Download Consulta: typeFacets:"Poster" Registros recuperados: 677 Data/hora

Consulta: typeFacets:"Poster"
Registros recuperados: 677
Data/hora: 09/06/2017 01:31:19
Characterization of watermelon fruitlet development
Provedor de dados: 35
Autores: Salman-Minkov, A.; Trebitsh, T.
Watermelon (Citrullus lanatus var. lanatus) fruit produce low amounts of ethylene during ripening and is therefore considered as a
non-climacteric fruit. Here we examined the involvement of ethylene in early stages of fruit development. Ethylene production
was high in ovary and young fruitlets but decreased at later stages of development. Increased fruit set was observed in plants
treated with ethylene biosynthesis inhibitor. To identify genes involved in the process we isolated genes encoding for the
rate-limiting enzyme in ethylene biosynthesis pathway, 1- aminocyclopropane-1-carcoxylate synthase (ACC synthase, ACS). The
expression pattern during early fruit development of watermelon ACS genes (CitACS) was analyzed. High CitACS1 transcript
level was...
Tipo: Poster
Palavras-chave: 1-Aminocyclopropane-1-cacoxylate synthase (ACS); Aminoethoxyvinyl-glycine (AVG); Citrullus lanatus;
Non-climacteric fruit; Watermelon; Fruit development; Ethylene.
Ano: 2008
URL: http://hdl.handle.net/2174/283
Development and characterization of Cucumis sativus-hystrix introgression lines exhibiting resistance
to downy mildew
Provedor de dados: 35
Autores: Zhou, X.-H.; Wan, H.-J.; Qian, C.-T.; Chen, J.-F.
Stable C. sativus-hystrix introgression lines with fourteen chromosomes, derived from the interspecific hybridization between a
wild relative of cultivated cucumber C. hystrix (2n=2x=24, HH) and a Chinese cucumber 'Beijingjietou' (C. sativus L., 2n=2x=14,
CC) were characterized using morphological, cytological, and SSR analysis. In morphology, those introgression lines were
characterized to have small-sized leaf, short fruit, and multi-branching habit which were closer to the wild parent (C. hystrix), and
to have a fertility as high as that of cultivated cucumber. Cytological observation showed that sister chromatids in at least one pair
of somatic chromosomes were delayed obviously in separation at late metaphase. At diakinesis, 0.2 tetravalents, 0.05...
Tipo: Poster
Palavras-chave: Cucumber; Cucurbits; Interspecific hybridization; SSR; Pseudoperonospora cubensis.
Ano: 2008
URL: http://hdl.handle.net/2174/230
Genetic diversity of Spanish melons (Cucumis melo) of the Madrid provenance
Provedor de dados: 35
Autores: Escribano, S.; Lázaro, A.; Staub, J.E.
The genetic diversity of five winter melon landraces having a historic presence in the town of Villaconejos, Spain (near Madrid)
and four reference accessions including one accession from snakemelon, was assessed using the allelic variation at 19 SSR loci.
Seventy-two polymorphic bands were scored which provided for adequate discrimination among the accessions examined. Cluster
analysis (UPGMA) employing SSR-based genetic similarity (GS, Jaccard similarity coefficient) data resulted in a dendrogram
with two major clades. Although winter melon accessions were represented in both clades, genetic differences among two Madrid
accessions and the other seven landraces were remarkable. In fact, this genetic difference (GS = 0.24; lack of genetic affinity)
was...
Tipo: Poster
Palavras-chave: Mediterranean country; Cucumis melo; SSRs; Genetic resource; Genetic distance; Multivariate analysis; Genetic
diversity.
Ano: 2008
URL: http://hdl.handle.net/2174/225
Comparative mapping of Cucurbita moschata and C. pepo using SSR markers
Provedor de dados: 35
Autores: Gong, L.; Lelley, T.
The first SSR-based genetic linkage map of C. moschata was created by integrating the maps of two F2 populations with one
common parent developed from the crosses Waltham Butternut (WB) × Nigerian Local (NL) and ZHOU (a hull-less type) × WB.
This integrated C. moschata map comprises 205 SSR markers and 2 morphological traits (Gr and n). The map is composed of 27
linkage groups with a marker density of 7 cM. Comparison of the C. moschata map and the published C. pepo map revealed a
high level of macro-synteny. Seventy-one common SSR markers between C. moschata and C. pepo are located in homologous
linkage groups. These markers representing orthologous loci in general have conserved orders and similar genetic distances. Four
SSR markers were mapped in...
Tipo: Poster
Palavras-chave: Microsatellite; Molecular mapping; Cucurbita; Hull-less seed; Green rind; Linkage map.
Ano: 2008
URL: http://hdl.handle.net/2174/276
Effective long-term storage methods for soft X-ray irradiated pollen, and the use of storage pollen
Provedor de dados: 35
Autores: Akutsu, M.; Kami, D.; Sugiyama, K.
An effective long-term storage method for active soft X-ray irradiated pollen for the production of seedless watermelon (Citrullus
lanatus) in diploid plants by using gas treatments is described. Soft X-ray irradiated pollen stored under N2 or CO2 gas, or under a
vacuum for 1 year had high pollen germination abilities. Also, pollen stored at -25ºC under N2 gas for 1 year and mixed with an
equal amount of ‘Marriage powder’ had similar results in the fruit produced. This result indicated that ‘Marriage powder’ was
useful as a pollen extender medium for watermelon. Soft X-ray irradiated pollen was stored at -25ºC for about 1 week, after which
the pollen was set in an incubator at 20, 25, 30, 35, or 40ºC under 50, 60, or 80 % relative humidity for 1 to 6...
Tipo: Poster
Palavras-chave: Mediterranean country.
Ano: 2008
URL: http://hdl.handle.net/2174/229
Cucumber hybrids type cornichon, obtained at the Vegetable Research and Development Station
Bacau-Romania
Provedor de dados: 35
Autores: Fălticeanu, M.; Ambarus, S.; Stoian, L.; Cristea, T.O.; Calin, M.
In the breeding programs from VRDS Bacau, Romania, two gynoecious cucumber hybrids (Cucumis sativus L.), cornichon type,
were obtained. The breeding methods utilized is the hybridization of two gynoecious stable and uniform lines with two
monoecious parental lines. The researches fulfilled with the purpose of determining the behavior of two gynoecious hybrids
obtained at VRDS Bacau in open field and plastic tunnels culture, revealed the potential production and fruits quality at the
hybrids ‘Cornişa F1’ and ‘Cornibac F1’.
Tipo: Poster
Palavras-chave: Cucumis sativus; Plant; Breeding; Gynoecy; Cucumber.
Ano: 2008
URL: http://hdl.handle.net/2174/241
How does the first fruit inhibit younger fruit set in cucurbits?
Provedor de dados: 35
Autores: Baniel, A.; Saraf-Levy, T.; Perl-Treves, R.
In this study we describe the inhibitory effect exerted by developing cucumber fruits on later-developing ovaries. Such pollinated
ovaries do not set fruit but do not degenerate readily, remaining in a "stand-by" state that can be reversed when older fruits are
removed. An increase in fruit set and decrease in inhibition was obtained by exogenous gibberellin and cytokinin treatment, and to
a lesser extent by auxin. A decrease in transcript levels of genes expressed during fruit set was apparent in inhibited ovaries.
Tipo: Poster
Palavras-chave: Cucumis sativus; Cucumber; Fruit set; Ovary; Gene expression.
Ano: 2008
URL: http://hdl.handle.net/2174/270
Construction of watermelon SSH cDNA libraries induced by Fusarium oxysporum and analysis of
expressed sequence tags
Provedor de dados: 35
Autores: Yong Xu; Shaogui Guo; Haiying Zhang; Guoyi Gong; Aijun Mao; Lihua Geng.
Suppression subtractive hybridization (SSH) cDNA libraries were constructed with watermelon root induced by F. oxysporum
race 1. The process of library construction was checked and analyzed; results showed that the technique was efficient in the
subtractive hybridization. 562 ESTs with good quality were assembled to 550 contigs with DNAStar 5.0 software. After function
annotation, the most prevalent category was disease and defense, which accounted for 33.5 % of the ESTs; the second category
was signal transduction which accounted for 13.1 %. Systemic acquired resistance (SAR) was supposed to be the important
element composing the resistance to F. oxysporum race 1 in PI 296341-FR after sequence analysis.
Tipo: Poster
Palavras-chave: Citrullus lanatus; Artificial inoculation; Suppression subtractive hybridization; Fusarium oxysporum;
Watermelon; DNA.
Ano: 2008
URL: http://hdl.handle.net/2174/273
Inheritance of type I glandular trichomes in Cucumis melo
Provedor de dados: 35
Autores: Palomares-Rius, F.J.; Sarria, E.; Alba, J.M.; Gómez-Guillamón, M.L.
A high density of glandular trichomes of Type I could contribute to enhance resistance to Aphis gossypii in melon breeding
programs with the Vat gene. To study the inheritance of this trait, a six-generation genetic family was obtained from the cross
between the accession TGR-1551, with high density of glandular trichomes and the Spanish cultivar ‘Bola de oro’ with low
trichome density. The genetic model estimated showed that the Type I trichome density followed an oligogenic inheritance with
important additive effect and strong epistatic effect between heterozygous loci. The values for broad sense heritability (H2) and
narrow sense heritability (h2) were 0.86 and 0.50, respectively, which made this character suitable for breeding.
Tipo: Poster
Palavras-chave: Aphis gossypii; Antixenosis; Heritability; Genetic model; Additive; Dominance; Epistasis.
Ano: 2008
URL: http://hdl.handle.net/2174/250
Cloning and expression analysis of rboh gene encoding respiratory burst oxidase in Citrullus
colocynthis
Provedor de dados: 35
Autores: Si, Y.; Kang, K.K.; Dane, F.
Drought stress is a major environmental factor influencing plant growth and development. Citrullus colocynthis is a very drought
tolerant cucurbit species with a deep root system. Differences in gene expression during drought were studied using cDNA-AFLP.
In this study, we focus on mRNA accumulation of drought-induced genes in C. colocynthis treated with PEG, abscisic acid
(ABA), salicylic acid (SA), jasmonic acid (JA) or NaCl. Two genes, CcrbohD and CcrbohF, encoding respiratory burst oxidase
proteins were cloned using RACE. Sequence comparison showed that the CcrbohD protein has a conserved region at the N
terminus with an EF-hand loop domain, characteristic of the RBO protein family. Phylogenetic analysis confirmed that CcrbohD
and CcrbohF belong to the...
Tipo: Poster
Palavras-chave: Drought stress; PEG; Plant hormone; Real-time RT-PCR; Bitter apple; Citrullus colocynthis.
Ano: 2008
URL: http://hdl.handle.net/2174/269
Transgenic resistance to RNA viruses in cucurbits is dependant on transgene construct and varies
between viruses
Provedor de dados: 35
Autores: Leibman, D.; Wolf, D.; Segev, O.; Raskin, A.; Gaur, R.; Saharan, V.; Zelcer, A.; Gal-On, A.
Cucurbit production worldwide is affected by modern agricultural technologies that require massive investments of capital and
knowledge. Viral diseases of cucurbit crops result in heavy yield losses, and may even jeopardize the production of these crops.
The classical crop breeding for disease resistance in cucurbits is severely hampered by the lack of natural sources of durable
resistance to some of the most destructive viruses. The generation of viral resistance by means of genetic engineering was reported
and widely implemented for several crops, including cucurbits. Our laboratories have been involved in the evaluation of several
genetic constructs for the generation of transgenic resistance to different groups of RNA viruses known to severely affect...
Tipo: Poster
Palavras-chave: Cucumber; Cucumis sativus; Cucumber fruit mottle mosais virus; Cucumber vein yellowing virus; Cucurbit
yellow stunting disorder virus; Zucchini yellow mosaic virus; Papaya ringspot virus; Transgenic plant.
Ano: 2008
URL: http://hdl.handle.net/2174/248
Gynoecy in bitter melon (Momordica charantia) for exploiting hybrid vigour
Provedor de dados: 35
Autores: Dey, S.S.; Behera, T.K.; Munshi, A.D.; Pal, A.; Rakshit, S.
Development of hybrids in bitter melon is expensive because of hand pollination but the utilisation of gynoecy is economical and
easier for exploiting hybrid vigour in bitter melon. A study was conducted to determine magnitude of heterosis in bitter melon by
making crosses on one gynoecious line, DBGY-201 with eight other inbreds. It was observed that all the hybrids showed
significant heterosis in desirable directions for traits like sex ratio, days to first picking, fruit weight, length and girth, yield per
plant and vine length. The gynoecious hybrid DBGY-201 × ‘Pusa Vishesh’ showed highest heterosis (-19 %) for earliness and the
hybrid DBGY- 201 × ‘Priya’ was reported to provide maximum heterosis for fruit length, weight and yield. These gynoecious...
Tipo: Poster
Palavras-chave: Cucurbit; Bitter melon; Heterosis; Breeding; Sex ratio; Yield; Gynoecy.
Ano: 2008
URL: http://hdl.handle.net/2174/261
Marker assisted selection of genes and QTLs for resistance combinations to Aphis gossypii in melon
Provedor de dados: 35
Autores: Thomas, S.; Mistral, P.; Chareyron, V.; Boissot, N.
The Vat gene in melon confers resistance to both aphid colonization and aphid transmission of several viruses. QTLs that provide
resistance to aphid were localized on the melon genome. We built genetic allelic combinations with/without the resistant allele at
the Vat locus and QTLs. These combinations (homozygous for the resistance loci) had a homogeneous genetic background for 90
% of the genome. Plants with different allelic combinations were infested by two Aphis gossypii genotypes NM1 and C9, and
observed for acceptance and biotic potential. The Vat gene reduced the acceptance by both aphid genotypes, but only reduced the
biotic potential of NM1. QTLs had a complementary effect on acceptance. To predict the durability of the resistance we plan to...
Tipo: Poster
Palavras-chave: Cucumis melo; Quantitative trait loci (QTL); Aphid; Aphis gossypii; Resistance durability; Vat gene.
Ano: 2008
URL: http://hdl.handle.net/2174/251
Potential of, and problems with, glabrous cucumber breeding
Provedor de dados: 35
Autores: Sakata, Y.; Yoshioka, Y.; Sugiyama, M.
In Japan, cucumber cultivars lacking warts and with very few spines are highly desired by the food service industry, as it is
believed that there are fewer germs on the surfaces of such cucumbers. To obtain a spineless cucumber cultivar, we have begun a
breeding program for glabrous cucumber. We present here information on the morphological characteristics of glabrous cucumber
accessions NCG71 and NCG90, and the yield performance of a glabrous trial accession that we bred, KA 2. We also discuss the
potential of, and possible problems with, glabrous cucumber.
Tipo: Poster
Palavras-chave: Breeding; Cucumis sativus; Hair; Spine; Morphological characteristic.
Ano: 2008
URL: http://hdl.handle.net/2174/264
Methods of isolation of Cucumis sativus and C. melo pollen grains and their utilization in in vitro
pollination
Provedor de dados: 35
Autores: Skálová, D.; Navrátilová, B.; Lebeda, A.
Optimizing manipulation with pollen grains is necessary for successful in vitro pollination. This pollination can be used for
overcoming crossing barriers in interspecific hybridization in the genus Cucumis. Pollen grains from Cucumis sativus and C. melo
were isolated by various methods. Different techniques of centrifugation were compared with direct isolation of pollen grains
from anthers. The viability of pollen grains was evaluated and their ability to form pollen tubes was tested. Three isolation media
(NLN, YST and VB) and two cultivation media (YS and CP) were used. Then pollen grains were cultivated with ovules of C.
sativus and the level of regeneration was observed. The growing and green ovules were considered as the lowest level and the
highest...
Tipo: Poster
Palavras-chave: Cucumis; Centrifugation; Interspecific hybridization; Pollinisation; Regeneration.
Ano: 2008
URL: http://hdl.handle.net/2174/232
Fusarium wilt infection in melon: a transcriptomic approach to characterize the genetic dialogue
between host and pathogen
Provedor de dados: 35
Autores: Szafranska, K.; Fusari, F.; Luongo, L.; Ferrarini, A.; Polverari, A.; Delledonne, M.; Ficcadenti, N.; Sestili, S.; Belisario,
A.
Fusarium oxysporum f. sp. melonis (Fom) causes Fusarium wilt of melon which is an economically important disease worldwide.
The most effective control measure to prevent Fusarium wilt is through host resistance. Four races of Fom are presently known (0,
1, 2, and 1.2), one of which, race 1.2, is able to overcome the resistance of commonly cultivated varieties. No genes have been
identified in melon that confer high levels of resistance to race 1.2. A transcriptomic approach has been undertaken by
cDNA-AFLP on melon plants of the cultivar ‘Charentais Fom-2’ infected with race 1 (avirulent) and race 1.2 (virulent), at five
time points, and the experiment was concluded 21 days after inoculation. The RNA from fungal colonies of the two races was also
included...
Tipo: Poster
Palavras-chave: Fusarium oxysporum f.sp. melonis; Cucumis melo; Resistance; Soilborne pathogen; Virulence.
Ano: 2008
URL: http://hdl.handle.net/2174/272
Molecular characterization of different Italian inodorus melon populations based on ISSR molecular
markers and preliminary SSR analysis
Provedor de dados: 35
Autores: Sestili, S.; Daniele, A.; Rosa, A.; Ferrari, V.; Belisario, A.; Ficcadenti, N.
Cucurbitaceae, or cucurbit family, are important crops widely distributed in the warmest areas of the world supplying humans
with edible products and useful fibres. Melon (Cucumis melo L.) is considered the most diversified species in the genus Cucumis.
The inodorus melon varieties, commonly known as “winter melons” for their capability to be preserved during the winter time, are
traditionally cultivated in the Mediterranean area and they have a relevant importance in the economy of the Italian southern
regions. The genetic diversity and relationships among 13 Italian inodorus accessions of different geographic origin were revealed
by using 90 ISSR primers and 18 SSR primer pairs. The DH line Nad-1 and the Charentais-T genotype, both belonging to the...
Tipo: Poster
Palavras-chave: Mediterranean country; Genetic resource; Cucumis melo; Fingerprinting; Genetic distance; Principal component
analysis; Inodorus melon.
Ano: 2008
URL: http://hdl.handle.net/2174/222
Cucurbitaceae genetic resources in the Czech gene bank. Current status of the collection
Provedor de dados: 35
Autores: Karlová, K.
The Crop Research Institute, Dept. of Vegetables and Special Crops in Olomouc is responsible for the conservation and
documentation of genetic resources of vegetable, medicinal, aromatic, and spice plants. Collections maintained by the department
in Olomouc include more than 10,000 accessions of about 430 botanical species and the collection of cucurbitaceous genetic
resources with 1,713 accessions potentially available is one of the largest. Unfortunately only about 40 % of them is already
regenerated. The collection is distributed in 11 species and the biggest part of collection shapes Cucumis sativus L. and Cucurbita
sp.
Tipo: Poster
Palavras-chave: Cucurbitacea; Regeneration; Storage; Characterization; Safe duplicate; Genetic resources.
Ano: 2008
URL: http://hdl.handle.net/2174/224
New Citrullus haplotypes at the tRNA-Val – rps12 locus of cpDNA
Provedor de dados: 35
Autores: Tóth, Z.; Gyulai, G.; Szabó, Z.; Gyulai, F.; Heszky, L.
Six new Citrullus haplotypes were identified at tRNA-Val – rps12 locus of chloroplast (cpDNA) genome in colocynth (Citrullus
colocynthis), citron melon (Citrullus lanatus citroides) and watermelon (Citrullus lanatus lanatus) cultivars. Ancient-DNAs
(aDNA) of seed remains excavated from two sites of the Middle Ages (13th-14th Cent. Debrecen and 15th Cent. Budapest,
Hungary) and a herbarium samples from the 19th Cent. (Pannonhalma, Hungary) were also investigated to track cpDNA evolution
back to the 13th-14th centuries with the final aim of molecular and morphological reconstruction of old varieties. Medieval
samples showed molecular similarity to current cultivars ‘Belyj dlinnij’, ‘Csárdaszállás’ ‘Klondike’, and ‘Kecskeméti vörös’
indicating the oldest...
Tipo: Poster
Palavras-chave: Watermelon; Citrullus; Citron melon; Colocynth; Chloroplast DNA (cpDNA); Haplotype.
Ano: 2008
URL: http://hdl.handle.net/2174/226
Characterization of the resistance to Fusarium oxysporum f. sp. melonis race 1.2 in Cucumis melo
‘BG-5384’
Provedor de dados: 35
Autores: Chikh-Rouhou, H.; González Torres, R.; Alvarez, J.M.
‘BG-5384’ is a melon cantalupensis accession which has been found to be resistant to Fusarium oxysporum f.sp. melonis. In this
work it is shown that ‘BG- 5384’ has a high level of resistance to F. oxysporum f.sp. melonis races 0, 1, and 2. The resistance to
race 1.2 appears to be polygenic controlled and partially dominant when the inoculation was done with the pathotype W of the
race 1.2, and recessive when the pathotype was Y, showing that this resistance shows some race specific effects.
Tipo: Poster
Palavras-chave: Mediterranean country; Melon; Fusarium wilt; Partial resistance; Physiological race; Cucumis melo.
Ano: 2008
URL: http://hdl.handle.net/2174/238
Sex expression-associated RAPD markers in pointed gourd (Trichosanthes dioica)
Provedor de dados: 35
Autores: Kumar, S.; Singh, B.D.; Sinha, D.P.; Rai, M.
DNA samples were extracted separately from 10 male and 10 female sexual progeny of pointed gourd (Trichosanthes dioica), and
3 plants from a parthenocarpic clone (IIVRPG-105); the DNAs were bulked by sex type. Forty-one random decamer primers were
screened with the three bulks in order to identify markers associated with sex expression. A total of 509 amplification products
were obtained of which six were associated with sex expression. These six markers were then tested with individual plant DNA
samples, and three sex-associated RAPD markers were identified. A 1000 bp amplification product from the primer OPC05 was
found to be present in all the male and absent from all the female and parthenocarpic plants. In contrast, a 400 bp amplification
product from...
Tipo: Poster
Palavras-chave: Trichosanthes dioica; RAPD; Sex expression; Sex-associated; Parthenocarpy.
Ano: 2008
URL: http://hdl.handle.net/2174/262
Genetic erosion in melon (Cucumis melo): a case study from Tunisia
Provedor de dados: 35
Autores: Elbekkay, M.; Hamza, H.; Haddad, M.; Ferchichi, A.; Kik, C.
This study reports on the analysis of 21 local melon cultivars (Cucumis melo L.) collected in the South of Tunisia which were
compared to three modern melon cultivars widely-grown in this area. The analysis was based on the morphological
characterization of fruits. Modern cultivars were significantly different from local germplasm as they were more firm and had
higher sugar content. Furthermore it was found that local germplasm was more variable, as a group, compared to the modern
cultivars which replace them steadily. This study clearly shows the need to safeguard and manage this precious local germplasm
both ex situ and in situ, as this material may contain valuable genes for future breeding activities and also future cultivation
practices. It can also...
Tipo: Poster
Palavras-chave: Mediterranean country; Fruit; Genetic resource; Biodiversity; Conservation; Cucumis melo.
Ano: 2008
URL: http://hdl.handle.net/2174/220
Cucurbit research in India: a retrospect
Provedor de dados: 35
Autores: Rai, M.; Pandey, S.; Kumar, S.
Cucurbits belong to family Cucurbitaceae, includes about 118 genera and 825 species. In India, a number of major and minor
cucurbits are cultivated, which share about 5.6 % of the total vegetable production. They are consumed in various forms i.e., salad
(cucumber, gherkins, long melon), sweet (ash gourd, pointed gourd), pickles (gherkins), and deserts (melons). In India, several
research institutes and universities have utilized a number of cultivated and wild species to develop improved varieties and
parental lines. About 112 open pollinated varieties of several cucurbits have been recommended for cultivation at national and
state levels. Among these, 48 improved varieties in 8 major cucurbits have been identified and recommended through All India...
Tipo: Poster
Palavras-chave: Cucurbitaceae; Cucurbitaceous vegetables; Germplasm; Hybrid; Production; Genetic resources; Biotic
resistance.
Ano: 2008
URL: http://hdl.handle.net/2174/223
Morphological and molecular diversity of 47 melon (Cucumis melo) cultivars compared to an extinct
landrace excavated from the 15th century
Provedor de dados: 35
Autores: Szabó, Z.; Gyulai, G.; Tóth, Z.; Heszky, L.
Morphological diversity of 47 melon (Cucumis melo L.) cultivars and landraces from Hungarian germplasm collection were
analyzed. Cluster analysis based on 26 morphological (quantitative and qualitative) traits revealed an extreme diversity among
accessions, however cultivars were clustered into three types of cantalupensis, reticulatus and inodorus. Molecular (SSR, ITS) and
morphological dendrograms were compared and the genotype of medieval sample was reconstructed
Tipo: Poster
Palavras-chave: Hungary; Cucumis melo; ADNA; Microevolution; SNP; Germplasm; Dendrogam; Genetic resource.
Ano: 2008
URL: http://hdl.handle.net/2174/219
Detection of two QTLs for fruit weight in cucumber (Cucumis sativus)
Provedor de dados: 35
Autores: Heang, D.; Sato, H.; Sassa, H.; Koba, T.
Cucumber has variations in traits of such as fruits with different weights, shapes, spine colors, etc. These traits are controlled by
either multiple or single genes. An F2 population with molecular markers such as AFLP and SSR markers was used to develop a
genetic linkage map of cucumber. The two parents have a large difference in traits which led us able to detect two QTLs, fw1 and
fw2, for fruit weight. Furthermore, a gene for spine morphology was also mapped on the linkage group 7. These results could be
useful for comparative genetic studies as well as marker assisted selection.
Tipo: Poster
Palavras-chave: AFLP marker; SSR marker; Genetic linkage map; Fruit weight.
Ano: 2008
URL: http://hdl.handle.net/2174/255
A new gene controlling resistance to Fusarium oxysporum f. sp. melonis races 0 and 2 in melon
Provedor de dados: 35
Autores: Oumouloud, A.; González Torres, R.; Arnedo Andrés, M.S.; Alvarez, J.M.
‘Tortuga’ is a cantalupensis accession of Spanish origin which has proven to be resistant to Fusarium oxysporum f.sp. melonis
races 0 and 2. In this work we report the results of an allellism test to assess the inheritance of this resistance. Resistance in
‘Tortuga’ seems to be controlled by two genes, one of them is the already described Fom-1, and the other is either a dominant one
linked to Fom-1, or an independent recessive factor. Further work will be needed to clarify the nature of this resistance.
Tipo: Poster
Palavras-chave: Mediterranean country; Cucumis melo; Fusarium wilt; Physiological races; Allelism test; Disease resistance;
Cantaloup.
Ano: 2008
URL: http://hdl.handle.net/2174/242
Cloning and characterisation of a CTR1-like gene in Cucurbita pepo
Provedor de dados: 35
Autores: Manzano, S.; Gómez, P.; Garrido, D.; Jamilena, M.
A homologue of CTR1, one of the key genes in the regulation of ethylene response pathway of Arabidopsis, has been cloned and
characterised in Cucurbita pepo. The Cup-CTR1 gene is predicted to encode for a protein containing the structural features of Map
kinase kinase kinases (MAPKKKs) and shares 58-85 % identity with CTR1-like proteins in Arabidopsis and other plant species.
Phylogenetic analysis indicates that Cup-CTR1 is more related to Arabidopsis CTR1 and related proteins in tomato, rose and
Delphinium, than to other plant MAPKKKs. The gene is expressed at various levels in all the tissues examined. During flower
development, Cup-CTR1 is up-regulated in male flowers but not in female flowers. Given that the expression of the gene is only
induced by...
Tipo: Poster
Palavras-chave: Zucchini; Ethylene; Flower development; Cucurbita pepo.
Ano: 2008
URL: http://hdl.handle.net/2174/267
Impending towards Egyptian consumer preference as melon fruit flesh visual and taste quality
definitions
Provedor de dados: 35
Autores: Glala, A.A.; Mostafa, B.E.; Omran, S.
This investigation was carried out on the fruits of 24 melon genotypes, six inbred lines, fifteen F1 hybrids from a half diallel cross
between these six lines, and three commercial hybrids (‘Ideal’, ‘KAM008’ and ‘KAM009’). The aim was to define the Egyptian
consumer preference for melon flesh visual and eating quality, through correlation analysis between some chemicals and panel
test results. There was a highly significant negative correlation between total acidity (TA) and non reducing sugar (NRS) content
with favorable taste and general acceptance by Egyptian consumers. A highly significant negative correlation was also observed
between flesh whiteness “L” and greenness “a” values with favorable color and general acceptance. A highly significant...
Tipo: Poster
Palavras-chave: Breeding; Fruit flesh; Taste; Color; Odor; General acceptance; Correlation; Fruit quality; Egyptian consumer.
Ano: 2008
URL: http://hdl.handle.net/2174/274
The utilization of honey bees for the production of seeds of cucumber, cornichon type
Provedor de dados: 35
Autores: Calin, M.; Ambarus, S.; Cristea, T.O.; Falticeanu, M.; Stoian, L.; Popa, C.M.; Dumbrava, M.M.
The paper presents the results of researches performed upon the use of honeybees in the seed production of three hybrids in
Cornichon type of Cucumis sativus (‘Cornisa’, ‘Cornibac’, and ‘Cornirom’). Honey-bees are very efficient in pollination of
cucumber flowers, resulting in an increase of seed quantities per fruit ranging from 150 % (‘Cornirom’) to 214 % (‘Cornisa’), as
compared to hand pollination.
Tipo: Poster
Palavras-chave: Cucumis sativus; Pollinisation; Seed production; Honey-bee.
Ano: 2008
URL: http://hdl.handle.net/2174/240
In vitro induction of haploid plants in unpollinated ovules, anther and microspore culture of Cucumis
sativus
Provedor de dados: 35
Autores: Suprunova, T.; Shmykova, N.
In order to increase the yield of haploid cucumber plants obtained from in vitro culture of unpollinated ovules, anther and
microspore, we have studied several factors: the nature and concentration of plant growth regulators, the genotypes, the flower
bud lengths, and the stages of microspore development. Among the different growth regulators tested, thidiazuron (TDZ) was the
best for gynogenesis induction with an optimal concentration of 0.2 mg.L-1. Out of the ten evaluated genotypes, only cultivar
‘Gordion’ was able to develop the haploid plant through in vitro gynogenesis. Based on the histological studies we found that the
best stages of the anther development for haploid induction are the late uninucleate microspore and the early bicellular pollen...
Tipo: Poster
Palavras-chave: Cucumis sativus; Gynogenesis; Androgenesis; Haploid plant; Microspore.
Ano: 2008
URL: http://hdl.handle.net/2174/233
Pleiotropic effect of sex expression on fruit shape in melon
Provedor de dados: 35
Autores: Abdelmohsin, M.E.; Pitrat, M.
In melon, monoecy is conferred by the dominant allele A. Many melon cultivars of different horticultural groups are
andromonoecious, a/a. For facilitating commercial production of F1 hybrid seeds, a monoecious female parent would be quite
useful. However, monoecy is almost always associated with a larger length-todiameter ratio of the fruit. We have tested the
hypothesis that monoecy itself, allele A, is responsible for the change in fruit shape by using two sets of
monoecious/andromonoecious near-isogenic lines: one derived by backcrossing A from a monoecious donor using the
andromonoecious ‘Charentais T’ as the recurrent parent and one using the residual heterozygosity (H-NIL) after 6 generations of
selfpollinating in a recombinant inbred line...
Tipo: Poster
Palavras-chave: Cucumis melo; Pleiotropy; Monoecy; Near-isogenic; Recombinant inbred line; Sex expression.
Ano: 2008
URL: http://hdl.handle.net/2174/263
Overview of potyvirus resistance in watermelon
Provedor de dados: 35
Autores: Guner, N.; Wehner, T.C.
Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is a major cucurbit crop that accounted for 7.5 % of the world
area devoted to vegetable production in 2003. Potyviruses are a major limiting factor in commercial watermelon production
worldwide. The major viruses affecting watermelon are Papaya ringspot viruswatermelon strain (PRSV-W), Watermelon mosaic
virus (WMV), and Zucchini yellow mosaic virus (ZYMV). Sources of resistance to PRSV-W have been reported. These were PI
(plant introduction) accessions from South Africa (PI 244017, PI 244018, PI 244019), from Zimbabwe (PI 482342, PI 482318, PI
482379), from Botswana (PI 485583), and from Nigeria (PI 595203). A single recessive gene controls resistance to PRSV-W,
with the gene symbol prv....
Tipo: Poster
Palavras-chave: ZYMV (Zucchini yellow mosaic virus); WMV (Watermelon mosaic virus); PRSV-W (Papaya ringspot virus
watermelon strain); Citrullus lanatus; Potyvirus; Cucurbit; Virus resistance.
Ano: 2008
URL: http://hdl.handle.net/2174/245
Relationship between genetic diversity and reproduction strategy in a sexually-propagated crop in a
traditional farming system, Citrullus lanatus var. citroides
Provedor de dados: 35
Autores: Minsart, L.-A.; Bertin, P.
Citrullus lanatus var. citroides (African melon) is a crop cultivated in sub- Saharan Africa for its dried seeds reported to be rich in
nutrients. In this project the relationship between its mode of reproduction and its genetic diversity will be established. This
relationship is particularly interesting as C. lanatus var. citroides has been evolving in a traditional farming system, under a
low-anthropic selection. On the one hand, the accurate reproduction strategies of this species will be determined by studying the
floral morphology, occurrence of autoincompatibility, rate of allogamy. On the other hand, the genetic structure inside different
accessions, and the associated population genetic flow will be established. This genetic structure of the...
Tipo: Poster
Palavras-chave: African melon; Watermelon; Citrullus lanatus var.citroïdes; Cucurbit; Molecular marker; SSR; Rate of
allogamy.
Ano: 2008
URL: http://hdl.handle.net/2174/227
Near-isogenic lines of melon with different climacteric behavior as a tool to characterize fruit
senescence traits
Provedor de dados: 35
Autores: Obando-Ulloa, J.M.; Jowkar, M.M.; Moreno, E.; Souri, M.K.; Dos Santos, N.; Sanmartin, P.; Bueso, M.C.; Kessler, M.;
Martinez, J.A.; Alarcon, A.; Nicolai, B.; Lammertyn, J.; Garcia-Mas, J.; Monforte, A.J.; Fernandez-Trujillo, J.P.
Aroma volatiles and fruit quality traits at harvest or after senescence were determined in a collection of near-isogenic lines (NILs)
with different climacteric behavior (two non-climacteric NILs more the parental non-climacteric ´Piel de sapo´ and the rest
climacteric). Data were analyzed by partial least squares discriminant analysis. In senescent fruit, four ester volatiles (particularly
benzyl acetate) helped to discriminate between climacteric and non-climacteric NILs. Aroma volatiles were more efficient for
discriminating by senescent or climacteric behavior than fruit quality traits, and flavor traits (dry matter, soluble solids content,
titratable acidity, and individual sugars and organic acid content) were more efficient than using other major...
Tipo: Poster
Palavras-chave: Aroma volatiles; Fruit over-ripening; Fruit quality; Multivariate discriminant analysis; Postharvest; Cucumis
melo; Quality traits; Firmness; Senescence.
Ano: 2008
URL: http://hdl.handle.net/2174/202
Assessment of stability of expression of various male-sterile genes in muskmelon in sub-tropical field
conditions
Provedor de dados: 35
Autores: Dhillon, N.P.S.; Kumar, J.
Five melon (Cucumis melo L.) progenies segregating for five male-sterile genes (ms-1, ms-2, ms-3, ms-4, and ms-5) along with
two male-fertile cultivars were evaluated for phenotypic variation in expression of fertility in sub-tropical field conditions, for two
years. Male-fertile plants of three progenies of ms-1, ms-2, and ms-3 were phenotypically unstable and produced more
male-sterile flowers than plants of normal male-fertile cultivars. Progenies of ms-4 and ms-5 were stable for the expression of
male-fertile plants.
Tipo: Poster
Palavras-chave: Cucumis melo; Phenotype; Stability; Hybrid; Male-sterility.
Ano: 2008
URL: http://hdl.handle.net/2174/260
Detection of cucumber parthenogenic haploid embryos by floating of immature seeds in liquid
medium
Provedor de dados: 35
Autores: Lotfi, M.; Salehi, S.
Only a small percentage of seeds arisen by irradiated pollen include haploid embryo. Inspecting the seeds one by one for rescuing
the embryos is a tedious and time consuming work which decreases haploid production efficiency in this method for cucurbit
plants. Cucumber seeds formed three weeks after pollination with irradiated pollen were floated in liquid medium for about 10
days before excision of the embryos. This innovative method allowed a better development of haploid embryos; they turned to
green and germinate like normal seeds and could be identified easily without the need of inspecting the seeds one by one. This
method permitted an easier detection and extraction of embryos in comparison with common approach, increased the number and
the quality...
Tipo: Poster
Palavras-chave: Cucurbit; Cucumber; Irradiated pollen; Liquid culture; Parthenogenesis; Doubled haploid.
Ano: 2008
URL: http://hdl.handle.net/2174/234
Electrophoretic spectra of seed storage protein in Cucumis melo and Citrullus vulgaris as a tool for
cultivar differentiation
Provedor de dados: 35
Autores: Vladova, R.; Zamfirova, M.; Andreev, T.; Krasteva, L.
Reduced seed storage proteins from 60 cultivars of melon (Cucumis melo) and 52 cultivars of watermelon (Citrullus lanatus) have
been investigated electrophoretically using polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The
cultivars are from the collection of the Institute of Plant Genetics Resources, Sadovo (Bulgaria). The data obtained suggest clearly
expressed differences in electrophoretic profiles of components of 7S globulins both for melon and watermelon cultivars. Four
phenotypic groups are proposed for melon cultivars (I, II, III, IV) and two (I, II) for watermelon cultivars. This information can be
used for cultivar differentiation.
Tipo: Poster
Palavras-chave: Cucumis melo; Watermelon; Melon; Citrullus lanatus; 7S globulins; Electrophoresis; Genetic resources;
Bulgaria; Cultivar differenciation.
Ano: 2008
URL: http://hdl.handle.net/2174/228
Phenotyping root response to complex diseases: the Monosporascus root rot/ vine decline of melons
Provedor de dados: 35
Autores: Roig, C.; Picó, B.; Fita, A.; Nuez, F.
Monosporascus root rot/vine decline is one of the major diseases of melon crop in warm habitats, caused by the pathogenic fungus
Monosporascus cannonballus. Resistance to this disease has been reported in several sources. However, the use of resistance in
breeding programs is prevented by difficulties in phenotyping the root response to the disease. The present study covers the
phenotyping of an F2 population of melon, derived from a cross between C. melo subsp. melo ‘Piel de sapo’ (susceptible to vine
decline) and C. melo subsp. agrestis ‘Pat81’ (partially resistant to vine decline), for root resistance to the fungus. Both,
conventional methods, based on the visual scoring of the severity of root lesions, and new technologies, color image analyses
and...
Tipo: Poster
Palavras-chave: Mediterranean country; Cucumis melo; Collapse; Image analysis; M. cannonballus; Soil-borne fungi; Real-time
PCR.
Ano: 2008
URL: http://hdl.handle.net/2174/237
Methodology of tetraploid induction plants and expression of microsatellite alleles in triploid
watermelon
Provedor de dados: 35
Autores: Omran, S.A.; Guerra-Sanz, J.M.; Garrido Cárdenas, J.A.
Methods to obtain tetraploid watermelon plants from germinating seeds by treatments with chromosome doubling chemicals have
been assayed and some tetraploid plants obtained by such treatments were pollinated with a diploid to obtain triploid watermelons.
Three concentrations each of dinitroaniline (12 to 15 mg.L-1) and colchicine (300 to 500 mg.L-1), using three exposure durations
(12 to 36 h), were compared for efficiency of tetraploid induction on germinating seeds of five watermelon cultivars. In all five
cultivars, the highest percentage of tetraploid plants was obtained using dinitroaniline at concentration of 12 mg.L-1 for 24 hrs.
The expression of the microsatellite alleles in a triploid obtained from crossing a tetraploid plant of ‘Sugar Baby’ with...
Tipo: Poster
Palavras-chave: Citrullus lanatus; Polyploidy; Dinitroaniline; Colchicine; Simple sequence repeats; Watermelon.
Ano: 2008
URL: http://hdl.handle.net/2174/235
Affecting cucurbit hormonal status by a ZYMV transient expression vector
Provedor de dados: 35
Autores: Davidovich, V.; Leibman, D.; Gal-On, A.; Perl-Treves, R.
Squash and cucumber plants were infected with ZYMV strains engineered to over-express enzymes involved in ethylene and
gibberellin biosynthesis. Presence of the inserted ACS gene within the viral RNA was transient and the insert was deleted after
20-40 days. Ethylene over-expressing plants produced very high ethylene levels and were severely stunted. Monoecious
cucumbers produced earlier, consecutive female flowers. Gibberellin over-expression was deduced from the observed phenotypic
change, plants were taller and flowered earlier.
Tipo: Poster
Palavras-chave: Zucchini yellow mosaic virus (ZYMV); GA20 oxidase; ACC synthase; Ethylene; Squash; Cucumber.
Ano: 2008
URL: http://hdl.handle.net/2174/281
Flexibility in Cucurbitaceae breeding management with an integrated research software
Provedor de dados: 35
Autores: Sillon, J.-F.; Royer, F.; Royer, Fl.
DORIANE SAS develops and commercializes integrated and modular software for research activity able to manage the breeding
data with a high level of flexibility. This software is able to manage complex “experiment cycles” and molecular markers data
required by Cucurbitaceae breeding. Thanks to two innovative concepts like "experiment cycle" and "multi level architecture",
DORIANE reached this objective building a well organized library adapted for the whole research department and a powerful tool
for assisted decision making. Moreover, its client-server architecture facilitates the transmission of information between
researchers and laboratories.
Tipo: Poster
Palavras-chave: Cucurbitaceae; Biotechnology; Breeding; Database; Experiments management; Molecular marker.
Ano: 2008
URL: http://hdl.handle.net/2174/253
Breeding of cucumber (Cucumis sativus) for resistance to multiple diseases and other traits
Provedor de dados: 35
Autores: Kushnereva, V.
The most effective and straightforward way of plant protection is the production of cucumber hybrids with resistance to multiple
diseases. Therefore, breeding of cucumber hybrids with a combination of defensive traits is a major objective. The accurate choice
of parental lines is the first step towards development of successful hybrids. A variety of methods were used in order to speed up
the process of inbred line development: a range of various planting times, planting in greenhouses and hot beds, screening of
germplasm for disease resistances under artificial inoculation as well as natural field conditions, high selection pressure,
backcrossing, multi-stage hybridization. As a result, we have developed cucumber lines and hybrids combining complex...
Tipo: Poster
Palavras-chave: Cucumber; Cucumis sativus; Podosphaera xanthii; Cladosporium cucumerinum; Pseudomonas lachrymans;
Parthenocarpy; Gynoecy; Resistance; Breeding.
Ano: 2008
URL: http://hdl.handle.net/2174/275
Status of soil-borne phytosanitary problems encountered in melon (Cucumis melo) in the main
producing regions of France
Provedor de dados: 35
Autores: Villeneuve, F.; Maignien, G.
French melon growers have found themselves confronted with melon root decay. Accordingly, Ctifl, in close collaboration with
the regional research stations and INRA, set up a study designed to gain greater knowledge of the various phytosanitary problems
and identify the probable cause(s). The principle of the study was to monitor pathogen distribution changes in melon. Three plots
were monitored and a number of samples from other plots were also studied (19 samples in 2003, 22 in 2004, 6 in 2005, 2 in 2006
and 25 in 2007). The symptoms that developed during the years of the study were identified based on this body of data. The
results show the prevalence of problems related to Fusarium oxysporum f. sp. melonis race 1-2 yellowing, often found together
with...
Tipo: Poster
Palavras-chave: Cucumis melo; Fusarium oxysporum f. sp. melonis; Fusarium wilt; Soil-borne disease; France; Disease
resistance.
Ano: 2008
URL: http://hdl.handle.net/2174/252
Influence of honey bees brood pheromone on the production of triploid watermelon
Provedor de dados: 35
Autores: Guerra Sanz, J.M.; Roldán Serrano, A.
Honey bee brood pheromone has been used for boosting the rate of flower visitation by honey bees in cultures of a triploid
watermelon cultivar with diploid plants as pollen-donors. The application of brood pheromone had several consequences on the
quality production parameters of the triploid culture, especially on the average of fruits per plant, the weight of fruits and on the
Brix degree, all these parameters were higher and with statistically different significance from the control. The foraging of the
bees was monitored by the number of visits to flowers and by the number of seeds per fruit of the pollen-donor plants: both
variables were higher in the plot with brood pheromone than in the control. This is the first time that brood pheromone has been...
Tipo: Poster
Palavras-chave: Apis mellifera; Pollen-donor plant; Diploid; Watermelon; Pollinisation; Citrullus lanatus.
Ano: 2008
URL: http://hdl.handle.net/2174/239
Melon fruit color: more than just looks
Provedor de dados: 35
Autores: Burger, Y.; Tadmor, Y.; Lewinsohn, E.; Meir, A.; Sa'ar, U.; Katzir, N.; Paris, H.S.; Schaffer, A.A.
Muskmelons and cantaloupes are climacteric fruits that lose the green color of their fruit rinds upon ripening. Their yellow or
orange appearance is easily recognized by consumers as a sign of ripeness. However, these melons have a short shelf life, as this
loss of chlorophyll is associated with ethylene synthesis. Observations and comparisons of these melons with the non-climacteric,
long-keeping, yellow-rinded casaba melons suggest that through genetic recombination it should be possible to develop cultivars
of muskmelons and cantaloupes combining the consumer-driven characteristic of non-green (yellow or orange) mature fruit color
with long shelf life.
Tipo: Poster
Palavras-chave: Cucumis melo; Chlorophyll; Shelf life; Fruit; Color; Climacteric fruit.
Ano: 2008
URL: http://hdl.handle.net/2174/259
Dioscorides’s bruonia melaina is Bryonia alba, not Tamus communis, and an Illustration labeled
bruonia melaina in the Codex Vindobonensis is Humulus lupulus not Bryonia dioica
Provedor de dados: 35
Autores: Renner, S.S.; Scarborough, J.; Schaefer, H.; Paris, H.S.; Janick, J.
The Cucurbitaceae genus Bryonia contains ten species that are distributed throughout the Mediterranean to North Africa and from
central Europe to Kazakhstan. References to the medicinal uses of species of Bryonia span two millennia, including two passages
in Dioscorides’s De Materia Medica, written in about 65 CE. An illustrated copy of this text, known as the Codex Vindobonensis
and dated 512 CE, is enriched with illustrations, including two labeled as bruōnia or bryonia. Here we argue that while
Dioscorides’s text clearly concerns the blackfruited B. alba and a red-fruited species, perhaps B. cretica or B. dioica, only one of
the plates in the Codex shows a species of Bryonia, while the other shows Humulus lupulus.
Tipo: Poster
Palavras-chave: Botanical illustration; European Cucurbitaceae; Medicinal plants; Pharmaceutical uses; Pliny the Elder; Bryonia
dioica; Genetic resource.
Ano: 2008
URL: http://hdl.handle.net/2174/218
The FT/TFL1 gene family in cucumber
Provedor de dados: 35
Autores: Sato, H.; Heang, D.; Sassa, H.; Koba, T.
In Arabidopsis thaliana, FT and TFL1 are known to affect phase transition from vegetative phase to reproductive phase. It is also
known that these genes also affect some growth habits such as flowering time and compactness. Especially, TFL1 and its
functional orthologs, CEN in snapdragon and SP in tomato, were demonstrated to regulate growth habit of indeterminate type or
determinate type. Cucumber cultivars also have two types of growth habit. Most of them were indeterminate types, however,
taking into account of the characteristics such as yield, early harvest, and robustness, determinate type might be ideal for
cultivating. In the present study, we identified one FT and five TFL1 homologs in cucumber and elucidated their genomic
organization,...
Tipo: Poster
Palavras-chave: Determinate type; Indeterminate type; Ortholog; Homolog; Arabidopsis thaliana; Cucumber.
Ano: 2008
URL: http://hdl.handle.net/2174/271
Preliminary research on drought resistance of wild and domestic Turkish watermelon accessions
Provedor de dados: 35
Autores: Karipcin, Z.; Sari, N.; Kirnak, H.
This project was conducted at GAPEYAM, Sanlıurfa, Turkey, in a semi arid region of Turkey. The aim was to determine the
effects of water stress on 85 watermelon accessions collected from different regions of Turkey. Two irrigation levels were
imposed to determine potential drought resistance of accessions. All plots in the beginning were irrigated with enough irrigation
water for healthy seed germination. The plants received enough irrigation until the period of true leaves. After the true leaves,
irrigation treatments were initiated. While S1 treatment received full irrigation based on depleted soil moisture in the root zone, S2
treatment received 50 % of S1. A new formula was developed to evaluate the drought resistance. For each accession, the ratio...
Tipo: Poster
Palavras-chave: Genetic resources; Irrigation level; Citrullus lanatus; C. colocynthis; C. lanatus var. citroides; C. rehmii;
Praecitrullus fistulosus; Drought resistance; Watermelon; Turkey; Water stress.
Ano: 2008
URL: http://hdl.handle.net/2174/277
A recessive gene conferring ethylene insensitivity and androecy in Cucurbita pepo
Provedor de dados: 35
Autores: Manzano, S.; Dominguez, V.J.; Garrido, D.; Gómez, P.; Jamilena, M.
The genetic and physiological analysis performed in the ‘Vegetable spaghetti’ (Veg) inbred line of Cucurbita pepo subsp. pepo
has indicated that its androecious phenotype is determined by a single recessive gene conferring ethylene insensitivity. The
production of female flowers in the androecious line starts much later than in normal varieties, and is lower than 30 %, with some
of the plants producing less than 5 % female flowers. The androecious trait segregates as a single recessive gene in F2 generation,
and cosegregates with a weak ethylene insensitive phenotype in seedlings. In fact, etiolated seedlings of the ‘Veg’ line and the
most androecious plants in the F2 generation produce more ethylene than the contrasting line, but are less sensitive to...
Tipo: Poster
Palavras-chave: Inheritance; Ethylene production; Sex expression; Cucurbita pepo; Androecy.
Ano: 2008
URL: http://hdl.handle.net/2174/280
Improving the genetic transformation efficiency of Cucumis melo subsp. melo ‘Piel de Sapo’ via
Agrobacterium
Provedor de dados: 35
Autores: Castelblanque, L.; Marfa, V.; Claveria, E.; Martinez, I.; Perez-Grau, L.; Dolcet-Sanjuan, R.
The effects of five Agrobacterium strains, two selection agents, and co-culture conditions were evaluated on the transformation
efficiency of three melon lines (‘T111’, ‘PS8’, ‘PNY’) belonging to the cultivar Cucumis melo subsp. melo ‘Piel de Sapo’, the C.
melo subsp. melo ‘Védrantais’ line, and the accession C. melo subsp. agrestis ‘PI 161375’. Transformation efficiencies for
accession ‘PI 161375’ (10.6 %) were higher than those obtained for ‘Piel de Sapo’ (0.1 %) or ‘Védrantais’ (3.1 %). Among the
‘Piel de Sapo’ lines, the highest rates of transformation were observed with ‘T111’. Selection with pmi solved the problem of
escapes encountered with nptII on ‘Piel de Sapo’. Results on the number of explants with GUS expression indicated that
co-culture at...
Tipo: Poster
Palavras-chave: Melon; Muskmelon; Near Isogenic Lines (NILs); Pmi; Agrobacterium; Genetic transformation; Piel de Sapo;
Cucumis melo subsp. melo; Transformation efficiency; Agrobacterium infection; Regeneration.
Ano: 2008
URL: http://hdl.handle.net/2174/284
Use of sporulation and other leaf and vine traits for evaluation of resistance to downy mildew in
cucumber
Provedor de dados: 35
Autores: Criswell, A.D.; Wehner, T.C.; Klosinska, U.; Kozik, E.
A higher level of downy mildew resistance is needed in cucumber (Cucumis sativus L.). One method for doing that would be to
combine different mechanisms of resistance into a single cultivar. Disease symptoms are expressed as necrotic spots, chlorotic
areas, amount of sporulation on the leaf underside, and stunting of plant growth. Methods for evaluation of necrosis, chlorosis, and
sporulation are available, but sporulation requires a lot of effort to evaluate, requiring spore counts on a hemacytometer under a
compound microscope. We evaluated two faster methods: a subjective rating under a dissecting scope, and a subjective rating with
the unaided (naked) eye. The naked eye was the fastest method, and it also had the lowest error variation in an experiment...
Tipo: Poster
Palavras-chave: Pseudoperonospora cubensis; Cucumis sativus; Necrosis; Chlorosis; Stunting; Downy mildew.
Ano: 2008
URL: http://hdl.handle.net/2174/243
Improving eating quality and carotenoid content of squash
Provedor de dados: 35
Autores: Noseworthy, J.; Loy, B.
The fruit of most cultigens of Cucurbita maxima and C. moschata squash are high in carotenoids, especially B-carotene and lutein,
both of which are important nutritionally. However, there have been no systematic studies to quantify the amount and types of
carotenoids in fruit tissues of breeding germplasm and popular cultivars. In the summer of 2007, seven inbred lines of C. maxima
and two op cultivars and five inbred lines of C. moschata were grown in replicated plots at research farms in Durham and
Madbury, New Hampshire (USA). Data were recorded at harvest and after 30 and 60 days of storage at 15oC on % mesocarp dry
weight (DW) and soluble solids (SS), both major attributes for determining acceptable eating quality. A visual estimation of
carotenoid...
Tipo: Poster
Palavras-chave: Cucurbita maxima; Cucurbita moschata; Butternut squash; Kabocha; Carotenoid.
Ano: 2008
URL: http://hdl.handle.net/2174/258
Morphological characterization of Korean and Turkish watermelon germplasm
Provedor de dados: 35
Autores: Huh, Y.C.; Solmaz, I.; Sari, N.
A total of 67 watermelon accessions of Korean (37 accessions) and Turkish (27 accessions) germplasm and 3 accessions of other
species were characterized for morphological characteristics. The accessions were characterized according to UPOV descriptor
list for 56 characters (6 seedling, 4 plant, 11 leaf, 5 flower, 23 fruit and 7 seed). Eight quantitative characters (hypocotyl length,
cotyledon width, cotyledon length, fruit weight, fruit length, fruit width, thickness of outer layer of pericarp and soluble solid
content) were also measured. According to the results of morphological characterization performed, the accessions displayed a
large diversity; however, plant growth habit and leaf blade flecking were constant characters for all the accessions. The...
Tipo: Poster
Palavras-chave: Mediterranean country; Genetic resource; Multivariate analysis; Citrullus lanatus; Citrullus lanatus var.
citroïdes; Citrullus colocynthis; Praecitrullus fistulosus; Watermelon.
Ano: 2008
URL: http://hdl.handle.net/2174/221
Root architecture variation in Cucurbita
Provedor de dados: 35
Autores: Fita, A.; Postma, J.; Picó, B.; Nuez, F.; Lynch, J.
Cucurbita species are employed as rootstocks for melons, watermelons, and cucumbers. The use of one or another species or
accession of Cucurbita as a rootstock results from germplasm availability and compatibility with the scion rather than on
systematic research of the root characteristics of different taxa. The objectives of the present work were to compare 23 Cucurbita
accessions belonging to 10 different species or subspecies (wild and cultivated) for their root architecture and their capacity to
form cluster roots under low P and low Fe conditions. Two experiments were conducted, the first consisting of growing the plants
in pouches to observe directly root growth in three treatments. One treatment was a full nutrient solution, another was in a...
Tipo: Poster
Palavras-chave: Cucurbitaceae; Root morphology; Rootstock; Cluster root; Root plasticity; Cucurbita.
Ano: 2008
URL: http://hdl.handle.net/2174/254
Morphological and RAPD marker evidence of gene flow in open-pollinated populations of Cucurbita
moschata interplanted with C. argyrosperma
Provedor de dados: 35
Autores: Cuevas-Marrero, H.; Wessel-Beaver, L.
The tropical pumpkins Cucurbita moschata Duchesne and C. argyrosperma Huber are often found growing together. Both C.
argyrosperma subsp. argyrosperma (the domesticated cushaw squash) and the wild species C. argyrosperma subsp. sororia (L.H.
Bailey) Merrick & Bates are found together in Central America. Several reports indicate that plants displaying a phenotype
combining traits of both species occur, suggesting gene flow between species. This research studied gene flow between species by
evaluating progenies from field plantings of C. argyrosperma (both subspecies) interplanted with C. moschata and allowed to
open-pollinate. The progenies evaluated were from C. argyrosperma seed parents. Morphological and species-specific RAPD
markers demonstrated...
Tipo: Poster
Palavras-chave: Pumpkin; Squash; Interspecific cross; Genetic compatibility; Cucurbitaceae; Pollinisation.
Ano: 2008
URL: http://hdl.handle.net/2174/231
Possible involvement of CsTypA1 in reproductive organ development of cucumber (Cucumis sativus)
Provedor de dados: 35
Autores: Barak, M.; Trebitsh, T.
Cucumber (Cucumis sativus) is a monoecious plant that is extensively studied with respect to floral sex determination. While the
genetic background, hormonal and environmental factors are well characterized, the molecular mechanisms regulating unisexual
flower development are not well understood. Initially a cucumber floral bud is bisexual and has the potential to develop into a
male or female flower. Using differential cDNA-AFLP analysis between plant apices of monoecious (predominantly male) and
gynoecious (female) cucumber plants, we isolated a cDNA that encodes a putative GTP binding protein tyrosine phosphorylated
protein A (CsTypA1). TypA genes are widely distributed in plants and prokaryotes. Bacterial TypA proteins are involved in
protein...
Tipo: Poster
Palavras-chave: Flower development; Floral sex; Ovary; Cucumis sativus; Cucumber; CDNA; Sex determination.
Ano: 2008
URL: http://hdl.handle.net/2174/282
A review of production systems on watermelon quality
Provedor de dados: 35
Autores: Davis, A.R.; Webber III, C.L.; Perkins-Veazie, P.; Ruso, V.; Lopez-Galarza, S.; Sakata, Y.
Cultural practices have been reported to affect quality and phytonutrient content of watermelon [Citrullus lanatus var. lanatus
(Thunb.) Matsum. & Nakai]. Knowing which cultivars perform well under various technologies and production systems, and
knowing how these systems affect quality and phytonutrient content is imperative to ensure high quality fruit. Organic production
and grafting are two cultural practices that are increasing among watermelon producers. Each of these technologies have the
potential to interact with cultivars to influence watermelon quality. This review discusses the effects organic culture, input level,
and grafting have on watermelon fruit quality.
Tipo: Poster
Palavras-chave: Citrullus lanatus; Lycopene; Brix; Quality; Organics; Grafting; Watermelon; Production system; Cultural
practices.
Ano: 2008
URL: http://hdl.handle.net/2174/279
Histological study of shoot organogenesis in melon (Cucumis melo L.) after genetic transformation
Provedor de dados: 35
Autores: Chovelon, V.; Restier, V.; Dogimont, C.; Aarouf, J.
Leave and cotyledon explants from two melon genotypes ‘Vedrantais’ and ‘Paul’ were cultured on different media and their
regeneration was followed during 60 days. High frequency of plant regeneration was observed with ‘Vedrantais’ cotyledons
cultured on MS medium added with BAP and 2-iP. Using this protocol, Agrobacterium mediated transformation was developed
and a significant reduction of the plant regeneration rate was observed. Explants histological analysis revealed the presence of
transformed meristematic areas but a rapid and premature cell vacuolization was observed. During plant regeneration,
meristematic cells were affected by important cytological damages: cell dislocation accompanied by cell death and final collapsus.
This disruption of...
Tipo: Poster
Palavras-chave: Cucumis melo; Agrobacterium tumefaciens; GUS uidA; Genetic transformation; Regeneration.
Ano: 2008
URL: http://hdl.handle.net/2174/285
Isolation of Cucurbita pepo ethylene receptors Cup-ETR1 and Cup-ERS1 and functional analysis
during fruit formation
Provedor de dados: 35
Autores: Payán, C.; Peñaranda, A.; Mariotti, B.; Garrido, D.; Jamilena, M.; Gómez, P.
The Zucchini morphotype of Cucurbita pepo is considered summer squash, and the fruits are harvested when still immature. The
formation of the fruit follows sequential processes commencing in the floral organs which must be strictly coordinated in order to
obtain a proper fruit. Lack of coordination in the growth of floral organs leads to unsuccessful fruit formation and yield loss.
Previous studies have indicated the role of ethylene in the regulation of flower and fruit formation. To study the regulation
mechanisms of this hormone during fruit formation, we have isolated homolog genes of ethylene receptors, named Cup-ETR1 and
Cup-ERS1. The study of the expression of these genes in ovary and fruit by Q RT-PCR showed a distinctive expression pattern
in...
Tipo: Poster
Palavras-chave: Fruit set; Zucchini cultivar; Growth coordination; Maturity; Cucurbita pepo; Ethylene receptor.
Ano: 2008
URL: http://hdl.handle.net/2174/266
Inheritance of tolerance to Aphis gossypii in C. melo TGR-1551 and its relation with resistance to
virus transmission
Provedor de dados: 35
Autores: Sarria, E.; Yuste-Lisbona, F.J.; Palomares, F.J.; López-Sesé, A.I.; Gómez-Guillamón, M.L.
Aphid tolerance in TGR-1551 is controlled by Vat gene according to the allelism test involving PI 414723. The existing relations
between aphid tolerance and antixenosis and between aphid tolerance and resistance to virus transmission were studied.
Tipo: Poster
Palavras-chave: Aphis gossypii; Cucumis melo; Melon; Susceptibility; No preference; Non-persistent virus; Allelism test; Vat
gene.
Ano: 2008
URL: http://hdl.handle.net/2174/249
Challenges and options in managing Phytophthora blight (Phytophthora capsici) of cucurbits
Provedor de dados: 35
Autores: Babadoost, M.; Tian, D.; Islam, S.Z.; Pavon, C.
There is no cucurbit cultivar with measurable resistance against Phytophthora blight, caused by Phytophthora capsici, available.
Genetic complexity of sources of Phytophthora resistance and variation in genetics of P. capsici are the serious challenge in
breeding for resistance to Phytophthora blight. At present, cultural practices and chemical use are the options for managing
Phytophthora blight of cucurbits. The most effective strategy for controlling P. capsici in cucurbits was an integrated approach of
crop rotation for ≥3 years, seed treatment with mefenoxam (0.42 ml Apron XL LS/kg of seed), avoiding the use of contaminated
water with P. capsici, and fungicide spray-applications. Among more than 50 fungicides tested, only dimethomorph (Acrobat,...
Tipo: Poster
Palavras-chave: Citrullus lanatus; Cucumis melo; Cucumis sativus; Cucurbita pepo; Cucurbita maxima; Cucurbita moschata;
Damping-off; Fruit rot; Phytophthora.
Ano: 2008
URL: http://hdl.handle.net/2174/247
Use of ethylene production as a marker for the selection of gynoecy in melon (Cucumis melo L.)
Provedor de dados: 35
Autores: Manzano, S.; Martínez, C.; Kraakman, P.; Jamilena, M.
Two different approaches have been used to analyze whether the measurements of ethylene produced by different plant organs
may constitute a good tool for the selection of gynoecy in melon (Cucumis melo). Firstly, the effects of treatments with either
ethylene or the ethylene inhibitor AVG on the sex expression of different gynoecious, monoecious and andromonoecious lines of
melon were compared. Secondly, the level of ethylene was measured in leaves, as well as apical and lateral meristems of different
gynoecious and monoecious lines of melon. The differences observed in the sensitivity of the analyzed gynoecious lines to
ethylene treatments suggested the existence of variation in the internal level of ethylene. In fact, leaves and apical meristems
from...
Tipo: Poster
Palavras-chave: Cucumis melo; Gynoecy; Sex expression; Ethylene; AVG.
Ano: 2008
URL: http://hdl.handle.net/2174/265
Detection of quantitative trait loci affecting short lateral branching in Cucumis melo
Provedor de dados: 35
Autores: Fukino, N.; Sugiyama, M.; Ohara, T.; Sainoki, H.; Kubo, N.; Hirai, M.; Matsumoto, S.; Sakata, Y.
Labor-saving techniques for pruning lateral branches are desirable in Japanese melon production. A short-lateral-branching line,
Nou4 was developed from a weed-type ‘LB-1’ (Cucumis melo var. agrestis). In this study, quantitative trait loci(QTL) analysis for
short lateral branching was conducted with a population of 94 F2 derived from a cross between Nou4 and normal-branching
cultivar ‘Earl’s Favourite (Harukei 3)’. A total of 114 markers including 94 SSRs, 2 CAPS, and 18 AFLPs were employed to
construct a linkage map with 13 linkage groups. Two QTLs controlling short lateral branching were identified on LG VII and LG
XI. The QTL on LG VII explained 14.8 % of the phenotypic variance with a LOD score of 3.2. The QTL on LG XI explained
42.2 % of the...
Tipo: Poster
Palavras-chave: Melon; Lateral shoot; Labor-saving; Genetic linkage map; QTL analysis; Phenotypic variance; Cucumis melo;
QTL.
Ano: 2008
URL: http://hdl.handle.net/2174/278
Attempt to select cucumber (Cucumis sativus L.) double haploid lines to downy mildew tolerance by
molecular markers
Provedor de dados: 35
Autores: Śmiech, M.; Sztangret-Wiśniewska, J.; Gałecka, T.; Korzeniewska, A.; Marzec, M.; Kolakowska, G.; Piskurewicz, U.;
Niemirowicz-Szczytt, K.
The main goal was to identify RAPD molecular markers associated with downy mildew resistance. RAPD markers that
differentiated susceptible and resistant H and DH plants were identified. Further research is needed to verify linkage between the
identified markers and the susceptible and resistant phenotypes.
Tipo: Poster
Palavras-chave: Pseudoperonospora cubensis; Haploid; Double haploid; RAPD; Cucumber sativus; Downy mildew; Resistance.
Ano: 2008
URL: http://hdl.handle.net/2174/244
New Czech pickling cucumber hybrids - comparison of tolerance to Zucchini yellow mosaic virus
(ZYMV)
Provedor de dados: 35
Autores: Svoboda, J.
Commonly grown cultivars of pickling cucumber (Cucumis sativus L.) in the Czech Republic are highly susceptible to Zucchini
yellow mosaic virus (ZYMV). New hybrids are bred to achieve resistant plants. The level of tolerance to ZYMV of three Czech
pickling cucumber hybrids 1/05, 9/05 and 12/05, was compared to four pickling and slicing cucumber cultivars ‘Othello’, ‘Melody
F1’, ‘Dasher’ and ‘Lili’. Young plants were artificially inoculated with the Czech highly pathogenic ZYMV isolate, ZYMV-H.
ELISA was used to determine the relative concentration of viral protein in leaves as the reciprocal value of the virus titer. The
hybrid 1/05 showed the highest degree of tolerance to ZYMV-H. The virus concentration measured in its leaves was four times
lower than in...
Tipo: Poster
Palavras-chave: Cucumis sativus; ELISA; Resistance; ZYMV; Tolerance.
Ano: 2008
URL: http://hdl.handle.net/2174/246
Harnessing Aquatic Yeasts For Developing A New Generation of Sunscreens
Provedor de dados: 17
Autores: Hycienth Braganca; Nandkumar Kamat.
Around 100 yeast genera and 800 species have been isolated and characterized. Nagahama (2006) has reviewed yeast biodiversity
in freshwater, marine and deep-Sea Environments. Our work aims at systematic biodiversity assessment of freshwater aquatic
yeasts from Goa with major focus on carotenogenic basidiomycetes yeasts which on exposure to potentially damaging levels of
solar ultraviolet radiation (UVR) accumulate photoprotective compounds (PPC) such as mycosporine-glutaminol-glucoside
(myc-glu-glu, peak absorption at 309-310nm) that server as sunscreens and /or antioxidant. These yeasts are a potential source of
a particularly diverse family of such substances, collectively referred to as mycosporine- like amino-acids (MAAs). This paper
presents the...
Tipo: Poster
Palavras-chave: Biotechnology; Ecology; Microbiology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4249/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
Molecular simulations to study the effect of pore geometry and structure on the adsorption of CH4/H2
mixtures in carbon pores
Provedor de dados: 17
Autores: Vasanth K. Kumar; Erich A. Müller; Francisco Rodriguez-Reinoso.
We used molecular simulations to study the effect of pore structure and geometry on the selectivity of carbon materials for the
adsorption of methane from a mixture of methane and hydrogen at 50 bar and 298 K. We modeled hydrogen as a more realistic
dumb-bell shaped fluid and methane as spherical Lennard-Jones sphere. The pore geometry studied includes the slit, nanotube,
random carbon structure and carbon pores that mimic a foam structure. Our results confirm that both the pore size and pore
structure have a significant effect on the selectivity for methane molecules. An array of nanotubes that have a closed structure has
the highest selectivity for methane molecules, followed by carbon foam, slit and random pore structures. Energetic and packing
effects...
Tipo: Poster
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6132/version/1
The Cell Cycle Ontology: an application ontology supporting the study of cell cycle control
Provedor de dados: 17
Autores: Erick Antezana; Vladimir Mironov; Mikel Egana; Robert Stevens; Ward Blondé; Bernard De Baets; Martin
Kuiper.
The Cell Cycle Ontology (CCO) is an application ontology that automatically captures and integrates detailed knowledge on the
cell cycle process by combining, interlinking and enriching knowledge from various sources. CCO uses Semantic Web
technologies, and it is accessible via the web for browsing, visualising, advanced querying, and computational reasoning. CCO
facilitates a detailed analysis of cell cycle related molecular network components. Through querying and automated reasoning, it
may provide new hypotheses to help steer a systems biology approach to biological network building. The ontology is available
on "http://www.cellcycleontology.org":http://www.cellcycleontology.org. Visual exploration can be done
via the BioPortal, the...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3563/version/1
Urban Creek flow, re-aeration and ecological health
Provedor de dados: 17
Autores: Peter Pollard; Sam Bagraith.
For two years we studied the health of a lowland freshwater ecosystem, Moggill Creek, flowing through the western suburbs of
Brisbane Qld, Australia. We found: Terrestrial organic carbon was most likely driving very high bacterial growth and respiration
rates that removed dissolved oxygen from the water. The diversity of fish and invertebrates was high and the overhanging riparian
vegetation cover limited algal and cyanobacterial production. Overall the creek was in fair to good health—Report
Grade“D”. Conclusion: Water column dissolved oxygen concentrations and Creek health relied on
environmental flow during rain to physically re-aerate the water to counter the high bacterial consumption of oxygen that resulted
from the...
Tipo: Poster
Palavras-chave: Ecology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4698/version/1
Information on Transcriptional Regulation and Signal Transduction of _Escherichia coli_ K-12
Integrated in the Database RegulonDB.
Provedor de dados: 17
Autores: Socorro Gama-Castro; Alberto Santos-Zavaleta; Martin Peralta-Gil; Verena Weiss; Heladia Salgado; Hilda Solano;
Julio Collado-Vides.
Since its inception, RegulonDB ("http://regulondb.ccg.unam.mx/":http://regulondb.ccg.unam.mx/) has
been a database that compiles information about the regulation of transcription initiation of _Escherichia coli_ K-12. However, we
are aware that transcriptional regulation is not an isolated process; instead, it is the response to the different environmental
conditions that trigger a series of concatenated reactions that end in transcriptional regulation, and it implies an adequate response
in terms of induced and repressed gene products. We are working now to include all these new data in RegulonDB. As a
consequence, transcriptional regulation in RegulonDB will be part of a unit that initiates with the signal, continues with the
signal...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5270/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
Structural characterization of an endoglucanase from _Serpula lacrymans_ var. lacrymans S7.9
Provedor de dados: 17
Autores: Csaba Zoltan Kibedi Szabo; Judit Galicza; Istvan Weyda; Csaba Dezso Andras.
Lately cellulase enzymes from fungi and also bacteria, have received much attention due to their application in bioethanol
production from lignocellulosic feedstock. Dry rot fungus (_Serpula lacrymans_) is known to be the most damaging destroyer of
indoor wood construction materials in temperate regions. Therefore the very recent sequencing of this fungus genome has opened
new possibilities. We describe here the analysis of the primary, secondary and tertiary structure of a 255 amino acid sequence
endoglucanase, from _S. lacrymans_ var. lacrymans S7.9, having a molecular weight of 26746. We also provide the amino acids
from the active site.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6575/version/1
Suppression of 12-O-tetradecanoylphorbol-13-acetate-induced ornithine decarboxylase activity by
resveratrol derivatives
Provedor de dados: 17
Autores: Suaib Luqman; Tamara P. Kondratyuk; Juma Hosino; Mark Cushman; John M. Pezzuto.
As
demonstrated
previously,
resveratrol
(3,4',5-trihydroxy-trans-stilbene)
inhibits
12-O-tetradecanoylphorbol-13-acetate (TPA)-induced ornithine decarboxylase (ODC), the key rate limiting enzyme in
mammalian polyamine synthesis. Using human bladder epithelial carcinoma HTB-24 cells in culture where resveratrol inhibits
induction with an IC50 of 8.8 µM, we now report potential metabolites demonstrate greater activity
[tetrabutylammonium (E)-4-(3,5-dihydroxystyryl)phenyl sulfate (IC50 1.2 µM),
3,5,4'-trisulfate (IC50 1.8
resveratrol tripotassium
µM), resveratrol tripotassium 3,4'-disulfate (IC50 1.8
µM), and resveratrol tripotassium 3,5-disulfate (IC50 2.3 µM)]. Based on RT-PCR...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6908/version/1
Genome-wide transcription analysis of interaction between the human macrophage and
Mycobacterium tuberculosis during concurrent drug administration by conventional and novel
methods
Provedor de dados: 17
Autores: Awadh Bihari Yadav; Amit K. Singh; Amit Misra.
Targeted drug delivery to alveolar macrophages harboring Mycobacterium tuberculosis (Mtb) holds promise of high efficacy
against pulmonary tuberculosis (TB). It was investigated whether inhalable microparticles (MP) can rescue macrophages from
‘alternative’ activation induced by pathogenic Mtb in addition to achieving targeted drug delivery. A
genome-wide transcription analysis (Affymetrix HG-U133 Plus 2.0 DNA microarray) of THP-1 cell line derived macrophages
was undertaken after exposing them to infection with 10 MOI of MTB H37Rv at 0, 12 and 24 hours post infection. The Molecular
markers of macrophage bactericidal activity were assayed in THP-1- and primary human peripheral blood mononuclear cell
(PBMC)-derived macrophages, in the...
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2453/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
PLA Microparticles for Pulmonary Delivery of AntiTB drugs: Biodistribution study
Provedor de dados: 17
Autores: Rahul Kumar Verma; Jatinder Kaur; Awadh Bihari Yadav; Kauslender Kumar; Amit Misra.
A dry powder inhalable (DPI) microparticles comprising anti-tuberculosis drugs incorporated in biodegradable polymers was
developed for the treatment of pulmonary tuberculosis (P. Muttil _et al_. 2007). Poly L-lactic acid (PLA) microparticles
incorporating a high payload of rifabutin and isoniazid were fabricated by spray drying (Buchi 190). Microparticles were
composed of PLA and the drugs (rifabutin and isoniazid) at a 2:1:1 weight ratio. Microparticles of desired high encapsulation
efficiency and sustained release characteristics were produced having a diameter range of 2-10 µm (Malvern
Mastersizer 2000). Differential scanning calorimetry (DSC) was carried out to study drug polymer interaction. The time course of
tissue biodistribution...
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2448/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
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
Ligand based virtual screening studies to design drug molecules for human PIN1 causing
cardiovascular disease
Provedor de dados: 17
Autores: C Ramana; Manne Munikumar; Amineni Umamaheswari.
PIN1 is a member of the cis/trans peptidyl-prolyl isomerase family which plays critical roles in cell-cycle regulation. Over
expression of PIN1 in endothelial cells causes cardiovascular disease. The present study has focused on computational analysis to
identify the potential inhibitors for PIN1. The human PIN1 crystal structure was retrieved from the protein data bank and prepared
using protein preparation wizard of Maestro v9.2. Fourteen PIN1 inhibitors reported in recent literature were acquired and
searched for structural analogs using Ligand.Info tool. 5675 PIN1 inhibitor analogs yielded were converted to 3D structures using
LigPrep with constraints of ADME evaluation and toxicity assessments. The 3D ligand dataset was docked to PIN1 through...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6604/version/1
The spatial temporal regime of stream flow of the conterminous U.S. in connection with indices of
global atmospheric circulation
Provedor de dados: 17
Autores: Boris Shmagin; Carol A. Johnston; Scott Bridgham.
Long-term stream flow records (1929-1988) from seventy one U.S. Geological Survey gauging stations with drainage area in
range 1000-10000 sq mi were analyzed using multivariate statistics. Factor analysis of average annual flow revealed seven
patterns of river runoff within seven distinct regions of the territory. This factor model reflected 69% variance of the initial matrix.
The second set of stream flow records (1939-1972) from ninety-seven gauging stations was used as control. This set contains all
seventy one from first one and additional stations with shorter observation period. Factor analysis of this expended set again
yielded seven factors (69% variance of the initial matrix) with very similar spatial distribution of gauging...
Tipo: Poster
Palavras-chave: Earth & Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/1382/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
Identification of a highly polymorphic tetranucleotide repeat locus (DXpS) at Xp and development of
a DXpS/HUMARA biplex methylation-based PCR assay that enhances detection of X-chromosome
inactivation
Provedor de dados: 17
Autores: Filipe B. Machado; Ester S. Ramos; Pamela C. Radic; Carlos D. de Brasi; Enrique Medina-Acosta.
The methylation-based PCR assay at the polymorphic (CAG)n repeat in exon 1 of the human androgen receptor _AR_ gene
(HUMARA) is a standard method for determination of the methylation state of alleles in active X (Xa) and inactive X (Xi)
chromosomes. HUMARA assay is endowed with heterozygosity rates ~85% worldwide. This means that in a proportion of
females it is uninformative. The HUMARA genotype is not neutral, being linked to Kennedy´s disease. Moreover,
allele designation and quantification from trinucleotide repeats demand normalizing for minor (stutter) products differing from the
original template by multiples of the repeat unit. Here, we report on the identification of a highly polymorphic tetranucleotide
repeat (named DXpS) mapping to...
Tipo: Poster
Palavras-chave: Biotechnology; Genetics & Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6633/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
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
Visualizing classification of natural video sequences using sparse, hierarchical models of
cortex.
Provedor de dados: 17
Autores: Steven P. Brumby; Michael I. Ham; Will A. Landecker; Garrett Kenyon; Luís M. A. Bettencourt.
Recent work on hierarchical models of visual cortex has reported state-of-the-art accuracy on whole-scene labeling
using natural still imagery. This raises the question of whether the reported accuracy may be due to the sophisticated,
non-biological back-end supervised classifiers typically used (support vector machines) and/or the limited number of images used
in these experiments. In particular, is the model classifying features from the object or the background? Previous work
(Landecker, Brumby, et al., COSYNE 2010) proposed tracing the spatial support of a classifier’s
decision back through a hierarchical cortical model to determine which parts of the image contributed to the classification,
compared to the...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5971/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
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
Pyrosequencing/Sanger Plant Genome Assembly (Limitations, Problems And Solutions) - On The
Way To Cucumber (Cucumis sativus L. cv. Borszczagowski) Draft Genome Sequence Publishing
Provedor de dados: 17
Autores: Rafal Woycicki; Zbigniew Przybecki.
Genome sequencing give us an opportunity to broaden the range and improve the quality of omics studies. New sequencing
technologies make it possible to achieve the sequencing reads 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 focus here on
the wide range of approaches undertaken to assemble the draft cucumber (Cucumis sativus L. cv. Borszczagowski) genome done
by using 12x coverage of pyrosequencing Titanium chemistry shotgun paired and unpaired reads combined with Sanger reads.
Tipo: Poster
Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4630/version/1
Positive Darwinian Selection And The Birth Of An Olfactory Receptor Clade In Teleost Fish
Provedor de dados: 17
Autores: Ashiq Hussain; Luis Saraiva; Sigrun Korsching.
Trace amine-associated receptors (TAARs) in mammals recently have been shown to function as olfactory receptors. We have
delineated the taar gene family in jawless, cartilaginous and bony fish (zero, two, and more than hundred genes, respectively). We
conclude that taar genes are evolutionary much younger than the related OR and ORA/V1R olfactory receptor families, which are
present already in lamprey, a jawless vertebrate. The two cartilaginous fish genes appear to be ancestral for two taar classes, each
with mammalian and bony fish (teleost) representatives. Unexpectedly, a whole new clade, class III, of taar genes originated even
later, within the teleost lineage. Taar genes from all three classes are expressed in subsets of zebrafish olfactory receptor...
Tipo: Poster
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6448/version/1
Ecotoxicological risk assessment of agriculture intensification in Argentinean cropping lands using a
fuzzy-logic based model
Provedor de dados: 17
Autores: Diego Ferraro.
Current agricultural models have an increasing dependence on non-renewable resources that have significant implications for the
ecosystem health. Pesticides are considered one main impact force that affects both the structure and functions of agroecosystems.
In this work we presented results from the application of an environmental pesticide risk assessment of a large database of
cropping systems in the Inland Pampa (Argentina) where, since 1990, the traditional mixed grazing–cropping
systems were being replaced by permanent agriculture and the intensification of pesticide use has increased significantly.
However, there is no clear awareness of the ecotoxicological risk associated with these land use changes. The ecotoxicological
risk on both...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5215/version/1
SBGN-ED - a tool for editing, validating, and translating of SBGN maps
Provedor de dados: 17
Autores: Tobias Czauderna; Christian Klukas; Astrid Junker; Falk Schreiber.
The recently proposed Systems Biology Graphical Notation (SBGN) provides a standard for the visual representation of
biochemical and cellular processes. SBGN helps to communicate biological knowledge more efficient and accurate between
different research communities in the life sciences. However, to support SBGN, methods and tools for editing, validating, and
translating of SBGN maps are necessary.

We present methods for these tasks, the tool
SBGN-ED, and an application example. SBGN-ED allows to create all three types of SBGN maps from scratch, to validate these
maps for syntactical and semantical correctness, to translate maps from the KEGG and MetaCrop databases into SBGN, and to
export SBGN maps into several file and...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4973/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
Pharmacophore Modeling and Binding Analysis for targeting Mycobacterium tuberculosis MurC
ligase
Provedor de dados: 17
Autores: Yogesh N; Jignesh P; Vivek K; C Gopi Mohan.
Despite the availability of effective chemotherapy and the moderately protective vaccine, new anti-Tuberculosis agents are
urgently needed to decrease the global incidence of Tuberculosis (TB). The resumption of TB, mainly caused by the emergence of
multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains and HIV epidemics, led to an increased need to
understand the molecular mechanisms of drug action and drug resistance, which should provide significant insight into the
development of newer compounds.

Based on this ground, computational studies of
Mtb-MurC enzyme inhibition were carried out to find out novel lead molecules against the same.
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4163/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
Exposing The Cancer Genome Atlas (TCGA) as a SPARQL endpoint
Provedor de dados: 17
Autores: Helena Deus.
Automated discovery of candidate biomarkers from multiple databases has been the central challenge in the Life Sciences in
general and in the study of systemic processes such as those documented by The Cancer Genome Atlas (TCGA) in particular.


The maturation of Semantic Web technologies offers solutions to those problems by
allowing the query to be defined by navigating a normally represented domains of discourse instantiated by the data.


We address the systems challenge of The Cancer 
Genome
Atlas initiative (http://cancergenome.nih.gov/), which generates a large scale repository of high throughput molecular biology data
generated and processed at 5 academic...
Tipo: Poster
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6303/version/1
Structure-based design of novel pyrazoles as aurora kinase A inhibitors.
Provedor de dados: 17
Autores: Mohane Coumar; Paritosh Shukla; Ajay Kumar Dixit; Jiun-Shyang Leou; John T. A. Hsu; Su-Ying Wu; Hsing-Pang
Hsieh.
Inhibition of Aurora kinase, a member of serine/threonine kinase involved in the regulation of cell division is emerging as a new
molecular targeted cancer treatment option. Three isoforms of Aurora kinase, A, B and C are known. Both Aurora A and B are
over expressed in many human cancers and are linked to chromosome instability, oncogenic transformation, tumour progression
and development of chemoresistance. Inhibitors of Aurora kinase, regardless of their kinase specificity spectrum have shown to
promote cancer cell death by induction of apoptosis and mitotic catastrophe. Based on the current success of Aurora kinase
inhibitors in the development of kinase-based cancer therapy, we have initiated a structure-based virtual screening for the
identification...
Tipo: Poster
Palavras-chave: Biotechnology; Cancer; Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/2769/version/1
Multiple Ontologies for Integrating Complex Phenotype Datasets
Provedor de dados: 17
Autores: Mary Shimoyama; Melinda Dwinell; Howard Jacob.
There has been an emergence of multiple large scale phenotyping projects in the rat model organism community as well as
renewed interest in the ongoing phenotype data generated by thousands of researchers using hundreds of rat strains worldwide.
Unfortunately, this data is scattered and is neither described nor formatted in a standardized manner. A system to integrate
complex phenotype data from multiple sources and facilitate data mining and analysis is being developed using multiple
ontologies.

*Introduction*
The potential value of integrating
phenotype data from multiple sources (different laboratories, varying techniques to measure similar phenotypes, multiple strains)
is enormous. Presented here is...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3554/version/2
SemanticSBML: a tool for annotating, checking, and merging of biochemical models in SBML format
Provedor de dados: 17
Autores: Wolfram Liebermeister; Falko Krause; Jannis Uhlendorf; Timo Lubitz; Edda Klipp.
Semantic annotations in SBML (systems biology markup language) enable computer programs to check and process biochemical
models based on their biochemical meaning. Annotations are an important prerequisite for model merging, which would be a
major step towards the construction of large-scale cell models. The software tool semanticSBML allows users to check and edit
MIRIAM annotations and SBO terms, the most common forms of annotation in SBML models. It uses a large collection of
biochemical names and database identifiers to support modellers in finding the right annotations. Annotated SBML models can
also be built from lists of chemical reactions. In model merging, semanticSBML suggests a preliminary merged model based on
MIRIAM annotations in the original...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3093/version/1
Identification of potent inhibitors for p38δ MAPkinase of human through in silico
analysis
Provedor de dados: 17
Autores: Naga Lakshmi M; Manne Munikumar; Dibyabhaba Pradhan; Amineni Umamaheswari.
P38δ Mitogen activated protein kinase is a serine/threonine protein kinase that participates in signaling cascades,
mediating cellular responses to cytokinines, UV radiation, hyperosmotic stress, inducing keratinocyte differentiation and
regulating apoptosis. Over expression of p38δ leads to tumor development by impairing the ERK1/2
–AP1 pathway that is critically linked to the control of cell proliferation and tumorigenesis on skin which was
experimentally proven in knockout mice. Therefore, herein, a computational approach was undertaken to design novel inhibitors
against p38delta for effective cancer therapy. The tertiary structure of p38δ was retrieved from a protein databank and
active sites were predicted from...
Tipo: Poster
Palavras-chave: Cancer; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5459/version/1
Phyloclimatic Modelling Can Estimate Ancestral Areas
Provedor de dados: 17
Autores: Chris Yesson; Alastair Culham.
Ancestral area selection is traditionally based on geographic patterns analyzed alongside phylogenetic data. The approach assumes
consistent climate and will only select areas from within present day distributions. The combination of observed distribution and
inferred climate preferences have been used to determine the potential distribution of species in the past, present and future. The
heritability of environmental niches, based on climate preferences, has been demonstrated, and ancestral niches have been
reconstructed using phylogenetic techniques. These techniques can be combined to estimate ancestral areas. Ancestral area
selection via environmental preference differs from traditional methods, as areas which are outside the current observed...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/478/version/1
PrOCoil - Advances in predicting two- and three-stranded coiled coils
Provedor de dados: 17
Autores: Carsten C. Mahrenholz*; Ingrid G. Abfalter*; Ulrich Bodenhofer; Rudolf Volkmer; Sepp Hochreiter.
*Overview* | Coiled coils are usually described as consisting of two up to seven α-helices that are wrapped around
each other. They can associate as either homomeric or heteromeric structures and bind in parallel or antiparallel topologies.
Another characteristic of all coiled coils is the periodic recurrence of a sequence [abcdefg]n called heptad repeat, where n denotes
the heptad number. In these repeats, a and d are hydrophobic amino acids at core positions crucial for the tertiary structure. In
contrast, the polar positions b, c, and f are hydrophilic and e and g are charged residues.
Due to their ability
to oligomerize, coiled coils are involved in a variety of important cellular functions, either on their own or as part of...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4677/version/1
Plant Metabolic Pathways in MetaCyc and SolCyc
Provedor de dados: 17
Autores: Anuradha Pujar; Ron Caspi; Naama Menda; Isaak Tecle; Peter Karp; Lukas Mueller.
MetaCyc is a metabolic encyclopedia of experimentally validated biochemical pathways curated from scientific literature, that
spans all organisms, with an emphasis on plants and microbes. The Pathway tools is a complex curation software suite that
enables curation of reactions, construction of pathways and annotation with one or more representative enzymes, that include
information such as substrate specificity, kinetic properties, activators, inhibitors, cofactor requirements, genes if cloned and links
to external databases. In addition curators are able to provide concise, review-level summaries and extensive literature citations.
The present database release includes more than 1200 pathways from more than 1549 organisms, 7312 reactions, 5127 enzymes,...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3192/version/1
The BioGRID Interaction Database
Provedor de dados: 17
Autores: Michael S. Livstone; Bobby-Joe Breitkreutz; Chris Stark; Lorrie Boucher; Andrew Chatr-Aryamontri; Rose Oughtred;
Julie Nixon; Teresa Reguly; Jennifer Rust; Andrew Winter; Kara Dolinski; Mike Tyers.
The goal of the Biological General Repository for Interaction Datasets (BioGRID) (http://www.thebiogrid.org) is to archive and
freely disseminate collections of genetic and protein interactions from major model organisms. BioGRID currently houses over
335,000 interactions curated from high-throughput datasets and individual focused studies found in the primary literature, as
derived from some 23,000 publications. Complete coverage of the entire literature for both the budding yeast _Saccharomyces
cerevisiae_ and the fission yeast _Schizosaccharomyces pombe_ has been achieved, resulting in the curation of over 246,000
interactions, and efforts to expand curation across multiple species are underway. Through collaborations with the Gene Ontology
(GO)...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5627/version/1
Precise Atomic Structures of Three Novel Nanomaterials in Nanotechnology, Biomedicine and
Cosmology: Graphene, Boron Nitride and Coronene
Provedor de dados: 17
Autores: Raji Heyrovska; Lakshmi Atchison; Sara Narayan.
Nanomaterials are currently of great importance in science, technology and commercial applications. Since these materials are
atomic layer thick and are a few square nanometers of area, a knowledge of their precise atomic structures will help in the exact
understanding of the properties at the nanoscale and in the fabrication and design of the nanomaterials for their many uses. Their
known inter-atomic distances have been used here to obtain the exact atomic radii of the component atoms and thereby their
precise atomic structures, for the first time. Considered here are three nanomaterials with hexagonal structures, but of quite
different properties, namely, graphene (an electrical conductor), boron nitride (an insulator) and coronene (indicators of life...
Tipo: Poster
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4357/version/1
Evaluation of diversity, specialization, and gene specificity in transcriptomes
Provedor de dados: 17
Autores: Octavio Martinez; Humberto Reyes-Valdés.
The transcriptome is a set of genes transcribed in a given tissue under specific conditions and can be characterized by a list of
genes with their corresponding frequencies of transcription. Transcriptome changes can be measured by counting gene tags from
mRNA libraries or by measuring light signals in DNA microarrays. Recently we proposed an approach to define and estimate the
diversity and specialization of transcriptomes and gene specificity. This approach can be useful for the determination and measure
of transcriptional networks. We defined transcriptome diversity as the Shannon entropy of its frequency distribution. Gene
specificity is defined as the mutual information between the tissues and the corresponding transcript, allowing detection of either...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3012/version/1
Time Trends for Agricultural Crop Production in Saskatchewan, Canada: 1905-2011
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Saskatchewan, Canada, with a total land area of 651,900 km^2^, is one of the world’s most productive agricultural
cropping regions. Approximately 44% of Canada's total cultivated farmland is in the province. In 2008, the total
export value of crops was CAD$8.34 billion. Over the past century, changing industry economics and advances in scientific,
technical, and engineering knowledge and practices have affected the amount and type of crops produced. The current work
examines time trends for agricultural crop production since Saskatchewan was created in 1905. While yields of all crops have
generally increased over time, total production trends vary widely by crop, warranting more detailed investigations into the
socio-economical and...
Tipo: Poster
Palavras-chave: Earth & Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6712/version/1
Epitopes in ChEBI - A Collaboration with the IEDB
Provedor de dados: 17
Autores: Zara Josephs; Marcus Ennis; Steve Turner; Gareth Owen; Bjoern Peters; Randi Vita; Christoph Steinbeck.
*ChEBI background:* Chemical Entities of Biological Interest (ChEBI) is a curated database of small chemical entities important
in biosystems. As well as a description of entities, it provides a semantically rich knowledge base; and an internal hierarchy that
organises
the
entities
by
their
molecular
structure
types
and
potential
rôles.

*The ChEBI-IEDB collaboration:* The Immune Epitope and
Analysis Resource (IEDB) is a project supported by contract from the National Institute of Allergy and Infectious Diseases
(NIAID). Its goal is to make epitope-related data on infectious diseases and immune disorders freely available to researchers
worldwide. In June 2009, ChEBI began working with the IEDB on a project aimed...
Tipo: Poster
Palavras-chave: Chemistry; Immunology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5094/version/1
Grofit: Fitting biological growth curves
Provedor de dados: 17
Autores: Matthias Kahm; Guido Hasenbrink; Hella Lichtenberg-Frate; Jost Ludwig; Maik Kschischo.
Growth experiments are routinely used to analyze basic properties of a given organism or cellular model. Similarly, within the
TRANSLUCENT project the characterization of cellular growth and particularly under conditions of high extra cellular potassium
or sodium is an important task. Any growth analysis should ideally reveal a relationship between the concentration of a
compound/substrate and its effect on a particular growth parameter. In view of the quite labor intensive analysis of hundreds of
growth curves - sometimes not revealing ideal relationships - the Grofit-software was developed to support biologists and such
approaches. Within the software package, specifically tailored regression and bootstrapping techniques are utilized to
statistically...
Tipo: Poster
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4508/version/1
QSAR studies on Withanolide analogs for anticancer activity
Provedor de dados: 17
Autores: Dharmendra Kumar Yadav; Feroz Khan; Rajender S. Sangwan.
Withanolides are a group of pharmacologically active compounds present in most prodigal amounts in roots and leaves of
Withania somnifera (Indian ginseng), one of the most important medicinal plants of Indian systems of medicine. Withanolides are
basically steroidal lactones (highly oxygenated C-28 phytochemicals) and similar to ginsenosides activity. Some of the
withanolides that have been reported possess immunomodulatory, and anticancer activities. In the present investigation, a
quantitative structure activity relationship (QSAR) model based on forward stepwise multiple linear regression (MLR) has been
developed against the MCF7, MCF7/BUS, and SK-Br-3 human solid tumor breast cancer cell lines. Relationship correlation
coefficient (r2) and cross...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6617/version/1
The Hymenoptera Genome Database
Provedor de dados: 17
Autores: Monica C. Munoz-Torres; Justin T. Reese; Christopher P. Childers; Anna K. Bennett; Jaideep P. Sundaram; Donald C.
Vile; Christine G. Elsik.
The Hymenoptera Genome Database (HGD) is an informatics resource supporting genomics of hymenopteran insect species. This
relational database implements open-source software and components providing access to curated data contributed by an
extensive, active research community. HGD includes the genome sequences and annotation data of honey bee _Apis mellifera_
and its pathogens ("http://BeeBase.org":BeeBase.org) the parasitoid wasp _Nasonia vitripennis_
("http://NasoniaBase.org":NasoniaBase.org) and a portal to the genomes of six species of ants. Together,
these species cover approximately 200 MY in the phylogeny of Hymenoptera, allowing to leverage genetic, genome sequence,
and gene expression data, as well as the...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5182/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
VO: Vaccine Ontology
Provedor de dados: 17
Autores: Yongqun He; Lindsay Cowell; Alexander D. Diehl; Harry Mobley; Bjoern Peters; Alan Ruttenberg; Richard H.
Scheuermann; Ryan R. Brinkman; Melanie Courtot; Chris Mungall; Zuoshuang Xiang; Fang Chen; Thomas Todd; Lesley
Colby; Howard Rush; Trish Whetzel; Mark A. Musen; Brian D. Athey; Gilbert S. Omenn; Barry Smith.
Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes
with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of
tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet
different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about
varied vaccine types and resources, and support advanced vaccine data analysis and inference. To address these problems, the
community-based Vaccine Ontology (VO,...
Tipo: Poster
Palavras-chave: Biotechnology; Immunology; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3552/version/1
Estimation of oxidative status in lymphocytes of type2 diabetes mellitus patients
Provedor de dados: 17
Autores: Awadhesh K Arya; Kamlakar Tripathi.
Introduction: Diabetes mellitus (DM) is a group of metabolic disorders which opens the door for many diseases leading to various
complications like neuropathy, nephropathy and retinopathy. Type 2 diabetes mellitus (T2DM) is associated with elevated level of
oxidative stress, which is one of the most important factors responsible for the development of chronic complications of this
disease. Antioxidants like reduced glutathione (GSH), superoxide dismutase (SOD) and catalase protects cells against oxidative
damage.

Purpose: Our present study suggests that hyperglycemia induced oxidative
stress leads to various complications in T2DM patients. Here we investigated oxidative stress markers in lymphocytes of healthy
control and...
Tipo: Poster
Palavras-chave: Immunology.
Ano: 2011
URL: http://precedings.nature.com/documents/5975/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
Mathematical Modeling of the Neuronal Processes in Sugar Addiction
Provedor de dados: 17
Autores: Andre Almeida; Hamed Celaymanian; Natalie Seel; Boris Zak; Hamid R. Noori.
It has already been demonstrated that the body responds to enhanced intake of sugar and is conducive to a natural form of
addiction. There are substantial neurochemical changes in the brain (especially dopamine and acetylcholine systems) similar to
other addictive drugs. A mathematical model comprised by a system of delayed leaky integrate-and-re equations is
established to simulate the effects of sugar on a reward-circuitry. Simulations with Neuron suggest agreement with the
neurobiological hypotheses of hyperactivity of neural systems due to binge sugar intake.
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5546/version/2
Envisioning a data reuse registry
Provedor de dados: 17
Autores: Heather A. Piwowar; Wendy W. Chapman.
Repurposing research data holds many benefits for the advancement of biomedicine, yet is very difficult to measure and evaluate.
We propose a data reuse registry to maintain links between primary research datasets and studies that reuse this data. Such a
resource could help recognize investigators whose work is reused, illuminate aspects of reusability, and evaluate policies designed
to encourage data sharing and reuse.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2152/version/1
Soil extracellular enzyme activities from a forest harvest and climate manipulation experiment in
central Pennsylvania
Provedor de dados: 17
Autores: Marshall D. McDaniel; Jason P. Kaye; Mary Ann V. Bruns; Margot W. Kaye.
We have previously shown that warming and wetting a post-harvest forest soil increased C and N mineralization rates. A series
of interacting processes may lead to these observed patterns including shifts in microbial allocation among extracellular enzymes.
We monitored soil extracellular enzyme activity (EEA) for 2.5 years in a post-harvest, climate manipulated field experiment. A 2
ha forest in Central Pennsylvania was whole-tree harvested in 2007 and climate manipulations of +2 °C (warmed), and
+20% mean monthly historical precipitation (wetted) were added to plots and in combination in a factorial design. The following
enzymes were quantified: β-1,4-glucosidase (BG), cellobiohydrolase (CBH), leucine aminopeptidase (LA),...
Tipo: Poster
Palavras-chave: Ecology; Microbiology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6254/version/1
Learning Features of Simple and Complex Cells: A Generative Approach via Multiplicative
Interactions
Provedor de dados: 17
Autores: Wentao Huang; Zhengping Ji; Garrett Kenyon.
We develop a hierarchical generative model to learn features of simple and complex cells in the primary visual cortex via
multiplicative interactions and address the problem of learning invariant visual representation from natural image sequences.
Generally, the overall objective of a generative sparse coding model (Olshausen and Field, Nature, 1996) is to reconstruct the
input *x* via a linear combination of feature bases *A = [A~1~,A~2~,...,A~M~]*, such that *x = As*, where s is the latent
representation with a sparse constraint. 
In the proposed model, we added another hidden layer with
complex cells to modulate the latent representation *s*, such that *s* is generated via an element-wise product of bottom-up
representation
*y =...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5943/version/1
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
Functional aspects of titanosaur osteoderms
Provedor de dados: 17
Autores: Thiago S. Marinho.
Though titanosaur osteoderms are not common findings, these elements are recorded widely in Gondwana and part of Laurasia.
This assembly known by the date offers few resources for studies on the ecology of this group of dinosaurs. Recently, some eggs
bearing titanosaur embryos with preserved skin, from Patagonia, Argentina, may shed some light on the function and disposition
pattern of these dermic bones. Some of the skin patches associated with the titanosaur embryos show two distinct patterns of
tuberosities: a longitudinal row and rosettes, both composed of closely attached tuberosities. These tuberosities do not seem to be
ossified, but this might be due to the ontogenetic stage of the titanosaurs. Here we propose that these tuberosities might have...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/508/version/1
The Gene Ontology Annotation (GOA) Database
Provedor de dados: 17
Autores: Rachael Huntley; Emily Dimmer; Daniel Barrell; David Binns; Rolf Apweiler.
The Gene Ontology (GO) is a well-established, structured vocabulary that has been successfully used for 10 years in the
annotation of proteins. GO terms, created in consultation with the biology community, are used to replace the multiple
nomenclatures used by scientific databases that can hamper data integration. Currently GO consists of more than 26,500 terms
distributed over three ontologies that describe the molecular function, biological process and subcellular location of a protein in a
generic
cell.

The
Gene
Ontology
Annotation
(GOA)
database
("http://www.ebi.ac.uk/GOA":http://www.ebi.ac.uk/GOA) aims to provide high-quality manual and
electronic GO annotations to proteins within the UniProt...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3154/version/1
Transgene effects on rhizodeposition: Evidence from molecular-chemical screening by Pyrolysis-Field
Ionisation Mass Spectrometry (Py-FIMS)
Provedor de dados: 17
Autores: Andre Schlichting; Christel Baum; Dana Zimmer; Peter Leinweber.
Rhizodeposition plays an important role in the C and N cycle of ecosystems, since it essentially reflects the interaction between
plant, soil and soil microorganisms. The molecular-chemical characterisation of rhizodeposition is often limited to selected
compound classes (e.g., carbohydrates and amino acids). A more comprehensive analytical approach is based on the
molecular-chemical “fingerprint” revealed by Pyrolysis-Field Ionisation Mass Spectrometry
(Py-FIMS).

The presented results give evidence of specific effects in conjunction
with soil type, crop, variety, transgenes and mycorrhizal colonisation on the molecular-chemical composition of rhizodeposition.
The experiments included various crops...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4440/version/1
Telomeres in Evolution and Development from Biosemiotic Perspective
Provedor de dados: 17
Autores: Guenther Witzany.
Whereas telomeres protect terminal ends of linear chromosomes, telomerases identify natural chromosome ends being different
from broken DNA. Although telomeres play a crucial role in the linear chromosome organisation of eukaryotic cells, their
molecular syntax descended from an ancient retroviral competence. This is an indicator for the early retroviral colonization of
large
double
stranded
DNA
viruses,
which
are
putative
ancestors
of
the
eukaryotic
nucleus.

This contribution will demonstrate an advantage of the biosemiotic approach
towards our evolutionary understanding of telomeres: focus on the genetic/genomic structures as language-like text which follows
combinatorial (syntactic), context-sensitive (pragmatic) and...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/932/version/2
Inhibiton of NFκB activation and aromatase activity by vanilloids: An in vitro and in
silico study
Provedor de dados: 17
Autores: Suaib Luqman; Abha Meena; Laura E. Marler; Tamara P. Kondratyuk; John M. Pezzuto.
Target-specific drugs, including natural products, offer promise for the amelioration of cancer and other human ailments with
reduced side-effects. Capsaicin, the pungent ingredient present in chillies (Capsicum annuum L.), and capsazepine, a synthetic
analogue of capsaicin (collectively referred to as vanilloids), are known to possess a variety of pharmacological and physiological
properties. In our continuous effort to discover cancer chemopreventive agents from natural products, we investigated the effect of
vanilloids on NFκB activation with stably transfected 293/NFκB-Luc human embryonic kidney cells
induced by treatment with tumor necrosis factor (TNFα), and aromatase activity. Capsaicin and capsazepine
blocked...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6913/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
The Trend of Wildlife Habitat Isolation due to the Development on Adjacent Areas of the Jirisan
National Park in Korea
Provedor de dados: 17
Autores: Sunghyun Lim; Chonghwa Park.
Background/Objectives/Methods
Jirisan national park (IUCN status 2) is the first national park (1967) and
the biggest national park (472km^2^) in Korea. In the first trial on the species restoration, since 2004, Asiatic Black Bears (Ursus
thibetanus ussuricus) reintroduced from North Korea and Russia have been conserved in the park. Development activities around
the Jirisan national park (JNP) have been isolating the habitat for many wildlife species. The objectives of this study are to
identify the trend of wildlife habitat isolation caused by the development activities in areas adjacent to the JNP, analyze the trend
of habitat fragmentation by using selected fragmentation indices and discuss landscape ecological implications of habitat...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3735/version/1
The relative importance of stabilizing mechanisms of coexistence
Provedor de dados: 17
Autores: Glenda M. Yenni; Xiao Xiao.
*Background/Question/Methods* 
Stabilizing mechanisms of coexistence, by definition, cause a species to
experience greater intraspecific competition than interspecific. This results in negative frequency-dependent growth rates for that
species causing a negative relationship between its relative frequency in the community and its growth rate in the next year. The
most crucial aspect of this negative relationship for persistence is that it enables a species to increase when rare. This has been
empirically demonstrated for pairwise interactions. However, in species-rich communities, the effects of competition are not
realistically pairwise. In cases where multiple species are competing for a resource, stabilizing mechanisms become...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3762/version/1
Exploring hidden dimensions of soil fungal biodiversity: A simple technique to detect soil fungi
resistant to antifungal compounds
Provedor de dados: 17
Autores: Sonashia Velho-Pereira; Nandkumar M. Kamat.
Soils are known to be ultimate and complex reservoirs of microbial diversity. The complex dimensions of bacterial and fungal
diversity in tropical soils and microbial community dynamics are underexplored. Isolation techniques aimed at Actinomycetes
generally employ highly selective media, powerful antibiotics and antifungal compounds to suppress undesirable bacteria and
fungi. However some soil fungi may show their resistance towards these antifungal compounds. During our work to explore soil
actinomycetes diversity, slides coated with Arginine Vitamin agar (AVA) incorporating a cocktail of antibiotics and antifungal
compounds such as Nystatin, Cycloheximide, Terbinafin, Griseofulvin, and Fluconazole were exposed to soil environment and
were retrieved at...
Tipo: Poster
Palavras-chave: Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4208/version/1
Towards reproducible MSMS data preprocessing, quality control and quantification
Provedor de dados: 17
Autores: Laurent Gatto; Kathryn S. Lilley.
The development of MSnbase aims at providing researchers dealing with labelled quantitative proteomics data with a transparent,
portable, extensible and open-source collaborative framework to easily manipulate and analyse MS2-level raw tandem mass
spectrometry data. The implementation in R gives users and developers a great variety of powerful tools to be used in a controlled
and reproducible way. Furthermore, MSnbase has been developed following an object-oriented programming paradigm: all
information that is manipulated by the user is encapsulated in ad hoc data containers to hide it's underlying
complexity. We illustrate the usage and achievements of our software using a published spiked-in data set in which varying
quantities of test proteins...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5010/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
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
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
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
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
Ontology for Biomedical Investigations
Provedor de dados: 17
Autores: Bjoern Peters; The OBI Consortium.
The goal of OBI is to enable a formal representation of biomedical investigations that captures the experimental evidence on
which their findings are based. The scope of OBI includes: materials made in and produced for investigations, research objectives,
experimental protocols, roles of people in investigations and processing and publication of data gathered in investigations. Use of
OBI will allow comparison of experimental data from the wide array of scientific disciplines represented by domain experts in the
OBI consortium. OBI follows the principles laid out by the OBO foundry, and integrates tightly with other foundry candidate
ontologies, such as GO (www.geneontology.org) and ChEBI (www.ebi.ac.uk/chebi/) whose terms are used to describe
biological...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3623/version/1
TMS, phosphenes and visual mental imagery: A mini-review and a theoretical framework
Provedor de dados: 17
Autores: Istvan Bokkon; Matthew Kirby; Amedeo D'Angiulli.
We reviewed the existing research linking visual mental imagery and phosphenes induced by TMS. We examined and contrasted
conditions (and parameters) under which intensity and amplitude of TMS application at various cortical sites along the ventral and
dorsal visual pathways: 1) induces the experience of visual images during perception and mental imagery, 2) interferes with or
facilitates perception and/or imagery in concurrent and dual task conditions, 3) correlates with self-reports such as vividness
ratings, and 4) reduces or has other selective effects on phosphene threshold in concomitance with perception and imagery. We
propose an interpretation of the results of this mini-review within a new biophysical framework for visual mental imagery based
on...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3244/version/1
Pre and post fire carbon dynamics in a Florida Scrub oak
Provedor de dados: 17
Autores: Rosvel Bracho; Cassondra Thomas; Jiahong Li; Thomas Powell; C. Ross Hinkle.
Scrub oak is a xeromorphic shrub ecosystem discontinuously distributed in coastal and inland Florida. It supports a high
biodiversity which includes a large number of endangered and threatened species. Its structural features are maintained by a fire
return cycle of 7 to 10 years which maintains the biodiversity. Management of fire prone ecosystems such as this raises the
question of whether the management strategy contributes to the system being a carbon sink or carbon source over the long-term.
We used eddy covariance and biometric approaches to measure carbon dynamics in a Florida scrub oak ecosystem located at
Kennedy Space Center in east Central Florida from April 2004 to December 2007. The study site was controlled burned in
February 2006. Two...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5223/version/1
Effects of habitat, microsite and seed density on recruitment limitation in native scrubland and scrub
undergoing restoration
Provedor de dados: 17
Autores: Elizabeth L. Stephens; Pedro F. Quintana-Ascencio; Maliha Beg.
*Background/Questions/Methods*
Recruitment influences population and community dynamics by
determining the replacement of older individuals, decreasing population expansion and reducing/excluding a species from a
community. There is insufficient information on the relative importance of mechanisms affecting seed availability and how
interactions between recruitment limitation, other life history stages and environmental variables affect plant demography. Seed
availability is pertinent to restoration projects, in which the establishment of native plant populations is a priority. We hypothesize
that seed and seedling dynamics are affected by seed production, predation, and microsite characteristics, which may differ among
habitats with...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3629/version/1
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
In-silico identification of potential antagonists for human Casein kinase II subunit alpha'
(CK2α2)
Provedor de dados: 17
Autores: Kanipakam Hema; Harika Meduru; Navya Pallapotu; Amineni Umamaheswari.
Human CK2α2 is an enzyme that belongs to the Serine/Threonine protein kinase family which is involved in signal
transduction. Over expression of CK2α2 causes kidney cancer therefore, human CK2α2 has been
identified as a drug target for the development of potential antagonists against cancer therapy. The existing human
CK2α2 inhibitors in clinical practice are having side effects like fatigue, diarrhea, nausea, anorexia and vomiting.
High-throughput virtual screening is one of the most common method used to identify lead compounds was implemented in the
present study to identify potential inhibitors of human CK2α2. The co-crystal structure of human CK2α2
was retrieved from the protein data bank. A...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6958/version/1
In-silico analysis of human IGFBP-4 involved in cardiovascular diseases
Provedor de dados: 17
Autores: Manne MuniKumar; Kavali Roopesh; Amineni Umamaheswari.
Cardiovascular disease is the major cause of disability and premature death throughout the world and contributes substantially to
the escalating costs of health care. Insulin like growth factor binding protein 4 (IGFBP-4) mainly belongs to the family of IGFB
protein. Over expression of IGFBP-4 leads to cardiovascular diseases namely stroke, acute myocardial infarction and heart failure.
IGFBP-4 serves as an effective drug target against cardiovascular disease. Hence, ligand based virtual screening was pursued in
the present study to propose potential inhibitors of IGFBP-4. Two published inhibitors were selected to initiate high throughput
virtual screening from small molecule databases namely, NCI, ChemBank, ChemPDB, AKos GmbH, Asinex Ltd and KEGG
ligand....
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6567/version/1
GENCODE: Creating a Validated Manually Annotated Geneset for the Whole Human Genome
Provedor de dados: 17
Autores: A. Bignell; A. Frankish; B. Aken; M. Diekhans; F. Kokocinski; M. Lin; M. Tress; J. Van Baren; I. Barnes; T. Hunt; D.
Carvalho-Silva; C. Davidson; S. Donaldson; J. Gilbert; E. Hart; M. Kay; R. Kinsella; D. Lloyd; J. Loveland; J. E. Mudge; C.
Snow; J. Vamathevan; L. Wilming; M. Brent; M. Gerstein; R. Guigó; R. Harte; M. Kellis; S. Searle; J. Harrow; T.
Hubbard.
The Human and Vertebrate Analysis and Annotation (HAVANA) group at the Wellcome Trust Sanger Institute produced the
manually annotated geneset for the Encyclopedia of DNA Elements (ENCODE) pilot project and, as part of the Gencode
subgroup, are reprising this role in the scale up to cover the whole human genome. Our manual annotation is checked
computationally and validated experimentally. Loci and transcripts predicted to be absent from the initial annotation are identified
by comparison with a number of state-of-the-art algorithms for identifying exons, splice sites, transcripts and pseudogenes. Where
novel features are confirmed the annotation is updated. Annotated coding transcripts are analysed to assess their coding potential
by investigating...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3155/version/1
Studies in preparation of banana wine (fruit wine)
Provedor de dados: 17
Autores: Surajbhan Sevda; Pramod Khartmol; Lambert Rodrigues.
Banana is a tropical fruit, which is grown abundantly in India. It is mainly composed of soluble sugars, starch and other
polysaccharides. The juice was extracted from the normal ripe fruits with the help of pectinase enzyme. Optimization of pectinase
treatment was done by RSM method. Wine was prepared by using two strains of Saccharomyces cerevisiae NCIM 3283
& NCIM 3046. The size of inoculum, effective pH, temperature, level of SO2 , level of DAP for both strains was
optimized. It was found that NCIM 3046 gave better results compared to the other strain. Soluble solids (SS), pH and specific
gravity decreased while titratable acidity (TA) increased with increasing length of fermentation of the juice. Sensory evaluation
results showed that banana...
Tipo: Poster
Palavras-chave: Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/5774/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
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
Robust information from phylogenetic trees?
Provedor de dados: 17
Autores: Carl Boettiger.
Traditional information criteria approaches can lead to misleading model choice in comparative phylogenetics. I present both
these weaknesses and a more robust comparison by likelihood ratio. I then discuss a new class of models to capture the transition
process between evolutionary regimes.
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4614/version/1
Potential effects of pollen from stacked Bt maize on non-target Lepidoptera in agrarian systems
Provedor de dados: 17
Autores: Mechthild Schuppener; Alan J. Slusarenko; Stefan Rauschen.
The cultivation of genetically engineered (GE) maize expressing Lepidopteran specific Bt proteins poses potential risk for
non-target butterflies. Pollen is dispersed by wind in the surroundings of maize fields, deposited on weeds and taken up by
non-target butterfly lavae. While MON810 contains low concentrations of Bt protein in pollen, this is not necessarily true for new
GE maize lines.

Species appropriate for a post market environmental monitoring
(PMEM) should (i) have a small host range to ensure a comprehensive inventory, (ii) be representative and (iii) be common in
agrarian landscapes. Rare species seem to be inappropriate (Aviron et al. 2009). We selected the Small Tortoiseshell (_Aglais
urticae_) and the...
Tipo: Poster
Palavras-chave: Earth & Environment; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4491/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 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
The Synthesis and Characterization of New, Robust Titanium (IV) Scorpionate Complexes
Provedor de dados: 17
Autores: Jared J. Gerschler-Zia; James F. Dunne; Aaron D. Sadow.
Titanium complexes possessing sterically encumbered ligands have allowed for the preparation of reactive moieties (imido,
alkylidene and alkylidyne species) relevant to reactions such as olefin polymerization and alkyne hydroamination. For this reason,
we have targeted robust scorpionate ancillary ligands to support reactive titanium centers. Thus, a series of titanium complexes
were synthesized using an achiral oxazoline-based scorpionate ligand, tris(4,4-dimethyl-2-oxazolinyl)phenyl borate [To^M^]^-^
as well as the related chiral ligand, tris(4-isopropyl-2-oxazolinyl)phenyl borate [To^P^]^-^. The complex [Ti(κ^3^To^M^)Cl~3~] was prepared in moderate yield (43%) by the rapid (<1 min at room temperature) reaction of
Li[To^M^] and...
Tipo: Poster
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4763/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
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
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
LifeWatch – A European e-Science and observatory infrastructure supporting access
and use of biodiversity and ecosystem data
Provedor de dados: 17
Autores: Mark Frenzel; Stefan Klotz; Alex Hardisty; Olaf Banki.
There are many promising earth and biodiversity-monitoring projects underway across the globe, but they often operate in
information islands, unable easily to share data with others. This is not convenient: It is a barrier to scientists collaborating on
complex,
cross-disciplinary
projects
which
is
an
essential
nature
of
biodiversity
research.


LifeWatch (www.lifewatch.eu) is an ESFRI (European Strategy Forum on Research
Infrastructures) initiative which has just entered its construction phase. It is aiming at new ways of collaboration, in an
open-access research environment to solve complex societal and scientific questions on biodiversity and ecosystems. It installs a
range of new services and tools to help the...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5843/version/1
Plant Transcription Factors @ uni-potsdam.de
Provedor de dados: 17
Autores: Diego Mauricio Riaño-Pachón; Ingo Dreyer; Slobodan Ruzicic; Bernd Mueller-Roeber.
We present the Plant Transcription Factor Database (PlnTFDB), and the putative complete set of TFs in the algae
_Chlamydomonas reinhardtii_, _Ostreococcus tauri_ and the vascular plants _Oryza sativa_ and _Arabidopsis thaliana_.
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/243/version/1
Soil Disturbance Increases Soil Microbial Enzymatic Activity in Arid Ecoregions
Provedor de dados: 17
Autores: Lori Kae Schwab-Uchanski; Adrian Unc; Mary Lucero.
Functional diversity of the soil microbial community is commonly used in the assessment of soil health as it relates to the activity
of soil microflora involved in carbon cycling. Soil microbes in different microenvironments will have varying responses to
different substrates, thus catabolic fingerprint information of each location-specific community can be obtained. The purpose of
this study was to evaluate total-soil enzymatic activity profiles across three disturbance regimes in an arid desert grassland in the
Southwestern United States. Microbial enzymatic activity was measured using the MicroResp™ system, which
measures respiration of microbes within whole soil samples supplemented with various carbon sources (simple and polymeric
sugars,...
Tipo: Poster
Palavras-chave: Ecology; Microbiology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6202/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
ECoG-based short-range recurrent stimulation techniques to stabilize tissue at risk of progressive
damage: Theory based on clinical observations
Provedor de dados: 17
Autores: Markus A. Dahlem; Felix M. Schneider; Jens P. Dreier; Anthony J. Strong; Eckehard Schoell.
We introduce theoretical concepts based on chaos control to stabilize in acute stroke the tissue at risk of progressive damage by
preventing adverse effects of waves of mass neuronal depolarization. Moreover, we present clinical electrocorticography (ECoG)
recordings of relevant signals suggested for the feedback control. The recordings are performed in combination with novel
subdural opto-electrode technology for simultaneous laser-Doppler flowmetry in patients with aneurysmal subarachnoid
haemorrhage (aSAH). In aSAH patients waves of spreading depolarization (SD) have a high incidence and cause hypoxia in tissue
at risk, and, importantly, the haemodynamic response is the inverse of that seen in healthy tissue. In previous clinical studies,
clusters of...
Tipo: Poster
Palavras-chave: Biotechnology; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3408/version/1
In-silico Predictive Mutagenicity Model Generation Using Supervised Learning Approaches
Provedor de dados: 17
Autores: Anurag Passi; Abhik Seal; OSDD Consortium; UC Abdul Jaleel.
With the advent of High Throughput Screening techniques, it is feasible to filter possible leads from a mammoth chemical space
that can act against a particular target and inhibit its action. Virtual screening complements the in-vitro assays which are costly
and time consuming. This process is used to sort biologically active molecules by utilizing the structural and chemical information
of the compounds and the target proteins in order to screen potential hits. Various data mining and machine learning tools utilize
Molecular Descriptors through the knowledge discovery process using classifier algorithms that classify the potentially active hits
for the drug development process.

Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6116/version/1
Theory of the Origin, Evolution, and Nature of Life
Provedor de dados: 17
Autores: Erik D. Andrulis.
Life is an inordinately complex unsolved puzzle. Despite significant theoretical progress, experimental anomalies, paradoxes, and
enigmas have revealed paradigmatic limitations. Thus, the advancement of scientific understanding requires new models that
resolve fundamental problems. Here, I present a theoretical framework that economically fits evidence accumulated from
examinations of life. This theory is based upon a straightforward and non-mathematical core model and proposes unique yet
empirically consistent explanations for major phenomena including, but not limited to quantum gravity, phase transitions of water,
why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of
sugars and...
Tipo: Poster
Palavras-chave: Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7050/version/1
The Evolution Ontology
Provedor de dados: 17
Autores: Adam M. Goldstein.
Existing ontologies model components of evolution, but none synthesize them or describe the framework of ideas used to
conceptualize evolution. The Evolution Ontology (EO) aims to do just this. EO models processes (e.g. natural selection); contexts
(e.g. habitats); the entities that undergo evolution; and the theories, methods, and disciplines of evolutionary science. Uses include
data curation, data mining, and literature curation, EO’s developers working on the latter two for works of Darwin
and the Biodiversity Heritage Library.
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3557/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
coli_.

*Introduction*
Phenotypes
organism
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
The Differences Between Products Of Gene Expression In Male, Female And Hermaphrodite
Cucumber Floral Buds (Cucumis Sativus L.)
Provedor de dados: 17
Autores: Magdalena Pawelkowicz; Ewa Siedlecka; Zbigniew Przybecki.
Cucumber is a species in which sex expression has been extensively studied. Sexual differentiation is controlled by genotypic and
environmental factors. The main genes responsible for sex determination have been described but the mechanism of their action
remains unexplained. In this study we attempted to find cDNA clones which can be connected with sex differentiation and flower
development
in cucumber. 
Two pairs of nearly isogenic lines: GY-3 (gynoecious –
FFMMGG) and HGY-3 (hermaphrodite - FFmmGG), B10 (monoecious - ffMMGG) and 2gg (gynoecious - FFMMgg) were used
to search for differences in gene expression in young (1 – 2mm) cucumber floral buds.
In
order to obtain differentially expressed cDNA...
Tipo: Poster
Palavras-chave: Biotechnology; Developmental Biology; Genetics & Genomics; Molecular Cell Biology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5605/version/1
Linking stoichiometric homeostasis with ecosystem structure, functioning, and stability
Provedor de dados: 17
Autores: Qiang Yu; Quansheng Chen; James Elser; Arianne Cease; Nianpeng He; Honghui Wu; Guangming Zhang; Jianguo
Wu; Yongfei Bai; Xingguo Han.
Ecosystem structure, functioning, and stability have been a focus of ecological and environmental sciences during the past two
decades. The mechanisms underlying their relationship, however, are not well understood. Based on comprehensive studies in
Inner Mongolia grassland, here we show that species-level stoichiometric homeostasis was consistently positively correlated with
dominance and stability on both 2-year and 27-year temporal scales and across a 1200-km spatial transect. At the community
level, stoichiometric homeostasis was also positively correlated with ecosystem function and stability in most cases. Thus,
homeostatic species tend to have high and stable biomass; and ecosystems dominated by more homeostatic species have higher
productivity...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5255/version/1
Docking studies to explore novel lead molecules for human Spleen tyrosine kinase involved in chronic
lymphocytic leukemia
Provedor de dados: 17
Autores: Naveen Kadaari; Dibyabhaba Pradhan; Manne Munikumar; Amineni Umamaheswari.
B-cell chronic lymphocytic leukemia (CLL) is the most prevalent B-cell malignancy in adults. Despite advances in treatment, the
disease remains incurable, warranting further efforts to identify novel molecular targets and inhibitors. Spleen tyrosine kinase
(SYK) plays a pivotal role for B-lymphocyte development and maturation in the B-cell receptor (BCR) signaling pathway and
hence represents a potential therapeutic target for CLL. The present study is directed towards finding novel inhibitors of SYK
through ligand based virtual screening. The co-crystal structure of SYK was investigated to locate active site residues (Glu-449,
Ala-451 Arg-498, Asn-499, Ser-511, and Asp-512). Five SYK specific published inhibitors (Gleevec, staurosporine, Bay61-3606,
R-406...
Tipo: Poster
Palavras-chave: Cancer; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5460/version/1
Pendent Drops at Elevated P & T
Provedor de dados: 17
Autores: Apostolos Georgiadis; Geoffrey Maitland; Martin Trusler; Sergei Kazarian; Alexander Bismarck.
Within the scope of producing clean fossil fuels by simultaneously tackling greenhouse gas emissions, the interfacial tension of
partially miscible phases containing CO~2~ is being investigated with the pendant drop method. Emphasis is given to
measurements at elevated pressures and temperatures, analogous to reservoir conditions. A high pressure apparatus consisting of a
view cell and high pressure capillary fittings is used for creating pendent drops at the desired conditions. A computer aided Drop
Shape Analysis system is used for capturing images of such drops, which are then analysed for the interfacial tension calculation
of the two phases with the KRUSS DSA software. The results acquired from the initial measurements conducted for the
H~2~O/CO~2~...
Tipo: Poster
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2636/version/1
Identification and Evolution of Transcription Factors in Stramenopiles
Provedor de dados: 17
Autores: Francisco Buitrago; Silvia Restrepo; Diego Riaño-Pachón.
Transcription factors (TFs) regulate spatial and temporal gene expression by binding to DNA and either activating or repressing
the action of RNA polymerases; in addition to TFs, other transcriptional regulators (TRs) participate in transcriptional modulation.
With the availability of genome sequences for several organisms and computational strategies for gene functional annotation, the
entire set of TFs and TRs can be identified, described, and compared between species and lineages. The diversity among
Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they are present in freshwater,
marine and terrestrial habitats and embrace many ecologically important algal (e.g. diatoms, brown algae, chrysophytes), and...
Tipo: Poster
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6672/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
Identification of new leads for human IGFBP-2: a therapeutic target for cardiovascular diseases
Provedor de dados: 17
Autores: Kanipakam Hema; I Vani Priyadarshini; Amineni Umamaheswari.
IGFBP-2, the largest member of insulin-like growth factor binding proteins family, is under-expressed in hazardous
cardiovascular diseases like obesity and type II diabetes mellitus, which upon aging leads to heart stroke. Therefore, IGFBP-2 has
been proposed as a possible target for the development of novel leads for cardiovascular disease therapy. High-throughput virtual
screening, one of the most common methods used to identify lead compounds was implemented here to identify potential
IGFBP-2 activators. The NMR (nuclear magnetic resonance) structure of human IGFBP-2 was retrieved from the protein data
bank. A 2D similarity search was performed for known IGFBP-2 activator TPA to acquire 383 structural analogs. The 3D
structural conversion and multiple...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6570/version/1
Improvement of PubMed Literature Searching using Biomedical Ontology
Provedor de dados: 17
Autores: Zuoshuang Xiang; Yongqun He.
PubMed articles are annotated using the Medical Subject Headings (MeSH) to increase search efficiency. However, MeSH
contains limited information on many biomedical domains (e.g., vaccine). Biomedical ontologies may be used to improve
PubMed searching capability. This study demonstrates that Vaccine Ontology (VO) can be used to significantly improve PubMed
searching efficacy in the vaccine domain. The recall and precision of the ontology-based literature mining approach are analyzed
and discussed.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3491/version/1
Grid technology for collaborative ontology development
Provedor de dados: 17
Autores: Stuart Aitken; Kemian Dang; Jonathan Bard.
In contrast with the centrally-organised curation of the Gene Ontology, many biological ontologies are developed by
loosely-organised groups who develop their ontology remotely. These groups tend to be formed from scientists and
bio-informaticians from research groups with a common interest, who want to create a resource that will be useful to the
community, rather than being formally mandated. Until recently, technological support for bio-ontology development relied on
stand-alone editors running on users’ desk- tops for creating new ontology versions (e.g. OBO-Edit, COBrA and
Protégé) and on private email, email lists and perhaps Wikis for the distribution of ontology files and
discussions. Clearly, much better use could be...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3186/version/1
The Jena Library of Biological Macromolecules - JenaLib
Provedor de dados: 17
Autores: Rolf Huehne; Juergen Suehnel.
The JenaLib database ("www.fli-leibniz.de/IMAGE.html":http://www.fli-leibniz.de/IMAGE.html) offers
value-added information for all Protein Data Bank (PDB) and Nucleic Acid Database (NDB) entries. This
includes:
(1) atlas pages and entry lists, (2) PDB sequence information extracted from atomic coordinates,
(3) PDB/UniProt sequence alignments that clearly indicate gaps, mutations, numbering irregularities and modified residues, (4)
integration of data on single amino acid polymorphisms (SAPs), PROSITE motifs, exon structure and SCOP/CATH/Pfam
domains with PDB, GO and taxonomy information, (5) display of these data in the sequence/alignment viewer and in the
Jmol-based molecule viewer Jena3D...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3114/version/1
Protective effect of (-) α-bisabolol on markers of oxidative stress in erythrocytes subjected
to oxidative insult
Provedor de dados: 17
Autores: Suaib Luqman; Suchita Srivastava.
(-)-α-bisabolol is a sesquiterpene alcohol found as a major component of essential oil of chamomile (Matricaria
recutita L., Chamomilla recutita L., Matricaria chamomilla L.; Family Asteraceae). Chamomile, one of the most ancient and
widely recognized herbs to mankind, has been used traditionally for centuries as an anti-inflammatory, antispasmodic,
carminative, mild astringent and healing medicine. It is also known to be very helpful as an external agent for encouraging the
rapid healing of ulcers and burns without infection, as well as persistent skin problems such as eczema and psoriasis. Since
clinical trials and human studies are limited, we have investigated the effect of (-)-α-bisabolol on markers of oxidative
stress in human...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6903/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
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
Nuclear DNA and protein content evaluation in Taxus plant cell cultures using multiparameter flow
cytometry
Provedor de dados: 17
Autores: Vishal Gaurav; Amit Shavit; Susan C. Roberts.
Plant cell cultures of Taxus provide the most reliable production methods for the anti-cancer drug paclitaxel. In order to
comprehend the inherent culture heterogeneity and production variability in cell cultures, it is essential that the cellular
metabolism is studied at the genomic level. Genomic stability in plant cell cultures is crucial as it affects cell growth and division,
metabolite accumulation and protein synthesis. A rapid and efficient method to prepare nuclei suspensions from aggregated cell
cultures of Taxus was employed. Methods were subsequently developed to simultaneously stain them for DNA and protein
content using Propidium Iodide and Fluorescein Isothiocyanate respectively. Flow cytometry was used to analyze and quantify the
DNA...
Tipo: Poster
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics & Genomics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3809/version/1
Margarine products quality monitoring using reflectance UV-VIS-SWNIR spectroscopy
Provedor de dados: 17
Autores: Rui C. Martins; Vitor V. Lopes; António A. Vicente.
Margarine is a term that can indicate any of a wide range of butter substitutes. Due to the great diversity of the raw material,
margarine end-product quality characteristics are expected to be highly diversified. This article proposes the use of reflectance
UV-VIS-SWNIR spectroscopy to monitor the margarine end-product quality properties. The main effort in this work was the
development of a fast monitoring procedure to assess the quality of the manufactured margarines. 
The study
was performed on two margarine products: regular margarine (less than 80% fat) and reduced-fat margarine (less than 60% fat).
The nine product samples were collected during the production line normal operating conditions on different days. The samples
had the...
Tipo: Poster
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2293/version/1
Evidence attribution in the UniProt Knowledgebase
Provedor de dados: 17
Autores: Michele Magrane; UniProt Consortium.
UniProtKB provides the scientific community with a comprehensive collection of protein sequence records containing extensive
curated information including functional and sequence annotation. This information is derived from a variety of sources such as
scientific literature and sequence analysis programs as well as data imported from automatic annotation systems and external
databases. To allow users to ascertain the origin of each data item in a UniProtKB record, an evidence attribution system is being
introduced which links each piece of information to its original source. This system allows users to trace the origin of all
information, to differentiate easily between experimental and computational data, and to assess data reliability. The current
system...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3129/version/1
Multiple Ontologies for Integrating Complex Phenotype Datasets
Provedor de dados: 17
Autores: Mary Shimoyama; Melinda Dwinell; Howard Jacob.
There has been an emergence of multiple large scale phenotyping projects in the rat model organism community as well as
renewed interest in the ongoing phenotype data generated by thousands of researchers using hundreds of rat strains worldwide.
Unfortunately, this data is scattered and is neither described nor formatted in a standardized manner. A system to integrate
complex phenotype data from multiple sources and facilitate data mining and analysis is being developed using multiple
ontologies.

*Introduction*
The potential value of integrating
phenotype data from multiple sources (different laboratories, varying techniques to measure similar phenotypes, multiple strains)
is enormous. Presented here is...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3554/version/1
MSTd Neurons Encode Nonlinear Combinations of Retinal and Extra-retinal Signals
Provedor de dados: 17
Autores: Lukas Brostek.
Neuronal activity in the dorsal Medial Superior Temporal area (MSTd) is assumed to depend on both retinal and extra-retinal
input. Most of the neurons show activity when presented with a moving large-field visual stimulus. In addition, many MSTd
neurons are activated during smooth pursuit eye movements even in the absence of retinal input. However, the interaction between
the retinal and extra-retinal input is not yet fully understood.
Here we present novel insights regarding the
tuning of MSTd neurons for combinations of different input variables using an information-theoretic approach. Neuronal tuning
functions can be expressed by the conditional probability of observing a spike given any combination of input variables.
However,...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5938/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
Resolving Stressful Relationships in Prehistory: Macroscopic and Histological Indicators of Growth
Disruption in Subadult Long Bones
Provedor de dados: 17
Autores: Gwen Robbins.
This poster provides a set of quadratic formulas for predicting body mass using the femoral midshaft in subadult skeletons. This
age-structured method has lower %SEE and is more efficient than estimating body mass from the bone ends (Ruff, 2007). This
poster demonstrates that estimates of body mass in subadult skeletons can be compared with stature to look at biocultural stress
levels in prehistoric populations. Finally a qualitative assessment of histological markers of growth disruption is provided for
individuals that demonstrate low bone mass for body size.
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2471/version/1
RNA Vaccine: novel approach for cancer treatment
Provedor de dados: 17
Autores: L K Dwivedi; Prateeksha Goswami; Kanika Bhalla.
Cancer is still an unsolved puzzle and a major cause of mortality and morbidity in the world. Today, about one in every thousand
people is dying due to cancer. No effective agent has yet been found which can cure cancer in its metastatic stage. However,
attempts in the shape of chemotherapy, immunotherapy and vaccines are made worldwide to find a remedy through a proper
regimen. In continuation, tumor specific mRNA has been introduced as part of vaccines in recent days. It is mostly used in
transfection with Dendritic Cells (DCs) for better effectiveness and safety. The DCs are selected for transfection because they are
highly potent Antigen Presenting Cells (APCs) with the ability to take up & process tumor antigen in peripheral blood
&...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5949/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
Ten thousand times faster: Classifying multidimensional data on a spiking neuromorphic hardware
system.
Provedor de dados: 17
Autores: Michael Schmuker; Daniel Brüderle; Sven Schrader; Martin Nawrot.
Discrimination of sensory inputs is a computational task that biological neuronal systems perform very efficiently. Assessing the
principles in those systems is a promising approach to develop technical solutions for many problems, such as data classification.
A particular problem here is to train a classifier in a supervised fashion to discriminate classes in multidimensional data. We
implemented a network of spiking neurons that solves this task using a neuromorphic hardware system, that is, analog neuronal
circuits on a silicon substrate. This system enables us to do high-performance computation in a biologically inspired way, with
spiking neurons as computational units. In this contribution, we illustrate solutions to technical challenges that occur...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6547/version/1
Exposing WikiPathways as Linked Open Data
Provedor de dados: 17
Autores: Andra Waagmeester; Helena Deus; Chris T. Evelo.
Biology has become a data intensive science. Discovery of new biological facts increasingly relies on the ability to find and match
appropriate biological data. For instance for functional annotation of genes of interest or for identification of pathways affected by
over-expressed genes. Functional and pathway information about genes and proteins is typically distributed over a variety of
databases and the literature.

Pathways are a convenient, easy to interpret way to
describe known biological interactions. WikiPathways provides community curated pathways. WikiPathways users integrate
their knowledge with facts from the literature and biological databases. The curated pathway is then reviewed and possibly
corrected or...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6679/version/1
Occurrence of Gastroliths in _Baurusuchus_ (Baurusuchidae, Mesoeucrocodylia) from Adamantina
Formation, Bauru Basin
Provedor de dados: 17
Autores: Felipe M. Vasconcellos; Leonardo Morato; Thiago Marinho; Ismar S. Carvalho.
The fossil record of Baurusuchidae Mesoeucrocodylia in the General Salgado county and its surroundings is one of the best
regarding preservation, completeness and articulation of skull and skeleton remains, including specimens that shown even the
most delicate bone structures and cartilaginous tissues. 

One of them, UFRJ DG
288-R, has preserved its skull and about 80% of its skeleton. During the removal of the rock matrix, on what should be the
specimen’s abdominal region, together with fragments of gastralia were observed some small well-polished
weathered angulous to subrounded clasts, presumed to be gastroliths. 

These xenoliths
occur in a restrict cluster, where at least...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1950/version/1
Telomeres in Evolution and Development from Biosemiotic Perspective
Provedor de dados: 17
Autores: Guenther Witzany.
Telomeres identify natural chromosome ends being different from broken DNA through differences in their
"molecular syntax" (M.Eigen) which determines the functions of reverse transcriptase and its integrated
RNA template, telomerase. Although telomeres play a crucial role in the linear chromosome organization of eukaryotic cells, their
molecular syntax descended from an ancient retroviral competence. This is an indicator for the early retroviral colonization of
large double stranded DNA viruses, which are putative ancestors of the eukaryotic nucleus.
This talk will
demonstrate certain advantages of the biosemiotic approach towards our evolutionary understanding of telomeres: focus on the
genetic/genomic structures as...
Tipo: Poster
Palavras-chave: Developmental Biology; Ecology; Genetics & Genomics; Microbiology.
Ano: 2007
URL: http://precedings.nature.com/documents/932/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
Modeling Pinus edulis growth in a changing climate: Carbon dioxide, growing season length, and
precipitation
Provedor de dados: 17
Autores: Susannah Tysor; George Koch; Amy Whipple.
Background/Question/Methods
Pinus edulis (pinyon pine) is a foundation tree species in the southwestern
United States that has experienced high levels of mortality in a drought extending from the mid-1990s to the present. Despite
high mortality levels, radial growth of pinyon pine in northern Arizona over the past century shows an increasing trend not found
in four centuries of preindustrial growth. Atmospheric carbon dioxide concentration ([CO2]) shows a strong correlation with
recent radial growth, and a simple linear AR(1) model with only [CO2] as a covariate explains average yearly growth well. No
climate variable except [CO2] has a consistent long-term trend that accounts for increasing radial growth, but growing season
and...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5193/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
The dynamic consequences of invasion: negative plant-soil feedbacks on natives increase ver the time
course of invasion
Provedor de dados: 17
Autores: Elizabeth H. Schultheis; Jennifer A. Lau.
*a) Background/Questions/Methods*
Exotic species can negatively impact native community members,
directly through interference competition, or indirectly by altering interactions between native species and other species such as
pathogens and mutualists. Soil microbial communities have been shown to respond to invasive species, yet are relatively stable
and may take time to respond to perturbations. For this reason, microbe-mediated effects of invasives on natives may take time to
develop and may change throughout the invasion process. Few studies have investigated how species interactions between natives
and exotics change during invasions.

_Acer platanoides_ was introduced into the US
from Europe in 1756...
Tipo: Poster
Palavras-chave: Ecology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5192/version/1
p63, p73, & p53 are Negative Regulators of Epithelial to Mesenchymal Transition (EMT),
Invasion & Metastasis
Provedor de dados: 17
Autores: Lakshmanane Boominathan.
It has recently been shown that microRNAs, such as miRs-145,192, and 215, are regulated by the tumor suppressor p53 through
their p53REs. Considering miRs-145, 192, and 215 promoters contain p53REs suggests that they could be transcriptional targets
of p63 and p73 as well. Remarkably, bioinformatics analysis of miRs-145, 192, and 215 targets suggests that they target ZEB2,
suggesting that p53, p63, and p73 by increasing the expression of miRs-192, 215, & 145, they could inhibit the
expression of ZEB2. ZEB2 has been shown to function as a repressor of the tumor suppressor E-cadherin, suggesting that p53,
p73, and p63 by suppressing the expression of ZEB2 through their transcriptional target miRs, they could increase the expression
of E-cadherin....
Tipo: Poster
Palavras-chave: Cancer; Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4109/version/1
Just-in-time assembly of cell-cycle protein complexes
Provedor de dados: 17
Autores: Lars J. Jensen; Ulrik de Lichtenberg; Thomas S. Jensen; Søren Brunak; Peer Bork.
Our comparative analysis of eukaryotic cell-cycle complexes reveals that the identity of the periodically expressed subunits differs
significantly between organisms and is often mirrored by changes in cell-cycle-dependent phosphorylation of the protein products.
This indicates that many different solutions have evolved for just-in-time assembly of the same molecular machines.
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2273/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
Gene Expression Profiling of the Hepatic Transcriptome in Presence of TNF-alpha
Provedor de dados: 17
Autores: Amit Kumar Pandey; Neha Munjal; Malabika Datta.
Diabetes mellitus, often simply termed Diabetes, is a syndrome characterized by disordered metabolism and high blood sugar. It is
caused due to low levels of insulin hormone or from abnormal resistance to insulin in its target tissues. World Health Organization
estimates that India will alone have 79.4 million diabetic patients in 2030. One of its major form Type 2 diabetes, is often
associated with obesity, hypertension, elevated cholesterol and metabolic syndrome. Changes in life style, such as consumption of
high-calorie diet and lack of exercise, have increased the global prevalence not only of diabetes but also of obesity. Type 2
diabetes is characterized by insulin resistance in target tissue, occurs due to several reasons and one of them being the...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2527/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
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
Money handling influences BMI: a survey of cashiers
Provedor de dados: 17
Autores: Shraddha Karve; Ketaki Shurpali; Neelesh Dahanukar; Maithili Jog; Milind Watve.
Money is a recent phenomenon in the evolutionary history of man and therefore no separate brain centre to handle money is likely
to have evolved. The brain areas activated by food reward and money reward are extensively overlapping. In an experimental
set-up, hunger was demonstrated to influence money related decisions and money related thoughts to influence hunger. This
suggests that the brain areas evolved for handling food related emotions are exapted to handle money and therefore there could be
a neuronal cross-talk between food and money. If this is true then attitude and behavior related to money and wealth could
influence obesity. We conducted a survey of 211 individuals working as full time cashiers in order to test whether ownership over
the cash,...
Tipo: Poster
Palavras-chave: Developmental Biology; Ecology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2708/version/1
PlnTFDB: Plant Transcription Factor Database – Update
Provedor de dados: 17
Autores: Diego Mauricio Riaño-Pachón; Luiz Gustavo Guedes Correa; Bernd Mueller-Roeber.
PlnTFDB is a publicly available computational resource comprising putative complete sets of transcription factors from plants.
The original database listed the putative complete sets of TFs from five different green plant (viridiplantae) species. Up to date,
summer 2007, PlnTFDB have had more than one hundred thousand hits from more than one thousand different clients, showing
the importance that this resource had acquired for the plant community. In this first major update, we extended the coverage of the
database to additional completed viridiplantae genomes, i.e., the moss _Physcomitrella patens_ and the rice _Oryza sativa_ spp
_indica_. The scope of PlnTFDB was broadened to encompass other eukaryote photosynthetic organisms, such as the
rhodophyte...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1094/version/1
(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
Modeling cardiac rhythm and heart rate using BFO and DOLCE
Provedor de dados: 17
Autores: Lynda Temal; Arnaud Rosier; Olivier Dameron; Anita Burgun.
This paper presents an application ontology for modeling cardiac rhythm and its anomalies such as tachycardia and bradycardia.
We use BFO and DOLCE as ontological reference framework in order to compare their impact on ontology design.



Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3558/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
Fluctuating population dynamics promotes the evolution of phenotypic plasticity
Provedor de dados: 17
Autores: Mario Pineda-Krch; Richard Svanbäck; Michael Doebeli.
An increasing number of studies are showing evidence in support of sympatric speciation. One basic question remains, however.
When a population has undergone a branching in its phenotype, is this due to an evolutionary branching in the underlying
genotype or due to phenotypic plasticity modifying a single genotype? Thus, phenotypic plasticity has come to be viewed as a trait
subject to selection, just like any other phenotypic character1,2. Here we present a model addressing the conditions under which a
predator phenotype experiencing selection for two alternative optimal phenotypes gives rise to genetically based phenotypic
branching or to phenotypic plasticity, allowing the corresponding genotype to give rise to two alternative, well-adapted...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/56/version/1
Ontologies for use in Systems Biology: SBO, KiSAO and TEDDY
Provedor de dados: 17
Autores: Nick Juty; Nicolas Le Novère; Dagmar Waltemath; Christian Knuepfer.
The use of computational modelling in the description and analysis of biological systems is at the heart of Systems Biology.
Besides the information stored in a core model, there is increasingly a need to provide additional semantic information: to identify
model components, to assist in biological interpretation of models, to define simulation conditions and to describe simulation
results. This information deficit can be addressed through the use of ontologies. We describe here three ontologies created
specifically to address the needs of the Systems Biology community in each sub-division, and illustrate their practical use with the
'Repressilator' model (Elowitz and Leibler, 2000).
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5122/version/1
Genome Network Project: An Integrated Genomic Platform
Provedor de dados: 17
Autores: Jose C. Clemente; So Nakagawa; Kazuho Ikeo; Takashi Gojobori.
With the objective of elucidating the structure of gene interactions in the human genome, the Genome Network Project has
generated a vast quantity of experimental data, mainly focusing on transcriptional control and transcription-factor related
protein-protein interactions (PPI). This data has been collected and organized into the Genome Network Platform
("http://genomenetwork.nig.ac.jp/":http://genomenetwork.nig.ac.jp/) at the National Institute of Genetics.
Expression data was obtained through CAGE (Cap Analysis Gene Expression), qRT-PCR, tiling array, microarray and short RNA
analysis, while PPI information was gathered through yeast two hybrid (Y2H), mammalian two hybrid (M2H) and _in vitro_ virus
(IVV) methods. The Genome Network...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3180/version/1
RDF Curator: A Novel Workflow that Generates Semantic Graph from Literature for Curation
Using Text Mining
Provedor de dados: 17
Autores: Yusuke Komiyama; Osamu Gotoh.
There exist few databases that enable cross-reference among various research fields related to bioenergy. Cross-reference is highly
desired among bioinformatics databases related to environment, energy, and agriculture for better mutual cooperation. By uniting
Semantic Graph, we can economically construct a distributed database, regardless of the size of research laboratories and research
endeavors.

Our purpose is to design and develop a workflow based on RDF
(Resource Description Framework) that generates Semantic Graph for a set of technical terms extracted from documents of
various formats, such as PDF, HTML, and plain text. Our attempt is to generate Semantics Graph as a result of text mining
including morphological...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5072/version/1
Novel developments in SBGN-ED and applications
Provedor de dados: 17
Autores: Tobias Czauderna; Eva Grafahrend-Belau; Astrid Junker; Anja Hartmann; Matthias Klapperstück; Falk
Schreiber.
Systems Biology Graphical Notation (SBGN, http://sbgn.org) [1] is an emerging standard for graphical representations of
biochemical and cellular processes studied in systems biology. Three different views (Process Description, Entity Relationship,
and Activity Flow) cover several aspects of the represented processes in different levels of detail. SBGN helps to communicate
biological knowledge more efficient and accurate between different research communities in the life sciences. However, to
support SBGN, methods and tools for editing, validating, and translating of SBGN maps are necessary.
We
present methods for these tasks and novel developments in SBGN-ED (www.sbgn-ed.org) [2], a tool which allows to create all
three types of SBGN maps...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6415/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
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
JSBML: a flexible and entirely Java-based library for working with SBML
Provedor de dados: 17
Autores: Nicolas Rodriguez; Marine Dumousseau; Andreas Dräger; Clemens Wrzodek; Alexander Dörr;
Sarah M. Keating; Akiya Jouraku; Nicolas Le Novère; Andreas Zell; Michael Hucka.
The XML-based Systems Biology Markup Language (SBML) is the de facto standard file format for the storage and exchange of
biochemical network models, and is supported by more than 180 software packages to date. Much of this success is due to its
clearly
defined
specifications
and
the
availability
of
libSBML,
a
portable,
robust,
and
easy-to-use
library.

LibSBML provides many methods for manipulating and validating SBML
files through its Application Programming Interface (API).
Originally written in C and C++, libSBML also provides
automatically-generated language bindings for Java, MATLAB, Perl, and many more. However, the platform independence of
Java is compromised in libSBML due to the fact that the language binding is...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6718/version/1
Normalization and Matching of Chemical Compound Names
Provedor de dados: 17
Autores: Martin Golebiewski; Jasmin Šarić; Henriette Engelken; Meik Bittkowski; Ulrike Wittig;
Wolfgang Müller; Isabel Rojas.
The identification of a chemical compound solely based on its name requires comprehensive chemical knowledge and often
extensive searches in chemical databases. However, it is crucial for the integration of biochemical data extracted from the
literature, since many publications exclusively describe a compound by its name. We have developed an application which
matches synonymic names of chemical compounds and thereby facilitates the bundling of corresponding data referring to the
same compound.

The tool that we have developed is based on natural language
processing (NLP) methods and applies rules to systematically normalize chemical compound names. Matching of synonymous
names is achieved by comparison of the normalized...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3322/version/1
Oncogenic Product HMGA1a Might Function as an Aberrant Splicing Inducer of Estrogen Receptor
[alpha] in Breast Cancer
Provedor de dados: 17
Autores: Kenji Ohe; Toshiaki Utsumi; Akila Mayeda.
Estrogen receptor (ER)-[alpha]46 is known as an important isoform for ER[alpha]. It inhibits the function of full length ER[alpha]
in MCF-7 mammary carcinoma cells and associated with cell cycle arrest. On the other hand, the oncogene _HMGA1_ (formally
_HMG I/Y_) is known to have increased expression in mammary carcinoma correlating with the degree of malignancy. We
present here that HMGA1a (HMG I) induces the exon skipped product, ER[alpha]46 mRNA, by tethering U1 snRNP to an
upstream pseudo 5' splice site, which is quite analogous to the PSI-mediated splicing regulation of _Drosophila_
P-element.

Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/4104/version/1
SGN Database: From QTLs to Genomes
Provedor de dados: 17
Autores: Isaak Y. Tecle; Naama Menda; Robert Buels; Lukas Mueller.
Quantitative trait loci (QTL) analysis is used to dissect the genetic basis underlying polygenic traits. Several public databases have
been storing and making QTL data available to research communities. To our knowledge, current QTL databases rely on manual
curation where curators read literature and extract relevant QTL information to store in databases. Evidently, this approach is
expensive in terms of expert manpower and time use and limits the type of data that can be curated. At the Solanaceae Genomics
Network (SGN) ("http://sgn.cornell.edu":http://sgn.cornell.edu), we have developed a database to store raw
phenotype and genotype data from QTL studies, perform, on the fly, QTL analysis using R/QTL statistical software...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3160/version/1
Rapid bioassay for evaluating enzyme production in fungal isolates from environmental sources
Provedor de dados: 17
Autores: Eleonora Bordo; Francesca Luziatellie; Silvia Crognale; Sara Marinari; Stefano Grego; Maurizio Ruzzi.
Fungal hydrolytic enzymes have a great potential due to the rapid development of enzyme technology and their industrial
applications. A fluorimetric microplate assay has been developed for measuring activity of β-D-exoglucanase,
β-D-glucosidase, α-D-glucosidase, β-N-acetyl-hexosaminidase, β-D-xylosidase
in diluted culture broth samples. The substrates used are conjugates of the highly fluorescent compounds 4-methylumbelliferone
(MUB) and thus product formation can be measured directly in the microplate without previous extraction and purification of the
product. The developed system was evaluated on eight fungal strains isolated from shrub species (Tamarix) that can be used in
phytoremediation. Depending...
Tipo: Poster
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/6217/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
Novel Techniques for Microspectroscopy and Chemical Imaging Analysis of Soybean Seeds and
Embryos
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng You; Doina M. Costescu.
Novel methodologies are currently being evaluated for the Chemical Analysis of soybean seeds as well as developing mature
soybean embryos by FT-IR/NIR Microspectroscopy. This is the first report of FT-NIR Chemical Images obtained with 1 micron
resolution. NIR spectra of Proteins, Oil and DNA fibers are obtained for regions as small as 1μ^2^.
Tipo: Poster
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Immunology;
Molecular Cell Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6591/version/2
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
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
Signaling Flux Redistribution concept can switch survival to apoptosis in cancer cells
Provedor de dados: 17
Autores: Daiki Yamada; Kentaro Hayashi; Vincent Piras; Masaru Tomita; Masa Tsuchiya; Kumar Selvarajoo.
The tumor necrosis factor related apoptosis-inducing ligand (TRAIL) induces apoptosis in certain types of carcinoma. However,
in majority of malignant tumors, it has no effect. Here we analyzed cell survival and apoptotic pathways triggered by TRAIL. A
computational model based on perturbation-response approach with mass-action equations was developed. All 48 parameter
values of the model were selected by genetic algorithm that minimizes deviation between experimental and simulation data for
human fibrosarcoma cells. Subsequently, we show in silico knock-down of a cell survival pathway molecule could potentially
enhance the activation of apoptosis through Signaling Flux Redistribution (SFR).
Tipo: Poster
Palavras-chave: Cancer; Immunology; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4375/version/1
The Immune Response in Patients with SARS: differential gene expression profiling.
Provedor de dados: 17
Autores: Peter Natesan Pushparaj; Jayapal J. Manikandan; Alirio Jose A. J. Melendez.
Severe acute respiratory syndrome (SARS) emerged in 2003, as a new epidemic form of life-threatening infection. As of 26th
September 2003, there were 8422 cases of SARS from 29 countries with 908 deaths (WHO). However, the pathogenesis of SARS
is poorly understood. To understand the host response to this pathogen, we profiled the gene expression patterns of peripheral
blood mononuclear cells (PBMC) from SARS patients compared to healthy controls using one of the latest techniques, high
density oligonucleotide expression probe array (HG-Focus array, Gene Chip, Affymetrix, Santa Clara, CA). High-density
oligonucleotide
microarray
is
a
promising
approach
for
high
throughput
analysis.
It
has
been
extensively
used in many areas of biomedical...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1145/version/1
Hypercytokinemia: Increased or decreased innate immunity?
Provedor de dados: 17
Autores: Milind Watve; Sonam Mandani; Prajakta Belsare.
The adipose tissue is an active endocrine organ which secretes proinflammatory cytokines and chemokines resulting into raised
serum levels. Hypercytokinemia has been interpreted as raised level of innate immunity and its evolution is interpreted as a
response to increased chances of infection under starvation conditions in which the thrifty phenotype evolved. If starvation and
infection challenges co-occurred during hunter gatherer life, thrifty genotype and infection resistant genotype may have
co-evolved. An inherent weakness of this explanation is that in obesity or insulin resistance there is no evidence of increased
resistance to infections. The raised levels of inflammatory cytokines have not been demonstrated to combat infections or enhance
wound...
Tipo: Poster
Palavras-chave: Ecology; Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/2710/version/1
Para-(benzoyl)-phenylalanine as a potential inhibitor against leptospirosis
Provedor de dados: 17
Autores: Dibyabhaba Pradhan; Vani Priyadarshini; Manne Munikumar; Amineni Umamaheswari.
Leptospirosis is a zoonotic disease of global concern caused by Leptospira interrogans. Subtractive genomic approach, metabolic
pathway analysis and multi strain genome comparisons of Leptospira interrogans serovars had proposed 88 common drug targets
from 5,124 genes of serovar Copenhageni and 4,727 genes of serovar Lai. Three potential drug targets (lpxC, lpxD and lpxB)
were identified from Lipid A biosynthesis process of lipopolysaccharide (LPS) biosynthesis pathway. Lipid A is one of the three
components of LPS that contains multiple hydrophobic fatty acid chains which anchor the LPS into the bacterial membrane.
Designing inhibitory drug molecules targeting Lipid A biosynthesis would dissolve the structural integrity of membrane structure
leading to...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5636/version/1
Where Is Scientific Evidence in Support of Refuge Size Reduction for Pyramided Bt Crops?
Provedor de dados: 17
Autores: Andrei Alyokhin.
Genetically modified plants expressing insecticidal Cry proteins originating from a soil-dwelling bacterium Bacillus thuringiensis
(Bt) provide a powerful tool for managing insect pests. Unfortunately, insect ability to develop resistance to insecticidal proteins
potentially jeopardizes its long-term efficiency. Review of registration materials submitted by plant biotech industry to the U.S.
Environmental Protection Agency and the existing scientific literature shows that currently available evidence in support of
reducing refuge for the pyramided genetically modified corn plants to 5% of the total crop area is essentially limited to predictions
of a single unpublished mathematical model developed “in-house” by the industry...
Tipo: Poster
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/6563/version/1
Towards automatic classification within the ChEBI ontology
Provedor de dados: 17
Autores: Janna Hastings; Paula de Matos; Marcus Ennis; Christoph Steinbeck.
*Background*
Appearing
in
a
wide
variety
of
contexts,
biochemical
'small
molecules' are a core element of biomedical data. Chemical ontologies, which provide stable identifiers and a shared
vocabulary for use in referring to such biochemical small molecules, are crucial to enable the interoperation of such data. One
such chemical ontology is ChEBI (Chemical Entities of Biological Interest), a candidate member ontology of the OBO Foundry.
ChEBI is a publicly available, manually annotated database of chemical entities and contains around 18000 annotated entities as
of the last release (May 2009). ChEBI provides stable unique identifiers for chemical entities; a controlled vocabulary in the form
of recommended names (which...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3525/version/1
Measurement & Prediction of Phase Behaviour of Carbon Dioxide Mixtures
Provedor de dados: 17
Autores: Esther Forte; Amparo Galindo; Livio G. Ruffine; J.P. Martin Trusler.
Acquiring a comprehensive understanding of the behaviour of carbon dioxide under reservoir conditions is essential for
optimizing its usage in enhanced oil recovery (EOR) and for developing sequestration schemes. In order to obtain this
understanding, it is necessary to study the physical properties and phase behaviour of mixtures of carbon dioxide with
hydrocarbons and brines under conditions of high pressure. In this work we are addressing both the experimental and the
theoretical aspects of this problem. A new apparatus, based on the static-analytical method, has been developed to measure phase
equilibrium. The equipment comprises a high-pressure cell with sapphire windows for visual observation and phase sampling,
with on-line gas chromatography...
Tipo: Poster
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2649/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
PRELIMINARY BASELINE SURVEY OF AVIFAUNAL DIVERSITY IN JIMMA ZONE,
SOUTH-WESTERN ETHIOPIA
Provedor de dados: 17
Autores: Haile Yineger; Kitessa Hundera; Bruktawit Abdu; Tifases Beyene; James Kuria Ndungu'; Cagan Hakki
Sekercioglu; Olivier Honnay; Bart Muys; Raf Aerts; Luc Lens.
Multidimensional poverty, which is deeply-rooted within least-developed African countries like Ethiopia, is forcing local people
to heavily rely on natural resources for their subsistent livelihoods. As a result, remaining wilderness areas in tropical Africa
which support huge but little known biological diversity, are subject to extensive habitat loss, fragmentation and degradation in
turn causing loss of plant and animal species and ecosystem services provided by them. Coffee forest fragment within the Jimma
Zone of Ethiopia cannot be expected to be an exception to such scenario. Taking this persistent problem into consideration, we
carried out a preliminary survey of bird biodiversity in selected areas of Jimma Zone during a short term bird ringing...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/4185/version/1
Prediction of novel inhibitors for human RNase1 involved in cardiovascular disease through in silico
screening
Provedor de dados: 17
Autores: Kanipakam Hema; Sadnala Giribabu; Sandeep Swargam; Amineni Umamaheswari.
Human pancreatic ribonuclease (RNase1) is a small digestive and pyramidine specific enzyme secreted by the pancreas. RNase1
contributes in the regulation of extracellular RNA by hydrolyzing RNA phosphodiester bonds. High levels of RNase1 in
cardiovascular disease patients project the enzyme as an attractive drug target. The known RNase1 inhibitors, citric acid and U1S
were searched for structural analogs from Ligand.info database to compile 783 ligands. The ligands' 3D structures and
their tautomeric states were generated using LigPrep. The 3424 prepared conformations were subjected to QikProp analysis and
filtered based on Lipinski rule of five and zero reactive functional group. The 3376 conformations with good ADME (absorption,
desorption,...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6527/version/1
Uberon: towards a comprehensive multi-species anatomy ontology
Provedor de dados: 17
Autores: Melissa A. Haendel; Georgios G. Gkoutos; Suzanna E. Lewis; Chris Mungall.
The lack of a single unified species-neutral ontology covering the anatomy of a variety of metazoans is a hindrance to translating
model organism research to human health. We have developed an Uber-anatomy ontology to fill this need, filling the gap between
the CARO upper-level ontology and species-specific anatomical ontologies.
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3592/version/1
Phylontal: Using Phylogenies to Align Phenotype Ontologies
Provedor de dados: 17
Autores: Peter Midford.
Phylontal is a simple approach to generating alignments of ontologies or constructs based on controlled vocabularies that
correspond to tips on a phylogeny. The method requires only a downpass (tips to root) and thus constructing alternative
alignments from multiple or uncertain phylogenies may be relatively inexpensive.
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4628/version/1
Standards and infrastructure for managing experimental metadata
Provedor de dados: 17
Autores: Philippe Rocca-Serra; Marco Brandizi; Eamonn Maguire; Nataliya Sklyar; Chris Taylor; Manon Delahaye; Richard
Evans; Susanna-Assunta Sansone.
*See
also
the
"related
presentation":http://precedings.nature.com/documents/3145/version/1*

W
e present an infrastructure that leverages synergistic reporting standards and ontologies^1,2,3,4,5^ to create a common structured
representation and storage mechanism for experimental metadata from biological and biomedical investigations ranging from
simple
single-assay
studies
to
complex,
methodologically
diverse
multi-assay
studies.


The infrastructure’s components include: a data capture and editing
tool (_ISAcreator_); validator (_ISAvalidator_); database (_BioInvestigation Index_); and converter (_ISAconverter_); and a
BioConductor analysis package...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3144/version/1
Residential irrigation as a driver of urban bird communities
Provedor de dados: 17
Autores: Bradley W. Schleder; Madhusudan Katti; Sarah Wallace.
*Background/Question/Methods*
The demand for fresh water has largely outpaced supply both globally
and locally with current water management policies unable to meet the needs of urban, agricultural, and industrial activities.
Irrigation is one of the many anthropogenic uses of water and is arguably the most important maintenance factor in a landscape.
This is particularly true in an arid climate, such as the Central Valley of California. Urban residents' decisions about
the design and maintenance of their landscapes affect bird species richness. Published research indicates that these decisions are
also affected by the residents' socioeconomic status. However, the driver of this relationship remains unknown. This
paper...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3617/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
Mathematical Modeling of the Neuronal Processes in Sugar Addiction
Provedor de dados: 17
Autores: Andre Almeida; Hamed Celaymanian; Natalie Seel; Boris Zak; Hamid R. Noori.
It has already been demonstrated that the body responds to enhanced intake of sugar and is conducive to a natural form of
addiction.
There
are
substantial
neurochemical
changes
in
the
brain
(especially
dopamine
and
acetylcholine
systems) similar to other addictive drugs. A mathematical model comprised by a system of
delayed leaky integrate-and-re equations is established to simulate the effects of sugar on a
reward-circuitry. Simulations with Neuron suggest agreement with the neurobiological hypotheses of hyperactivity of neural
systems due to binge sugar intake.
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5546/version/1
GabiPD: Gabi Primary Database - a plant integrative ‘omics’ database in
GABI-FUTURE
Provedor de dados: 17
Autores: Diego Mauricio Riaño-Pachón; Axel Nagel; Robert Wagner; Elke Weber; Birgit Kersten.
GabiPD ("http://gabi.rzpd.de":http://gabi.rzpd.de) was established within GABI-I and further developed in
GABI-II and constitutes a repository and analysis platform for a wide array of heterogeneous data arising from high throughput
experiments developed by members of the GABI/WPG community. Currently, data from different fronts (genomics,
transcriptomics, proteomics, metabolomics) are incorporated in GabiPD, representing 14 different biological species. Last year
GabiPD moved to the Max Planck Institute of Molecular Plant Physiology. In the progressing GABI-FUTURE phase, the GabiPD
team has been creating a more integrative data view, expanding the tools and information provided by our well-known
GreenCards. Links to different...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1684/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
The NCI-Nature Pathway Interaction Database: A cell signaling resource.
Provedor de dados: 17
Autores: Shiva Krupa; Kira Anthony; Jeffrey R. Buchoff; Matthew Day; Timo Hannay; Carl F. Schaefer.
The Pathway Interaction Database (*PID*, http://pid.nci.nih.gov) is a freely available
collection of curated
and peer-reviewed signaling pathways composed of human
biomolecular interactions and cellular processes.
Created in a collaboration between the
U.S. National Cancer Institute and Nature Publishing Group, the
database
is
a
research
tool
for
cell
biologists,
biochemists,
computational
biologists
and
bioinformaticians.
The PID offers a range of tools to facilitate pathway exploration. Users can browse
the
pre-defi
ned
set
of
pathways
and
also
create
interaction
network
maps
centered
on
a single molecule of interest or an extensive list...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1311/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
Structural Analysis of Polarizing Indels Argues the Root of the Tree of Life is Near the Chloroflexi
Provedor de dados: 17
Autores: Ruben E. Valas; Philip E. Bourne.
Determining which branches of the tree of life have derived features narrows down the possible location of the root. Currently the
polarization of indels done by Lake _et al_.^1-5^ and the polarizing transitions of Cavalier-Smith^6^ arrive at contradictory
positions for the root of the tree. We have analyzed the sequence based indel arguments using protein structure wherever
possible. Structure strongly supports some of the polarizations, but in other indels it argues for a different conclusion. We
conclude that there is no contradiction between Lake _et al_. and Cavalier-Smith; the root of the tree of life must be near the
Chloroflexi.

Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3290/version/1
Optimizing automated preprocessing streams for brain morphometric comparisons across multiple
primate species
Provedor de dados: 17
Autores: Daniel Mietchen; Robert Dahnke; Christian Gaser.
Introduction: MR techniques have delivered images of a wide array of species, ranging from invertebrates to birds to elephants
and whales. However, their potential to serve as a basis for comparative brain morphometric investigations has rarely been tapped
so far (Christidis and Cox, 2006; Van Essen & Dierker, 2007). In order to address one of the potential reasons behind
this, we tested various automated segmentation streams (using CARET, FSL and lab-written code) that have been mainly
designed
for
applications
in
humans,
with
the
aim
of
optimizing
them
for
comparisons
across
multiple
species.

Methods: T1-weighted MR images from individuals representing 11 primate
species have been acquired by Rilling and Insel...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4511/version/1
Using SeaWiFS and In Situ Data for HAB Prediction in the Northern Gulf of Mexico: Decision Tree
Analysis
Provedor de dados: 17
Autores: Dan Holiday; Greg Carter.
To date, 13 potential HAB species have been detected in coastal waters of Mississippi and Alabama, including representatives of
the diatom genera Pseudo-nitzschia and Chaetoceros, and dinoflagellate genera Karenia, Gonyaulax, Akashiwo, Karlodinium, and
Prorocentrum. This study investigates the potential of satellite remote sensing (SeaWiFS) to predict environmental conditions
leading to the formation of HABs in these turbid coastal waters. Phytoplankton populations and water quality were monitored in
situ at 3 to 6 week intervals and 17 locations in Mobile Bay and the Mississippi Sound from December, 2004, through June, 2006.
SeaWiFS imagery corresponding with in situ collections was acquired. Non-parametric multivariate analyses determined
relationships...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3607/version/1
Standardization in UniProtKB/Swiss-Prot
Provedor de dados: 17
Autores: Serenella Ferro Rojas; Anne Morgat; UniProt Consortium.
Within the UniProt consortium, the UniProtKB/Swiss-Prot knowledge base provides the international community with a stable,
comprehensive, fully classified, richly and accurately annotated protein sequence database that is fully operable with other
databases. Annotation relates to function(s) of the protein (their catalytic activity and the corresponding metabolic pathway(s) in
which the protein may be involved), their cellular location, their interactions with other cellular components, etc.


It is challenging to unify the way we annotate proteins, to ensure consistency and to
describe data unambiguously. It is also highly valuable both for querying the database and for analyzing high-throughput data
(expression data for...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3214/version/1
Serum profiling and biomarker discovery of rat mammary tumors using mass-coded abundance tags
(MCAT)
Provedor de dados: 17
Autores: Craig Rowell; Glen Puckett; Kevin Raorty; Marion Kirk; Landon Wilson; Sam Wang; Mark Carpenter; Coral A.
Lamartiniere.
Advances in Mass-spectrometry techniques allow for the rapid processing and evaluation of complex biological mixtures such as
blood/serum. These samples represent a protein rich environment as well as a sentinel monitoring system of the entire organism.
The central tenet of these studies is that changes in the microenvironment of a tissue, brought about by a disease process, will lead
to sufficient changes in the protein and peptide pattern of the serum, such that the differences can be accurately detected and
correctly associated with a particular disease state. Using mass-spectrometry approaches we have developed techniques that
allow us to compare samples from tumor-free and tumor present serum samples simultaneously to find biomarkers that indicate...
Tipo: Poster
Palavras-chave: Cancer.
Ano: 2008
URL: http://precedings.nature.com/documents/2032/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
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
Enzyme activities and glyphosate biodegradation in a riparian soil affected by simulated saltwater
incursion
Provedor de dados: 17
Autores: Changming Yang; Mengmeng Wang.
Soil salinization due to saltwater incursion, is a major threat to biochemical activities and thus strongly alters biogeochemical
processes in a freshwater riparian of coastal estuary region. A pot incubation experiment was conducted to investigate the effects
of simulated saltwater incursion on some key enzymatic activities and biodegradation dynamics of herbicide glyphosate in a
riparian soil in Chongming Island located in the Yangtze River estuary, China. The results showed that saltwater addition with
10% artificial seawater significantly increased the biodegradation efficiency of glyphosate with the lowest residual concentration
among all the treatments. However, glyphosate degradation was markedly decreased in the riparian soil with high levels of...
Tipo: Poster
Palavras-chave: Microbiology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6187/version/1
P-POD, The Princeton Protein Orthology Database, as a Tool for Identifying Gene Function
Provedor de dados: 17
Autores: Michael S. Livstone; Rose Oughtred; Sven Heinicke; Fan Kang; Benjamin Vernot; Aiton Goldman; Dannie Durand;
David Botstein; Kara Dolinski.
P-POD, the Princeton Protein Orthology Database, classifies proteins from model organisms and medically-important organisms
into families of homologs and provides curated evidence from the literature addressing these relationships. The web page for
each protein family includes a phylogenetic tree, sequence alignment, and cross-references to disease-related papers from SGD,
papers
describing
complementation
experiments,
and
OMIM
gene
and
disease
information.

As participants in the Gene Ontology Consortium’s
Reference Genome project, we seek to provide a consistent centralized method to identify orthologous proteins. We have
expanded P-POD to include the protein complement of the twelve Reference Genomes. In...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3119/version/1
Neural Modulation by Rhythm Induced Temporal Expectations
Provedor de dados: 17
Autores: Gustavo Rohenkohl; Anna Dal Molin; Anna C. Nobre.
Time is an essential dimension of our experience, framing human behaviour at scales ranging from the millisecond organization of
motor actions to circadian rhythms cycle, and beyond. Nevertheless, the mechanisms by which the brain keeps time and uses
temporal information to organise behaviour remain unknown. Whereas the principles of the organisation of spatial cognition in the
human brain are emerging, the same is not true for temporal cognition. The current study tested the influence of temporal
expectations on attentional orienting to moving targets. In this task, a ball appeared at the left side of a screen and moved across
the screen in steps following either a regular or irregular rhythm. After reaching an occluding band, the ball was temporarily...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2956/version/1
Habitat use of Northern Map Turtles (Graptemys geographica) in an altered system, the
Susquehanna River, Maryland (USA)
Provedor de dados: 17
Autores: Teal M. Richards; Richard A. Seigel.
*_Background/Question/Methods_*

Riverine
turtle
populations
are
declining
worldwide and many of these species have been extirpated from large areas of their range. In Maryland, the northern map turtle
(Graptemys geographica) occurs only in the lower Susquehanna River, which is the eastern edge of its range. The northern map
turtle is a Maryland state endangered species and had not been seen in Maryland since the early 1990’s. The
Susquehanna River is divided by a hydroelectric dam and is heavily used for recreational activities, both of which may negatively
impact turtles. To determine the status of map turtles in Maryland, we performed visual encounter surveys for basking turtles at 12
sites from April to...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3680/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
Optimal decision bounds for probabilistic population codes and time varying evidence
Provedor de dados: 17
Autores: Jan Drugowitsch; Rubén Moreno-Bote; Alexandre Pouget.
Decision making under time constraints requires the decision maker to trade off between making quick, inaccurate decisions and
gathering more evidence for more accurate, but slower decisions. We have previously shown that, under rather general settings,
optimal behavior can be described by a time-dependent decision bound on the decision maker’s belief of being
correct (Drugowitsch, Moreno-Bote, Pouget, 2009). In cases where the reliability of sensory information remains constant over
time, we have shown how to design diffusion models (DMs) with time-changing boundaries that feature such behavior. Such
theories can be easily mapped onto simple neural models of decision making with two perfectly anti-correlated neurons, where
they predict the...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5821/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
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
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
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
Rice Genes in Oryzabase
Provedor de dados: 17
Autores: Yukiko Yamazaki; Rie Tsuchiya; Yuka Takahashi; Takao Asanuma; Yo Shidahara; Shingo Sakaniwa.
In addition to maintaining a rice gene list, Oryzabase, a database of rice science, has also been hosting a website to submit newly
identified genes. The current rice gene dictionary is based on a traditional rice trait gene dictionary and extended through time
with new genes which are manually retrieved from journal articles. Currently over 4000 genes are listed. However it is still
insufficient in both quantity and quality. 


Recently we started to apply automated
extraction before manual annotation to enhance the efficiency of gene extraction. To improve the quality of information, we
started collecting relevant DNA accessions and LOCUS-ID. In Oryzabase, we try to employ the help of users to overcome this
information...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5069/version/1
semanticSBML 2.0 - A Collection of Online Services for SBML Models
Provedor de dados: 17
Autores: Falko Krause; Timo Lubitz; Marvin Schulz; Edda Klipp.
semanticSBML 2.0 is a collection of online services for the processing of biochemical networks in the SBML (Systems Biology
Markup Language) document format. It allows users to edit SBO (Systems Biology Ontology) and RDF based MIRIAM
(Minimum Information Required in the Annotation of Models) annotations, check for semantic validity, compare and merge
SBML documents, and to create submodels. Given an annotated SBML document similar SBML documents can be retrieved from
the BioModels Database via a ranked similarity search. Further features of semanticSBML 2.0 include graph visualization of
SBML documents, parameter balancing, creation of SBML documents using shorthand SBML, and an interface to the BioModels
Database that allows the comparison of document...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5402/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
Populational analysis of Saccharomyces cerevisiae strains from different appellations of origin and
grape varieties by microsatellite analysis.
Provedor de dados: 17
Autores: Leonor Pereira; Filomena L. Duarte; Paulo T. Ramos; Maria F. Alemão; Paula Gomes; Ana C. Gomes;
Susana Sousa; Sofia Machado; Manuel Santos; Margarida Casal; Dorit Schuller.
The objective of the present study was to evaluate populational relationships among Saccharomyces cerevisiae strains isolated
from some of the Portuguese most important grapevine varieties in different appellations of origin, using polymorphic
microsatellites. 
One hundred ninety two grape samples were collected during the 2006 and 2007 harvest
season in the Vinho Verde (grape varieties: Arinto, Alvarinho, Avesso, Loureiro, Touriga Nacional) Bairrada (grape varieties:
Arinto, Baga, Castelão Francês, Maria Gomes, Touriga Nacional) Alentejo (grape varieties,
Aragonês, Trincadeira, Touriga Nacional), Terras do Sado (grape variety Castelão) Bucelas (grape variety
Arinto) and Estremadura (grape varieties:...
Tipo: Poster
Palavras-chave: Ecology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/2290/version/1
The locomotion pattern of Baurusuchus salgadoensis Carvalho, Nobre & Campos, 2005
and the distribution of Baurusuchidae in Gondwanaland
Provedor de dados: 17
Autores: Felipe M. Vasconcellos; Thiago S. Marinho; Ismar S. Carvalho.
Baurusuchus salgadoensis Carvalho, Nobre & Campos, 2005 is a ziphodont mesoeucrocodylian closely related to the
Sebecosuchia. Cranial features indicate that this species had terrestrial predatory habits. The postcranial skeleton of B.
salgadoensis show distinctive characteristics when compared to extant Crocodylomorpha. The dorsal vertebrae are close
articulated with short and craniocaudally expanded neural spines, specially the posterior ones. The sacral vertebrae are robust and
have the lateral processes highly fused to the ilium. The anterior caudal vertebrae are robust as the sacral ones but their neural
spines are more stout, anteriorlly expanded and higher. The close articulation of the dorsal vertebrae may indicate a less flexible
dorsal...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/808/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
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
Surface Modified Ultrathin Polyelectrolyte Nanoreservoir for Delivery of Proteins: Evaluation in
Terms of Controlled Release and Biocompatibility
Provedor de dados: 17
Autores: Girish Kumar Gupta; Vikas Jain; Prabhat Ranjan Mishra.
The proposed ultrathin polyelectrolyte nanoreservoir (UPN) was fabricated in two combinations by alternate layering of
polyelectrolytes poly (allylamine hydrochloride) along with sodium poly (styrene sulfonate) (PAH/PSS)5 and sodium alginate
(PAH/SA)5
using porous calcium carbonate as a template using layer-by-layer adsorption technique with the subsequent
template removal at low pH. We studied the possibility whether remnant intact nanoreservoir could be suited for encapsulation as
well as delivery vehicle for protein such as bovine serum albumin as a model. To tune biocompatibility with biological cells the
assembled surface was modified using pluronic (F-68) by adsorption and possible hydrophobic interaction. The prepared system
was characterized for...
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2548/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
Results of a Wildlife Toxicology Workshop held by Smithsonian Institution: Identification
& Prioritization of Problem Statements
Provedor de dados: 17
Autores: K. Christiana Grim; Mark Jankowski; Alonso Aguirre; Val Beasley; Anne Fairbrother; Sarah Gerould; Barnett Rattner;
Teri Rowles; Steve Monfort; Shirlee Tan.
*Background/Question/Methods*
On March 13-15, 2007 nearly 50 scientists and administrators from the
US and Canada participated in a Smithsonian-sponsored Wildlife Toxicology Workshop. Invitees were from academic,
government, conservation and private organizations and were selected to represent the diverse disciplines that encompass wildlife
toxicology. The workshop addressed scientific and policy issues, strengths and weaknesses of current research strategies,
interdisciplinary and science-based approaches in the study of complex contaminant issues, mechanisms for disseminating data to
policy-makers, and the development of a partner network to meet the challenges facing wildlife toxicology over the next decade.
Prior to the meeting,...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3684/version/1
The TA-p73 functions as a Lung tumor suppressor by increasing the expression of miRNA, let-7
Provedor de dados: 17
Autores: Lakshmanane Boominathan.
I have previously proposed that TA-p73-depenedent tumor suppressor pathway could inhibit the development of lung
adenocarcinoma. This hypothesis is strongly supported by a recent finding showing that TA-p73 specific knockout mice are
prone to lung adenocarcinoma. However, the p73-dependent tumor suppressor pathway remains ill defined. It has been shown
that let-7 cluster is highly expressed in normal lung. Loss of let-7 expression: a) is common in Non-small cell lung carcinoma;
and b) enhances lung tumor formation, indicating that it could function as a lung tumor suppressor. Based on these facts, I
hypothesized that let-7 could be a transcriptional target of p73. To confirm this hypothesis, I have analyzed the let-7 cluster
promoters using TRASFAC...
Tipo: Poster
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4252/version/1
Prediction of Evolutionarily important catalytic amino acid of Mycobacterium tuberculosis
O-Succinylbenzoate synthase through in silico mutational analysis
Provedor de dados: 17
Autores: Babajan B; Chaitanya M; Anuradha CM; Suresh Kumar Chitta.
The emergence of tuberculosis resistant to multiple, first- and second-line antibiotics poses challenges to a global control strategy
that relies on standard drug treatment regimens. The high drug-resistant strains of Mycobacterium tuberculosis (Mtb) have been
implicated in outbreaks and have been found throughout the world; a comprehensive understanding, the magnitude of this threat
requires an accurate assessment of the worldwide burden of resistance. In an attempt to design anti-TB drugs, the target chosen is
a key enzyme of Mtb, O-Succinylbenzoate synthase (OSBS), which is an attractive target for its role in electron transport chain as
OSBS is not available in humans. An attempt has been to built the 3-D structure of Mtb-OSBS using online Swiss model...
Tipo: Poster
Palavras-chave: Biotechnology; Microbiology; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3776/version/1
Hemodynamic and electrophysiological evidence of resting-state network activity in the primate
Provedor de dados: 17
Autores: Allen Ardestani; Wei Shen; Felix Darvas; Arthur Toga; Joaquin Fuster.
An expanding body of literature describes the existence of concerted brain activations in the absence of any external stimuli.
Resting-state networks have been identified and demonstrated to be modulated during the performance of specific cognitive
operations. However, despite mounting evidence the possibility still remains that those correlated signal fluctuations reflect
non-neural phenomena. In order to isolate functionally relevant spontaneous coactivations, we utilized a multi-level sampling
approach to obtain co-registered brain signals across a range of sampling resolution and sensitivity. Surface and local field
potentials, hemodynamic signals (near-infrared spectroscopy, NIRS), and cell spiking were recorded from dorsolateral prefrontal
and...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2562/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
Introduction to Medical Genetics
Provedor de dados: 17
Autores: Atif A. Baig.
Medical genetics is the key to modern biochemistry and underlying mechanisms of many diseases.
Tipo: Poster
Palavras-chave: Genetics & Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6596/version/1
The Eukaryote Genome Annotation Platform at Genoscope
Provedor de dados: 17
Autores: Betina M. Porcel; Franck Aniere; Sylvain Bonneval; Benjamin Noel; Jean-Marc Aury; Corinne Da Silva; Olivier
Jaillon; France Denoeud; Claude Scarpelli; Jean Weissenbach; Patrick Wincker; François Artiguenave.
The Genoscope annotation workflow for eukaryote genomes relies on evidence from ab initio gene models predictions combined
with homology searches, using collections of expressed sequences - full length cDNAs, ESTs or massive-scale mRNA sequences
from the same or closely related organisms – proteins or other genomic sequences. Global analysis of these drafts or
complete sequences are then combining both approaches in the form of gene prediction data integration using GAZE, capable to
identify a majority of the existing gene features. Although of very good quality, gene-modelling remains still tentative at the end
of the process. Even though computational predictors are useful on large scale annotation for global genomics analysis, there is
no...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3457/version/1
Post-market monitoring: legal framework in Brazil and first results
Provedor de dados: 17
Autores: Marcia A. Melo; Ederson A. Kido; Paulo P. Andrade.
Brazil is presently (2010) the second largest producer of Genetically Modified (GM) crops. The legal framework to support both
research activities and the commercial release of Genetically Modified Organisms (GMOs) is, however, very recent, as the
Biosafety Law dates back from 2005. After the indispensable risk analysis, done by National Technical Committee for Biosafety
(CTNBio), a GM plant can be approved for commercial release. Nevertheless, as stated in the Normative Resolution nr. 5 (NR-5),
2008, the post-market monitoring is mandatory. However, the first GM crop in Brazil, the herbicide tolerant soybean, was
harvested in 2005. The CTNBio asked, then, for a monitoring plan and the applicant designed a complex study focused on
case-specific monitoring....
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4528/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
Structural analysis of outer membrane beta-stranded porins using B-factor
Provedor de dados: 17
Autores: Abhishek Kumar; S Krishnaswamy.
Computational and statistical analysis has formed a large component of the biophysical efforts put forth to understand protein
structure and function, due to the diversity and complexity of their structure. Outer membrane proteins form a diverse and
complex set of proteins. Of these, porins that allow passage of molecules across the membrane interface have been analyzed here
from a biophysical and structural perspective. The objective of this study is to analyze the structural organization of porins using
atomic temperature factor as a parameter. Generally atomic temperature factors of molecules from crystal structures indicate the
degree of mobility or disorder seen in the crystal structure. As good crystal structures have lesser possibilities of errors...
Tipo: Poster
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/2803/version/1
Precipitation in Aberdeen, SD: data analysis approach
Provedor de dados: 17
Autores: Boris Shmagin.
Daily, monthly, and annual sums of precipitation for Aberdeen, South Dakota, from 1890-2008 were analyzed using univariate
and multivariate statistical methods (primary statistical analysis, factor analysis, time-series analysis: shift detection and simplified
Fourier analysis - SFA) and provided descriptions of the variability (stochastic and cyclic or oscillatory) for monthly and annual
sums of precipitation. The goal was to describe the natural variability in three scales, then to use this to forecast extremes, such as
the spring 2007 flooding event that occurred in Aberdeen. The part of the variability that may be explained for sums of
precipitation seasonality by factor model is 57%. The single time series relations of the main cyclic component to...
Tipo: Poster
Palavras-chave: Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3197/version/2
Text Mining in Full Text Articles -- Methodical and Represenation Issues
Provedor de dados: 17
Autores: Roman Klinger; Robert Pesch; Theo Mevissen; Juliane Fluck.
In many cases, information from abstracts of biomedical publications is not sufficient for annotation of database entries.
Therefore, text mining systems supporting curators of biodatabases should be able to process full text articles. Beside the technical
problems arising from full text parsing, the representation of the annotated full text is an important issue. Journal articles are
mostly electronically available in PDF or HTML format. Also with more easily manageable XML formats, readers would like to
have a visualisation of annotations and semantic enrichment directly in the PDF or HTML. We summarize the technical problems
arising from parsing of HTML and PDF journal full texts and show first results of visualisation in both formats.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3141/version/1
The MEROPS Database
Provedor de dados: 17
Autores: Neil D. Rawlings; Alan J. Barrett.
Many proteins undergo important post-translational proteolytic processing to remove targeting signals and activation peptides, and
most proteins undergo proteolytic inactivation and catabolism. The enzymes that hydrolyse the peptide bonds in proteins and
peptides
are
known
as
peptidases,
proteases
or
proteolytic
enzymes.
The
MEROPS
database
("http://merops.sanger.ac.uk":http://merops.sanger.ac.uk) presents the classification and nomenclature of
peptidases, their inhibitors and substrates. In 1993 we proposed the scheme for the classification of peptidases that has been
internationally accepted, and in 1996 we established the MEROPS database. Protein inhibitors have been included in the
database since 2004. About 2% of the genes in a...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3103/version/1
The Relationship between the UniProt Knowledgebase (UniProtKB) and the IntAct Molecular
Interaction Databases
Provedor de dados: 17
Autores: Yasmin Alam-Faruque.
IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are
derived from literature curation or direct user submission and all experimental information relating to binary
protein-protein
interactions is entered into the IntAct database by curators, via a web-based editor.
Interaction information is added to the SUBUNIT comment and the RP line of the relevant publication within the UniProtKB
entry. There may be a single INTERACTION comment present within a UniProtKB entry, which conveys information relevant to
binary protein-protein interactions. This is automatically derived from the IntAct database and is updated on a triweekly basis.
Interactions can be derived by...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3936/version/1
It was (not) me: Causal Inference of Agency in goal-directed actions
Provedor de dados: 17
Autores: Tobias Beck; Carlo Wilke; Barbara Wirxel; Dominik Endres; Axel Lindner; Martin A. Giese.
Summary: 
The perception of one’s own actions depends on both sensory information and
predictions derived from internal forward models [1]. The integration of these information sources depends critically on whether
perceptual consequences are associated with one’s own action (sense of agency) or with changes in the external
world that are not related to the action. The perceived effects of actions should thus critically depend on the consistency between
the predicted and the actual sensory consequences of actions. To test this idea, we used a virtual-reality setup to manipulate the
consistency between pointing movements and their visual consequences and investigated the influence of this manipulation on
self-action...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5858/version/2
Novel phytosynthesis of nanoparticles using Indigeneous Australian Plants
Provedor de dados: 17
Autores: N V K V Prasad Tollamadugu; S R Venkata Kambala; Benjamin Convery; Ravi Naidu.
Nanoparticles are considered to be the building blocks of nanotechnology. Biosynthesis of nanoparticles using plant material is an
exciting and relatively new developing research area in nanobiotechnology. In the present study, Eucalyptus leaves were collected
from Olive pink botanical garden, Alice Springs, Australia and were used to synthesize silver nanoparticles. Cubical structured
and well monodispersed silver nanoparticles were formed with an average size of 50nm. The formed silver nanoparticles are
found to have promising applications in medicine as good antimicrobial agents. To the best of our knowledge this is the first
report on exploiting indigeneous Australian plant sources for the synthesis of metallic nanoparticles.
Tipo: Poster
Palavras-chave: Developmental Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6307/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
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
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.
has
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
Obesity as a perceived social signal
Provedor de dados: 17
Autores: Manasee Mankar; Radhika Joshi; Prajakta Belsare; Maithili Jog; Milind Watve.
Fat accumulation has been classically considered as a means of energy storage. Obese people are theorized as metabolically
‘thrifty’, saving energy during times of food abundance. However, recent research has highlighted
many neuro-behavioral and social aspects of obesity, with a suggestion that obesity, abdominal obesity in particular, may have
evolved as a social signal. We tested here whether body proportions, and abdominal obesity in particular, are perceived as signals
revealing personality traits. 

Faceless drawings of three male body forms namely lean,
muscular and feminine, each with and without abdominal obesity were shown in a randomized order to a group of 222
respondents. A list of 30...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2711/version/1
Present and future of proteomics data curation at the PRIDE database
Provedor de dados: 17
Autores: Juan Antonio Vizcaino; Henning Hermjakob; Lennart Martens.
Significant progress has been made in improving the accessibility and utility of the large amounts of generated high-throughput
proteomics data by the introduction of publicly available proteomics repositories. One such repository is PRIDE (the
‘PRoteomics
IDEntifications’
database,
"http://www.ebi.ac.uk/pride":http://www.ebi.ac.uk/pride). PRIDE stores mass spectrometry related data,
including
peptide
and
protein
identifications,
mass
spectra
and
valuable
additional
metadata.

At present, data curation in PRIDE is limited to data submission support.
The format in which all submissions need to take place is PRIDE XML. Mass spectrometry derived data is very heterogeneous in
terms of...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3222/version/1
Impact of tissue microstructure on a model of cardiac electromechanics based on MRI data
Provedor de dados: 17
Autores: Valentina Carapella; Vicente Grau; Pras Pathmanathan; Kevin Burrage.
Cardiac motion is a vital process as it sustains the pumping of blood in the body. For this reason motion abnormalities are often
associated with severe cardiac pathologies. Clinical imaging techniques, such as MRI, are powerful in assessing motion
abnormalities
but
their
connection
with
pathology
often
remains
unknown.

Computational models of cardiac motion, integrating imaging data, would
thus be of great help in linking tissue structure (i.e. cells organisation into fibres and sheets) to motion abnormalities and to
pathology. Current models, though, are not able yet to correctly predict realistic cardiac motion in the healthy or diseased
heart.

Our hypothesis is that a more realistic...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6594/version/1
Sisseton Wahpeton College Student Internship – Learning About Water Quality
Assessment, Geospatial Technologies, Landuse Classification and Statistical Analysis
Provedor de dados: 17
Autores: Brendon Barker; Destinee Eastman; Steven Farmer, Jr.
Three student interns from Sisseton Wahpeton College and their advisor Karla Witt worked with researchers from South Dakota
State University to explore the hypothesis that satellite imagery could be used as a tool to evaluate water quality in lakes on the
Sisseton Wahpeton Reservation. Interns constructed their own Secchi disks and used them to measure transparency in lakes and
mark the locations with a global positioning system (GPS) on days when satellite imagery was available. A geographic
information system (GIS) was used to relate field measurements to satellite images. The students also conducted monthly water
quality sampling on Pickerel, Enemy Swim and Clear Lakes to determine current trophic state. Existing land use maps for
Pickerel Lake were...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5340/version/1
R tools for MicroRNA pathway analysis
Provedor de dados: 17
Autores: Anwesha Dutta; Pooja Mandaviya; Rasanpreet Kaur; Sandeep Mallya.
In the early 2000s, microRNAs (miRNAs) were discovered as segments of a new class of highly conserved and small non-coding
RNA molecules of 20-25 nucleotides that are transcribed from DNA.
They do not translation into proteins,
rather they inhibit protein expression by binding to the 3’untranslated regions (3’ UTRs) of specific
mRNA targets (that is/are complementary to them) and guiding their translational repression or complete degradation and gene
silencing. With this, miRNAs provide a second level of regulation beyond primary gene expression. Integrative study of cellular
pathways is pivotal to understanding the functions of individual genes and proteins in terms of systems and processes that
contribute to normal...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5918/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
Functional analysis of βC1 protein encoded by Tomato leaf curl Java virus, a
monopartite begomovirus
Provedor de dados: 17
Autores: Pradeep Sharma; Tatsuya Kon; Masato Ikegami.
Tomato leaf curl disease is among the most important limiting factors that affect tomato production in world wide including south
East Asia. Recently, we have isolated tomato leaf curl Java virus, a whitefly-transmitted monopartite begomovirus, which belongs
to the family Geminiviridae. ToLCJAV have been shown to be associated with a novel signal stranded DNA satellite, known as
[beta]DNA. Post transcriptional gene silencing (PTGS) in plants is a natural defense response against virus infections, and as a
counter defense strategy, viruses have evolved to encode silencing suppressor proteins. The present work we have identified the
suppressor activities encoded by [beta]C1 protein encoded by ToLCJAV DNA[beta] satellite, which poses a serious threat to...
Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3317/version/1
Optimizing automated preprocessing streams for brain morphometric comparisons across multiple
primate species
Provedor de dados: 17
Autores: Daniel Mietchen; Robert Dahnke; Christian Gaser.
INTRODUCTION

MR techniques have delivered images of brains from a wide array
of species, ranging from invertebrates to birds to elephants and whales. However, their potential to serve as a basis for
comparative brain morphometric investigations has rarely been tapped so far (Christidis and Cox, 2006; Van Essen &
Dierker, 2007), which also hampers a deeper understanding of the mechanisms behind structural alterations in
neurodevelopmental disorders (Kochunov et al., 2010). One of the reasons for this is the lack of computational tools suitable for
morphometrci comparisons across multiple species. In this work, we aim to characterize this gap, taking primates as an...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4511/version/2
Homology modeling and docking studies to explore the novel drug for monocyte differentiation
antigen CD14
Provedor de dados: 17
Autores: Bhimisetty Reshma; Sandeep Swaragam; Amineni Umamaheswari.
Monocyte differentiation antigen CD14 belongs to the leucine rich family. Elevated levels of monocyte differentiation antigen
CD14 and toll-like receptor 4 (TLR4) play a major role in inflammatory response and cause ischemic heart diseases, neuropathic
pain and LPS (endotoxin) induced septic shock. IAXO compounds (IAXO-101, IAXO-102 and IAXO-103) inhibit the
CD14-dependent and TLR4-independent signaling pathways but they have severe side effects. Due to unavailability of human
monocyte differentiation antigen CD14 crystal structure, 3D structure was constructed based on template structure (1WWL) using
Modeler 9v9. The modeled structure was refined, energy minimized and validated. Binding site residues of human monocyte
differentiation antigen CD14 were...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6580/version/1
siRNA knockdown of SPHK1 in vivo protects mice from systemic, type-I Allergy.
Provedor de dados: 17
Autores: Jayapal J. Manikandan; Peter Natesan P. N. Pushparaj; Alirio Jose A. J. Melendez.
Systemic anaphylaxis is considered to be a typical immediate hypersensitivity response, determined by the activation of immune
cells,
via antigen-induced aggregation of IgE-sensitized FcεRI cells. Perhaps most the
important cells, in the immediate hypersensitivity responses, are mast cells. We have previously shown that SPHK1 plays a key
role in the intracellular signaling pathways triggered by FceRI aggregation on human
mast cells. More
recently, we performed a genome-wide gene expression profiling of human mast cells, sensitized with IgE alone, or stimulated by
FcεRI aggregation. We found that sphingosine kinase 1 (SPHK1) was one
of genes activated at
the earlier stages of mast cell...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Pharmacology.
Ano: 2007
URL: http://precedings.nature.com/documents/1147/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
Examining the uses of shared data
Provedor de dados: 17
Autores: Heather A. Piwowar; Douglas B. Fridsma.
Background

Many initiatives and repositories exist to encourage the sharing of research data, and
thousands of microarray gene expression datasets are publicly available. Many studies reuse this data, but it is not well understood
which datasets are reused and for what purpose.


Methods

Materials and
We trained a machine-learning algorithm to automatically classify full-text gene expression
microarray studies into two classes: those that generated original microarray data (n=900) and those which only reused data
(n=250). We then compared the Medical Subject Heading (MeSH) terms of two classes to identify MeSH topics which were overor under-represented by publications with...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/425/version/2
Opposite effects of two zinc(II) dithiocarbamates on NF-kB pathway
Provedor de dados: 17
Autores: Boris Cvek; Zdenek Dvorak; Jan Taraba; Lukas Muller; Radim Vrzal; Jitka Ulrichova.
Inhibiting nuclear factor-kappaB (NF-kB) activation in anticancer and antiinflammatory therapy is of topical interest. Current
research in molecular biology has dramatically advanced in the understanding of the cellular events involved in NF-kB induction.
Dithiocarbamates, in particular diethyldithiocarbamate and pyrrolidinedithiocarbamate, have been known and widely used as
strong inhibitors of NF-kB signaling pathway for more than ten years. Their activity is frequently thought to be due to chelating of
zinc or copper present in serum supplemented in the culture medium. Zinc(II) diethyldithiocarbamate (Et2Zn) and zinc(II)
dibenzyldithiocarbamate (Bz2Zn) were prepared by direct synthesis in aqueous millieu. They were structurally characterized by
X-ray...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2007
URL: http://precedings.nature.com/documents/735/version/1
Examining the uses of shared data
Provedor de dados: 17
Autores: Heather A. Piwowar; Douglas B. Fridsma.
Background

Many initiatives and repositories exist to encourage the sharing of research data, and
thousands of microarray gene expression datasets are publicly available. Many studies reuse this data, but it is not well understood
which datasets are reused and for what purpose.


Methods

Materials and
We trained a machine-learning algorithm to automatically classify full-text gene expression
microarray studies into two classes: those that generated original microarray data (n=900) and those which only reused data
(n=250). We then compared the Medical Subject Heading (MeSH) terms of two classes to identify MeSH topics which were overor under-represented by publications with...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/425/version/1
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
Power laws, memory capacity, and self-tuned critical branching in an LIF model with binary synapses
Provedor de dados: 17
Autores: Christopher T. Kello; Bryan Kerster.
Both fluctuations and distributions of spontaneous neural spiking activity have been observed to closely follow a variety of power
laws. Multiple explanations have been offered for each observation, but few lead to mechanisms that encompass their widespread
occurrence. A canonical, leaky integrate-and-fire model is presented in which synapses are updated based on the timing of preand post-synaptic spikes in order to maintain a state of critical branching. Results showed that 1) the self-tuning algorithm
maintained critical branching under a range of parameters; 2) power laws were obtained in spiking activity fluctuations (1/f
scaling), size distributions of network bursts (neural avalanches), and temporal correlations in interspike intervals (Allan...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5893/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
Mining PubMed for Biomarker-Disease Associations to Guide Discovery
Provedor de dados: 17
Autores: Walter J. Jessen; Katherine T. Landschulz; Thomas G. Turi; Rachel Y. Reams.
Biomedical knowledge is growing exponentially; however, meta-knowledge around the data is often lacking. PubMed is a
database comprising more than 21 million citations for biomedical literature from MEDLINE and additional life science journals
dating back to the 1950s. To explore the use and frequency of biomarkers across human disease, we mined PubMed for
biomarker-disease associations. We then ranked the top 100 linked diseases by relevance and mapped them to medical subject
headings (MeSH) and, subsequently, to the Disease Ontology. To identify biomarkers for each disease, we queried Covance
BioPathways, an online data resource that maps commercial biomarker assays to biological and disease pathways. We then
integrated pathways-based information to...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6941/version/1
Lipid models for united-atom molecular dynamics simulations of protein
Provedor de dados: 17
Autores: Andreas Kukol.
Molecular dynamics (MD) simulations of biomolecules are performed at various levels of atomic detail from all-atom models to
coarse grained models. United-atom models are at an intermediate level, in which non-polar hydrogen atoms are subsumed into
their adjacent carbon-atom reducing the number of particles for a DPPC lipid molecule by 60%. United-atom models of the lipids
DPPC, DMPC, POPC and POPG in the GROMOS96 53a6 force field were developed, that reproduced experimental properties of
lipid bilayers without assumption of a constant surface area or inclusion of surface pressure. In the absence of experimental data
a	surface	per lipid area for the negatively charged POPG of 0.700±0.007 nm2 was
obtained	that is higher than...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5977/version/1
Orienting Attention Based on Long-Term Memory Improves Perceptual Discriminations
Provedor de dados: 17
Autores: E. Zita Patai; Jennifer Summerfield; Anling Rao; Anna C. Nobre.
The role of attentional orienting in daily life is to selectively deploy both behavioural and neural resources towards events, based
on continually changing task goals and expectations, in order to optimize performance. In the following experiment, we show that
attentional orienting is influenced by long-term memories in a perceptual discrimination task. In the learning phase, participants
were trained on 120 ecologically valid natural scenes, of which 80 contained a target. Their task was to locate the target (a small
key) on the screen by clicking on it with the mouse. One or two days later, participants completed a cued perceptual
discrimination task. The same scenes that were studied before, but without any targets, were presented as cues (50 ms...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2960/version/1
Structure Prediction and Functional Characterization of ERG Proteins Involved in Ergosterol
Biosynthetic Pathway of Candida albicans
Provedor de dados: 17
Autores: Sudeep Roy; Suaib Luqman; Ashok Sharma.
The ERG proteins and enzymes of the ergosterol biosynthetic pathway has been the subject of intensive investigation as a target
for several classes of antifungal agents used to treat C. albicans infection. Over the past few decades, a number of drugs and
inhibitors with wide spectrum of activity, low toxicity and defined targets have been introduced. Several lines of evidence suggest
that allylamines targets squalene epoxidase (ERG1), morpholines affects sterol C8-C7 isomerase (ERG2) and sterol reductase
(ERG24), azoles inhibits a cytochrome P450 (ERG11) responsible for the 14 α-demethylation of lanosterol and C-5
sterol desaturase (ERG3) and polyenes binds to ergosterol that leads to the damage of cell plasma membrane, ensuing in leakage
of...
Tipo: Poster
Palavras-chave: Microbiology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6709/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
SC1/PRDM4 recruits PRMT5 to control the timing of neural precursor differentiation in developing
neural stem cells
Provedor de dados: 17
Autores: Alexandra Chittka; Ursula Grazini.
During cortical development, neural stem cells (NSCs) switch from proliferative to neuron-generating asymmetric divisions. Here
we investigated the role of Schwann cell factor 1 (SC1/PRDM4), a transcriptional repressor highly expressed in the developing
nervous system, during NSCs development. We found that SC1 protein levels were down-regulated in newly differentiating
neurons, while remaining high in undifferentiated NSCs, suggesting an asymmetric inheritance of SC1. Knockdown of SC1 in the
NSCs led to precocious differentiation of neurons and its overexpression led to an increase in Nestin-expressing precursors. We
found that SC1, through its amino-terminus, recruits the chromatin modifier PRMT5, a histone arginine methyltransferase that
catalyses...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4926/version/1
Modeling long-range interactions across the visual field in stereo correspondence
Provedor de dados: 17
Autores: Jenny C. A. Read.
When the eyes are converged, most objects in the visual scene will have a significant vertical disparity as measured at the retina.
The pattern of vertical disparity across the retina is largely independent of object depth, depending mainly on the particular eye
position
adopted.
Recently,
Phillipson
and
Read
(2010,
European
Journal
of
Neuroscience,
doi:10.1111/j.1460-9568.2010.07454.x) showed that humans are better at achieving stereo correspondence when the vertical
disparity field indicated infinite viewing distance, even when the physical viewing distance was just 30cm. They interpreted this
as indicating that disparity encoding is optimized for long viewing distances, and is not updated to reflect changes in eye posture.
Their results also indicated a...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5840/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
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/1
Improving metabolite evaluation in integrated pathway analysis
Provedor de dados: 17
Autores: Rasanpreet Kaur; Anwesha Dutta; Martina Kutmon; Martijn Iersel; Chris Evelo.
Biological molecules such as proteins and metabolites interact to accomplish a biological function and to respond to
environmental stimuli. Pathways capture this information derived through scientific experimentation and data analysis. They
contain information about genes that appear in complexes, the interacting genes, the directionality of the interactions (e.g.
inhibitors versus activators), the cellular locations where the reactions occur, and the metabolites that are affected by the
processes. Using our open-source pathway analysis platform, PathVisio, we will connect pathway analysis to different quantitative
approaches already in development for metabolic network modeling, such as flux balance analysis and dynamic simulation. In
order to use...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6970/version/1
Modulation of auditory responses by modality-specific attention in rat primary auditory cortex
Provedor de dados: 17
Autores: Lung-Hao Tai; Anthony M. Zador.
How does attention modulate sensory representations? In order to probe the underlying neural mechanisms, we established a
simple rodent model of modality-specific attention. Here we describe results of experiments in freely moving rats in which we
have used tetrodes to record neural responses in primary auditory cortex (area A1) while subjects performed this
behavior.

Subjects were first trained to perform distinct auditory and olfactory two
alternative forced-choice (2AFC) tasks.
Training and testing were conducted in a custom three-poke computer-controlled
behavioral apparatus. Subjects initiated trials with a center-poke, which triggered presentation of a tone (either 5 or 15 Hz), an
odor (either R(-)-2-Octanol or...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2354/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
Timing feedback-inhibition of the male reproductive hormone axis
Provedor de dados: 17
Autores: Ritu R. Malik; Shailesh S. Tondwal; K Subramanian Venkatesh; Gopal Gupta; Amit Misra.
Hormonal methods of male contraception have addressed feedback-inhbition of the cascade of hormones that has evolved to
regulate sperm production but high concentrations of testosterone (T) in the blood have not worked satisfactorily. We
hypothesized that an episodic event, such as degranulation of gonadotropin-releasing hormone (GnRH) neurons in the
hypothalamus, could be as well inhibited by episodic interference as by continuously-applied suppression. We used a
computational model of hypothalamus-pituitary-gonad axis described by Veldhuis et al. to test the hypothesis that episodic
administration of T would inhibit GnRH and/or luteinizing hormone (LH) secretion. A set of stochastic differential equations
model feedback as well as feed-forward actions of...
Tipo: Poster
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2648/version/1
HP-23: Co-ordinated Regulation of Gene Expression in H. Pylori in Response to Low pH and Iron
Limiting Growth Conditions
Provedor de dados: 17
Autores: Ananya Gupta; Sergey Ustinov; Kaveh Mashayekhi; Anthony P. Moran.
Establishing a successful infection within the gastric environment and its varied and changing niches requires adaptation achieved
through regulation of bacterial gene expression. In the gastric environment in addition to the low pH Helicobacter pylori is
required to adapt to conditions of iron limitation. In this study, we used cDNA microarrays to identify genes whose expression
was altered when the bacterium was grown under differing conditions of pH (5 versus 7) and iron limitation. cDNA microarray
analyses following exposure to different growth conditions were carried out for three H. pylori strains 26695 (gastritis-associated),
J99 (ulcer-associated) and AG-1 (atrophic gastritis-associated). Genes were identified whose expression was acid pH-dependent...
Tipo: Poster
Palavras-chave: Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/5842/version/1
OntoCAT - a simpler way to access ontology resources
Provedor de dados: 17
Autores: Tomasz Adamusiak; Tony Burdett; K Joeri van der Velde; Niran Abeygunawardena; Despoina Antonakaki; Helen
Parkinson; Morris Swertz.
OntoCAT is an open source package developed to simplify the task of querying heterogeneous ontology resources. It supports
local ontologies in OBO and OWL format as well as public repositories NCBO BioPortal and EBI Ontology Lookup Service
(OLS). It is available from "http://ontocat.sourceforge.net":http://ontocat.sourceforge.net
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4666/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
Functional annotation of human parvovirus b19 proteome and Molecular docking of VP1 protein
with Teniposide
Provedor de dados: 17
Autores: Amburu Praneetha; Dibyabhaba Pradhan; Vani Priyadarshini; Amineni Umamaheswari.
Parvovirus B19 is a common source of infection with a seroprevalence of 60-70% in the adult population. Human parvovirus
causes several distinct clinical syndromes such as erythema, polyarthritis resembling rheumatoid arthritis, vasculitis, hydrops
fetalis, myocarditis etc. Recent years have witnessed manifest increase in clinical knowledge of parvovirus B19-associated
complications, diagnosis and treatment. Traditional immunosuppressive therapy being unsuccessful, anti-viral therapy might be
worthy of consideration. Functional annotation of human parvoviral proteome may provide insights into role of viral proteome in
its survival and pathogenic mechanisms. Availability of whole proteome in the open source aided functional annotation of protein
using...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5170/version/1
Virtual Fly Brain: An ontology-linked schema of the Drosophila Brain
Provedor de dados: 17
Autores: David J. Osumi-Sutherland; Mark Longair; J. Douglas Armstrong.
Drosophila neuro-anatomical data is scattered across a large, diverse literature dating back over 75 years and a growing number of
community databases. Lack of a standardized nomenclature for neuro-anatomy makes comparison and searching this growing
data-set extremely arduous. 

A recent standardization effort (BrainName; Manuscript
in preparation) has produced a segmented, 3D model of the Drosophila brain annotated with a controlled vocabulary. We are
formalizing these developments to produce a web-based ontology-linked atlas in which gross brain anatomy is defined, in part, by
labeled volumes in a standard reference brain.

We have developed new relations that
allow us to use this...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3980/version/1
In silico comparative analysis of conserved genes expressed in solanaceous plants under abiotic
stresses
Provedor de dados: 17
Autores: sanchita gupta; sunita singh dhawan; ashok sharma.
The gene expression data was studied in order to analyze genes involved in different abiotic stresses in solanaceous plants. Salt,
temperature (heat & cold) and drought are the main abiotic stresses to the plants. Abiotic stress responses are important
for sessile organisms like plants because they have to cope with environmental changes to survive. The idea was to analyze those
differentially expressed genes, which show common expression in response to different abiotic stress conditions in each plant.
Mitogen activated protein kinases (MAPK) are important mediators in signal transmission, connecting the perception of external
stimuli to cellular responses. In plants, MAPKs plays a major role in the signaling of abiotic stresses. The expression...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6717/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
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
Insilico based designing of short peptide and ligands for calcineurin receptor
Provedor de dados: 17
Autores: Vishwamhabr V. Bhandare; T. G. Jagtap; M. M. Pillai; P. S. Patil.
Calcineurin is a target protein for Cyclosporin A (CsA) an immunosuppressive drug which prevents transplant rejection. CsA has
complex structure of 11 amino acids, a cyclic structure with uncommon amino acids, and can’t be chemically
synthesized. CsA can be synthesized commercially by using fermentation. One report shows chemical synthesis of CsA with
partial success (Jason and Diver, 2002). In view of this it is proposed to model a peptide and ligand as an alternate for CsA with
the same function and can be chemically synthesized. The target for Cyclosporin is Cyclophilin which forms a ternary complex
with calcineurin (CN). An in silico study concludes that all four peptides (1 wild + 3 mutant) were found to bind in the catalytic
site of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6072/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
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
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
Wormbase Curation Interfaces and Tools
Provedor de dados: 17
Autores: Xiaodong Wang.
Curating biological information from the published literature can be time- and labor-intensive especially without automated
tools. WormBase1 has adopted several curation interfaces and tools, most of which were built in-house, to help curators recognize
and extract data more efficiently from the literature. These tools range from simple computer interfaces for data entry to
employing scripts that take advantage of complex text extraction algorithms, which automatically identify specific objects in a
paper and presents them to the curator for curation. By using these in-house tools, we are also able to tailor the tool to the
individual needs and preferences of the curator. For example, Gene Ontology Cellular Component and gene-gene interaction
curators...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5112/version/1
Implications of single-neuron gain scaling for information transmission in networks
Provedor de dados: 17
Autores: Julijana Gjorgjieva; Michael Famulare; Rebecca Mease; William J. Moody; Adrienne L. Fairhall.
Summary: 

Many neural systems are equipped with mechanisms to efficiently encode
sensory information. To represent natural stimuli with time-varying statistical properties, neural systems should adjust their gain
to the inputs' statistical distribution. Such matching of dynamic range to input statistics has been shown to maximize
the information transmitted by the output spike trains (Brenner et al., 2000, Fairhall et al., 2001). Gain scaling has not only been
observed as a system response property, but also in single neurons in developing somatosensory cortex stimulated with currents of
different amplitude (Mease et al., 2010). While gain scaling holds for cortical neurons at the end of the first post-natal...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5860/version/1
Future Predictions of _Cyclamen_ Distribution in the Mediterranean Region
Provedor de dados: 17
Autores: Claudia Ciotir; Chris Yesson; Alastair Culham.
_Cyclamen_ (Myrsinaceae) occupy the Mediterranean region, with highest diversity in Greece and Turkey, with a few species
endemic to islands. _Cyclamen_ species have a phenological preference for dry summers and wet winters. A recent study
developed models of the climatic niches of _Cyclamen_. These models were projected into future climate scenarios for 2050. The
area of climatic suitability for every _Cyclamen_ species is predicted to decrease. A limited dispersal capacity places them at high
risk of extinction. Half of the species are threat ened with extinction due to their potential area loss, indicating that conservation
and protection for these species has to be implemented by adding them to the red list.
Tipo: Poster
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3066/version/1
Identification of Unique proteins of Candida albicans as Antifungal Drug Targets
Provedor de dados: 17
Autores: Himanshu Tripathi; Abha Meena; Feroz Khan; Suaib Luqman.
There are growing examples of drug resistance in the fungal pathogens to evade antifungal drugs by developing mutation in the
key targeted enzymes and high expression of drug transporter genes including ABC transporters and MFS transporters. This led to
the urgent need to identify novel (unique or essential to fungus) targets that can be used in development of potential antifungal
drugs. We have used a comparative genomics approach to find out novel targets in opportunistic fungus, Candida albicans
responsible for severe infection in immunocompromised humans. To identify novel targets we have analyzed available total
14,633 protein sequences (proteome) of C. albicans [SC5314] retrieved through RefSeq, an experimentally curated reference
sequence database...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6619/version/1
The Army of One (Sample): the Characteristics of Sampling-based Probabilistic Neural
Representations
Provedor de dados: 17
Autores: Pietro Berkes; Richard E. Turner; Jozsef Fiser.
There is growing evidence that humans and animals represent the uncertainty associated with sensory stimuli and utilize this
uncertainty during planning and decision making in a statistically optimal way. Recently, a nonparametric framework for
representing probabilistic information has been proposed whereby neural activity encodes samples from the distribution over
external variables. Although such sample-based probabilistic representations have strong empirical and theoretical support, two
major issues need to be clarified before they can be considered as viable candidate theories of cortical computation. First, in a
fluctuating natural environment, can neural dynamics provide sufficient samples to accurately estimate a stimulus? Second, can
such a code...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5811/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
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
Microbial responses to changes in land use
Provedor de dados: 17
Autores: Rebecca C. Mueller; Klaus Nüsslein; Jorge Rodrigues; James Tiedje; Vivian Pellizari; Brigitte Feigl;
Brendan Bohannan.
Background/Question/Methods
Land use change is one of the greatest threats to biodiversity worldwide.
This
is
especially
true
for
land
use
change
that
results
in
the
destruction
of
intact
forest,
or
"deforestation”. Deforestation is causing a loss of biological diversity on an unprecedented scale,
especially in the Tropics. It is unclear how the majority of the biodiversity on Earth – microbial biodiversity
– is responding to these extraordinary rates of deforestation. I will provide an overview of our current understanding
of microbial responses to deforestation. I will focus, as an example, on our current research regarding the effects of deforestation
on the diversity of arbuscular mycorrhizal...
Tipo: Poster
Palavras-chave: Ecology; Microbiology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5505/version/1
Reactome - a knowledgebase of human biological pathways
Provedor de dados: 17
Autores: Peter D'Eustachio; David Croft; Bernard de Bono; Gopal Gopinath; Marc Gillespie; Bijay Jassal; Lisa
Matthews; Esther Schmidt; Imre Vastrik; Guanming Wu; Suzanna Lewis; Ewan Birney; Lincoln Stein.
Pathway curation is a powerful tool for systematically associating gene products with functions. Reactome (www.reactome.org) is
a manually curated human pathway knowledgebase describing a wide range of biological processes in a computationally
accessible manner. The core unit of the Reactome data model is the Reaction, whose instances form a network of biological
interactions through entities that are consumed, produced, or act as catalysts. Entities are distinguished by their molecular
identities and cellular locations. Set objects allow grouping of related entities. Curation is based on communication between
expert authors and staff curators, facilitated by freely available data entry tools. Manually curated data are subjected to quality
control and peer...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1281/version/1
Homology modeling and in silico screening of inhibitors for human CD5 antigen-like protein involved
in cardiovascular disease
Provedor de dados: 17
Autores: Varala Sravani; S Rajitha Reddy; Amineni Umamaheswari.
CD5L (CD5 antigen -like) is a secreted glycoprotein that belongs to the SRCR (scavenger receptor cysteine rich) group B family
of proteins that regulate leukocyte function. Over expression of human CD5L leads to Kawasaki disease and atherosclerosis. In
the quest of designing novel inhibitors against CD5L, homology models for the protein were predicted based on crystal structures
of 1BY2, 2OYA and 2OY3 as multiple templates using Modeller 9v9. The CD5L homology models were selected using GA341
score, DOPE score, PROCHECK and ProSA to select the best model. The selected CD5L model was analyzed using CASTp to
locate the largest ligand binding pocket. Five known inhibitors of human CD5L were searched for structural analogs from
Ligand.Info Meta database. The...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6586/version/1
Elevated CO2 and O3 Effects on Fine-Root Life Span in Ponderosa Pine
Provedor de dados: 17
Autores: Donald L. Phillips; Mark G. Johnson; David T. Tingey; Marjorie J. Storm.
Atmospheric carbon dioxide (CO2) and ozone (O3) concentrations are rising, which may have opposing effects on tree C balance
and allocation to fine roots. More information is needed on interactive CO2 and O3 effects on roots, particularly fine-root life
span, a critical demographic parameter and determinant of soil C and N pools and cycling rates. We conducted a study in which
ponderosa pine (Pinus ponderosa) seedlings were exposed to two levels of CO2 and O3 in sun-lit controlled-environment
terracosms for three years. Minirhizotrons were used to monitor individual fine roots in three soil horizons every 28 days.
Proportional hazards regression was used to analyze effects of CO2, O3, diameter, depth, and season of root initiation on
fine-root...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3703/version/1
JSBML: a flexible and entirely Java-based library for working with SBML
Provedor de dados: 17
Autores: Andreas Dräger; Nicolas Rodriguez; Marine Dumousseau; Alexander Dörr; Clemens Wrzodek;
Roland Keller; Sebastian Fröhlich; Nicolas Le Novère; Andreas Zell; Michael Hucka.
The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer
models of biological processes in text files. In order to perform model simulations, graphical visualizations and other software
manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior
implementations of SBML APIs, JSBML has been designed from the ground up for the Java™ programming
language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for
Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and
Versions through Level 3 Version...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6372/version/1
Identifiers.org/MIRIAM Registry annotation and cross-referencing framework
Provedor de dados: 17
Autores: Nick Juty; Camille Laibe; Nicolas Le Novere.
We describe the MIRIAM Registry, which forms a foundation layer database upon which persistent, unambiguous and perennial
identifiers of data can be built. We describe the existing MIRIAM URI identifiers, and the newly minted resolvable, parallel forms
of these identifiers which use Identifiers.org URLs.
Tipo: Poster
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6396/version/1
UIMA in the Biocuration Workflow: A coherent framework for cooperation between biologists and
computational linguists
Provedor de dados: 17
Autores: Bart Mellebeek; Carlos Rodriguez-Penagos; Laura Ines Furlong.
As collaborating partners, Barcelona Media Innovation Centre and GRIB (Universitat Pompeu Fabra) seek to combine strengths
from Computational Linguistics and Biomedicine to produce a robust Text Mining system to generate data that will help
biocurators in their daily work. The first version of this system will focus on the discovery of relationships between genes, SNPs
(Single Nucleotide Polymorphisms) and diseases from the literature.

A first challenge
that we were faced with during the setup of this project is the fact that most current tools that support the curation workflow are
complex, ad-hoc built applications which sometimes make difficult the interoperability and results sharing between research
groups from...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3171/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
The statistics of contour fragments in natural scenes
Provedor de dados: 17
Autores: Josh Merel; Gasper Tkacik; Adam Gifford; Jason Prentice; Vijay Balasubramanian.
Summary: Recent electrophysiology recordings in macaque V4/IT suggest that single neuron response to synthetic closed
contours can be largely captured by models which only consider a small number of contour fragments (Brincat and Connor 2004).
Motivated by this experimental work, we sought firstly to characterize the statistics of contour fragments in natural scenes, and
secondly
to
generate
synthetic
images
which
reflect
the
measured
contour-fragment
statistics.

To detect contour fragments, we defined a set of feature detectors which
respond only in the presence of two edges co-occurring at a fixed relative angle – implemented as a logical
‘AND’ of two Gabor-like, laplacian-of-gaussian...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6366/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
Porous Chitsan-Gelatin Scaffolds Embedded with PLGA Nanoparticles for Bone Repair
Provedor de dados: 17
Autores: Vijay Kumar Nandagiri; Piergiergio Gentile; Valeria Chiono; Clara Muttu; Gianluca Ciardelli; Franco Maria
Montevecchi; Ziebun Ramtoola.
Bone regeneration can be accelerated by localized delivery of appropriate growth factors/bio active molecules. Localized delivery
can be achieved by incorporating bioactive molecules within biodegradable particulate carrier system followed by embed them in
a suitable porous scaffolds. These carrier system facilitates the impregnated growth factor(s) to release at a desirable rate and
concentration, and to linger at injury sites for a sufficient time to recruit progenitors and stimulate tissue healing processes. In this
study, an attempt has been made to engraft the porous chitosan-gelatin scaffolds with PLGA nanoparticles for localized delivery
of bioactive components. Scaffolds loaded with PLGA nanoparticles were subjected to physical and mechanical...
Tipo: Poster
Palavras-chave: Developmental Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4728/version/1
Terminizer - Assisting Mark-Up of Text Using Ontological Terms
Provedor de dados: 17
Autores: David Hancock; Norman Morrison; Giles Velarde; Dawn Field.
We present a tool that automatically detects ontological terms in free text. Once candidate terms have been identified the results
are displayed either overlaid on the original text or in a list organised by the ontology and frequency. The user can interactively
accept or reject each match, or try to find a more appropriate match by exploring the network of ontology concepts themselves. In
typical ontological resources, the parent(s) of a term represent broader concepts whilst the children of a term represent more
specific concepts. In this way, the suggested match can used as a starting point for the user to find a more suitable term. The
ontology browser interface incorporates a graphical visualisation which uses Flash to present an interactive view of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3128/version/1
MMsPred: a bioactivity and toxicology predictive system
Provedor de dados: 17
Autores: Joel Masciocchi; Luca Pireddu; Ricardo Medda; Piergiorgio Palla; Matteo Floris; Luca Pani; Patricia Rodriguez-Tome.
In the last decade, the development and use of new methods in combinatorial chemistry and high-throughput screening has
dramatically increased the number of known biologically active compounds. Paradoxically, the number of drugs reaching the
market has not followed the same trend, often because many of the candidate drugs present poor qualities in absorption,
distribution, metabolism, excretion, and toxicological properties (ADME-Tox). The ability to recognize and discard bad
candidates early in the drug discovery steps would save lost investments in time and money. Machine learning techniques could
provide solutions to this problem.
The goal of my research is to develop classifiers that accurately
discriminate between active and inactive...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4188/version/1
Envelope protein as molecular target for YFV (Yellow fever virus) drug discovery
Provedor de dados: 17
Autores: Manne Munikumar; Dibyabhaba Pradhan; I. Vani Priyadarshini; Amineni Umamaheswari.
Yellow fever (YF), a mosquito-borne viral haemorrhagic fever, is one of the most lethal viral diseases. Despite the availability of
vaccines, yellow fever virus (YFV) strikes an estimated 2, 00,000 persons world-wide each year and causes 30,000 deaths
approximately. There are no approved antiviral therapies for the treatment of YFV disease in humans. YFV 17D strain RNA
genome is of 10,862 nucleotides, which encodes three structural proteins (C, PrM, and E) and seven nonstructural proteins (NS1,
NS2A, NS2B, NS3, NS4A, NS4B, and NS5). Identification of different protein functions facilitates a mechanistic understanding
of YFV infection and opens novel means for drug development. Functional assignment of complete YFV proteome was done
through support Vector...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5151/version/1
Responses of soil nitrite-oxidizers to global environmental changes
Provedor de dados: 17
Autores: Audrey Niboyet; Eléonore Attard; Laure Barthes; Christopher B. Field; Nadine Guillaumaud; Bruce A.
Hungate; Paul W. Leadley; Catherine Lerondelle; Thomas Pommier; Maria Tourna; Akihiko Terada; Franck Poly; Xavier Le
Roux.
Background/Question/Methods
There is increasing evidence that global change can alter the structure of
plant
communities with large impacts on the functioning of terrestrial ecosystems. However, little is known
about the impact of global change on soil microbial communities. In particular, the response of soil nitrite-oxidizers
microorganisms that mediate the second step of nitrification, a key process of the nitrogen cycle, has never been
investigated.
Here, we examined the effects of four main global environmental changes on the activity, the
abundance and the diversity of soil nitrite-oxidizers in an annual grassland ecosystem as part of the Jasper Ridge Global Change
Experiment (CA, USA). This...
Tipo: Poster
Palavras-chave: Ecology; Microbiology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5509/version/1
Snow Cover in South Dakota: Statistical analysis of spatiotemporal diversity
Provedor de dados: 17
Autores: Boris Shmagin; Carol A. Johnston.
Snow distribution and accumulation influence many human activities and the dynamic sustainability of ecological systems. Snow
cover distribution analysis is a second research step towards creating a Atlas of Climate and Water Resources for SD (temperature
analysis was presented last year). We analyzed the regional diversity of monthly total snowfall based on long-term data obtained
from the High Plains Regional Climate Center for South Dakota. Multidimensional statistical methods were used, and the results
presented for the State of South Dakota. 

The sets of initial matrixes were compiled
with snow observations for the state. The first type of initial matrix of time series {Xt*n}, where t = number of years (67) and n
=...
Tipo: Poster
Palavras-chave: Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1826/version/1
The Neural Control Mechanisms Underlying Memory-Guided Attention
Provedor de dados: 17
Autores: Ian C. Gould; Mark G. Stokes; Kathryn Atherton; Anna C. Nobre.
The control mechanisms that guide selective attention are typically examined in response to explicit attentional cues. In everyday
life, however, the focus of attention is more typically guided according to past experiences than direct instruction. We therefore
developed a novel behavioural paradigm to examine the neural substrate of memory-guided attentional orienting. Participants first
learn the location of target stimuli hidden within naturalistic scenes. After the target locations have been learned, participants then
perform an attention-orienting task. Each experimental trial begins with a cue stimulus, consisting of the memory scene presented
without the target stimulus. A test scene is then presented, with a 50% probability of a target stimulus...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2955/version/1
LibSBGN: Electronic Processing of SBGN maps
Provedor de dados: 17
Autores: Martijn P. van Iersel; Sarah E. Boyd; Frank Bergmann; Stuart Moodie; Falk Schreiber; Tobias Czauderna; Emek Demir;
Nicolas Le Novère; Anatoly Sorokin; Huaiyu Mi; Augustin Luna; Ugur Dogrusoz; Yukiko Matsuoka; Akira
Funahashi; Hiroaki Kitano; Mirit I. Aladjem; Michael L. Blinov; Alice C. Villéger.
Introduction

Graphical representations of participants and their relationships are
essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously,
it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical
Notation (SBGN) has been developed.

As SBGN is becoming more widely adopted,
and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange
using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need
for a toolset that...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/4967/version/2
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
Regulation of virulence in Francisella tularensis by small non-coding RNAs
Provedor de dados: 17
Autores: Guillaume Postic; Eric Frapy; Marion Dupuis; Iharilalao Dubail; Jonathan Livny; Alain Charbit; Karin L. Meibom.
Using a cDNA cloning and sequencing approach we have shown that Francisella tularensis expresses homologues of several small
RNAs
(sRNAs) that are well-conserved among diverse bacteria. We have also discovered two abundant
putative sRNAs that share no sequence similarity or conserved genomic context with any previously annotated regulatory
transcripts. Deletion of either of these two loci led to significant changes in the expression of several mRNAs that likely include
the cognate target(s) of these sRNAs. Deletion of these sRNAs did not, however, significantly alter F. tularensis growth under
various stress conditions in vitro, its replication in murine cells, or its ability to induce disease in a mouse model of F. tularensis
infection.
Tipo: Poster
Palavras-chave: Genetics & Genomics; Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/5965/version/1
The role of Havana and communities in the manual curation of unfinished vertebrate genomes
Provedor de dados: 17
Autores: Denise R. Carvalho-Silva; Chao-Kung Chen; Adam Frankish; James Gilbert; Leo Gordon; Toby Hunt; Mustapha
Larbaoui; Jane E. Loveland; Jonathan Mudge; Harminder Sehra; Catherine Snow; Charlie Steward; Marie Marthe Suner; Mark
Thomas; Laurens Wilming; Jennifer Harrow.
Manual
annotation‭
"‬museum‭"
(‬the‭
‬model
of
annotation‭)
‬relies on a small group of specialized curators to catalogue and classify genes according to their functional
roles.‭ This‬ is both costly and time consuming and therefore is used only for model organisms with
sufficient funding.‭ ‬Smaller research communities often have to rely on other models of
annotation,‭
‬mainly
automated
annotation‭
"‬factory‭"
(‬the‭
‬model,‭
‬e.g.‭...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3102/version/1
Screening of different species of Bacillus against broad spectrum antibiotics
Provedor de dados: 17
Autores: Vivek Bajpai; Yamini Singh Sisodia; Pallavi Sharma; Pankaj Jain.
Sewage is waste suspended in water that is intended to flow away from a community. Sewage effluent contains a wide range of
pathogenic microorganisms which may pose health hazards to the human population when they are discharged into the
environment. This study is carried out to systematically examine the pathogenic microorganisms in sewage samples isolated from
the Shekhawati region of Rajasthan. For this purpose a survey was carried out at the Sewage Treatment plant of the Mody Institute
of Technology & Science, Laxmangarh, Sikar. In this survey we isolated 26 bacterial strains and identified them using
biochemical and molecular methods. Different biochemical tests were performed during the study and in molecular identification
by DNA isolation,...
Tipo: Poster
Palavras-chave: Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/6677/version/1
The direct and indirect effects of the red imported fire ant (Solenopsis invicta) on seed fate in the
longleaf pine ecosystem
Provedor de dados: 17
Autores: Margaret Shearin; L K. Kirkman; Ronald Carroll.
Invasion of non-native ants potentially disrupts natural relationships of native ants and ant-dispersed plants. These relationships
may be affected directly through seed collection, or indirectly though impacts on the native ant community.
Solenopsis invicta
(the red imported fire ant), a widespread invasive of the southeastern United States, negatively impacts human health, agriculture,
and wildlife. The impacts of S. invicta on native plant communities are less understood, partially because the invasions are
usually coupled with human disturbance of soil or vegetation. The longleaf pine ecosystem is one of the few native communities
successfully invaded by S. invicta. In a natural stand of longleaf pine with native groundcover we determined the...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5217/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
Worm Annotation in the UniProt Knowledgebase (UniProtKB)
Provedor de dados: 17
Autores: Duncan J. Legge; UniProt Consortium.
The nematode worm, _Caenorhabditis elegans_, was the first multicellular organism to be sequenced. Its genome was published in
1998, providing an impetus for gene and protein annotation. Recently, the genome of _C. briggsae_ has been sequenced. This has
given bioinformaticans the opportunity to study comparative genomics between two highly similar organisms. Currently, there are
12 species of _Caenorhabditis_ in UniProtKB and over 700 nematode species, including some of interest to parasitology.
Functional and sequence annotation from literature and sequence analysis tools are included in each curated record. _C. elegans_
has a relatively small genome size, short life span and a transparent body, making it ideal for knock-out/RNAi studies. Thus many
_C....
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3157/version/1
Plant regulation of microbial enzyme production in situ
Provedor de dados: 17
Autores: Colin Averill; Adrien C. Finzi.
Soil extracellular enzymes regulate the rate at which complex organic forms of nitrogen (N) become bio-available. Much research
has focused on the limitations to heterotrophic enzyme production via lab incubations, but little has been done to understand the
limitations to enzyme production in situ. We created root and symbiotic mycelia exclusion treatments using mesh in-growth bags
in the field to isolate the effect of roots and other portions of the microbial community on enzyme production. When fertilized
with complex protein N we found increases in N-degrading enzyme concentrations only when root in-growth was allowed. No
response was observed when complex N was added to root-free treatments. Expanding on economic rules of microbial element
limitation...
Tipo: Poster
Palavras-chave: Ecology; Microbiology; Earth & Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6353/version/1
Learning to discount transformations as the computational goal of visual cortex
Provedor de dados: 17
Autores: Joel Z. Leibo; Jim Mutch; Tomaso Poggio.
It has been long recognized that a key obstacle to achieving human-level object recognition performance is the problem of
invariance. The human visual system excels at factoring out the image transformations that distort object appearance under
natural conditions. Models with a cortex-inspired architecture such as HMAX as well as nonbiological convolutional neural
networks are invariant to translation (and in some cases scaling) by virtue of their wiring. The transformations to which this
approach has been applied so far are _generic_; a single example image of any object contains all the information needed to
synthesize a new image of the transformed object. In contrast, viewpoint and illumination transformations depend on the
object's 3D...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6078/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
Genome activity profiling of monomeric-IgE and Fc-epsilon-RI-aggregation on human mast cells
reveals a complex network of genes involved in inflammatory responses.
Provedor de dados: 17
Autores: Jayapal J. Manikandan; Alirio Jose P. N. Melendez; Peter Natesan A. J. Pushparaj.
Mast cell activation, mediates type-1 allergic responses, one of the most powerful reactions of the immune system. However, mast
cells activation is becoming increasingly linked to inflammatory, autoimmunity, and to adaptive immunity by regulating T-cell
activation.
Here we analyzed the gene expression pattern in IgE-sensitized and FcεRI
aggregation on human mast cells. Our data revealed coordinated changes in gene expression. We observed increased expression of
gene-transcripts involved in allergic, innate and adaptive
immune responses. Among the most prominent
findings is the increased expression of transcripts encoding for MIP3a, SPARCL1, AREG, IL18, CCL1, TNFRSF9, IL1b,
CX3CR1, PTGER3, MIF, MMP12, ADORA3,...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1150/version/1
ODIN: An Advanced Interface for the Curation of Biomedical Literature
Provedor de dados: 17
Autores: Fabio Rinaldi; Simon Clematide; Gerold Schneider; Martin Romacker; Therese Vachon.
We
present
*ODIN*
(Ontogene
Document
biomedical
literature,
developed
INspector):
within
a
the
system
scope
for
of
interactive
the
curation
of
"*SASEBio*
project":http://www.ontogene.org/projects/sasebio/ (Semi-Automated Semantic Enrichment of the Biomedical
Literature), as a collaboration between the "OntoGene group":http://www.ontogene.org/ at the University
of Zurich and the NITAS/TMS group of Novartis Pharma AG. The purpose of the system is to allow a human annotator/curator to
leverage upon the results of an advanced text mining system in order to enhance the speed and effectiveness of the annotation
process. 

The OntoGene system takes as input a document (e.g a...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5169/version/1
Does the Density of Invasive Rusty Crayfish Affect Stream Macroinvertebrates?
Provedor de dados: 17
Autores: Mark Kuhlmann; Anthony Prisciondaro; Megan Irland; Greg Hamilton; Sara Caldwell; Ryan Oliver.
Rusty crayfish (_Orconectes rusticus_) have invaded streams of the upper Susquehanna River catchment (New York, USA),
replacing native crayfish and probably increasing overall crayfish density. Crayfish are important consumers and agents of
disturbance in aquatic communities, so the introduction and expansion of rusty crayfish could affect the invaded community
through the change in crayfish species composition, the increase in crayfish density, or some combination of the two. Other
macroinvertebrates are prey of, competitors with, or subject to disturbance by crayfish and so are likely to be affected by changes
in the crayfish assemblage. We conducted correlative field sampling and an enclosure experiment to investigate the effects of
invading _O....
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3701/version/1
Towards more Challenging Problems for Ontology Matching Tools
Provedor de dados: 17
Autores: Ernesto Jimenez-Ruiz; Bernardo Cuenca Grau.
We motivate the need for challenging problems in the evaluation of ontology matching tools. To address this need, we propose
mapping sets between well-known biomedical ontologies that are based on the UMLS Metathesaurus. These mappings could be
used as a basis for a new track in future OAEI campaigns (http://oaei.ontologymatching.org/).

Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6612/version/1
Genome sequence and genetic linkage analysis of Shiitake mushroom _Lentinula edodes_
Provedor de dados: 17
Autores: Hoi Shan Kwan; Chun Hang Au; Man Chun Wong; Jing Qin; Iris Sze Wai Kwok; Winnie Wing Yan Chum; Pui Ying
Yip; Kin Sing Wong; Lei Li; Qian Li Huang; Wen Yan Nong.
_Lentinula edodes_ (Shiitake/Xianggu) is an important cultivated mushroom. Understanding the genomics and functional
genomics of _L. edodes_ allows us to improve its cultivation and quality. Genome sequence is a key to develop molecular genetic
markers for breeding and genetic manipulation. We sequenced the genome of _L. edodes_ monokaryon L54A using Roche 454
and ABI SOLiD genome sequencing. Sequencing reads of about 1400Mb were de novo assembled into a 40.2 Mb genome
sequence. We compiled the genome sequence into a searchable database with which we have been annotating the genes and
analyzing the metabolic pathways. In addition, we have been using many molecular techniques to analyze genes differentially
expressed during development. Gene ortholog groups...
Tipo: Poster
Palavras-chave: Genetics & Genomics.
Ano: 2012
URL: http://precedings.nature.com/documents/6855/version/1
Invasional conflict: Do invasive insect herbivores mediate the effects of enemy release for their
invasive plant hosts?
Provedor de dados: 17
Autores: Kerry R. Bohl; Peter Stiling.
Although many factors have been proposed that potentially contribute to invasion success in plants, it remains unclear why some
species successfully establish and become dominant while others do not. The most often cited explanation for the success of
invasive plants worldwide is the enemy release hypothesis (ERH), which maintains that populations are kept in check by their
co-evolved natural enemies in their native range, but are released from this regulation in the new range. Although there is
evidence that introduced plant species often experience a decrease in damage by herbivores in the novel range, it is uncertain if
this decrease affects plant productivity. The purpose of this study was 1) to determine if the invasive plant _Eugenia uniflora_...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3716/version/1
New fungal sources for α-L-Rhamnosidase: an important enzyme used in the synthesis of
drugs and drug precursors
Provedor de dados: 17
Autores: Vinita Yadav; Kapil Deo Singh Yadav.
Two fungal strains were isolated and tentatively identified as Penicillium VY and Aspergillus VY. All the isolated species show
the maximum production on third day in a liquid culture media. The pH optimum was found to be 10.0 for Penicillium VY and
11.0 for Aspergillus VY. The temperature optima were 50ºC in both the cases. The enzyme produced by Penicillium
VY was found to be stable in the pH range 3.0-7.0 and 3.0–6.0 in case of Aspergillus VY. The enzyme does not
loose activity up to 40º C in case of Penicillium VY and 40ºC in case of Aspergillus VY if exposed for 1
h.

Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/2560/version/1
The influence of different excipients and storage procedures on hCG (human Corionic Gonadotropin)
as evidenced by spectrophotometry
Provedor de dados: 17
Autores: Daniel Oscar Belluscio; Sergio Ariel Vaney.
Our studies concluded that changes in either PH, temperature, electrolytes, excipients, alcohol or silver modify the chemical
structure of hCG as evidenced by UV-Spectrophotometry.
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5919/version/1
The community of herbivorous arthropods as an indicator for biological control function in the Post
Market Environmental Monitoring of the cultivation of stacked Bt maize
Provedor de dados: 17
Autores: Eva Schultheis; Alan J. Slusarenko; Stefan Rauschen.
In field experiments on the potential impacts of the genetically engineered Bt maize events MON 810, MON 88017, and MON
89034 x MON 88017, data were gathered on a diverse range of non-target organisms (NTO). These experiments were performed
at different trial locations since 2001.

Surveying herbivores serves two purposes: (i)
to assess direct effects on these NTO, and (ii) indirectly analyse disturbances in the biological control function of natural enemies
(Sanvido et al., 2009).

Herbivores of interest for this approach should be exposed to
the
Bt
proteins,
representative
for
the
maize
biocoenosis,
and
of
considerable
densities
using
standardised
methods.
Plant bugs...
Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4492/version/1
p-hydroxybenzoic acid inhibited photosynthetic efficiency, yield and non-photochemical fluorescence
quenching in Lactuca sativa
Provedor de dados: 17
Autores: M. Iftikhar Hussain; Luis Gonzalez; Manuel Joaquin Reigosa.
The p-hydroxybenzoic acid (BA) is a widespread phenolic compound often cited as allelochemical [1], released into soil by root
exudates of _Avena fatua_ [2], leaf leachates, and decomposed plant tissues of _Triticum aestivum_ L. [3]. Because of the
herbicidal potential of BA on crops [4] and weed species [5], commercially available BA was tested on photosynthetic efficiency,
yield and non-photochemical fluorescence quenching in _Lactuca sativa_ in a glass house study. The stock solution (3mM) of BA
was made in Methanol: Water (20:80). Methanol was evaporated in a rotary vaporizer and stock solution was adjusted to
concentration of 1.5 mM. Lettuce (_Lactuca sativa_ L. cv. Great Lakes California) seeds were grown in perlite culture in plastic
pots, irrigated...
Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4573/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
Sociobiological Control of Plasmid copy number
Provedor de dados: 17
Autores: Mukta Watve; Milind Watve.
Background:
All known mechanisms and genes responsible for the regulation of plasmid replication lie with
the plasmid rather than the chromosome. It is possible therefore that there can be copy-up mutants. Copy-up mutants will have
within host selective advantage. This would eventually result into instability of bacteria-plasmid association. In spite of this
possibility low copy number plasmids appear to exist stably in host populations. We examined this paradox using a computer
simulation model.

Model:
Our multilevel selection model
assumes a wild type with tightly regulated replication to ensure low copy number. A mutant with slightly relaxed replication
regulation can act as a...
Tipo: Poster
Palavras-chave: Ecology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/2016/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
Polyelectrolyte multilayer assembly bearing ketoprofen for transdermal delivery
Provedor de dados: 17
Autores: Rachna Gupta; Preeti Yadav; Subhini A. Saraf.
A novel microencapsulation technology based on layer-by-layer assembly has been extensively studied and used for controlled
delivery of drug microcrystal having poor aqueous solubility and low bioavailability. A non-steroidal anti-inflammatory drug
ketoprofen (KF)was selected for encapsulation using biodegradable and biocompatible polyions and synergistically the fabricated
system was embedded in gel matrix for topical application. Topical application of the drugs at the pathological sites offer potential
advantages of delivering the drug directly to the site of action and thus producing high tissue concentrations of the drug.
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3849/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
Transcriptional complex assembly represented in SBGN PD
Provedor de dados: 17
Autores: Alexander Mazein; Steven Watterson; Peter Ghazal.
This poster shows how transcriptional complex assembly can be represented in SBGN Process Description language. Example:
LPS-induced TNF-alpha enhancer complex formation.
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4984/version/1
Weight matrix based identification of terpene synthases conserved motifs in Arabidopsis thaliana
proteome
Provedor de dados: 17
Autores: Suchita Srivastava; Suaib Luqman; Feroz Khan.
Terpenes comprise the most diverse collection of natural products. Out of more than 30,000 individual terpenoids identified, at
least half are synthesized by plants. A relatively small, but quantitatively significant, number of terpenoids are involved in primary
plant metabolism. However, the vast majorities are classified as secondary metabolites; compounds not required for plant growth
and development but presumed to have an ecological function in communication or defense and are widely used in industrial
applications. Terpene hydrocarbon scaffolds are generated by the action of the mechanistically intriguing family of mono-,
sesqui-, and diterpene synthases collectively termed as terpene synthases, that catalyze multistep reactions with
diphosphorylated...
Tipo: Poster
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6909/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
Towards a web-based simulation experiment description repository
Provedor de dados: 17
Autores: Michael Guravage; Roeland M. H. Merks.
Modellers are producing more and more complex models. Unless these models are sufficiently characterised and made available
to the research community their reuse will be minimal, and reproducing simulation experiments incorporating them will prove
problematic. Consensus on the content and form of experiment recipes that combine models and simulations will encourage model
sharing and facilitate reuse.

A set of guidelines specifying the 'Minimum
Information About a Simulation Experiment'(MIASE) proposes a common set of information necessary to reproduce
simulation experiments that incorporate quantitative models.

We have instantiated
these guidelines in a web-based...
Tipo: Poster
Palavras-chave: Plant Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6346/version/1
Increased flood frequency and magnitude decreases density of a stream-breeding salamander in
urbanized watersheds
Provedor de dados: 17
Autores: Kyle Barrett; Craig Guyer.
Background/Question/Methods
As urbanization increases across the globe, more ecologists have taken note
of its consequences to stream systems. Sufficient data have been collected to document repeated patterns in urbanized streams for
many abiotic parameters, aquatic insects, and fish. For example, we now know that urbanized streams experience more frequent
and intense spates as a result of increased runoff form impervious surfaces in the urban watershed. The spates eventually lead to a
more incised and wider stream bed. Such abiotic shifts consistently result in decreased aquatic invertebrate and fish diversity.
More recently, stream-breeding salamanders have been observed to decrease in density in urban areas. We monitored the density
of...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3972/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
eagle-i: An Ontology-Driven Framework For Biomedical Resource Curation And Discovery
Provedor de dados: 17
Autores: Erik Segerdell; Melanie L. Wilson; Ted Bashor; Daniela Bourges-Waldegg; Karen Corday; H. Robert Frost; Tenille
Johnson; Christopher J. Shaffer; Larry Stone; Carlo Torniai; Melissa A. Haendel.
The
eagle-i
Consortium
("http://www.eagle-i.org/home":www.eagle-i.org/home)
comprises
nine
geographically and ethnically diverse universities across America working to build a federated network of research resources.
Biomedical research generates many resources that are rarely shared or published, including: reagents, protocols, instruments,
expertise, organisms, training opportunities, software, human studies, and biological specimens. The goal of eagle-i is to improve
biomedical research by helping researchers more easily find scientific resources that are difficult to discover, reducing
time-consuming and expensive duplication of resources. Now in early development, the system will ultimately expand to include
research resources at...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5176/version/1
Molecular Static and Dynamic Analyses reveal Flaw in Murine Model used by US FDA to Detect
Drug Carcinogenicity
Provedor de dados: 17
Autores: Trevor Marshall.
The US FDA currently accepts carcinogenicity studies of pharmaceutical drugs based on murine models. In addition to 6 month
studies with p53(+/-) and ras.H2 transgenic mice, lifetime studies (typically 2 years) in WT mice or rats are also considered as
evidence that a drug lacks carcinogenic activity. This model is not always exhaustive. For example, during the acceptance testing
of the ARB Olmesartan[1], possible carcinogenicity observed in hamsters was not able to be duplicated in rats, or in transgenic
mice. We have previously used the static molecular modeling of AutoDock to demonstrate that Olmesartan has agonostic activity
in the PDB:1DB1 model of the human VDR Nuclear Receptor[2], while it has antagonistic activity in the PDB:1RK3 model of the
rat...
Tipo: Poster
Palavras-chave: Biotechnology; Cancer; Immunology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/52/version/1
Evaluating experiential education through an intertidal ecology field trip.
Provedor de dados: 17
Autores: Kate E. Lowry; Cynthia Wilber; Rodolfo Dirzo.
*Background/Question/Methods*

Stanford SEEDS and the Jasper Ridge Biological
Preserve have worked together with Redwood High School to implement an experiential ecology education program. The
Redwood Environmental Academy of Leadership(REAL) is designed to bring underserved high school students out of the
classroom and into the outdoors to create a unique and effective learning experience. Though the program focuses on riparian
ecosystem restoration, the course curriculum is interdisciplinary and designed to inspire continuation high school students to
attend college or pursue environmental careers. Through a SEEDS special grant, REAL students were taken to Fitzgerald Marine
Reserve in Half Moon Bay, California, to learn...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3875/version/1
NamesforLife Semantic Resolution Services for the Life Sciences
Provedor de dados: 17
Autores: Charles T. Parker; Dorothea K. Taylor; Kara Mannor; Sarah Wigley; Nicole Osier; Catherine Lyons; George M. Garrity.
A major challenge in bioinformatics, life sciences, and medicine is using correct and informative names. While this sounds simple
enough, many different naming conventions exist in the life sciences and medicine that may be either complementary or
competitive with other naming conventions. For a variety of reasons, proper names are not always used, leading to an accumulated
semantic ambiguity that readers of the literature and end users of databases are left to resolve on their own. This ambiguity is a
growing problem and the biocuration community is aware of its consequences. 

To
assist those confronted with ambiguous names (which not only includes researchers but clinicians, manufacturers, patent
attorneys, and others...
Tipo: Poster
Palavras-chave: Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5137/version/1
Xenopus and Zebrafish Annotation in the UniProt Knowledgebase (UniProtKB)
Provedor de dados: 17
Autores: Rebecca E. Foulger; UniProt Consortium.
The African clawed frog Xenopus laevis and the zebrafish Danio rerio have both proved to be good model organisms for studying
early vertebrate cellular and developmental biology. More recently, the related western clawed frog Xenopus tropicalis has
become a popular choice in the laboratory, since its shorter life style and diploid genome make it more amenable to genetic
analysis. Ongoing sequencing of the X. tropicalis and D. rerio genomes, together with the growing number of EST/cDNA
projects, is generating large amounts of sequence data and revealing many human developmental and disease genes that have
counterparts in fish and frog.

UniProtKB/Swiss-Prot curates Xenopus and zebrafish
proteins with functional and sequence...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3153/version/1
MIRIAM Resources: a robust annotation and cross referencing framework
Provedor de dados: 17
Autores: Camille Laibe; Nick Juty; Nicolas Le Novère.
_Background_
More than ever, the era of data integration has highlighted the key requirement to reference
specific data in an unambiguous and perennial way, in order to enable community-level sharing, development, exchange and reuse
of information. In the field of Systems Biology, which is concerned with creating quantitative models of biological processes,
these requirements have directly led to the creation of the Minimal Information Required In the Annotation of Models (MIRIAM,
"http://biomodels.net/miriam/":http://biomodels.net/miriam/). MIRIAM provides a specific set of
guidelines
that
can
be
implemented
within
any
format.

_Objectives_
To...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5128/version/1
DARPP-32 is a robust integrator of dopamine and glutamate signals
structured
modelling
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
Theta rhythmicity enhances learning in adaptive STDP
Provedor de dados: 17
Autores: Christian Albers Albers; Joscha Schmiedt; Klaus Pawelzik.
The classical STDP window captures changes of a synaptic weight in response to the relative timing of a pre and a postsynaptic
spike (see e.g. Bi and Poo, 1998). Due to its static nature, however, it cannot account for nonlinear interactions between spikes.
Several theoretical studies offer dynamic formulations for STDP, for example by modulating the synaptic weight change by
variables like synaptic calcium concentration (Shouval et al., 2002) or somatic depolarisation (Clopath et al., 2010), or by
introducing spike triplet interactions (Pfister and Gerstner, 2006). Here, we propose a new model which is formulated as a set of
differential equations (Schmiedt et al., 2010). The weight change is given by a differential Hebbian learning rule, which
reproduces...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5855/version/1
FAIRE-seq data analysis of Chlamydomonas reinhardtii under carbon deprivation
Provedor de dados: 17
Autores: David Urbina-Gómez; Flavia Vischi Winck; Bernd Müller-Röber; Diego Mauricio
Riaño-Pachón.
For the genome-wide identification of nucleosome depleted regions under carbon deprivation, we analyze an available set of data
from an assay of formaldehyde-assisted isolation of regulatory elements followed by sequencing (FAIRE-seq). Mapping to the
sequenced nuclear genome of C.reinhardtii, followed by the identification of the enrichment-sequenced fragments was performed.
We examined the location of these fragments relative to annotated genes. The related genes were associated to the corresponding
Gene-Ontology (GO), for an evaluation of over-representate GO categories. Some genes, link with functions or locations, that
have been previous described, indicating the success of the method finding carbon-metabolism related fragments.
Tipo: Poster
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7035/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
MitoWheel, visualizing the human mitochondrial genome
Provedor de dados: 17
Autores: Gábor Zsurka; Attila Csordás.
So far researchers, web users were restricted to non-intuitive and visually poor text based databases every time they wanted to
take a look on the mitochondrial DNA and find a region of interest. But with MitoWheel the situation is about to change.
MitoWheel is a graphical representation of the circular human mitochondrial genome available on the web at
"http://mitowheel.org":http://mitowheel.org.

The
human
mitochondrial DNA is a 16569 basepair long, circular molecule and this very circularity is the basic idea behind MitoWheel. The
mitochondrial genome can be represented with a wheel and by spinning this wheel users can quickly scan through, browse and
identify the particular regions. The spinning is...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3167/version/1
Molecular evidence for Toxoplasma gondii in the brain of striped dolphins (Stenella coeruleoalba)
stranded along the Ligurian Sea coast of Italy
Provedor de dados: 17
Autores: Donato Traversa; Angela Di Cesare; Cristina Casalone; Barbara Iulini; Walter Mignone; Cristiana Tittarelli; Umberto
Proietto; Silvana Meloni; Giulia Buffatello; Fiona Forster; Seamus Kennedy; Giovanni Di Guardo.
Toxoplasma gondii is a protozoan agent of increasing concern for both free-ranging and captive cetaceans. Nonetheless,
information on epidemiology, biology, genetics and pathogenic potential of T. gondii for aquatic mammals is incomplete. This
work provides molecular evidence for T. gondii in the brain tissue from five striped dolphins (Stenella coeruleoalba) found
stranded in 2007-2008 along the Ligurian Sea coast of Italy. These animals showed a more or less severe, subacute to chronic, non
purulent, multifocal meningo-encephalitis. Additionally, the cerebral parenchyma of 3 animals harboured protozoan cysts and
zoites which were immunohistochemically linked to T. gondii. Consequently, a preliminary molecular investigation was
undertaken to confirm the...
Tipo: Poster
Palavras-chave: Ecology; Genetics & Genomics; Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4930/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
Identification of transcription factor genes and their correlation with the high diversity of
Stramenopiles
Provedor de dados: 17
Autores: Francisco Buitrago; Silvia Restrepo; Diego Riaño-Pachón.
In this study we identify, and classify into families, transcription factors (TFs) and other transcriptional regulators (TRs) in
genome sequences available from the Stramenopile group. For this we exploit the presence of protein domains and their
combinations to build rules in the form of boolean rules, that are specific for each family of TFs and TRs. We found a correlation
between the family size and some traits that has been described to be involved in the complexity of organisms. Furthermore, we
found specific gains, losses and families that shows higher abundance in different lineages, which may be involved in the
regulation of specific traits for some Stramenopile species.
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7002/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
IUPHAR-DB: An Expert-Curated, Peer-Reviewed Database of Receptors and Ion Channels
Provedor de dados: 17
Autores: Joanna L. Sharman; Valerie A. Hale; Rebecca Hills; Edward M. Rosser; Martin Jones; Stuart D. Greenhill; Anthony J.
Harmar; NC - IUPHAR.
The International Union of Basic and Clinical Pharmacology database (IUPHAR-DB) integrates peer-reviewed pharmacological,
chemical, genetic, functional and anatomical information on the 354 non-sensory G protein-coupled receptors (GPCRs), 71
ligand-gated ion channel subunits and 141 voltage-gated ion channel subunits encoded by the human, rat and mouse genomes.
These genes represent the targets of about a third of currently approved drugs and are a major focus of drug discovery and
development programs in the pharmaceutical industry. Individual gene pages provide a comprehensive description of the genes
and their functions, with information on protein structure, ligands, expression patterns, signaling mechanisms, functional assays
and biologically...
Tipo: Poster
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3230/version/1
Individual and seasonal variation in the diet of the endangered Barton Springs Salamander (Eurycea
sosorum): An application of stable isotope analysis to the conservation of an endangered species
Provedor de dados: 17
Autores: J. Hayley Gillespie.
It is well known that many species show strong temporal variation in diet. Long-term dietary trends may be important in assessing
the effects of ecological change such as global warming, land use change, or introductions of invasive species. Short-term
variation in food sources or prey selection may be crucial for understanding population dynamics in poorly understood species.
The Barton Springs Salamander (_Eurycea sosorum_) is an endangered species endemic to four small spring outflows in
downtown Austin, Texas. This species remains aquatic throughout life and inhabits benthic rocky substrate. While little is known
about its foraging ecology, _E. sosorum_ is assumed to be a generalist predator with the abundant amphipod _Hyalella azteca_ as
its primary...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3598/version/1
In Silico Analysis To Explore Novel Inhibitors For Human Proto-oncogene Tyrosine Protein Kinase
Src
Provedor de dados: 17
Autores: Nagapriya Mahanandi; Dibyabhaba Pradhan; Amineni Umamaheswari.
The first oncogene and the first non receptor tyrosine kinase, Src, plays a key role in cell morphology, motility, proliferation and
survival. Over expression of Src kinase activity disrupts the RAS pathway in signaling pathway, where it loses its ability to
hydrolyse GTP and thus, leads to cancer. A wide range of evidences indicated that Src-signaling was important in the oncogenesis
of prostate cancer and other tumours. Src-signaling is involved in androgen-induced proliferation of prostate cancer in cancer
tissue of patients having castration-refractory prostate cancer. Once prostate cancer becomes castration-resistant, bone metastases
become significant problem for which treatment options are limited. As Src is involved in multiple signaling pathways,...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4905/version/1
Factors influencing immature Dermacentor variabilis burdens on white-footed mice (Peromyscus
leucopus)
Provedor de dados: 17
Autores: Tad Dallas; Stephanie Fore; Hyun-Joo Kim; Mary Peng; Jake Henderson; Georgia Mueller; Laura Fielden.
The host-parasite relationship is an important and complex ecological interaction.
Parasite load affects
pathogen transfer and can influence host fitness. Mice were
live trapped in three night trapping sessions
conducted on two permanent grids
every other month from June 2006 to December 2008. Grids were
established in
an old field and an early successional forest each with 104 sampling points.
Data
were
analyzed
had
significant
effects
with
on
negative
tick
load
binomial
(P
=0.012
regression.
and
P
Gender
=0.029,
and
body
size
both
respectively),
with
males
and
larger hosts harboring more immature ticks. However, body size and gender...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3713/version/1
GenColors: Annotation and comparative genomics made easy
Provedor de dados: 17
Autores: Marius Felder; Alessandro Romualdi; Gernot Gloeckner; Matthias Platzer; Juergen Suehnel.
GenColors is a web-based software/database system initially aimed at an improved and accelerated annotation of prokaryotic
genomes making extensive use of genome comparison (Romualdi et al., _Bioinformatics_ 2005; Romualdi et al., _Methods Mol.
Biol._ 2007). It offers a seamless integration of data from ongoing sequencing projects and annotated genomic sequences obtained
from GenBank. With GenColors dedicated genome browsers containing a group of related genomes can be easily set up and
maintained. The tool has been efficiently used for sequenceing and annotating the Borrelia garinii genome and is currently applied
to a number of other ongoing genome projects on _Legionella_, _Pseudomonas_ and _E. coli_ genomes. Examples for freely
accessible...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3111/version/1
Family values: Maternal care in rattlesnakes is more than mere attendance
Provedor de dados: 17
Autores: Melissa Amarello; Jeffrey J. Smith; John Slone.
Parental care is important in many diverse taxa because of its positive impact on the parent's fitness. Relatively
simple forms of parental care, such as female attendance and defense, which is present in many squamate reptiles, will likely
provide insight into the evolution of more complex forms observed in crocodilians, birds, and mammals. Historically,
observations of adult and newborn rattlesnakes in close proximity were dismissed as mere coincidence of live-birth, and only
recently acknowledged as examples of parental care. In 2010, we monitored 11 pregnant Arizona black rattlesnakes (_Crotalus
cerberus_): 4 solitary individuals and 2 aggregations composed of three and four individuals. We documented various forms of
parental care,...
Tipo: Poster
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6671/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 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
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
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
Lyme Borreliosis During Pregnancy
Provedor de dados: 17
Autores: András Lakos; Norbert Solymosi.
One of the authors (AL) presented a poster on 34 pregnancies of maternal Lyme borreliosis (Lb) in 1995. It was striking that
untreated Lb associated with higher probability of adverse outcome but the number of patients were small and the statistical power
was low. We have recently published a paper on 95 maternal Lb and the outcome of their pregnancies. Since the closure of the
database for that manuscript the number of the pregnant women with Borrelia infection observed in our Centre increased to 124,
and the statistical analysis strengthened our previous doubtful observations and reached significant results in important aspects by
now. This series is the largest study to date on this topic. Treatment was administered parenterally to 87 (70%) women and...
Tipo: Poster
Palavras-chave: Microbiology.
Ano: 2012
URL: http://precedings.nature.com/documents/7027/version/1
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
Ligand Based Virtual Screening to Design Novel Human MEK1 Protein Inhibitors for Potential
Development of Drugs Against Melanoma
Provedor de dados: 17
Autores: Vijayasree Potluri; Dibyabhaba Pradhan; Amineni Umamaheswari.
The Ras-dependent Raf/MEK/ERK signaling pathway is a major regulator of cell proliferation and survival. Hyper activation of
the pathway is frequently observed in human malignancies as a result of aberrant activation of receptor tyrosine kinases or
mutations in RAF (V600E). MEK1 is dual-specificity tyrosine/threonine protein kinases found in the pathway. The RAF
mutation (present in 50% of melanomas) have been shown to be highly dependent on MEK1 activity and also MEK1 is the only
acknowledged activator of ERK, making them attractive targets for therapeutic intervention. In view of its importance,
identification of potent inhibitor against MEK1 may be valuable to design effective drugs against melanoma. Inhibitors for human
MEK1 reported till dates have...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4901/version/1
Open Source Kinesin-1 Stochastic Simulation and Gliding Assay Tracking Software
Provedor de dados: 17
Autores: Lawrence J. Herskowitz; Anthony L. Salvagno; Brian P. Josey; Andy Maloney; Steven J. Koch.
Kinesin-1 (conventional kinesin) is a homodimeric motor protein important for axonal transport. It has been well studied through
ensemble and single-molecule assays. However, the enzymatic stepping cycle is complex, with many rate constants that are
modulated by interaction of the two motor domains. This makes it difficult to predict how changes in a given rate constant may
affect observable properties such as processivity, velocity, or stall force. We have written a simulation of kinesin walking using a
Stochastic Simulation Algorithm. The model allows for interactions between the heads, and includes states that are not considered
part of the normal cycle. This adds to the complexity of the model but also allows for probing rare events, such as those that...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4468/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
PathwayAnalyser: A Systems Biology Tool for Flux Analysis of Metabolic Pathways
Provedor de dados: 17
Autores: Karthik Raman; Nagasuma Chandra.
Stoichiometric and constraint-based analyses of metabolic pathways have been gaining ground in the recent past with the increase
in the quality and number of pathway databases available and the curation of genome-scale metabolic models. Genome-scale
metabolic models of several organisms such as _Escherichia coli_, _Saccharomyces cerevisiae_ and _Staphylococcus aureus_
have already been constructed. Flux Balance Analysis (FBA) and Minimisation of Metabolic Adjustment (MoMA) are two of the
popular techniques for the constraint-based analysis of metabolic pathways.

We have
developed a computational tool, PathwayAnalyser, for the analysis of metabolic pathways, particularly by FBA and MoMA.
PathwayAnalyser interfaces with the...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1868/version/1
In vitro shoot regeneration from cotyledon of redgram
Provedor de dados: 17
Autores: Telugu Raghavendra; Palagiri Sudhakar; K Balakrishna Reddy; Keerthi Venkaiah; Putta Latha; Tollamadugu NVKV
Prasad; Lakkireddi Prasanthi.
Pigeonpea is one of the most popular legume grains in the world, especially in the Indian sub-continent. Keeping in view the
importance of the crop, an efficient protocol for rapid in vitro plant regeneration from cotyledon of redgram has been reported in
this paper. The concentraion of the hormones played an important role in shoot and root regeneration.
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7041/version/1
IMGT/Automat: the strategy for the annotation of human and mouse cDNA nucleotide sequences of
IG and TR
Provedor de dados: 17
Autores: Géraldine Folch; Joumana Jabado-Michaloud; Fatena Bellahcene; Laetitia Regnier; Véronique
Giudicelli; Marie-Paule Lefranc.
The cDNA sequences of immunoglobulins (IG) and T cell receptors (TR) represent more than one half of the sequences in the
IMGT^®^ nucleotide database IMGT/LIGM-DB^1^ and 75% of them are from human and mouse. A few cDNA are
germline but the great majority results from a V-D-J or V-J gene rearrangement, spliced to a C gene. The IG and TR genes have
been studied extensively in IMGT^®^ ("http://www.imgt.org":http://www.imgt.org) ^2^, which
allowed to set up their nomenclature and the corresponding germline reference sequences. These standardized reference directory
sets (one for each group of each locus) and the IMGT-ONTOLOGY axioms and derived concepts^3^ are the key elements
indispensable to perform the annotation of IG...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3159/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
Identification of Potent Leads for Human cAMP Dependent Protein Kinase Catalytic Subunit Alpha:
A Strategic Application of Virtual Screening for Cancer Therapeutics
Provedor de dados: 17
Autores: Sandeep Swargam; Dibyabhaba Pradhan; Amineni Umamaheswari.
The advancement in therapeutic applications focused on specific macromolecular compounds of deregulated cell signaling
pathways bestowed novel approach to design the ligands as drug molecules against several life threatening diseases such as
Cancer. In humans, protein kinase A is one of the important kinases those were involved in cell signaling mechanism. cAMP,
G-proteins and ATP molecules were required for activation of protein kinase A (PKA), upon activation, PKA catalytic subunits
(PRKACA,PRKACB and PRKACG) undergoes many cellular functions like cell proliferations, cell cycle regulation, and survival
of cells through acting on many substrates. Overexpression of extracellular cAMP dependent protein kinase A catalytic subunits
(PRKACA) causes severe...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4903/version/1
Suppression of TNF-α induced NFκB activity by gallic acid and its
semi-synthetic alkyl-gallates: Possible role in cancer chemoprevention
Provedor de dados: 17
Autores: Suaib Luqman; Mauro C. C. Morais; Tamara P. Kondratyuk; Maicon S. Petronio; Luis
S. Silva; Vanderlan S. Bolzani; Christiane
P. Soares; John
O. Regasini; Dulce
H.
M. Pezzuto.
NFκB, a transcription factor, regulates the expression of a number of genes involved in carcinogenesis. Thus, agents
that can suppress NFκB activation have the potential to suppress carcinogenesis. In the present investigation, gallic
acid was isolated from Alchornea glandulosa (Euphorbiaceae) and eight semi-synthetic alkyl gallates were prepared from the
reaction of the corresponding alcohols with gallic acid at 80oC for 48 h in good yields (70-97%). All the compounds were
evaluated against TNF-α-induced NFκB activation with stable transfected 293/NFκB-Luc
human embryonic kidney cells. Treatment of cells with gallic acid and the gallate esters (20 µg/ml) significantly
reduced TNF-α...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6922/version/1
Endothelial Massive Calcium Accumulation Death (MCAD): Mechanism, Target, and Predictive
Biomarker for Anti-Angiogenic Therapy
Provedor de dados: 17
Autores: Larry Weisenthal.
We cultured human umbilical vein endothelial cells with bevacizumab, with tyrosine kinase inhibitors known to be AA, and with
traditional cytotoxic drugs. The images below show that, in the presence of physiological saline and non-favorable culture
conditions, the vast majority of the endothelial cells undergo a "non-specific" type of cell death (NSCD),
not associated with calcium accumulation, but with loss of cell membrane integrity, allowing uptake of the Fast Green dye,
staining these dead dells a pale blue green. In the presence of known AA agents (e.g. bevacizumab, some TK inhibitors) a large
percentage of the endothelial cells undergo death associated with massive calcium accumulation (MCAD), with these cells
staining...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6647/version/1
Is the new cognitive neuroscience of social inequality equal? Deconstructing the current
neurocognitive research on children’s attention
Provedor de dados: 17
Autores: Amedeo D'Angiulli; Pavel Grebenkov.
The relation between socioeconomic status (SES) and various outcomes, such as cognitive ability, behavior, social skills and
health, has been studied for over half a century. The general consensus in interpreting the results as been that low SES is
necessarily associated with cognitive and/or behavioral pathologies or deficits. Contrary to this deficit hypothesis new evidence
suggests that the differences between low- and high-SES populations may be due to cognitive preferences associated with the
social context where children develop. Much of this evidence has come from developmental neuroimaging studies on attention
and executive control generally showing that despite differences between low- and high-SES children in neural correlates, there
are no...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4470/version/1
LogMap 2.0: towards logic-based, scalable and interactive ontology matching
Provedor de dados: 17
Autores: Ernesto Jimenez-Ruiz; Bernardo Cuenca Grau; Yujiao Zhou.
In this paper we present a much improved version of LogMap, a highly scalable ontology matching system with
‘built-in’ reasoning and diagnosis capabilities. LogMap 2.0 is not only more scalable and robust than
its predecessor, but it also provides the necessary infrastructure for domain experts to interactively contribute to the matching
process.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6670/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
Effect of a single Dialysis session on plasma Lp(a) levels in patients on Maintenance haemodialysis
Provedor de dados: 17
Autores: Varikasuvu Seshadri Reddy; MM Suchitra; Prabhakar E. Reddy; Aparna R. Bitla; Siva V. Kumar; PVLN Srinivasa Rao.
Background: 
Cardiovascular disease (CVD) is a major cause of mortality in End stage renal disease
(ESRD) patients on Maintenance haemodialysis (MHD). Lp (a), is a specialized form of glycoprotein-LDL-cholesterol complex
and is an independent risk factor for myocardial infarction. The risk is related to its atherogenic and thrombogenic properties. The
present study was taken up to evaluate changes in Lp(a) and Lipid profile in patients undergoing hemodialysis session.


Methodology: 
Twenty seven patients with end stage renal
disease who were on maintenance hemodialysis were included. Plasma samples were collected hourly during a dialysis session
with polysulfone membrane using bicarbonate...
Tipo: Poster
Palavras-chave: Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6473/version/1
Ecophysiological traits of grasses: resolving the effects of photosynthetic pathway and phylogeny
Provedor de dados: 17
Autores: Samuel H. Taylor; Mark Rees; Stephen P. Hulme; Rob Freckleton; Brad S. Ripley; F. I. Woodward; Colin P. Osborne.
C4 photosynthesis is an important example of convergent evolution in plants, having arisen in eudicots, monocots and diatoms.
Comparisons between such diverse groups are confounded by phylogenetic and ecological differences, so that only broad
generalisations can be made about the role of C4 photosynthesis in
determining ecophysiological traits.
However, 60% of C4 species occur in the grasses (Poaceae) and molecular phylogenetic techniques confirm that there are between
8 and 17 independent origins of C4 photosynthesis in the Poaceae. In a screening experiment, we compared leaf physiology and
growth traits across several major
independent C3 & C4 groups within the Poaceae, asking 1)
which traits differ...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3937/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
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
Human Transcript Database Search Showed Existence Of Extremely Short Introns
Provedor de dados: 17
Autores: Makoto Shimada; Noriko Haraguchi; Akila Mayeda.
Since pre-mRNA splicing is processed by a spliceosome that is a huge complex consists of RNAs and as many as 200 proteins, it
is considered that minimum intron size is limited by molecular size of the spliceosome. To understand splicing mechanism, we
investigate human intron size distribution using annotated transcriptome database, H-InvDB. Distribution of obtained intron
length shows that there is a mode at 83 nt in length with 4049 transcripts and number of introns decreases drastically in shorter
than 65 nt, where numbers of transcripts in each locus also decrease. However, some introns less than 65 nt are observed, both
shows high Codon Adaptation Index (CAI) and also observed orthologous transcripts in other mammals. These suggests that
there is a...
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5115/version/1
Spatial navigation and multiscale representation by hippocampal place cells
Provedor de dados: 17
Autores: Jason S. Prentice; Josh Merel; Vijay Balasubramanian.
Hippocampal lesions are known to impair success in navigation tasks. While such tasks could be solved by memorizing complete
paths from a starting location to the goal, animals still perform successfully when placed in a novel starting position. We propose
a navigation algorithm to solve the latter problem by exploiting two facts about hippocampal organization: (1) The size of the
place fields of hippocampal place cells varies systematically along the dorsoventral axis, with dorsal place cells having smaller
place fields than ventral (Kjelstrup et. al. 2008); and (2) the theta oscillation propagates as a traveling wave from dorsal to ventral
hippocampus (Lubenov and Siapas, 2009). Taken together, these observations imply that the hippocampal...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6379/version/1
Toward a complete model of radial growth in Pinus edulis: the effects of CO2 and prior years
Provedor de dados: 17
Autores: C. Susannah Tysor; Amy Whipple; George Koch.
_Pinus edulis_ (piñon pine) is found across 35% of the Colorado Plateau and is a foundation species in the
piñon-juniper woodlands of the Southwest. Piñon pine mortality in the recent drought has been high and
climate change models forecast a warmer future for the region, which will increase piñon pine water stress. In order to
predict the fate of piñon pine, we must understand how various climatic factors influence piñon growth.
Tree rings provide a climate sensitive record of growth ideal for exploring the relationship between growth and climate. We used
78 piñon pine trees cored at Red Mountain in northern Arizona in 1998 to predict tree ring width and piñon
pine mortality, using...
Tipo: Poster
Palavras-chave: Ecology; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3613/version/1
The Molecular In Silico Dissection of Cancer using TCLASS and its Application in the Identification
of the Tissue of Origin of Cancers of Unknown Primary Site
Provedor de dados: 17
Autores: Torik Ayoubi.
Traditional cancer diagnosis relies on a combination of clinical and histo-pathological data. In many cases, however, the
morphology of in particular metastatic cancer is not discriminative enough for correct diagnosis. In addition, the morphology of
tumor cells do not provide information on aberrant molecular pathways that may be used to specifically target the tumor like the
application of Herceptin to breast cancers with amplification in the ERBB2 gene. With the completion of the human genome
project, molecular pathology has dramatically increased its arsenal of novel molecular biomarkers that can be used to determine
the phenotype of tumors. Gene expression profiling using high-density microarray technology is an extremely powerful tool to...
Tipo: Poster
Palavras-chave: Biotechnology; Cancer; Genetics & Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5300/version/1
Evolution of Thriftiness: An analytical viewpoint
Provedor de dados: 17
Autores: Prajakta Belsare; Milind Watve.
We examine here, using a simple mathematical model, the conditions under which thrifty genes or fetal programming could
evolve. Obesity and related disorders are thought to have their roots in metabolic thirftiness that evolved to combat periodic
starvation. The failure to detect any thrifty genes and the association of low birth weight with type 2 diabetes, caused a shift in the
concept from thrifty gene to thrifty phenotype and fetal programming. This hypothesis assumes that intra-uterine undernutrition
programs the body to be thrifty, predicting and preparing for starvation in later life. However, there are reproductive costs
associated with thriftiness. Results of the model suggest that under no condition thrifty and non-thrifty genes would co-exist...
Tipo: Poster
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2709/version/1
Phenotypic Plasticity and the Invasiveness of Three _Taraxacum_ Species
Provedor de dados: 17
Autores: Jing Luo; John Cardina.
*Background/Question/Methods* 
Many factors have been found to be associated with the success of
invasive species. Phenotypic plasticity, the ability of a plant genotype to respond to different environmental conditions by
producing different phenotypes, is thought to play an important role plant invasions. In three major experiments, I tested the
hypothesis that the invasive _Taraxacum officinale_ (common dandelion) and its non-invasive congener _T. laevigatum_ will
exhibit different phenotypic plasticity in germination, growth, and reproduction. I also proposed that their responses to various
environments could be used to assess the invasive behavior of a potential crop species: _T....
Tipo: Poster
Palavras-chave: Ecology; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3767/version/1
The Effect of Retro-Cueing on an ERP Marker of VSTM Maintenance
Provedor de dados: 17
Autores: Alexandra M. Murray; Bo-Cheng Kuo; Mark G. Stokes; Anna C. Nobre.
Previous research has found that Contralateral Delay Activity (CDA) is correlated with the number of items maintained in Visual
Short Term Memory from one visual field (VF) (Vogel & Machizawa, 2004).
CDA is usually elicited by a
to-be-remembered array after a prospective cue (pro-cue) signalling the relevant side of the visual display, and is interpreted as a
putative electrophysiological signature of WM maintenance. Attention can also be directed to the contents of VSTM, after the
presentation of a visual array, using a retroactive cue (retro-cue) (Nobre, Griffin, & Rao, 2008). Because retro-cueing
directs attention within a memory trace, potentially reducing the load of items to be maintained, we hypothesised that this would...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2958/version/1
Soil Microbial Community Composition and Enzyme Activity Responses to an Intensive
SilvopastoralSystem of Colombia
Provedor de dados: 17
Autores: Victoria E. Vallejo; Richard P. Dick; Arbeli Ziv; Wilson Terán; Fabio Roldán.
Extensive cattle production occupies more than 27% of the rural landscapes in Latin America, and nowadays is considered as a
major driver of tropical deforestation. Conventional monoculture pasture (CP) systems have degraded soils and caused negative
environmental impacts. Recent years have shown increasing interest in the development of alternatives to the CP with a high
efficiency of internal resource use and thus lower input requirement and cost. To address this, intensive silvopastoral systems
(ISS) have been developed where trees are integrated with crops, pastures, and cattle for environmental and economic benefits.
Soil microbial communities drive nutrients cycling and play an essential role in maintaining and improving soil quality; however,
little...
Tipo: Poster
Palavras-chave: Ecology; Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/6265/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
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
Plant Functional Types and Plant Trait Measurements in the Eastern Ghats, South India
Provedor de dados: 17
Autores: K. Anupama; A. Stephen; S. Aravajy; G. Orukaimani.
Classifying terrestrial plant species on the basis of function rather than on taxonomy facilitates addressing ecological questions at
the scale of ecosystems, landscapes or Biomes. The concept of plant functional types (PFTs) helps handle taxonomic diversity, as
it groups together species that share common attributes with respect to, e.g. life-form, phenology and bioclimatic limits. For some
time now, large international efforts promoted by the IGBP-GCTE programme are underway to measure for a large number of
species a shortlist of significant plant traits that would underlie such functional plant classification systems. The idea here is to
help address vegetation responses to and vegetation effects on environmental changes such as climate changes, but...
Tipo: Poster
Palavras-chave: Ecology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/941/version/1
Looking at the Beginnings: Enquiries about Emergence of Cognition in Evolution
Provedor de dados: 17
Autores: Walter Riofrio.
Trying to understand when and how the cognitive phenomena arise in evolution continues being a hard problem of confronting.

One important task is to find the ways in which we will be able to arrive at those explanations that will
enable us to understand how living beings put together perceived sensory information as well as how they represent it.

In this presentation, we address some conceptual questions involved in the relationships between sensorial
information perceived by brains and its representational capacities. 

Tipo: Poster
Palavras-chave: Ecology; Molecular Cell Biology; Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/413/version/1
Structural insight to Streptococcus mitis thymidylate kinase: a potential common drug target of
infective endocarditis
Provedor de dados: 17
Autores: Vani Priyadarshini; Dibyabhaba Pradhan; Manne Munikumar; Amineni Umamaheswari.
The incidence of infective endocarditis (IE) represents the fourth leading cause of life-threatening infectious disease with a yearly
incidence of 15,000 to 20,000 new cases despite advances in antimicrobial therapy, development of better diagnostic and surgical
techniques. The diverse group of causative microbes of IE is one of major obstacle towards development of effective
antimicrobial drug. This has triggered exploration of common potential novel drug target from available whole genome sequences
of predominant pathogens causing IE in SVIMS hospital through comparative subtractive genomic approach and metabolic
pathway analysis. Streptococcus mitis is the most predominant IE pathogen in SVIMS hospital. Thymidylate kinase of
Streptococcus mitis plays a...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5158/version/1
Wikis in the classroom: Properties and potential uses of this collaborative learning tool
Provedor de dados: 17
Autores: Jayna L. DeVore; Kristen K. Cecala; John C. Maerz.
Background/Question/Methods 
Student engagement is tied to course performance and information
retention. Shifting the focus of the classroom from a lecture-based approach to a student-centered learning environment is one
way to achieve this goal. One tool that can be used to allow student contribution to the content and direction of a course is a
wiki. Wikis are highly flexible collaborative websites that can be structured to meet course needs and allow multiple users to
contribute to site content. They provide a platform where real-time editing can be performed in a flexible
'topical' format. They are intended to promote group learning through collaboration rather than isolated
reflection, and can provide another...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5244/version/1
HEAT: a New Tool for Gene Set Enrichment Analysis Using Comprehensive Annotation of Human
Genes in H-InvDB
Provedor de dados: 17
Autores: Tadashi Imanishi; Akiko O. Noda; Miho Sera.
H-InvDB Enrichment Analysis Tool (HEAT) is a new data-mining tool for gene set enrichment analysis based on comprehensive
annotations of human genes in H-InvDB.
HEAT searches for H-InvDB annotations that are significantly enriched in a
user-defined gene set, as compared with the entire H-InvDB representative transcripts. The advantage of HEAT is the wide
variety of annotation items used for its analysis: chromosomal bands, InterPro functional domains, Gene Ontology terms, KEGG
pathways, H-InvDB gene families/groups, SCOP structural domains, subcellular localization predicted by using the Wolf-PSORT
program, tissue-specific gene expression as defined in the H-ANGEL database, and transcription factor binding sites in promoter
regions based on JASPAR. HEAT...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5185/version/1
Hypothesis: Klotho can decouple insulin resistance from the associated pathophysiology
Provedor de dados: 17
Autores: Milind Watve; Ulfat Baig.
A very fundamental paradox of insulin resistance is that in a wide variety of animal models impairment of insulin signaling
increases life span. But in humans it increases the risk of a range of fatal disorders. The Klotho protein appears to resolve this
paradox. Overexpression of the Klotho gene increases longevity in mammals by inducing insulin resistance. But the Klotho
protein is simultaneously anti-inflammatory, antioxidant and pro-angiogenesis. A number of other studies have indicated that
systemic inflammation, angiogenesis dysfunction and oxidative stress are the main causes of pathological complications of
diabetes. The Klotho protein has demonstrated that insulin resistance can be decoupled from these pathogenic mechanisms and if
decoupled it...
Tipo: Poster
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5420/version/1
Update On The Zebrafish Genome Project
Provedor de dados: 17
Autores: J P Almeida-King; S Donaldson; G K Laird; D M Lloyd; H K Sehra; J E Collins; K Howe; B Reimholz; J Torrance; S
Trevanion; D Stemple; I Barroso; J G R Gilbert; E Griffiths; J E Loveland; R Storey; J L Harrow; T Hubbard.
The zebrafish genome, which consists of 25 linkage groups and is ~1.4Gb in size, is being sequenced, finished and analysed in its
entirety at the Wellcome Trust Sanger Institute. The manual annotation is provided by the Human and Vertebrate Analysis and
Annotation (HAVANA) group and is released at regular intervals onto the Vertebrate Genome Annotation (Vega) database
("http://vega.sanger.ac.uk":http://vega.sanger.ac.uk) and may be viewed as a DAS source in Ensembl
("http://www.ensembl.org/Danio_rerio":http://www.ensembl.org/Danio_rerio).


Our annotation is compiled in close collaboration with the Zebrafish Information
Network (ZFIN)...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3105/version/1
Type II Aerobic Methane Oxidizing Bacteria (AMOB) Drive Methane Oxidation in Pulsed Wetlands
as Indicated by 13C-Phospholipid Fatty Acid Composition
Provedor de dados: 17
Autores: Taniya Roy Chowdhury; Richard Dick.
Methane (CH4) is a potent greenhouse gas and management strategies have been proposed to limit CH4 emissions from
freshwater wetlands. The methanotrophic bacteria can intercept much of the CH4 produced by methanogenic archaea and thus
management protocols for wetlands could conceivably include manipulations not only to limit the production of CH4 by
methanogens, but also to enhance the consumption of CH4 by benthic or planktonic methanotrophs. The hydrological
characteristic of a wetland is a major determinant of the CH4 emission rates. A major consideration for CH4 production is
whether a wetland is static or flowing (wetlands connected to rivers and streams). Very little is known about the effects of
hydrologic pulsing on wetland carbon dynamics and...
Tipo: Poster
Palavras-chave: Ecology; Microbiology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6291/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 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
Prediction Of Cancer Possibility By Pattern Recognition And Statistical Study Of Expression Of Gene
Level Of Cancer Cells
Provedor de dados: 17
Autores: Medhavi Mallick; Devang Odedra.
The activity of the p53 tumor-suppressor protein has a key role in controlling both cancer and aging: under activity encourages the
growth of cancer, and over activity can accelerate the aging process. The p53 protein is a tumor suppressor encoded by a gene
whose disruption is associated with approximately 50 to 55 percent of human cancers. The p53 protein acts as a checkpoint in the
cell cycle, either preventing or initiating programmed cell death (Apoptosis). p53 regulating genes MDM2, PARP, Oncogenicras,
and p21 etc play a crucial role in tumor suppression.
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5624/version/1
H-InvDB: A Comprehensive Annotation Resource For Human Transcriptome
Provedor de dados: 17
Autores: Chisato Yamasaki; Jun-ichi Takeda; Takuya Habara; Makoto Ogawa; Akiko Noda; Ryuichi Sakate; Katsuhiko
Murakami; Tadashi Imanishi; Takashi Gojobori.
H-Invitational Database (H-InvDB: "http://www.h-invitational.jp/":http://www.h-invitational.jp/) is a
comprehensive annotation resource for human transcriptome. By extensive analyses of all human transcripts, we provide curated
annotations of human genes, transcripts and proteins that include gene structures, alternative splicing isoforms, non-coding
functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure,
genetic polymorphisms, relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein
interactions (PPIs) and gene families/groups. The latest release of H-InvDB (release 7.0) provides annotation for 296,912 human
transcripts in...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5271/version/1
Integral presentation of Experimental Results and Bioinformatic Analyses on _Ciona_ _intestinalis_
Proteins
Provedor de dados: 17
Autores: Kouki Yonezawa; Keisuke Ueno; Katsuhiko Mineta; Toshinori Endo.
For the aim of facilitating biologists to find new knowledge through the comprehensive proteomic and transcriptomic data of
_Ciona intestinalis_, we have been developing an intuitive and integral view of experimental and bioinformatic results for each
protein, which, unlike on human proteins, was incomplete for _Ciona_ proteins. In the presentation, we integrated in a view the
experimental results of 2D-PAGE analyses done at Shimoda Marine Research Center, University of Tsukuba, 3D-view of
expressions (3DPL) done by Hotta _et al_., and cross-references with JGI version 1 and ENSEMBL. A total of 1,673 entries of
2D-PAGE and 57 of 3DPL are currently contained in CIPRO database. The information is summarized in a single page for a
protein. Together with...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5088/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
Multidimensional structure of stream flow regime in a hierarchy of landscapes within the U.S. Great
Lakes basin
Provedor de dados: 17
Autores: Boris Shmagin; Carol Johnston; Scott Bridgham.
Stream flow data were used to evaluate a landscape hierarchy ranging from the Ontonagon River watershed (OW) to the upper
peninsula of Michigan (MUP) to the entire Great Lakes basin (GLB). Flow records (1926-1988) were obtained for 45 USGS
gauging stations within the GLB with drainage areas of 100-1450 sq. mi. Data were arranged in five initial matrixes with number
of time series from 14 to 45. Factor analysis of average annual flow revealed from three to six patterns of stream runoff within
distinct regions of the GLB. A typical watershed was selected to represent each of the five distinct regions identified for the period
1956-88, and its data were used to analyze monthly average flow values. This analysis identified two to five groupings of months
with...
Tipo: Poster
Palavras-chave: Earth & Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/1371/version/1
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
Safety evaluation of Asparagus racemosus: a commonly used herb of Ayurvedic Medicine in Charles
Foster rats
Provedor de dados: 17
Autores: Debabrata Chanda; K Patider; Anirban Pal; Suaib Luqman; D U. Bawankule; D N. Mani; Narayan P. Yadav.
Asparagus racemosus Willd., one of the most important medicinal plants, is regarded as a ‘rasayana’
in the Ayurvedic system of medicine and has been recommended for use as a galactagogue, aphrodisiac, anodyne, diuretic and
nerve tonic since time immemorial, necessitating its incorporation into a number of important Ayurvedic formulations like
Shatavarikalpa, Phalaghrita and Vishnutaila. However, data regarding safety or toxicity of Asparagus racemosus in animal
systems is lacking. Hence, the present experiment envisaged acute and sub-acute toxicity of Asparagus racemosus root aqueous
extract in adult Charles Foster rats following the guidelines of OECD including parameters like observational, hematological,
biochemical and...
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6921/version/1
The eDAL Suite: Tools and Concepts for Primary Data Citation
Provedor de dados: 17
Autores: Matthias Lange; Christian Colmsee; Steffen Flemming; Jinbo Chen; Matthias Klapperstück; Uwe Scholz.
Retrieval and citation of primary data is the important factor in the approaching age of “data science”.
Digital data are easily shared, and just as easily wiped or lost. The problem of keeping on-line data accessible
and
retrievable is especially difficult for SME like plant breeders plant biotech companies as well as
research projects in this domain.
Intension of eDAL is the provisioning of an information retrieval and data
citation infrastructure that meets the requirements of the “data science” age and implements a
re-usable platform for data retrieval, data
citation, and data publication. Like a shopping cart, the idea is to
combine a search engine and a...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4935/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
Precipitation in Aberdeen, SD: data analysis approach
Provedor de dados: 17
Autores: Boris Shmagin; Carol A. Johnston; Dennis Todey.
The daily, monthly and annual sum of precipitation was analyzed for station Aberdeen-Airport, South Dakota (NOAA COOP
#390020) with traditional normative statistical descriptions of precipitation variability and with methods of data analysis. The goal
for research was formulated as finding a way to forecast extremes, such as the flooding of Aberdeen in May 2007 after a 30-hour,
8.42 inch rain event. Daily data were available, analyzed and cannot be considered as having any use for the forecast. The
observations of 1423 monthly sums of precipitation have the following characteristics: mean = 1.802 in.; geometric mean = 0.856
in.; median = 1.26 in.; minimum = 0.0; maximum = 12.39 in. Simplified Fourier analysis was performed for monthly data, and 31
cyclic...
Tipo: Poster
Palavras-chave: Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3197/version/1
The Latest Information and Perspective of Human Gene and Protein Database (HGPD) as Human
Proteome Study
Provedor de dados: 17
Autores: Yukio Maruyama; Yoshifumi Kawamura; Takao Isogai; Nobuo Nomura; Naoki Goshima.
HGPD ("http://www.HGPD.jp/":http://www.HGPD.jp/) is a unique database that stores information on a
set of human Gateway entry clones in addition to protein expression data. HGPD was launched in November 2008 and, since then,
33,275 human Gateway entry clones have been constructed from ORFs of full-length cDNAs, thus representing the largest
collection in the world. Sequence information and protein expression of Gateway entry clones can also be retrieved from HGPD.
The majority of analysis data for cDNA sequences in HGPD are shared with the FLJ Human cDNA Database
("http://flj.hinv.jp/v01/cgi/index.cgi":http://flj.hinv.jp/v01/cgi/index.cgi), which was constructed as human
cDNA sequence analysis database focusing on mRNA...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5070/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
Information on Transcriptional Regulation and Signal Transduction of _Escherichia coli_ K-12
Integrated in the Database RegulonDB.
Provedor de dados: 17
Autores: Socorro Gama-Castro; Alberto Santos-Zavaleta; Martin Peralta-Gil; Verena Weiss; Heladia Salgado; Hilda Solano;
Julio Collado-Vides.
Since its inception, RegulonDB ("http://regulondb.ccg.unam.mx/":http://regulondb.ccg.unam.mx/) has
been a database that compiles information about the regulation of transcription initiation of _Escherichia coli_ K-12. However, we
are aware that transcriptional regulation is not an isolated process; instead, it is the response to the different environmental
conditions that trigger a series of concatenated reactions that end in transcriptional regulation, and it implies an adequate response
in terms of induced and repressed gene products. We are working now to include all these new data in RegulonDB. As a
consequence, transcriptional regulation in RegulonDB will be part of a unit that initiates with the signal, continues with the
signal...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5270/version/2
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
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
Phyloclimatic Modelling: Phylogenies, Palaeo-climate and Environmental Preferences
Provedor de dados: 17
Autores: Chris Yesson; Alastair Culham.
A new technique is demonstrated for the interpretation of the role played by climate in plant diversity through the optimisation of
climate variables on phylogenetic trees. This is achieved by calculating climate preferences for individual species based on
established bioclimatic modelling techniques using point
distribution data from distributed sources. We
demonstrate a new technique for optimising the component parameters on phylogenetic trees. These parameters can be
re-combined into
bioclimatic models for ancestral nodes throughout the phylogenetic tree. The combination
of DNA-sequence data and the fossil record is used to establish time-calibrated phylogenies. Using these chronograms,
bioclimatic models can in turn...
Tipo: Poster
Palavras-chave: Ecology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/145/version/1
Tumor necrosis factor and caspase in response to soluble or microparticle-incorporated drugs in
Mycobacterium tuberculosis infection
Provedor de dados: 17
Autores: Awadh Bihari Yadav; Amit Misra.
We compared the effects of microparticles (MP) containig anti-tubercular drugs and those of the drugs themselves on the host
macrophage (MΦ) response to infection with Mycobacterium tuberculosis H37Ra (Mtb). 
Mice
infected intravenously with M. tb. were either administered rifampicin and isoniazid by oral gavage or through inhalation of
biodegradable MP containing the two anti-tubercular drugs. Bronchoalveolar lavage (BAL) was perfomed to recover lung
MΦ, which were cultured and the supernatant analysed for TNFα by ELISA. The murine MΦ
cell line J774 or the human monocyte line THP-1 differentiated with phorbol myristate were infected in vitro and treated with MP
or soluble drugs. The kinetics of...
Tipo: Poster
Palavras-chave: Immunology; Pharmacology.
Ano: 2007
URL: http://precedings.nature.com/documents/1190/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
NPO: Ontology for Cancer Nanotechnology Research
Provedor de dados: 17
Autores: Dennis Thomas; Rohit Pappu; Nathan Baker.
We present the design and development of NanoParticle Ontology (NPO). The ontology is implemented in the Ontology Web
Language (OWL). The domain terms in NPO currently represent entities, which describe knowledge about physical, chemical,
and functional properties of nanoparticles characterized in cancer nanotechnology research. The upper-level of NPO is formed
using terms from the Basic Formal Ontology (BFO).
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3515/version/1
Quest for the descent of the Escherichia coli outbreak strain TY2482 – out of Germany?
Provedor de dados: 17
Autores: Tiruvayipati S. Avasthi; Narender Kumar; Ramani Baddam; Singamaneni H. Devi; Lothar H. Wieler; Niyaz Ahmed.
The recent outbreak of the Escherichia coli infection in north Germany reportedly has killed 35 people and sickened about 4000.
Infections were reported in 2001 and 2002 in Germany and Central Africa respectively. In order to dissect all possible connections
among the three infection/outbreak strains and to extract the most virulent genes responsible for the augmented pathogenicity of
the present German strain (2011), whole genome sequence data of the two isolates (E. coli TY_2482 & LB226692)
were analyzed. We report that the German outbreak strain isolated in 2011 is a seasoned clone of the 2002 isolate sequenced from
Central Africa (55989) and perhaps a direct descendent of the German EAEC strain reported in 2001 infection cases.
Tipo: Poster
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6034/version/1
Productivity and forage quality of a phytodiverse semi-natural grassland under various
management regimes
Provedor de dados: 17
Autores: Tatiana From; Ute K. Petersen; Johannes Isselstein.
Grassland management experiment (GrassMan) was set up in 2008 on a permanent semi-natural grassland in the Solling uplands,
Germany. The main research focus is on the ecosystem functioning of the phytodiverse grassland (e.g. productivity and forage
quality, water and nutrient fluxes). The aim of our study was to analyse the effects of vegetation composition and functional
diversity on productivity and forage quality of the semi-natural permanent grassland. Variation in sward composition was
achieved by herbicide application and resulted in three sward types: control sward type (without herbicide application),
monocot-reduced and dicot-reduced. Further management factors included different nutrient input levels (without fertilizer and
180-30-100 kg/ha of...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6622/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
"public"...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5175/version/1
Investigation of the Adsorption Characteristics of Antimony, Cadmium, and Lead by Nano- and
Microparticle Titania
Provedor de dados: 17
765
Autores: Jared Zia; Dula Amarasiriwardena; Baoshan Xing.
The utilization of nanotechnology is expected to rise greatly within the next decade. The increasing ubiquity of nanotechnology,
coupled with the fact that the toxicity of a nanomaterial is partially dependent on its adsorbed components, emphasizes the general
importance, and environmental significance, of nanomaterial adsorption studies. Using nanoparticle titania (and microparticle
titania for comparison), a series of adsorption experiments were performed. The antimony, lead, and cadmium adsorption capacity
of nanoparticle titania was compared to that of microparticle titania. During a typical adsorption experiment, a known amount of
nanomaterial was shaken with a solution containing a known concentration of antimony, lead, and cadmium. Following an...
Tipo: Poster
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3698/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
Root-associated fungal communities colonizing two dominant semiarid grasses: Hilaria sp. and Stipa
sp.
Provedor de dados: 17
Autores: Miriam I. Hutchinson; Jayne Belnap; Jose Herrera; Robert Sinsabaugh; Andrea Porras-Alfaro.
We conducted a preliminary survey of the fungal communities associated with roots of Stipa hymenoides and Hilaria jamesii, two
grasses native to the southwestern United States. Root samples from 10 different plants were collected at a semiarid grassland in
Utah. Fungal communities were assessed using microscopic and molecular methods. Roots were cleared with KOH and stained
using blue ink to visualize mycorrhizal and endophytic fungi. A total of 100 root segments were surface sterilized and plated on
malt
extract
agar
with
antibiotics.
Fungal
endophytes
were
identified
using
nrITS
primers.

Results/Conclusions

Microscopi
c analyses showed that all root samples from both Hillaria and Stipa...
Tipo: Poster
Palavras-chave: Ecology; Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/3679/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
Host factors affecting abomasal parasites in Alpine Ibex
Provedor de dados: 17
Autores: Roberta Ceccarelli; Valentina Valenti; Paolo Lanfranchi; Nicola Ferrari.
Alpine ibex is characterized by strong sexual differences, both morphological and in population dynamics. Host sex has been
shown to strongly affect parasite load with males usually more infected than females. Moreover ibex exhibit a peculiar pattern of
survival with subadult males having a slow growing rate coupled with high survival which rapidly decline in old individual. This
peculiar life history has been suggested to have been developed as adaptation to an harsh environment. In this way by investing
fewer resources in growing the ibex can direct more energy in survival. At the same time the investment in immunodefence can
change over the age. To verify the hypothesis that sex and age affect parasite infection, we analysed the abomasal parasite...
Tipo: Poster
Palavras-chave: Ecology; Microbiology; Earth & Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3805/version/1
The Opisthokonta and the Ecdysozoa may be clades: An update on Philip et al. (2005)
Provedor de dados: 17
Autores: Marko Prous.
To test the monophyly of Opisthokonta (animal-fungal clade) and Ecdysozoa (nematode-arthropod clade), Philip et al [Mol. Biol.
Evol. 22: 1175–1184 (2005)] used sequence data from 10 eukaryotic genomes (an alveolate, a plant, two
ascomycetous yeasts, a nematode, two dipterans, and three vertebrates). Strict criteria were used to select genes for phylogenetic
analyses: single-gene families were identified and from these families, genes capable of recovering the uncontroversial parts of the
phylogenetic tree (for example animal and vertebrate monophyly) were selected. Only five single-copy genes were found to be
universally distributed across the analyzed taxa and capable of recovering all the uncontroversial parts of the tree. Phylogenetic...
Tipo: Poster
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3306/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
Network-based analyses of Huntington’s Disease
Provedor de dados: 17
Autores: Ravi K. Kalathur; Matthias E. Futschik.
The use of high-throughput technologies has provided us with large amounts of data for _Huntington's disease_ (HD),
especially at the gene and protein levels. As phenotypic changes in HD may not just be due to the activity of individual genes but
interrelated alterations of whole molecular networks, it is important to systematically analyse and represent accumulated data in a
network-based approach.

Methods: To analyse and visualise protein interaction
networks
through
a
dedicated
database
to
HD,
we
have
established
"HDNetDB":
http://hdnetdb.sysbiolab.eu. This platform will not only help to understand molecular mechanisms better, but also assist in
identifying potential molecular markers...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7090/version/1
Grid Potential Analysis and Docking Studies on a Dataset of N-Arylsulfonyl-3-AcetylIndoles as
Anti-HIV Agent
Provedor de dados: 17
Autores: Surendra Kumar; Meena Tiwari.
A grid potential analysis employing the AutoGPA module in MOE2009.10 was performed on a dataset of 42 molecules of
N-arylsulfonyl-3-acetylindoles as anti-HIV agent. The molecular docking simulations were also employed to position the
inhibitors to their binding site to determine the most appropriate binding mode for different conformations of molecule. The
uniqueness of AutoGPA module is that it automatically builds the 3D-QSAR model on the pharmacophore based molecular
alignment. The best AutoGPA 3D-QSAR model obtained in the present study gives the cross-validated q2 value of 0.588 and
r2pred value of 0.701 among the fifty six 3D-QSAR model developed. Furthermore, the steric and electrostatic contour maps for
AutoGPA model along with the 3D structure of...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6932/version/1
Niche Overlap and Diet Breadth: Can bumble bee (Bombus spp.) foraging behavior reveal species
vulnerabilities?
Provedor de dados: 17
Autores: Rosemary Malfi; T'ai Roulston.
Within the last two decades, notable shifts have taken place within the bumble bee (_Bombus_ spp.) communities of North
America: some species have experienced substantial, rapid declines, while others appear to be stable or even experiencing range
expansion. Studies from the UK and Europe implicate the loss of natural habitat and associated floral resources in overall bumble
bee declines and species losses. Research also indicates that loss of host plants disproportionately impacts species with narrower
diet breadths, and that these species are more likely to be long-tongued (presumably due to the reduction of long-tubed floral
hosts). In contrast, species with more generalized diets have been shown to be more abundant. In this study we examined
resource...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6482/version/1
IMGT/GENE-DB: genomic reference sequences for human and mouse IG and TR genes and alleles
Provedor de dados: 17
Autores: Fatena Bellahcene; Géraldine Folch; Joumana Jabado-Michaloud; Chantal Ginestoux; Patrice Duroux;
Véronique Giudicelli; Marie-Paule Lefranc.
The immunoglobulin (IG) and T cell receptor (TR) major loci span about 6 Megabases (Mb) of the human genome on
chromosomes 2, 7, 14 and 22, and 9 Mb in mouse on chromosomes 6, 12, 13, 14 and 16. There are seven major loci: three IG loci
(IGH, IGK, IGL) and four TR loci (TRA, TRB, TRG, TRD), with a distinct repartition of the variable (V), diversity (D), joining
(J) and constant (C) genes. The human genome comprises a total number of 608-665 IG and TR genes (371-422 IG and 237-243
TR), depending on the haplotypes, per haploid genome ^1, 2^ of which 531-588 genes are located in the major loci (distributed in
369-418 V, 32 D, 105-109 J and 25-29 C genes). There are also 77 orphons (68 IG and 9 TR) including two processed IG genes,
outside the major loci. The...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3158/version/1
Requirements for a single cell mechanism of entorhinal "grid field" activity:
role of dendritic oscillators and coupling
Provedor de dados: 17
Autores: Michiel W. H. Remme; Máté Lengyel; Boris S. Gutkin.
The responses of rat medial entorhinal cortical neurons form characteristic grid patterns as a function of the
animal’s position. A recent model of grid fields proposes a mechanism based on intrinsic single cell properties. It
relies on interference patterns emerging from multiple distinct and independent oscillations maintained in the dendritic tree of the
cell. Here we examine the requirements necessary to implement this idealized mechanism in a biophysically realistic model. We
find that appropriate grid field-formation by a single cell is exquisitely sensitive to intra-dendritic interactions. Mathematical
analysis shows how these effects depend on properties of the dendritic oscillators and the (active) membrane segments that
connect them....
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3338/version/1
GreenPhylDB: A Gene Family Database for plant functional Genomics
Provedor de dados: 17
Autores: Matthieu G. Conte; Marie-Angélique Laporte; Christophe Périn; Mathieu Rouard.
With the increasing number of genomes being sequenced, a major objective is to transfer accurate annotation from characterised
proteins to uncharacterised sequences. Consequently, comparative genomics has become a usual and efficient strategy in
functional genomics. The release of various annotated genomes of plants, such as _O. sativa_ and _A. thaliana_, has allowed
setting up comprehensive lists of gene families defined by automated methods. However, like for gene sequence, manual curation
of gene families is an important requirement that has to be undertaken. GreenPhylDB comprises protein sequences of 12 plant
species fully sequenced that were grouped into homeomorphic families using similarity-based methods. Clusters are finally
processed by...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3136/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
Seasonal priority effects: Implications for invasion and restoration in California coastal sage scrub
Provedor de dados: 17
Autores: Claire E. Wainwright; Elsa E. Cleland.
Competition from exotic annual grasses (EAGs) threatens native plant communities in California. Coastal sage scrub communities
have substantially diminished in area over the last century, in some instances by greater than 90%, while EAGs continue to
proliferate. Several mechanisms may explain the success of EAGs, including the suppression of native seedlings by accumulated
litter, exhaustion of soil moisture, and low seed production or dispersal of natives. 
The timing and
magnitude of rainfall plays a significant role in determining the survival and reproduction of plant species in Mediterranean
ecosystems. Populations of annuals fluctuate greatly from year to year, corresponding with variability in autumn precipitation.
EAGs in...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5224/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
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
Functional differentiation within the monkey cortex as revealed by near-infrared spectroscopy
Provedor de dados: 17
Autores: Allen Ardestani; Felix Darvas; Jens Steinbrink; Arthur Toga; Joaquin M. Fuster.
The role of prefrontal cortex in working memory (WM) is well established. However, questions remain regarding the topography
and “domain-specific differentiation” of different types of information processing in the cortex.
While it has been theorized that dorsolateral (DPFC) and ventrolateral (VPFC) prefrontal cortex preferentially process spatial and
object WM, respectively, both electrophysiological evidence in the monkey and neuroimaging in the human have largely failed to
demonstrate such regional differentiation. In this study we use near-infrared spectroscopy (NIRS) to detect functional changes,
across relatively large cortical cell populations, simultaneously from prefrontal and posterior parietal cortices. Imaging data...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1673/version/1
Plants at risk from climate change
Provedor de dados: 17
Autores: Chris Yesson; Alastair Culham.
The popular garden flower Cyclamen grows natively in the Mediterranean. Climate change could make the region unsuitable for
18/21 species in 50 years time. Ant-dispersed Cyclamen can’t hope to migrate to suitable new areas without
assistance.

Background: The impact of global climate change on plant distribution,
speciation and extinction is of current concern. Examining species climatic preferences via bioclimatic niche modelling is a key
tool to study this impact. There is an established link between bioclimatic niche models and phylogenetic diversification. A next
step is to examine future distribution predictions from a phylogenetic perspective. We present such a study using Cyclamen
(Myrsinaceae), a group...
Tipo: Poster
Palavras-chave: Ecology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/150/version/1
SciNetS Search : Inference Search over an Integrated Life-sciences Database Based on the Semantic
Web
Provedor de dados: 17
Autores: Norio Kobayashi; Manabu Ishii; Yuko Yoshida; Yuko Makita; Akihiro Matsushima; Yoshiki Mochizuki; Tetsuro
Toyoda.
Integration of various omics databases is a fundamental approach for comprehensive understanding of life phenomena.
Scientists’ Networking System (SciNetS) is a Semantic Web-based data repository that realises database integration
by collecting metadata of databases described as a set of triples consisting of two bio-items such as gene and ontology terms and a
semantically defined relationship between these bio-items.
These triples are curated from various life-sciences databases
including gene-publication relationships manually curated from MEDLINE and gene-phenotype relationships extracted from
published databases by computer programs. SciNetS internally forms a metadata network by maximally concatenating...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5083/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
Examining the uses of shared data
Provedor de dados: 17
Autores: Heather A. Piwowar; Douglas B. Fridsma.
Does your research area re-use shared datasets?
*
synergy and efficient resource use
*
facilitate re-use
*
Re-using data has many benefits, including research
Some research areas have tools, communities, and practices which
Identifying these areas will allow us to learn from them, and apply the lessons to areas
which
underutilize
the
sharing
and
re-purposing
investigators


of
scientific
data
between
Which datasets?
This preliminary analysis
examines the re-use of microarray gene expression datasets. Thousands of microarray gene expression datasets have been
deposited in publicly available databases. 
Many studies reuse this data,...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/425/version/3
How can cells in the anterior medial face patch be viewpoint invariant?
Provedor de dados: 17
Autores: Joel Z. Leibo; Jim Mutch; Tomaso Poggio.
In a recent paper, Freiwald and Tsao (2010) found evidence that the responses of cells in the macaque anterior medial (AM) face
patch are invariant to significant changes in viewpoint. The monkey subjects had no prior experience with the individuals depicted
in the stimuli and were never given an opportunity to view the same individual from different viewpoints sequentially. These
results cannot be explained by a mechanism based on temporal association of experienced views. Employing a biologically
plausible model of object recognition (software available at cbcl.mit.edu), we show two mechanisms which could account for
these results. First, we show that hair style and skin color provide sufficient information to enable viewpoint recognition without...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5845/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
Prediction of Soil Organic Properties in a Diverse Population of Ohio Soils Using Near Infrared
Reflectance Spectroscopy Analysis
Provedor de dados: 17
Autores: Warren Dick; Aditi Sengupta.
A Near Infrared Spectroscopy (NIRS) method was used to predict soil organic carbon and amino sugar concentrations, and
β-Glucosidase and β-Glucosaminidase activity in 184 diverse soils of Ohio. The measured variable
values were calibrated to NIR spectral data with partial least squares regression analysis. The multivariate models developed were
validated using the full cross validation method and the test set method with a test set size of 50 samples. Statistical analysis of the
spectral data was done using the multivariate analysis software Unscrambler 8.0 (CAMO Inc). The first differential transformation
of the NIR region (1100-2498 nm) gave good results. The NIRS method predicted well the organic carbon (OC) and amino
sugar...
Tipo: Poster
Palavras-chave: Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6248/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
The effect of temperature, soil nitrogen and gastropods on _Thuja plicata_ growth and reproduction
Provedor de dados: 17
Autores: Anna O'Brien; Jannke HilleRisLambers; Ailene Ettinger.
Humans are changing the environment. For example, nitrogen deposition, rising temperatures, and non-native species are
influencing plant communities. These changes have and will continue to affect trees, thus, understanding the response of species
to global change will help conservationists plan for the future. Urban areas already experience higher temperatures, elevated
CO~2~, greater nitrogen levels, and more non-native species compared to rural areas. The response of trees to urban parks and
park edges can therefore be used as a proxy for the net effects of global change on trees. We investigate the growth and
reproduction of _Thuja plicata_, a native Pacific Northwest conifer, in both urban and rural forest fragments to understand global
change...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5446/version/1
Logical Operation Based Literature Association with Genes and its application, PosMed.
Provedor de dados: 17
Autores: Yuko Makita; Rinki Bhatia; Mrinalini Deshpande; Akihiro Matsushima; Manabu Ishii; Yoshiki Mochizuki; Yuko
Yoshida; Norio Kobayashi; Testuro Toyoda.
PosMed prioritizes candidate genes for positional cloning by employing our original database search engine GRASE, which uses
an
inferential
process
similar
to
an
artificial
neural
network
comprising
documental
neurons
(or
'documentrons') that represent each document contained in databases such as MEDLINE and OMIM
(Yoshida, _et al_. 2009, Makita, _et al_. 2009). PosMed immediately ranks the candidate genes by connecting phenotypic
keywords to the genes through connections representing gene–gene interactions other biological relationships, such
as metabolite–gene, mutant mouse–gene, drug–gene, disease–gene, and
protein–protein interactions, ortholog data, and...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5071/version/1
In silico identification of potential inhibitors for human aurora kinase b
Provedor de dados: 17
Autores: Mahesh Babu G; Pradeep N.; Dibyabhaba Pradhan; Manne MuniKumar; Amineni Umamaheswari.
Cell cycle progression through mitosis and meiosis involves regulation by serine/threonine kinases from the aurora family. Aurora
kinase b (Aurkb) is mainly involved in the proper segregation of chromosomes during mitosis as well as meiosis. However, over
expression of Aurkb leads to the unequal distribution of genetic information creating aneuploid cells, a hallmark of cancer. Thus,
Aurkb can be used as an effective molecular target for computer-aided drug discovery against cancer. Existing Aurkb inhibitors
are less efficient, hence an in silico work was carried out to identify novel potent inhibitors. Three published inhibitors azd1152,
zm447439 and N-(4-{[6-methoxy-7-(3-morpholin-4-ylpropoxy) quinazolin- 4-yl] amino} phenyl) benzamide were subjected to...
Tipo: Poster
Palavras-chave: Cancer; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5458/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
In silico comparative study of epitopes predicted from different strains of genus parvovirus.
Provedor de dados: 17
Autores: Rahul B. Chamute; Mahadev A. Jadhav; Anant Patil.
Parvoviruses are typically linear, non-segmented single-stranded DNA viruses, with an average genome size of 5000 nucleotides.
Parvoviruses are some of the smallest viruses found in nature. Some have been found as small as 23 nm. Many types of
mammalian species have a strain of parvovirus associated with them. Parvoviruses tend to be specific about the taxon of animal
they will infect, but this is a somewhat flexible characteristic. Thus, all strains of parvovirus will affect dogs, wolves, and foxes,
but only some of them will infect human. Parvovirus is treated with the help of vaccines but the traditional vaccine development
process is very expensive and unsafe, with the help of insilico software tools and databases we can predict the epitopes of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5574/version/1
In Silico Analysis and Identification of Potent Inhibitors for Human Serine/Threonine Protein Kinase
PIM-3 Involved in Hepatic Cancer
Provedor de dados: 17
Autores: Prasanna Kumar Guttala; Dibyabhaba Pradhan; Amineni Umamaheswari.
PIM3 belongs to a family of proto oncogenes that encode serine/threonine protein kinases in human. Pim-3 is involved in cell
cycle progression, suppression of apoptosis and proliferation of human hepatoma cell lines. During normal cell cycle progression,
Bcl-2 associated death promoter (BAD protein) inactivates Bcl-2 and Bcl-xL there by promoting apoptosis. However,
phosphorylation of BAD protein by Pim-3 leaves Bcl-2 free to inhibit Bax-triggered apoptosis. Thus, designing inhibitors against
Pim-3 would stop BAD phosphorylation, hence would be highly useful for development of novel means of cancer therapeutics.
Computer aided drug designing approach was followed here to explore lead molecules targeting human Pim-3. For this, proteomic
nature and phylogeny...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4899/version/1
UniProt in RDF: Tackling Data Integration and Distributed Annotation with the Semantic Web
Provedor de dados: 17
Autores: Nicole Redaschi; UniProt Consortium.
The UniProt knowledgebase (UniProtKB) is a comprehensive repository of protein sequence and annotation data. We collect
information from the scientific literature and other databases and provide links to over one hundred biological resources. Such
links between different databases are an important basis for data integration, but the lack of a common standard to represent and
link information makes data integration an expensive business. At UniProt we have started to tackle this problem by using the
Resource Description Framework ("http://www.w3.org/RDF/":http://www.w3.org/RDF/) to represent our
data. RDF is a core technology for the World Wide Web Consortium's Semantic Web activities...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3193/version/1
The System Biology Format Converter
Provedor de dados: 17
Autores: Gaël Jalowicki; Nicolas Rodriguez; Martina Kutmon; Jean-Baptiste Pettit; Lu Li; Arnaud Henry; Kedar Nath
Natarajan; Camille Laibe; Chris T. Evelo; Nicolas Le Novère.
The System Biology Format Converter (SBFC) aims is to provide a generic framework that potentially allows any conversion
between two formats. Interoperability between formats is a recurring issue in Systems Biology. Although there are various tools
available to convert models from one format to another, most of them have been independently developed and cannot easily be
combined, specially to provide support for more formats. The framework is written in Java and can be used as a standalone
executable. This is a collaborative project and we hope that developers will provide support for more formats by creating new
modules.SBFC allows anyone to easily add new converters and to integrate existing converters with a minimum of changes. We
will also allow to...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6363/version/1
SNIPER SHOT PEGylation: TGase mediated site-specific conjugation of PEG to proteins
Provedor de dados: 17
Autores: Abhijeet Satwekar.
Commercially available recombinant protein drugs often cause immune reactions in the body which reduces their efficiency.
Protein drugs can be PEGylated, (attachment of polyethylene glycol) to overcome this problem. PEGylation increases
bioavailability by reduced immune reactions and decreased renal clearance [1]. So far the traditional approaches for PEGylation
involve harsh reaction conditions which provide a heterogeneous product (PEG attached randomly to different sites) along with
the formation of several byproducts. Due to heterogeneity, the PEGylated protein drug faces challenge for FDA approval.
Therefore, there is an immense need to develop an approach which could generate a homogeneous PEGylated protein drug.

The...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5671/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
Exploring The Hidden Realms Of Global Biodiversity: Interesting Endophytic Yeast Flora From
Floral Ovaries
Provedor de dados: 17
Autores: Nandkumar Kamat; Shweta S. Saudagar.
Soil is considered the ultimate reservoir of all the microbiota and specifically the yeasts. However their association with different
plant organs and at different developmental stages is not fully explored. Although about 1000 yeast species have been identified,
exploration of various microhabitats such as plant storage organs, flowers, nectar, and tree sap is expected to yield a large number
of novel species, including interesting endophytic yeasts(Carlos & Gabor, 2006). Angiosperms are considered the most
diverse group of the plant kingdom comprising of about 250,000 species (Kenrick, 1999). As part of an exhaustive exploration of
yeasts associated with angiosperm flowers, specific attention was paid to floral ovaries to detect the presence of...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Ecology; Genetics & Genomics; Microbiology; Plant Biology; Evolutionary
Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6268/version/1
The Importance of Modularity in Bioinformatics Tools
Provedor de dados: 17
Autores: Martina Kutmon; Martijn P. van Iersel; Thomas Kelder; Chris T. Evelo.
In the last decade the amount of Bioinformatics tools has increased enormously. There are tools to store, analyse, visualize, edit or
generate biological data and there are still more in development. Still, the demand for increased functionality in a single piece of
software must be balanced by the need for modularity to keep the software maintainable. In complex systems, the
conflicting
demands
of
features
and
maintainability
are
often
solved
by
plug-in
systems.

For example Cytoscape, an open source platform for Complex-Network
Analysis and Visualization, is using a plug-in system to allow the extension of the application without changing the core. This not
only allows the integration of new functionality...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6113/version/1
Screening Of Antibiotic Producing Microorganism From Rhizoshphere Soil, Their Antibiotic
Production And Characterization
Provedor de dados: 17
Autores: Vishwambhar V. Bhandare; Sandip Mahadev Chavre.
Rhizosphere soil samples were preferred as it contains most of the prospective antibiotic producers. In an attempt to screen out
new potent antibiotic producers from soil, the Rhizobium species was isolated. Antibiotic produced by shake flask culture is found
to be effective against both gram positive and gram negative organisms. This product was found to be a very promising antibiotic
when assayed biologically. UV treatment showed positive effect on antibiotic production. The molecular structure of the antibiotic
was identified by using advanced analytical techniques like UV Visible spectroscopy, FTIR, GCMS, NMR spectroscopy.
Tipo: Poster
Palavras-chave: Biotechnology; Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/6101/version/1
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
Phenoscape: Ontologies for Large Multi-species Phenotype Datasets
Provedor de dados: 17
Autores: Peter Midford; Paula Mabee; Todd Vision; Hilmar Lapp; Jim Balhoff; Wasila Dahdul; Cartik Kothari; John Lundberg;
Monte Westerfield.
The Phenoscape project is developing ontologies and tools to integrate morphological and genomic data to address comparative
questions in evolutionary biology. We are currently curating 81 publications describing ~5000 phenotypic characters in 4,000
species of Ostariophysian fishes, and will be making our database of ontology-based annotations concurrently with this meeting
via a web-based interface at "http://kb.phenoscape.org":http://kb.phenoscape.org.
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3594/version/1
In silico design of potent agonists for human PPAR γ
Provedor de dados: 17
Autores: Navya Pallapotu; Divya M; Kanipakam Hema; Amineni Umamaheswari.
Peroxisome proliferator-activated receptor (PPAR γ) acts as a key regulator on adipocyte differentiation and glucose
homeostasis. PPAR γ has been implicated in the pathology of type 2 diabetes. As human PPAR γ
activity is considered important in improving insulin sensitivity, in silico screening was carried out to find potent agonists for
human PPAR γ protein. The co-crystal structure of PPAR γ, solved through X-Ray diffraction method
was retrieved from the protein data bank. Four PPAR γ agonists selected from literature were submitted to subsequent
2D searching protocol using Ligand.Info, which yielded 1699 structural analogs. The PPAR γ co-crystal structure and
ligand dataset were...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6957/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
Microparticles specific for lung delivery: in-vivo drug distribution in monkeys
Provedor de dados: 17
Autores: Rahul Verma; Amit Misra.
In spite of extensive research in tuberculosis (TB), it is still one of the major infectious diseases and cause of high mortality
worldwide. To enhance efficacy with lower dosing, newer drug delivery systems has been developed which provide targeted drug
delivery and controlled release at the primary site of infection, i.e., the lung macrophage. Our lab has previously reported poly(D,
L-lactic acid) (PLA) microparticles containing rifabutin (RFB) and isoniazid (INH) for pulmonary delivery and explored various
facets of treatment with microparticle DPI. We have utilized this dry powder aerosol drug delivery system to deposit drugs
directly at the site of infection in lungs and have been investigating such DPI as a novel approach to increase therapeutic...
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7061/version/1
Long-term Benefits of GM crops: Potential for Diabrotica Suppression in Europe using Bt Maize
Provedor de dados: 17
Autores: Nicholas P. Storer; Peter Schlotter; Kevin L. Steffey.
Transgenic crops producing insecticidal proteins from _Bacillus thuringiensis_ (Bt) have been widely adopted since 1996 in the
United States of America to combat important pests of maize and cotton. There is growing evidence that several target pest
populations have been dramatically reduced in areas where the Bt crops have been most intensively adopted over multiple years.
The evidence is most dramatic for nonmigratory monophagous and oligophagous species that show high mortality on Bt crops,
such as European corn borer (_Ostrinia nubilalis_), and tobacco budworm (_Heliothis virescens_). Bt cotton is currently being
used in the southwestern USA as part of an area-wide eradication program for pink bollworm (_Pectinophora gossypiella_).
Single, stacked, and...
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4447/version/1
The Eukaryotic Linear Motif Resource (ELM): Regulatory Sites in Proteins
Provedor de dados: 17
Autores: Francesca Diella; Allegra Via; Claudia Chica; Katja Luck; Catherin M. Gould; Toby J. Gibson.
Linear motifs are short and evolutionarily variable sequence patterns associated with particular functions often involving
post-translational modifications, such as phosphorylation, acetylation, glycosylation, targeting signals for cellular compartments,
protein cleavage sites and protein–protein interaction.

Experimentally
they are often neglected because their short length (4-10 residues long), and the fact that they often reside in disordered regions in
proteins makes them difficult to detect. For a similar reason, using the sole regular expression to detect linear motifs matches in
sequences has almost no predictive power because they are both statistically insignificant and prone to massive...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3152/version/1
Allele-specific primer based identification of dimeric alpha-amylase inhibitor
Provedor de dados: 17
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
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
Learning complex tasks with probabilistic population codes
Provedor de dados: 17
Autores: Richard E. Turner; Pietro Berkes; Jozsef Fiser.
Recent psychophysical experiments imply that the brain employs a neural representation of the uncertainty in sensory stimuli and
that probabilistic computations are supported by the cortex. Several candidate neural codes for uncertainty have been posited
including Probabilistic Population Codes (PPCs). PPCs support various versions of probabilistic inference and marginalisation in
a neurally plausible manner. However, in order to establish whether PPCs can be of general use, three important limitations must
be addressed. First, it is critical that PPCs support learning. For example, during cue combination, subjects are able to learn the
uncertainties associated with the sensory cues as well as the prior distribution over the stimulus. However, previous...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5838/version/1
Local statistics in natural scenes predict the saliency of synthetic textures
Provedor de dados: 17
Autores: Gasper Tkacik; Jason S. Prentice; Jonathan D. Victor; Vijay Balasubramanian.
To represent behaviorally relevant information efficiently, neural circuits in sensory periphery are matched to the first and
second-order statistical structure of natural inputs. The retina, for example, removes stimulus components that are predictable (and
therefore uninformative), and transmits what is unpredictable (and therefore informative). Here we show that this efficient coding
principle applies to complex aspects of natural scenes, and to central visual processing (Tkačik et al, PNAS 2010).


The aspect of natural scenes that we examine in detail is texture in image patches.
Texture is determined partly by the distribution of light intensities and partly by the spatial organization of light across...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6009/version/1
Inflammation, DNA-centered radicals, and oxidative genotoxicity: The role of HOCl produced by
myeloperoxidase in carcinogenesis
Provedor de dados: 17
Autores: Sandra E. Gomez-Mejiba; Zili Zhai; Dario C. Ramirez.
Myeloid cells (macrophages and neutrophils) infiltrate and synthesize myeloperoxidase (MPO) in sites of inflammation,
producing gentotoxicity. In RAW 264.7 macrophages, bacterial lipopolysaccharide (LPS) induces superoxide radical anion,
nuclear
deformation
(nuclear
protuberances),
MPO
synthesis,
biomolecule
oxidation
and
cell
death.
“Freezing” LPS-triggered macrophage activation with the nitrone spin trap 5,5-dimethyl-1-pyrroline
N-oxide (DMPO) prevented cell activation and death. Oxidation of proteins and genomic DNA was also blocked, with formation
of protein- and DNA-DMPO nitrone adducts, as analyzed by immuno-spin trapping with a polyclonal anti-DMPO serum.
Interestingly, confocal microscopy analysis of these cells showed that...
Tipo: Poster
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/4047/version/1
The Attentional Routing Circuit: Receptive Field Modulation Through Nonlinear Dendritic
Interactions
Provedor de dados: 17
Autores: Bruce Bobier; Terrence C. Stewart; Chris Eliasmith.
We present a model of attentional routing called the Attentional Routing Circuit (ARC) that extends an existing model of spiking
neurons with dendritic nonlinearities. Specifically, we employ the Poirazi et al. (2003) pyramidal neuron in a population coding
framework. ARC demonstrates that the dendritic nonlinearities can be exploited to result in selective routing, with a decrease in
the
number
of
cells
needed
by
a
factor
of
~5
as
compared
with
a
linear
dendrite
model.

Routing of attended information occurs through the modulation of
feedforward visual signals by a cortical control signal specifying the location and size of the attended target. The model is fully
specified in spiking single cells. Our approach differs...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5817/version/1
ENA as an Information Hub
Provedor de dados: 17
Autores: Petra ten Hoopen; Ruth Akhtar; Richard Gibson; Bob Vaughan; Nadeem Faruque; Guy Cochrane.
The European Nucleotide Archive (ENA; "http://www.ebi.ac.uk/ena/":http://www.ebi.ac.uk/ena/) is a
comprehensive repository for public nucleotide sequence data from nearly four hundred thousand taxonomic nodes. Together with
partners in the International Nucleotide Sequence Database Collaboration (INSDC; EBI, NCBI and DDBJ) we provide a broad
spectrum of sequences, from raw reads (Sequence Read Archive data class), assembled contigs (Whole Genome Shotgun data
class), assemblies of EST transcripts (Transcriptome Shotgun Assembly data set), to partial or complete assembled nucleic acid
molecules with functional annotation derived from direct and third party experimental evidence (Standard and TPA data classes,
respectively). Resources beyond...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5108/version/1
Reactome - a knowledgebase of human biological pathways
Provedor de dados: 17
Autores: Bijay Jassal; Esther E. Schmidt; Guanming Wu; Imre Vastrik; David Croft; Bernard de Bono; Gopal Gopinath; Marc
Gillespie; Steven Jupe; Gavin O'Kelly; Lisa Matthews; Phani V. Garapati; Michael Caudy; Alexander Kanapin; Bruce
May; Shahana Mahajan; Ewan Birney; Peter D'Eustachio; Lincoln Stein.
Reactome ("http://www.reactome.org":http://www.reactome.org) is an expert-authored, peer-reviewed
knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current
release includes 2921 human proteins, 2871 reactions and 4167 literature citations. This curated dataset is integrated with a
functional interaction network assembled computationally from non-curated sources of information including protein-protein
interactions, gene co-expression, and gene ontology annotations, providing access. A new entity-level pathway viewer and
improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied
high-throughput data...
Tipo: Poster
Palavras-chave: Chemistry; Genetics & Genomics; Immunology; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3200/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: 2008
URL: http://precedings.nature.com/documents/2643/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
What's in an 'is a' link?
Provedor de dados: 17
Autores: William R. Hogan.
Introduction

Several
researchers
have
demonstrated
that
current
medical
terminologies and ontologies use relations in inconsistent and ambiguous ways,[1] despite Woods’ seminal work
that first illustrated the problem.[2] The goal of the present work is to catalog the different ways in which SNOMED CT uses the
_is a_ relation. The rationale for creating the catalog is to serve as a basis for systematically improving the semantics of
terminologies
and
ontologies
so
as
to
improve
their
accessibility
inference.

Methods

I
to
machine
reviewed
the
literature to find ontological mistakes that change the interpretation of the _is a_ relation, without...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3462/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
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
SBRML- A Markup Language for Encoding Systems Biology Results
Provedor de dados: 17
Autores: Joseph O. Dada.
Background:
The wide acceptance of Systems Biology Markup Language (SBML) as standard format for
models of biochemical systems makes it possible to build, share, evaluate and develop biochemical models cooperatively.
However, there is currently no standard format for encoding the results of computational analyses of systems biology models. To
address this issue, we present here the Systems Biology Results Markup Language (SBRML), an XML-based format for
representing systems biology results. SBRML provides a means of representing computational simulation results as well as
encoding experimental data in the context of a particular model.

Methods
& Results:
SBRML is based on XML...
Tipo: Poster
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6351/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
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
Exploring binding site of human RBP4 towards discovery of novel inhibitor for treatment of
cardiovascular diseases
Provedor de dados: 17
Autores: C Lakshmi Narayana Rao; LA Raziya Beevi; Amineni Umamaheswari.
Retinol binding proteins (RBPs) are transport proteins that act by solubilizing and protecting their labile ligands in aqueous
spaces. In addition, RBPs have diverse and specific functions in regulating the disposition, metabolism and activities of retinoids.
Elevated levels of retinol-binding protein 4 (RBP4) are observed in cardiovascular disease conditions, which prompts it as a
potential drug target. Therefore, computational approach methods were implemented herein to design a novel inhibitor for RBP4.
Crystal structure (2wq9) of RBP4 was retrieved and investigated to locate retinol binding site residues (Lys29, Pro32, Leu35,
Phe36, Leu37, Phe45, Ala55, Ala57, Met73, Val74, Gly75, Met88, Try90, His104, Gln117, Arg121, Try133, Phe135, Phe137).
Five...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6587/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
GUDMAP - An Online GenitoUrinary Resource
Provedor de dados: 17
Autores: Chris Armit; Simon Harding; Jamie A. Davies; Jane Armstrong; Jane Brennan; Sue Lloyd-MacGilp; Derek Houghton;
Mehran Sharghi; Xingjun Pi; Y. Cheng; Bruce Aronow; Kevin Gaido; Sean Grimmond; Peter Koopman; Jim Lessard; Melissa
Little; Andy McMahon; Cathy Mendelsohn; Steve Potter; Michelle Southard-Smith; Duncan Davidson.
The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the
scientific
and
medical
community
with
gene
expression
data
and
tools
to
facilitate
research
(see
"www.gudmap.org":http://www.gudmap.org). The data provided by GUDMAP includes large _in situ_
hybridization screens (wholemount and section) and expression microarray analysis of components of the developing mouse
urogenital system (including laser-captured material and FACS-isolated cells from transgenic reporter mice). In addition, a
high-resolution anatomy ontology has been developed by members of the GUDMAP consortium to describe the subcompartments
of the developing murine genitourinary tract....
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3297/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
Models of Multifunctional Central Pattern Generators: Polyrhythmic Bursting
Provedor de dados: 17
Autores: Andrey Shilnikov.
We demonstrate a motif of three reciprocally inhibitory cells that is able to produce multiple patterns of bursting rhythms.
Through the examination of the qualitative geometric structure of two-dimensional maps for phase lag between the cells we reveal
the organizing centers of emergent polyrhythmic patterns and their bifurcations, as the asymmetry of the synaptic coupling is
varied. The presence of multistability and the types of attractors in the network are shown to be determined by the duty cycle of
bursting. This analysis does not require knowledge of the equations that model the system, and so provides a powerful new
approach to studying regulatory networks. Thus, the approach is applicable to a variety of biological phenomena beyond motor
control.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5800/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 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
Managing Bio-Models: Model Storage, Retrieval, Ranking and Versioning
Provedor de dados: 17
Autores: Ron Henkel; Dagmar Waltemath; Olaf Wolkenhauer.
In this poster, we present our experience with techniques for the management of bio-models (i.e. XML-encoded computational
models of biological systems) in repositories. These techniques support users to find, access, adapt and then re-submit models tasks which are essential for the reuse of models in systems biology. Here, we focus on model retrieval, the ranking of search
results and concepts to track the history of a model through version control. These concepts have so far not been sufficiently
addressed in existing systems.
To validate our techniques, we have been implemented a framework called
Sombi. The underlying database called mDB is tailored towards a fine-grained storage of the model and its annotations. The
design is...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6325/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
STRING and STITCH: known and predicted interactions between proteins and chemicals
Provedor de dados: 17
Autores: Lars J. Jensen; Michael Kuhn; Manuel Stark; Samuel Chaffron; Christian von Mering; Peer Bork.
Information on protein-protein and protein-chemical interactions is essential for understanding cellular functions. The STRING
and STITCH web resources integrate interaction evidence derived from pathways, automatic literature mining, primary
experimental data, and genomic context. The resulting interaction networks cover 1.5 million proteins from 373 organisms and
68,000 chemicals.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2265/version/1
QSAR & DOCKING APPROACH - POTENTIAL WAY TO NEW DRUG
DEVELOPMENT
Provedor de dados: 17
Autores: Ajeet Ajeet.
With today's need for discovering and developing new drug molecules, it is necessary to accept ways to save time and
wet lab essentials. To this end, the QSAR and molecular docking approach is used widely by us. This poster describes steps for
developing a new or modified moiety of a drug molecule.

Tipo: Poster
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7071/version/1
(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
Neuronal plasticity: cell-based strategy for target identification and validation
Provedor de dados: 17
Autores: Ana Mingorance-Le Meur; Timothy P. O'Connor.
While growing neurites are relatively plastic during development, their plasticity levels drop rapidly as neurons mature and
become integrated into neuronal networks. As a consequence, the central nervous system ability to reorganize itself in response to
injury or disease is insufficient. One of the main limitations for the design of therapeutic strategies to enhance neurite sprouting
following neurological diseases is our poor understanding of the mechanisms underlying neurite structural plasticity.


To overcome this limitation, we have implemented a strategy to identify,
characterize and validate the most therapeutically relevant drug targets to modulate neuronal plasticity. This strategy is based on
the hypothesis...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/2780/version/1
Learning a Bayesian prior in interval timing
Provedor de dados: 17
Autores: Hansem Sohn; Sang-Hun Lee.
Behavioral studies on perceptual learning (PL) often attributed an improvement in task performance to an enhancement in sensory
processing of stimuli. However, the framework of Bayesian inference suggests that perceptual improvements can arise from
learning-induced changes either in a likelihood function or in a prior expectation for sensory input. We developed and adapted
Bayesian observer models to long-term changes in interval timing (IT) performance by human subjects to assess relative
contributions of the prior and likelihood to PL of IT.

While subjects were viewing a
small bar that drifted for a while and disappeared, we estimated subjective time intervals ([DELTA]Ts) from
subjects’ natural reactions to...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5804/version/1
Tuberculosis vaccine: pipeline approaches and future prospective
Provedor de dados: 17
Autores: L K Dwivedi; Ankita Singh; Poonam Yadav.
Tuberculosis (TB), despite anti-mycobacterial therapies and vaccine, is a deadly infectious disease with about 12 million incident
cases worldwide. Existing Bacillus Calmette-Guérin (BCG) vaccine is unquestionably inexpensive, safe and effective
against severe forms of childhood TB but appears to be limited in effectiveness against adult pulmonary disease in endemic areas.
Genetic variation in the population is the major obstruction inhibiting validation of biomarkers for protective human immunity
against TB. Since current TB cases are presenting new challenges with threats of HIV co-infection therefore various attempts at a
global platform are being made to develop a new modified vaccine against it. Consequently, Modified Vaccinia Ankara virus...
Tipo: Poster
Palavras-chave: Immunology.
Ano: 2011
URL: http://precedings.nature.com/documents/5950/version/1
Soil extracellular enzyme activities from a forest harvest and climate manipulation experiment in
central Pennsylvania
Provedor de dados: 17
Autores: Marshall D. McDaniel; Jason P. Kaye; Mary Ann V. Bruns; Margot W. Kaye.
We have previously shown that warming and wetting a post-harvest forest soil increased C and N mineralization rates. A series
of interacting processes may lead to these observed patterns including shifts in microbial allocation among extracellular enzymes.
We monitored soil extracellular enzyme activity (EEA) for 2.5 years in a post-harvest, climate manipulated field experiment. A 2
ha forest in Central Pennsylvania was whole-tree harvested in 2007 and climate manipulations of +2 °C (warmed), and
+20% mean monthly historical precipitation (wetted) were added to plots and in combination in a factorial design. The following
enzymes were quantified: β-1,4-glucosidase (BG), cellobiohydrolase (CBH), leucine aminopeptidase (LA),...
Tipo: Poster
Palavras-chave: Ecology; Microbiology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6254/version/2
Hyperinsulinemia and insulin resistance : What comes first ?
Provedor de dados: 17
Autores: Pramod P. Patil; Milind M. Watve.
Background

1)	Classical
explanation
:
Classical
explanation of diabetic pathophysiology states that obesity induced insulin resistance develops first and is followed by
compensatory hyperinsulinnemia. Further insulin resistance leads to prolonged, increased secretary demand on beta cells
leading
to
subsequent
secondary
beta
cell
failure,
diabetes^2^.

2)	
giving
rise
Neurobehavioral
to
hyperglycaemia
origin
and
hypothesis
:
The Neurobehavioral origin hypothesis suggests that insulin resistance mediates a shift from muscle
dependent (soldier) to brain dependent (diplomat) strategies of making a livelihood. If nutrient limitation...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5416/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
Rule Responder: A Rule-Based Semantic eScience Service Infrastructure
Provedor de dados: 17
Autores: Adrian Paschke; Zhili Zhao.
To a large degree information and services for chemical e-Science have become accessible -anytime, anywhere -but not
necessarily useful. The Rule Responder eScience middleware is about providing information consumers with rule-based agents to
transform existing information into relevant information of practical consequences, hence providing control to the end-users to
express in a declarative rule-based way how to turn existing information into personally relevant information and how to react or
make automated decisions on top of it.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5632/version/1
Soil Microbial Biomass And Activity In A Cork Oak Savanna
Provedor de dados: 17
Autores: Maria C. Caldeira; David Fangueiro; Xavier Lecomte; Miguel N. Bugalho; João P. Coutinho;
João S. Pereira.
Cork oak savannas are composed by a sparse tree canopy (30-70 trees/ha) and a grassland understory predominantly composed of
C3 annuals that survive the hot and dry Mediterranean summers as seeds in the soil. Microbial communities can be more or less
efficient at converting organic substrates into microbial biomass carbon depending on the quantity and quality of organic matter
inputs. The cork oak savannas have two distinct types of plant litter that can affect soil microbial biomass and activity differently:
herbaceous litter and the more recalcitrant woody plant litter resulting from the trees. Spatial variability of soil microbial biomass
and activity due to the tree-grassland component of cork oak savannas were evaluated in order to better understand...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5401/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
Enzyme activities in brown forest soils after introduction of Bacillus thuringiensis-based
bioinsecticides
Provedor de dados: 17
Autores: Hasmik S. Movsesyan; Arevik M. Sargsyan; Naira P. Ghazaryan.
Much attention in the complex of forest pest control methods nowadays is devoted to the application of biological preparations,
especially to bacterial formulations produced on the base of Bacillus thuringiensis (BT) that in addition to their high biological
effectiveness against injurious insects are safe for man, homoiоtherms, beneficial insects and fish. As is known only
20-40% of sprayed preparation influences directly on pests while its 60-80% by different ways eventually penetrates into the soil.
Taking into account also the fact that usage norm of commercial bacterial preparations makes up to 1-3 kg ha^-1^ and that
preparation powder contains 45-100 billion viable spores g^-1^ it becomes evident that as a result of spraying huge quantity...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6426/version/1
Site-Specific Modification Of Proteins Mediated By Transglutaminase
Provedor de dados: 17
Autores: Abhijeet Satwekar.
Transglutaminase (TGase) catalyzes an acyl transfer reaction between the [gamma]-carboxamide group of glutamine (Gln) and
the [epsilon]-amino group of lysine (Lys) residues to form a stable amide bond. The TGase reaction can be used for
bioconjugation of an amino-derivative of poly-ethylene glycol (PEG) to protein drugs, leading to PEGylated proteins that display
increased bioactivity and stability. The procedure was shown to lead to site-specific bioconjugation of few proteins, thus offering
a valid alternative to the chemical methods of PEGylation in current use (1). Moreover, TGase can be used for site-specifically
labeling proteins with fluorescent groups at the level of Gln or Lys for diagnostic applications. The TGase attack is not entirely
dependent...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6000/version/1
H-InvDB release 6, a comprehensive annotation resource for human genes and transcripts
Provedor de dados: 17
Autores: Chisato Yamasaki; Katsuhiko Murakami; Jun-ichi Takeda; Yoshiharu Sato; Akiko Noda; Ryuichi Sakate; Takuya
Habara; Hajime Nakaoka; Fusano Todokoro; Akihiro Matsuya; Tadashi Imanishi; Takashi Gojobori.
H-Invitational Database (H-InvDB; "http://www.h-invitational.jp/":http://www.h-invitational.jp/) is an
integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated
annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional
RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic
polymorphisms, relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions
(PPIs) and gene families/groups. The latest release of H-InvDB (release 6.0) provide annotation for 219,765 human transcripts in
43,159 human gene...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3251/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
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
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
Open Source Drug Discovery
Provedor de dados: 17
Autores: Jyoti Yadav; OSDD Consortium.
Tuberculosis is a ravaging disease killing one person in every 1.5 minutes in India alone. Someone in the world is newly infected
with TB bacilli every second. Overall, one-third of the world's population is currently infected with the TB bacillus.
Left untreated, each person with active TB disease will infect on average between 10 and 15 people every year. 450 000 new
MDR-TB cases are estimated to occur every year. Estimated 5% of TB patients are HIV infected. Although the complete genome
sequence of the causative pathogen _Mycobacterium tuberculosis_ was published about a decade ago and many years of
painstaking efforts have been invested, we are still far from having a good, fast acting drug and vaccine which confers long lasting
protection....
Tipo: Poster
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2537/version/1
Literature Triage and Indexing in the Mouse Genome Informatics (MGI) Group
Provedor de dados: 17
Autores: Randal P. Babiuk; Dale A. Begley; Susan M. Bello; Dirck W. Bradt; Donna L. Burkart; Howard Dene; Alexander D.
Diehl; Harold J. Drabkin; Jacqueline H. Finger; Terry F. Hayamizu; David P. Hill; Michelle Knowlton; Debra M. Krupke; Ira Lu;
Lois J. Maltais; Monica McAndrews-Hill; Terrence F. Meehan; Li Ni; Hiroaki Onda; Dmitry Sitnikov; Constance M. Smith;
Cynthia L. Smith; Monika Tomczuk.
The Mouse Genome Informatics (MGI; "http://www.informatics.jax.org":http://www.informatics.jax.org)
group is comprised of several collaborating projects including the Mouse Genome Database (MGD) Project, the Gene Expression
Database (GXD) Project, the Mouse Tumor Biology (MTB) Database Project, and the Gene Ontology (GO) Project. Literature
identification and collection is performed cooperatively amongst the groups.

In recent
years many institutional libraries have transitioned from a focus largely on print holdings to one of electronic access to journals.
This change has necessitated adaptation on the part of the MGI curatorial group. Whereas the majority of journals covered by the
group used to be...
Tipo: Poster
Palavras-chave: Cancer; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology;
Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3246/version/1
Novel protein antigen (JHP940) from the genomic plasticity region of Helicobacter pylori induces
TNF-alpha and Interleukin- 8 secretion by human macrophages
Provedor de dados: 17
Autores: Niyaz Ahmed; Ayesha Alvi; Mohammed Rizwan.
Plasticity region of the H. pylori genome comprises strain specific gene loci. We performed genotyping and functional biology of
one such locus (jhp940) that was previously found to be functionally unknown but present in gastric cancer associated strains
from many different countries. We found its geographic prevalence to be independent of cagA presence and disease status.
Cloning, expression and purification of the JHP940 revealed a novel, ~36kDa protein in biologically active form. The same
induced strong and significant levels of TNF-alpha and Interleukin-8 in human macrophages. Induction of these cytokines by
JHP940 points to its putative role in chronic gastric inflammation and various other outcomes of H. pylori infection including
gastric cancer.
Tipo: Poster
Palavras-chave: Immunology; Microbiology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/864/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
Inhaled Insulin: Intrapulmonary or Intranasal?
Provedor de dados: 17
Autores: Danish Ahmed; Sweta Kumari; Shruti Mishra; Shivangi Jaiswal.
Initial attempts delivered the insulin hormone intramuscularly, intravenously, and eventually subcutaneously. Other routes of
administration of the drug were explored. These included oral, rectal, sublingual, buccal, transdermal, vaginal, intramuscular,
intrapulmonary, and intranasal delivery systems. The purpose of these latter studies was to determine a noninjectable method to
deliver insulin to patients with type 1 and 2 diabetes that would effectively lower blood sugar, control hemoglobin A1c (in much
later studies), and allow patients a simpler, less invasive, and more direct control oftheir underlying disease process.  In
January 2006 the United States Food and Drug Administration approved Exubera (Pfizer Pharmaceuticals, New York, NY) as...
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7115/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
Hierarchical inference of disparity
Provedor de dados: 17
Autores: Ivana Tosic; Bruno A. Olshausen.
Disparity selective cells in V1 respond to the correlated receptive fields of the left and right retinae, which do not necessarily
correspond to the same object in the 3D scene, i.e., these cells respond equally to both false and correct stereo matches. On the
other hand, neurons in the extrastriate visual area V2 show much stronger responses to correct visual matches [Bakin et al, 2000].
This indicates that a part of the stereo correspondence problem is solved during disparity processing in these two areas. However,
the mechanisms employed by the brain to accomplish this task are not yet understood. Existing computational models are mostly
based on cooperative computations in V1 [Marr and Poggio 1976, Read and Cumming 2007], without exploiting the...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5824/version/1
Investigations on biological activity of Vetiveria zizanioides L. Nash, a palingenesis of some important
findings in miracle grass
Provedor de dados: 17
Autores: Suaib Luqman.
Vetiveria zizanioides L. Nash synonymously known as Chrysopogon zizanioides L. Roberty (Family: Poaceae/Graminae), widely
cultivated in the tropical regions of the world, is a miraculous grass native to India first developed for soil and water conservation
by the World Bank during mid 1980s. Popularly known as ‘KHUS’, it is the major source of the
well-known oil of vetiver, which is used in medicine, cosmetics and in perfumery making agarbattis, soaps, soft drinks, pan
masala. Being a major constituent of ‘Rasayana’ in Ayurveda, different parts of the vetiver plant have
traditionally been used by the Indian tribes for treating various ailments, diseases and disorders including boils, burns, epilepsy,
fever,...
Tipo: Poster
Palavras-chave: Cancer; Microbiology; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6904/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
Retinal adaptation to spatial correlations
Provedor de dados: 17
Autores: Kristina D. Simmons; Jason S. Prentice; Jan Homann; Gasper Tkacik; Philip C. Nelson; Vijay Balasubramanian.
The classical center-surround retinal ganglion cell receptive field is thought to remove the strong spatial correlations in natural
scenes, enabling efficient use of limited bandwidth. While early studies with drifting gratings reported robust surrounds
(Enroth-Cugell and Robson, 1966), recent measurements with white noise reveal weak surrounds (Chichilnisky and Kalmar,
2002).
This might be evidence for dynamical weakening of the retinal surround in response to decreased spatial correlations,
which would be predicted by efficient coding theory. Such adaptation is reported in LGN (Lesica et al., 2007), but whether the
retina also adapts to correlations is unknown.


We tested for adaptation by
recording...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6344/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
Phantom Pain Reduction by Non-ionizing Electromagnetic Treatment
Provedor de dados: 17
Autores: Istvan Bokkon.
Based on our years of experience testing a technique called non-ionizing Electromagnetic-Own-Signal-Treatment (EMOST), here,
we present our preliminary results for phantom pain reduction by this method under clinical circumstances. Our preliminary
results showed not only a reduction in phantom pain in patients but also a marked improvement in their sleep and mood quality
after the treatments. Here, we also suggest that some of the important effects of our method may be achieved via the redox balance
of the body and redox-related neural plasticity. However, low-frequency and intensity electromagnetic fields can potentially
provide useful methods for the treatment of various problematic disorders and can play important roles in public health of the
21st...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4989/version/1
Precise Atomic Structures of two Important Molecules in Biochemistry:
Provedor de dados: 17
Autores: Raji Heyrovska; Saraswathi Narayan; Lakshmi Atchison.
This work celebrates the “International Year of Chemistry – 2011”, by providing
“for the first time”, the structures at the atomic level of two important molecules, namely, ascorbic
acid and aspirin. Ascorbic acid, also known as vitamin C, was discovered as a cure for scurvy which claimed many human lives
and hence got its name. It is also supposed to be an antioxidant and to prevent flu. Aspirin is synthesized from salicylic acid and is
widely used as a remedy for flu and has other medical uses such as saving the lives of cardiac patients as an anticoagulant of
blood. The biochemistry and chemistry of both these compounds have been evolving for nearly a century ever since their
discoveries. Here, the...
Tipo: Poster
Palavras-chave: Chemistry; Developmental Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5966/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
In Silico Characterization of Tomato leaf curl Joydebpur virus (ToLCJV) DNA-A Proteins
Provedor de dados: 17
Autores: Rajneesh Prajapat; Avinash Marwal; Anurag Sahu; Rajarshi Kumar Gaur.
We retrieved six protein sequences of Tomato leaf curl Joydebpur virus (ToLCJV) DNA-A [FJ345402] from GenBank-NCBI
(ACJ03821, ACJ03822, ACJ03823, ACJ03824, ACJ03825 and ACJ03826) which were used for computational modeling
structure prediction. Ramachandran plot of ACJ03826-AC4 had maximum 73.3% and ACJ03822-AV1 had 71% residues in core
region therefore these models cannot be placed in a good quality category. ACJ03824-AC2 had only 18.6% residues in core and
13.6% residues in disallowed regions and therefore it was the least stable protein. Verify-3D graph profile scores for selected
ToLCJV proteins were greater than zero. Therefore all the verify-3D graph corresponds to an acceptable environment for the
model. Findings of the present study provide a base...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6658/version/1
Homology Modeling of Human α~2A~-Adrenoceptor
Provedor de dados: 17
Autores: Jignesh Patel; Gourja G; Vivek Kumar; Yogesh Narkhede; Shikhar Gupta; C. Gopi Mohan.
α~2A~-adrenoceptor (ADA2A) is a membrane bound receptor which has been classified as the member of larger
superfamily G-protein coupled receptors (GPCRs); also known as seven transmembrane (7-TM) domains receptor. Around 50%
drugs currently available in the market exert their effects through GPCRs. Membrane proteins are difficult to crystallize as
compared to soluble proteins. There is a need of 3D-structure of ADA2A to understand
binding modes of various agonists and
antagonists and hence homology model of ADA2A was developed. Homology model of ADA2A constructed based on crystal
structure of β~2~-adrenoceptor. The crystal structure of β~2~-adrenoceptor (PDB ID: 2RH1) was used as
template, which has good sequence identity...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4106/version/1
Letting the Cat Out of the Bag: OBO and the Semantic Web
Provedor de dados: 17
Autores: John E. Rose.
The
tools
developed
to
work
with
an
expanding
number
of
biomedical
ontologies
are
all
directed
“inward,” back toward the scientists. The Semantic Web is an effort to assign meaning to data
available on the internet resulting in a universal platform of knowledge exchange. For the Open Biomedical Ontologies to become
a part of the Semantic Web, a more “outward-looking” tool is required. A prototype, AmiGA, based
on 21 ontologies with over 600,000 terms,
has been constructed.

Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3527/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
Quest for the descent of the Escherichia coli outbreak strain TY2482 – out of Germany?
Provedor de dados: 17
Autores: Tiruvayipati S. Avasthi; Narender Kumar; Ramani Baddam; Niyaz Ahmed.
The recent outbreak of the Escherichia coli infection in north Germany reportedly has killed 35 people and sickened about 4000.
Infections were reported in 2001 and 2002 in Germany and Central Africa respectively. In order to dissect all possible connections
among the three infection/outbreak strains and to extract the most virulent genes responsible for the augmented pathogenicity of
the present German strain (2011), whole genome sequence data of the two isolates (E. coli TY_2482 & LB226692)
were analyzed. We report that the German outbreak strain isolated in 2011 is a seasoned clone of the 2002 isolate sequenced from
Central Africa (55989) and perhaps a direct descendent of the German EAEC strain reported in 2001 infection cases.
Tipo: Poster
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6034/version/2
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
Prevalence and Patterns of Microarray Data Sharing
Provedor de dados: 17
Autores: Heather A. Piwowar; Wendy W. Chapman.
Sharing research data is a cornerstone of science. Although many tools and policies exist to encourage data sharing, the
prevalence with which datasets are shared is not well understood. We report our preliminary results on patterns of sharing
microarray data in public databases.

The most comprehensive method for measuring
occurrences of public data sharing is manual curation of research reports, since data sharing plans are usually communicated in
free text within the body of an article. Our early findings from manual curation of 100 papers suggest that 30% of investigators
publicly share their full microarray datasets. Of these, 70% of the datasets are deposited at NCBI's Gene Expression
Omnibus (GEO) database,...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1701/version/1
Quantitative Preparative Native Continuous Polyacrylamide Gel Electrophoresis (QPNC-PAGE)
Provedor de dados: 17
Autores: Bernd Kastenholz.
QPNC-PAGE, or quantitative preparative native continuous polyacrylamide gel electrophoresis, is a high-resolution technique
applied in biochemistry and bioinorganic chemistry to separate proteins by isoelectric point. This variant of gel electrophoresis is
used by biologists to isolate active or native metalloproteins in biological samples and to resolve properly and improperly folded
metal cofactor-containing proteins in complex protein mixtures.
Tipo: Poster
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1782/version/1
Ontology-driven International Maize Information System (IMIS) for Phenotypic and Genotypic Data
Exchange
Provedor de dados: 17
Autores: Rosemary Shrestha; Hector Sanchez; Claudio Ayala; Peter Wenzl; Elizabeth Arnaud.
The Consultative Group on International Agricultural Research (CGIAR; http://www.cgiar.org/) centres have developed the
International Crop Information System (ICIS; http://www.icis.cgiar.org) for the management and integration of global information
on genetic resources, and germplasm improvement for any crop. The Maize breeding programs at CIMMYT
(http://beta.cimmyt.org/) have different software tools to manage phenotypic, genotypic, and environmental information for their
experiments generated worldwide. These tools have the capacity of collecting information in the field, wet lab, and store it into
different relational databases. The IMIS (http://imis.cimmyt.org/confluence/display/IMIS/Crop+Finder) is an implementation of
the ICIS, which is a...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5029/version/1
HMGA1a induces aberrant splicing of estrogen receptor α in MCF-7 breast cancer cells
Provedor de dados: 17
Autores: Kenji Ohe; Toshiaki Utsumi; Akila Mayeda.
The well known transcription factor, HMGA1a, also known as an oncogene, causes aberrant splicing of Presenilin-2 found in
sporadic Alzheimer's disease, through sequence specific RNA binding. Since HMGA1 protein levels correlate with
tumorigenic malignancy, we are interested in the potential of HMGA1a as an aberrant splicing factor in cancer. The N-terminal
truncated isoform of Estrogen Receptor alpha, ERα46, is known to increase expression when breast cancer cells
(MCF-7) become hyperconfluent. Transiently expressed HMGA1a induced ERα46 mRNA expression. Plasmid
driven micro RNA containing the presenilin-2 HMGA1a RNA binding site and a micro RNA nuclear localization signal
(miR_HMGBS_NLS), inhibited ERα46 mRNA...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4104/version/2
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
HGNC: The Why and How of Standardised Gene Nomenclature
Provedor de dados: 17
Autores: Ruth Seal; Susan Gordon; Michael Lush; Mathew Wright; Elspeth Bruford.
The HUGO Gene Nomenclature Committee (HGNC) aims to approve a unique gene symbol and gene name for every human
gene.
Standardisation of gene symbols is necessary to allow researchers and curators to refer to the same gene without
ambiguity. Consistent use of gene symbols in publications and across different websites makes it easy for researchers to find all
relevant information for a particular gene and facilitates data mining and retrieval. For each gene that we name we curate
relevant information including symbol aliases, chromosomal location, locus type, sequence accessions and links to relevant
databases. Therefore, our website is a central resource for human genetics. 
 
We
endeavour to approve gene symbols that...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3182/version/1
The GABI Primary Database: GABIPD - Integration of Plant 'Omics'-Data in
Gene Context
Provedor de dados: 17
Autores: Diego Mauricio Riaño-Pachón; Axel Nagel; Jost Neigenfind; Robert Wagner; Rico Basekow;
Elke Weber; Sabrina Kleessen; Birgit Kersten.
GabiPD ("http://www.gabipd.org/":http://www.gabipd.org/) at the Max Planck Institute of Molecular Plant
Physiology constitutes a repository and analysis platform of genomic, transcriptomic, proteomic, and metabolomic plant data
provided by the GABI community (Riaño-Pachón et al., 2009). Beside the data, current versions of useful
tools are being made accessible via GabiPD, such as MapMan (Usadel et al., 2005) and SATlotyper (Neigenfind et al., 2008).
Access to GabiPD is provided via either the web interface or WebServices.

In
GabiPD, twenty different plant species are currently represented with the model plant A. thaliana on top followed by the crop
plants S. tuberosum and H. vulgare....
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3218/version/1
How do we quantify biodiversity? All the evidence in one place.
Provedor de dados: 17
Autores: Olga Lyashevska.
Biodiversity is a multi-dimensional concept that is represented by a large variety of measures. This complexity and lack of
consistency limits the development of a coherent scientific understanding of biodiversity and how properties, such as ecosystem
services, may depend on it. Here, I demonstrate that the formal discipline of creating a relational database (RDB) for information
about biodiversity and its measures, is a useful tool in organising such knowledge into coherent sense. Following steps of the
logical database design and data normalization to build a RDB, results in a formal definition of biodiversity within a well defined
concept structure; mapping rules between the concepts of biodiversity and entities of RDB and a consistent information...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3327/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/1
Ornithine decarboxylase activity, a clinical biomarker for evaluating cancer chemopreventive efficacy
of phytomolecules
Provedor de dados: 17
Autores: Nusrat Masood; Vijaya Dubey; Suaib Luqman.
Biomarkers of cancer have made a strong traipse in predicting the disease pattern and contributed significantly to the
understanding of tumour state, progression, characteristics and response to therapies. Polyamines such as putrescine, spermine and
spermidine are cationic biomolecules essential for the cell cycle function and serve as excellent biomarkers of tumour progression.
The polyamine biosynthesis is tightly regulated by ornithine decarboxylase, a highly inducible enzyme specific to pH,
temperature, time and substrate concentration. The expression of this enzyme is very high during cell transformation and tumour
progression leading to elevated level of polyamines. To measure the activity of ornithine decarboxylase an improved, easy,
simple,...
Tipo: Poster
Palavras-chave: Cancer; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6643/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
Identifying Copy Number Variations based on Next Generation Sequencing Data by a Mixture of
Poisson Model
Provedor de dados: 17
Autores: Karin Schwarzbauer; Günter Klambauer; Andreas Mayr; Sepp Hochreiter.
Next generation sequencing (NGS) technologies have profoundly impacted biological research and are becoming more and more
popular due to cost effectiveness and their speed. NGS can be utilized to identify DNA structural variants, namely copy number
variations
(CNVs)
which
showed
association
with
diseases
like
HIV,
diabetes
II,
or
cancer.

There have been first approaches to detect CNVs in NGS data, where most of
them detect a CNV by a significant difference of read counts within neighboring windows at the chromosome. However these
methods suffer from systematical variations of the underlying read count distributions along the chromosome due to biological
and technical noise. In contrast to these global methods, we locally...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4716/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
Immunogenetic sequence annotation based on IMGT-ONTOLOGY
Provedor de dados: 17
Autores: Joumana Jabado-Michaloud; Géraldine Folch; Fatena Bellahcene; François Ehrenmann; Patrice
Duroux; Véronique Giudicelli; Marie-Paule Lefranc.
IMGT/LIGM-DB^1^ is the first and the largest IMGT^®^ database^2^ in which are managed, analysed and annotated
more than 136,000 immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and 235 other vertebrate
species (April 2009). The expert annotation of these sequences and the added standardized knowledge are based on
IMGT-ONTOLOGY, the first ontology developed in the field of immunogenetics and immunoinformatics.^3^ The annotation of
immunogenetic sequences requires important expertise, owing to the unusual structure (non-classical exon/intron structure) of the
IG and TR genes and characteristic chain synthesis owing to DNA V-J and V-D-J rearrangements. The way to annotate these
sequences depends on the molecular type...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3165/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
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
Predictive context biases perceptual selection during binocular rivalry
Provedor de dados: 17
Autores: Rachel N. Denison; Michael A. Silver.
Prediction may be a fundamental principle of sensory processing, such that the brain continuously generates predictions about
forthcoming sensory information. However, little is known about how prediction contributes to the selection of a conscious
percept from among competing alternatives. Here, we used binocular rivalry to investigate the effects of prediction on perceptual
selection. In binocular rivalry, incompatible images presented to the two eyes result in a perceptual alternation between the
images, even though the visual stimuli remain constant. If predictive signals influence the competition between neural
representations of rivalrous images, this influence should generate a bias in perceptual selection that depends on predictive
context. To...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5816/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
Reacquainting two cultures. Preventing a de-elsification of European nutrigenomics?
Provedor de dados: 17
Autores: Bart Penders.
Sir Charles Snow, being a writer and a scientist, felt that he "was moving among two groups - comparable in
intelligence, identical in race, not grossly different in social origin, earning about the same incomes, who had ceased to
communicate at all"(Snow, 1993 [1959], p.2). He called these two groups, the two cultures, referring to those in the
natural sciences and those in the humanities. 
Many argue that this division is an awful thing. This poster
discusses strategies to reacquaint the two cultures in the case of genomics.
Tipo: Poster
Palavras-chave: Genetics & Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3981/version/1
Recovery kinetics of winter stressed conifers: The effects of growth light environment, extent of the
season, and species.
Provedor de dados: 17
Autores: Amy Verhoeven.
Evergreens undergo a dramatic reduction in their maximal photochemical efficiency (measured as Fv/Fm) during winter, which is
largely due to increases in a sustained form of thermal energy dissipation. Upon removing winter-stressed leaves to room
temperature and low light, Fv/Fm recovers over several days and can include both a rapid phase (reversing in minutes) and a slow
phase (reversing over days). Both phases are associated with reversal of sustained energy dissipation. Preliminary examination
of recovery of evergreens monitored in January in Minnesota showed an absence of the rapid component to recovery. Our goal
was to monitor recovery kinetics of sun and shade evergreens in Minnesota throughout winter in order to assess whether the rapid
phase of...
Tipo: Poster
Palavras-chave: Earth & Environment; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5323/version/1
LBFO: toward an artificial language for ontology development
Provedor de dados: 17
Autores: Leonard F. Jacuzzo.
The syntax of LBFO represents the initial step toward the creation of a rigorously characterized, recursively defined, artificial
language for the sole purpose of ontology development. The underlying idea is that maximally fruitful application of ontology
requires accurate representation of reality in accordance with current textbook science. Hence, creating a robust, accurate
representation of reality is a fundamental concern. 
An ontology represents general types of entities and
relations between them. A domain ontology represents the general types and relations for a given domain of research. A top-level
ontology represents the general types of entities in any domain of research. Ontologies serve many purposes in computerized...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4001/version/1
LibSBGN: Electronic Processing of SBGN maps
Provedor de dados: 17
Autores: Martijn P. van Iersel; Sarah E. Boyd; Frank Bergmann; Stuart Moodie; Falk Schreiber; Tobias Czauderna; Emek Demir;
Nicolas Le Novère; Anatoly Sorokin; Huaiyu Mi; Augustin Luna; Ugur Dogrusoz; Yukiko Matsuoka; Akira
Funahashi; Hiroaki Kitano; Mirit I. Aladjem; Michael L. Blinov; Alice C. Villéger.
Introduction

Graphical representations of participants and their relationships are
essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously,
it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical
Notation (SBGN) has been developed.

As SBGN is becoming more widely adopted,
and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange
using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need
for a toolset that...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4967/version/1
The SOL Genomics Network Model: Making Community Annotation Work
Provedor de dados: 17
Autores: Naama Menda; Isaak Tecle; Anuradha Pujar; Aureliano Bombarely; Tom York; Adri Mills; Joseph Gosselin; Robert
Buels; Lukas Mueller.
The concept of community annotation is a growing discipline for achieving participation of the research community in depositing
up‐to‐date knowledge in biological databases.
The Solanaceae Genomics
Network ("SGN":http://sgn.cornell.edu/) is a clade‐oriented database (COD) focusing on
plants of the nightshade family, including tomato, potato, pepper, eggplant, and tobacco, and is one of the bioinformatics nodes of
the international tomato genome sequencing project. One of our major efforts is linking Solanaceae phenotype information with
the underlying genes, and subsequently the genome. As part of this goal, SGN has introduced a database for locus names and
descriptors, and a database for...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3134/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
In silico design of novel leads for inhibition of human beta-2-microglobulin
Provedor de dados: 17
Autores: Pallapotu Navya; Dibyabhaba Pradhan; 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 pharmacological properties leading to
intolerable side effects. Hence, ligand based virtual screening protocol of CADD method was pursued 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/6569/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
Tumor suppressors function as a bottleneck against cellular reprogramming into iPS cells
Provedor de dados: 17
Autores: Lakshmanane Boominathan.
Generating individual specific pluoripotent stem cells from differentiated cells is essential for regenerative medicine. Here, I
propose that the tumor suppressor TA-p73/p63-dependent microRNA network may inhibit self-renewal and reprogramming. It
has recently been shown that C-terminal NHL domain of TRIM32, an ubiquitin ligase, binds to Argonaute 1(Ago-1, a component
of RNA information silencing complex) and thereby the complex TRIM32-Ago1 promotes the efficiency of processing of
microRNA-134. 
Bioinformatics analysis of TRIM32 promoter revealed five p73/p63 binding sites in the
TRIM32 promoter, indicating that it could be a transcriptional target of TA-p73/p63. This data suggests a possibility that the
TA-p73/p63, by increasing the...
Tipo: Poster
Palavras-chave: Cancer; Genetics & Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/4113/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
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
Natural Diet of an Australian Freshwater Pipefish
Provedor de dados: 17
Autores: Andrew W. Jones; Lars G. Rudstam; Thomas S. Rayner.
Globally, the family Syngnathidae (seahorses and pipefish) is recognized as being both under threat from anthropogenic pressures
and poorly studied. Of the 47 species that are listed on the IUCN Red List, 33 are currently listed as ‘data
deficient’, with inadequate information available to make an assessment of their risk of extinction. Within Australia,
this has prompted environmental assessments of specific fisheries, as well as a number of recent ecological studies of marine
syngnathids. However, no work has been published on the continent’s four freshwater species. To begin to remedy
this, a thorough analysis of the feeding habits of one such species was conducted. Twenty-two specimens of _Hippichthys
heptagonus_...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/329/version/1
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
Estimation of extracellular lipase enzyme produced by thermophilic bacillus sp. isolated from arid
and semi-arid region of Rajasthan, India
Provedor de dados: 17
Autores: Deeksha
Gaur; Pankaj Kumar
Jain; Yamini Singh Sisodia; Vivek Bajpai.
Thermophilic organisms can be defined as microorganisms which are adapted to live at high temperatures. The enzymes produce
by thermophilic bacteria are capable of catalyzing biochemical reactions at high temperatures. Thermophilic bacteria are able to
produce thermostable lipase enzymes capable of degradation of lipid at temperatures higher than those of mesophilic bacteria.
Therefore, the isolation of thermophilic bacteria from natural sources and their identification are quite useful in terms of
discovering thermophilic lipase enzymes. Due to great temperature fluctuation in hot arid and semi-arid regions of Rajasthan, this
area could serve as a good source for new thermophilic lipase producing bacteria with novel industrially important properties.
The...
Tipo: Poster
Palavras-chave: Biotechnology; Microbiology.
Ano: 2012
URL: http://precedings.nature.com/documents/7072/version/1
PMEM of carabid beetles in the agro-ecosystem: Prospects and problems
Provedor de dados: 17
Autores: Kai U. Priesnitz; Ullrich Benker.
The comparison of carabid communities sampled at three different field sites during 5 years of ecological biosafety research
provides useful information for the design of a post market environmental monitoring of this arthropod family. Each evaluated
field site demonstrated a unique composition of carabid species. A baseline for the carabid beetle communities would therefore be
necessary for each field site to detect any changes in its composition over time. Aside from the influence of the location, the
impacts of weather, the date of sampling and of course the chosen sampling method have to be considered. A standardized method
is a basic requirement for a replicable assessment. The number of traps per square meter, and the size and the design of the traps...
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4445/version/1
Implementation Methods for Estimating Haplotypes with Grid Computing Technology
Provedor de dados: 17
Autores: Zafri Muhammad; Sanjaya KC; Phua Kia Kien.
Introduction: PHASE is a software for haplotype reconstruction and recombination rate estimation from population data and
implements the methods for estimating haplotypes from population genotype data. This software require enormous computing
power due to the complexity algorithms used. Recent advancement in grid computing and multi-core processing technology has
resulted
in
the
creating
of
virtual
supercomputers
computations).

Method:
(that
PHASE
are
version
capable
2.0
of
was
massive
downloaded
parallel
from
PHASE’s homepage (http://stephenslab.uchicago.edu/software.html), and installed on 10 Apple iMac computers
(20 CPUs) running Mac OS 10.5 using Apple™ Xserve as a controller. A PHP web-based...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4168/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
Paclitaxel delivery by micro/nano encapsulation using layer-by-layer assembly
Provedor de dados: 17
Autores: Girish Kumar Gupta; Vikas Jain; Prabhat Ranjan Mishra.
A novel formulation of paclitaxel (PTX) has been developed by providing multilayer assembly over drug loaded porous CaCO3
microparticles (CaCO3 MP) using combination of biocompatible and biodegradable polyelectrolytes (PE’s). PTX
was encapsulated into the nanopores of preformed CaCO3 MP prepared by the co-precipitation method. Infrared (IR) and X-ray
diffraction (XRD) provides evidences that PTX has been encapsulated into nanopores of CaCO3 MP and not crystallized on the
surface. PTX loaded CaCO3 MP (CaCO3-PTX) was found to be highly stabilized against thermal decomposition as evinced by
thermo gravimetric analysis (TGA) indicating decomposition at 600°C and 250°C for CaCO3-PTX and
PTX respectively. The multilayer assembly over...
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/2812/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/1
Ontology Mapping of PATO to YATO for the improvement of interoperability of quality description
Provedor de dados: 17
Autores: Hiroshi Masuya; Nobuhiko Tanaka; Kazunori Waki; Tatsuya Kushida; Kouji Kozaki; Riichiro Mizoguchi.
To facilitate broad interoperability for phenotype information between different ontological frameworks, we developed a
reference ontology, PATO2YATO_Quality, with the careful mapping of terms of PATO which is a quality ontology commonly
used for biological phenotype annotation to the latest top-level ontology, YATO, which represents advanced modeling of
quality-related concepts. As a result, YATO framework enabled to describe changes of phenotypic qualities along the courses of
time in ontologically correct way and sophisticated classification and representation of interrelationships among quality-related
concepts to provide fully integration of qualitative values and quantitative values obtained from phenotyping experiments and
advanced representation...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3508/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
Intact mitochondria migrate in membrane tubular network connections formed between human stem
cells
Provedor de dados: 17
Autores: Attila Csordas; Attila Cselenyák; Ferenc Uher; Marianna Murányi; Simone Hennerbichler; Heinz
Redl; Márk Kollai; Zsombor Lacza.
The hypothesis of mitochondrial transfer between eukaryotic animal cells is intriguing, although its route of action and
physiological role is unknown. Our goal was to examine intercellular connections among several types of stem cells and to
observe whether intact functional mitochondria may travel via these connections. Time-lapse laser scanning confocal microscopy
has shown that human amnion-derived stem cells as well as bone marrow derived mouse and human mesenchymal stem cells
form cell-to-cell connections via a tubular membrane network. The maximal length of these micrometer-thick tubes is around 180
?m. Interestingly, freshly isolated amniotic epithelial stem cells did not form these connections, only after several passages when
the morphology of...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/44/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
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
Ecology of Environmental Education: Feedbacks, Education, and Resilience
Provedor de dados: 17
Autores: Keith G Tidball; Marianne Krasny.
The ecology education community has focused on the suite of knowledge and competencies that constitute environmental literacy,
including self-knowledge, evidence-based habits of mind, and ecological concepts and connections (Jordan et al., 2009). Whereas
the environmental education (EE) community also is concerned with knowledge, it further embraces goals related to changing
attitudes and behavior. In both of these sub-disciplines, educational researchers most often focus on outcomes of specific
interventions. Less attention has been paid to the interrelations among the ecological or environmental education activities
themselves and the larger social-ecological system. This poster will explore the notion of an ecology of EE, and will attempt to
situate EE...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5199/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
Logical implications for regulatory relations represented by verbs in biomedical texts
Provedor de dados: 17
Autores: Sine Zambach.
Relations used in biomedical ontologies can be very general or very specific in respect to the domain. However some relations are
used widely in for example regulatory networks. This work focuses on positive and negative regulatory relations, in particular
their usage expressed as verbs in different biomedical genres and the properties of the relations.
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3560/version/1
Roots and Emergence of Cognition in Evolution
Provedor de dados: 17
Autores: Walter Riofrio.
Trying to understand when and how the cognitive phenomena arise in evolution continues being a hard problem of confronting.
One important task is to find the ways in which we will be able to arrive at those explanations that will enable us to understand
how living beings put together perceived sensory information as well as how they represent it. In this presentation, we address
some conceptual questions involved in the relationships between sensorial information perceived by brains and its representational
capacities. 

Tipo: Poster
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/413/version/2
Is there a Weed Shift in Roundup Ready Maize?
Provedor de dados: 17
Autores: Arnd Verschwele.
The cultivation of transgenic glyphosate-resistant crop varieties can simplify weed control in crops such as maize and others. On
the other hand, the repeated use of broadly effective herbicides like glyphosate, especially in the same crop, can have a negative
effect on biodiversity. Additionally there is a risk for a spread of more tolerant or even resistant weed
species.

It was the aim of a 6-years field study (2003-2008) to investigate weed
effects of use of glyphosate in a continuous transgenic herbicide-resistant maize rotation at three sites in Germany. These sites
differed significantly in terms of soil, climate and initial weed spectrum. The studies focussed on the comparison between local
herbicide standards and...
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4527/version/1
Resin duct density and size predicts mortality in ponderosa pine trees of Northern Arizona
Provedor de dados: 17
Autores: Jeffrey M. Kane; Thomas E. Kolb.
In the presence of herbivores, plants must allocate a portion of their accumulated carbon towards defense to survive.
For
example, trees susceptible to bark beetle attack are primarily reliant on resin production for protection. Tree mortality may be
reflected by individual differences in the ability of plants to produce defensive structures and compounds. We compared the
radial growth rates, resin duct production, density, and size between living and dead ponderosa pine trees in northern Arizona
using standard dendrochronology techniques. As a result, we found four main findings: 1) living ponderosa pines had 33% more
resin ducts than dead pines (t = 2.97, P < 0.003); 2) resin duct size was 13% larger in living than in dead pines (t =
3.00,...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3736/version/1
Resource Mediated Competition of two South Texas Natives: _Acacia berlandieri_ and _Trichloris
pluriflora_
Provedor de dados: 17
Autores: Sara J. Roach; Paul N. Jurena.
*Background/Question/Methods* 
_Acacia berlandieri_, an early-successional C~3~ woody shrub legume,
and _Trichloris pluriflora_, a late-successional/climax C~4~ mid-tall grass, reside in similar habitats and have both been
documented in Texas for over 150 years. This study examines the resource mediated above and below ground competition within
and between these species, which may illuminate some of the dynamics involved in the encroachment of woody shrub species into
the former grasslands. These species, started from seed, were grown outdoors (5 replicates/treatment) using sandy clay loam soil
in plastic lined 15×15 cm pots for 155 days and watered daily. Half of these pots received 12.5%
Hoagland’s solution as a...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3774/version/1
WormBase - Nematode Biology and Genomes
Provedor de dados: 17
Autores: Paul Davis; WormBase Consortium.
WormBase is the major public online database resource for the _Caenorhabditis_ research community. The database was
developed primarily for the nematode _C. elegans_ but expanded to host genomes and biological data from other closely related
nematode species including _C. briggsae_, _C. remanei_, _C. brenneri_, _C. japonica_ and _Pristionchus pacificus_. WormBase
has developed tools to mine the data held within the database and compare the hosted species. Over the years we have developed a
variety of curation pipelines which often begin in a "first-pass" literature curation step. This involves a
brief overview of the literature before directing it to specialised data curators who extract all relevant information. Curators focus
on...
Tipo: Poster
Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3127/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
The guardians of the genome dependent tumor suppressor miRNAs network
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. Here I present a number of models that illustrates how the TA-p73/p63 could
function as tumor suppressors. Remarkably, the guardians—p53, p63, and p73—of the genome are in
control of most of the known tumor suppressor miRNAs. 
TA-p73/p63 and p53, by suppressing the
expression of c-Myc through TRIM32 and miR-145, they could up regulate the expression of tumor suppressor microRNAs, such
as miR-15/16a, miR-29, miR-34, miR-26, let-7a/d/g, miR-30b/c/d/e, miR-146a, and a number of tumor suppressor genes. It
appears that p53/TA-p73/p63-mediated repression...
Tipo: Poster
Palavras-chave: Cancer; Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4112/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
The Effect of Urbanization on Bumble Bee Communities in Greater Philadelphia
Provedor de dados: 17
Autores: Rosemary L. Malfi; Neal M. Williams.
Bumble bees (Bombus spp.) are among the most important wild pollinators in temperate ecosystems in North America and
Europe, and are believed to be vital to the functioning of the pollination networks in which they occur. Accordingly, evidence of
their overall decline in Europe and more selective decline in the U.S. has raised concern about the long term persistence of many
species. Human-induced changes in land use, including the loss of natural and semi-natural habitat and associated floral
resources, are purported causes in several cases. Declines prompted an investigation of this potential trend in the urbanized
landscape in and surrounding Philadelphia, PA. We surveyed the species richness and abundance of bumble bee communities in
ten half-ha...
Tipo: Poster
Palavras-chave: Ecology; Earth & Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5341/version/1
Seeds banks of desert annuals in an aridity gradient in the southern Atacama Desert
Provedor de dados: 17
Autores: Diego A. Sotomayor; Julio R. Gutiérrez.
*Background/Question/Methods*
Annual plant communities are important components of the biodiversity
found in the coastal southern Atacama Desert in Chile. Moreover, they are an important economic resource for the human
communities living in that area. These plant communities develop, after heavy rainfall episodes, a phenomenon locally known as
the “blooming of the desert”. Although the minimum rainfall thresholds for these plants to emerge are
relatively well known, little is known about their seed banks, its composition, dynamics and variation across the latitudinal aridity
gradient from south to north. This system is interesting to study species coexistence, as well as, to look for exotic plants invasion,
since...
Tipo: Poster
Palavras-chave: Ecology; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3619/version/1
It was (not) me: Causal Inference of Agency in goal-directed actions
Provedor de dados: 17
Autores: Tobias F. Beck; Carlo Wilke; Barbara Wirxel; Dominik Endres*; Axel Lindner; Martin A. Giese*.
Summary: 
The perception of one's own actions depends on both sensory information and
predictions derived from internal forward models [1]. The integration of these information sources depends critically on whether
perceptual consequences are associated with one’s own action (sense of agency) or with changes in the external
world that are not related to the action. The perceived effects of actions should thus critically depend on the consistency between
the predicted and the actual sensory consequences of actions. To test this idea, we used a virtual-reality setup to manipulate the
consistency between pointing movements and their visual consequences and investigated the influence of this manipulation on
self-action...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5858/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
Human Heart Development Pathways
Provedor de dados: 17
Autores: Samuel Sklar; Alexander Pico.
This pathway has been largely adapted from an article by Deepak Srivastava, Cell. 2006 Sep 22;126(6):1037-48. In this pathway
are known transcription factors, miRNAs and regulatory proteins that impact the regional specificity of the human heart.
Activating signals are indicated by arrows while inhibitory signals are indicated by T-bars. Special thanks to Kim Cordes for her
assistance in revising this pathway, based on recent heart development research. A live version of the pathway can be found at
http://www.wikipathways.org/index.php/Pathway:WP1591
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6500/version/1
Names on Nodes: Automating the Application of Taxonomic Names within a Phylogenetic Context
Provedor de dados: 17
Autores: T. Michael Keesey.
_Names on Nodes_^1^ is an open‑source^2^ Flex application which utilizes a mathematical approach to automate
the application of phylogenetically‑defined names to phylogenetic hypotheses. Phylogenetic hypotheses are
modeled as directed, acyclic graphs, and may be read from bioinformatics or graph files (NEXUS, NexML, Newick, and
GraphML) or created de novo. Hypotheses may also be merged from multiple sources. _Names on Nodes_ stores hypotheses as
MathML, an XML‑based language for representing mathematical content and presentation. Phylogenetic definitions
may be constructed using a visual editor and exported in MathML. Thus, it is possible to create a dictionary of defined names and
automatically apply them to phylogenetic...
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4653/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
Invasive Plant (_Microstegium vimineum_) Reduces Abundance and Richness of Insect Communities
Provedor de dados: 17
Autores: Maria Carolina Simao; Jennifer Rudgers; S. Luke Flory.
Plant invasions are known to have negative impacts on native plant communities, yet their effects on higher trophic levels have
not been well documented. Past studies investigating the effects of invasive plants on herbivores and carnivores have been largely
observational in nature and thus lack the ability to tease apart whether differences are a cause or consequence of the invasion. In
addition, understanding how plant traits and plant species compositions change in invaded habitats may increase our ability to
predict when and where invasive plants will have effects that cascade to animals. We experimentally introduced a non-native plant
(_Microstegium vimineum_, Japanese stiltgrass) to evaluate impacts on arthropods. We also investigated possible...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3651/version/1
Normalization And Matching Of Chemical Compound Names
Provedor de dados: 17
Autores: Martin Golebiewski; Meik Bittkowski; Henriette Slogsnat; Jasmin Saric; Isabel Rojas; Wolfgang Müller.
We have developed ChemHits (http://sabio.h-its.org/chemHits/), an application which detects and matches synonymic names of
chemical compounds. The tool is based on natural language processing (NLP) methods and applies rules to systematically
normalize chemical compound names. Subsequently, matching of synonymous names is achieved by comparison of the
normalized name forms. The tool is capable of normalizing a given name of a chemical compound and matching it against
names in (bio-)chemical databases, like SABIO-RK, PubChem, ChEBI or KEGG, even when there is no exact
name-to-name-match.
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6505/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
GOAssay: from Gene Ontology to Assays IDentifiers - Towards Automatic Functional Annotation of
PubChem BioAssays
Provedor de dados: 17
Autores: Rajarshi Guha; Julien Gobeill; Patrick Ruch.
OBJECTIVES: We report on a experiment to functionally annotate PubChem assays using the Gene Ontology Categorizer
(GOCat). 

METHODS and MATERIALS: The assays are processed to filter out non
functional information, then the textual content is sent to the categorizer, which provide a ranked list of GO descriptors based on a
GOA-learned association model. 

RESULTS: The GO descriptors are regarded as
irrelevant for only 18% of the assays. 

CONCLUSION: Semantic enrichment of
PubChem assays with functional
genomics categories seems effective at least to navigate PubChem assays.


AVAILABILITIES: the database is hosted by the...
Tipo: Poster
Palavras-chave: Chemistry; Genetics & Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3176/version/1
GO faster ChEBI with Reasonable Biochemistry
Provedor de dados: 17
Autores: Duncan Hull.
Chemical Entities of Biological Interest (ChEBI) [1] is a database and ontology that represents knowledge about more than 15,000
small molecules and their biochemistry. The database does not currently use description logic reasoning or OWL, but is
investigating this possibility for better, cheaper and faster ontology development in the future. This poster describes four specific
problems and solutions to reasoning in ChEBI: 1. Using necessary and sufficient conditions 2. identifying inconsistencies 3.
Improving alignment with the the Gene Ontology (GO) 4. Reasoning with chemical structures.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2435/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
Predicting Temporal Patterns In The Environment: Toward Primitive Mechanisms Of Learning,
Memory, And Generalization
Provedor de dados: 17
Autores: Matthew C. Jones; Tim Curran; Michael C. Mozer; Matt Wilder.
Across a wide range of cognitive tasks, recent experience influences subsequent behavior. For example, when individuals
repeatedly perform a speeded two-alternative choice task, response latencies vary dramatically based on the immediately
preceding sequence. These sequential dependencies (SDs) have been interpreted as adaptation to the statistical structure of an
uncertain, changing environment (e.g., Jones & Sieck, 2003; Mozer, Kinoshita, & Shettel, 2007; Yu
& Cohen, 2009), and can shed light on how individuals learn and represent structure in binary stimulus sequences.
Heretofore, theories have posited that SDs arise from rapidly (exponentially) decaying memory traces of various environmental
statistics (e.g., Cho et al.,...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5796/version/1
Time Trends for Livestock Production in Saskatchewan, Canada: 1905-2011
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Saskatchewan, Canada, with a total land area of 651,900 km^2^, is one of the world’s most productive agricultural
regions. A broad variety of livestock are raised in the province, including cattle, pigs, poultry, sheep/goats, llama, ostrich, elk,
deer, and bison. In 2010, the total revenue from the Saskatchewan livestock sector was CAD$1.6 billion. Over the past century,
changing industry economics and advances in scientific, technical, and engineering knowledge and practices have affected the
amount and type of livestock produced. The current work examines time trends for livestock production since Saskatchewan was
created in 1905. While production trends vary widely by livestock type, most sectors display clearly increasing amounts of
industry...
Tipo: Poster
Palavras-chave: Earth & Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6714/version/1
Predicting the Congener-Specific Environmental Behaviour of Perfluorinated Acid Contaminants
Using Semi-Empirical Computational Methods
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest; Ken J. Friesen.
Perfluorinated acids (PFAs) are contaminants detected worldwide in a range of abiotic and biotic environmental matrices. The two
major classes of PFAs include the perfluorinated carboxylic acids (PFCAs) and perfluorinated sulfonic acids (PFSAs), both of
which are considered persistent and potentially bioaccumulative. Current research and regulatory efforts are focussed on the
straight-chain members of each PFA class and homologue group, primarily because these congeners are the major components of
technical mixtures and are also available as pure standards. However, the numerous potential branched congeners in each PFA
class represent a poorly understood family of environmental contaminants whose environmental and toxicological properties may
be more...
Tipo: Poster
Palavras-chave: Chemistry; Earth & Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1956/version/1
The neuron as a population of ion channels: the emergence of a stochastic and history dependent
mode
Provedor de dados: 17
Autores: Daniel Soudry; Ron Meir.
Experiments show that synaptically isolated cortical neurons, stimulated with periodic extra-cellular current pulses for long
durations, respond in a complex irregular and history dependent manner - over a large range of timescales (from seconds to days).
With the aim of finding a biophysical explanation to these results, we developed a general novel scheme to analytically solve
conductance based Hodgkin-Huxley like models under pulse stimulation, and derived closed-form expressions for the transient
behavior, firing rates and firing patterns of the neuron. Using this approach we were able to reproduce most experimental results
using only slow sodium inactivation - with the important exceptions of the irregular behavior and the large range of timescales....
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5799/version/1
PDBWiki
Provedor de dados: 17
Autores: Henning Stehr; Jose Duarte; Michael Lappe; Jong Bhak; Dan Bolser.
*Background:* The success of community projects such as Wikipedia has recently prompted a discussion about the applicability
of such tools in the life sciences. However, there is currently no consensus about how best to achieve this
goal.

*Methodology/Principal Findings:* Here we present a community knowledge
base for the annotation of biological molecular structures that addresses some of these issues. This Wiki-style database consists of
one structured page for each entry in the the Protein Data Bank (PDB) and allows users to attach categorised comments and
discussions to the entries. The core data for each entry is shown as a summary and can be used for searching and navigation via
categories. A user-editable list of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3123/version/1
Modeling miRNA regulation in signaling networks: miR-34a regulation of the p53/Sirt1 module
Provedor de dados: 17
Autores: Xin Lai.
Micro RNAs are a family of small regulatory RNAs whose function is to regulate the activity and stability of specific messenger
RNA targets through post-translational regulatory mechanisms. We studied a signaling module composed by p53, Sirt1 and the
small regulatory miRNA, miR-34a, based on the integration of experimental evidence and quantitative data, with mathematical
modeling. We further used the model to investigate different possible designs of the silencing mechanisms exerted by miR-34a on
Sirt1, and to simulate the dynamics of the system under pathological conditions of deregulation of its components.


Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5123/version/1
Lead identification and docking studies of metastatic protein human mitogen activated protein kinase
kinase4
Provedor de dados: 17
Autores: Harika Meduru; Dibyabhaba Pradhan; Manne Munikumar; Amineni Umamaheswari.
Human dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4) is a direct activator of MAP kinases in response to
various environmental stresses or mitogenic stimuli. Upon phosphorylation, MAP2K4 has been shown to activate MAPK8,
MAPK9 and MAPK14/p38 but not MAPK1/ERK2 or MAPK3/ERK1. Over expression of MAP2K4 causes carcinogenic effects,
such as ovarian cancer, colorectal cancer, prostate cancer and pancreatic cancer. Our present study was carried out to design a
potent drug molecule against MAP2K4 to control over expression. As there is no experimentally determined structure for
MAP2K4, the homology modeling technique of Modeller9v7 was implemented to generate a MAP2K4 3D model based on the
co-crystal structure of MAP2K6 (PDB ID: 3FME) with...
Tipo: Poster
Palavras-chave: Cancer; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5457/version/1
GabiPD: GABI primary database - a plant integrative 'omics' database
Provedor de dados: 17
Autores: Diego Mauricio Riaño-Pachón; Axel Nagel; Robert Wagner; Jost Neigenfind; Elke Weber; Svenja
Diehl; Birgit Kersten.
The GABI Primary Database, GabiPD, was established eight years ago in the frame of the German initiative for Genome Analysis
of the Plant Biological System (Genomanalyse im biologischen System Pflanze, GABI), funded by the German Federal Ministry
of Education, Research and Technology (BMBF) as well as a number of private enterprise companies. The main goal of GabiPD
is to collect, integrate, visualize and link primary information from GABI projects. GabiPD, in contrast to other plant databases
constitutes a repository and analysis platform for a wide array of heterogeneous data arising from high-throughput experiments in
several plant species. Currently, data from different 'omics' fronts are incorporated in GabiPD (i.e.,
genomics,...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2221/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
Searching BioModels Database
Provedor de dados: 17
Autores: Ron Henkel; Dagmar Waltemath; Andre Peters; Lukas Endler; Nicolas le Novère.
*Aim*

The increasing number of computational models of biological systems
demands a better support for search facilities. One possible improvement is to enable ranked retrieval of models based on existing
model annotation. 
 
Applying existing Information Retrieval (IR)
techniques to computational models, we have implemented a new search strategy in BioModels Database. In this search strategy
the index of search terms contains not only the model descriptions in the database, but is expanded by including ontological and
textual information about a model and its constituents retrieved from external sources. To add more background knowledge, we
additionally index the abstracts of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4985/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
The Role of Bio-Ontologies in Data-Driven Research: A Philosophical Perspective
Provedor de dados: 17
Autores: Sabina Leonelli.
This project aims to reach a philosophical understanding of the role played by theory in the practices of data dissemination and
re-use that characterise data-driven research. Bio-ontologies have the potential to play the epistemic role of theories in this
context, insofar as they (1) express the knowledge underlying data-driven research and (2) guide such research towards future
discoveries.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3646/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
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
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
GillespieSSA: A user-friendly stochastic simulation package for R
Provedor de dados: 17
Autores: Mario Pineda-Krch.
GillespieSSA is a package for the statistical computing and graphics language and environment R. GillespieSSA provides a
simple to use and extensible interface to several stochastic simulation algorithms for generating simulated trajectories of finite
population continuous-time model. Currently it implements Gillespie’s exact stochastic simulation algorithm
(Direct method) and several approximate methods (Explicit tau-leap, Binomial tau-leap, and Optimized tau-leap). The package
also contains a library of template models that can be run as demo models and can easily be customized and extended. Currently
the following models are included, decaying-dimerization reaction set, linear chain system, logistic growth model, Lotka
predator-prey model,...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3673/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
Expression profile of genes involved in hydrogen sulphide liberation by _Saccharomyces cerevisiae_
grown under different nitrogen concentrations
Provedor de dados: 17
Autores: Ana Mendes-Ferreira; Catarina Barbosa; Marcel.lí del Olmo; Arlete Mendes-Faia; Cecília
Leão.
The present work aims to elucidate molecular mechanisms underlying hydrogen sulphide production in _S. cerevisiae_ associated
to nitrogen deficiency. To assess, at a genome-wide level, how the yeast strain adapted to the progressive nitrogen depletion and
to nitrogen re-feeding, gene expression profiles were evaluated during fermentation at different nitrogen concentrations, using the
DNA array technology. The results showed that most MET genes displayed higher expression values at the beginning of both
control and N-limiting fermentation, just before the time at which the release of sulphide was observed. MET genes were
downregulated when yeast stopped growing which could associate MET gene expression levels with cell growth. The over
expression of MET...
Tipo: Poster
Palavras-chave: Biotechnology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/2736/version/1
Short and long distance translocations: Movement and survival in eastern box turtles (_Terrapene
carolina carolina_)
Provedor de dados: 17
Autores: Scott D. Farnsworth; Richard A. Seigel; Patrick W. Cain.
*Background/Question/Methods*

Human development represents a serious threat to
wildlife populations through continued habitat loss and incidental mortality from construction activities. Resource managers
responsible for protecting species with legal status or high public profile are faced with difficult decisions on how to best manage
populations located in construction zones. One approach to mitigate mortalities is to relocate individuals. The effectiveness of
translocation for reptiles and amphibians has been questioned, with studies often reporting higher mortality and increased
movements of translocated individuals. Translocations of reptiles and amphibians have primarily involved moving animals long
distances,...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3678/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
Effect of hyperglycemia on inflammatory markers in patients with Type 2 Diabetes
Provedor de dados: 17
Autores: Rajeev Goyal; Abul F. Faizy; Najmul Islam.
The role of inflammation in causation of both Diabetes and its complications has gained acceptance. Initially, hyperglycemia was
thought to be the factor causing inflammation, but recently, obesity has gained attraction as probable cause of inflammation. We
have studied the levels of markers of inflammation in Diabetic patients, with uncontrolled hyperglycemia, before and after
treatment. The results indicate that hyperglycemia significantly causes increase in inflammatory markers like TNF-α
and IL-6, which further contribute to pathogenesis of Diabetes mellitus type 2 as well as its complications such as atherosclerosis
and neuropathy.
Tipo: Poster
Palavras-chave: Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/1567/version/1
T Cell Receptor Gamma and Delta Gene Rearrangements in T-cell Acute Lymphoblastic Leukemia in
South India and Quantitation of Minimal Residual Disease
Provedor de dados: 17
Autores: Sudhakar Natarajan; Nirmala K. Nancy; Rajalekshmy Kamalalayam; Rajkumar Thangarajan.
Background: T cell-Acute Lymphoblastic Leukemia (T-ALL) arises by clonal proliferation of lymphoid precursors arrested at
particular stage of differentiation. The incidence of T-ALL in India is 37-43% of ALL. In this study, TCR gamma (TCRG) and
TCR delta (TCRD) gene rearrangements were detected in diagnostic samples of ALL. Those clonal rearrangements detected at
diagnosis are used as clonal markers for the quantitation of minimal residual disease (MRD) in follow up samples.


Patients and Methods: BM/PB from 54 T-ALL patients (34 pediatrics and 20 adults)
at diagnosis, treated by MCP 841 protocol were studied. Median age of the patients was 13. The frequency of clonal TCRG and
TCRD gene rearrangements were studied by...
Tipo: Poster
Palavras-chave: Cancer; Immunology.
Ano: 2010
URL: http://precedings.nature.com/documents/5274/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
Intra-specific variation in plant hydraulic sectoriality along a latitudinal gradient
Provedor de dados: 17
Autores: Angela Zeng; Roberto Salguero-Gomez; Agustin Santos-Alvarez; Amy Zanne; Brenda Casper.
High temperatures and nutrient limitations in deserts challenge plant survival. Large temperature oscillations and droughts typical
of cold deserts can result in cavitation, the precipitation of dissolved air within a xylem vessel. If xylem vessels are closely
packed, then a cavitation event may expand to neighboring vessels, resulting in runaway embolism, and potentially paralyze the
vital functions of the plant.

Hydraulic sectoriality, where the plant is functionally composed of
independent hydraulic units, has been suggested as a strategy to decrease the risk associated with cavitation. This can occur by
increasing xylem vessel isolation and/or increasing the physical modularity of the plant. Furthermore, hydraulic sectoriality...
Tipo: Poster
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5277/version/1
Novel Techniques for Microspectroscopy and Chemical Imaging Analysis of Soybean Seeds and
Embryos
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng You; Doina M. Costescu.
Novel
methodologies
are
currently
being
evaluated
for
the
Chemical
Analysis
of
soybean seeds as well as developing 
mature soybean embryos by FT-IR/NIR
Microspectroscopy. This is the first report of FT-NIR Chemical Images obtained with 1 micron resolution. NIR spectra of
Proteins, Oil and DNA fibers are obtained for regions as small as 1μ^2^.
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Molecular Cell Biology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6591/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
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
Implementation of computational methods for designing potential inhibitors against human
p38α protein
Provedor de dados: 17
Autores: Durga Devi M; Dibyabhaba Pradhan; Manne Munikumar; Amineni Umamaheswari.
p38α, a non-receptor serine/threonine kinase, plays an essential role in cell proliferation, cell differentiation,
apoptosis, production of cytokines such as IL1β and TNFα, senescence and tumorigenesis. Over
expression of p38α enhances the production of cytokines, leading to inflammation causing cancers. Therefore, the
protein p38α is selected as a target for the inhibition of progression of inflammatory cancers. SB203580, BIRB796,
2H-quinolizine-2-one, 7-alkyl-1,5-bis–aryl-pyrazolo pyridinones, aML3403, N-pyrimidyl amides, Fused pyrazoles,
SD0006, 4-3-(4-fluoro phenyl )-1H-pyrazol-4-yl)pyridine are the nine published inhibitors for the p38α, but they
show side effects like liver...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5456/version/1
Status and habitat requirements of Physaria thamnophila, an endangered species of Tamaulipan
thornscrub
Provedor de dados: 17
Autores: Norma Fowler; Dana Price; Christopher Best; Alice Hempel.
	Physaria (Lesquerella) thamnophila (Brassicaceae; henceforth Physaria) is an endangered herbaceous perennial plant
of remnant patches of Tamaulipan thornscrub near the southern Texas border. Six years of censuses of four populations of
Physaria were analyzed. Quantitative data were collected to describe the plant community in the four sites. There was no
overall trend in population size, but fluctuations in observed numbers of plants among years were extremely large: a single census
cannot provide a reliable assessment of a population of this species. Seedling numbers were positively related with shrub canopy
cover. However, there were many more Physaria plants in the brush-cleared portion of one site than in its uncleared portion.
Seedling...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3656/version/1
Maximization of learning speed in motor cortex due to neuron redundancy
Provedor de dados: 17
Autores: Ken Takiyama; Masato Okada.
Many kinds of redundancies play important roles in the motor system. Many combinations of muscle activity can generate an
identical movement. One of the functional and computational roles of this muscle redundancy is to control joint impedance for
stabilizing movements against applied external perturbation. Many combinations of joint angles can yield an identical fingertip
position. A functional and computational role of this kinematic redundancy is to ensure motor accuracy, if a joint angle is
perturbed, by adjusting redundant ones. Neurons are overwhelmingly more numerous than muscles in our motor system.
However, an open question remains as to what the functional and computational roles of this neuron redundancy are. To generate
desired motor commands,...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5867/version/1
Subtyping of Dengue Viruses using Return Time Distribution based Appproach
Provedor de dados: 17
Autores: Pandurang Kolekar; Mohan Kale; Urmila Kulkarni-Kale.
Dengue virus (DENV) is the causative agent of Dengue Hemorrhagic Fever and Dengue Shock Syndrome, and continues to
represent a major public health hazard. DENVs are antigenically classified in four serotypes and each serotype is further divided
into respective genotypes. The association between DENV subtypes and the kind & severity of disease caused by them
is known. Experimental and computational approaches for subtyping are routinely used for the purpose of diagnosis and treatment
of DENV, in addition to the study of phylodynamics. All virus-specific molecular subtyping tools make use of sequence
alignments at backend. But as the volume of molecular data increases, alignment-dependent methods become computationally
intensive. Hence, the need for...
Tipo: Poster
Palavras-chave: Biotechnology; Genetics & Genomics; Immunology; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5590/version/1
Pepper yellow leaf curl Indonesia virus, a new bipartite begomovirus species that belongs to distinct
clade of Old World geminiviruses
Provedor de dados: 17
Autores: Pradeep Sharma1,2; J. Sakata2; Y. Shibuya2; Masato Ikegami2.
Begomoviruses are currently emerging as a major threat to vegetable production in many tropical and subtropical regions
worldwide. Pepper yellow leaf curl disease (PepYLCD) has been noticed in many Capsicum annum L. producing regions from
East Asia especially from Indonesia and causes devastating damage to pepper crop production since 2000. In this study we have
cloned and sequenced complete nucleotide of begomoviruses from pepper exhibiting leaf curling and bright yellowing symptoms.
Besides, we also determined the occurrence of disease on tomato evoking leaf curl symptoms and ageratum with yellow vein type
of symptoms. On the basis of genome organization and sequence homology, these viruses were designated as Pepper yellow leaf
curl Indonesia virus...
Tipo: Poster
Palavras-chave: Biotechnology; Genetics & Genomics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4162/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
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