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Rogers Mark F - - 2012
We propose a method for predicting splice graphs that enhances curated gene models using evidence from RNA-Seq and EST alignments. Results obtained using RNA-Seq experiments in Arabidopsis thaliana show that predictions made by our SpliceGrapher method are more consistent with current gene models than predictions made by TAU and Cufflinks. ...
Jacobberger James W - - 2012
An imprecise quantitative sense for the oscillating levels of proteins and their modifications, interactions, and translocations as a function of the cell cycle is fundamentally important for a cartoon/narrative understanding for how the cell cycle works. Mathematical modeling of the same cartoon/narrative models would be greatly enhanced by an open-ended ...
Lei Guoqing - - 2012
Prediction of ribonucleic acid (RNA) secondary structure remains one of the most important research areas in bioinformatics. The Zuker algorithm is one of the most popular methods of free energy minimization for RNA secondary structure prediction. Thus far, few studies have been reported on the acceleration of the Zuker algorithm ...
Mavelli Fabio - - 2012
Over the last two decades, lipid compartments (liposomes, lipid-coated droplets) have been extensively used as in vitro "minimal" cell models. In particular, simple and complex biomolecular reactions have been carried out inside these self-assembled micro- and nano-sized compartments, leading to the synthesis of RNA and functional proteins inside liposomes. Despite ...
Rozov Roye - - 2012
RNA-Seq is a technique that uses Next Generation Sequencing to identify transcripts and estimate transcription levels. When applying this technique for quantification, one must contend with reads that align to multiple positions in the genome (multireads). Previous efforts to resolve multireads have shown that RNA-Seq expression estimation can be improved ...
Sacomoto Gustavo A T - - 2012
In this paper, we address the problem of identifying and quantifying polymorphisms in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the fundamental idea that each polymorphism corresponds to a recognisable pattern in a De Bruijn graph constructed from the RNA-seq reads, we ...
Günther Oliver P - - 2012
Biomarker panels derived separately from genomic and proteomic data and with a variety of computational methods have demonstrated promising classification performance in various diseases. An open question is how to create effective proteo-genomic panels. The framework of ensemble classifiers has been applied successfully in various analytical domains to combine classifiers ...
Pinheiro Felipe L - - 2012
A new and unusual specimen of a probable azhdarchoid pterosaur is described for the Early Cretaceous (Albian) Romualdo Formation of Brazil. The specimen consists of a palate that, although fragmentary, has a unique morphology differing from all other known pterosaurs with preservation of palatal elements. The new specimen probably indicates ...
Tan Mingfeng - - 2012
Computational identification of transcription factor binding sites (TFBSs) is a rapid, cost-efficient way to locate unknown regulatory elements. With increased potential for high-throughput genome sequencing, the availability of accurate computational methods for TFBS prediction has never been as important as it currently is. To date, identifying TFBSs with high sensitivity ...
Chiu Jimmy Ka Ho - - 2012
Current RNA secondary structure prediction approaches predict prevalent pseudoknots such as the H-pseudoknot and kissing hairpin. The number of possible structures increases drastically when more complex pseudoknots are considered, thus leading to computational limitations. On the other hand, the enormous population of possible structures means not all of them appear ...
Jeffries Clark D CD Renaissance Computing Institute, CB 3127, University of North Carolina at Chapel Hill, - - 2012
This paper includes a conceptual framework for cell cycle modeling into which the experimenter can map observed data and evaluate mechanisms of cell cycle control. The basic model exhibits qualitative stability, meaning that regardless of magnitudes of system parameters its instances are guaranteed to be stable in the sense that ...
Chen Gang - - 2012
Conventional functional magnetic resonance imaging (FMRI) group analysis makes two key assumptions that are not always justified. First, the data from each subject is condensed into a single number per voxel, under the assumption that within-subject variance for the effect of interest is the same across all subjects or is ...
Dillon Robin L - - 2011
Since the 9/11 terrorist attacks, there has been an increase in public discussion regarding U.S. domestic intelligence activities. Domestic intelligence activities focus on gathering information about potential threats from individuals within the United States, and completely rational members of the public can have different opinions about the acceptability of various ...
Ezcurra Martín D - - 2011
Late Mesozoic palaeobiogeography has been characterized by a distinction between the northern territories of Laurasia and the southern landmasses of Gondwana. The repeated discovery of Gondwanan lineages in Laurasia has led to the proposal of alternative scenarios to explain these anomalous occurrences. A new biogeographical model for late Mesozoic terrestrial ...
Sallan Lauren Cole - - 2012
Adaptive radiations, bouts of morphological divergence coupled with taxonomic proliferation, underpin biodiversity. The most widespread model of radiations assumes a single round, or 'early burst', of elevated phenotypic divergence followed by a decline in rates of change or even stasis. A vertebrate-specific model proposes separate stages: initial divergence in postcranial ...
Faria Nuno R NR Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium. - - 2012
Human immunodeficiency virus type 2 (HIV-2) emerged in West Africa and has spread further to countries that share socio-historical ties with this region. However, viral origins and dispersal patterns at a global scale remain poorly understood. Here, we adopt a Bayesian phylogeographic approach to investigate the spatial dynamics of HIV-2 ...
Cant Michael A - - 2012
Abstract Evolutionary conflict arises at all levels of biological organization and presents a barrier to the evolution of cooperation. This barrier can be overcome by mechanisms that reduce the disparity between the fitness optima of subunits, sometimes called the "battleground" of conflict. An alternative, unstudied possibility is that effort invested ...
Uhls Yalda T - - 2011
In line with Greenfield's (2009) theory of social change and human development, current popular preadolescent TV shows suggest that fame, an individualistic goal, is an important and achievable aspiration (Uhls & Greenfield, 2011). Such messages may be particularly salient for preadolescents, ages 10-12. This study used focus groups and mixed ...
Eskofier Bjoern M - - 2011
The classification of gait patterns has great potential as a diagnostic tool, for example, for the diagnosis of injury or to identify at-risk gait in the elderly. The purpose of the paper is to present a method for classifying group differences in gait pattern by using the complete spatial and ...
Schlick Tamar - - 2012
Understanding the structural organization of eukaryotic chromatin and its control of gene expression represents one of the most fundamental and open challenges in modern biology. Recent experimental advances have revealed important characteristics of chromatin in response to changes in external conditions and histone composition, such as the conformational complexity of ...
Woodland Ryan J - - 2011
Seasonal oscillations in the carbon (δ(13)C) and nitrogen (δ(15)N) isotope signatures of aquatic algae can cause seasonal enrichment-depletion cycles in the isotopic composition of planktonic invertebrates (e.g., copepods). Yet, there is growing evidence that seasonal enrichment-depletion cycles also occur in the isotope signatures of larger invertebrate consumers, taxa used to ...
Hückstädt L A - - 2011
Identifying individuals' foraging strategies is critical to understanding the ecology of a species, and can provide the means to predict possible ecological responses to environmental change. Our study combines stable isotope analysis and satellite telemetry to study the variability in individual foraging strategies of adult female southern elephant seals (Mirounga ...
Barry Michael J - - 2011
The aim of this study was to demonstrate a novel method for measuring the effects of toxicants on the behavior of groups of unmarked fish. Ctrax is an open source Python-based machine vision program that was originally designed to track fruit flies (Drosophila). The effects of the fish anaesthetic quinaldine ...
Riera J - - 2011
Spontaneous calcium (Ca(2+)) oscillations (SCOs) in astrocytes might be a crucial signaling for the multipurpose role of this type of cell in several brain functions. To interpret experimental data of astrocytic SCOs, which has been largely observed in the last decade, several groups have attempted to accommodate biophysical models that ...
Alves Maria Cecilia Goi Porto - - 2011
OBJECTIVE: To identify the advantages and disadvantages of using segments compared to a complete address list, for the selection of households in a multistage cluster sampling in slums. METHODOLOGICAL PROCEDURES: A qualitative study was performed in four slums selected by the São Paulo Municipal Health Survey of 2008, and the ...
Baine Ann-Marie T - - 2011
A reliable model of fulminant liver failure (FLF) is urgently required in this research field. This study aimed to develop a murine FLF model. We used three groups of male C57BL/6 mice: control, with azoxymethane treatment (AOM group), and with galactosamine and tumor necrosis factor-alpha treatment (Gal+TNF-alpha group). The effects ...
Eadie John McA - - 2011
Conspecific brood parasites lay their eggs in the nests of other females in the same population, leading to a fascinating array of possible ‘games’ among parasites and their hosts (Davies 2000; Lyon & Eadie 2008). Almost 30 years ago, Andersson & Eriksson (1982) first suggested that perhaps this form of ...
Merz Erin L - - 2011
Interactions among the dimensions of the Five Factor Model (FFM) have not typically been evaluated in mental health research, with the extant literature focusing on bivariate relationships with psychological constructs of interest. This study used latent profile analysis to mimic higher-order interactions to identify homogenous personality profiles using the FFM, ...
Myers Nicholas D - - 2011
The purpose of this article was to provide a substantive-methodological synergy of potential importance to future research in sport and exercise psychology. The substantive focus was to improve the measurement of coaching efficacy by developing a revised version of the coaching efficacy scale (CES) for head coaches (N = 557) ...
Yi Nengjun - - 2011
Complex diseases and traits are likely influenced by many common and rare genetic variants and environmental factors. Detecting disease susceptibility variants is a challenging task, especially when their frequencies are low and/or their effects are small or moderate. We propose here a comprehensive hierarchical generalized linear model framework for simultaneously ...
Kosakyan Anush - - 2011
We used Cytochrome Oxidase Subunit 1 (COI) to assess the phylogenetic relationships and taxonomy of Nebela sensu stricto and similar taxa (Nebela group, Arcellinida) in order to clarify the taxonomic validity of morphological characters. The COI data not only successfully separated all studied morphospecies but also revealed the existence of ...
Zecca Giovanni - - 2011
Wild grapes are woody climbers, found mostly in temperate regions of the northern hemisphere, comprising the genus Vitis. Despite its importance, the evolutionary history of Vitis is still contentious. Past studies have led to conflicting hypotheses about the phylogeny, speciation events, and biogeographic history of the genus. Here we investigate ...
Lewis Thomas - - 2011
Using self-consistent field theory (SCFT), we study the conformational properties of polyelectrolyte dendrimers. We compare results for three different models of charge distributions on the polyelectrolytes: (1) a smeared, quenched charge distribution characteristic of strong polyelectrolytes; (2) a smeared, annealed charge distribution characteristic of weak polyelectrolytes; and (3) an implicit ...
Wooten J A - - 2011
Comparing niche divergence among closely related taxa can yield important insights into the ecological distinctiveness of genetically similar forms, and identify the processes that are responsible for diversification in such organisms. Here, we apply newly developed techniques for analysing niche divergence to assess how ecologically distinct a group of closely ...
Xue Jianping - - 2011
NHANES subjects self-identified as "Asian, Pacific Islander, Native American, or multiracial" (A/P/N/M) have higher levels of blood organic mercury than other racial/ethnic groups; however, the reasons for this have been unclear. This research uses exposure modeling to determine the reasons for elevated blood methylmercury (MeHg) levels, and also extends previous ...
Purse B V - - 2011
Culicoides biting midges (Diptera: Ceratopogonidae) vector a wide variety of internationally important arboviral pathogens of livestock and represent a widespread biting nuisance. This study investigated the influence of landscape, host and remotely-sensed climate factors on local abundance of livestock-associated species in Scotland, within a hierarchical generalized linear model framework. The ...
Chen Zhe Z Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510, USA. - - 2012
To measure the dosimetric properties of the Model AgX100 ¹²⁵I source for interstitial brachytherapy. The photon energy spectrum emitted by the AgX100 source was measured using a high-resolution germanium spectrometer customized for low-energy brachytherapy source spectrometry. The dose distribution around the source was measured using the 1×1×1 mm³ lithium fluoride ...
Spence Jeffrey S - - 2011
Linear statistical models are used very effectively to assess task-related differences in EEG power spectral analyses. Mixed models, in particular, accommodate more than one variance component in a multisubject study, where many trials of each condition of interest are measured on each subject. Generally, intra- and intersubject variances are both ...
Creane Arthur - - 2011
Many soft biological tissues contain collagen fibres, which act as major load bearing constituents. The orientation and the dispersion of these fibres influence the macroscopic mechanical properties of the tissue and are therefore of importance in several areas of research including constitutive model development, tissue engineering and mechanobiology. Qualitative comparisons ...
Chen Yu-Cheng - - 2012
The objective of this exposure assessment was to reconstruct cumulative historical exposures for workers who have been exposed to multiple chemicals and chemical groups to better understand a cluster of brain cancers within a research and development lab. Chemicals of interest, including acrylates, bis-chloromethyl ether (BCME), chloromethyl methyl ether (CMME), ...
Cabreira Sergio F - - 2011
Post-Triassic theropod, sauropodomorph, and ornithischian dinosaurs are readily recognized based on the set of traits that typically characterize each of these groups. On the contrary, most of the early members of those lineages lack such specializations, but share a range of generalized traits also seen in more basal dinosauromorphs. Here, ...
Brown Ottilia - - 2011
The use of religion and spirituality in psychotherapy has been a contentious issue for decades. This paper explores and describes whether psychologists would use religion and spirituality in psychotherapy as well as enablers and barriers in this regard. A qualitative exploratory descriptive method was followed using purposive sampling to obtain ...
Sereysky Jedd B - - 2012
The purpose of this study was to develop and validate an in vivo mouse model of tendon fatigue and use this model to investigate and quantify the physical manifestations of fatigue damage in mouse tendon. Patellar tendons of C57BL/6J mice were fatigue loaded at 2 Hz to three endpoints (4 ...
Chapman Kathryn L - - 2011
The changing environment of monoclonal antibody (mAb) development is impacting on the cost of drug development and the use of experimental animals, particularly non-human primates (NHPs). The drive to reduce these costs is huge and involves rethinking and improving nonclinical studies to make them more efficient and more predictive of ...
Richards D P - - 2011
The composition of snake venoms shows a high degree of variation at all taxonomic levels, and natural selection for diet has been implicated as a potential cause. Saw-scaled vipers (Echis) provide a good model for studying this phenomenon. The venoms of arthropod feeding species of Echis are significantly more toxic ...
Fulk George D - - 2011
Purpose: The purpose of this study was to determine the ability of a novel shoe-based sensor that uses accelerometers, pressure sensors, and pattern recognition with a support vector machine (SVM) to accurately identify sitting, standing, and walking postures in people with stroke. Methods: Subjects with stroke wore the shoe-based sensor ...
Andrés Amara - - 2011
The present study explores the usefulness of dyadic quantification of group characteristics to predict team work performance. After reviewing the literature regarding team member characteristics predicting group performance, percentages of explained variance between 3% and 18% were found. These studies have followed an individualistic approach to measure group characteristics (e. ...
Ikiugu Moses N - - 2011
Occupational therapists are often reluctant to use single theoretical conceptual practice models to guide practice because they recognise the limitation of individual models in addressing clients' occupational performance issues. However, there is a dearth of eclectic methods of guiding theoretical model combination in the profession. The effectiveness of one such ...
Smith Stephen A - - 2011
Molluscs (snails, octopuses, clams and their relatives) have a great disparity of body plans and, among the animals, only arthropods surpass them in species number. This diversity has made Mollusca one of the best-studied groups of animals, yet their evolutionary relationships remain poorly resolved. Open questions have important implications for ...
Krauss Inga - - 2011
BACKGROUND: Gait analysis is an important instrument in clinical research and results should be objective. The purpose of this study was to quantify clinical outcomes of two biomechanical models with different anatomical coordinate systems and angle decomposition strategies for knee joint kinematics. METHODS: The study was designed to compare a ...
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