyroglobulin (Tg), thyroperoxidase (TPO), offers the possibility of radioiodine therapy to
non-iodide-concentrating tumor because the expression of iodide metabolism-associated proteins in thyroid are mediated by the
thyroid transcription factors TTF-1 and Pax-8. The human TTF-1 and Pax-8 gene were transducted into the human thyroid
carcinoma (K1 and F133) cells by the recombinant adenovirus, AdTTF-1 and AdPax-8. Reexpression of NIS mRNA and protein,
but not TPO and Tg mRNA and protein, was detected in AdTTF-1-infected F133 cells, following with increasing radioiodine
uptake (6.1~7.4 times),...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2011
URL: http://precedings.nature.com/documents/6546/version/1
Combustion Analysis of a Meteorite Debris
Provedor de dados: 17
Autores: Saheeb Ahmed Kayani.
In this research paper, nature and origins of a meteorite debris identified near village Lehri in district Jhelum, Pakistan have been
determined. Total carbon content of a specimen of the meteorite debris is determined using combustion analysis and this
abundance has been compared with values reported in literature to establish likely origins of the debris.
Tipo: Poster
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5066/version/2
Combustion Analysis of a Meteorite Debris
Provedor de dados: 17
Autores: Saheeb Ahmed Kayani.
In this research paper, nature and origins of a meteorite debris identified near village Lehri in district Jhelum, Pakistan have been
determined. Total carbon content of a specimen of the meteorite debris is determined using combustion analysis and this
abundance has been compared with values reported in literature to establish likely origins of the debris.
Tipo: Poster
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5066/version/1
Comment on “On the Doubly Hydrogen Bonded Dimer of 7-Azaindole (0.1 M) as a
Model for DNA Base Pairs in Acetonitrile Solutions at Rt”
Provedor de dados: 17
Autores: Oh-Hoon Kwon; Omar F. Mohammed.
In continuation of comments by Catalán, the latest here questions the steady-state emission spectra of 7-azaindole, and
hence the validity of non-concerted proton transfer. In this comment, we show that his results are at fault and not supportive of his
claims. We provide possible causes of the misleading claims, including the contamination of the solvent with water moisture. We
conclude by calling for an end to such practice, which is counter productive, as it does not follow the scholarly approach of
science.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/2522/version/1
Comment on "Embryological evidence identifies wing digits in birds as digits 1, 2, and
3."
Provedor de dados: 17
Autores: Xing Xu; Jonah Choiniere; Corwin Sullivan; Fenglu Han.
Tamura et al. (Science, 11 Febuary 2011, p. 753) claim that the three avian wing digits should be identified as digits I-III based on
new embryological data and suggest that these identifications help to remove the conflict between the paleontological data and
developmental data concerning the homology of the avian digits. However, their results are not novel, and the authors fail to
address the critical problems relating to this interesting issue.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6433/version/1
Comment on Lobell et al "Climate Trends and Global Crop Production Since
1980"
Provedor de dados: 17
Autores: Mikhail A. Semenov; Peter R. Shewry.
Lobel et al (ScienceXpress) analysed changes in global yields which can be attributed to climate change trend, and reported a
5.5% decline in global wheat production since 1980. We have failed to confirm these results using a process-based crop model,
which showed no decline in wheat yield since the 1950s at two European sites. The Lobel et al conclusions are not valid due to the
limitations of the regression analysis used.
Tipo: Manuscript
Palavras-chave: Earth & Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6289/version/1
Comment to "Endogenous Viral Etiology of Prion Diseases"
Provedor de dados: 17
Autores: Claudiu Bandea.
This note is intended as a comment to a paper in Nature Precedings entitled "Endogenous viral etiology of prion
diseases":http://precedings.nature.com/documents/3887/version/1 . Because it contains illustrations that could not be
displayed in the comments section of that paper, I’m posting this comment here as a PDF document.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Immunology; Microbiology; Neuroscience; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/4101/version/1
Comments and Suggestions for Improvement of the Archon Genomics X PRIZE Validation Protocol
Provedor de dados: 17
Autores: Alexander Wait Zaranek; Tom Clegg; Ward Vandewege; Joseph V. Thakuria.
This document is a comment on the X PRIZE validation protocol written by Kedes et al. (2011).
We propose several
modifications which we think will improve the fairness and transparency of the contest while keeping the cost of the validation
process under control.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5766/version/1
Comments on “Assessing future risk: quantifying the effects of sea level rise on storm
surge risk for the southern shores of Long Island, New York”
Provedor de dados: 17
Autores: David A. Burton.
Tide gauge and satellite data indicate that the rate of sea level rise has not increased significantly in response to the last 3/4
century of CO2 emissions, so there is no reason to expect that it will do so in response to the next 3/4 century of CO2 emissions.
The best prediction for sea level in the future is simply a linear projection of the history of sea level at the same location in the
past. For Long Island, that is about 7-8 inches by 2080.
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2012
URL: http://precedings.nature.com/documents/7067/version/1
Common Transactivation Motif 9aaTAD recruits multiple general co-activators TAF9, MED15, CBP
and p300
Provedor de dados: 17
Autores: Martin Piskacek.
More than 2000 transcription factors are involved in the human gene regulation to provide cellular function and development.
Transactivation domain, TAD, mediates the interaction of transcription factors with general transcriptional co-activators such as
TAF9, MED15, CBP and p300. Recently reported NMR-data for interactions of these co-activators with transcription factors
reveal tightly binding of KIX and TAZ domains to common 9aaTAD motif. Nine-amino-acid Trans-Activation Domain, 9aaTAD,
defines a transactivation domain common to a large super-family of eukaryotic transcription factors represented in yeast by Gal4,
Oaf1, Pdr1, Rtg3, Pho4, Gln3, Gcn4 and in mammals by p53, E2A, NFAT, NFkB, HSF1, NF-IL6, MLL, EBNA2, VP16. The
9aaTAD family was derived from...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3488/version/2
Common Transactivation Motif 9aaTAD recruits multiple general co-activatorsTAF9, MED15, CBP
and p300
Provedor de dados: 17
Autores: Martin Piskacek.
More than 2000 transcription factors are involved in the human gene regulation to provide cellular function and development.
Transactivation domain, TAD, mediates the interaction of transcription factors with general transcriptional co-activators such as
TAF9, MED15, CBP and p300. Recently reported NMR-data for interactions of these co-activators with transcription factors
reveal tightly binding of KIX and TAZ domains to common 9aaTAD motif. Nine-amino-acid Trans-Activation Domain, 9aaTAD,
defines a transactivation domain common to a large super-family of eukaryotic transcription factors represented in yeast by Gal4,
Oaf1, Pdr1, Rtg3, Pho4, Gln3, Gcn4 and in mammals by p53, E2A, NFAT, NFkB, HSF1, NF-IL6, MLL, EBNA2, VP16. The
9aaTAD family was derived from...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3488/version/1
Commonness and rarity of species: Does species' rank influence contribution to ecosystem
function?
Provedor de dados: 17
Autores: Meha Jain; Case Prager; Dan Flynn; Caroline Devan; Georgia Hart; Farshid Ahrestani; Dan Bunker; Matt Palmer; Sean
Smukler; Jason Sircely; Shahid Naeem.
Across the globe, biodiversity loss is occurring at an unprecedented rate. Rare species are especially susceptible to extinction,
given that they typically have small population sizes and restricted geographic ranges, are less adaptable to disturbances, and are
greater habitat specialists. However, while rare species may be prone to extinction, it remains unclear whether the loss of rare
species is important to ecosystem function. In addition, it is important to consider the way in which rarity is defined, given that
there are multiple definitions of rarity based on a species' geographic range, habitat specificity, and abundance in a
community. Therefore, to better understand the contribution of rare species to community function, our study has...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5243/version/1
Community content building for evolutionary biology: Lessons learned from LepTree and
Encyclopedia of Life
Provedor de dados: 17
Autores: Cynthia Parr; Dana Campbell; John Park.
Online resources to aid large-scale ecological and evolutionary biology are beginning to take root, only a decade behind fields
such as genomics and molecular biology. One barrier has been a long tradition, in evolutionary biology at least, of work by
individuals on the order of a few hundred of species rather than the thousands or hundreds of thousands necessary to understand
the general evolutionary or ecological processes that explain species characteristics and distributions. Advances in collaborative
and semantic software offer promise – it should be possible to develop high quality online species-level datasets for
comparative analyses and even to integrate, via machine reasoning, across highly customized datasets. In this talk we will...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4603/version/1
Community curation on WikiPathways: How we assist knowledge collection
Provedor de dados: 17
Autores: Chris Evelo.
Biologists typically use knowledge represented as pathways to better understand the results of genomics experiments. Through
integration of data from different omics techniques with what we already know, statistical evaluation and subsequent data
visualization the results often start to make sense. An important problem is that we often do not have the relevant pathways, or
they may be incomplete or not suitable for usage by analytical tools. Wikipathways is meant to be an answer to the problems
described above. It uses mediawiki technology and dedicated open source java code to allow biologists to edit pathway content on
the web. We assist this process through the development of helpful software like a Diff tool, Go and KEGG converters, portal
mechanism,...
Tipo: Presentation
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3115/version/1
Community dynamics generates complex epidemiology through self-induced amplification and
suppression
Provedor de dados: 17
Autores: Zhenyuan Zhao; Juan Pablo Calderon; Chen Xu; Pak Ming Hui; Neil Johnson.
The development of quantitative models of outbreaks is key to their eventual control, from human and computer viruses through
to social (and antisocial) activities. Standard epidemiological models can reproduce many general features of outbreaks.
Unfortunately, the large temporal fluctuations which often dominate real-world data are thought to require more complicated,
system-specific models involving super-spreaders, specific social network topologies and rewirings, and birth-death processes.
However we show here that these large fluctuations have a generic explanation in terms of underlying community dynamics.
Communities increasing (or decreasing) in size, act as instantaneous amplifiers (or suppressors) yielding a complex temporal
evolution whose...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2030/version/1
Community Outreach through Genomics Education Partnership
Provedor de dados: 17
Autores: Ramana Madupu; Anne G. Rosenwald; A. Malcolm Campbell; Satish C. Bhalla; Granger Sutton.
The J Craig Venter Institute (JCVI) has recently partnered with undergraduate university faculty to expand the scope of education
and outreach program as part of the NIAID’s BRC initiative, by joining forces with faculty members participating
in the Genomics Education Partnership (GEP). The goal of the GEP is to provide opportunities for undergraduate students to
participate in genomics research and gain hands on experience. Faculty members trained on annotation methodologies and tools
during the Prokaryotic Annotation Workshop conducted at JCVI, impart their knowledge in the classroom as part of the semester
course. As a pilot project, we are currently collaborating with 3 groups lead by a faculty member, spread across 3 universities in
the...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3149/version/1
Community-level analysis of anthropogenic impacts on rocky shore communities in Sri Lanka
Provedor de dados: 17
Autores: Ashoka D. K. H. Manage.
Human activities threat seashore communities in many areas of the world and their impacts on coastal ecosystem are a matter of
increasing concern. Present study describes the anthropogenic disturbances on the rocky shore community structure by comparing
the benthic communities of disturbed and non-disturbed areas in Sri Lanka where rocky shores remain virtually untouched so far
by experimental studies. Impacts of human disturbances; trampling, handling and exploitation on the community structure of
rocky macro benthic assemblages were tested in high-, mid- and low-intertidal area by stratified sampling method at Rumassala
marine sanctuary and adjacent two localities at either side of the marine sanctuary, Galle and Unawatuna. Univariate measures,
log...
Tipo: Manuscript
Palavras-chave: Ecology; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2317/version/1
Comparative density functional theory study on the relative gas phase enthalpies and free energies of
formation for the mono- through hepta-halogenated (X=F, Cl, Br) anthraquinones
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas phase standard state (298.15 K, 1 atmosphere) relative enthalpies and free energies of formation were calculated for all monothrough hepta-halogenated (X=F, Cl, Br) anthraquinone congeners using the B3LYP, BHandHLYP, M062X, PBE0, and B97D
density functionals with the 6-311++G(d,p) basis set. All levels of theory yielded similar results with strong intra- and
inter-method correlations for both the relative enthalpy and free energy values and the corresponding thermodynamic stability
rank. Within each homolog group, the most thermodynamically stable isomers are those which maximize substitution at the lateral
positions (2, 3, 7, and 8) versus the less stabilizing peri positions (1, 4, 6, and 9), while also minimizing destabilizing adjacent
substitution...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5153/version/1
Comparative Enumeration Gene Expression
Provedor de dados: 17
Autores: Leonardo Varuzza; Carlos A. D. E. B. Pereira.
This paper is about differential gene expression measured by transcript counting methods such as SAGE or MPSS. It introduces
two significance tests for detection of differential expressed tags: frequentist and Bayesian. Under the frequentist view, it is
proposed a test that computes the critical level as a function of each tag total frequency. Under the Bayesian view the Full
Bayesian Significance Test is used considering the logistic normal distribution. The two proposed significance levels, the
frequentist and the Bayesian, are compared for a data set with four libraries. The linking function between them is a Beta
distribution function with mean 0.39 and standard deviation 0.30.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2002/version/1
Comparative functional genomics approach for the annotation of proteins in Unclassified Halophilic
archaeon DL31
Provedor de dados: 17
Autores: N S. Sardeshmukh; S G. Sanmukh; E Nakkeeran.
The structure, function and sub-cellular location prediction for the unknown proteins from Unclassified Halophilic archaeon DL31
were carried out for characterization of the proteins in their respective families. The 991 genes for hypothetical proteins in
Halophilic archaeon DL31 chromosome were predicted by the application of computational methods and Bioinformatics web
tools. The structure predictions for 206 unknown proteins were possible whereas functions were predicted in 825 protein
sequences. The function prediction for the proteins were done by using Bioinformatics web tools like CDD-BLAST,
INTERPROSCAN and PFAM by searching protein databases for the presence of conserved domains. The Sub-cellular location
predictions were done for all the unknown...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6784/version/1
Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions
Provedor de dados: 17
Autores: Pedro Beltrao; Luis Serrano.
Protein interaction networks are an important part of the post-genomic effort to integrate a part-list view of the cell into
system-level understanding. Using a set of 11 yeast genomes we show that combining comparative genomics and secondary
structure information greatly increases consensus-based prediction of SH3 targets. Benchmarking of our method against positive
and negative standards gave 83% accuracy with 26% coverage. The concept of an optimal divergence time for effective
comparative genomics studies was analyzed, demonstrating that genomes of species that diverged very recently from
_Saccharomyces cerevisiae_ (_S. mikatae_, _S. bayanus_, and _S. paradoxus_), or a long time ago (_Neurospora crassa_ and
_Schizosaccharomyces pombe_), contain less...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/16/version/1
Comparative Litter Quality and Recalcitrance Among Native Grasses and the Invasive,
Non-indigenous KR Bluestem (_Bothriochloa ischaemum_)
Provedor de dados: 17
Autores: Amanda Benbow; Kelly G. Lyons.
KR Bluestem (_Bothriochloa ischaemum_) is a non-indigenous, invasive, C4 grass that was introduced throughout the
Midwestern and Southwestern U.S. short- to midgrass prairies with the aim of improving degraded rangelands. The aggressive
nature of KR bluestem has led to dramatic alterations of natural and managed ecosystems. Comparative studies of decomposition
often show that non-indigenous, invasive plant species have higher rates of nutrient cycling than indigenous species; however, KR
bluestem appears to deviate from this trend. Large amounts of litter are observed in KR-dominated grasslands as compared to
intact native grasslands, suggesting that the species has a relatively lower decomposition rate and may slow nutrient cycling in
these systems....
Tipo: Presentation
Palavras-chave: Ecology; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3614/version/1
Comparative methods in R hackathon
Provedor de dados: 17
Autores: Brian O'Meara; Michael Alfaro; Charles Bell; Benjamin Bolker; Marguerite Butler; Peter Cowan; Damien
de Vienne; Richard Desper; Joseph Felsenstein; Luke Harmon; Christoph Heibl; Andrew Hipp; Gene Hunt; Thibaut Jombart;
Steve Kembel; Hilmar Lapp; Scott Loarie; Wayne Maddison; Peter Midford; David Orme; Emmanuel Paradis; Sam Price; Dan
Rabosky; Brian Sidlauskas; Stacey Smith; Dave Swofford; Todd Vision; Peter Waddell; Amy Zanne; Derrick Zwickl.
The R statistical analysis package has emerged as a popular platform for implementation of powerful comparative methods to
understand the evolution of organismal traits and diversification. A hackathon was organized to bring together active R developers
as well as end-users working on the integration of comparative phylogenetic methods within R to actively address issues of data
exchange standards, code interoperability, usability, documentation quality, and the breadth of functionality for comparative
methods available within R. Outcomes included a new base package for phylogenetic trees and data, a public wiki with tutorials
and overviews of existing packages, code to allow Mesquite and R to interact, improvement of existing packages, and increased...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2126/version/1
Comparative semiempirical, ab initio, and DFT study on the thermodynamic properties of linear and
branched PFSA/Fs, PFCA/Fs, and perhydroalkyl sulfonic acids, alkanes, and alcohols
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
A systematic and comprehensive semiempirical, Hartree-Fock (HF) ab initio, and B3LYP density functional theory (DFT) study
was conducted on the relative thermodynamic properties of various linear and branched perfluorinated and perhydrogenated alkyl
compounds. The semiempirical AM1, PM3, and PM6 methods all consistently and accurately predict that branched alkyl
compounds will generally be more thermodynamically stable than their linear counterparts. In contrast, HF and B3LYP
calculations with the 6-31G(d,p), 6-31++G(d,p), and 6-311++G(d,p) basis sets predict that linear isomers will be more stable than
branched analogs. These different linear versus branched perfluoroalkyl/perhydroalkyl thermodynamic property trends between
semiempirical and ab initio/DFT...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3928/version/1
Comparative study on the gas to solution phase solvation free energies of model combustion flue gas
compounds (N~2~, O~2~, CO~2~, H~2~O, SO~2~, and CO) in 178 organic solvents using the
IEFPCM-UFF, CPCM, and SMD implicit solvent models at the Gaussian-4 (G4) level of theory
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas to solution phase Gibbs free energies of solvation at 298.15 K for transfer of six representative combustion flue gas
compounds (N~2~, O~2~, CO~2~, H~2~O, SO~2~, and CO) were calculated at the Gaussian-4 (G4) level of theory using the
IEFPCM-UFF, CPCM, and SMD implicit solvent models for 178 organic solvents. The IEFPCM-UFF and CPCM models yield
similar free energies of solvation for all six compounds in each of the solvents considered, having maximum absolute intra-solvent
deviations <1.6 kJ mol^-1^. Substantial free energy of solvation differences were observed between the
IEFPCM-UFF/CPCM and SMD models, with maximum absolute intra-solvent deviations up to 45.5 kJ mol^-1^. The
IEFPCM-UFF and CPCM models displayed strong free energy of...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5227/version/1
Comparative theoretical investigation on the isomerization energies of long-chain perfluoroalkanes: A
case study with perfluorooctane sulfonic acid congeners
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
The gas and solution phase relative thermodynamic stabilities of the 89 perfluorooctane sulfonic acid (PFOS) congeners play an
important role in assessing whether synthetic conditions for commercial mixtures are under thermodynamic or kinetic control, and
in calculating various physico-chemical properties for these important industrial compounds and environmental contaminants. In
the present study, 4,272 gas and solvent phase (water and n-octanol) calculations were conducted at various levels of
semiempirical (PM6), density functional (B3LYP, B97D, PBE1PBE [PBE0], and M062X functionals with the 6-311++G(d,p)
basis set), and second order Moller-Plesset perturbation (MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p)) theory and the SMD,
IEFPCM-UFF, and CPCM implicit...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5353/version/1
Comparative theoretical investigation on the isomerization energies of long-chain perfluoroalkanes: A
case study with perfluorooctanoic acid congeners
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
The gas and solution phase relative thermodynamic stabilities of the 39 linear and branched perfluorooctanoic acid (PFOA)
congeners in both their acid and anionic forms were calculated at various levels of density functional (B3LYP, wB97XD, and
M062X
functionals
with
the
6-311++G(d,p)
basis
set)
and
second
order
Moller-Plesset
perturbation
(MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p)) theory using the SMD implicit solvation model. The B3LYP functional does not
accurately model the expected trends in thermodynamic stability of PFOA isomers with linear versus branched perfluoroalkyl
chains. Calculations obtained with the M062X and MP2 model chemistries suggest these theoretical methods may be more
appropriate for relative thermodynamic stability studies on...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/5528/version/1
Comparing and Explaining Public Acceptance Of Ecological Forestry in Tasmania and the U.S.
Pacific Northwest
Provedor de dados: 17
Autores: Robert Ribe; Rebecca Ford; Kath Williams.
Major controversies have erupted in recent years about extensive and intensive timber harvesting programs in Tasmania and the
U.S. Pacific Northwest. These conflicts have centered on ecological impacts and both regions have responded by adopting
similar programs of “ecological forestry.”
Both programs emphasize the retention of varying
amounts of trees in aggregated or dispersed patterns within harvests, and seek to “life boat”
mature-forest habitat functions across some harvest prescriptions. Are these programs garnering similar public acceptance? Do
people with similar ideologies judge the acceptability of forests similarly in both regions? Do perceptions differ between regions
due to differences in...
Tipo: Presentation
Palavras-chave: Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3744/version/1
Comparison of Cholesterol Lowering Diets: Apple, Casein Cytochrom P450 protein and Cholesterol
7α Hydroxylase Activities in Hamsters
Provedor de dados: 17
Autores: Rakesh Sharma; Rakesh K. Tandon.
Lithogenic diet, casein and apple fiber diets were fed to hamsters for 3-5 weeks. For control group, animals were fed on normal
Purina chow without any supplement. The cholesterol lowering effect of lithogenic diet, casein and apple diets were compared.
After dietary regimen, animals were screened for any gall stone formation. The isolated liver microsomes were separated from
animals and tested for the cholesterol-7α Hydroxylase (CH) enzyme activity measurement in all three groups. The
control animals did not show any gall stone formation and their CH enzyme activities were normal. The lithogenic diet showed
significantly enhanced CH enzyme activities while animals fed on casein and apple diet regimen showed moderate increase in
microsomal CH...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4205/version/1
Comparison of computationally- and manually-assigned Gene Ontology annotations to improve
functional characterization of gene products.
Provedor de dados: 17
Autores: Maria Costanzo; Rama Balakrishnan; Karen Christie; Eurie Hog; Julie Park; J. Michael Cherry.
The Gene Ontology (GO) describes molecular functions, biological processes, and cellular components of gene products using
controlled-vocabulary terms that are related to each other in a structure that facilitates computing on GO annotations within and
across species. Experimentally-based GO annotations that are manually curated from the literature are often used to predict the
functions of related uncharacterized proteins. The accuracy of such annotations is thus critically important, particularly for a
well-studied model organism such as _Saccharomyces cerevisiae_ which is frequently used as the source of the experimental data.


Comparison of experimentally-based annotations with those predicted by
computational methods...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5095/version/1
Comparison of Efficiency of Photodynamic Diagnostics with Topical Use of the 3% and 15%
Aminolevulinic Acid in the Detection of Vulvar Lesions
Provedor de dados: 17
Autores: Agnieszka Mazdziarz; Habib Alkhalayla; Aleksandra Zielinska; Beata Spiewankiewicz.
The objective of the study was evaluating the efficiency of the photodynamic method PDD (photodynamic diagnosis) in the
detection of vulvar lesions when two concentrations of the photosensitizer were used ( 3%- and 15%-aminolevulinic acid ), as
well as evaluating the efficiency of this method when compared to the efficiency of vulvoscopy, against the result of histological
examination. Two concentrations of the 5-ALA cream ( aminolevulinic acid ) - 3% and 15% - were used in the PDD testing. The
study group was divided into two subgroups A and B. In subgroup A the 15% eucerine - based cream was used. In subgroup B the
3% ALA gel with addition of 2% DMSO was used. The photosensitizer was applied to the vulva four to six hours before the
examination. In order...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2011
URL: http://precedings.nature.com/documents/6272/version/1
Comparison of histopathologicalfeatures of Vibrio cholerae O1 El Tor
andO139 Bengal infections in rabbit intestinal mucosa
Provedor de dados: 17
Autores: Atif A. Baig.
Vibrio cholerae is the causative agent of the infectious disease, cholera. The bacteria adhere to the mucosal membrane and release
cholera toxin, leading to watery diarrhea. There are >100 serovars of V. cholerae, but the O1 and O139 serovars are the
main causative agents of cholera. The present study aimed to compare the severity of intestinal mucosal infection caused by O1 El
Tor and O139 V. cholerae in a rabbit ileal loop model.
The results showed that although the fluid
accumulation was similar in the loops inoculated with O1 and O139 V. cholerae, the presence of blood was detected only in the
loops inoculated with the O139 serovar. Serosal hemorrhage was confirmed by histopathological examination and the loops
inoculated with...
Tipo: Presentation
Palavras-chave: Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/6418/version/1
Comparison of Plasmid yield between L.B. and using Molasses as a medium
Provedor de dados: 17
Autores: Nitin Sharma; Purshottum Kaushik.
During the initial studies I have found that the molasses may be a good alternative to costly L.B media where one can manipulate
the C/N ratio as per requirement of cell. Molasses is one of the best alternatives as it is cheap and can be easily manipulated.
Escherichia coli is a bacterium that is commonly found in the lower intestine of warm-blooded animals. it is possible to produce
vaccine by molasses medium. The paper is opening a new face of study.
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3897/version/1
Competent intermediate hosts and genetic re-assortment: what does the ferret and raccoon model tell
us about influenza pandemic risk?
Provedor de dados: 17
Autores: Paul Alexander.
Avian influenza virus (AI) strains such as H5N1 and H9N2 are endemic among birds and poultry globally and mainly within
Eurasia. Human cases have been reported yet the transmission among humans has been inefficient. While swine and pigs have
functioned as the primary intermediate host and genetic re-assorter of AI virus, other intermediate and competent hosts may be
emerging. This could be potentially disastrous for humans should this lead to the generation of a pandemic strain. This letter to the
editor highlights recent findings of AI spread among ferrets and raccoons and the real prospect of genetic re-assortment and
evolution among these intermediate non-avian species that could lead to a pandemic strain. These hosts revealed efficient
transmission to...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/2506/version/1
Competition between spiders and pitcher plants? Prey availability and trophic interactions in bogs
Provedor de dados: 17
Autores: Clarisse Hart; Jonathan Mejia; Nicholas J. Gotelli; Aaron M. Ellison.
Web-building spiders (e.g. _Frontinella communis_ and _Neriene radiata_) and northern pitcher plants (_Sarracenia purpurea_)
are co-occurring sit-and-wait predators that may compete for shared arthropod prey. We evaluated prey availability and capture
rates by web-weaving spiders and pitcher plants in a headwater stream box complex (Harvard Pond) in central Massachusetts. We
established 40 plots with spider and pitcher plant removal treatments, and collected arthropod prey captured by open pitcher
plants, pitfall traps, and sticky traps in those plots. 

The removal of web-building
spiders significantly changed the distribution of prey captured by the pitcher plants (Chi-square test: P = 2.2 × 10-16 at
Harvard...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3662/version/1
Complex Systems Analysis of Arrested Neural Cell Differentiation during Development and
Analogous Cell Cycling Models in Carcinogenesis
Provedor de dados: 17
Autores: I C. Baianu; V. I. Prisecaru.
A new approach to the modular, complex systems analysis of nonlinear dynamics of arrested neural cell Differentiation--induced
cell proliferation during organismic development and the analogous cell cycling network transformations involved in
carcinogenesis is proposed. Neural tissue arrested differentiation that induces cell proliferation during perturbed development and
Carcinogenesis are complex processes that involve dynamically inter-connected biomolecules in the intercellular, membrane,
cytosolic, nuclear and nucleolar compartments. Such 'dynamically inter-connected' biomolecules form
numerous inter-related pathways referred to as 'molecular networks'. One such family of signaling
pathways contains the cell...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Molecular Cell
Biology; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7101/version/1
Complex Systems Analysis of Arrested Neural Cell Differentiation during Development and
Analogous Cell Cycling Models in Carcinogenesis
Provedor de dados: 17
Autores: V. I. Prisecaru; I C. Baianu.
A new approach to the modular, complex systems analysis of nonlinear dynamics of arrested neural cell Differentiation--induced
cell proliferation during organismic development and the analogous cell cycling network transformations involved in
carcinogenesis is proposed. Neural tissue arrested differentiation that induces cell proliferation during perturbed development and
Carcinogenesis are complex processes that involve dynamically inter-connected biomolecules in the intercellular, membrane,
cytosolic, nuclear and nucleolar compartments. Such 'dynamically inter-connected' biomolecules form
numerous inter-related pathways referred to as 'molecular networks'. One such family of signaling
pathways contains the cell...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Molecular Cell
Biology; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7101/version/2
Complex Systems Analysis of Cell Cycling Models in Carcinogenesis
Provedor de dados: 17
Autores: I. C. Baianu.
A new approach to the modular, complex systems analysis of nonlinear dynamics in cell cycling network transformations
involved in carcinogenesis is proposed. Carcinogenesis is a complex process that involves dynamically inter-connected
biomolecules in the intercellular, membrane, cytosolic, nuclear and nucleolar compartments that form numerous inter-related
pathways referred to as networks.
The variable biotopology of such dynamic networks is highly complex,
and has a number of interesting properties that can be formally characterized at one level of organization by mathematical
structures called 'biogroupoids'. 
One such family of pathways contains the cell
cyclins. Cyclins are proteins that link several...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Immunology;
Molecular Cell Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6205/version/1
Complex Systems Biology of Organisms
Provedor de dados: 17
Autores: I. C. Baianu.
Complex Systems Biology models and theories are axiomatically defined in terms of concrete categories and organismic
supercategories (OS) to include both complete self-reproduction of logically defined pi-entities founded in Quine's
logic and dynamic system diagrams subject to both algebraic and topological transformations. Mathematical models of complex
organisms are expressed in terms of category theory and organismic supercategories (OS). OS theories have applications in:
Bioinformatics, Developmental Biology, Genomics and Molecular Cell Biology
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7044/version/1
Composition of Biochemical Networks using Domain Knowledge
Provedor de dados: 17
Autores: Martin Goodfellow; John Wilson; Ela Hunt.
Graph composition has applications in a variety of practical applications. In drug development, for instance, in order to understand
possible drug interactions, one has to merge known networks and examine topological variants arising from such composition.
Similarly, the design of sensor nets may use existing network infrastructures, and the superposition of one network on another can
help with network design and optimisation. The problem of network composition has not received much attention in algorithm
and database research. Here, we work with biological networks encoded in Systems Biology Markup Language (SBML), based on
XML syntax. We focus on XML merging and examine the algorithmic and performance challenges we encountered in our work
and the...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4966/version/1
Compressibility of Calcium Nitride to 137 Kb
Provedor de dados: 17
Autores: Michael J. Bucknum.
A compressibility study was carried out of calcium nitride using a powdered sample in a diamond anvil cell with a
Debeye-Scherrer camera at Cornell High Energy Synchrotron Source (CHESS) in 1992. This is the first such high pressure study
of the equation of state of calcium nitride reported in the literature.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1771/version/1
Compressibility of Calcium Nitride to 137 Kb
Provedor de dados: 17
Autores: Michael J. Bucknum.
[alpha]-Ca3N2 as an opaque, red-brown crystalline powder lying in the cubic Ia-3 space group, was placed into a specially
designed glove box under nitrogen atmosphere, along with powdered f.c.c. Au, and carefully loaded within the [beta]-brass gasket
of a conventional high pressure diamond anvil cell (DAC). The powdered samples were then sealed under nitrogen atmosphere to
a
pressure
of
8.40
Kb
and
taken
to
Cornell
High
Energy
Synchrotron
Source
where
conventional
Debeye-Scherrer diffraction photographs were recorded at 8.40, 91.0 and 137 Kb. The
pressure of the sample was monitored by using the equation of state of Au, and no phase change from the Ia-3 structure was
observed in the sample of powdered [alpha]-Ca3N2 up to a pressure of 137...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1771/version/4
Compressibility of Calcium Nitride to 137 Kb
Provedor de dados: 17
Autores: Michael J. Bucknum.
A compressibility study was carried out of calcium nitride using a powdered sample in a diamond anvil cell with a
Debeye-Scherrer camera at Cornell High Energy Synchrotron Source (CHESS) in 1992. This is the first such high pressure study
of the equation of state of calcium nitride reported in the literature.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1771/version/3
Compressibility of Calcium Nitride to 137 Kb
Provedor de dados: 17
Autores: Michael J. Bucknum.
A compressibility study was carried out of calcium nitride using a powdered sample in a diamond anvil cell with a
Debeye-Scherrer camera at Cornell High Energy Synchrotron Source (CHESS) in 1992. This is the first such high pressure study
of the equation of state of calcium nitride reported in the literature.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1771/version/2
Computational binding mechanism of Mycobacterium tuberculosis UDP-NAG enolpyruvyl
transferase (MurA) with inhibitors fosfomycin, cyclic disulfide analog RWJ-3981, pyrazolopyrimidine
analog RWJ-110192, purine analog RWJ-140998, 5-sulfonoxy-anthranilic aci
Provedor de dados: 17
Autores: C. M. Anuradha; B. Babajan; M. Chaitanaya; C. Rajasekhar; Suresh Kumar Chitta.
Worldwide, tuberculosis (TB) remains the most frequent and important infectious disease causing morbidity and death. One-third
of the world's population is infected with Mycobacterium tuberculosis (Mtb), the etiologic agent of TB. In this
context, TB is in the top three, with malaria and HIV being the leading causes of death from a single infectious agent, and about
two million deaths are attributable to TB annually. The bacterial enzyme MurA catalyzes the transfer of enolpyruvate from
phosphoenolpyruvate (PEP) to uridine diphospho-N-acetylglucosamine (UNAG), which is the first committed step of bacterial
cell wall biosynthesis. In this work, 3D structural model of Mtb-MurA enzyme has been developed, for the first time, by
homology modeling and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3731/version/1
Computational methods in cancer gene networking
Provedor de dados: 17
Autores: Edwin Wang.
In the past few years, many high-throughput techniques have been developed and applied to biological studies. These techniques
such as “next generation” genome sequencing, chip-on-chip, microarray and so on can be used to
measure gene expression and gene regulatory elements in a genome-wide scale. Moreover, as these technologies become more
affordable and accessible, they have become a driving force in modern biology. As a result, huge amount biological data have
been produced, with the expectation of increasing number of such datasets to be generated in the future. High-throughput data are
more comprehensive and unbiased, but ‘real signals’ or biological insights, molecular mechanisms
and biological principles...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2737/version/1
Computational Prediction and Analysis of the NAPP - DR6 Interaction: Implications for
Alzheimer's Research
Provedor de dados: 17
Autores: Josheph Audie; Sergei Ponomarev.
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that involves a devastating clinical course and
lacks an effective treatment. A biochemical model for neuronal development that might have implications for AD, recently
proposed by Nikolaev and co-workers, hinges on a novel protein-protein interaction between the death cell receptor six (DR6)
ectodomain and an N-terminal fragment of amyloid precursor protein (NAPP). The model provides a coherent and satisfying
framework for better understanding AD pathophysiology. Moreover, the DR6-NAPP interaction offers a tempting target for novel
pharmacological intervention. Given all of this, we constructed a structural model of the DR6-NAPP interaction using the
neurotrophin p75 receptor as...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4545/version/1
Computational Studies Of Huntington Protein: Classification & Binding Pattern
Determination
Provedor de dados: 17
Autores: Nitin M. R. Chitranshi; Shipra M. S. Gupta.
Huntington's disease (HD) is a dominantly inherited neurodegenerative disorder characterized by progressive motor
deficits, psychiatric deterioration, worsening chorea, cognitive impairment due to neuronal cell loss in the basal ganglia, cerebral
cortex, and its fragments interactions with themselves and other biomolecules that results in aggregates , transcriptional repression
, oxidative injury and mitochondrial dysfunction . The repeat domain of Huntingtin interacting protein (HIP) 14 (PDB id 3eu9) is
used to study the structure based drug design. We made the selection of 50 different small molecules which were screened out
through various fixed parameters and applied descriptors to generate the model for molecules that shows the drug likeness...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5581/version/1
Computational system biology
Provedor de dados: 17
Autores: Ankit Geete.
Systems biology is a multi-disciplinary field that deals with mechanisms involved in complex biological processes
by considering them as integrated systems of multiple interacting components. The huge amount of data involved in this study
necessitates the use of computational tools.
Tipo: Presentation
Palavras-chave: Biotechnology; Genetics & Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7104/version/1
Computer aided drug design studies to explore novel antagonist of human myotrophin
Provedor de dados: 17
Autores: Sandeep Swargam; K Mahesh; Amineni Umamaheswari.
Human myotrophin is the smallest ankyrin repeat protein implicated as a factor to induce cardiac hypertrophy. Activation of
myotrophin was observed during acute myocardial infarction (MI). In acute coronary syndrome (ACS) patients, myotrophin acts
as a self-governing predictor of major adverse cardiac events (MACE). Therefore, human myotrophin serves as an effective drug
target for discovery of new potential drugs. Recent human myotropin inhibitors have poor pharmalogical properties leading to
intolerable side effects. Hence, ligand based virtual screening protocol of CADD method was persuaded in the present study to
propose new class potential myotrophin inhibitors. Docking was done by using Schrödinger software suite 2010
(maestro v9.1), docked...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6562/version/1
Computer simulations on the sympatric speciation modes for the Midas cichlid species complex
Provedor de dados: 17
Autores: Karen Luz-Burgoa; Suzana Moss de Oliveira; Jorge de Sá Martins.
Cichlid fishes are one of the best model system for the study of evolution of the species. Inspired by them, in this paper we
simulated the splitting of a single species into two separate ones via random mutations, with both populations living together in
sympatry, sharing the same habitat.
We study the ecological, mating and genetic conditions needed to reproduce the
polychromatism and polymorphism of three species of the Midas Cichlid species complex. Our results show two scenarios for the
A. Citrinellus speciation process, one with and the other without disruptive natural selection. 
In the first
scenario, the ecological and genetic conditions are sufficient to create two new species, while in the second the mating and
genetic...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/798/version/1
Computerized Protein Modeling and Molecular Docking Analysis of Human Proto Oncogene
Tyrosine Protein Kinase YES for Discovery of Novel Lead Molecules
Provedor de dados: 17
Autores: Karuna J. Jaya Sai; Dibyabhaba Pradhan; Amineni Umamaheswari.
Human proto-oncogene tyrosine-protein kinase YES (YES) is a non receptor kinase belongs to Src family. This gene lies in close
proximity to thymidylate synthase gene on chromosome 18, and a corresponding pseudogene has been found on chromosome 22.
In hepatocellular carcinoma and colorectal carcinoma elevated human YES activity was observed. Inhibitors of human YES
reported till date are in clinical trials and associated with several side effects. The present study was mainly aimed in homology
modeling of human YES and discovery of novel lead molecules that inhibit YES kinase more efficiently with fewer side effects.
Virtual screening and docking techniques were applied to identify novel lead molecule of YES kinase. As there was no reported
human YES...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4902/version/1
Computing the inverse of the neurophysiological spike-response transform
Provedor de dados: 17
Autores: Vladimir Brezina; Estee Stern; Keyla Garcia-Crescioni; Mark W. Miller; Charles S. Peskin.
Consider the transform from a discrete neuronal spike train to a continuous neurophysiological response such as postsynaptic
membrane voltage or muscle contraction. Often, we can record only the response. Here we therefore ask about the inverse of
this transform: given the response, how can we estimate from it the spike train that produced it? In previous work, we have
developed a kernel-based "decoding" method for system identification of the forward transform. Using
several variant approaches based on this method, here we demonstrate how to identify the spike train, in the minimal case from
just the response, with synthetic as well as real synaptic and neuromuscular data.
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3472/version/1
Concentration-dependent free radical scavenging and ferric reducing ability of Vetiveria zizanioides
(L.) Nash: Protective effect of vetiver root extract during oxidative stress
Provedor de dados: 17
Autores: Suaib Luqman; Ritesh Kumar; Shubhangi Kaushik; Suchita Srivastava; Mahendra P. Darokar; Suman P. S.
Khanuja.
Vetiveria zizanioides, popularly known as ‘KHUS’ grass, has been known to India since ancient
times. It is the major source of well-known oil of vetiver, which is used in medicine and in perfumery. A concentration-dependent
ferric reducing, free radical scavenging and antioxidant activity of two genotypes, namely KS 1 and gulabi of vetiver (Vetiveria
zizanioides L. Nash) root, were evaluated by using in vitro assays: the ferric reducing antioxidant power (FRAP), 1,
1-Diphenyl-2-picrylhydrazyl (DPPH), total phenolic content (TPC), total antioxidant capacity (TAC) and reducing power (RP)
assay. A positive co-relation was observed between FRAP, DPPH and TPC of cv KS 1, whereas TAC and RP showed a negative
co-relation. A significant...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6920/version/1
Concentrations and profiles of melatonin and serotonin in fruits and vegetables during ripening: A
mini-review
Provedor de dados: 17
Autores: Sierra Rayne.
Melatonin and serotonin are important phytochemicals with hormonal, antioxidant, immunoactive, and neuroactive biological
properties, and have been identified and quantitated in a broad range of fruits, vegetables, and derivative products. Relatively little
is known about the temporal profiles of these compounds during fruit and vegetable development. Improved knowledge in this
area would help guide our understanding of fundamental plant physiology, as well as potentially facilitate better control of
melatonin and serotonin concentrations and relative abundances in functional foods. The current work synthesizes the current
state-of-the-art regarding the presence and trends of these compounds during fruit and vegetable development. The literature
reflects...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4722/version/1
Concentrations of Polychlorinated Biphenyls (PCBs), Polychlorinated Dibenzo-p-dioxins and Furans
(PCDD/Fs), and Polybrominated Diphenyl Ethers (PBDEs) as Functions of Sample Depth in Killer
Whale (Orcinus orca) Blubber
Provedor de dados: 17
Autores: Michael G. Ikonomou; Sierra Rayne; Norman F. Crewe.
Concentrations of polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), and
polybrominated diphenyl ethers (PBDEs) were examined as a function of depth in killer whale (Orcinus orca) blubber samples.
Lipid-normalized concentrations of PCBs, PCDD/Fs, and PBDEs did not display significant variation with depth in three distinct
blubber layers (outer, central, and inner). Significantly more variation in contaminant concentrations were observed with depth on
a wet weight basis for the killer whale sample. The current study indicates that non-invasive microdart biopsy sampling methods
commonly used for monitoring contaminants in marine mammals yield representative details on contaminant burdens for
chlorinated and...
Tipo: Manuscript
Palavras-chave: Chemistry; Ecology; Earth & Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/638/version/1
Conceptual model of E. coli transcriptional machinery
Provedor de dados: 17
Autores: Anatoly Sorokin; Timur Dzhelyadin; Svetlana G. Kamzolova.
At the moment one type of analysis of transcription regulatory networks (TRNs) in prokaryotes is topological analysis of graph
structure of possible regulatory interaction links (see for example [1]). That type of analysis takes into account possibility links
that designate the fact that one gene product in some conditions can modulate transcription of the other. The benefit of such
approach is that it is allow analyzing TRN at the whole cell level. At the same type it is known that at least some responses are
regulated by abundance of elements of transcription machinery [2-3]. We have developed conceptual model of whole cell E. coli
TRN with SBGN ER, SBGN PD and SBGN AF languages [4]. That model is the first step towards incorporation of some
quantitative...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6341/version/1
Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2
Sub-clades
Provedor de dados: 17
Autores: Henry L. Niman; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong
Kong in 1997 1,2. The number of confirmed human cases now exceeds 300, and the associated Case Fatality Rate exceeds 60% 3.
The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases
4-7. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases
that lack an editing function, thereby resulting in antigenic drift 8. We report here the concurrent acquisition of the same
polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, and Ghana. These changes are not easily
explained by the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/459/version/1
Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2
Sub-clades
Provedor de dados: 17
Autores: Henry L. Niman; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong
Kong in 1997. The number of confirmed human cases now exceeds 300, and the associated Case Fatality Rate exceeds 60%. The
genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases. The
gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an
editing function, thereby resulting in antigenic drift. We report here the concurrent acquisition of the same polymorphism by
multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, and Ghana. These changes are not easily explained by the
current...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/459/version/2
Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2
Sub-clades
Provedor de dados: 17
Autores: Henry Niman; Mona M. Aly; Abdel-Satar Arafa; Nasr El-Sayed; Ahmed E. Nayel; Ahmed S. Abdelghani; Hala M.
Esmat; Gregory A. Raczniak; Mensah Agyen-Frempong; William K. Ampofo; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong
Kong in 1997 1,2. The number of confirmed human cases now exceeds 300 and the associated Case Fatality Rate exceeds 60% 3.
The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases
4-7. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases
that lack an editing function, thereby resulting in antigenic drift 8. We report here the concurrent acquisition of the same
polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, Kuwait, and Ghana. These changes are not
easily...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/459/version/4
Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2
Sub-clades
Provedor de dados: 17
Autores: Henry L. Niman; Magdi D. Saad; Mona M. Aly; Jeffery Tjaden; Kenneth C. Earhart; Marshall R. Monteville;
Moustafa M. Mansour; Nasr El-Sayed; Ahmed E. Nayel; Ahmed S. Abdelghani; Hala M. Esmat; Emad M. Labib; Ehab A.
Ayoub; Abdelattar Arafa; Gregory A. Raczniak; Mensah Agyen-Frempong; William K. Ampofo; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong
Kong in 1997. The number of confirmed human cases now exceeds 300, and the associated Case Fatality Rate exceeds 60%. The
genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases. The
gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an
editing function, thereby resulting in antigenic drift. We report here the concurrent acquisition of the same polymorphism by
multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, and Ghana. These changes are not easily explained by the
current...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Ecology; Genetics & Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/459/version/3
Concurrent, Collaborative Ontology Building with Collaborative
Protégé (CP)
Provedor de dados: 17
Autores: Daniel Schober.
Creation of an ontology according to some common plan is best accomplished collaboratively. This is sometimes contradicted by
the distribution of the ontology’s developers. An obvious solution therefore is to build collaboration into ontology
development tools. Such support necessarily includes both the technical means to perform editing operations upon an ontology,
but also support for the communication that makes collaboration such a vital part of much ontology development. To investigate
the distributed, collaborative ontology engineering process and the corresponding capabilities of the Collaborative Protege 3 (CP)
tool, members of the OntoGenesis network came together and enriched the Ontology of Biomedical Investigations (OBI) with
new...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3516/version/1
Congener specific organic carbon normalized soil and sediment-water partitioning coefficients for the
C1 through C8 perfluorinated alkylsulfonic and alkylcarboxylic acids
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Organic carbon normalized soil and sediment-water partitioning (Koc) coefficients were estimated for all C1 through C8
perfluorinated alkylsulfonic acid (PFSA) and alkylcarboxylic acids (PFCA) congeners. The limited experimental Koc dataset for
the straight chain C7 through C10 PFCAs and C8 and C10 PFSAs was correlated to SPARC and ALOGPS computationally
estimated octanol-water partitioning constants and used to predict Koc values for both branched and linear C1 through C8
isomers. All branched and linear congeners in this homologue range are expected to have Koc values>1, leading to
their accumulation in organic matter on sediments and soils, retardation during ground and pore water flow, and the preferential
association with dissolved organic...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3011/version/1
Congener specific organic carbon normalized soil and sediment-water partitioning coefficients for the
C~1~ through C~8~ perfluoroalkyl carboxylic and sulfonic acids
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Organic carbon normalized soil and sediment-water partitioning coefficients (K~oc~) were estimated for all C~1~ through C~8~
perfluoroalkyl carboxylic (PFCA) and sulfonic (PFSA) acid congeners. The limited experimental K~oc~ dataset for the straight
chain C~7~ through C~10~ PFCAs and C~8~ and C~10~ PFSAs was correlated to SPARC and ALOGPS computationally
estimated octanol-water partitioning / distribution constants and used to predict K~oc~ values for both branched and linear C~1~
through C~8~ isomers. Branched and linear congeners in this homologue range are generally expected to have K~oc~ values
>1, leading to their accumulation in organic matter on sediments and soils, retardation during ground and pore water
flow, and the preferential...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3011/version/2
Congener-Specific Numbering Systems for the Environmentally Relevant C4 through C8
Perfluorinated Homologue Groups of Alkyl Sulfonates, Carboxylates, Telomer Alcohols and Acids,
and Their Derivatives
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest; Ken J. Friesen.
We introduce a congener-specific numbering system for the C4 through C8 perfluorinated homologue groups of alkyl sulfonates,
carboxylates, telomer alcohols and acids, and their derivatives. Increasing length of the carbon chain beyond C3 leads to a
corresponding rapid increase in the number of potential isomers (C4 =4, C5 =8, C6 =17, C7 =39, and C8 =89 congeners). There is
a need for clear and unambiguous chemical shorthand to ensure accuracy and consistency in the future perfluorinated alkyl
substance (PFA) literature, and to correct previous misconceptions that may have restricted research efforts into developing
full-congener PFA analysis. If adopted by the research community, introduction of a numbering system at this relatively early
stage of...
Tipo: Poster
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1957/version/2
Congener-Specific Numbering Systems for the Environmentally Relevant C4 through C8
Perfluorinated Homologue Groups of Alkyl Sulfonates, Carboxylates, Telomer Alcohols and Acids,
and Their Derivatives
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest; Ken J. Friesen.
We introduce a congener-specific numbering system for the C4 through C8 perfluorinated homologue groups of alkyl sulfonates,
carboxylates, telomer alcohols and acids, and their derivatives. Increasing length of the carbon chain beyond C3 leads to a
corresponding rapid increase in the number of potential isomers (C4 =4, C5 =8, C6 =17, C7 =39, and C8 =89 congeners). There is
a need for clear and unambiguous chemical shorthand to ensure accuracy and consistency in the future perfluorinated alkyl
substance (PFA) literature, and to correct previous misconceptions that may have restricted research efforts into developing
full-congener PFA analysis. If adopted by the research community, introduction of a numbering system at this relatively early
stage of...
Tipo: Poster
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1957/version/1
Connecting Carbon Capture with Oceanic Biomass Production
Provedor de dados: 17
Autores: Chen Wang.
The climate change believed by anthropogenic emission is not isolated but tightly coupled with other issues including biodiversity
loss and ocean acidification etc., and in order to prevent the potential serious impacts, both political and technological methods are
being tried for greenhouse mitigation. Dimming the income sunlight by some “geoengineering”
approaches currently seem ruinously expensive and technically difficult, and would not prevent the increase of greenhouse gases
(GHGs) in atmosphere and ocean acidification, so capturing carbon to reduce the environmental concentration of carbon dioxide
(CO2) and promoting renewable energy development for the reduction of using fossil fuels are very necessary. Biofuels derived
from...
Tipo: Manuscript
Palavras-chave: Chemistry; Ecology; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5161/version/1
Connecting Seed Lists of Mammalian Proteins Using Steiner Trees
Provedor de dados: 17
Autores: Amelia G. White; Avi Ma'ayan.
Multivariate experiments and genomics studies applied to mammalian cells often produce lists of genes or proteins altered under
treatment/disease vs. control/normal conditions. Such lists can be identified in known protein-protein interaction networks to
produce subnetworks that “connect” the genes or proteins from the lists. Such subnetworks are
valuable for biologists since they can suggest regulatory mechanisms that are altered under different conditions. Often such
subnetworks are overloaded with links and nodes resulting in connectivity diagrams that are illegible due to edge overlap. In this
study, we attempt to address this problem by implementing an approximation to the Steiner Tree problem to connect seed lists of
mammalian...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1768/version/1
Connectivity reflects coding: A model of voltage-based spike-timing-dependent-plasticity with
homeostasis
Provedor de dados: 17
Autores: Claudia Clopath; Lars Büsing; Eleni Vasilaki; Wulfram Gerstner.
Electrophysiological connectivity patterns in cortex often show a few strong connections in a sea of weak connections. In some
brain areas a large fraction of strong connections are bidirectional, in others they are mainly unidirectional. In order to explain
these connectivity patterns, we use a model of Spike-Timing-Dependent Plasticity where synaptic changes depend on presynaptic
spike arrival and the postsynaptic membrane potential. The model describes several nonlinear effects in STDP experiments, as
well as the voltage dependence of plasticity under voltage clamp and classical paradigms of LTP/LTD induction. We show that in
a simulated recurrent network of spiking neurons our plasticity rule leads not only to receptive field development, but also to...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3362/version/1
Consciousness and subjective time: a plausible auditory approach
Provedor de dados: 17
Autores: Sepehr Ehsani.
The perception of time is an indispensable facet of human consciousness, and may in fact be dynamically present in primates and
other species, albeit with different manifestations. Moreover, contrary to the physical measures of time, cognitive temporal
perception may be subjectively affected by both internal and environmental cues. Here we review the evidence for the potential
role of the auditory system in shaping the cortical measures of time, and propose possible auditory methods for studying this
aspect of consciousness.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5941/version/1
Consciousness as Recursive, Spatiotemporal Self-Location
Provedor de dados: 17
Autores: Frederic Peters.
At the phenomenal level, consciousness can be described as a singular, unified field of recursive self-awareness, consistently
coherent in a particular way; that of a subject located both spatially and temporally in an egocentrically-extended domain, such
that conscious self-awareness is explicitly characterized by I-ness, now-ness and here-ness. The psychological mechanism
underwriting this spatiotemporal self-locatedness and its recursive processing style involves an evolutionary elaboration of the
basic orientative reference frame which consistently structures ongoing spatiotemporal self-location computations as i-here-now.
Cognition computes action-output in the midst of ongoing movement, and consequently requires a constant self-locating...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2444/version/1
Consciousness as Recursive, Spatiotemporal Self-Location
Provedor de dados: 17
Autores: Frederic Peters.
At the phenomenal level, consciousness can be described as a singular, unified field of recursive self-awareness, consistently
coherent in a particular way; that of a subject located both spatially and temporally in an egocentrically-extended domain, such
that conscious self-awareness is explicitly characterized by I-ness, now-ness and here-ness. The psychological mechanism
underwriting this spatiotemporal self-locatedness and its recursive processing style involves an evolutionary elaboration of the
basic orientative reference frame which consistently structures ongoing spatiotemporal self-location computations as i-here-now.
Cognition computes action-output in the midst of ongoing movement, and consequently requires a constant self-locating...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2444/version/2
Consensus virtual screening approaches to predict protein ligands
Provedor de dados: 17
Autores: Andreas Kukol.
In order to exploit the advantages of receptor-based virtual screening, namely time/cost saving and specificity, it is important to
rely on algorithms that predict a high number of active ligands at the top ranks of a small molecule database. Towards that goal
consensus methods combining the results of several docking algorithms were developed and compared against the individual
algorithms. Furthermore, a recently proposed rescoring method based on drug efficiency indices was evaluated. Among AutoDock
Vina 1.0, AutoDock 4.2 and GemDock, AutoDock Vina was the best performing single method in predicting high affinity ligands
from a database of known ligands and decoys. The rescoring of predicted binding energies with the water/butanol partition
coeffcient...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5979/version/1
Conservation Pakage for Modal Ecorace
Provedor de dados: 17
Autores: Ajit Kumar Sinha.
Conserving biodiversity is about genetic variety, species, habitats and ecosystems. All are important, but it is often most
appropriate, practical and effective to focus on species. With modern conservation awareness, there is a welcome and popular
commitment to maintaining the diversity of species in India. Nevertheless, over the last 50 years, we have witnessed the severe
decline of many once widespread and familiar species, such as tropical Tasar silkworm Antherea mylitta D. Conservation is not
just about avoiding extinctions, but about restoring or recovering species populations to secure levels and preventing other species
from reaching such a perilous situation in the first place. Species, by their very nature, have specific ecological requirements....
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6162/version/1
Considerate Approaches to Achieving Sufficiency for ABC Model Selection
Provedor de dados: 17
Autores: Chris Barnes; Sarah Filippi; Michael Stumpf; Tom Thorne.
ABC methods have gained popularity in situations where traditional methods which involve explicit evaluation of likelihoods are
either too cumbersome or fail outright. This, almost by definition means that for any interesting real-world scenario we have no or
little recourse to sufficient statistics, which had previously been central to ABC approaches and their derivation. In the context of
model selection this can have particularly undesirable consequences if we have to compress the data through the use of summary
statistics. In this talk we discuss complementary approaches that allow us to address this problem in a principled manner, and
outline the scenarios where ABC model selection is unproblematic. We will argue that many of the most interesting...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5952/version/1
Consortium Building For PEM MFC Using Synthetic Media As Substrate
Provedor de dados: 17
Autores: Muralidharan Ayyappan; Dimpal Parida; Arti Yadav; Ramya Mohandass.
Microbial production of electricity is an important form of bioenergy since Microbial Fuel cells (MFC) offer the possibility of
extracting electric current from a wide range of organic wastes and renewable biomass. Factors affecting the MFC operational
effectiveness are the MFC design and the bacterial metabolism and electron transfer. The purpose of this study is to identify
species which are responsible for electricity generation so as to build a suitable consortium and to investigate the relative
efficiencies between the microbial consortiums. Enrichment by repeated transfer of a bacterial consortium harvested from the
anode compartment of a MFC with synthetic media as a substrate increased the output from an initial level of 34 mA to a maximal
level of...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/6632/version/1
Consortium for Functional Glycomics Overview
Provedor de dados: 17
Autores: James C. Paulson.
This presentation provides an overview of the Consortium for Functional Glycomics.
Tipo: Presentation
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/11/version/1
Constraint-Guided Workflow Composition Based on the EDAM Ontology
Provedor de dados: 17
Autores: Anna-Lena Lamprecht; Stefan Naujokat; Bernhard Steffen; Tiziana Margaria.
Methods for the automatic composition of services into executable workflows need detailed knowledge about the application
domain, in particular about the available services and their behavior in terms of input/output data descriptions. In this paper we
discuss how the EMBRACE data and methods ontology (EDAM) can be used as background knowledge for the composition of
bioinformatics workflows. We show by means of a small example domain that the EDAM knowledge facilitates finding possible
workflows, but that additional knowledge is required to guide the search towards actually adequate solutions. We illustrate how
the ability to flexibly formulate domain-specific and problem-specific constraints supports the workflow development process.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5397/version/1
Constraints of FL Motif on the Targeting and Function of Sodium-Bicarbonate Cotransporter 1
Provedor de dados: 17
Autores: Hong C. Li; Ali Shawki; YoonKyung Park; Emily Y Li; Kyung-Soo Hahm; Joel H. Collier; Bryan Mackenzie;
Manoocher Soleimani.
A C-terminal dihydrophobic FL motif plays a vital role in the basolateral targeting of sodium bicarbonate cotransporter 1. To
further characterize the role of dihydrophobic FL motif, 1). the FL motif in wild type (PFLS) was reversed to LF (PLFS), 2). the
FL motif (PFLS) was shifted upstream (FLPS), and 3). the FL motif (PFLS) was shifted downstream (PSFL). The wild type
(PFLS) and its mutant (PLFS) were exclusively expressed on the basolateral membrane by con-focal microscopy, however, the
mutant (FLPS) and (PSFL) were predominantly mistargeted to the apical membrane and the cytoplasm, respectively. Functional
studies showed that the mutant (PSFL) displayed a remarkably reduced current (p value<0.05 vs wild type). The
mutant (PSFL) displayed a...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1638/version/1
Constructing ABC summary statistics: semi-automatic ABC
Provedor de dados: 17
Autores: Paul Fearnhead; Dennis Prangle.
To analyze complex datasets efficiently, ABC algorithms require well-chosen low dimensional summary statistics of the data. We
present a method to construct appropriate summary statistics for ABC in a semi-automatic manner. Previous attempts at this have
been based around constructing statistics that are sufficient (or approximately sufficient). However, in most real applications it is
difficult to know if low-dimensional sufficient statistics exist, or how to approximate them if they do. We take an alternative
approach of aiming for summary statistics which will enable inference about certain parameters of interest to be as accurate as
possible.  This talk describes our method, the underpinning theory, and promising empirical results on a range...
Tipo: Presentation
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5959/version/1
Construction of direction selectivity in V1: from simple to complex cells
Provedor de dados: 17
Autores: Timm Lochmann; Tim Blanche; Daniel A. Butts.
Despite detailed knowledge about the anatomy and physiology of the primary visual cortex (V1), the immense number of
feed-forward and recurrent connections onto a given V1 neuron make it difficult to understand how the physiological details relate
to a given neuron’s functional properties. Here, we focus on a well-known functional property of many V1 complex
cells: phase-invariant direction selectivity (DS). While the energy model explains its construction at the conceptual level, it
remains unclear how the mathematical operations described in this model are implemented by cortical circuits. To understand how
DS of complex cells is constructed in cortex, we apply a nonlinear modeling framework to extracellular data from macaque V1.
We use a...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5861/version/1
Contaminant Trapping Behind Large Dams: A Mini-Review
Provedor de dados: 17
Autores: Sierra Rayne; Ken J. Friesen.
It appears likely that the installation of many large dams on major rivers worldwide over the past century has led to large and
complex contaminant loadings becoming trapped in the sediments behind these dams. Future planned large dam removal efforts or
unintentional breaches may result in substantial contaminant releases downstream. We review the current state of the art regarding
knowledge of contaminant loadings behind large dams and potential downstream impacts following dam breaches.
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2965/version/1
Context-based generation of kinetic equations with SBMLsqueezer 1.3
Provedor de dados: 17
Autores: Andreas Dräger; Sandra Nitschmann; Alexander Dörr; Johannes Eichner; Michael J. Ziller;
Andreas Zell.
The development of predictive, quantitative models constitutes a common task in today‘s systems biology. To
obtain a mathematical model description for the simulation of gene-regulatory, signaling, and metabolic networks, kinetic
equations are required for each reaction within the network. Deriving and assembling these formulas is a complicated,
time-consuming, and error-prone process that requires knowledge about the structure of interactions, consistently choosing a rate
law for each type of reaction, and assignment of appropriate units to all parameters. In many cases, thermodynamic dependencies
between the parameters have to be taken into account. For multi compartment models, the concentration units of reacting species
have to be converted...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4983/version/1
Control in technological systems and physical intelligence: an emerging theory
Provedor de dados: 17
Autores: Bradly Alicea.
The transduction and processing of physical information is becoming important in a range of research fields, from the design of
materials and virtual environments to the dynamics of cellular microenvironments. Previous approaches such as morphological
computation/soft robotics, neuromechanics, and embodiment have provided valuable insight. This work approaches haptic,
proprioception, and physical sensing as all part of the same subject. In this presentation, three design criteria for applying physical
intelligence to engineering applications will be presented. These criteria have several properties in common, which inspires two
types of end-effector model: stochastic (based on a spring) and deterministic (based on a piezomechanical array). The
generalized...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5910/version/1
Control of cell division in the adult brain by heparan sulfates in fractones and vascular basement
membranes
Provedor de dados: 17
Autores: Frederic Mercier; Vanessa Douet.
Regulation of cell division in adult tissues and organs requires the coordination of growth factors at the surface of
potentially-dividing cells in specific anatomic loci named germinal niches. However, the biological components and physiological
system that control growth factors in the germinal niches are unknown. In the adult brain, no function has been attributed to
fractones, the fractal-shaped extracellular matrix structures located in the subventricular zone (SVZ) next to neural stem and
progenitor cells. Here, we show that BMP-7 (bone morphogenetic protein-7) and FGF-2 (fibroblast growth factor-2) modulate cell
division in the SVZ only if the growth factors bind to heparan sulfates localized in fractones and adjoined vascular basement
membranes....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5444/version/1
Control of konzo in the Democratic Republic of Congo
Provedor de dados: 17
Autores: J. Howard Bradbury; Chretienne Mandombi; D Nahimana; J. P. Banea; Ian C. Denton; N Kuwa.
Konzo is an upper motor neuron disease that causes irreversible paralysis of the legs mainly in children and young women^1,2^,
due to consumption of large amounts of cyanogens from poorly processed cassava, the staple food of tropical Africa^3^. Konzo
occurs in the Democratic Republic of Congo (DRC),Mozambique, Tanzania, Cameroon, Central African Republic and Angola. In
March 2010 the wetting method, which removes cyanogens from cassava flour^4,5,6^, was taught to and used by the mothers of
Kay Kalenge village. This reduced the total cyanide content of cassava flour to the FAO/WHO limit of 10ppm^7^. Cyanogen
intake of school children, monitored by urinary thiocyanate analyses, decreased from mean values of 332 to 130
μmole/L. The percentage of...
Tipo: Manuscript
Palavras-chave: Chemistry; Neuroscience; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6520/version/1
Control over stress induces plasticity of individual prefrontal cortical neurons: A conductance-based
neural simulation
Provedor de dados: 17
Autores: Juan A. Varela; Jungang Wang; Andrew L. Varnell; Donald C. Cooper.
Behavioral control over stressful stimuli induces resilience to future conditions when control is lacking. The medial prefrontal
cortex(mPFC) is a critically important brain region required for plasticity of stress resilience. We found that control over stress
induces plasticity of the intrinsic voltage-gated conductances of pyramidal neurons in the PFC. To gain insight into the underlying
biophysical mechanisms of this plasticity we used the conductance- based neural simulation software tool, NEURON, to model
the increase in membrane excitability associated with resilience to stress. A ball and stick multicompartment conductance-based
model was used to realistically fit passive and active data traces from prototypical pyramidal neurons in neurons in rats...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6267/version/1
Controlling sap-sucking insect pests with recombinant endophytes expressing plant lectin
Provedor de dados: 17
Autores: Xiuyun Zhao; Gaofu Qi; Xianfang Zhang; Nan Lan; Xinrong Ma.
We developed a novel pest management strategy, which uses endophytes to express anti-pest plant lectins. Fungal endophyte of
Chaetomium globosum YY-11 with anti-fungi activities was isolated from rape seedlings, and bacterial endophytes of SJ-10
(Enterobacter sp.) and WB (Bacillus subtilis) were isolated from rice seedlings. Pinellia ternate agglutinin gene was cloned into
SJ-10 and WB for expression by a shuttle vector, and YY-11 was mediated by Agrobacterium tumefaciens. Positive transformants
were evaluated using PCR and Western blot assay. Recombinant endophytes colonized most of crops, and resistance of rice
seedlings, which were inoculated with the recombinant endophytic bacteria, to white backed planthoppers was dramatically
enhanced by decreasing...
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4862/version/1
Convergence of atmospheric and North Atlantic CO2 trends on multidecadal timescales
Provedor de dados: 17
Autores: Galen McKinley; Amanda Fay; Taro Takahashi; Nicolas Metzl.
The oceans’ carbon uptake substantially reduces the rate of anthropogenic carbon accumulation in the atmosphere1,
and thus slows global climate change. Some diagnoses of trends in ocean carbon uptake have suggested a significant weakening in
recent years2-8, while others conclude that decadal variability confounds detection of long-term trends9-11. Here, we study
trends in observed surface ocean partial pressure of CO2 (pCO2) in three gyre-scale biomes of the North Atlantic, considering
decadal to multidecadal timescales between 1981 and 2009. Trends on decadal timescales are of variable magnitudes and depend
sensitively on the precise choice of years. As more years are considered, oceanic pCO2 trends begin to converge to the trend in...
Tipo: Manuscript
Palavras-chave: Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5993/version/1
Cooperative effect of ribosomal protein s19 and Pim-1 kinase on murine c-Myc expression and
myeloid/erythroid cellularity
Provedor de dados: 17
Autores: Anne-Sophie Frojmark; Jitendra Badhai; Joakim Klar; Maria Thuveson; Jens Schuster; Niklas Dahl.
Diamond Blackfan anemia (DBA) is a bone marrow failure syndrome associated with heterozygous mutations in the ribosomal
protein S19 (RPS19) gene in a subgroup of patients. One of the interacting partners with RPS19 is the oncoprotein PIM-1 kinase.
We intercrossed Rps19+/- and Pim-1-/- mice strains to study the effect from the disruption of both genes. The double mutant
(Rps19+/-Pim-1-/-) mice display normal growth with increased peripheral white- and red blood cell counts when compared to the
w.t. mice (Rps19+/+Pim-1+/+). Molecular analysis of bone marrow cells in Rps19+/-Pim-1-/- mice revealed up-regulated levels
of c-Myc and the anti-apoptotic factors Bcl2, BclXL and Mcl-1. This is associated with a reduction of the apoptotic factors Bak
and Caspase 3 as...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2882/version/1
Copper and other heavy metals in specialized crops and their effects on soil coenosis
Provedor de dados: 17
Autores: Anna Steindl; Thomas Strumpf; Frank Riepert.
The background of the project are claims of the EU regulation to generate reliable data considering the extent of copper
contamination
in
soils
of
specialized
crops
in
order
to
decide
about
copper
restrictions
in
organic
farming.

2522 single soil samples were collected on 85 vineyard and 13 hop areas
with different management histories. Samples were taken from sites presently under cultivation, formerly cultivated, and sites
without anthropogenic copper contamination as control, indicating natural background values. In addition to Aqua Regia
extraction for determining total copper contents, available plant copper content was analyzed in NH~4~NO~3~ extraction. Soil
parameters such as pH-value, C/N ratio, soil type etc....
Tipo: Presentation
Palavras-chave: Chemistry; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5737/version/1
Copper induced peroxidase, CCPP form Caribbean copper plant
Provedor de dados: 17
Autores: Reetesh Kumar.
Plant peroxidase exhibit broad substrate specificity and is active in a wide range of pH and temperature, and in the presence of
organic compounds as well as other additives. The peroxidase is known to be involved in many physiological and regulatory
processes in plants. This ppt presents an introduction on plant peroxidase and their applications. A purification protocol has been
developed and the purified protein, named as CCPP is biochemically and physiologically characterized. The physiochemical
properties such as molecular weight, isoelectric point have been experimentally determined. The enzymatic efficiency has been
evaluated through temperature optimum, pH optimum, Km and other enzymatic properties along with spectroscopic parameters
like circular...
Tipo: Presentation
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6410/version/1
Copyrights and digitizing the systematic literature: the horror... the horror...
Provedor de dados: 17
Autores: N. Dean Pentcheff.
It is time for us to take full advantage of the investment that our societies have made in documenting the biodiversity of the world.
It is time for us to fully, and legally, make systematic literature available worldwide. Using U.S. "Fair Use"
guidelines, we can.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4644/version/1
(Corrected) Osmotic stress and water isotope effects in kinesin-1 gliding motility assays
Provedor de dados: 17
Autores: Steven J. Koch; Andy Maloney; Lawrence J. Herskowitz.
The osmotic pressure and kinetic properties of water play important roles in biomolecular interactions. As pointed out by
Parsegian, Rand, and Rau, these crucial roles are often overlooked[1]. In some fields, osmotic stress and isotope effects have
been exploited for probing the role water plays in binding interactions of biomolecules. To our knowledge, there have been no
studies of osmotic stress and water isotope effects for kinesin, and only a handful for myosin. We're currently using
the gliding motility assay to see whether we can extract new information about kinesin-1 / microtubule interactions by changing
osmotic stress and water isotopes. We will describe our open-source, automated analysis platform for extracting microtubule
gliding...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4479/version/2
(Corrected) Osmotic stress and water isotope effects in kinesin-1 gliding motility assays
Provedor de dados: 17
Autores: Steven J. Koch; Andy Maloney; Lawrence J. Herskowitz.
The osmotic pressure and kinetic properties of water play important roles in biomolecular interactions. As pointed out by
Parsegian, Rand, and Rau, these crucial roles are often overlooked[1]. In some fields, osmotic stress and isotope effects have
been exploited for probing the role water plays in binding interactions of biomolecules. To our knowledge, there have been no
studies of osmotic stress and water isotope effects for kinesin, and only a handful for myosin. We're currently using
the gliding motility assay to see whether we can extract new information about kinesin-1 / microtubule interactions by changing
osmotic stress and water isotopes. We will describe our open-source, automated analysis platform for extracting microtubule
gliding...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4479/version/3
(Corrected) Speed effects in gliding motility assays due to surface passivation, water isotope, and
osmotic stress.
Provedor de dados: 17
Autores: Andy Maloney; Lawrence J. Herskowitz; Steven J. Koch.
The molecular motor kinesin-1, an ATPase, and the substrate it walks along, microtubules, are vital components of eukaryotic
cells. Kinesin converts chemical energy to linear motion as its two motor domains step along microtubules in a process similar to
how we walk. Cells create systems of microtubules that direct the motion of kinesin. This directed motion allows kinesin to
transport various cargoes inside cells.

During the stepping process, the kinesin motor
domains bind and unbind from their binding sites on the microtubules. Binding and unbinding rates of biomolecules are highly
dependent on hydration and exclusion of water from the binding interface. Osmotic stress will likely strongly affect the binding
and...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4469/version/3
(Corrected) Speed effects in gliding motility assays due to surface passivation, water isotope, and
osmotic stress.
Provedor de dados: 17
Autores: Andy Maloney; Lawrence J. Herskowitz; Steven J. Koch.
The molecular motor kinesin-1, an ATPase, and the substrate it walks along, microtubules, are vital components of eukaryotic
cells. Kinesin converts chemical energy to linear motion as its two motor domains step along microtubules in a process similar to
how we walk. Cells create systems of microtubules that direct the motion of kinesin. This directed motion allows kinesin to
transport various cargos inside cells.

During the stepping process, the kinesin motor
domains bind and unbind from their binding sites on the microtubules. Binding and unbinding rates of biomolecules are highly
dependent on hydration and exclusion of water from the binding interface. Osmotic stress will likely strongly affect the binding
and...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4469/version/2
Correlation between Ground Level Ultra-Violet Radiation & Lower Atmospheric Aerosol
Load
Provedor de dados: 17
Autores: Shweta Yadav; Ankit Tandon.
UV radiation is known to affect many biological and chemical processes, and is largely detrimental to individual organisms.
Specific concerns include increase in the incidence of skin cancer, ocular damage, and other health effects in humans and other
animals; damage to terrestrial and oceanic vegetation; changes in the chemistry of the lower atmosphere e.g. photochemical smog
formation. Present study was undertaken to monitor lower atmospheric aerosol load with Respirable Dust Sampler and ultraviolet
radiation with UV-radiometer in the ambient environment of Delhi. PM10 (< 10 µm) and SPM
(> 10 µm) samples collected for the period of the study (8 weeks, 2 samples per week, total 16 samples).
Hourly UV Fluxes (UV-B...
Tipo: Poster
Palavras-chave: Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2677/version/1
Correlation between Pineal Activation and Religious Meditation Observed by Functional Magnetic
Resonance Imaging
Provedor de dados: 17
Autores: Chien-Hui Liou; Chang-Wei Hsieh; Chao-Hsien Hsieh; Si-Chen Lee; Jyh-Horng Chen; Chi-Hong Wang.
The human brain possesses plenty of functions but little is known about its scientific relationship with mind and spirit.
Conferences^1,2^ focused on the connection between science and religion were held very recently in which neuroscientists,
Buddhist scholars and Dalai Lama discussed attention, mental imagery, emotion, mind, brain functions and meditation, suggesting
religious meditation offers an effective means to investigate the mystery of mind and spirit. In the past decade, scientists struggled
to obtain brain mappings for various meditation styles using different brain imaging techniques and stimulating results have been
observed^3-17^. In this letter we report that, together with other brain regions, pineal body exhibit significant activation...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1328/version/1
Correlations between experimental and theoretical adiabatic ionization energies for organic
compounds and rate constants for atmospheric reactions with hydroxyl radicals
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Adiabatic ionization energy (AIE) calculations were performed at the AM1, PM3, PM6, PDDG, HF/QZVP, and B3LYP/QZVP
levels of theory on 722 atmospherically relevant organic compounds with available experimental rate constants for atmospheric
reactions with hydroxyl radicals (k~OH~). From the starting set of molecules, a final suite of 114 mono- and polyfunctionalized
compounds provided converged neutral and cationic geometries without imaginary frequencies for all six levels of theory. NIST
evaluated AIEs were available for 54 compounds, providing mean absolute AIE prediction errors of 0.31 (AM1), 0.28 (PM3),
0.50 (PM6), 0.36 (PDDG), 1.22 (HF/QZVP), and 0.20 eV (B3LYP/QZVP). Modest correlations were found between the
experimental (r=-0.68, SE=0.81) and...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5447/version/1
Cortical activity modulation of language processing by dynamic optimization of task complexity and
functional restrictions
Provedor de dados: 17
Autores: Shantanu Ghosh; Amrita Basu; Subash Khushu; Senthil S. Kumaran.
Language, regarded as a hierarchical cognitive code activated by functional operational modes of the brain by most
neuropsychologists, is characterized by increased cognitive load in successively higher levels of processing. Language
comprehension is posited to be executed through symbolic-iconic information being encoded neurally as modulated phenomena,
and can be studied _in vivo_ by functional brain imaging. Using a lexical decision-making task in conjunction with syntactic error
correction that effectively isolated the regulatory neural substrate of processing structural-functional information, and minimizing
the possible confounds of gender and proficiency, functional magnetic resonance imaging (fMRI) was performed on bilingual
volunteers to ascertain...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3941/version/1
Cortical Bone Ontogeny: Activity, Nutritional Stress and Archaeology
Provedor de dados: 17
Autores: Gwen Robbins.
This poster introduces the idea that femoral compact bone growth and development demonstrates a very different pattern among
infants and children in a contemporary sample of well-nourished active children versus archaeological samples of stressed,
malnourished children.
Tipo: Poster
Palavras-chave: Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2470/version/1
Cortical responses reflecting inhibition of return (IOR): a magnetoencephalographic study
Provedor de dados: 17
Autores: Akiko Hashimoto; Yasuyuki Takeshima; Koji Inui; Ryusuke Kakigi.
Inhibition of return (IOR) is a phenomenon whereby the reaction time (RT) to detect a second stimulus (target) presented at the
same location as the first stimulus (cue) is longer than when the target is presented at an un-cued location. In the present study, we
investigated cortical activities under a standard IOR paradigm by recording visual evoked magnetic fields (VEFs). In Experiment
1, subjects directed their attention to the target at the periphery of the screen and the RT was measured. In Experiment 2, they paid
attention to the center of the screen and the RT was not measured. In both experiments, the peak latency of the major deflection of
VEFs in the occipito-temporal area was greater for the cued target than un-cued target. This is the first...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2063/version/1
Corticofugal projections from the anterior olfactory nucleus target olfactory bulb principal cells
Provedor de dados: 17
Autores: Kurt R. Illig.
The anterior olfactory nucleus (AON) is a cortical structure reciprocally connected with the olfactory bulb (OB) and the piriform
cortex. Here, using small extracellular and intracellular injections to trace the terminal projections in the OB from individual cells
in the rat AON, and examining the morphology and distribution of these projections, I report that these projections appear to
preferentially target and directly synapses with mitral cells. These findings suggests that the AON acts to modulate incoming
olfactory information based on ongoing processing, perhaps in a way that tunes the OB to signal the presence of particular odors.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6641/version/1
Cosmetic Use of Botulinum Toxin-A Affects Processing of Emotional Language
Provedor de dados: 17
Autores: David Havas; Arthur Glenberg; Karol Gutowski; Mark Lucarelli; Richard Davidson.
Language can evoke powerful emotions and influence consequent actions in readers, but the mechanisms underlying interactions
of language and emotion are largely unknown. Since Darwin, emotional expressions have been implicated in emotional cognition,
experience and understanding, but the functional role of the affective periphery is difficult to test. In a first experiment, facial
electromyography revealed that silent reading of emotional (angry, sad, and happy) sentences automatically elicits differential
patterns of activity in facial muscles used in expression of corresponding emotions (smiling and frowning). In a second
experiment, temporary paralysis of the facial muscle corrugator supercilli (responsible for producing a frown) hindered
processing,...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3683/version/1
Cost effective mass multiplication of Gymnema sylvestre in hydroponic system
Provedor de dados: 17
Autores: Raju Karthic; Sundaram Seshadri.
Present experiment was designed with an objective to develop a cost efficient mass multiplication method for Gymnema sylvestre
using hydroponic system. A plastic tub, with polyethylene cover, containing 1/10 strength of MS salts supplemented with Indole
butyric acid (IBA) at different concentrations (0.5, 1.0, 2.5 mg/L) was studied. Medium containing 0.5mg/L of IBA produced
highest rooting (66%) with 96 % survival. This protocol will serve as an alternative to the existing in vitro and clonal
multiplication protocols.
Tipo: Manuscript
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3770/version/1
Co-transformation of Oil Palm Using Agrobacterium-Mediated Transformation
Provedor de dados: 17
Autores: Vu Le.
Agrobacterium-mediated transformation is being used as an alternative method for improving the conventional breeding. In this
study, immature embryos (IEs) of oil palm are chosen as explants for transformation. β-glucuronidase (gus) and green
fluorescence protein (GFP) were harbored by the two plasmids pCAMBIA 1304 and pCAMBIA 1302 respectively. The results
were obtained at least four days after transformation. The IEs placing in the N6O medium for 7 days were then co-cultivated with
A.tumefaciens suspension within 30 mins and then incubated in the dark for 1 day. In single transformation, GUS assay revealed
that about 64% transient transformation frequency was obtained for IEs two weeks after co-cultivation, GFP activity was recorded
as 41.67%...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/5441/version/1
Counting absolute number of molecules using unique molecular identifiers
Provedor de dados: 17
Autores: Teemu Kivioja; Anna Vähärautio; Kasper Karlsson; Martin Bonke; Sten Linnarsson; Jussi
Taipale.
Advances in molecular biology have made it easy to identify different DNA or RNA species and to copy them. Identification of
nucleic acid species can be accomplished by reading the DNA sequence; currently millions of molecules can be sequenced in a
single day using massively parallel sequencing. Efficient copying of DNA-molecules of arbitrary sequence was made possible by
molecular cloning, and the polymerase chain reaction. Differences in the relative abundance of a large number of different
sequences between two or more samples can in turn be measured using microarray hybridization and/or tag sequencing. However,
determining the relative abundance of two different species and/or the absolute number of molecules present in a single sample
has proven much...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics & Genomics; Molecular Cell Biology;
Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5903/version/1
Coupling of capillary RBC flow failure with neuronal depolarization
Provedor de dados: 17
Autores: Minoru Tomita; Yutaka Tomita; Haruki Toriumi; Miyuki Unekawa; Norihiro Suzuki.
RBC (oxygen-carrier) behaviour in the cerebrocortical microvasculature during K^+^-induced cortical spreading depression
(CSD) was examined in urethane-anesthetized male Wistar rats (n=10). The movements of FITC-labeled RBCs in single
capillaries in the cortical region were traced with a high-speed camera laser scanning confocal fluorescence microscope and
analyzed with Matlab domain software, KEIO-IS2, to obtain the velocities of all labeled RBCs appearing in local capillaries
during CSD wave propagation. We found that CSD induced periodic decreases in both RBC number and velocity until RBCs
halted or disappeared for 3.3 +/- 2.3 s, and then RBC flow was restored. The RBC flow stall was statistically significant (P
< 0.05). During capillary flow...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3220/version/1
Coupling perception and action using probabilistic control
Provedor de dados: 17
Autores: Constantin A. Rothkopf; Paul Schrater.
Although there is a long tradition of separating perception, decision making and action, the theoretical conditions for such a
separation are very restrictive and not applicable even to the most basic every day tasks in humans. Instead, all uncertainties
relating states of the world to observations, actions to future states and rewards, and actions to observations need to be considered
in order to act optimally. In the most general formulation this can be formalized as a partially observable Markov decision process
(POMDP).

We consider the task of intercepting a moving ball for which a multitude
of previous studies has shown that humans use a constant bearing angle strategy. Here we manipulated the observation function
in...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6566/version/1
Courtship plasticity reveals the evolution of dialects in allopatric fish populations
Provedor de dados: 17
Autores: Cesar Gonzalez Zuarth; Adriana Vallarino; Constantino Macias Garcia.
Traditionally, reproductive isolation between disjoint populations has been thought to emerge as a result of the accumulation of
different mutations, genetic drift, or through the effects of natural and sexual selection^1^. Alternatively, the ability of an
organism to express different phenotypes depending on the environment (i.e. phenotypic plasticity) could produce reproductive
isolation^2,3^. Sexually selected traits are expected to be phenotypically plastic and can result in modifications of the species
recognition system and thus originate new species^4^. Here we show that the population-characteristic male courtship behaviour
of a fish (Girardinichthys multiradiatus) is modified in the presence of females from other populations, that this is due to...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2155/version/1
Covalently bound substrate at the regulatory site triggers allosteric enzyme activation
Provedor de dados: 17
Autores: Steffen Kutter; Manfred Weiss; Georg Wille; Ralph Golbik; Michael Spinka; Stephan König.
The mechanism by which the enzyme pyruvate decarboxylase from yeast is activated allosterically has been elucidated. A total of
seven three-dimensional structures of the enzyme, of enzyme variants or of enzyme complexes form two yeast species (three of
them reported here for the first time) provide detailed atomic resolution snapshots along the activation coordinate. The prime
event is the covalent binding of the substrate pyruvate to the side chain of cysteine 221, thus forming a thiohemiketal. This
reaction causes the shift of a neighbouring amino acid, which eventually leads to the rigidification of two otherwise flexible loops,
where one of the loops provides two histidine residues necessary to complete the enzymatically competent active site...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1639/version/1
COX inhibition: Catalepsy and Striatum Dopaminergic-GABAergic-Glutamatergic
Neurotransmission
Provedor de dados: 17
Autores: Hadi Fathi-Moghaddam; Mehdi Shafiee Ardestani; Meysam Shafiee Ardestani; Davood Barzegar-Pourshuraki; Amin
Gravand; Latifeh Navidpour; Hojat Ebrahiminik; Abbas Shafiee.
Selective COX-2 and COX-1 inhibitors were administered (i.p. acutely) to normal and parkinsonian rats, followed by the analysis
of the striatal dopamine, GABA and glutamate concentrations using the microdialysis technique, simultaneously, the catalepsy of
animals was evaluated. Selective COX-2 inhibition showed improving effects on the catalepsy followed by decreasing the
striatum glutamatergic-GABAergic and enhancing the dopaminergic neurotransmission. Nonetheless COX inhibition had no
significant improving effects on damaged Substantia Nigra Pars Compacta (SNc) neurons.
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/1481/version/1
Creatine kinase in energy metabolic signaling in muscle
Provedor de dados: 17
Autores: Olav Kongas; Johannes H. G. M. van Beek.
There has been much debate on the mechanism of regulation of mitochondrial ATP synthesis to balance ATP consumption during
changing cardiac workloads. A key role of creatine kinase (CK) isoenzymes in this regulation of oxidative phosphorylation and in
intracellular energy transport had been proposed, but has in the mean time been disputed for many years. It was hypothesized that
high-energy phosphoryl groups are obligatorily transferred via CK; this is termed the phosphocreatine shuttle. The other important
role ascribed to the CK system is its ability to buffer ADP concentration in cytosol near sites of ATP hydrolysis.


Almost all of the experiments to determine the role of CK had been done in the
steady state, but...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1317/version/1
Creating a Translational Medicine Ontology
Provedor de dados: 17
Autores: Christine Denney; Colin Batchelor; Olivier Bodenreider; Sam Cheng; John Hart; John Hill; John Madden; Mark Musen;
Elgar Pichler; Matthias Samwald; Sándor Szalma; Lynn Schriml; David Sedlock; Larisa Soldatova; Koji Sonoda;
David Statham; Holger Stenzhorn; Patricia L. Whetzel; Elizabeth Wu; Susie Stephens.
*Abstract*
We, participants in the Translational Medicine Ontology activity of the World Wide Web
Consortium’s
Health
Care
and
Life
Sciences
Interest
Group
("http://esw.w3.org/topic/HCLSIG":http://esw.w3.org/topic/HCLSIG) and members of the National Center
for Biomedical Ontology ("http://bioontology.org/":http://bioontology.org/), are developing a high-level,
patient-centric ontology for translational medicine which will draw on existing domain ontologies and allow the integration of
data
throughout
the
drug
process.

*Introduction*
The
development
pharmaceutical
industry
has
historically focused on the development of novel blockbuster drugs....
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Neuroscience;
Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3686/version/1
Creating “fire-smart” forest stands and landscapes
Provedor de dados: 17
Autores: Paulo Fernandes.
Wildland fire is an important feature of the Mediterranean Basin. Past fire incidence has been limited by landscape diversity and
the intensity of biomass use. Fire activity and the meteorological component of fire danger have increased during the last decades,
but the fire regime modification was primarily fuel-driven, i.e. caused by changes in land cover and land use. Fire-smart forests
and landscapes are resistant to fire spread and resilient to its occurrence. In cultural landscapes where fires are seldom allowed to
spread "fire smartness" is attained through proactive management by either treating fuels in fire-prone
vegetation types or decreasing the importance of those vegetation types in the landscape. The presentation overviews...
Tipo: Presentation
Palavras-chave: Ecology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6245/version/1
Creating and improving detoxification pathways for interpretation of toxicogenomics data
Provedor de dados: 17
Autores: Pieter Giesbertz; Jonas Hummel; Stan Gaj; Danyel Jennen; Thomas Kelder; Chris Evelo; Joost van Delft; Jos Kleinjans.
Current high-throughput technology in genomics creates a large amount of biological data. Bioinformatics approaches are directed
towards understanding such data on a systems biology level. Advanced mathematical methods like principal component analysis,
clustering, neural networks, support vector machine (SVM) approaches and neural networks can help to find patterns in the data.
However, to really understand the data the patterns must be combined with existing knowledge. One of the approaches to do so is
to associate these data to functional classifications such as can be found in the Gene Ontology. Other methods focus on using
biological pathways coming from both public and private pathway databases like KEGG, WikiPathways, Reactome, and
MetaCore. Some of...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4575/version/1
Crinumin, a novel substitute of chymotrypsin, may control pancreatic insufficiency and
inflammation: Purification and characterization
Provedor de dados: 17
Autores: Kunwar Awaneesh Singh; Chandan Singh; G.R.K. Rao; M.V. Jagannatham.
Crinumin, a glycosylated serine protease with chymotrypsin like catalytic specificity was purified from a medicinally important
plant _Crinum asiaticum_ of family _Amaryllidaceae_. Ethno-botanical information and Pharmacological studies confirming
about the presence of active bio- molecules in the _Crinum_ played crucial role in injury, inflamed joint, local pain and arthritis.
Biomedical research suggests chymotrypsin was not only used as digestive aid but also helpful in the above disease. These
findings support towards the crinumin may be the active bio-molecule. Crinumin shows activity over a wide range of pH (4.5-11.5
and optimum at 8.5), temperature (75 °C and optimum at 70 °C) and is also functional against chaotrophs,
organic...
Tipo: Poster
Palavras-chave: Pharmacology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4339/version/1
Critical Concentration Gradient Model of Bacterial Cell Division
Provedor de dados: 17
Autores: Aijaz A. Rashid; Perminder P. Sing.
Critical concentration gradient model is helpful in understanding the mechanism of Z-ring formation. The distribution of positive
and negative regulators of Z-ring formation in cell is not random but well programmed. The positive and negative regulators in
cell lead to a critical concentration gradient from mid cell to the poles. The critical concentration of FtsZ required for Z-ring
assembly at the centre of cell is less than that at the poles. So FtsZ starts polymerizing at cell centre and afterwards by cooperative
association of more and more monomers leads to the Z-ring formation. Simultaneously during Z-ring formation the recruitment of
other accessory proteins takes place, leading to the formation of a stable divisome complex.
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4659/version/1
Critical dynamics in homeostatic memory networks
Provedor de dados: 17
Autores: Sakyasingha Dasgupta; J. Michael Herrmann.
Critical behavior in neural networks characterized by scale-free event distributions and brought about by self-regulatory
mechanisms such as short-term synaptic dynamics or homeostatic plasticity, is believed to optimize sensitivity to input and
information transfer in the system. Although theoretical predictions of the spike distributions have been confirmed by in-vitro
experiments, in-vivo data yield a more complex picture which might be due to the in-homogeneity of the network structure,
leakage in currents or massive driving inputs which has so far not been comprehensively covered by analytical or numerical
studies.

We address these questions by the study of a neural model of memory that
allows for storage and...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5829/version/1
Critical nutritional stress among adult tribal populations of West Bengal and Orissa, India.
Provedor de dados: 17
Autores: Samiran Bisai; Kaushik Bose.
This paper deals with cross-sectional studies carried out during the period 2004-2007. It is based on eight data sets of tribals of
Paschim Medinipur and Bankura Districts of West Bengal and Keonjhar District of Orissa. The tribes include Bhumijs, Kora
Mudis, Lodhas, Santals, Bathudis and Savars. Height and weight were measured following standard techniques. The body mass
index (BMI) was computed following standard equation. Nutritional status (chronic energy deficiency, CED) was evaluated
using internationally accepted cut-off values of BMI. We followed the World Health Organization's classification
(1995) of the public health problem of low BMI, based on adult populations worldwide. Our results show that, in general, among
the tribes...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth & Environment; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7068/version/1
Critical nutritional stress among adult tribal populations of West Bengal and Orissa, India.
Provedor de dados: 17
Autores: Samiran Bisai; Kaushik Bose.
This paper deals with cross-sectional studies carried out during the period 2004-2007. It is based on eight data sets of tribals of
Paschim Medinipur and Bankura Districts of West Bengal and Keonjhar District of Orissa. The tribes include Bhumijs, Kora
Mudis, Lodhas, Santals, Bathudis and Savars. Height and weight were measured following standard techniques. The body mass
index (BMI) was computed following standard equation. Nutritional status (chronic energy deficiency, CED) was evaluated
using internationally accepted cut-off values of BMI. We followed the World Health Organization's classification
(1995) of the public health problem of low BMI, based on adult populations worldwide. Our results show that, in general, among
the tribes...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth & Environment; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7068/version/2
Critical studies on systematics of Murdannia lanuginosa (Wall. EX C. B. Cl) Brueck.
(Commelinaceae)
Provedor de dados: 17
Autores: M D. Nandikar; R V. Gurav.
_Murdannia lanuginosa_ (C. B. Cl.) Brucek. (Commelinaceae), an endemic plant to Western Ghats of Peninsular India. It is
categorized as regionally endangered taxon owing to its restricted habitat and low population status in ateritic plateaus of
Maharashtra and Karnataka. It is observed in higher abundance in lateritic plateaus and hilly slopes at an altitude range of 900 to
1600 m. _M. lanuginosa_ found on open grassy plateaus along with herbs like _M. simplex_, _M. versicolor_, _Ischaemum
impressum_, _Glyphochloa forficulata_, _Paspalum canarae_, _Smithia bigemina_, _S. purpurea_, _Rotala densiflora_,
_Pogostemon deccanensis_, etc. Extent of occurrence of _M. lanuginosa_ estimated to be 4,000 sq. km and found only at few
locations. This paper presents...
Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4619/version/2
Critical studies on systematics of Murdannia lanuginosa (Wall. EX C. B. Cl) Brueck.
(Commelinaceae)
Provedor de dados: 17
Autores: M D. Nandikar; R V. Gurav.
_Murdannia lanuginosa_ (C. B. Cl.) Brucek. (Commelinaceae), an endemic plant to Western Ghats of Peninsular India. It is
categorized as regionally endangered taxon owing to its restricted habitat and low population status in ateritic plateaus of
Maharashtra and Karnataka. It is observed in higher abundance in lateritic plateaus and hilly slopes at an altitude range of 900 to
1600 m. _M. lanuginosa_ found on open grassy plateaus along with herbs like _M. simplex_, _M. versicolor_, _Ischaemum
impressum_, _Glyphochloa forficulata_, _Paspalum canarae_, _Smithia bigemina_, _S. purpurea_, _Rotala densiflora_,
_Pogostemon deccanensis_, etc. Extent of occurrence of _M. lanuginosa_ estimated to be 4,000 sq. km and found only at few
locations. This paper presents...
Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4619/version/1
Crossing Disciplinary Boundaries to Understand Human Drivers of Environmental Threats
Provedor de dados: 17
Autores: Eugene A. Rosa; Thomas Dietz.
A wide range of ecological studies affirms the cumulative damage to ecosystem capital and services around the globe. They also
point to the overwhelming role that anthropogenic or human drivers play in global ecological damage. The MAHB is intended to
combine what we know about human drivers of environmental threats with what the social sciences know about changing human
behavior and institutions.
A variety of social sciences have taken up the first task of identifying the key human
activities—at both the local, cumulative level and at the systemic level—most responsible for global
environmental change. Considerable progress has been made in our understanding of land use and land cover change, of
vulnerability, resilience, and...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5251/version/1
Crossing Lilium Orientals of different ploidy creates Fusarium-resistant hybrid
Provedor de dados: 17
Autores: Zheng Sixiang; Wu Hongzhi; Zhao Yan; Liu Feihu.
Oriental hybrid lily is of great commercial value, but it is susceptible to Fusarium disease that causes a significant loss to the
production. A diploid Oriental hybrid resistant to Fusarium, Cai-74, was diploidized from triploid obtained from the offspring of
tetraploid
(from
‘Star
Fighter’)
and
diploid
(‘Con
Amore’,
‘Acapulco’) by screening the hybrids of different cross combinations following inoculating Fusarium
oxysporum to the tissue cultured plantlets in a greenhouse. By analyzing saponins content in bulbs of a number of lily genotypes
with a known Fusarium resistance, it was found that the mutant Cai-74 had a much higher content of saponin than its parents.
Highly resistant wild _L....
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4830/version/1
Cross-modal facilitation of visual and tactile motion
Provedor de dados: 17
Autores: David Burr; Giulio Sandini; Monica Gori.
Robust and versatile perception of the world is augmented considerably when information from our five separate sensory systems
is combined. Much recent evidence has demonstrated near-optimal integration across senses, but it remains unclear at what level
the integration occurs, at a "sensory" or "decisional" level. Here we show that
non-informative "pedestal" motion stimuli in one sensory modality (vision or touch) selectively lowers
thresholds in the other, to the same degree as pedestals in the same modality: strong evidence for functionally important
cross-sensory integration at early levels of sensory processing.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2675/version/1
Cross-Product Extensions of the Gene Ontology
Provedor de dados: 17
Autores: Christopher J. Mungall; Michael Bada; Tanya Z. Berardini; Jennifer Deegan; Amelia Ireland; Midori A. Harris; David
P. Hill; Jane Lomax.
The Gene Ontology is being normalized and extended to include computable logical definitions. These definitions are partitioned
into mutually exclusive cross-product sets, many of which reference other OBO Foundry ontologies. The results can be used to
reason over the ontology, and to make cross-ontology queries.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3496/version/1
Crosstalk and the spectrum of biological global broadcasts: Toward generalization of the Baars
consciousness model across physiological subsystems
Provedor de dados: 17
Autores: Rodrick Wallace.
Once cognitive biological phenomena are recognized as necessarily having 'dual' information sources, it is
easy to show that the information theory chain rule implies isolating coresident information sources from crosstalk requires more
metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to dynamic
global broadcasts of interacting cognitive biological processes analogous to, but slower than, consciousness, itself included within
the paradigm. The argument is closely analogous to the well-studied exaptation of noise to trigger stochastic resonance
amplification in physiological systems.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Immunology; Molecular Cell Biology; Neuroscience; Evolutionary
Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6898/version/1
Cryopreservation of a whole liver
Provedor de dados: 17
Autores: Zohar Gavish; Amir Arav; Menahem Ben-Haim.
Preservation of vascularized organs such as the liver is limited to 24hrs. before destructive processes disqualify it for
transplantation. This narrow time window prevents surgeons from performing optimal pathogen screening and matching tests
which often lead to re-transplantation. Numerous problems are associated with viably freezing and thawing a whole liver:
complicated geometry, poor heat transfer, release of latent heat and the difficulty of generating a uniform cooling rate. Our past
success led us to apply our novel freezing technique to a larger solid organ, the liver. Whole livers were frozen/thawed using a
directional solidification apparatuses; viability was tested by means of integrity and functionality in vitro and in auxiliary liver...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2007
URL: http://precedings.nature.com/documents/1352/version/1
Cryopreservation of cell/hydrogel constructs based on a new cell-assembling technique
Provedor de dados: 17
Autores: Xiaohong Wang; Huirong Xu; Yongnian Yan; Renji Zhang.
Organ manufacturing products hold the promise to be used widely in the future for complex organ failings. The cryopreservation
of the product is a very important step in the commercialization activities. In this article, a new cell cryopreservation technique,
whereby, cryoprotectants were directly incorporated into the cell/hydrogel constructs, prototyped according to the predesigned
structure and then subjected to a special freezing/thawing process. The rheological and hydration properties of the
cryopreservation systems indicated that the hydratabilities of the gelatin/alginate hydrogels were greatly increased while the
eutectic temperatures were greatly decreased by the addition of glycerol. Dextran-40 was found to be effective to improve the
cell...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3722/version/1
Cu2+ uptake by Chlorococcum hemicolum - A Xeric Chlorophycean Alga
Provedor de dados: 17
Autores: Mr. Harish; S. Sundaramoorthy; Devendra Kumar; S.G. Vaijapurkar.
Bioremediation of copper by xeric chlorophycean bioremediator, Chlorococcum hemicolum was investigated. The growth rates at
various concentrations of Cu2+ were assessed in terms of protein level and 8 mg L-1 (37.67 % level in growth kinetics) is the
tolerance limit. Absorption/adsorption kinetics was estimated after 240 hrs of Cu2+ treatments. Absorptions were higher than
adsorption with maximum accumulation factor (AF) of 1.40. The Cu2+ concentration and absorption were linearly related (r =
0.99; p>0.01). Other biochemical parameters like total sugar, chlorophyll and carotenoids were also quantified to
correlate the state of metabolism and these exhibited reduction due to heavy metal stress.
Tipo: Manuscript
Palavras-chave: Ecology; Earth & Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5657/version/1
Cueing in a perceptual task causes long-lasting interference that generalizes across context to affect
only late perceptual learning and is remediated by the passage of time
Provedor de dados: 17
Autores: Ramesh Rajan.
Perceptual learning, the improvement in sensory discriminations with practise, is also subject to stimulus-specific interference
from temporal jitter in a learning session or manipulations applied between or immediately after sessions. We demonstrate a novel
form of perceptual interference where even a brief cueing exposure to a complex speech-in-noise task produces a forward
interference on subsequent speech-in-noise learning. This potent interference generalizes across cueing context but specifically
affects only late learning in the subsequent task, is resistant to the remediating effects of sleep and persists across an overnight
delay involving sleep, and can be evoked by a single exposure 1 day before the learning. Learning in the speech-in-noise task...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2387/version/1
Cunningham: a BLAST Runtime Estimator
Provedor de dados: 17
Autores: James R. White; Malcolm Matalka; W. Florian Fricke; Samuel V. Angiuoli.
BLAST is arguably the single most important piece of software ever written for the biological sciences. It is the core of most
bioinformatics workflows, being a critical component of genome homology searches and annotation. It has influenced the
landscape of biology by aiding in everything from functional characterization of genes to pathogen detection to the development
of novel vaccines. While BLAST is very popular, it is also often one of the most computationally intensive parts of bioinformatics
analysis. In our workflows, BLAST typically takes the majority of cpu time, and we need to parallelize to finish in a reasonable
time frame. Waiting for BLAST to finish without having any clue of how long it’s going to take is kind of
depressing, and...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5593/version/1
Cunningham: a BLAST Runtime Estimator
Provedor de dados: 17
Autores: James R. White; Malcolm Matalka; W. Florian Fricke; Samuel V. Angiuoli.
BLAST is arguably the single most important piece of software ever written for the biological sciences. It is the core of most
bioinformatics workflows, being a critical component of genome homology searches and annotation. It has influenced the
landscape of biology by aiding in everything from functional characterization of genes to pathogen detection to the development
of novel vaccines. While BLAST is very popular, it is also often one of the most computationally intensive parts of bioinformatics
analysis. In our workflows, BLAST typically takes the majority of cpu time, and we need to parallelize to finish in a reasonable
time frame. Waiting for BLAST to finish without having any clue of how long it’s going to take is kind of
depressing, and...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5593/version/2
Curating Genetic Association Literature for Common Diseases
Provedor de dados: 17
Autores: Elana Silver; Eran Halperin; Kord M. Kober; Badri Padhukasahasram; Nila Patil; Michelle Sommargren; Dietrich A.
Stephan; Daryl J. Thomas; Heather Trumbower; Michele Cargill.
Papers describing genetic associations with common diseases are currently being published at a rapid rate. These new papers add
to an already large body of literature which includes candidate gene studies, genome wide association studies, review papers, and
meta-analyses. Related papers describe the basic epidemiology of these common diseases, as well as interactions between genes
and environment, other genes, and drugs (pharmacogenomics), all of which may affect disease predisposition and management.


As the field of personalized genomics continues to grow and mature, this body of
literature is being synthesized in various ways. One aspect of utmost importance is to track gene-disease associations over time to
see if...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3174/version/1
Curation and annotation for BioModels Database, a resource of published quantitative kinetic models
Provedor de dados: 17
Autores: Chelliah Vijayalakshmi; Lukas Endler; Camille Laibe; Chen Li; Nicolas Le Novère.
BioModels Database ("http://www.ebi.ac.uk/biomodels/":http://www.ebi.ac.uk/biomodels/) is a free
resource for storing, viewing and retrieving published, peer-reviewed, quantitative models of biochemical and cellular systems. As
a storage format, BioModels Database uses the Systems Biology Markup Language (SBML), but also allows submission and
export of models in various other commonly used formats.

To offer scientists reliable
information, models are curated to comply with the MIRIAM (Minimal Information Requested In the Annotation of biochemical
Models) standard. This curation process involves verification of the model structure, the parameter and variable values and its
mathematical relations....
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3124/version/1
Curation at the NCBI: Genomes, Genes, & Sequence Standards
Provedor de dados: 17
Autores: Garth Brown; Catherine Farrell; Jennifer Hart; Melissa Landrum; Donna Maglott; Bonnie Maidak; Michael Murphy;
Terence Murphy; Bhanu Rajput; Kim D. Pruitt; Lillian Riddick; David Webb; Janet Weber; Wendy Wu.
The National Center for Biotechnology Information (NCBI) provides curation support for many genomes, and disseminates
information in several resources including Entrez Gene, reference sequences (RefSeq), the Consensus CDS (CCDS) database, and
the Genome Reference Consortium (GRC). These projects are supported by several collaborations to provide:1) support to the
international consortium maintaining the assemblies for human and mouse (GRC); 2) sequence standards for chromosomes,
genes, transcripts and proteins (RefSeq); 3) reports of integrated information including nomenclature, publications, phenotypes
and diseases, sequences, ontologies, interactions (Gene); and 4) identification of proteins that are consistently annotated on the
human and mouse...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3287/version/1
Curation of NISEED, an integrative framework for the digital representation of embryonic
development
Provedor de dados: 17
Autores: Delphine Dauga; Olivier Tassy; Fabrice Daian; Daniel Sobral; Patrick Lemaire.
NISEED (Network for In situ Expression and Embryological Data) is a generic infrastructure for the creation, maintenance and
integration of molecular and anatomical information on model organisms. We applied it to ascidians which are marine
invertebrate chordates. These animals constitute model organisms of choice for developmental biology because their embryos
develop with a small number of cells and an invariant lineage, allowing their study with a cellular level of resolution. In
ANISEED (Ascidian NISEED), embryogenesis of ascidian is represented at the level of the genome via functional gene
annotations, cis-regulatory elements or gene expression data, at the level of the cell by representing its morphology, fates, lineage,
and relations with its...
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3168/version/1
Curcumin Functions as a Positive Regulator of miRNA Processing & a Negative Regulator
of Cancer Stem Cell Proliferation
Provedor de dados: 17
Autores: Lakshmanane P. Boominathan.
Identifying agents that inhibit the proliferation of cancer stem cells is of great importance in cancer biology. Curcumin has been
shown to function as an anti-cancer agent. One of the tumor suppressors that appear to be induced in response to curcumin
treatment is p53. A recent study suggests that curcumin increases the expression of miRNAs, such as miR-22, miR-181a, b, c,
miR-34, miR-103, and miR-21.
Intriguingly, miR-34, 181b, c, miR-103, miR-21, and miR-24 have been identified as
transcriptional targets of the tumor suppressor p53. This data suggests a possibility that curcumin, by inducing the expression of
p53, it could increase the expression of these microRNAs. A number of groups have shown that c-Myc, Sox-2, Klf-4, Oct-4,
Sox-2, Nanog, and...
Tipo: Poster
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/4110/version/1
Current State of JUMMP
Provedor de dados: 17
Autores: Martin Gräßlin.
In computational biology there is a strong need to exchange quantitative models of biological processes in a standardized way. For
storing and retrieving peer-reviewed models the BioModels Database has been available for several years. But at the moment
there is no tool available to bring a model from development in the lab directly to the peer-reviewed online
resource.

The JUMMP (JUst a Model Management Platform) project aims at
providing a generic model management platform for any standardized model file. Through a well-elaborated security layer models
can be developed and shared privately and later on be made available to the curation process and the broader community. Each
change to a model is recorded in a version...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6371/version/1
Current status of herbal and their future perspectives
Provedor de dados: 17
Autores: Ramar Perumal R. Samy; Ponnampalam Gopalakrishnakone.
Traditional medicine is the synthesis of therapeutic experience of generations of practicing physicians of indigenous systems of
medicine. Throughout the history of mankind, many infectious diseases have been treated with herbals. The traditional medicine is
increasingly solicited through the tradipractitioners and herbalists in the treatment of infectious diseases. Among the remedies
used, plant drugs constitute an important part. A number of scientific investigations have highlighted the importance and the
contribution of many plant families i.e. Asteraceae, Liliaceae, Apocynaceae, Solanaceae, Caesalpinaceae, Rutaceae, Piperaceae,
Sapotaceae used as medicinal plants. Medicinal plants play a vital role for the development of new drugs (export and import...
Tipo: Manuscript
Palavras-chave: Pharmacology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1176/version/1
Cutting the trees to save the forest: The Finch Pruyn working forest
Provedor de dados: 17
Autores: Rachel Neugarten; Steven Wolf; Rich Stedman.
The past two decades have seen sales of millions of acres of commercial forest land in the United States. Changed ownership
often results in altered forest management, parcelization or development. Such changes have profound implications for forest
species and ecosystems, as well as the timber industry, recreational opportunities, and local and regional economies. An emerging
strategy seeks to protect lands through complex public-private partnerships involving state agencies, conservation organizations,
and commercial investors. By definition, these partnerships have both environmental and socioeconomic goals; as such, they
represent contemporary experiments in sustainable development applied to forested landscapes. As this approach is a recent
innovation,...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3690/version/1
Cyclin kinase inhibitor p21: a mediator of immune tolerance: direct and indirect evidence
Provedor de dados: 17
Autores: Ashwani Khanna.
*Background:* Uncontrolled proliferation of T-cells is considered a barrier to the induction of transplantation tolerance by T
regulatory cells. Therefore, cyclin kinase inhibitor p21, one of the most potent inhibitors of cell proliferation, may exert an
important role in the induction/generation of T regulatory cells.
*Methods:* CD4^+^CD25^+^ and
CD4^+^CD25^-^ cells were isolated from normal healthy blood donors (n=6), p21^-/-^ mice (n=9) and wild type mice (n=9).
Proliferation with and without cyclosporine was quantified by ^3^H-thymidine uptake assay (expressed as counts per minute) and
FoxP3 mRNA was studied by real-time quantitative RT-PCR. 
*Results:* The difference in proliferation
(p<0.003) among...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2009
URL: http://precedings.nature.com/documents/3378/version/1
D2RQ Platform – Treating Non-RDF Databases as Virtual RDF Graphs
Provedor de dados: 17
Autores: Radoslaw Oldakowski.
D2RQ is a complete solution to map and expose relational databases as RDF.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5660/version/1
DARPP-32 is a robust integrator of dopamine and glutamate signals
Provedor de dados: 17
Autores: Nicolas Le Novere; Eric Fernandez; Renaud Schiappa; Jean-Antoine Girault.
Integration of neurotransmitter and neuromodulator signals in the striatum plays a central role in the functions and dysfunctions of
the basal ganglia. DARPP-32 is a key actor of this integration in the GABAergic medium-size spiny neurons, in particular in
response to dopamine and glutamate. When phosphorylated by cAMP-dependent protein kinase (PKA) DARPP-32 inhibits
protein phosphatase-1 (PP1), whereas when phosphorylated by cyclin-dependent kinase 5 (CDK5) it inhibits PKA. DARPP-32 is
also regulated by casein kinases and by several protein phosphatases. These complex and intricate regulations make simple
predictions of DARPP-32 dynamic behaviour virtually impossible. We used detailed quantitative modelling of the regulation of
DARPP-32 phosphorylation to...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2006
URL: http://precedings.nature.com/documents/9/version/1
D-aspartate exerts an opposing role upon age-dependent NMDAR-related synaptic plasticity and
memory decay
Provedor de dados: 17
Autores: Francesco Errico; Robert Nistico'; Antimo D'Aniello; Sandra Sivilia; Michela Giustizieri;
Francesco Napolitano; Enza Topo; Giorgio Bernardi; Laura Calza; Nicola Mercuri; Alessandro Usiello.
In the present study, we demonstrated that D-aspartate acts as an _in vitro_ and _in vivo_ neuromodulatory molecule upon
hippocampal NMDAR transmission. Accordingly, we showed that this D-amino acid, widely expressed during embryonic phase,
was able to strongly influence hippocampus-related functions at adulthood. Thus, while up-regulated levels of D-aspartate
increased LTP and spatial memory in four-month old adult mice, the prolonged deregulation of this molecule in thirteen-month
old animals induced a substantial acceleration of age-dependent decay of synaptic plasticity and cognitive functions. Moreover,
we highlighted a role for D-aspartate in enhancing NMDAR-dependent synaptic plasticity through an inducible
"turn-on/turn-off-like...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1891/version/1
Data Basin Climate Center: sharing and manipulating spatial information on the web
Provedor de dados: 17
Autores: Dominique Bachelet; James Strittholt; Tosha Comendant.
Monitoring datasets is essential to detect changes that are occurring and identify thresholds that cause them, but scientists around
the world are now generating large volumes of data that vary in quality, format, supporting documentation, and accessibility.
Moreover, diverse models are being run at various spatial and temporal scales to try and understand past climate variability and its
impacts, generate future climate and land use scenarios, and project potential future impacts to the planet. Conservation
practitioners and land managers are struggling to synthesize this wealth of information, identify relevant and usable datasets, and
translate evolving science results into on-the-ground climate-aware strategies.
In partnership with...
Tipo: Presentation
Palavras-chave: Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5256/version/2
Data Basin Climate Center: sharing and manipulating spatial information on the web
Provedor de dados: 17
Autores: Dominique Bachelet; James Strittholt; Tosha Comendant.
Monitoring datasets is essential to detect changes that are occurring and identify thresholds that cause them, but scientists around
the world are now generating large volumes of data that vary in quality, format, supporting documentation, and accessibility.
Moreover, diverse models are being run at various spatial and temporal scales to try and understand past climate variability and its
impacts, generate future climate and land use scenarios, and project potential future impacts to the planet. Conservation
practitioners and land managers are struggling to synthesize this wealth of information, identify relevant and usable datasets, and
translate evolving science results into on-the-ground climate-aware strategies.
In partnership with...
Tipo: Presentation
Palavras-chave: Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5256/version/1
Data citation in the wild
Provedor de dados: 17
Autores: Valerie Enriquez; Sarah Walker Judson; Nicholas M. Walker; Suzie Allard; Robert B. Cook; Heather A. Piwowar;
Robert J. Sandusky; Todd J. Vision; Bruce E. Wilson.
Consistent attribution of research data upon reuse is necessary to reward the original data-producing investigators, reconstruct
provenance, and inform data sharing policies, tool requirements, and funding decisions. Unfortunately, norms for data attribution
are varied and often weak. As part of the DataONE 2010 summer internship program, three interns studied the policies, practice,
and implications of current data attribution behavior in the environmental sciences. We found that few policies recommend
robust data citation practices: in our preliminary evaluation, only one-third of repositories (n=26), 6% of journals (n=307), and 1
of 53 funders suggested a best practice for data citation. We manually reviewed 500 papers published between 2000 and...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5452/version/1
Data Curation in Biology - Past, Present and Future
Provedor de dados: 17
Autores: Janet Thornton.
Data curation has been critical in the development of biology from Darwin and Linnaeus to UniProt, the careful collection and
organisation of data has been the spring from which new hypotheses and understanding have emerged. In this presentation, I will
describe how we have used data curation in my own research group - and also present an overview of curation at the EBI. With
new technical developments and the move towards the semantic web, the role of curation in the future needs to develop to take
advantage of these new opportunities. This will be discussed.
Tipo: Presentation
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3225/version/1
Data, Databases, and Communities
Provedor de dados: 17
Autores: Matthew Day.
Overview
*
Publishing
landscape
and
challenges
*
Nature
gateways
and
databases
* NCI-Nature Pathway Interaction Database
* A few other communication
tools
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2884/version/1
Data integration in myGrid with Taverna
Provedor de dados: 17
Autores: Duncan Hull.
Many areas of life sciences research involve integrating terabytes of heterogeneous, 
distributed and
autonomous data available on the Web. The myGrid project has addressed 
these challenging problems by
developing and applying novel grid and semantic web 
services technology to life science data integration,
particularly genome annotation and 
microarray analysis. This presentation outlines the past, present and
future of the Taverna workflow system.

Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/331/version/1
Data Management Plan for Monogram BioSciences
Provedor de dados: 17
Autores: Christos J. Petropoulos.
This is the data plan for access to data underlying published reports by Monogram BioSciences.
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics & Genomics; Immunology; Microbiology; Pharmacology; Bioinformatics; Evolutionary Biology;
Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5668/version/1
Data Mining for Simple Sequence Repeats in Oil Palm Expressed Sequence Tags
Provedor de dados: 17
Autores: Aikkal Riju; Vadivel Arunachalam.
Expressed Sequence Tags or ESTs are small pieces of DNA sequence that are generated by sequencing either one or both ends of
an expressed gene. ESTs provide researchers with a quick and inexpensive route for discovering new genes, for obtaining data on
gene expression and regulation, and for constructing genome maps. Oil palm EST sequences as available in public domain are
downloaded. They were grouped and made contigs using CAP3 and Phrap. Microsatellite repeats are located using 5 softwares
(MISA, TRA, TROLL, SSRIT, SSR primer). Among the 5 methods MISA is found to be the best. It can elucidate the compound
repeat also. Frequency and total number (202) of SSR were detected. Mononucleotide repeat is more abundant especially
‘A/T’...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3581/version/1
Data mining of protein families using common peptides
Provedor de dados: 17
Autores: Assaf Gottlieb; Uri Weingart; David Horn.
Predicting the function of a protein from its sequence is typically addressed using sequence-similarity. Here we propose a
motif-based approach, using supervised motif extraction from protein sequences belonging to one functional family. The resulting
deterministic motifs form Common Peptides (CPs) that characterize this family, allow for data mining of its proteins and facilitate
further partition of the family into clusters
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2189/version/1
Data Mining of the Coffee Rust Genome
Provedor de dados: 17
Autores: David Octavio Botero-Rozo; William Giraldo; Alvaro Gaitan; Marco Cristancho; Diego M. Riaño-Pachon;
Silvia Restrepo.
The genomes of nine isolates of _Hemileia vastatrix_, the causal agent of coffee leaf rust were sequenced by Illumina and 454.
Quality control, cleaning and _de novo_ assemblies of data were performed. Since isolates were obtained from the field and it is
not possible to produce axenic cultures of _H. vastatrix_, MEGAN software was used to evaluate contamination levels and to
select contigs with fungal similarities. Mitochondrial contigs were identified and annotated by comparing this assembly against
the _Puccinia_ genome. Furthermore, two transcriptomes from isolates of _H. vastatrix_ were assembled to complement the
genomic data.
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7034/version/1
Data sharing: What about epidemiological cohorts?
Provedor de dados: 17
Autores: Marcel Goldberg; Marie Zins.
General-purpose population-based cohorts can be powerful scientific platforms. The Gazel Cohort Study, a French cohort of
20,000 adults followed-up since more than 20 years, was designed as an open epidemiologic laboratory, hosting more than 40
nested research projects from French and international teams.
Formal rules were elaborated to define the
way that the Gazel database can be accessed.
One of the main problems faced by the Gazel team members is
scientific recognition of their work, as the large majority of the publications come from external research groups.
Tipo: Presentation
Palavras-chave: Genetics & Genomics; Earth & Environment; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5575/version/1
Data submission and curation for caArray, a standard based microarray data repository system
Provedor de dados: 17
Autores: X Bian; J Klemm; A Basu; J Hadfield; R Srinivasa; T Parnell; S Miller; W Mason; D Kokotov; M Duncan; P Duvall; L
Gurses; T Boal; L Misquitta; D Swan; R Wysong; A Klink; A Johnson; G Fontenay; J Liu; M Colbert; G Komatsoulis.
caArray is an open-source, open development, web and programmatically accessible array data management system developed at
National Cancer Institute. It was developed to support the exchange of array data across the Cancer Biomedical Informatics Grid
(caBIG™), a collaborative information network that connect scientists and practitioners through a shareable and
interoperable infrastructure to share data and knowledge. caArray adopts a federated model of local installations, in which data
deposited are shareable across caBIG™. 

Comprehensive in annotation
yet easy to use has always been a challenge to any data repository system. To alleviate this difficulty, caArray accepts data upload
using the...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3138/version/1
Dating the cyanobacterial ancestor of the chloroplast
Provedor de dados: 17
Autores: Luisa Falcon; Susana Magallon; Amanda Castillo.
Cyanobacteria have played a pivotal role in the history of life on Earth being the first organism to carry out oxygenic
photosynthesis, which changed atmospheric chemistry and allowed the evolution of Eukarya. Chloroplasts are the cellular
organelles of photoautotrophic eukaryotes in which photosynthesis is conducted. Although the initial suggestion from
Mereschkowsky (1905) that cyanobacteria are the ancestors of chloroplasts was greeted with skepticism, the idea is now widely
accepted. Here we attempt to resolve and date the cyanobacterial ancestry of the chloroplast using phylogenetic analysis and
molecular clocks, because until now, the long-standing question of, from which, among the vast diversity of cyanobacteria, did
chloroplasts evolve, has not...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3696/version/1
Day-length is central to maintaining consistent seasonal diversity in marine bacterioplankton
Provedor de dados: 17
Autores: Jack A. Gilbert; Paul Somerfield; Ben Temperton; Susan Huse; Ian Joint; Dawn Field.
Marine bacterial diversity is vast, but seasonal variation in diversity is poorly understood. Here we present the longest bacterial
diversity time series consisting of monthly (72) samples from the western English Channel over a 6 year period (2003-2008) using
747,494 16SrDNA-V6 amplicon-pyrosequences. Although there were characteristic cycles for each phylum, the overall
community cycle was remarkably stable year after year. The majority of taxa were not abundant, although on occasion these rare
bacteria could dominate the assemblage. Bacterial diversity peaked at the winter solstice and showed remarkable synchronicity
with day-length, which had the best explanatory power compared to a combination of other variables (including temperature and
nutrient...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4406/version/1
DDBJ Activities: Contribution to the Research in Information Biology
Provedor de dados: 17
Autores: Jun Mashima; Takehide Kosuge; Toshihisa Okido; Yuichi Kodama; Kazuho Ikeo; Hideaki Sugawara; Yoshio Tateno;
Takashi Gojobori.
DDBJ (DNA Data Bank of Japan; "http://www.ddbj.nig.ac.jp/":http://www.ddbj.nig.ac.jp/)started its
database activities in 1986. From the beginning, DDBJ has been one of INSDC (International Nucleotide Sequence Database
Collaboration; "http://www.insdc.org/":http://www.insdc.org/) that is a tripartite collaboration with
EMBL-Bank/EBI and GenBank/NCBI.The total base number of the primary nucleotide sequence data collected and distributed by
INSDC exceeded 100 Gbases in August 2005. Since then it took only three years for the total base number to be doubled (200
Gbases). Now, the collaboration is being expanded to Traces (DNA sequence chromatograms) and Short Reads (raw reads data
from 454, Solexa, SOLiD etc). DDBJ is also...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3211/version/1
DDBJ Sequence Read Archive / DDBJ Omics Archive
Provedor de dados: 17
Autores: Yuichi Kodama; Satoshi Saruhashi; Eli Kaminuma; Hideaki Sugawara; Toshihisa Takagi; Kousaku Okubo; Yasukazu
Nakamura.
Massively parallel sequencers become widespread and produce unprecedented amounts of sequence reads in many biological
fields. DNA Data Bank of Japan (DDBJ) has constructed the international sequence database collaboration (INSDC) together
with EBI and NCBI. In 2008, DDBJ has established the DDBJ Read Archive (DRA) to archive raw output data from the new
sequencing platforms. DRA archives and provides the raw data sets together with the other two INSDC partners the Sequence
Read Archive (SRA) at NCBI and the European Sequence Read Archive (ERA) at EBI. These new sequencing platforms are also
used to count DNA/RNA molecules instead of microarray experiment because of their higher accuracy. Since 2004, DDBJ has
operated CIBEX as a repository database for...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5085/version/1
Death of human tumor endothelial cells in vitro through a probable calcium-associated mechanism
induced by bevacizumab and detected via a novel method
Provedor de dados: 17
Autores: Larry Weisenthal; Haddy Liu; Constance Rueff-Weisenthal.
We isolated three dimensional cell clusters from fresh human solid tumors and also isolated human neoplastic and normal
lymphatic cells. Cells were cultured for 96 hours with and without bevacizumab and other agents. At concentrations of
bevacizumab which completely removed VEGF from the culture medium, dead microvascular cells were detected through Fast
Green/H&E staining as previously described. These peculiar staining characteristics suggested the involvement of
calcium, and this was confirmed through staining with Alizarin red S. Using Alizarin staining as a marker for endothelial cell
death permitted the use of public domain image analysis software which resulted in a sensitive and specific system for identifying
active pharmaceuticals which...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2010
URL: http://precedings.nature.com/documents/4499/version/1
Debugging Mappings between Biomedical Ontologies: Preliminary Results from the NCBO BioPortal
Mapping Repository
Provedor de dados: 17
Autores: Jyotishman Pathak; Christopher Chute.
The ability to provide semantic mappings between multiple large biomedical ontologies is considered as a very important, albeit
labor-intensive and error-prone task. To facilitate such a process, several approaches for collaborative ontology mapping building
and sharing have been proposed in the recent past. However, despite the improvements in community-wide mappings
development, more often the mapping rules are redundant, incoherent, and at times, incorrect. In this paper, we present an
approach for identifying such “erroneous mappings” using Distributed Description Logics.
Specifically, we illustrate how logical reasoning can be used to discover semantic inconsistencies caused by erroneous mappings,
and provide preliminary results...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3455/version/1
Debugging Mappings between Biomedical Ontologies: Preliminary Results from the NCBO BioPortal
Mapping Repository
Provedor de dados: 17
Autores: Jyotishman Pathak; Christopher Chute.
The ability to provide semantic mappings between multiple large biomedical ontologies is considered as a very important, albeit
labor-intensive and error-prone task. To facilitate such a process, several approaches for collaborative ontology mapping building
and sharing have been proposed in the recent past. However, despite the improvements in community-wide mappings
development, more often the mapping rules are redundant, incoherent, and at times, incorrect. In this paper, we present an
approach for identifying such “erroneous mappings” using Distributed Description Logics.
Specifically, we illustrate how logical reasoning can be used to discover semantic inconsistencies caused by erroneous mappings,
and provide preliminary results...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3456/version/1
Decadal-scale changes in seagrass coverage on the Mississippi barrier islands, northern Gulf of
Mexico
Provedor de dados: 17
Autores: Gregory A. Carter; G. Alan Criss; Gabriel A. Blossom; Patrick D. Biber.
Seagrasses provide habitat for a wide variety of aquatic species, and reduce coastal erosion via sediment stabilization. The areal
coverage of seagrass beds on the Mississippi barrier islands appears to have declined substantially since the 1960s. However,
difficulties in sampling benthic vegetation, differences among previous studies in survey methods, and a lack of data on
year-to-year variation in coverage have impeded quantitative study of this decline. Thus, the goal of the present study was to
utilize historical remote sensing data to quantitatively determine changes in seagrass (predominantly Halodule wrightii Ascherson)
coverage on the Mississippi barrier islands. Analyses were limited to imagery acquired during late summer through autumn,
when...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3669/version/1
Deciphering the genome structure and paleohistory of _Theobroma cacao_
Provedor de dados: 17
Autores: Xavier Argout; Jerome Salse; Jean Marc Aury; Gaetan Droc; Jerome Gouzy; Mathilde Allegre; Cristian Chaparro;
Thierry Legavre; Mark Guiltinan; Siela Maximova; Michael Abrouk; Florent Murat; Olivier Fouet; Julie Poulain; Manuel Ruiz;
Yolande Roguet; Maguy Rodier-Goud; Jose Fernandes Barbosa-Neto; Francois Sabot; Dave Kudrna; Jetty Siva S. Ammiraju;
Stephan C. Schuster; John E. Carlson; Erika Sallet; Schiex T.; Anne Dievart; Melissa Kramer; Laura Gelley; Zi Sh;
Aurélie Bérard; Christopher Viot; Michel Boccara; Ange Marie Risterucci; Valentin Guignon; Xavier
Sabau; Michael Axtell; Zhaorong Ma; Yufan Zhang; Spencer Brown; Mickael Bourge; Wolfgang Golser; Xiang Song; Didier
Clement; Ronan Rivalan; Mathias Tahi; Joseph Moroh Akaza; Bertrand Pitollat; Karina Gramacho; Angélique
D’Hont; Dominique Brunel; Diogenes Infante; Ismael Kebe; Pierre Costet; Rod Wing; W. Richard McCombie;
Emmanuel Guiderdoni; Francis Quetier; Olivier Panaud; Patrick Wincker; Stephanie Sidibe-Bocs; Claire Lanaud.
We sequenced and assembled the genome of _Theobroma cacao_, an economically important tropical fruit tree crop that is the
source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described
genes, with 82% of them anchored on the 10 _T. cacao_ chromosomes. Analysis of this sequence information highlighted specific
expansion of some gene families during evolution, for example flavonoid-related genes. It also provides a major source of
candidate genes for _T. cacao_ disease resistance and quality improvement. Based on the inferred paleohistory of the T. cacao
genome, we propose an evolutionary scenario whereby the ten _T. cacao_ chromosomes were shaped from an ancestor through
eleven chromosome...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics & Genomics; Plant Biology; Evolutionary Biology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4908/version/1
Deciphering the phylogenetic history of neuroserpin orthologs across metazoans by analysis of
synteny and rare genomic characters
Provedor de dados: 17
Autores: Abhishek Kumar; Hermann Ragg.
The superfamily of serine proteinase inhibitors (serpins) is involved in wide arrays of fundamental biological processes such as
blood coagulation, complement activation, fibrinolysis, angiogenesis, inflammation and tumor suppression. The average protein
size of a serpin family member is 350-400 amino acids, but gene structure varies in terms of number and position of exons and
introns. All known serpins can be grouped into 16 clades and 10 orphan sequences. Vertebrate serpins can be conveniently
classified into six sub-groups, based on three independent biological features - genomic organization, diagnostic amino acid sites
and rare indels.
The objective of this study was to elucidate the phylogenetic kinships of serpins involved
in...
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2496/version/1
Declarative modelling in the ecological and environmental sciences
Provedor de dados: 17
Autores: Robert Muetzelfeldt.
Most simulation models in ecological and environmental research are implemented as computer programs in a conventional
programming language.
This brief paper argues for a radically different approach, based on the representation of the model
structure, relationships and equations in a declarative format (e.g. XML).
Simulation code can then be generated from this, but
in addition the model can be displayed and processed in a wide range of useful ways, greatly increasing the efficiency and
effectiveness of the modelling process.
Tipo: Manuscript
Palavras-chave: Ecology; Earth & Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/17/version/1
Decoding Sequence Classification Models for Acquiring New Biological Insights
Provedor de dados: 17
Autores: Ulrich Bodenhofer; Andreas Kothmeier; Ingrid G. Abfalter; Carsten C. Mahrenholz; Sepp Hochreiter.
Classifying biological sequences is one of the most important tasks in computational biology. In the last decade, support vector
machines (SVMs) in combination with sequence kernels have emerged as a de-facto standard. These methods are theoretically
well-founded, reliable, and provide high-accuracy solutions at low computational cost. However, obtaining a highly accurate
classifier is rarely the end of the story in many practical situations. Instead, one often aims to acquire biological knowledge about
the principles underlying a given classification task. SVMs with traditional sequence kernels do not offer a straightforward way of
accessing this knowledge.

In this contribution, we propose a new approach to
analyzing...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4708/version/1
Decoding the Design Principles of Amino Acids and the Chemical Logic of Protein Sequences
Provedor de dados: 17
Autores: B. Jayaram.
That only 20 amino acids occur naturally accounting for the structural and functional diversity of proteins remains a mystery. We
show here that this is a consequence of the action of a symmetry group, identify the presence of hydrogen bond donor groups,
presence of sp3 hybridized [gamma] carbons, absence of [delta] carbons and linearity as properties central to side chain design
and quantify the chemical logic of protein sequences.
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2135/version/1
Decomposing CO2 emissions data into a pair of logistic growth pulses
Provedor de dados: 17
Autores: Gleb G. Alexandrov.
Numerous scenarios of emissions growth presume that it can not grow infinitely: there are certain limits that may not or must not
be exceeded. Applying the theory of pulsing logistic growth, I detected two pulses of logistic growth. This led me to the
conclusion that constructing a scenario of emissions growth one should pay attention to the fact that limits to their growth do not
remain constant.
Tipo: Poster
Palavras-chave: Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4306/version/1
Decrease in gyrase A protein expression in _E. coli_ cells inhibited by antisense ribozymes
Provedor de dados: 17
Autores: Shilpakala Sainath Rao; Malathi Raghunathan.
RNase P complexed with external guide sequence (EGS) represents a novel nucleic-acid-based gene interference approach to
modulate gene expression. Nucleic acid-based gene interference technologies represent promising strategies for specific inhibition
of mRNA sequences of choice. Recently, small interfering RNAs have been implicated in inducing endogenous RNase of the
RNA-induced silencing complex in the RNA interference pathway to inhibit gene expression and growth of several human
viruses. We report down regulation of protein expression of _E. coli_ gyrase A, an essential gene for DNA supercoiling and
antibiotic susceptibility in BL21 (DE3) strain of _E. coli_, using Ribonuclease P based external guide sequence (EGS) technique.
EGS directed against...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2408/version/1
Decrease of vanillin sucrose intake by victorious and defeated mice: development of anhedonia?
Provedor de dados: 17
Autores: Natalia N. Kudryavtseva; Natalia P. Bondar; Irina L. Kovalenko; Damira F. Avgustinovich.
Hedonic reactions to various rewards play a key role in various forms of motivated behavior. The influence of repeated experience
of social victories or defeats in daily agonistic interactions between male mice on voluntary consumption of vanillin sucrose
solution used as hedonic reinforcer was studied. Intake of vanillin sucrose solution was shown to decrease in the winners and
losers exposed to social confrontations as compared with the controls. Three days of deprivation failed to restore the intake of
vanillin sucrose solution to the control level in the losers and did so in the winners. The results obtained imply that similar
reaction of animals to a hedonic non-drug reinforcer may have different motivational origin depending on positive or negative...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/988/version/1
Defective FoxP3+ Treg cell differentiation in the gut of Type 1 Diabetic patients
Provedor de dados: 17
Autores: Ester Badami; Chiara Sorini; Margherita Coccia; Laura Molteni; Andrea Mario Bolla; Marina Scavini; Alberto Mariani;
Emanuele Bosi; Marika Falcone.
Environmental factors that act at the intestinal level such as diet, drugs, and microflora have a high impact on the pathogenesis of
autoimmune Type 1 Diabetes (T1D), but it is still unclear how the gut milieu affects autoimmunity outside the intestine. Here we
show that peripheral FoxP3+ Treg cell differentiation, a mechanism that takes place in the gut and is crucial to maintain systemic
immune tolerance, is impaired in T1D patients. These results provide the first evidence that gut mucosa alteration could
predispose to autoimmune T1D by affecting systemic immune regulation.
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2010
URL: http://precedings.nature.com/documents/4417/version/1
Deficiency of interleukin-1 receptor antagonist causes spontaneous femoral artery aneurysms
Provedor de dados: 17
Autores: Kikuo Isoda; Tomiharu Niida; Harumi Kondo; Fumikaka Ohsuzu.
Interleukin (IL) -1, a proinflammatory cytokine, increases in aneurysm, and the IL-1 receptor antagonist (IL-1Ra) modulates IL-1
activity endogenously. We show here that IL-1Ra-deficiency in hematopoietic cells disrupts immune system homeostasis and
causes spontaneous femoral artery aneurysms in mice lacking interventions such as drugs or surgery. Thus, IL-1Ra-deficient mice
provide easy observations with age and diminish mortality that typically follows surgical procedures. Furthermore, since
IL-1Ra-deficient mice contain the entire spectrum of lesions observed during inflammatory aneurysm, this mouse model likely
will provide numerous opportunities to study the pathogenesis and therapy of inflammatory aneurysm.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2826/version/1
Delayed-Type hypersensitivity to latex: Computational prediction of MHC class II epitopes on latex
allergens
Provedor de dados: 17
Autores: Bell R. Eapen.
Delayed type hypersensitivity to natural rubber latex is rare compared to IgE mediated immediate reactions. Binding of allergens
to MHC Class II is a crucial step in the presentation of antigens to CD4+ T Cells responsible for delayed reactions. Computational
prediction of MHC class II epitopes on thirteen known latex allergens using SMM-align method revealed strong binding with
several alleles. This shows that latex allergens are capable of initiating delayed type hypersensitivity in susceptible
individuals.

Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2931/version/1
Deletion of the rat trpc4 gene and its influence on motivated responding for natural reward
Provedor de dados: 17
Autores: William D. Klipec; Bridget Deeney; Claire Williamson; Kami Wenzel; Phuong Nguyen; Eric Ostertag; Donald C.
Cooper.
TRPC4 ion channels are expressed extensively in corticolimbic brain regions and a subpopulation of midbrain dopamine neurons.
TRPC4 knockout (KO) rats show reduced sociability and social exploration, but show no differences in simple and complex
strategic learning compared to normal wild type (WT) rats. Using water reward, we found no differences between TRPC4-KO and
WT rats in the break point on a progressive ratio schedule of reinforcement. Although deletion of the trpc4 gene alters social
interaction/anxiety it does not appear to affect motivation for natural rewards. Current experiments are underway testing the role
of trpc4 gene deletion on cocaine reward (see www.neuro-cloud.net/nature-precedings/klipec3 for updates and collaborations).
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/7109/version/1
Deletion of the trpc4 gene and its role in simple and complex strategic learning
Provedor de dados: 17
Autores: William D. Klipec; Phuong Nguyen; Bridget Deeney; Claire Williamson; Kami Wenzel; Jessica Stumme;
Marissa Collins; Abby Drish; Laura Swenson; Eric Ostertag; Donald C. Cooper.
The TRPC4 ion channel is expressed extensively in corticolimbic and a subpopulation of midbrain dopamine neurons. While
TRPC4 knockout (KO) rats exhibit reduced sociability and social exploration, little is known about the role of TRPC4 in
motivation and learning. To identify a function for TRPC4 channels in learning processes  we tested TRPC4 KO and
normal wild
type
(WT)
rats.
TRPC4
KO
and
WT
rats
exhibited
no
differences
in
Y-­maze learning or simple discrimination learning. Furthermore, on a more complex serial reversal shift
task designed  to assess strategic learning where the reward and non-­reward cues were repeatedly reversed
between training sessions both TRPC4 KO and WT rats  ...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6929/version/1
Delving into Vertebrate Serpins for Understanding their Evolution
Provedor de dados: 17
Autores: Abhishek Kumar.
The superfamily of serine proteinase inhibitors (serpins) is involved in an array of fundamental biological processes such as blood
coagulation, cell differentiation, cell migration, complement activation, embryo implantation, fibrinolysis, angiogenesis, and
inflammation, and tumor suppression. Vertebrate serpins can be conveniently classified into six sub-groups, based on three
independent biological features - genomic organization, diagnostic amino acid sites and rare indels. The present vertebrate serpins
are derived from an original serpin most probably by intron insertion and we are trying to reconstruct the phylogeny of vertebrate
serpin and looking for the reconstruction of original vertebrate gene(s). We started with fish genomes and characterized...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3050/version/1
Demographic vital rates and population growth: rethinking the relationship in a harvested elk
population
Provedor de dados: 17
Autores: Jonathan M. Conard; Philip S. Gipson.
Understanding the nature of the relationship between demographic vital rates and the rate of population change (λ) is
important for determining effective strategies for population management and conservation. We examined the relative impacts of
various demographic vital rates on λ within the range of temporal vital rate variability observed in a harvested
population to test the hypotheses that adult survival rates in ungulates are relatively invariant when compared to other vital rates
and that variability in calf survival has a greater influence on rates of population change than adult survival. Vital rates were
estimated for an elk (_Cervus elaphus_) population at Fort Riley, Kansas from October 2003 – February 2007. The...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3609/version/1
Dendritic spike induction of postsynaptic cerebellar LTP
Provedor de dados: 17
Autores: Marco Canepari; Kaspar E. Vogt.
The architecture of parallel fiber (PF) axons contacting cerebellar Purkinje neurons (PNs) retains spatial information over long
distances. PF synapses can trigger local dendritic calcium spikes, but whether and how this calcium signal leads to plastic changes
that decode the PF input organization is unknown. By combining voltage and calcium imaging, we show that PF-elicited calcium
signals, mediated by voltage-gated calcium channels, increase non-linearly during high-frequency bursts of electrically constant
calcium spikes because they locally and transiently saturate the endogenous buffer. We demonstrate that these non-linear calcium
signals, independently of NMDA or metabotropic glutamate receptor activation, can induce PF long-term potentiation (LTP)....
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2020/version/1
Denitrification Hotspots and N20 Flux in Fluvial Systems
Provedor de dados: 17
Autores: Julia Hyman; Arthur Gold; Kelly Addy; Ken Forshay; Paul Mayer; Peter Groffman.
a)	Background/Question/Methods
Watersheds have a profound capacity to retain and remove
nitrogen (N) inputs before entering coastal waters thereby minimizing eutrophication and hypoxia in estuarine waters. Research
suggests that much of this N cycling occurs within aquatic ecosystems, e.g., lakes, streams and wetlands, which may become
“hotspots” of nitrous oxide (N2O) production. We examined the effects of woody debris on nitrate
removal and denitrification rates in streams of different N enrichment levels. Three different standardized substrates (fresh wood
blocks, bundles of naturally occurring streambed wood, and clay‐fired blocks) that were expected to vary in their
pool of labile carbon were...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5284/version/1
Density alteration in non-physiological cells
Provedor de dados: 17
Autores: Yu Liu; Yuan-Chang Zhu; Bin-Bin Wu; Xiao-Hua Wu; Fei-Fei Lan; Jian-Ge Wei; Ming Wang; Hai-Cheng Li; Lin-Na
Li; Ju-Xiang Li; Jia Fei.
In the present study an important phenomenon of cells was discovered: the change of intracellular density in cell's
response to drug and environmental factors. For convenience, this phenomenon is named as "density alteration in
non-physiological cells" ( DANCE). DANCE was determined by discontinuous sucrose gradient centrifugation
(DSGC), in which cells were separated into several bands. The number and position of the bands in DSGC varied with the change
of cell culture conditions, drugs, and physical process, indicating that cell's response to these factors was associated
with alteration of intracellular density. Our results showed that the bands of cells were molecularly different from each other, such
as the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6541/version/1
Density Functional Study on the Stability and Reactivity of Pt(100) and Pt(111) Surfaces Modified by
Ni Atoms
Provedor de dados: 17
Autores: María López; Eduardo Castro.
DFT study on the the stability and reactivity of Pt(100) and Pt(111) surfaces modified by nickel UPD monolayer deposition
have been carried out. We used the binding energy calculation of bimetallic structures versus the cohesion energy of the bulk
adsorbate to quantify the underpotential shift (ΔEupd) to determine the stability of the bimetallic systems. The
reactivity of the clean and modified surface was analized by energy levels of the highest occupied molecular orbital (HOMO),
softness and local softness. We concluded that the stability of Pt(100)25Ni9 and Pt(111)25Ni10 bimetallic structures cannot be
explained by excess of the metal- substrate binding energy but the instability can be explained by structural effects. We found
that...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3909/version/1
Density functional theory calculation of interaction between bisphosphate and farnesyl pyrophosphate
synthase
Provedor de dados: 17
Autores: Kazuki Ohno; Kenichi Mori; Yohsuke Hagiwara; Masaya Orita; Makoto Takeuchi.
Bisphosphonates (BPs) are the most widely used and effective treatment for osteoporosis and Pagets disease of the bone. To date,
a number of BPs-namely alendronate, risedronate, and minodronate-have been launched to market. Nitrogen-BPs (N-BPs) act by
inhibiting the enzyme farnesyl pyrophosphate synthase (FPPS), and several crystal structures of complexes between FPPS and
N-BPs have been identified. Understanding the physical basis of the binding between proteins and small molecules is an important
goal in both medicinal chemistry and structural biology. Here, we conducted density functional theory calculations for BPs and
their surrounding residues and were able to successfully reproduce experimental results qualitatively. In addition, we found that
both...
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4867/version/1
Dentate Gyrus
Provedor de dados: 17
Autores: Allen Institute for Brain Science; Rachel A. Dalley; Lydia L. Ng; Angela L. Guillozet-Bongaarts.
This report contains a gene expression summary of the dentate gyrus (DG), derived from the Allen Brain Atlas (ABA) _in situ_
hybridization mouse data set. The structure's location and morphological characteristics in the mouse brain are
described using the Nissl data found in the Allen Reference Atlas. Using an established algorithm, the expression values of the
dentate gyrus were compared to the values of the macro/parent-structure, in this case the hippocampal region, for the purpose of
extracting regionally selective gene expression data. The genes with the highest ranking selectivity ratios were manually curated
and verified. 50 genes were then selected and compiled for expression characterization. The experimental data for each gene may
be...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2095/version/1
Depolarization increases cellular light transmission
Provedor de dados: 17
Autores: Minoru Tomita; Norihiro Suzuki; Yutaka Tomita; Haruki Toriumi; Takashi Osada; Miyuki Unekawa; Jemal
Tatarishvili.
Application of optical methods to human brain tissue in vivo, e.g., measuring oxyhemoglobin and deoxyhemoglobin concentration
changes with near-infrared spectroscopy (NIRS), requires the a priori assumption that background optical properties remain
unchanged during measurements1,2. However, fundamental knowledge about light scattering by brain cells per se remains sparse;
many factors influence light transmission changes through living brain tissue, bringing into question what is being measured. We
have observed slow wave-ring spreads of light transmission changes on the rat cerebral cortex during potassium-induced cortical
spreading depression (CSD) and ascribed them to squeezing-out of blood from capillaries by swollen brain cells3,4. However, in
rat...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2001/version/1
Description of a method for localizing swarming mosquitoes and other insects in 3D space with
visualizations
Provedor de dados: 17
Autores: Nicholas C. Manoukis.
Male mosquitoes swarm to find mates, but the characteristics of these swarms have not yet been quantitatively analyzed in the
field. This paper describes a simple method used recently to localize individual Anopheles gambiae in a swarm via stereoscopic
image analysis of video footage swarms recorded in Doneguebougou, Mali. The methods described here represent a streamlining
of simple triangulation for insect localization in the hope that other researchers will be able to apply the method for studying
fundamental questions about flying insects or other taxa.

Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2599/version/1
Description of variation of genlculate's features of _Phyllodiaptomustunguidus_ shen et
Tai and sex-linked inheritance of Calanoida in freshwater
Provedor de dados: 17
Autores: Sheng-Xing Long; Xiao-Ming Gou; Pin-Hua Xia; Qi-Fei Ren; San Wan; Chuan Chen.
In the present paper, variation of genlculate's features of _Phyllodiaptomustunguidus_ shen et Tai of Calanoida are
described.The authors find that the right first antenna of female species has changed into genlculate and first antenna of male
species changed into genlculate, which can be explained by X-sex-linked inheritance. This isn't a disease but a genetic
characteristic that is better for the living of the species.
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/3003/version/1
Desiderata for an ontology of diseases for the annotation of biological datasets.
Provedor de dados: 17
Autores: Olivier Bodenreider; Anita Burgun.
There is a plethora of disease ontologies available, all potentially useful for the annotation of biological datasets. We define seven
desirable features for such ontologies and examine whether or not these features are supported by eleven disease ontologies. The
four ontologies most closely aligned with our desiderata are Disease Ontology, SNOMED CT, NCI thesaurus and UMLS.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3531/version/1
Design and construction of a new Drosophila species, D.synthetica, by synthetic regulatory evolution
Provedor de dados: 17
Autores: Eduardo Moreno.
Here, I merge the principles of synthetic biology^1,2^ and regulatory evolution^3-11^ to create a new species^12-15^ with a
minimal set of known elements. Using preexisting transgenes and recessive mutations of Drosophila melanogaster, a transgenic
population arises with small eyes and a different venation pattern that fulfills the criteria of a new species according to
Mayr's "Biological Species Concept"^7,10^. The genetic circuit entails the loss of a
non-essential transcription factor and the introduction of cryptic enhancers. Subsequent activation of those enhancers causes
hybrid
lethality.
The
transition
from
"transgenic
organisms"
towards
"synthetic
species", such as Drosophila...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6511/version/1
Design and development of a Europe-wide case specific monitoring method
Provedor de dados: 17
Autores: Angelika Ziegler; Wenke Mönkemeyer; Ralf Wilhelm; Kerstin Schmidt.
Directive 2001/18 EC demands the cultivation of genetically modified organisms (GMO) to be accompanied by post-market
environmental monitoring (PMEM). It is composed of a general surveillance for unanticipated adverse effects and case specific
monitoring (CSM), which is set up to reduce substantial uncertainties in relevant risk scenarios identified in the environmental
risk assessment. PMEM should also allow early identification of potential long-term effects of cultivating GMOs. It should
facilitate decisions in risk management.
In this project, a method for a Europe-wide CSM was to be
developed. Starting with critical questions from ERA, exposure scenarios (first for non target organisms, later for all other
partitions of the ERA) were...
Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4472/version/1
Design and Implementation of the UniProt Website
Provedor de dados: 17
Autores: Eric Jain; Isabelle Phan; Severine Duvaud; Elisabeth Gasteiger; Nicole Redaschi; Maria J. Martin; Peter McGarvey;
Amos Bairoch.
The UniProt consortium is the main provider of protein sequence and annotation data for much of the life sciences community.
The "www.uniprot.org":http://www.uniprot.org website is the primary access point to this data and to
documentation and basic tools for the data. This paper discusses the design and implementation of the new website, which was
released in July 2008, and shows how it improves data access for users with different levels of experience, as well as to machines
for programmatic access.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2611/version/1
Design of a dynamic model of genes with multiple autonomous regulatory modules by evolution in
silico
Provedor de dados: 17
Autores: Alexander V. Spirov; David M. Holloway.
A new approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is
proposed. The approach is based on Genetic Algorithms, with new crossover operators especially designed for these purposes.
The approach exploits the subbasin-portal architecture of the fitness functions suitable for this kind of evolutionary modeling. The
effectiveness of the approach is demonstrated on a series of benchmark tests.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3913/version/1
Design of a dynamic model of genes with multiple autonomous regulatory modules by evolution in
silico
Provedor de dados: 17
Autores: Alexander V. Spirov; David M. Holloway.
A new approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is
proposed. The approach is based on Genetic Algorithms, with new crossover operators especially designed for these purposes.
The approach exploits the subbasin-portal architecture of the fitness functions suitable for this kind of evolutionary modeling. The
effectiveness of the approach is demonstrated on a series of benchmark tests.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/3913/version/2
Design of carbon dioxide storage
Provedor de dados: 17
Autores: Martin J. Blunt.
Carbon capture and storage (CCS) – the collection of carbon dioxide (CO~2~) from industrial sources and its
injection underground – is an important technology to reduce CO~2~ emissions to the atmosphere, mitigating
climate change. The North Sea, with mature hydrocarbon fields and saline aquifers offers an attractive storage location for
CO~2~ produced by the UK’s gas and coal-fired power plants. The principal concern with CCS is to ensure that
the CO~2~ does not leak into the oceans or atmosphere over hundreds or thousands of years. We propose a storage strategy
where CO~2~ and brine are injected together followed by brine injection alone. We predict that using this technique around 95%
of the CO~2~ can be rendered...
Tipo: Presentation
Palavras-chave: Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2628/version/1
Design of RNAi reagents for invertebrate model organisms and human disease vectors
Provedor de dados: 17
Autores: Thomas Horn; Michael Boutros.
RNAi has become an important tool to silence gene expression in a variety of organisms, in particular when classical genetic
methods are missing. However, application of this method in functional studies has raised new challenges in the design of RNAi
reagents in order to minimize false positive and false negative results. Since the performance of reagents can be rarely validated
on a genome-wide scale, improved computational methods are required that consider experimentally derived design parameters.
Here, we describe computational methods for the design of RNAi reagents for invertebrate model organisms and human disease
vectors, such as Anopheles. We describe procedures on how to design short and long double-stranded RNAs for single genes, and
evaluate...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6665/version/1
Design of selective peptide antibiotics by using the sequence moment concept
Provedor de dados: 17
Autores: Davor Juretic; Nada Ilic; Damir Vukicevic; Nikolinka Antcheva; Alessandro Tossi.
New antibiotics against multidrug-resistant bacteria are urgently needed, but rapid acquisition of resistance limits their usefulness.
Endogenous antimicrobial peptides (AMPs) with moderate selectivity, but multimodal mechanism of action, have remained
effective against bacteria for millions of years. Their therapeutic application, however, requires optimizing the balance between
antibacterial activity and selectivity, so that rational design methods for increasing selectivity are highly desirable. We have
created training (n=36) and testing (n=37) sets from frog-derived AMPs with determined therapeutic index (TI). The
'sequence moments' concept then enabled us to find a one-parameter linear model resulting in a good
correlation between...
Tipo: Manuscript
Palavras-chave: Biotechnology; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3068/version/1
Design of selective peptide antibiotics by using the sequence moment concept
Provedor de dados: 17
Autores: Davor Juretic; Nada Ilic; Damir Vukicevic; Nikolinka Antcheva; Alessandro Tossi.
Withdrawn

Incomplete data
Tipo: Manuscript
Palavras-chave: Biotechnology; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3068/version/2
Designing L-Systems for making three and six open reading frames from the leading strand of a single
DNA molecule
Provedor de dados: 17
Autores: Arunava Goswami; Rajneesh Singh; Pabitra Choudhury; Sk. Sarif Hassan Hassan.
Current molecular biology dogma (except alternative splicing) suggests that leading strand of DNA produces mRNA and usually
the leading strand gives one ORF (ORF) among the available six ORFs. We attempted to break this rule where three and six ORFs
from the leading strand will be formed by designing L-Systems, originally proposed to study symmetry of biological world. We
thought this would revolutionize the world of synthetic biology. While doing so, we found L-System containing
A→T, T→G, C→A, and G→C, i.e., single nucleotide production rule will stop
growing after one nucleotide. L-System containing either (a) A→TG, T→GC, C→GA,
G→TC or (b) A→CTG,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4844/version/1
Designing nature reserves in the face of uncertainty
Provedor de dados: 17
Autores: Michael McCarthy; Colin Thompson; Hugh Possingham.
Conservation reserves are one of the most important tools for managing biodiversity. Ever since Diamond, based on theory of
island biogeography, proposed that a single large reserve was preferable to several small reserves of the same total area, there has
been an enduring debate about the veracity of his assertion. The so-called SLOSS debate - should we have a Single Large reserve
Or Several Small reserves - features in every conservation text book and is central to conservation theory. Population dynamic
models suggest that the design that minimizes the risk of extinction of species is case-specific, with the optimal number of
reserves ranging between one and very many. Uncertainty is pervasive in ecology, but, the previous analyses of the SLOSS
debate...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3387/version/1
Designing Novel Lead Molecules For Human Ribosomal Protein S6 Kinase Beta-1 Involved In
Cancers: Ligand Based Virtual Screening Approach
Provedor de dados: 17
Autores: Nainaru Ganesh; Dibyabhaba Pradhan; Amineni Umamaheswari.
Protein kinases are clinically relevant and attractive drug targets for most of the cancerous diseases. Ribosomal protein s6 kinase
(P70s6 kinase) is a mitogen activated Ser/Thr protein kinase, essential for cell growth, G1 cell cycle progression and cell survival.
Human P70s6 kinase is involved in different signaling pathways and phosphorylates the downstream S6 protein of the 40S
ribosomal subunit there by controlling the translational activity. Over expression of human P70s6 or rapid amplification of gene
(RPS6KB1) leads to rapid cell proliferation causing cancer in various organs of humans like colon, breast, ovary, etc. The over
expression is principally due to activation of some phosphorylating sites or ATP binding sites in the domain regions. In the...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4906/version/1
Designing Potent Inhibitors Of Human p38γ For Effective Breast Cancer Therapy
Provedor de dados: 17
Autores: Natarajan Pradeep; Dibyabhaba Pradhan; Amineni Umamaheswari.
Oncogenic constitutive enzyme human p38γ is a serine/threonine protein kinase, activated through phosphorylation
by environmental stress and pro-inflammatory cytokines responses. Breast cancer, hepatoma, colon cancer, atherosclerotic lesion
(coronary artery lesion / hardening of artery), hypertension and inflammations are some of the diseases caused by human
p38γ due to over expression. Over expression of the protein in turn induces anti-apoptosis and inflammatory
responses, increased malignant transformation and cell differentiation. Thus, designing potent inhibitors against p38γ
would be highly practicable for development of novel means of breast cancer therapeutics. Extensive preclinical data and
proteomic analysis support...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4904/version/1
Desynchronization of pathological low-frequency brain activity by the hypnotic drug zolpidem.
Provedor de dados: 17
Autores: Stephen D. Hall; Naoki Yamawaki; Alison E. Fisher; Ralf P. Clauss; Gavin L. Woodhall; Ian M. Stanford.
Reports of the beneficial effects of the hypnotic imidazopyridine, zolpidem, described in persistent vegetative state^1, 2^ have
been replicated recently in brain-injured and cognitively impaired patients^3-7^. Previous single photon emission computed
tomography (SPECT) studies have suggested that sub-sedative doses of zolpidem increased regional cerebral perfusion in affected
areas^5,
8^,
implying
enhanced
neuronal
metabolic
activity;
which
has
led
to
speculation
that
zolpidem
'reawakens' functionally dormant cortex. However, a neuronal mechanism by which this hypnotic drug
affords benefits to brain injured patients has yet to be demonstrated. Here, we report the action of sub-sedative doses of zolpidem
on neuronal network oscillatory...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/1966/version/1
Detecting differential usage of exons from RNA-Seq data
Provedor de dados: 17
Autores: Simon Anders; Alejandro Reyes; Wolfgang Huber.
RNA-Seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding
the regulation of these processes requires comparisons between treatments, tissues or conditions. For the analysis of such
experiments, we present _DEXSeq_, a statistical method to test for differential exon usage in RNA-Seq data. _DEXSeq_ employs
generalized linear models and offers good detection power and reliable control of false discoveries by taking biological variation
into account. An implementation is available as an R/Bioconductor package.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6837/version/1
Detecting differential usage of exons from RNA-Seq data
Provedor de dados: 17
Autores: Simon Anders; Alejandro Reyes; Wolfgang Huber.
RNA-Seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding
the regulation of these processes requires sensitive and specific detection of differential isoform abundance in comparisons
between conditions, cell types or tissues. We present DEXSeq, a statistical method to test for differential exon usage in RNA-Seq
data. DEXSeq employs generalized linear models and offers reliable control of false discoveries by taking biological variation into
account. DEXSeq detects genes, and in many cases specific exons, that are subject to differential exon usage with high sensitivity.
We demonstrate the versatility of DEXSeq by applying it to several data sets. The method facilitates the study of...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6837/version/2
Detection of BCR-ABL kinase domain mutations in CD34+ cells from newly diagnosed chronic phase
CML patients and their association with imatinib resistance
Provedor de dados: 17
Autores: Zafar Iqbal; Ijaz Shah; Aamer Aleem; Mubashar Naqvi; Ammara Tahir; Tariq Gill; Abid Taj; Abdul Qayyum; Najeeb
ur-Rehman; Muhammad Ferhan; Mudassar Iqbal; Muhammad Khalid; Weng Qin; Ahmad Khalid; Mahwish Khan; Shahid Baig;
Abid Jamil; Tanveer Akhtar; Muhammad Abbad; Riaz ul-Haq.
BCR-ABL kinase domain (KD) mutations, the most common cause of imatinib resistance, are infrequently detected in newly
diagnosed chronic-phase chronic myeloid leukemia (CP-CML) patients. Recent studies indicate pre-existing mutations (PEMs)
can be detected in a higher percentage of CML patients using CD34+ stem/progenitor cells, and these mutations may correlate
with imatinib resistance. We investigated KD mutations in CD34+ stem cells from 100 CP-CML patients by multiplex ASO-PCR
and sequencing ASO-PCR products at the time of diagnosis. PEMs were detected in 32/100 patients and included F311L, M351T,
and T315I. After a median follow-up of 30 months (range 8-48), all patients with PEMs exhibited imatinib resistance. Of 68
patients without PEMs, 24...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics & Genomics; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6645/version/1
Detection of genetic diversity among Indian strains of _Xanthomonas campestris_ pv.
_mangiferaeindicae_ using PCR-RAPD
Provedor de dados: 17
Autores: Ram Kishun; Vijai Kumar Gupta.
The randomly amplified polymorphic DNA (RAPD) technique was used to investigate the genetic diversity in 6 strains of
_Xanthomonas campestris_ pv. _mangiferaeindicae_ (_Xcmi_), the causal pathogen of mango bacterial canker disease (MBCD).
The RAPD analysis was also intended to identify molecular markers, specific to the species to develop PCR-based markers for
detection of _Xcmi_ in mango field and planting materials. Twenty RAPD primers (CP 1-CP 20) were evaluated to establish
molecular characters and genetic variability in the genome of _Xcmi_. Among these, only 4 were found efficient for development
of reproducible banding pattern. It has been observed that the largest and smallest amplified RAPD products were of 2.036 and
0.201 kbp. A total of 136...
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/2403/version/1
Detection of Metabolites by Proton Ex Vivo NMR, in Vivo MR Spectroscopy Peaks and Tissue
Content Analysis: Biochemical-Magnetic Resonance Correlation: Preliminary Results
Provedor de dados: 17
Autores: Rakesh Sharma; Madan Rehani; Arun Agrawala.
*Aim*: Metabolite concentrations by in vivo magnetic resonance spectroscopy and ex vivo NMR spectroscopy were compared
with
excised
normal
human
tissue
relaxation
times
and
tissue
homogenate
contents.

*Hypothesis*: Biochemical analysis combined with NMR and MR
spectroscopy defines better tissue analysis.

*Materials and Methods*: Metabolites
were measured using peak area, amplitude and molecular weights of metabolites in the reference solutions. In normal brain and
heart autopsy, muscle and liver biopsy tissue ex vivo NMR peaks and spin-lattice (T1) and spin-spin (T2) relaxation times, were
compared with diseased tissue NMR data in meningioma brain, myocardial infarct heart,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4121/version/1
Detection of MicroRNAs in Dried Serum Blots
Provedor de dados: 17
Autores: Santosh K. Patnaik; Reema Mallick; Sai Yendamuri.
MicroRNAs are short RNAs which can be utilized as biomarkers for a variety of conditions. They are detectable in serum, and
changes in the levels of circulating microRNAs have been associated with different diseases. We tested for the presence of
microRNAs in serum that is dried on paper and stored unrefrigerated instead of being kept frozen. MicroRNAs were readily
detectable in such blots, and their detectability was improved by using paper made of cellulose instead of glass fiber, and by
re-hydrating dried blots with Trizol™ instead of water, phosphate-buffered saline, or guanidine hydrochloride before
RNA extraction. MicroRNA preservation was not diminished by drying of blots at 37, 45 or 60 ºC instead of room
temperature or by...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4785/version/1
Detection of Nonlinear Effects in Gene Expression Pathways
Provedor de dados: 17
Autores: Andreas Mayr; Djork-Arne Clevert; Sepp Hochreiter.
One of the main topics in systems biology is to model genetic pathways. Genes of a pathway, which show linear dependencies of
their expression values, are easy to identify to belong to the pathway. However, if feedback loops or signal cascades are present,
gene expression values of pathway genes can be nonlinearly dependent on the expression values of other genes in the pathway. In
this situation such genes are hard to detect as belonging to the pathway because nonlinearity and noise must be
distinguished.

We propose an algorithm to infer nonlinear network elements in
pathways from microarray data. Our model assumes, that gene expression values, belonging to one pathway, are mainly driven by
one single latent factor. We...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4715/version/1
Detection of Stomach Cancer by TV-Endoscope Colour Enhancement Image Processing
Provedor de dados: 17
Autores: Masaki Miyamoto.
Using modern TV-endoscope equipment, we have experimented image processing in several ways. This time, we designed new
image processing unit called “Color Subtracted Enhancement
image processing unit”. This
unit　was made by combining the RGB-Subtraction　image processing device with the color
enhancement image processing device. The　RGB-subtraction device is an analogue unit that　enables
us to remove the visible red, green and blue peaks from the image. We can subtract the images R-G, R-B, G-R, B-R, B-G simply
by changing the switches. The color enhancement device (developed by Olympus optical corporation inc.) is a digital processing
unit that lets us reinforce any of these colors. This...
Tipo: Poster
Palavras-chave: Cancer.
Ano: 2008
URL: http://precedings.nature.com/documents/2255/version/1
Detection of substrate binding motifs for morphine biosynthetic pathway intermediates in novel
wound inducible (R,S)-reticuline 7-O-methyltransferase of Papaver somniferum
Provedor de dados: 17
Autores: Sonal Mishra; Abha Meena; Sema Singh; Dharmendra Kumar Yadav; Feroz Khan; Rakesh K. Shukla.
The benzylisoquinoline alkaloids (BIA) comprise a large and diverse group of nitrogen-containing secondary metabolites with
about 2500 compounds identified in plants. BIA biosynthesis begins with the condensation of the tyrosine derived precursors
dopamine and p-hydroxyphenylacetaldehyde to (S)-norcoclaurine. Subsequent regiospecific O- and N-methylations and aromatic
ring hydroxylation lead to (S)-reticuline, which is the central intermediate for almost all BIAs. For morphinan alkaloid
biosynthesis, (S)-reticuline undergoes an inversion of stereochemistry to (R)-reticuline, followed by C-C phenol coupling
catalyzed by a unique cytochrome P450-dependent monooxygenase to yield salutaridine. The cDNA sequence of enzymes leading
to (S)-reticuline, as well as...
Tipo: Poster
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5790/version/1
Detection of Sugarcane Yellow Leaf Luteovirus of India
Provedor de dados: 17
Autores: Rajarshi K. Gaur; G.P Rao; Axel Lehrer.
A luteovirus was found associated with midrib yellowing symptoms of sugarcane in India. The virus was earlier identified as
sugarcane yellow leaf virus (SCYLV) on the basis of particle morphology and serological relationships. In this study, we
attempted molecular characterization of an Indian isolate of SCYLV through reverse trascriptase-polymerase chain reaction
(RT-PCR). Comparison showed that the deduced amino acid sequence share 98% homology with an isolate from Texas (cultivar
CC85-964) and 100% homology with corresponding sequences of an Australian isolate of SCYLV (found in cultivar CP 65-357).
Phylogenetic analysis also suggests that the coat protein of the SCYLV genome possesses different taxonomic affinities with other
members of the family...
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3388/version/1
Detection strategies for non-authorized GMO products on the European market
Provedor de dados: 17
Autores: Patrick Gürtler; Esther Meissner; Ulrich Busch.
Import and planting of biotech crops is strictly regulated in Europe. In order to observe these strict regulations, an efficient
surveillance of the European market is required. In Europe, data on authorised biotech crops from foreign countries are on hand,
however, only scarce information on non-authorised biotech crops is available. Experience of the last years has shown that
non-authorized biotech crops (e.g. biotech-papaya, Bt10-maize, LL601-rice and Bt63-rice) were detected on the European market.
The Bavarian Health and Food Safety Authority is responsible for the detection of illegal imports and for labelling control of Food
and Feed in Bavaria (Germany). The quantitative real-time PCR is the method of choice for the detection of genetic...
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4444/version/1
Detection systems cross reacting with peptides - Analysis at the amino acid level
Provedor de dados: 17
Autores: Carsten C. Mahrenholz; Victor Tapia; Rolf Stigler; Rudolf Volkmer.
There are several methods commonly used to measure protein-protein interactions and binding affinities. Quite contrary to most of
these methods, protein- and peptide arrays on cellulose membranes or glass slides are suitable for high-throughput measurement,
as they provide a higher density of probes and a multitude of peptide-protein interactions can be measured in parallel [1]. The
most important application of the SPOT synthesis technique is to simultaneously detect a high number of peptides that have a
strong binding affinity to defined targets. The validity of the results, however, depends on the ability of the detection system to
indicate binding events whilst not interfering with the experiment itself through cross reaction. We tested three common...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4448/version/1
Determination of adsorptive and diffusive properties of carbon dioxide - methane - water in coal-like
structures using molecular simulations
Provedor de dados: 17
Autores: Alaaeldin Salih; Erich A. Müller.
This work employs molecular modeling to simulate both the equilibrium and kinetic behavior pertaining adsorption/desorption
and permeation of carbon dioxide within the enhanced coal bed methane (ECBM) process and the corresponding CO~2~
sequestration processes in deep coal mines. The coal structure is modeled on the basis of a carbon, nanotubes, slit pores and more
realistic “virtual” carbons. (from bottom up in the figure) The grand canonical Monte Carlo method is
used to simulate the adsorption isotherms and isosteric heats of adsorption of the methane-carbon dioxide-water ternary mixture
into the carbon structure, while Molecular Dynamics is applied to the same systems to study the competitive diffusion properties
of these fluids...
Tipo: Presentation
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2625/version/1
Determination of Isoflavone Contents for Selected Soybean Lines and Soy Foods by Fourier
Transform Near Infrared Reflectance Spectroscopy
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng You; Randall L. Nelson.
Soybean isoflavones are of considerable interest in relation to their possible health effects in human diets. Rapid and economical
determination of soybean isoflavone contents is essential for breeding and selection of soybean seeds with optimal isoflavone
levels for food applications. Fourier Transform Near Infrared Spectroscopy (FT-NIR) calibrations were developed for rapid and
reliable analysis of soybean isoflavone content. Our isoflavone calibrations are characterized by low standard errors
(<0.02%) and high degrees of correlation (>99%).
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Genetics & Genomics; Immunology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6194/version/1
Determination of linkage disequilibrium region suggests association of the ancient haplotype, hX with
neural function
Provedor de dados: 17
Autores: Makoto Shimada; Tsutomu Kanasashi.
Modern human populations are known to contain "ancient haplotypes" that originated from archaic humans
by hybridization. Some of them had been reported before the development of human genomic diversity databases, such as
HapMap. Consequently, some of them have no information about linkage disequilibrium (LD) regions. Because genetic
information within LD is tightly linked, to know LD region containing ancient haplotypes will be useful to estimate basic
parameters of admixture events, and to infer biological functions that linked with the ancient haplotypes. One of these ancient
haplotypes, haplotype X (_hX_) was found in a 10.1 kb-region located on Xp11.22, which diverged at 1.4 M years ago, with low
diversity within the cluster in...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6737/version/1
Determination of Mineralogical Contents of a Bangle Shard from an Indus Valley Settlement through
X-ray Diffraction Analysis
Provedor de dados: 17
Autores: Saheeb Ahmed Kayani; Rehan ul Haq Siddiqui.
Some initial results of XRD testing of a bangle shard collected from Harrappa, an Indus Valley settlement located in Pakistan, are
presented. The mineralogical structure of the bangle shard includes montmorillonite, gypsum, and quartz.
Tipo: Manuscript
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6127/version/2
Determination of Mineralogical Contents of a Bangle Shard from an Indus Valley Settlement through
X-ray Diffraction Analysis
Provedor de dados: 17
Autores: Saheeb Ahmed Kayani; Rehan ul Haq Siddiqi.
Some initial results of XRD testing of a bangle shard collected from Harrappa, an Indus Valley settlement located in Pakistan are
presented. The mineralogical structure of the bangle shard includes montmorillonite, gypsum, and quartz.
Tipo: Manuscript
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6127/version/1
Determination of Soybean Oil, Protein and Amino Acid Residues in Soybean Seeds by High
Resolution Nuclear Magnetic Resonance (NMRS) and Near Infrared (NIRS)
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng You; Doina Costescu; P R. Lozano; Valentin Prisecaru; Randall
L. Nelson.
A detailed account is presented of our high resolution nuclear magnetic resonance (HR-NMR) and near infrared (NIR) calibration
models, methodologies and validation procedures, together with a large number of composition analyses for soybean seeds. NIR
calibrations were developed based on both HR-NMR and analytical chemistry reference data for oil and twelve amino acid
residues in mature soybeans and soybean embryos. This is our first report of HR-NMR determinations of amino acid profiles of
proteins from whole soybean seeds, without protein extraction from the seed. It was found that the best results for both oil and
protein calibrations were obtained with a Partial Least Squares Regression (PLS-1) analysis of our extensive NIR spectral data,
acquired...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Ecology; Genetics & Genomics; Molecular Cell
Biology; Bioinformatics; Plant Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7053/version/1
Determinative atom model and the nature of chemical bond
Provedor de dados: 17
Autores: Wanchung Hu.
Quantum mechanics including Schrodinger and Dirac’s equations are used to describe the atom model. However,
the basic assumption assuming electron energy can be described by E=h’w is wrong. If E=h’w, then
the total energy of the electron will be E=rmv^2 in contrary to E=rmc^2 from special relativity. Here, I propose a new atom model
integrating frame-dragging force, centrifugal force, electrostatic force, and magnetic force. In this new model, the proton group
and neutron group in atomic nucleus are rotating in different direction. Thus, they provide equal and opposite frame-dragging
force for orbiting electrons. The electrons are orbiting in the equator plane of nucleus. There is no net force or net acceleration
for...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6719/version/1
Deterministic individual-based cellular automata modelling of single species population dynamics
Provedor de dados: 17
Autores: Lev Kalmykov; Vyacheslav Kalmykov.
This presentation was created to characterise foundations of cellular automata modelling of single species population dynamics.
We show models of single species population growth based on deterministic birth-death-regeneration process and demonstrate a
relationship between fecundity rate and population growth rate. Our models provide mechanistic simulation of logistic-like and
double logistic-like curves of population growth that is not possible in the classical Verhulst model (logistic growth model). This
method is deterministic individual-based and is based on logical “if-then” statements only. As this
method is bottom-up mechanistic and provides a direct visual insight into dynamics of complex systems, we used it to study...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6661/version/1
Deterministic Separation of Cancer Cells from Blood at 10 mL/min
Provedor de dados: 17
Autores: Kevin Loutherback; Joseph D'Silva; Liyu Liu; Amy Wu; Robert Austin; James Sturm.
Circulating tumor cells (CTCs) and circulating clusters of cancer and stromal cells have been identified in the blood of patients
with malignant cancer and can be used as a diagnostic for disease severity, assess the efficacy of different treatment strategies and
possibly determine the eventual location of metastatic invasions for possible treatment. There is thus a critical need to isolate,
propagate and characterize viable CTCs and clusters. Here, we present a microfluidic device for mL/min flow rate,
continuous-flow capture of viable CTCs from blood using deterministic lateral displacement arrays. We show here that a
deterministic bump array can be designed such that it will isolate with efficiency greater than 85% CTCs over a large range in
sizes from...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2012
URL: http://precedings.nature.com/documents/6861/version/1
Developing a Mammalian Behaviour Ontology
Provedor de dados: 17
Autores: Tim Beck; John M. Hancock; Ann-Marie Mallon.
The use of the Entity + Quality (EQ) model in phenotypic descriptions is dependent on the use of specialised domain ontologies to
define the entity under observation. A domain currently lacking a specialised ontology is mammalian behaviour, and so the
Mammalian Behaviour Ontology is being constructed to address this. Top-level class distinctions are made between behavioural
activities and behavioural functions of individuals, and those between two or more individuals. The ontology is manually
developed and encourages contributions from domain experts.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3565/version/1
Developing a Text Mining Prototype for the Comparative Toxicogenomics Database Biocuration
Process
Provedor de dados: 17
Autores: Thomas C. Wiegers.
Understanding interactions between environmental chemicals and genes provides insights into the mechanisms of chemical action,
disease susceptibility, therapeutic drug interactions, and toxicity. The Comparative Toxicogenomics Database (CTD;
http://ctd.mdibl.org) is a web-based resource that integrates diverse information for the cross-species analysis of chemical, gene,
and disease relationships. Much of the data contained in CTD is manually gathered by biocurators; CTD integrates data curated
manually from over 10,000 scientific documents. CTD biocurators manually curate chemical-gene and chemical/gene-disease
interactions from the scientific literature using controlled vocabularies. Unfortunately, there are many more scientific documents
available...
Tipo: Presentation
Palavras-chave: Genetics & Genomics; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3142/version/1
Developing an application ontology for annotation of experimental variables –
Experimental Factor Ontology
Provedor de dados: 17
Autores: James Malone; Tomasz Adamusiak; Ele Holloway; Helen Parkinson.
The Experimental Factor Ontology ("www.ebi.ac.uk/efo":http://www.ebi.ac.uk/efo) is an application
focused ontology modelling the experimental factors in ArrayExpress. The ontology has been developed to increase the richness
of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic
annotation and to integrate external data. The methodology employed in the development of EFO involves construction of
mappings to multiple existing domain specific ontologies, such as the Disease Ontology and Cell Type Ontology.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3806/version/1
Developing Language Abilities by a Non-verbal Training : A fMRI Study
Provedor de dados: 17
Autores: Laurent Lefebvre; Danielle Balériaux; Philippe Paquier; Francis Lowenthal.
The language ability is a critical aspect of experimental design in functional imaging studies. Today, it is commonly accepted that
the brain structures underlying the language are more distributed than the traditional Broca’s and
Wernicke’s areas. Currently, some other areas as the premotor cortex, the supplementary motor area, the cerebellum
or subcortical structures, notably, are recognised. However, a lesser studied question is to define if it is possible to observe a
reorganisation of the activation observed during language tasks when the subjects have been trained to develop non-verbal
abilities. Particularly, Bates and Ellman (1996) claim that probabilistic regularities are the basis of the language acquisition
processing.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1904/version/1
Developing ontologies in decentralised settings
Provedor de dados: 17
Autores: Alexander Garcia; Kieran O’Neill; Leyla J. Garcia; Phillip Lord; Robert Stevens; Oscar Corcho; Frank
Gibson.
This paper addresses two research questions: “How should a well-engineered methodology facilitate the
development of ontologies within communities of practice?” and “What methodology should be
used?” If ontologies are to be developed by communities then the ontology development life cycle should be better
understood within this context. This paper presents the Melting Point (MP), a proposed new methodology for developing
ontologies within decentralized settings. It describes how MP was developed by taking best practices from other methodologies,
provides details on recommended steps and recommended processes, and compares MP with alternatives. The methodology
presented here is the product of direct first-hand...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3231/version/1
Developing Ontology Support for Human Malaria Control Initiatives
Provedor de dados: 17
Autores: Daramola Olawande; Fatumo Segun.
Malaria is one of the most common infectious diseases and an enormous public health problem in Sub-Sahara Africa, Asia and
parts of America. In this paper, we discuss the development of the Human Malaria Control Ontology (HMCO) which contains
general information on Malaria and epidemiological information that can help in the formulation of effective malaria control
policies. The HMCO is aimed at providing interoperability support for the knowledge management of malaria control initiatives,
and serve as an open semantic web infrastructure for malaria research and treatment.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3591/version/1
Developing Predictive Molecular Maps of Human Disease through Community-based Modeling
Provedor de dados: 17
Autores: Jonathan M. J. Derry; Lara M. Mangravite; Christine Suver; Matt Furia; David Henderson; Xavier Schildwachter;
Jonathan Izant; Solveig K. Sieberts; Michael R. Kellen; Stephen H. Friend.
The failure of biology to identify the molecular causes of disease has led to disappointment in the rate of development of new
medicines. By combining the power of community-based modeling with broad access to large datasets on a platform that
promotes reproducible analyses we can work towards more predictive molecular maps that can deliver better therapeutics.
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5883/version/1
Development and application of molecular and bioinformatic tools for the genetic monitoring of wild
beets
Provedor de dados: 17
Autores: Matthias Enders; Lothar Frese; Marion Nachtigall.
Crop Wild Relatives (CWR) are an economically important plant genetic resource (PGR) for plant breeding. One strategy to
conserve PGR in the natural habitat (in situ) is the genetic reserve technique. This approach protects the existing intraspecific
diversity and allows, in contrast to the ex situ approaches, the emergence of new diversity. 
The genetic
reserve conservation technique will be tested in practice with the Genus _Beta_ within the framework of the EU Project
“AEGRO”. _Beta patula_ (Ait.) (BP) and _Beta vulgaris_ (L.) _maritima_ (Arcang.) (BVM) are used
as models. Both species are important resources for sugar beet breeding. BP is a rare and endangered species with a very limited
habitat. In contrast BVM...
Tipo: Presentation
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5742/version/1
Development and Characterization of Eudragit RS 100 Loaded Microsponges and its Colonic Delivery
Using Natural Polysaccharides
Provedor de dados: 17
Autores: Vikas Jain; Ranjit Singh.
In the present work, paracetamol loaded eudragit based microsponges were prepared using quasi-emulsion solvent diffusion
method. The compatibility of the drug with various formulation components was established. Process parameters were analyzed in
order to optimize the formulation. Shape and surface morphology of the microsponges were examined using scanning electron
microscopy.
The
colon
specific
formulations
were
prepared
by
compression
coating
of
microsponges
with
pectin:hydroxypropylmethylcellulose (HPMC) mixture followed by tabletting. The in vitro dissolution studies were done on all
formulations and the results were evaluated kinetically and statically. The kinetics of release study showed that the release data
followed Higuchi matrix and the main...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3676/version/2
Development and Characterization of Eudragit RS 100 Loaded Microsponges and its Colonic Delivery
Using Natural Polysaccharides
Provedor de dados: 17
Autores: Vikas Jain; Ranjit Singh.
In the present work, paracetamol loaded eudragit based microsponges were prepared using quasi-emulsion solvent diffusion
method. The compatibility of the drug with various formulation components was established. Process parameters were analyzed in
order to optimize the formulation. Shape and surface morphology of the microsponges were examined using scanning electron
microscopy.
The
colon
specific
formulations
were
prepared
by
compression
coating
of
microsponges
with
pectin:hydroxypropylmethylcellulose (HPMC) mixture followed by tabletting. The in vitro dissolution studies were done on all
formulations and the results were evaluated kinetically and statically. The kinetics of release study showed that the release data
followed Higuchi matrix and the main...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3676/version/1
Development and comparison of ECC-rtPCR with in vivo method to determine the viability and
infectivity of Giardial cysts
Provedor de dados: 17
Autores: M. Khalid Ijaz; Absar Alum; Basel Sbai; Hamas Asaad; Joseph Rubino.
Globally, Giardia is one of the major cause of diarrheal illnesses and rapid diagnostic methods differentiating infectious cysts are
critical for developing intervention strategies through contaminated surfaces, food and water. This is currently hampered by lack
of an in vitro model. We evaluated mRNA expression in trophozoites and their attachment to a CaCo2 (C2bb) cell monolayer
and changes in trans-cellular resistance as an indicator of Giardia viability and infectivity. Heat shock mRNA in Giardia cysts
and variant specific protein (VSP) mRNA in trophozoites were quantified by RT-PCR. When compared with neonatal mice
infectivity, the attachment of trophozoites to cell monolayers, expression of VSP, and changes in the trans-cellular resistance,
the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology; Microbiology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5501/version/1
Development and Evaluation of an Efficient Process for the Detoxification of Jatropha Oil and Meal
Provedor de dados: 17
Autores: Sarthak Gaur; Balaji Viswanathan; Rachadaporn Seemamahannop; Shubhender Kapila; Neil L. Book.
The poster deals with an often mentioned bioenergy plant - Jatopha curcas. The potential of the plant as a sustainable energy
source has been hampered by toxicity of its oil and protein rich seeds. The research done by our group describes a simple process
for detoxification of the protein rich Jatropha meal thereby making it suitable for animal feed. The process will accelerate use of
Jatropha as an energy and feed source thereby enhancing its economic viability. 

Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6118/version/1
Development and validation of a method for the detection of altered resistance in transgenic plants
against herbivore-pathogen-complexes
Provedor de dados: 17
Autores: Nadine Drechsler; Antje Habekuß; Thomas Thieme; Jörg Schubert.
Enhanced or reduced uptake of viruses by vectors and changes in resistance level can be sensitive indicators for metabolic
changes in transgenic plants caused by the new trait and not observed by conventional methods. In addition, the plant
transformation process itself can lead to such changes. To be able to investigate this hypothesis in cereals we decided to use two
highly important insect-transmitted viruses infecting them - _Barley yellow dwarf virus_ (BYDV) and _Wheat dwarf virus_
(WDV). Corresponding molecular tools for their quantification in plants as well as virus vectors had to be developed.

Both viruses cause similar symptoms: dwarfing, stunting, leaf discoloration leading to yield losses or death
of plant. BYDV...
Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4493/version/1
Development and validation of an analysis method for the detection of altered resistance in transgenic
plants to herbivore-pathogen-complexes
Provedor de dados: 17
Autores: Anja Hühnlein; Jörg Schubert; Thomas Thieme.
Genetically modified plants (GMPs) have to pass several safety evaluations before they can be approved but identification of
undesired changes in metabolism is hard to achieve due to its complexity. Such unexpected changes could be reflected by changes
in virus resistance and feeding behaviour of herbivores such as aphids. Altered behaviour can be determined by so- called life
table statistics where e. g. the lifetime and the reproduction rate are analysed. Such experiments are time consuming and costly.
The behaviour alterations should also be detectable by changes in virus uptake und transmission. Thus, quantitative detection
methods are needed in order to measure the absolute virus content in plants and in aphids. _Potato leafroll virus_ (PLRV) and...
Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4473/version/1
Development of a Decision Support System (DSS) for an integrated test system towards the effective
and competitive risk assessment on transgenic plants
Provedor de dados: 17
Autores: Christine Höflich; Andreas Müller; Jörg Schmidtke; Kerstin Schmidt; Inge
Broer.
Transgenic plants need specific approaches to analyse their potential impact on environment and consumer. The procedures used
to date are often too extensive and time-consuming and associated with high costs. The BioOK network was established to
develop an effective and competitive risk assessment on transgenic plants based on interdisciplinary research. New and effective
methods for the risk assessment were established which focus on transgene-specific effects measured in in vitro systems in the
laboratory or greenhouse whenever possible. Nevertheless event-specific field experiments have to be carried out in addition to
implement
environmental
effects
e.g.
on
non-targets
or
the
variability
of
transgene
expression.

The...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4438/version/2
Development of a Decision Support System (DSS) for an integrated test system towards the effective
and competitive risk assessment on transgenic plants
Provedor de dados: 17
Autores: Christine Höflich; Andreas Müller; Jörg Schmidtke; Kerstin Schmidt; Inge
Broer.
Transgenic plants need specific approaches to analyse their potential impact on environment and consumer. The procedures used
to date are often too extensive and time-consuming and associated with high costs. The BioOK network was established to
develop an effective and competitive risk assessment on transgenic plants based on interdisciplinary research. New and effective
methods for the risk assessment were established which focus on transgene-specific effects measured in in vitro systems in the
laboratory or greenhouse whenever possible. Nevertheless event-specific field experiments have to be carried out in addition to
implement
environmental
effects
e.g.
on
expression.

The...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4438/version/1
non-targets
or
the
variability
of
transgene
Development of a method for phenotyping Black Rot (_Guignardia bidwellii_) resistance on grapevine
(_Vitis_ spp.)
Provedor de dados: 17
Autores: Friederike Rex; Iris Fechter; Ludger Hausmann; Reinhard Töpfer.
Black Rot of grapevine is caused by the Ascomycet _Guignardia bidwellii_. The pathogen was introduced from North America to
Europe in the 19th century. Since 2002, increased effects of the disease have been noticed, causing significant yield losses in the
region of Mosel and infections in all German wine-growing regions. For that reason, it is important to breed Black Rot-resistant
grapevine cultivars. A method has been developed to characterize lots of vines in a fast and reliable way concerning their
susceptibility. Initial data has been collected and can be used for genetic analysis (here QTL). The aim of the project is to develop
a molecular marker correlating with Black Rot resistance which can be used to select juvenile plants and therefore support...
Tipo: Presentation
Palavras-chave: Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5743/version/1
Development of a new method to preserve caprine cauda epididymal spermatozoa in-situ at -10
degrees Centigrade
Provedor de dados: 17
Autores: Uttam Datta; M Chandrasekar; Manik Lal Hembram; Raju Dasgupta.
Electrolyte free mediums prepared with soybean lecithin-glycerol,Coenzyme Q10–glycerol and soybean
lecithin-Coenzyme Q10-glycerol were inoculated separately into ligated cauda epididymides, equilibrated 2 h at 5 degree
centigrade, wrapped with aluminium foils along with testis and freezed at -10 degree centigrade.Spermatozoan characters were
evaluated 7 and 21 days after thawing at 38.5 degree centigrade in a water bath for 5 min. Spermatozoan characters were
diminished gradually and significantly (P<0.001, P<0.05) between the mediums and observation days.
Soybean lecithin-CoenzymeQ10-glycerol effectively protected spermatozoa against cold shock where spermatozoan progressive
motility, livability, hypo-osmotic swelling...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3377/version/1
Development of a sampling regime for research with environmental relevance based on variability of
transgene expression in plants
Provedor de dados: 17
Autores: Carla Struzyna-Schulze; Heike Mikschofsky; Wenke Mönkemeyer; Jörg Schmidtke; Kerstin
Schmidt; Inge Broer.
Transgenic plants often produce proteins that are unknown in conventional crops. Therefore, it requires a fundamental analysis
before approval of a new genetically modified plant is given. Since the EFSA-guidelines for risk assessment on transgenic plants
provide only recommendations but no detailed instructions, we wanted to develop a valid test scheme that defines sample size and
sampling organ to enable a statically valid and efficient analysis of transgene expression and its variability. The scheme will be
based on data obtained for the variability in expression i. of different recombinant proteins in one variety; ii. of different
integration sites of one transgene in one variety; iii. of the same recombinant protein between different varieties and...
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4443/version/1
Development of an Ontology of Microbial Phenotypes (OMP)
Provedor de dados: 17
Autores: Michelle Giglio; Chris Mungall; Peter Uetz; Lanlan Yin; Johannes Goll; Deborah Siegele; Marcus Chibucos; James Hu.
*Abstract*
Phenotypic data are routinely used to elucidate gene and protein function in most organisms
amenable to experimental manipulation. However, although phenotype ontologies exist for many eukaryotic model organisms, no
standardized system exists for the capture of phenotypic information in bacteria. We propose to build an Ontology of Microbial
Phenotypes
and
use
it
to
annotate
the
prokaryotic
model
organism
coli_.

*Introduction*
Phenotypes
are
_Escherichia
the
observable
characteristics of an organism that result from the combination of a particular genotype and a particular environment, and thus are
a basic and fundamental aspect of the biology of all organisms. The awesome power...
Tipo: Poster
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3639/version/1
Development of Future Habitat Suitability Models for the Swift fox (Vulpes velox) in the American
Southwest
Provedor de dados: 17
Autores: Jennifer Redman; Michael T. Calkins; Mark C. Andersen; Kenneth G. Boykin.
The Swift fox (Vupes velox) is a habitat specialist species of short or mixed grass prairie. We used bioclimatic envelope models
and
habitat
suitability
models
under
three
future
climate
scenarios
(based
on
CO2
emission
rates)
from
"www.climatewizard.org":http://www.climatewizard.org to fit species distribution models, using the
maximum entropy method. Current suitable habitat for the swift fox covers an area of 161,984 km2. Under the future climate
scenarios the habitat decreases by 27% in the low emission scenario, 63% for medium emissions, and 53% in the high emissions
scenario. This decrease in suitable habitat corresponded to an overall decrease in total grassland landcover. The current total area
of grassland is 423,440 km2. Under...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3717/version/1
Development of GCP Ontology for Sharing Crop Information
Provedor de dados: 17
Autores: Rosemary Shrestha; Ramil Mauleon; Reinhard Simon; Jayashree Balaji; Stephanie Channelière; Adriana
Alercia; Martin Senger; Kevin Manansala; Thomas Metz; Guy Davenport; Richard Bruskiewich; Graham McLaren; Elizabeth
Arnaud.
The
Generation
Challenge
Programme
(GCP
–
"http://www.generationcp.org":http://www.generationcp.org) is a globally distributed crop research
consortium directed toward crop improvement through the application of comparative biology and genetic resources
characterization
to
plant
breeding.
GCP
adopted
the
development
paradigm
of
a
‘model-driven
architecture’ to achieve the interoperability and integration of diverse GCP data types that are available through
distributed data sources and consumed by end-user data analysis tools. Its objective is to ensure semantic compatibility across the
Consortium that will lead to the creation of robust global public goods from GCP research results....
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3087/version/1
Development of human limbs.
Provedor de dados: 17
Autores: Alexander Ermolenko.
This work offers a new view on the developmental history of tetrapods. It proposes an original evolution model of human limbs
based on metameric formation of osteogenic buds in accordance to primary segmentation and biplanar symmetry. While going
through evolution, osteogenic buds initially identical to each other were changing their sizes, realigning, regressing, uniting while
keeping the direction of the formation in accordance to the following formula (taking into account sesamoid
bones):
2; 1; 2; 3; 2; 3; 5; 5; 8; 8 (in the upper limb together with the upper limb girdle); 3; 2; 3; 2; 1; 2; 8; 8;
5; 5 (in the lower limb together with the pelvic bones).
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5539/version/1
Development of Incentives for Data Sharing in Ecology, Evolution, and Organismal Biology
Provedor de dados: 17
Autores: Clifford S. Duke.
Ready access to data is a key concern in both basic research and problem-solving in the biological sciences, as the scale and scope
of the questions that researchers ask expand, and as global problems demand data collected from around the world. With a grant
from the National Science Foundation, from 2004 through 2009, the Ecological Society of America (ESA) has led a series of five
workshops on data sharing, to help the ecology, evolution, and organismal biology communities find common ground on how to
make data more readily discoverable and accessible in their own disciplines. The most recent of these focused in the development
of incentives for data sharing, both at the individual and organizational level. This presentation will summarize the workshop...
Tipo: Presentation
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3647/version/1
Development of Integrative Bioinformatics Applications using Cloud Computing resources and
Knowledge Organization Systems (KOS).
Provedor de dados: 17
Autores: Jonas Almeida; Helena Deus; Wolfgang Maass.
Use of semantic web abstractions, in particular of domain neural Knowledge Organization Systems (KOS), to manage distributed,
cloud
based,
integrative
bioinformatics
infrastructure.
This
presentation
derives
from
recent
publication:

Almeida JS, Deus HF, Maass W. (2010) S3DB core: a framework for
RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics. 2010 Jul 20;11(1):387. [PMID
20646315].

These PowerPoint slides were presented at Semantic Web Applications
and Tools for Life Sciences December 10th, 2010, Berlin, Germany (http://www.swat4ls.org/2010/progr.php), keynote 9-10 am.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5537/version/1
Development of Java based graphical user interface for Diagnosis of Hepatitis UsingI Mixture of
Expert
Provedor de dados: 17
Autores: M Shankaracharya; Suchitra Kumari; Ambarish S. Vidyarthi.
Hepatitis is deadly, and the fifth leading cause of death after heart disease, stroke, chest disease and cancer. Worldwide, 1.5
million deaths per year have been estimated. Detection of hepatitis is a big problem for general practitioners. An expert doctor
commonly makes decisions by evaluating the current test results of a patient or by comparing the patient with others with the
same condition with reference to the previous decisions. Many machine learning and data mining techniques have been designed
for the automatic diagnosis of hepatitis. However, no one tool is available to the general population for the diagnosis of Hepatitis.
Hence, a graphical user interface-enabled tool needs to be developed, through which medical practitioners can feed patient...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7093/version/1
Development of Neural Electromagnetic Ontologies (NEMO): Ontology-based Tools for
Representation and Integration of Event-related Brain Potentials
Provedor de dados: 17
Autores: Gwen A. Frishkoff; Paea LePendu; Robert M. Frank; Haishan Liu; Dejing Dou.
We describe a first-generation ontology for
representation and integration of event-related brain potentials
(ERPs). The ontology is designed following OBO “best practices” and is augmented with tools to
perform ontology-based labeling and annotation of ERP data, and a database that enables semantically based reasoning over these
data. Because certain high-level concepts in the ERP domain are illdefined, we have developed methods to support coordinated
updates to each of these three components. This approach consists of “top-down” (knowledge-driven)
design and implementation, followed by “bottom-up” (data-driven) validation and refinement. Our
goal is to build an ERP...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3458/version/1
Development of Novel Calibrations for FT-NIR Analysis of Protein, Oil, Carbohydrates and
Isoflavones in Foods
Provedor de dados: 17
Autores: I Baianu; Jun Guo.
The development of calibration methodology for novel FT-NIRS analysis of soybean-based foods is presented together with
high-precision NIRS spectra and composition measurements in terms of proteins, oil and carbohydrates in soybean-based
foods/soy foods.

Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Pharmacology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6317/version/1
Developments in CFG glycan and pathogen polysaccharide arrays
Provedor de dados: 17
Autores: Ola Blixt.
This presentation summarizes developments in glycan and pathogen polysaccharide arrays at the Consortium for Functional
Glycomics (CFG).
Tipo: Presentation
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/12/version/1
Diabetes and kidney cancer: A direct or indirect association?
Provedor de dados: 17
Autores: Rohit P. Ojha; Eva L. Evans; Tabatha N. Powell; Bahij S. Nuwayhid; Zuber D. Mulla.
A positive association between diabetes and kidney cancer has been reported in several investigations, but it is unclear whether
diabetes or its complications account for this association. Recent advances in estimating direct associations may be useful for
elucidating the association between diabetes and kidney cancer. Therefore, we performed a case-control analysis to evaluate
whether the direct association between diabetes and kidney cancer is the primary concern in this exposure-outcome relation.
Discharge data (with International Classification of Diseases – 9 codes) from 2001 for hospitals throughout Florida
were used to construct a case-control population of inpatients aged ≥45 years. Cases (n=1,909) were inpatients
with...
Tipo: Poster
Palavras-chave: Cancer.
Ano: 2010
URL: http://precedings.nature.com/documents/4922/version/1
Diagnostic robustness of DNA microarrays in the classification of acute leukemia
Provedor de dados: 17
Autores: Marie Loh; Adrian Mondry.
Countless statistical methods have been described for the analysis of DNA microarrays, and each yields distinct results. This
raises the question whether DNA microarrays are robust diagnostic tools.

In order to
address this issue, we compared five formally similar statistical tests for gene selection on a single data set derived from acute
leukemia patients. Inter-test agreement of gene selection, of sample classification and with standard clinical diagnosis was
calculated using Cohen's κ-score.

The inter-test agreement
scores were 0.15 < κ < 0.68 for gene selection, and 0.60 < κ
< 0.89 for sample classification....
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics & Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1056/version/1
Diamagnetic levitation enhances growth of liquid bacterial cultures by increasing oxygen availability
Provedor de dados: 17
Autores: Camelia E. Dijkstra; Oliver J. Larkin; Paul Anthony; Michael R. Davey; Laurence Eaves; Catherine E. D. Rees; Richard
J. A. Hill.
Diamagnetic levitation is a technique that uses a strong, spatially-varying magnetic field to reproduce aspects of weightlessness,
on the Earth. We used a superconducting magnet to levitate growing bacterial cultures for up to 18 hours, to determine the effect
of diamagnetic levitation on all phases of the bacterial growth cycle. We find that diamagnetic levitation increases the rate of
population growth in a liquid culture and reduces the sedimentation rate of the cells. Further experiments and microarray gene
analysis show that the increase in growth rate is due to enhanced oxygen availability. We also demonstrate that the magnetic field
that levitates the cells also induces convective stirring in the liquid. We present a simple theoretical model,...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4216/version/2
Diamond nanowires, a new approach towards next generation electrochemical gene sensor platforms
Provedor de dados: 17
Autores: Nianjun Yang; Hiroshi Uetsuka; Jiuhong Yu; Eiji Osawa; Norio Tokuda; Christoph Nebel.
A novel bio-sensing platform is introduced by combination of a) geometrically controlled DNA bonding using vertically aligned
diamond nano-wires and b) the superior electrochemical sensing properties of diamond as transducer material. Ultra-hard
vertically aligned diamond nanowires are electrochemically modified to bond phenyl linker-molecules to their tips which provide
mesospacing for DNA molecules on the transducer. The nano-wires are generated by reactive ion etching of metallically boron
doped atomically smooth single crystalline CVD diamond. Surface properties are characterized by atomic force, scanning electron
and scanning tunneling microcopy. Electro- and biochemical sensor properties are investigated using cyclic and differential
pulse...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/1714/version/1
Dibutyltin Disrupts Glucocorticoid Receptor Function and Impairs Glucocorticoid-induced
Suppression of Cytokine Production
Provedor de dados: 17
Autores: Christel Gumy; Charlie Chandsawangbhuwana; Anna A. Dzyakanchuk; Denise V. Kratschmar; Michael E. Baker; Alex
Odermatt.
_Background_. Organotins are highly toxic and widely distributed environmental chemicals. Dibutyltin (DBT) is used as
stabilizer in the production of polyvinyl chloride plastics, and it is also the major metabolite formed from tributyltin (TBT) _in
vivo_. DBT is immunotoxic, however, the responsible targets remain to be defined. Due to the importance of glucocorticoids in
immune-modulation,
we
investigated
whether
DBT
could
interfere
with
glucocorticoid
receptor
(GR)
function.
_Methodology_. We used HEK-293 cells transiently transfected with human GR as well as rat
H4IIE hepatoma cells and native human macrophages and human THP-1 macrophages expressing endogenous receptor to study
organotin effects on GR function. Docking of organotins was...
Tipo: Manuscript
Palavras-chave: Immunology; Pharmacology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2312/version/1
Dicroidium: no more a Triassic Gondwana index fossil
Provedor de dados: 17
Autores: Ashwini Srivastava; Rashmi Srivastava; Deepa Agnihotri.
A large number of _Dicroidium_-frond, considered as the marker of Early Triassic Gondwana flora, are discovered for the first
time with well preserved cuticle from Early Permian (Lower Gondwana) sequence of Barakar Formation, Satpura Gondwana
Basin, India. The presence of _Dicroidium_ in Late Permian mixed floral zone of Jordan has been viewed as its possible origin in
paleotropics but the evidence in hand exhibits its Gondwanic derivation and threatens the recognition of _Dicroidium_ flora for
Middle Gondwana in association with Lower Gondwana Glossopteris and Upper Gondwana Ptilophyllun flora.
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4777/version/1
Did nature also choose arsenic?
Provedor de dados: 17
Autores: Felisa Wolfe-Simon; Paul C. W. Davies; Ariel Anbar.
All
known
life
requires
phosphorus
(P)
in
the
form
of
inorganic
phosphate
(PO<sub>4</sub><sup>-</sup>
P<sub>i</sub>)
and
phosphate-containing
organic
or
molecules.
P<sub>i</sub> serves as the backbone of the nucleic acids that constitute genetic
material and as the major repository of chemical energy for metabolism in polyphosphate bonds. Arsenic (As) lies directly below
P on the periodic table and so the two elements share many chemical properties, although their chemistries are sufficiently
dissimilar that As cannot directly replace P in modern biochemistry. Arsenic is toxic precisely because As and P are similar...
Tipo: Manuscript
Palavras-chave: Chemistry; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1482/version/1
Dielectric Constant of Liquids (Fluids) Shown to be Simple Fundamental Relation of Density over
Extreme Ranges from - 50^o^ to + 600^o^C, Believed Universal
Provedor de dados: 17
Autores: William L. Marshall.
Examinations of past complex theoretical equations describing isothermal dielectric constants (_[epsilon]_) of liquids show that
none describe experiments throughout and that only a two-constant equation of density is required. The dielectric susceptibility
(_[epsilon]_ – 1) as a simple exponential function of density is shown here to describe _[epsilon]_ for both polar and
non-polar organic liquids over all available experimental ranges from 0.50 to 1.2 g cm^-3^ and temperatures to 400^o^C. For
water above 0.25 g cm^-3^, the equation describes the excellent dielectric-constant formulation of Fernández, et al.,
(1997) throughout its experimental range [-35 to +600^o^C; to 1000 MPa (10000 Atm)] and even when diluted by...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2474/version/1
Dielectric Constant of Water Discovered to be Simple Function of Density over Extreme Ranges from
– 35 to + 600^o^C and to 1200 MPa (12000 Atm.), Believed Universal
Provedor de dados: 17
Autores: William L. Marshall.
The experimental static dielectric constants (_[epsilon]_) of water formulated by Fernández, et al., (1997-International
Association for the Properties of Water and Steam, IAPWS), –35 to 600^o^C; 0.1 to 1200 MPa, are discovered to be
closely described throughout by a simple equation of density (_[rho]_), presented here, and agreeing with their reported calculated
(extrapolated) values to 923^o^C. Eight limiting boundary conditions are observed. Values of _[epsilon]_ follow isothermal
straight-line slopes of log (_[epsilon]_ – 1) vs log _[rho]_ down to densities of 0.25 g cm^-3^ water, even in
dioxane-water solutions.
At lower densities, all slopes curve asymptotically in approaching unity, while becoming unity
throughout...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2472/version/1
Diet, Genetic Factors, and the Gut Microbiome in Crohn's Disease
Provedor de dados: 17
Autores: Gary D. Wu; James D. Lewis; Frederic D. Bushman.
This manuscript is part of a pilot effort on the part of NIH staff and the Nature publishing group to provide a more convenient
archive for "marker papers" to be published. These "marker papers" are designed
to provide the users of community resource data sets with information regarding the status and scope of individual community
resource projects. For further information see editorial in September 2010 edition of Nature Genetics (Nature Genetics, 42, 729
(2010)), and the Nature Precedings HMP summary page.

Project IDs: 46313,
46879
Publication moratorium: 1 year


We propose to
investigate the hypothesis that consistent changes...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics & Genomics; Immunology; Microbiology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5006/version/1
Diet of Northern Map Turtles (_Graptemys geographica_): Relationship to Sexual Dimorphism and
Potential Impacts of an Altered River System in Maryland
Provedor de dados: 17
Autores: Teal Richards-Dimitrie; Richard Seigel.
Last recorded in Maryland in the early 1990’s, the Northern Map Turtle (_Graptemys geographica_) is listed as
state endangered and is currently only known in the lower Susquehanna River drainage. This river is divided by a hydroelectric
dam, used for recreation, and has increasing shoreline development, all of which may negatively impact this population. Knowing
this population’s diet and if alterations to the river affect their prey base is important to understanding the
species’ current status. Northern Map Turtles are mostly molluscivorous but will also consume other invertebrates.
Studies have shown that map turtle species will subsidize their diet with invasive mussels, potentially decreasing dietary diversity.
The...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/4840/version/1
Diet transition to a high-fat diet for 3 weeks reduces brain omega-3-fatty acid levels, alters BDNF
signaling and induces anxiety & depression-like behavior in adult rats
Provedor de dados: 17
Autores: Sandeep Sharma; Yumei Zhuang; Fernando Gomez-Pinilla.
Background: The consumption of diets high in calories and low in nutrient value is becoming increasingly common in modern
society, which can lead to metabolic disorders like diabetes and obesity, and potentially to psychiatric disorders. We have
performed studies to assess how the shift from a healthy diet rich in omega-3 fatty acids to a diet rich in saturated fatty acid affects
the substrates for brain plasticity and function, and anxiety and depression-like behavior. Methods: Pregnant rats were fed with
omega-3 supplemented diet from their 2nd day of gestation period as well as their male pups for 12 weeks. Afterwards, the
animals were randomly assigned to either a group fed on the same diet or a group fed on a high-fat diet (HFD) rich in saturated
fats...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Neuroscience; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6950/version/1
Difference in response reliability predicted by STRFs in the cochlear nuclei of barn owls
Provedor de dados: 17
Autores: Louisa J. Steinberg; Jose L. Pena.
The brainstem auditory pathway is obligatory for all aural information. Brainstem auditory neurons must encode the level and
timing of sounds, as well as their time-dependent spectral properties, the fine structure and envelope, which are essential for sound
discrimination. This study focused on envelope coding in the two cochlear nuclei of the barn owl, nucleus angularis (NA) and
nucleus magnocellularis (NM). NA and NM receive input from bifurcating auditory nerve fibers and initiate processing pathways
specialized in encoding interaural time (ITD) and level (ILD) differences, respectively. We found that NA neurons, though unable
to accurately encode stimulus phase, lock more strongly to the stimulus envelope than NM units. The spectrotemporal receptive...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5798/version/2
Difference in response reliability predicted by STRFs in the cochlear nuclei of barn owls
Provedor de dados: 17
Autores: Louisa J. Steinberg; Jose L. Pena.
The brainstem auditory pathway is obligatory for all aural information. Brainstem auditory neurons must encode the level and
timing of sounds, as well as their time-dependent spectral properties, the fine structure and envelope, which are essential for sound
discrimination. This study focused on envelope coding in the two cochlear nuclei of the barn owl, nucleus angularis (NA) and
nucleus magnocellularis (NM). NA and NM receive input from bifurcating auditory nerve fibers and initiate processing pathways
specialized in encoding interaural time (ITD) and level (ILD) differences, respectively. We found that NA neurons, though unable
to accurately encode stimulus phase, lock more strongly to the stimulus envelope than NM units. The spectrotemporal receptive...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5798/version/1
Differences in the gene expression profile of human monocytic cells activated by high and low affinity
Fc-gamma-receptors.
Provedor de dados: 17
Autores: Jayapal J. Manikandan; Renji Reghunathan; Alirio Jose Melendez; Peter Natesan Pushparaj.
Receptors for the constant (Fc) region of immunoglobulin G, play an important role in linking the humoral and cellular arms of
immune response. Three different classes of receptors have been defined, FcγRI (CD64), FcγRII (CD
32), and FcγRIII (CD16). We have previously shown that in a human monocyte model (IFNγ-primed
U937 cells), FcγRI and FcγRII stimulation trigger two very distinct intracellular signalling pathways.
Here we show for the first time, the use of oligonucleotide microarrays to investigate the overall gene-expression profile of human
monocytes triggered with FcγRI or FcγRII. Our data indicate that several interesting genes are
differentially expressed in response...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1149/version/1
Differences of morphological and ecological characters among lineages of Chilean Rhinocryptidae in
relation an sister lineage of Furnariidae.
Provedor de dados: 17
Autores: Alejandro Correa Rueda; Jorge Mpodozis; Michel Sallaberry.
Eight species of Rhinocryptidae are recognized from Chile. Moreover, morphological, ecological and behavioral differences
among two lineages of _Scytalopus_ and two species of _Pteroptochos_ are unclear. According to our results, there are no
decisive criteria differentiating among subspecific sister taxa of _Scelorchilus albicollis_, _S. rubecula_ and _Pteroptochos
megapodius_. Here we discuss the speciation of the chilean Rhinocryptidae based in their behaviour. We propose a new
methodology based on ecological and behavioural patterns in order to understand the concept of speciation in this group of
birds.

Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1606/version/2
Differences of morphological and ecological characters among lineages of Chilean Rhinocryptidae in
relation an sister lineage of Furnariidae.
Provedor de dados: 17
Autores: Alejandro Correa Rueda; Jorge Mpodozis; Michel Sallaberry.
Eight species of Rhinocryptidae are recognized from Chile. Moreover, morphological, ecological and behavioral differences
among two lineages of _Scytalopus_ and two species of _Pteroptochos_ are unclear. According to our results, there are no
decisive criteria differentiating among subspecific sister taxa of _Scelorchilus albicollis_, _S. rubecula_ and _Pteroptochos
megapodius_. Here we discuss the speciation of the chilean Rhinocryptidae based in their behaviour. We propose a new
methodology based on ecological and behavioural patterns in order to understand the concept of speciation in this group of
birds.

Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1606/version/1
Differences of morphological and ecological characters among lineages of Chilean Rhinocryptidae in
relation an sister lineage of Furnariidae.
Provedor de dados: 17
Autores: Alejandro Correa Rueda; Jorge Mpodozis; Michel Sallaberry.
Eight species of Rhinocryptidae are recognized from Chile. Moreover, morphological, ecological and behavioral differences
among two lineages of Scytalopus and two species of Pteroptochos are unclear. According to our results, there are no decisive
criteria differentiating among subspecific sister taxa of Scelorchilus albicollis, S.rubecula and Pteroptochos megapodius. Here
we discuss the speciation of the chilean Rhinocryptidae based in their behaviour and we carried out an integrated analysis with
specie outgroup Cinclodes oustaleti (Furnariidae). We propose a new methodology
patterns
in
order
to
understand
the
concept
of
based on ecological and behavioural
speciation
in
this
group
of
birds.



Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1606/version/3
Different Approaches For Protein Engineering In Industrial Biotechnology
Provedor de dados: 17
Autores: Israr Khan; Muhammad Waheed Akhtar.
Protein engineering is the novel field which has wide applications from pharmaceutics, industry, commercial, laundry and
research. It may apply rational design or non rational design or both. Site directed mutagenesis is a classical approach involving
the protein folding principles and as such different techniques involving multidisciplinary research and broad knowledge is
required involving biocomputing of complex data obtained from various sequencing projects and prediction of the future protein
structure either chemically or genetically modified. Non rational mutagenesis or directed evolution involves random mutations in
the gene encoding protein or shuffling the genes encoding different domains producing a random set of numerous large libraries
of...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/5601/version/1
Differential expression analysis for sequence count data
Provedor de dados: 17
Autores: Simon Anders; Wolfgang Huber.
Motivation: High throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq),
protein-DNA binding (ChIP-Seq), cell counting. Statistical inference of differential signal in these data needs to take into account
their natural variability throughout the dynamic range. When the number of replicates is small, error modeling is needed to
achieve statistical power. 

Results: We propose an error model that uses the negative
binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The
method controls type-I error and provides good detection power.

Availability: A free
open-source...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4282/version/1
Differential expression analysis for sequence count data
Provedor de dados: 17
Autores: Simon Anders; Wolfgang Huber.
*Motivation:* High-throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq),
protein-DNA binding (ChIP-Seq) or cell counting (barcode sequencing). Statistical inference of differential signal in such data
requires estimation of their variability throughout the dynamic range. When the number of replicates is small, error modelling is
needed to achieve statistical power.

*Results:* We propose an error model that uses
the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count
data.
The
method
controls
type-I
error
and
provides
good
detection
power.


*Availability:* A free...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4282/version/2
Differential Gene Expression of Human Mast cell Activation Reveals Gene profiles of Innate and
Adaptive Immunity.
Provedor de dados: 17
Autores: Jayapal J. Manikandan; Reghunathan Renji; Peter Natesan Pushparaj; Alirio Jose Melendez.
High-density oligonucleotide microarray is a promising approach for high throughput analysis. It has been extensively used in
many areas of biomedical research. Immunoglobulin E (IgE) mediated allergic response (type-1 hypersensitivity) is one of the
most powerful reactions of the immune system. Tissue Mast Cells (MCs) and circulating basophils are the major effector cells in
these reactions. By dissecting the regulatory circuitry of mast cells by analyzing the genome wide effects of antigen stimulation
triggered by FcεRI, offers a potential for finding novel genes as ‘targets’ for therapeutic
intervention. In this work, we tried to study the gene expression pattern in IgE sensitized and FcεRI cross linked
cord...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1148/version/1
Differential photosynthetic adaptation between size-classes of Spruce and Fir juveniles help to
explain the co-existence of the two species.
Provedor de dados: 17
Autores: Edgard Bontempo e Silva; Toshihiko Hara; Akihiro Sumida; Kiyomi Ono.
Background/Question/Methods

_Abies
sachalinensis_
(Sakhalin
Fir)
and
_Picea
glehnii_
(Glehn’s Spruce) are major components of the sub-boreal forests of Hokkaido, Japan. Similar Spruce-Fir forests can
be found in many other places in the northern hemisphere and will probably be impacted by global warming. Therefore, detailed
knowledge of these species’ physiology and life-history strategies at different growth stages is important to
understand present communities and to support reliable prediction of possible consequences of global climate change.

Accordingly, the objective of this study was to establish relations between community dynamics,
life-history strategies and photosynthetic adaptation of...
Tipo: Poster
Palavras-chave: Ecology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5298/version/1
Diffusion Approximations for Demographic Inference: DaDi
Provedor de dados: 17
Autores: Ryan N. Gutenkunst; Ryan D. Hernandez; Scott H. Williamson; Carlos D. Bustamante.
Models of demographic history (population sizes, migration rates, and divergence times) inferred from genetic data complement
archeology and serve as null models in genome scans for selection. Most current inference methods are computationally limited to
considering simple models or non-recombining data. We introduce a method based on a diffusion approximation to the joint
frequency spectrum of genetic variation between populations. Our implementation, DaDi, can model up to three interacting
populations and scales well to genome-wide data. We have applied DaDi to human data from Africa, Europe, and East Asia,
building the most complex statistically well-characterized model of human migration out of Africa to date.
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4594/version/1
Digital BioCuration: A Question of Balance
Provedor de dados: 17
Autores: James Ostell.
Curation of biomedical data has come to encompass a broad range of activities and considerations, which include the building of
digital archives, making decisions on the relative value and longevity of one dataset vs another, editing data records manually,
performing or assessing computational processes over very large sets of data, and grappling with issues of web usability and data
standards. People who consider themselves biological curators may range from a single domain expert, who develops a collection
which reflects their personal judgments and priorities, to groups of people supporting large, long term public resources such as
GenBank, RefSeq, or PubMed, and everything in between. Finding the right balance between objective measures of quality and...
Tipo: Presentation
Palavras-chave: Genetics & Genomics; Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3257/version/1
Digital Image Analysis of Actinomycetes Colonies as a Potential Aid for Rapid Taxonomic
Identification
Provedor de dados: 17
Autores: Sonashia Velho-Pereira; Nandkumar M. Kamat.
High frequency isolation of actinomycetes poses a challenge for the taxonomists hence simple and rapid identification methods
are required. Our work to catalogue biodiversity of actinomycetes of Goa yielded several distinct morphotypes. After their
tentative identification, the feasibility to distinguish these using digital image analyses (DIA) was explored. Digital images of wild
colony morphotypes were processed using public domain SCION image analysis software. DIA revealed some intricate digital
characters. A combination of these with standard morphological and microscopic characters could be potentially useful for
preparing a digital identification key of the actinomycetes strains with potential application in rapid taxonomic identification.
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4209/version/1
Dimension-based attention in the recognition of facial identity and facial expression
Provedor de dados: 17
Autores: Zhicheng Lin.
Although the human visual system is constantly flooded with sensory information, the brain is remarkable in inferring structures
from the massive inputs and selectively attending to behaviorally relevant information. However, how the two processes interact
remains largely unknown. Can top-down attention efficiently select the task-relevant dimension (e.g. gender) during face
recognition to override interference in the task-irrelevant dimension (e.g. expression)? To address this issue, participants were
asked to classify real face images according to gender or expression, which were preceded by other faces (masked priming task)
or words (face-word Stroop task). Results show that face classification was 1) affected by the task-relevant but not the...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2222/version/1
Direct fluorophore conjugation to genomic DNA for microarray-based epigenomic profiling
Provedor de dados: 17
Autores: Vineet Gupta.
A methodology for microarray based epigenomic profiling is presented. The method relies on platinum-based fluorescence
labeling reagents for direct (non-enzymatic) labeling of DNA and RNA. This is a work in progress and only preliminary data is
presented here.
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Chemistry; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/444/version/1
Direct submission system and literature annotation of rice genes in Oryzabase
Provedor de dados: 17
Autores: Yukiko Yamazaki; Rie Tsuchiya; Takao Asanuma; Yo Shidahara; Shingo Sakaniwa.
Oryzabase ("http://www.shigen.nig.ac.jp/rice/oryzabase/":http://www.shigen.nig.ac.jp/rice/oryzabase/) is a
comprehensive rice science database ^1^. It houses a variety of genetic resources, relevant literatures, gene dictionary, DNA
sequences, and basic information such as developmental biology and anatomy. In order to keep the gene dictionary up-to-date,
literature annotation has been conducted manually since 1995. However as the publication of journal articles increases year by
year after genomic sequences were released, it became more difficult to update the dictionary timely and in high quality without
sufficient annotators. To overcome this difficulty, we applied machine learning and text-mining to extract known and unknown
genes...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3164/version/1
Discovery of multiple lead compounds as M2 inhibitors through the focused screening of a small
primary amine library.
Provedor de dados: 17
Autores: Wenhui Hu; Shaogao Zeng; Chufang Li; Yanling Jie; Zhiyuan Li; Ling Chen.
The discovery of new anti-influenza drugs is urgent, particularly considering the recent threat of swine flu. In this study, the
influenza virus M2 protein was expressed in HEK293 cells and shown to have selective ion channel activity for monovalent ions.
The anti-influenza virus drug amantadine hydrochloride significantly attenuated the inward current induced by hyperpolarization
of HEK293 cell membranes. Although adamantine derivatives are the only M2 drugs for influenza virus A, their use is limited in
the US due to drug resistance. Here we report the discovery of multiple M2 inhibitor lead compounds that were rapidly generated
through focused screening of a small primary amine library. The screen was designed using a scaffold-hopping strategy based
on...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3688/version/1
Discovery of the Principal Cystic Fibrosis Mutation (F508del) in Ancient DNA from Iron Age
Europeans
Provedor de dados: 17
Autores: Philip Farrell; Cedric Le Marechal; Claude Ferec; Malika Siker; Maria Teschler-Nicola.
The most common, life-threatening autosomal recessive disease of Europeans and Euro-Americans, cystic fibrosis (CF), occurs
predominately in patients with the F508del mutation.1 Although F508del is currently detectable as a single allele in 1/30-1/40
Europeans2-4 and Euro-Americans,5 it has not been determined what heterozygote selective advantage(s) might account for its
relatively high prevalence. Indirect evidence6 suggests that this mutation was present in Brittany at least 3000 years ago, but no
direct analyses of ancient DNA have been reported to identify F508del and clarify its frequency in prehistoric inhabitants of
Europe. Here we show that F508del was present in 3 of 32 Iron Age inhabitants of Austria from whom DNA could be recovered
from molar...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1276/version/1
Discovery of transcription factor binding sites through integration of generic motif finders
Provedor de dados: 17
Autores: Edward Wijaya; Siu-Ming Yiu; Thanh Son Ngo; Rajaraman Kanagasabai; Wing-Kin Sung.
Locating transcription factor binding sites is a key step in understanding gene regulation. Due to its importance, many _de novo_
motif-finding methods have been proposed. Individually, these motif finders perform unimpressively overall based on
Tompa's benchmark datasets. Moreover, these motif finders vary in their definitions of what constitute a motif, and in
their methods for finding statistically overrepresented motifs. There is no clear way for biologists to choose the motif finder that is
most suitable for their task. The purpose of this work is to describe a method called MotifVoter to identify transcription factor
binding sites by integrating the results found by motif finders of different models. Validation of our method on...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1251/version/1
Discriminatory power of MicroResp^TM^ analyses across variable spatial scales in semiarid
ecological zones
Provedor de dados: 17
Autores: Mohammad E. W. Tahtamouni; Adrian Unc; Mary Lucero; Sa'eb Khresat.
Indirect assessment of enzymatic activity potential via substrate induced respiration is a common tool used to evaluate variability
in soil microbial activity induced by environmental or management variables. The MicroResp™ method for total soil
sample catabolic profiling has been employed to estimate divergence in microbial activities under contrasting conditions. Here we
evaluate the potential for the method to discriminate across samples exposed to similar ecological conditions at distinct
geographical locations, and across samples exposed to distinct soil management conditions. Samples used in this report came from
four spatially distinct arid or semi arid locations in New Mexico, USA and Jordan. For all scales of comparison, similar...
Tipo: Poster
Palavras-chave: Ecology; Microbiology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6204/version/1
Discussion on preservation mechanism of Yersinia pestis by Citellus undulatus
Provedor de dados: 17
Autores: Cunning Qian; Jichun Lin; Yuming Feng; Xiaoxue Zhang; Cheng Wang; Gang Lei.
Studies prove that plague in _Citellus undulatus_ exists in the nature with the pattern of successive prevalence every year.
_Citellophilus tesquorum altaicus_ is not only the main transmission vector, but also the reservoir of _C. undulatus_ plague. And
the latter can spread _Yersinia pestis_. The fact challenges to the traditional theory of natural focus and carries out a theory
breakthrough.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3260/version/1
Disordered proteins and network disorder in network descriptions of protein structure, dynamics and
function. Hypotheses and a comprehensive review
Provedor de dados: 17
Autores: Peter Csermely; Kuljeet Singh Sandhu; Eszter Hazai; Zsolt Hoksza; Huba J. M. Kiss; Federico Miozzo; Daniel V.
Veres; Francesco Piazza; Ruth Nussinov.
During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review
the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global
network disorder on changes in protein structure and dynamics. We introduce a new classification of protein networks into
‘cumulus-type’,
i.e.,
those
similar
to
puffy
(white)
clouds,
and
‘stratus-type’, i.e., those similar to flat, dense (dark) low-lying clouds, and relate these network types
to protein disorder dynamics and to differences in energy transmission processes. In the first class, there is limited overlap
between the modules, which implies higher...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5608/version/1
Dispersal of _Aedes aegypti_: field study in temperate areas and statistical approach
Provedor de dados: 17
Autores: Paula Bergero; Carlos A. Ruggerio; Rubén Lombardo; Nicolás Schweigmann; Hernán
Solari.
We studied the dispersion of _Aedes aegypti_ during egg laying in natural conditions. Two independent experiments involving
mosquitoes dispersing from urbanization towards adjacent un-urbanized areas were carried out and analyzed in statistical terms.
We find relations between stochastic variables related to the egg laying mosquito activity (ELMA), useful to assess dispersion
probabilities, despite the lack of knowledge of the total number of ovipositions in the zone. We propose to evaluate the activity as
minus the logarithm of the fraction of negative ovitraps at different distances from buildings. We also estimate the average
number of eggs laid per oviposition using a regression between the ELMA and the number of eggs found. Three zones with
different...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2012
URL: http://precedings.nature.com/documents/6960/version/1
Disruptive Strategies for Removing Drug Discovery Bottlenecks
Provedor de dados: 17
Autores: Sean Ekins; Chris L. Waller; Mary P. Bradley; Antony J. Williams.
Drug Discovery is shifting focus from the industry to outside partners and in the process creating new bottlenecks, suggesting the
need for a more disruptive overhaul. Technologies like high throughput screening (HTS) have moved to a larger number of
academic and institutional laboratories in the US, with little apparent coordination or consideration of the outputs and creating a
translational gap. While there have been collaborative public private partnerships in Europe to share pharmaceutical data, the USA
has lagged behind. Sharing precompetitive computational models may be the next frontier to provide more confidence in the
quality of the leads produced and attract investment. We suggest there needs to be an awareness of what research is going on in...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology; Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/6961/version/1
Dissecting the Biological Motherboard (Systems Biology and Beyond)
Provedor de dados: 17
Autores: Abhay Krishna; Ajit Narayanan.
Genome-scale molecular networks, including gene pathways, gene regulatory networks and protein interactions, are central to the
investigation of the nascent disciplines of systems biology and bio-complexity. Dissecting these genome-scale molecular networks
in its all-possible manifestations is paramount in our quest for a genotype-input phenotype-output application which will also take
environment-genome interactions into account.

Machine learning approaches are now
increasingly being used for reverse engineering such networks. Our work stresses the importance of a system approach in
biological research and how artificial neural networks are at the forefront of Artificial Intelligence techniques that are
increasingly...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2003/version/1
Dissecting the mechanisms of learning-by-doing in Drosophila
Provedor de dados: 17
Autores: Björn Brembs; Wolfgang Plendl.
At the heart of learning-by-doing lies a well-known psychological phenomenon: information will be remembered better if it is
actively generated rather than passively read or heard. First described in humans, this generation effect can also be observed in
various animal models. However, the neurobiological mechanisms underlying the generation effect are unknown. Here we show
that two reciprocal interactions between its active and passive components contribute to the generation effect in flies. One
interaction consists of the active (skill-learning) component facilitating the passive (fact-learning) component. Fact-learning, on
the other hand, inhibits skill-learning. Experiments with adenylyl cyclase I deficient _rutabaga_ mutant flies revealed that the...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1354/version/1
Dissociation of Alzheimer's morphological pathology from cognitive impairment
Provedor de dados: 17
Autores: Tohru Hasegawa; Nobuyuki Mikoda.
We observed the Alzheimer's morphological pathology, amyloid production induces Alzheimer's
cognitive impairment, was dissociated from the cognitive impairment. The earlier Alzheimer's pathological changes
can be induced in normal C57BL mice, by B6 deficient feeding 4 months with no amyloid, and this cognitive and memory
impairments were completely inhibited by anti-homocysteic acid antibody. According to Koch's postulate, if a
pathogen of Alzheimer's disease is administrated to the normal animal, we would observe the Alzheimer's
cognitive impairment in the normal animal. We actually have observed this cognitive impairment in normal C57BL male mice
with no amyloid. From our observations, it is suggested...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2949/version/1
Distinct cytokine patterns in Occult Hepatitis C and Chronic Hepatitis C Virus Infection
Provedor de dados: 17
Autores: Nasser Mousa; Nashwa Abousamra; Azza Azza Abdel-Aziz; Yahia Gad; Mona Elhadidy; Mohamed Abd-elmaksoud.
Background & Aim: 
The immunopathogenesis of chronic hepatitis C virus (HCV) infection is a
matter of great controversy. The imbalance of T-helper lymphocyte cell cytokine production was believed to play an important
pathogenic role in chronic viral hepatitis. Occult hepatitis C infection is regarded as a new entity that should be considered when
diagnosing patients with a liver disease of unknown origin. The aim of this study was to determine serum T-helper 1 and T-helper
2 cytokine production in patients with occult HCV infection and its role in pathogenesis versus chronic viral hepatitis C
infection.

Methods: 
Serum levels of cytokines of T-helper 1
(IL-2, IFN-[gamma]) and...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2011
URL: http://precedings.nature.com/documents/6654/version/1
Distribution of ABO blood groups and Rh(D) factor among the Brahmin and Kushwaha populations
of Jhansi District(U.P)
Provedor de dados: 17
Autores: Nawab John Dar; Ankit Srivastava; Farooq A. Dar.
The distribution of ABO blood groups and Rh(D) factor has been studied among the Brahmin and Kushwaha populations of
Jhansi Uttar Pradesh. The A,B,O and AB blood group percentage in Brahmins was recorded as 20.88%, 36.64%, 37.02% and
10.44% .The Rh(D) positive percentage was 96.20% and Rh(d) negative 3.79%. In Kushwaha population the percentage of A,B,O
and AB was recorded as 25.65%, 30.26%, 31.25% and 12.82% respectively. The Rh (D) positive was recorded as 97.36% and
Rh(d) negative as 2.63%. The allele frequency of ABO among Brahmins was 0.198, 0.266, 0.536 and in Kushwaha the allele
frequency of ABO was recorded as 0.251, 0.278, and 0.471 respectively. So the prevalence of the ABO from the area under study
can be shown with a general formula as...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6362/version/1
DNA expression microarrays may be the wrong tool to identify biological pathways
Provedor de dados: 17
Autores: Adrian Mondry; Marie Loh; Alessandro Giuliani.
DNA microarray expression signatures are expected to provide new insights into patho- physiological pathways. Numerous
variant statistical methods have been described for each step of the signal analysis. We employed five similar statistical tests on
the same data set at the level of gene selection. Inter-test agreement for the identification of biological pathways in BioCarta,
KEGG and Reactome was calculated using Cohen’s k- score. The identification of specific biological pathways
showed only moderate agreement (0.30 < k < 0.79) between the analysis methods used.
Pathways
identified by microarrays must be treated cautiously as they vary according to the statistical method used.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1036/version/1
DNA Genealogy, Mutation Rates, and Some Historical Evidences Written in Y-Chromosome
Provedor de dados: 17
Autores: Anatole Klyosov.
Origin of peoples in a context of DNA genealogy is an assignment of them to a particular tribe (all members of which belong to a
certain haplogroup) or its branch (a lineage), initiated in a genealogical sense by a common ancestor and an estimation of a time
span between the common ancestor and its current descendants. We have developed an approach to kinetics of haplotype
mutations in non-recombinant segments of the Y-chromosome and illustrated it with a number of haplotype series related to
various populations (timespans to common ancestors shown as years before the present): Basques R1b1b2 (4,050), near thirty of
European countries R1a1 (between 4,100 and 4,825), India R1a1 (3,675), the Arabian Peninsula R1a1 (3,750), South India
Chenchu R1a1 (3,200 and...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2733/version/1
DNA Sequence Evolution through Integral Value Transformations
Provedor de dados: 17
Autores: Sk Sarif Hassan; Pabitra Pal Choudhury; Ranita Guha; Shantanav Chakraborty; Arunava Goswami.
In deciphering the DNA structures, evolutions and functions, Cellular Automata (CA) do have a significant role. DNA can be
thought of as a one-dimensional multi-state CA, more precisely four states of CA namely A, T, C, and G which can be taken as
numerals 0, 1, 2 and 3. Earlier, G.Ch. Sirakoulis et al reported the DNA structure, evolution and function through quaternary logic
one dimensional CA and the authors have found the simulation results of DNA evolutions with the help of only four linear CA
rules. The DNA sequences which are produced through the CA evolutions, however, are seen by our research team not to exist in
the established databases of various genomes although the initial seed (initial global state of CA) was taken from the database.
This...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5729/version/1
DNA SEQUENCE PATTERNS
Provedor de dados: 17
Autores: Sriram Kannan.
There is significance in the molecular weight derived sequence patterns of adenosine, guanosine, cytosine, thymine, methyl
cytosine and hydroxyl methyl cytosine if one has to consider the molecular events holistically by including single nucleotide
polymorphisms, tumor suppressor gene activity like that of ten eleven translocation gene, CpG methylation, miRNA SNP patterns
and SNPs neighboring CpGs. This research article focuses on observing simulation results of validated SNPs in a sequence using
substitution patterns of molecular weight of A, G, C, T, 5OHC, 5MC. The outcome helped to bring out positions in a DNA
sequence where in validated bi allelic SNPs were never found to occur and SNPs neighboring methylated CpGs do show
disconcordance and a...
Tipo: Presentation
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4933/version/1
DNA sequences classification and computation scheme based on the symmetry principle
Provedor de dados: 17
Autores: Xiao-Gang Song; Wen-Yuan Qiu.
The DNA sequences containing multifarious novel symmetrical structure frequently play crucial role in how genomes work. Here
we present a new scheme for understanding the structural features and potential mathematical rules of symmetrical DNA
sequences using a method containing stepwise classification and recursive computation. By defining the symmetry of DNA
sequences, we classify all sequences and conclude a series of recursive equations for computing the quantity of all classes of
sequences existing theoretically; moreover, the symmetries of the typical sequences at different levels are analyzed. The
classification and quantitative relation demonstrate that DNA sequences have recursive and nested properties. The scheme may
help us better discuss the...
Tipo: Manuscript
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3116/version/1
DNALinux Virtual Desktop Edition
Provedor de dados: 17
Autores: Sebastian Bassi; Virginia V. C. Gonzalez.
The new version of DNALinux (VDE) is presented. DNALinux VDE is a departure from traditional distributions since it uses a
virtual machine to bundle together the operating system and bioinformatics applications. The main advantage of this approach is
that a virtualized environment doesn't affect a installed system. With a virtual machine a Linux system can be run
under a Windows system, provided that the virtual machine player is installed. The included programs are listed and specifications
to add more programs are explained. We believe that DNALinux could be used as a standardized virtual machine for learning,
using, developing and testing bioinformatics applications.
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/670/version/1
DNA^+Pro^: an Improved Progressive Multiple Sequence Alignment Algorithm for Evolutionary
Analysis Using Combined DNA-Protein Sequences
Provedor de dados: 17
Autores: Xiaolong Wang; Shuang-yong Xu; Deming Gou.
Alignment of DNA and protein sequences is a basic tool in the study of evolutionary, structural and functional relationship among
macromolecules. Present sequence alignment methods are somewhat error-prone, often producing systematic bias. Errors in
sequence alignments sometimes lead to subsequent misinterpretation of evolutionary, structural and functional information in
genes, proteins and genomes. In traditional sequence alignment algorithms, alignments of DNA and protein sequences are
conducted separately. It has been long believed that the phylogenetic signal disappears more rapidly from DNA sequences than
from encoded proteins. It is therefore generally preferable to align sequences at the amino acid level. Here we present a new...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4898/version/1
Do enzyme activities during decomposition follow predicted patterns? A test of the conceptual model
of litter decay.
Provedor de dados: 17
Autores: Zachary L. Rinkes; Michael N. Weintraub; Jared L. DeForest; Daryl L. Moorhead.
Surprisingly, there remains a paucity of research examining specific interactions between the relationship between microbial
community behavior and plant litter chemistry during decomposition. A more mechanistic understanding of the relationship
between these drivers will ultimately help determine the trajectory of litter decomposition and the conditions in which soils serve
as either a source or sink for atmospheric C. In order to examine these relationships, a laboratory incubation was established using
_Acer saccharum_ litter and a sandy soil (< 1.5% organic matter). Extracellular enzyme activities
([BETA]-glucosidase, N-acetyl glucosaminidase, leucine-amino peptidase, acid phosphatase, phenol oxidase, and peroxidase)
were monitored on a...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6226/version/1
Do not log-transform count data
Provedor de dados: 17
Autores: Robert B. O'Hara; Johan Kotze.
1. Ecological count data (e.g., number of individuals or species) are often log-transformed to satisfy parametric test
assumptions.
2. Apart from the fact that generalized linear models are better suited in dealing with count
data, a log-transformation of counts has the additional quandary in how to deal with zero observations. With just one zero
observation (if this observation represents a sampling unit), the whole dataset needs to be fudged by adding a value (usually 1)
before transformation. 
3. Simulating data from a negative binomial distribution, we compared the outcome
of fitting models that were transformed in various ways (log, square-root) with results from fitting models using Poisson and
negative binomial...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/4136/version/1
Do they or don't they? A synthesis of microbial response to environmental change
Provedor de dados: 17
Autores: Teri C. Balser.
Background/Question/Methods
Microbial communities have long been thought to possess infinite plasticity,
yet evidence in recent years increasingly indicates compositional resistance to change.
While this discovery
may largely be due to the changing nature of soil biological research – with its move beyond single-season and
single-factor experiments, it nevertheless highlights a critical area in current ecosystem studies and soil microbial ecology. Do
they
or
don't
they
change?
When?
Under
what
circumstances?
And
does
it
matter?

Results/Conclusions
In this talk I review microbial
community compositional shifts. First I address general microbial response...
Tipo: Presentation
Palavras-chave: Ecology; Microbiology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5504/version/1
Docking and QSAR Studies of Camptothecin Derivatives as Inhibitor of DNA Topoisomerase-I
Provedor de dados: 17
Autores: Dharmendra K. Yadav; Feroz Khan; Santosh K. Srivastava.
Camptothecin (CPT) is a cytotoxic quinoline alkaloid which inhibits the DNA enzyme Topoisomerase-I (Topo-I) and has shown
remarkable anticancer activity in preliminary clinical trials. The major limitation is its low solubility and high adverse reaction. In
the studied work, we performed molecular docking of CPT derivatives against Topo-I and developed the quantitative structure
activity relationship (QSAR) model for anticancer activity screening. For QSAR, we used CPT and other anticancer drugs with its
IC50 values. We used a total of forty seven anticancer drugs as training set and eight compounds as test set and thirty derivatives
of CPT as query set. Total of fifty two chemical descriptors were used for the quantitative data calculation. Only four...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5773/version/1
Docking studies to explore novel inhibitors against human beta-site APP cleaving enzyme (BACE-1)
involved in Alzheimer’s disease
Provedor de dados: 17
Autores: S Anjum Mobeen; Manne Munikumar; Amineni Umamaheswari.
Alzheimer’s disease (AD) is one of the most prominent neurodegenerative disorders, particularly in elder persons
over 65 age. It is characterized by progressive cognitive deterioration together with declining activities. Amyloid precursor protein
(APP) cleaves at A-beta (Aβ) peptide by rate limiting factor of Beta-site APP cleaving enzyme (BACE-1) in
amyloidogenic pathway. Elevated level of BACE-1 leads to the accumulation of an insoluble form of Aβ peptides
(Senile Plaques), an important hallmark in the pathogenesis of Alzheimer disease. Five published inhibitors of BACE-1,
thiazolidinediones, rosiglitazone, pioglitazone, Sc7 and tartaric acid are available with poor pharmacological properties and
intolerable side effects....
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6964/version/1
Docking studies to explore novel lead molecules for human Spleen tyrosine kinase involved in chronic
lymphocytic leukemia
Prove