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Wolfe Kevin C KC Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United - - 2012
Several different mechanical models of double-helical nucleic-acid structures that have been presented in the literature are reviewed here together with a new analysis method that provides a reconciliation between these disparate models. In all cases, terminology and basic results from the theory of Lie groups are used to describe rigid-body ...
Seo Sangjae - - 2012
KOSMOS is the first online morph server to be able to address the structural dynamics of DNA/RNA, proteins and even their complexes, such as ribosomes. The key functions of KOSMOS are the harmonic and anharmonic analyses of macromolecules. In the harmonic analysis, normal mode analysis (NMA) based on an elastic ...
Touleimat Nizar - - 2012
Background: Huge progress has been made in the development of array- or sequencing-based technologies for DNA methylation analysis. The Illumina Infinium(®) Human Methylation 450K BeadChip (Illumina Inc., CA, USA) allows the simultaneous quantitative monitoring of more than 480,000 CpG positions, enabling large-scale epigenotyping studies. However, the assay combines two different ...
Mollazadeh-Beidokhti Laleh - - 2012
We studied the dynamical behavior of a mononucleosome under tension using a theoretical model that takes into account the nucleosomal geometry, DNA elasticity, nonspecific DNA-protein binding, and effective repulsion between the two DNA turns. Using a dynamical Monte-Carlo simulation algorithm, we demonstrate that this model shows a behavior that for ...
Anderson James Wj - - 2012
ABSTRACT: BACKGROUND: Stochastic Context-Free Grammars (SCFGs) were applied successfully to RNA secondary structure prediction in the early 90s, and used in combination with comparative methods in the late 90s. The set of SCFGs potentially useful for RNA secondary structure prediction is very large, but a few intuitively designed grammars have ...
Iancu Ovidiu D OD Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239-3098, USA. - - 2012
RNA-Seq experiments have shown great potential for transcriptome profiling. While sequencing increases the level of biological detail, integrative data analysis is also important. One avenue is the construction of coexpression networks. Because the capacity of RNA-Seq data for network construction has not been previously evaluated, we constructed a coexpression network ...
Lebon Florence - - 2012
A multi-disciplinary approach was used to identify the first pharmacophore model for KCC2 blockers: several physico-chemical studies such as XRD and NMR were combined to molecular modelling techniques, SAR analysis and synthesis of constrained analogues in order to determine a minimal conformational space regrouping few potential bioactive conformations. These conformations ...
Loinger Adiel - - 2012
Two major classes of small regulatory RNAs--small interfering RNAs (siRNAs) and microRNA (miRNAs)--are involved in a common RNA interference processing pathway. Small RNAs within each of these families were found to compete for limiting amounts of shared components, required for their biogenesis and processing. Association with Argonaute (Ago), the catalytic ...
Chen Jonathan L - - 2012
Thermodynamic parameters for GU pairs are important for predicting the secondary structures of RNA and for finding genomic sequences that code for structured RNA. Optical melting curves were measured for 29 RNA duplexes with GU pairs to improve nearest neighbor parameters for predicting stabilities of helixes. The updated model eliminates ...
Zabet Nicolae Radu - - 2012
Gene activity is mediated by site-specific transcription factors (TFs). Their binding to defined regions in the genome determines the rate at which their target genes are transcribed. We present a comprehensive computational model of the search process of TF for their genomic target site(s). The computational model considers: the DNA ...
Dimitrieva Slavica - - 2012
Commonly used RNA folding programs compute the minimum free energy structure of a sequence under the pseudoknot exclusion constraint. They are based on Zuker's algorithm which runs in time O(n(3)). Recently, it has been claimed that RNA folding can be achieved in average time O(n(2)) using a sparsification technique. A ...
Chuah Tong Kuan - - 2012
This paper presents a termination criterion for active contour that does not involve alteration of the energy functional. The criterion is based on the area difference of the contour during evolution. In this criterion, the evolution of the contour terminates when the area difference fluctuates around a constant. The termination ...
Sim Adelene Y L AY Department of Applied Physics, Stanford University, Stanford, CA 94305-4090, USA. - - 2012
Ribonucleic acid (RNA) molecules play important roles in a variety of biological processes. To properly function, RNA molecules usually have to fold to specific structures, and therefore understanding RNA structure is vital in comprehending how RNA functions. One approach to understanding and predicting biomolecular structure is to use knowledge-based potentials ...
An Guohua - - 2012
We conducted a pharmacokinetic (PK) study of mitoxantrone (Novantrone®), a clinically well-established anticancer agent, in mice and developed a mechanism-based PBPK (physiologically based pharmacokinetic) model to describe its disposition. Mitoxantrone concentrations in plasma and six organs (lung, heart, liver, kidney, spleen, and brain) were determined after a 5 mg/kg i.v. dose. ...
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 KD Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, - - 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 ...
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