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Vanegas Pamela L PL Department of Chemistry, Saint Louis University, Saint Louis, Missouri 63103, United - - 2012
Currently, several models for predicting the secondary structure of RNA exist, one of which is free energy minimization using the Nearest Neighbor Model. This model predicts the lowest-free energy secondary structure from a primary sequence by summing the free energy contributions of the Watson-Crick nearest neighbor base pair combinations and ...
Weitz Maximilian - - 2012
With the help of only two enzymes-an RNA polymerase and a ribonuclease-reduced versions of transcriptional regulatory circuits can be implemented in vitro. These circuits enable the emulation of naturally occurring biochemical networks, the exploration of biological circuit design principles and the biochemical implementation of powerful computational models.
Svetlov Vladimir - - 2012
In their commentary, Klyuyev and Vassylyev dispute a model of transcription inhibition by tagetitoxin (Tgt) proposed by us based on biochemical analysis and computational docking. We maintain that, although an alternative explanation can be provided for any single observation reported by us, taken together our results support a model in ...
Wan Lin - - 2012
RNA-Seq is widely used in biological and biomedical studies. Methods for the estimation of the transcript's abundance using RNA-Seq data have been intensively studied, many of which are based on the assumption that the short-reads of RNA-Seq are uniformly distributed along the transcripts. However, the short-reads are found to be ...
Antin Jonathan F - - 2012
The purpose of this research effort was to compare older driver and non-driver functional impairment profiles across some 60 assessment metrics in an initial effort to contribute to the development of fitness-to-drive assessment models. Of the metrics evaluated, 21 showed statistically significant differences, almost all favoring the drivers. Also, it ...
Zhang Jian - - 2012
In this work we develop an approach for predicting the tertiary structures of RNA fragments by combining an RNA nucleobase discrete state (RNAnbds) model, a sequential Monte Carlo method, and a statistical potential. The RNAnbds model is designed for optimizing the configuration of nucleobases with respect to their preceding ones ...
Mittal Vinay K - - 2012
The rapid expansion in the quantity and quality of RNA-Seq data requires the development of sophisticated high-performance bioinformatics tools capable of rapidly transforming this data into meaningful information that is easily interpretable by biologists. Currently available analysis tools are often not easily installed by the general biologist and most of ...
Hansen Kasper D - - 2012
The ability to measure gene expression on a genome-wide scale is one of the most promising accomplishments in molecular biology. Microarrays, the technology that first permitted this, were riddled with problems due to unwanted sources of variability. Many of these problems are now mitigated, after a decade's worth of statistical ...
Sim Adelene Y L AY Department of Applied Physics, Stanford University, Stanford, CA 94305, - - 2012
We develop a unique algorithm implemented in the program MOSAICS (Methodologies for Optimization and Sampling in Computational Studies) that is capable of nanoscale modeling without compromising the resolution of interest. This is achieved by modeling with customizable hierarchical degrees of freedom, thereby circumventing major limitations of conventional molecular modeling. With ...
Fongsatitkul Prayoon - - 2012
Energy generation from methane (CH(4)) is one of the primary targets of the anaerobic digestion process. Consequently, the focus of this study was to investigate the effect on CH(4) production of total solids (TS) loading (measured as % TS) and hydraulic residence time (HRT) during the treatment of the organic ...
Tuffrey-Wijne Irene - - 2012
OBJECTIVES: To develop a model for breaking bad news that meets the needs of people with intellectual disabilities (IDs). DESIGN: A two-phase qualitative study featuring: (I) focus group meetings, on-line focus groups and one-to-one interviews; (II) structured feedback from participants and other stakeholders. SETTING: Participants were drawn from National Health ...
Friedman Alinda - - 2012
Our mental representation of the world is far from objective. For example, western Canadians estimate the locations of North American cities to be too far to the west. This bias could be due to a reference point effect, in which people estimate more space between places close to them than ...
de Carvalho João P M - - 2012
Introduction.  Anencephaly is the most severe neural tube defect in human fetuses. There is an increasing need for tissue replacement in chronic diseases and reconstructive surgeries. Fetal tissues have been used as a substitute for native organs. Aim.  The aim of this article was to compare the structure and morphology ...
Cano-Sancho G - - 2012
HT-2 toxin (HT2) and T-2 toxin (T2) are mycotoxins produced in several cereals by species of Fusarium. The aim of the present study was to assess the exposure of Catalonian population to the combined mycotoxins T2 and HT2. Three different approaches were considered to handle the left censored data: (1) ...
van Zomeren Martijn - - 2012
To explain the psychology behind individuals' motivation to participate in collective action against collective disadvantage (e.g., protest marches), the authors introduce a dynamic dual pathway model of approach coping that integrates many common explanations of collective action (i.e., group identity, unfairness, anger, social support, and efficacy). It conceptualizes collective action ...
Ong Nicole T NT School of Kinesiology, The University of British Columbia, Vancouver, BC V6T 1Z1, - - 2012
The presence of after-effects in adaptation tasks implies that an existing internal model has been updated. Previously, we showed that although observers adapted to a visuomotor perturbation, they did not show after-effects. In this experiment, we tested 2 further observer groups and an actor group. Observers were now actively engaged ...
Yang J - - 2012
In this paper, a group-sensitive multiple kernel learning (GS-MKL) method is proposed for object recognition to accommodate the intra-class diversity and the inter-class correlation. By introducing the group between the object category and individual images as an intermediate representation, GS-MKL attempts to learn group-sensitive multi-kernel combinations together with the associated ...
Pyron R A - - 2012
For studies investigating trait evolution, there are at least two important questions. First, have traits under consideration influenced cladogenesis and extinction in the group? Second, how do fossil data alter inferences about trait evolution or diversification-rate dynamics? However, relatively few studies have assessed these questions. Here, we use recently developed ...
Woess Wolfgang - - 2012
This is a continuation of the study, begun by Ceccherini-Silberstein and Woess (2009) [5], of context-free pairs of groups and the related context-free graphs in the sense of Muller and Schupp (1985) [22]. The graphs under consideration are Schreier graphs of a subgroup of some finitely generated group, and context-freeness ...
Grabowski Tomasz - - 2012
Aim of the present study was an attempt to find a correlation between physicochemical structure of veterinary drugs and the maximum residue limit (MRL) for muscle tissue of food producing animals. Direct correlation and analysis in quintile groups for 52 physicochemical parameters were performed. An internal validation using leave-one-out cross-validation ...
Gunz Philipp - - 2012
The globular braincase of modern humans is distinct from all fossil human species, including our closest extinct relatives, the Neandertals. Such adult shape differences must ultimately be rooted in different developmental patterns, but it is unclear at which point during ontogeny these group characteristics emerge. Here we compared internal shape ...
Kira Ibrahim A - - 2012
Abstract The paper discusses varieties of group therapies with refugees and torture survivors and the logic behind enhancing traditional group therapies to fit the unique experiences of refugees and torture survivors. It discusses some lessons learned from practice and from empirical research and some recommended adaptations. Finally, it discusses the ...
Hashimoto Elizabeth M - - 2012
The log-Burr XII regression model for grouped survival data is evaluated in the presence of many ties. The methodology for grouped survival data is based on life tables, where the times are grouped in k intervals, and we fit discrete lifetime regression models to the data. The model parameters are ...
Mancuso Nicholas - - 2012
This paper addresses the problem of reconstructing viral quasispecies from next-generation sequencing reads obtained from amplicons (i.e., reads generated from predefined amplified overlapping regions). We compare the parsimonious and likelihood models for this problem and propose several novel assembling algorithms. The proposed methods have been validated on simulated error-free HCV ...
Jamal Salma - - 2012
MicroRNAs (miRNA) are small endogenously transcribed regulatory RNA which modulates gene expression at a post transcriptional level. These small RNAs have now been shown to be critical regulators in a number of biological processes in the cell including pathophysiology of diseases like cancers. The increasingly evident roles of microRNA in ...
Lawlor Kynan T - - 2012
Expanded DNA repeat sequences are known to cause over 20 diseases, including Huntington's disease, several types of spinocerebellar ataxia and myotonic dystrophy type 1 and 2. A shared genetic basis, and overlapping clinical features for some of these diseases, indicate that common pathways may contribute to pathology. Multiple mechanisms, mediated ...
Kadota Koji - - 2012
High-throughput sequencing, such as ribonucleic acid sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) analyses, enables various features of organisms to be compared through tag counts. Recent studies have demonstrated that the normalization step for RNA-seq data is critical for a more accurate subsequent analysis of differential gene expression. Development of ...
Zhang Junfeng - - 2012
A pair of fly impressions is described as a new species of a new genus, Orientisargus illecebrosusgen. et sp. n., referred to a new family Orientisargidaefam. n. within Archisargoidea of Brachycera, Diptera. The systematic position of Orientisargidae is discussed. Daohugosargusgen. n. is proposed for Sharasargus eximius KY Zhang et al., ...
McKeown Meghan - - 2012
Revwattsia fragilis (Watts) D.L. Jones (Dryopteridaceae), originally described as a Polystichum Roth by the pioneer Australian botanist Reverend W.W. Watts in 1914, is a rare epiphytic fern endemic to northeastern Queensland, Australia. Known from only a few populations, it is restricted to tropical rainforests in the Atherton Tablelands. We used ...
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 ...
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