Últimos itens adicionados do Acervo: Proceedings Nature

Nature é uma das mais prestigiosas e antigas revistas científicas do mundo: sua primeira edição é de 4 de novembro de 1869. Entre as inúmeras descobertas científicas publicadas na Nature estão a dos raios X, da estrutura em dupla hélice do ADN e o buraco na camada de ozônio.

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‣ The disease mutation A77V in Ryanodine receptor RyR2 induces changes in energy conduction pathways in the protein

Burak Erman; Nazan Walpoth
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Energetically responsive residues of the 217 amino acid N-terminal domain of the cardiac Ryanodine receptor RyR2 are identified by a simple elastic net model. These residues lie along a hydrogen bonded path through the protein. The evolutionarily conserved residues of the protein are all located on this path or in its close proximity. All of the residues of the path are either located on the two Mir domains of the protein or are hydrogen bonded to them. Two calcium binding residues, E171 and E173, are proposed as potential binding residues, based on insights gained from the elastic net analysis of another calcium channel receptor, the inositol 1,4,5-triphosphate receptor, IP3R. Analysis of the disease causing A77V mutated RyR2 showed that the path is disrupted by the loss of energy responsiveness of certain residues.

‣ Exposing WikiPathways as Linked Open Data

Andra Waagmeester; Helena Deus; Chris T. Evelo
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
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 enriched. Different tools (e.g. Pathvisio and Cytoscape) support the integration of WikiPathways-knowledge for additional tasks, such as the integration with personal data sets. Data from WikiPathways is increasingly also used for advanced analysis where it is integrated or compared with other data, Currently, integration with data from different biological sources is mostly done manually. This can be a very time consuming task because the curator often first needs to find the available resources...

‣ The Rise of Consortia

Neil E. Caporaso; Siiri N. Bennett
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
We provide some observations on the role of consortia in GWAS. We include 2 surveys (addressed to GWAS Investigators and to GWAS Consortia) sent to GWAS investigators in the spring of 2011. Tables and figures derived from the data are included. We also provide a summary table with some basic data on 110 consortia. We invite the community to visit the WikiGene site (http://www.wikigenes.org/GWAS/consortia.html) where this data may be further corrected and updated.

‣ The Role of Cognitive Dissonance in Social Networks

Henrique Akiba; Alvaro Machado Dias; Eduardo Oda; Ricardo Ikeda; Mauri Oliveira
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Context: The principles behind the process of creating new, spontaneous sequences out of previously ordered non-declarative stimuli have been scarcely addressed and, for such reason, remain highly unknown. Objective: This paper has four interconnected goals: (1) Introduce a new software-based neuropsychological test that can be used as a means to assess key aspects of the way people order and reorder non-declarative stimuli, based upon cognitive dissonance principles; (2) introduce a mathematical approach to the latter in ordering/re-ordering of non-declarative stimuli; (3) assess whether the principles of cognitive dissonance in ordering/re-ordering hold for a cohort of young adults with upper socio-economic level; (4) access the extent to which the same holds for children and adolescents and trace a curve of maturation of cognitive dissonance in ordering/re-ordering. Methods: Our multi-age and multi-language social Network Test implies the two stages, first the subject must order figures of human faces in order of preference, next, the software provides him with different pairs of figures which the subject must fulfill in order to built the intermediate arrays that he believe to interconnect the original pair. Our mathematical model is centered around the relation defined by increases in the distance separating these different pairs of figures in the initial order (distances 1...

‣ Structural changes in intestinal enteroendocrine cells after ileal interposition in normal rats

Gilmara S. Aguiar-Yamaguchi; João-Luiz M. C. Azevedo; Marcelo C. Carlini; Paolo H. B. Lourenco; Wellington Cardia; Maria T. S. Alves; Aparecida E. Hirata; Lucas P. F. F. Leal; Bianca Marigliani; Linda O. A. Bernardes; Karina F. Neves; Rudy N. Rocha;
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
INTRODUCTION: No therapeutic approach has significantly impacted the progression of diabetes. As early improvement of glicaemic control is observed after bariatric surgeries, there is currently a search for surgical procedures that can promote euglycemia also in non-obese patients. Glicaemic control can be achieved by increasing the blood concentration of GLP-1, a hormone produced by L cells that are more densely concentrated in the terminal ileum. The interposition of ileal segment to a more anterior region (proximal jejunum) can promote a greater stimulation of the L cells by poorly digested food, increasing the production of GLP-1 and reflecting on glicaemic control. AIMS: To investigate long-term histological modifications of intestinal mucosa of rats submitted to interposition of ileum segment to a proximal region (jejunum). METHODS: Forty 8-week old male Wistar-EPM1 rats (Rattus norvegicus albinus) were randomly distributed into 3 groups: the Interposition Group (IG) was subjected to ileal interposition, the Sham Group (SG) was subjected to sham operations, and the Control Group (CG) was not subjected to surgery. All animals were followed until the 60th postoperative day (8 postoperative week) when they were euthanized. Segments of jejunum and ileum from all groups were collected and analyzed by optical microscopy and immunohistochemistry. RESULTS: No structural nor histological changes in intestinal L cells in the interposed intestinal segment and other intestinal segments were noted after ileal interposition surgery. CONCLUSION: As L cells endocrine characteristics were likely maintained...

‣ MAP7D2 is a brain expressing X-linked maternal imprinted gene in humans

Yo Niida; Akihiro Yachie
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Increasing evidence suggests imprinted genes influence mouse and human behaviors and cognitive functions. Unlike autosomal imprinted genes, X-linked imprinted genes are expressed in a sex-dependent manner because of male hemizygosity. Therefore, these genes could directly affect sex-specific brain functions and sex-biased vulnerability to psychiatric disorders such as autism1. Comparing lymphoblastoid cell lines (LCL) and peripheral blood mononuclear cells (PBMC) from healthy adult male and females, we identified MAP7 domain containing 2 (MAP7D2) as the first human X-linked imprinted gene. Both in LCL and PBMC, MAP7D2 expression was significantly suppressed in males by maternal imprinting. In each female LCL clone, MAP7D2 was expressed higher in paternally derived allele and was affected by X-chromosome inactivation. In female PBMC, however, reactivation of maternal MAP7D2 alleles was observed. MAP7D2 was expressed specifically in the brain among human tissues with unique isoforms. These results predict a crucial role of MAP7D2 for human sex-dependent neurobiological traits.

‣ Modularization for the Cell Ontology

Christopher J. Mungall; Melissa A. Haendel; Amelia Ireland; Shahid Manzoor; Terry Meehan; David Osumi-Sutherland; Carlo Torniai; Alexander D. Diehl
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
One of the premises of the OBO Foundry is that development of an orthogonal set of ontologies will increase domain expert contributions and logical interoperability, and decrease maintenance workload. For these reasons, the Cell Ontology (CL) is being re-engineered. This process requires the extraction of sub-modules from existing OBO ontologies, which presents a number of practical engineering challenges. These extracted modules may be intended to cover a narrow or a broad set of species. In addition, applications and resources that make use of the Cell Ontology have particular modularization requirements, such as the ability to extract custom subsets or unions of the Cell Ontology with other OBO ontologies. These extracted modules may be intended to cover a narrow or a broad set of species, which presents unique complications. We discuss some of these requirements, and present our progress towards a customizable simple-to-use modularization tool that leverages existing OWL-based tools and opens up their use for the CL and other ontologies.

‣ Taking shortcuts with OWL using safe macros

Christopher J. Mungall; Alan Ruttenberg; David Osumi-Sutherland
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Accurate representation of complex domains such as biology demands powerful and expressive ontology languages such as OWL. However, the complex nested class expressions required for modeling can be a hindrance to ontology authoring and adoption. These class expressions can appear opaque to domain experts, and even users proficient in OWL can benefit from some kind of syntactic sugar or "short-cut" strategy, especially when authoring large ontologies. One solution is to have domain experts fill in simple templates (for example, in Excel) and translate the results into more complex axioms, but this has the disadvantage of being disconnected from full ontology authoring and reasoning environment. We present here a method of specifying shortcut properties directly in OWL. These shortcut properties can be used in similar ways as object properties within the OWL environment, with the resulting simple axioms translated automatically to more complex axioms via macro expansion. We describe some example scenarios where this is of use in authoring existing bio-ontologies. One of the main implications of this work is a way to simplify the translation between OBO format and OWL...

‣ Precise Molecular Structures of Cysteine, Cystine, Hydrogen-Bonded Dicysteine, Cysteine Dipeptide, Glutathione and Acetyl Cysteine Based on Additivity of Atomic Radii

Raji Heyrovska
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Structures of molecules are usually represented by arbitrary line drawings, ball and stick or space filling models. In recent years, the author found that using the appropriate radii of atoms and ions, bond lengths in inorganic, organic and biomolecules and of hydrogen bonds are exact sums of the radii of the adjacent atoms and or ions. This additivity of atomic radii was shown to hold also for the bond lengths in the twenty essential amino acids. On this basis, the atomic structures of the very important molecules mentioned in the title, have been presented here for the first time. It is hoped that these precise structures and their dimensions will shed new light into their role in biochemistry, pharmaceutical chemistry, environmental chemistry, biomedicine and in the mechanism of protein folding.

‣ Amino acid features: a missing compartment of prediction of protein function

Esmaeil Ebrahimie; Mansour Ebrahimi; Mahdi Ebrahimi
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Enormous computational efforts have been carried out to predict structure and function of protein. However, nearly all of these efforts have been focused on prediction of function based on primary nucleic acid sequence or modeling 3D structure of protein from its nucleic acid sequence. In fact, it seems that amino acid attributes, which is an intermediate phase between DNA/RNA and advanced protein structure, has been missed. From 2010, we examined the possibility of precise prediction of structural protein function based on amino acid features by improving the following three aspects of amino acid research: (1) Increasing the number of computationally calculated amino acid features, (2) Testing different feature selection (attribute weighting) algorithms and selection of the most important amino acid attributes based on the overall conclusion of algorithms, (3) Examining different supervised and unsupervised data mining (machine learning) algorithms, and (4) Joining attribute weighting with different data mining algorithms. We applied the discovered procedure in different biological examples including: protein thermostability, halostability, prediction of function of heavy metal transporters, cancer diagnosis and prediction...

‣ Temporal trends in groundwater levels from Saskatchewan, Canada

Sierra Rayne; Kaya Forest
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Groundwater resources play a key role in supplying water for domestic, industrial, agricultural, and ecological functions on the Canadian prairies. The current study investigates potential temporal trends in groundwater levels for the Canadian province of Saskatchewan over the past several decades. Overall, the large majority of areally distributed stations throughout Saskatchewan with increasing groundwater level time trends suggests that this hydrogeological resource is growing in quantity and is not under current threat from depletion.

‣ A hydrometric analysis of the Moose Jaw River near Burdick (05JE006): Temporal trends and frequency analyses for mean, minimum, and maximum flows

Sierra Rayne; Kaya Forest
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
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 and October. There is ambiguity as to whether statistically significant negative time trends in overwinter period mean monthly flows and monthly minimum/maximum flows for the hydrometric station are real or whether they represent a change in measurement technique/calibration during the mid-/late-1980s.

‣ Nasal Bacterial Microbiome: Probing a Healthy Porcine Family

Min Yue; Weicheng Bei; Huanchun Chen
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Upper respiratory tract (URT) infection caused the leading and devastating diseases in pigs. It was believed that the normal microbiome of URT plays a vital role in health and disease development. As the entry point of the URT, little knowledge of bacterial microbiome in porcine nasal was known. A cultivation-independent approach directly to 16s ribosomal RNA genes enabled us to reveal the nasal bacterial community, structure and diversity. Here, we found that an unprecedented 207 phylotypes were characterized from 933 qualified clones, indicating the variable, species richness but particularly dominant bacterial microbiome. The dominant species were from genus Comamonas and Acinetobacter, which constitute core normal bacterial microbiome in porcine nasal. Moreover, a set of swine specific pathogens and zoonotic agents were detected in the swine nasal microbiome. Collectively, we provided a snapshot of our current knowledge of the community structure of porcine nasal bacterial ecosystem in a healthy family that will further enhance our view to understand URT infection and public health.

‣ Field Trial Experiment Of Artificial Diet On Tasar Silkworm, Anthereaea myltta D.

Alok Sahay; Subrat Satpathy; Shashi Sharan
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
An indoor and outdoor experiment was conducted at Shyamsunderpur, Mayurbhanj, Odhisa to test the efficacy of the artificial diet, Tasar Amrit on the young aged Antheraea mylitta silkworm larvae. The results of the experiment reveal that survival and effective rate of rearing (ERR) was higher when larvae were brushed on Tasar Amrit (75 and 42.45%) in contrast to complete outdoor rearing (44 and 33.56 %). Uniform moulting was also observed in the larvae fed with Tasar Amrit.

‣ Trans-Disciplinary Protein Binding Of Drug: Docking Approach

Ajeet Ajeet
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
The purpose of present work is to introduce the binding of existing drugs to the trans-disciplinary protein with the help of docking procedures. Docking procedures allows virtually screening a database of compounds and predict the strongest binder based on various scoring functions. This work has been performed with the help of Molegro Virtual docker, in which two drugs are docked with their corresponding and non-corresponding (trans-disciplinary) protein. Results reveals that the protein-ligand interaction energy, hydrogen bond energy and MolDock scores provided by molegro virtual docker, between legands (Levodopa and Acyclovir) and trans-disciplinary proteins have been equivalent or even better than that of between legands and corresponding proteins.

‣ A Long-Term Analysis of the Moose Jaw Climate Station (4015322/4015320): Temporal Trends and Frequency Analyses for Temperatures, Precipitation, and Wind Speed

Sierra Rayne; Kaya Forest
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
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 during winter, and decreasing during October. Significant declines are occurring in the mean of homogeneous wind speeds during April, May, June, July, September, November, and December, as well as on an annual basis and during spring, summer, and autumn. Frequency distributions of monthly, seasonal, and annual climate variables were generated to facilitate more reliable risk analyses for agricultural activities and hydrologic modeling efforts.

‣ A New General Allometric Biomass Model

Wei Sheng Zeng; Shou Zheng Tang
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
To implement monitoring and assessment of national forest biomass, it is becoming the trend to develop generalized single-tree biomass models suitable for large scale forest biomass estimation. Considering that the theoretical biomass allometric model developed by West et al. [1,2] was statistically different from the empirical one, the two parameters in the most commonly used biomass equation M=aDb were analyzed in this paper. Firstly, based on the knowledge of geometry, the theoretical value of parameter b was deduced, i.e., b=7/3(≈2.33), and the comparison with many empirical studies conducted throughout the globe indicated that the theoretical parameter could describe soundly the average allometric relationship between aboveground biomass M and D (diameter on breast height). Secondly, using five datasets of aboveground biomass which consisted of 1441 M-D pairs of sample trees, the new general biomass allometric model was validated. Finally, the relationship between parameter a and wood density p was analyzed, and the linear regression was developed. The new model, which is not only simple but also species-specific, offers a feasible approach on establishment of generalized biomass models for regional and national forest biomass estimation.

‣ Assessment Of Response To Heart Failure Therapy: Ventricular Volume Changes Versus Shape Changes

Srilakshmi Adhyapak; V.Rao Parachuri
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
The prolate ellipsoid left ventricular geometry is crucial for its unique contraction and relaxation patterns. Perturbations in optimal cardiac function preceding overt heart failure ensue when this ellipsoid shape assumes a more spherical configuration. This stage of spherical configuration, prior to overt dilatation, is when therapy should be intensified. The dynamic shape changes during the cardiac cycle of systole and diastole in valvular regurgitations when ventricular volumes are within normal range have proved that shape changes are clearly dissociated from volume changes in the early stages. In the scenario of advanced heart failure, several therapeutic interventions have been tried with variable success. These therapies aim at decreasing the ventricular equator, and hence its volume. However, the ventricular shape may still be spherical leading to suboptimal function. The aim in any therapy for heart failure should be therefore to achieve near normal left ventricular anatomy and physiology, with shape assessment as the surrogate marker of therapeutic success.

‣ Bias Correction in Logarithmic Regression and Comparison with Weighted Regression for Nonlinear Models

Wei Sheng Zeng; Shou Zheng Tang
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Non-linear models with heteroscedasticity are commonly used in ecological and forestry modeling, and logarithmic regression and weighted regression are usually employed to estimate the parameters. Using the single-tree biomass data of three large samples, the bias correction in logarithmic regression for non-linear models was studied and comparison between logarithmic regression and weighted regression was discussed in this paper. Firstly, the imminent cause producing bias in logarithmic regression was analyzed, and a new correction factor was presented with which three commonly used bias correction factors were examined together, and the results showed that the correction factors presented here and derived by Baskerville (1972) should be recommended, which could insure the corrected model to be asymptotically consistent with that fitted by weighted regression. Secondly, the fitting results of weighted regression for non-linear models, using the weight function based on residual errors of the model estimated by ordinary least squares (OLS) and the general weight function (w=1/ƒ(x)2) presented by Zeng (1998) respectively, were compared with each other that showed two weight functions worked well and the general function was more applicable. It was suggested that the best way to fit non-linear models with heteroscedasticity would be using weighted regression...

‣ A New General Allometric Biomass Model

Wei Sheng Zeng; Shou Zheng Tang
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
To implement monitoring and assessment of national forest biomass, it is becoming the trend to develop generalized single-tree biomass models suitable for large scale forest biomass estimation. Considering that the theoretical biomass allometric model developed by West et al. [1,2] was statistically different from the empirical one, the two parameters in the most commonly used biomass equation M=aDb were analyzed in this paper. Firstly, based on the knowledge of geometry, the theoretical value of parameter b was deduced, i.e., b=7/3(~2.33), and the comparison with many empirical studies conducted throughout the globe indicated that the theoretical parameter could describe soundly the average allometric relationship between aboveground biomass M and D (diameter on breast height). Secondly, using five datasets of aboveground biomass which consisted of 1441 M-D pairs of sample trees, the new general biomass allometric model was validated. Finally, the relationship between parameter a and wood density p was analyzed, and the linear regression was developed. The new model, which is not only simple but also species-specific, offers a feasible approach on establishment of generalized biomass models for regional and national forest biomass estimation.