bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diets high in fermentable protein and fibre alter tight junction protein composition with minor effects on barrier function in piglet colon
Authors: Richter Jan F. , Pieper Robert , Zakrzewski Silke S. , Günzel Dorothee , Schulzke Joerg D. , Van Kessel Andrew G. 
Published: November 2013

Protein fermentation end products may damage the colonic mucosa, which could be counteracted by dietary inclusion of fermentable carbohydrates (fCHO). Although fermentable crude protein (fCP) and fCHO are known to affect microbial ecology, their interactive effects on epithelial barrier function are unknown. In the present study, in a 2 × 2 factorial experiment, thirty-two weaned piglets were fed low-fCP/low-fCHO (14·5 % crude protein (CP)/14·5 % total dietary fibre (TDF)), low-fCP/high-fCHO (14·8 % CP/16·6 % TDF), high-fCP/low-fCHO (19·8 % CP/14·5 % TDF) and high-fCP/high-fCHO (20·1 % CP/18·0 % TDF) diets. After 21–23 d, samples of proximal and distal colonic mucosae were investigated in Ussing chambers with respect to the paracellular and transcytotic passages of macromolecules and epithelial ion transport. The high-fCHO diets were found to reduce the permeability of the distal colon to the transcytotic marker horseradish peroxidase (HRP, 44 kDa;P <0·05) and also reduce the paracellular permeation ofN-hydroxysuccinimide-biotin into the submucosa (443 Da;P <0·05), whereas that of HRP was decreased by the high-fCP diets (P <0·01). Short-circuit current (active ion transport), transepithelial resistance (barrier function) and charge selectivity were largely unaffected in both the segments. However, the high-fCP diets were found to suppress the aldosterone-induced epithelial Na channel activity (P <0·01) irrespective of fCHO inclusion. The high-fCP diets generally reduced the expression of colonic claudin-1, claudin-2 and claudin-3 (P <0·01), while that of claudin-4 was increased by the high-fCHO diets (P <0·01). The high-fCHO diets also altered the ratio between occludin forms (P <0·05) and increased the expression of tricellulin in the proximal colon, which was not observed with high-fCP diets. In conclusion, dietary fCHO and fCP exerted few and largely independent effects on functional measurements, but altered tight junction protein composition in a compensatory way, so that colonic transport and barrier properties were only marginally affected.
The role of EDEM2 compared with EDEM1 in ricin transport from the endoplasmic reticulum to the cytosol
Authors: Słomińska-Wojewódzka Monika , Pawlik Anna , Sokołowska Iwona , Antoniewicz Jakub , Węgrzyn Grzegorz , Sandvig Kirsten 
Published: November 2013

EDEM1 [ER (endoplasmic reticulum)-degradation-enhancing α-mannosidase I-like protein 1] and EDEM2 are crucial regulators of ERAD (ER-associated degradation) that extracts non-native glycoproteins from the calnexin chaperone system. Ricin is a potent plant cytotoxin composed of an A-chain (RTA) connected by a disulfide bond to a cell-binding lectin B-chain (RTB). After endocytic uptake, the toxin is transported retrogradely to the ER, where the enzymatically active RTA is translocated to the cytosol in a similar manner as misfolded ER proteins. This transport is promoted by EDEM1. In the present study we report that EDEM2 is also involved in ricin retrotranslocation out of the ER. However, the role of EDEM1 and EDEM2 in ricin transport to the cytosol seems to differ. EDEM2 promotes ricin retrotranslocation irrespectively of ER translocon accessibility; moreover, co-immunoprecipitation and pull-down studies revealed that more ricin can interact with EDEM2 in comparison with EDEM1. On the other hand, interactions of both lectins with RTA are dependent on the structure of the RTA. Thus our data display a newly discovered role for EDEM2. Moreover, analysis of the involvement of EDEM1 and EDEM2 in ricin retrotranslocation to the cytosol may provide crucial information about general mechanisms of the recognition of ERAD substrates in the ER.
Appropriation and Explosion in Reforming Language-Games: A Model for Discursive Change
Authors: Mansouri-Zeyni Sina , Rahebi Mohammad-Ali 
Published: November 2013

The two of us wroteAnti-Oedipustogether. Since each of us was several, there was already quite a crowd.—Deleuze and Guattari,A Thousand PlateausWith the linguistic turn came an ever-increasing tendency to see language as the locus where truths are born, passed along, or modified. As such, postmodern theories have proved highly compatible with postcolonial studies, which have inspired studies of modern Iran as a country that was colonized, only not officially. However, the latter seem to have fallen for extreme abstraction where metaphysical claims abound: presuming constructivist views of language but failing to present a tangible framework, these studies discuss “discursive change” without giving a clue as to what either discourse or change is. Convinced as such, we have adopted Wittgenstein's idea of language-games to present a tangible model for discursive change.
Determining Optimum Temperature for Growth and Survival of Laboratory-Propagated Juvenile Freshwater Mussels
Authors: Carey Caitlin S , Jones Jess W , Hallerman Eric M , Butler Robert S 
Published: November 2013

Abstract
The effects of temperature on growth and survival of laboratory-propagated juvenile freshwater mussels of two federally endangered species, the Cumberlandian combshell Epioblasma brevidens and oyster mussel E. capsaeformis, and one nonlisted species, the wavy-rayed lampmussel Lampsilis fasciola, were investigated to determine optimum rearing temperatures for these species in small water-recirculating aquaculture systems. Juveniles 4–5 months old were held in downweller buckets at five temperatures. Growth and survival of juveniles were evaluated at 2-week intervals for 10 sampling events. At the end of the 20-week experiment, mean growth at 20, 22, 24, 26, and 28°C was, respectively, 0.75, 2.22, 3.27, 4.23, and 4.08 mm for Cumberlandian combshell; 1.35, 3.73, 3.81, 4.90, and 4.70 mm for oyster mussel; and 2.09, 3.96, 4.99, 5.13, and 4.87 mm for wavy-rayed lampmussel juveniles. Generally, temperature was positively correlated with growth of juveniles. Final mean maximum growth occurred at 26°C for all three species, although no significant differences in growth were detected between 26°C and 28°C. The relationship between temperature and survival of juveniles was less clear. Final survival was 82.5, 89.0, 91.0, 89.5, and 93.5% for Cumberlandian combshell; 73.0, 83.5, 78.0, 78.0, and 68.1% for oyster mussel; and 75.0, 89.5, 87.0, 86.5, and 89.5% for wavy-rayed lampmussel juveniles at the five temperature treatments, respectively. Based on the species used in this study, results indicate that 26°C is the optimum temperature to maximize growth of juvenile mussels in downweller bucket systems. The ability to grow endangered juveniles to larger sizes will improve survival in captivity and upon release into the wild and will reduce time spent in hatcheries. As a result, hatcheries can increase their overall production and enhance the likelihood of success of mussel population recovery efforts by federal and state agencies, and other partners.
Parallel content-based sub-image retrieval using hierarchical searching
Authors: Yang Lin , Qi Xin , Xing Fuyong , Kurc Tahsin , Saltz Joel , Foran David J. 
Published: November 2013

Abstract
Motivation: The capacity to systematically search through large image collections and ensembles and detect regions exhibiting similar morphological characteristics is central to pathology diagnosis. Unfortunately, the primary methods used to search digitized, whole-slide histopathology specimens are slow and prone to inter- and intra-observer variability. The central objective of this research was to design, develop, and evaluate a content-based image retrieval system to assist doctors for quick and reliable content-based comparative search of similar prostate image patches.
Method: Given a representative image patch (sub-image), the algorithm will return a ranked ensemble of image patches throughout the entire whole-slide histology section which exhibits the most similar morphologic characteristics. This is accomplished by first performing hierarchical searching based on a newly developed hierarchical annular histogram (HAH). The set of candidates is then further refined in the second stage of processing by computing a color histogram from eight equally divided segments within each square annular bin defined in the original HAH. A demand-driven master-worker parallelization approach is employed to speed up the searching procedure. Using this strategy, the query patch is broadcasted to all worker processes. Each worker process is dynamically assigned an image by the master process to search for and return a ranked list of similar patches in the image.
Results: The algorithm was tested using digitized hematoxylin and eosin (H&E) stained prostate cancer specimens. We have achieved an excellent image retrieval performance. The recall rate within the first 40 rank retrieved image patches is ∼90%.
Availability and implementation: Both the testing data and source code can be downloaded from http://pleiad.umdnj.edu/CBII/Bioinformatics/.
Contact: lin.yang@uky.edu
SBML and CellML translation in Antimony and JSim
Authors: Smith Lucian P. , Butterworth Erik , Bassingthwaighte James B. , Sauro Herbert M. 
Published: November 2013

Abstract
Motivation: The creation and exchange of biologically relevant models is of great interest to many researchers. When multiple standards are in use, models are more readily used and re-used if there exist robust translators between the various accepted formats.
Summary: Antimony 2.4 and JSim 2.10 provide translation capabilities from their own formats to SBML and CellML. All provided unique challenges, stemming from differences in each format’s inherent design, in addition to differences in functionality.
Availability and implementation: Both programs are available under BSD licenses; Antimony from http://antimony.sourceforge.net/ and JSim from http://physiome.org/jsim/.
Contact: lpsmith@u.washington.edu
PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra
Authors: Kertész-Farkas Attila , Reiz Beáta , Vera Roberto , Myers Michael P. , Pongor Sándor 
Published: November 2013

AbstractMotivation: Tandem mass spectrometry has become a standard tool for identifying post-translational modifications (PTMs) of proteins. Algorithmic searches for PTMs from tandem mass spectrum data (MS/MS) tend to be hampered by noisy data as well as by a combinatorial explosion of search space. This leads to high uncertainty and long search-execution times.Results: To address this issue, we present PTMTreeSearch, a new algorithm that uses a large database of known PTMs to identify PTMs from MS/MS data. For a given peptide sequence, PTMTreeSearch builds a computational tree wherein each path from the root to the leaves is labeled with the amino acids of a peptide sequence. Branches then represent PTMs. Various empirical tree pruning rules have been designed to decrease the search-execution time by eliminating biologically unlikely solutions. PTMTreeSearch first identifies a relatively small set of high confidence PTM types, and in a second stage, performs a more exhaustive search on this restricted set using relaxed search parameter settings. An analysis of experimental data shows that using the same criteria for false discovery, PTMTreeSearch annotates more peptides than the current state-of-the-art methods and PTM identification algorithms, and achieves this at roughly the same execution time. PTMTreeSearch is implemented as a plugable scoring function in the X!Tandem search engine.Availability: The source code of PTMTreeSearch and a demo server application can be found at http://net.icgeb.org/ptmtreesearch.Contacts: pongor@icgeb.orgSupplementary information: Supplementary materials are available at Bioinformatics online.
Bayesian network prior: network analysis of biological data using external knowledge
Authors: Isci Senol , Dogan Haluk , Ozturk Cengizhan , Otu Hasan H. 
Published: November 2013

Abstract
Motivation: Reverse engineering GI networks from experimental data is a challenging task due to the complex nature of the networks and the noise inherent in the data. One way to overcome these hurdles would be incorporating the vast amounts of external biological knowledge when building interaction networks. We propose a framework where GI networks are learned from experimental data using Bayesian networks (BNs) and the incorporation of external knowledge is also done via a BN that we call Bayesian Network Prior (BNP). BNP depicts the relation between various evidence types that contribute to the event ‘gene interaction’ and is used to calculate the probability of a candidate graph (G) in the structure learning process.
Results: Our simulation results on synthetic, simulated and real biological data show that the proposed approach can identify the underlying interaction network with high accuracy even when the prior information is distorted and outperforms existing methods.
Availability: Accompanying BNP software package is freely available for academic use at http://bioe.bilgi.edu.tr/BNP.
Contact: hasan.otu@bilgi.edu.tr
Supplementary Information: Supplementary data are available at Bioinformatics online.
Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors
Authors: Wilson Mandy L. , Okumoto Sakiko , Adam Laura , Peccoud Jean 
Published: November 2013

Abstract
Motivation: Expression vectors used in different biotechnology applications are designed with domain-specific rules. For instance, promoters, origins of replication or homologous recombination sites are host-specific. Similarly, chromosomal integration or viral delivery of an expression cassette imposes specific structural constraints. As de novo gene synthesis and synthetic biology methods permeate many biotechnology specialties, the design of application-specific expression vectors becomes the new norm. In this context, it is desirable to formalize vector design strategies applicable in different domains.
Results: Using the design of constructs to express genes in the chloroplast of Chlamydomonas reinhardtii as an example, we show that a vector design strategy can be formalized as a domain-specific language. We have developed a graphical editor of context-free grammars usable by biologists without prior exposure to language theory. This environment makes it possible for biologists to iteratively improve their design strategies throughout the course of a project. It is also possible to ensure that vectors designed with early iterations of the language are consistent with the latest iteration of the language.
Availability and implementation: The context-free grammar editor is part of the GenoCAD application. A public instance of GenoCAD is available at http://www.genocad.org. GenoCAD source code is available from SourceForge and licensed under the Apache v2.0 open source license.
Contact: peccoud@vt.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing
Authors: Doi Koichiro , Monjo Taku , Hoang Pham H. , Yoshimura Jun , Yurino Hideaki , Mitsui Jun , Ishiura Hiroyuki , Takahashi Yuji , Ichikawa Yaeko , Goto Jun , Tsuji Shoji , Morishita Shinichi 
Published: November 2013

Abstract
Motivation: Long expansions of short tandem repeats (STRs), i.e. DNA repeats of 2–6 nt, are associated with some genetic diseases. Cost-efficient high-throughput sequencing can quickly produce billions of short reads that would be useful for uncovering disease-associated STRs. However, enumerating STRs in short reads remains largely unexplored because of the difficulty in elucidating STRs much longer than 100 bp, the typical length of short reads.
Results: We propose ab initio procedures for sensing and locating long STRs promptly by using the frequency distribution of all STRs and paired-end read information. We validated the reproducibility of this method using biological replicates and used it to locate an STR associated with a brain disease (SCA31). Subsequently, we sequenced this STR site in 11 SCA31 samples using SMRTTM sequencing (Pacific Biosciences), determined 2.3–3.1 kb sequences at nucleotide resolution and revealed that (TGGAA)- and (TAAAATAGAA)-repeat expansions determined the instability of the repeat expansions associated with SCA31. Our method could also identify common STRs, (AAAG)- and (AAAAG)-repeat expansions, which are remarkably expanded at four positions in an SCA31 sample. This is the first proposed method for rapidly finding disease-associated long STRs in personal genomes using hybrid sequencing of short and long reads.
Availability and implementation: Our TRhist software is available at http://trhist.gi.k.u-tokyo.ac.jp/.
Contact: moris@cb.k.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
RNAseqViewer: visualization tool for RNA-Seq data
Authors: Rogé Xavier , Zhang Xuegong 
Published: November 2013

Abstract
Summary: With the advances of RNA sequencing technologies, scientists need new tools to analyze transcriptome data. We introduce RNAseqViewer, a new visualization tool dedicated to RNA-Seq data. The program offers innovative ways to represent transcriptome data for single or multiple samples. It is a handy tool for scientists who use RNA-Seq data to compare multiple transcriptomes, for example, to compare gene expression and alternative splicing of cancer samples or of different development stages.
Availability and implementation: RNAseqViewer is freely available for academic use at http://bioinfo.au.tsinghua.edu.cn/software/RNAseqViewer/
Contact: zhangxg@tsinghua.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences
Authors: Sreeskandarajan Sutharzan , Flowers Michelle M. , Karro John E. , Liang Chun 
Published: November 2013

Abstract
Summary: Palindromic sequences, or inverted repeats (IRs), in DNA sequences involve important biological processes such as DNA–protein binding, DNA replication and DNA transposition. Development of bioinformatics tools that are capable of accurately detecting perfect IRs can enable genome-wide studies of IR patterns in both prokaryotes and eukaryotes. Different from conventional string-comparison approaches, we propose a novel algorithm that uses a cumulative score system based on a prime number representation of nucleotide bases. We then implemented this algorithm as a MATLAB-based program for perfect IR detection. In comparison with other existing tools, our program demonstrates a high accuracy in detecting nested and overlapping IRs.
Availability and implementation: The source code is freely available on (http://bioinfolab.miamioh.edu/bioinfolab/palindrome.php)
Contact: liangc@miamioh.edu or karroje@miamioh.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
RelateAdmix: a software tool for estimating relatedness between admixed individuals
Authors: Moltke Ida , Albrechtsen Anders 
Published: November 2013

Abstract
Motivation: Pairwise relatedness plays an important role in a range of genetic research fields. However, currently only few estimators exist for individuals that are admixed, i.e. have ancestry from more than one population, and these estimators fail in some situations.
Results: We present a new software tool, RelateAdmix, for obtaining maximum likelihood estimates of pairwise relatedness from genetic data between admixed individuals. We show using simulated data that it gives rise to better estimates than three state-of-the-art software tools, REAP, KING and Plink, while still being fast enough to be applicable to large datasets.
Availability and implementation: The software tool, implemented in C and R, is freely available from www.popgen.dk/software.
Contact: albrecht@binf.ku.dk
Supplementary information: Supplementary data are available at Bioinformatics online.
AVIA: an interactive web-server for annotation, visualization and impact analysis of genomic variations
Authors: Vuong Hue , Stephens Robert M. , Volfovsky Natalia 
Published: November 2013

Abstract
Motivation: The plethora of information that emerges from large-scale genome characterization studies has triggered the development of computational frameworks and tools for efficient analysis, interpretation and visualization of genomic data. Functional annotation of genomic variations and the ability to visualize the data in the context of whole genome and/or multiple genomes has remained a challenging task. We have developed an interactive web-based tool, AVIA (Annotation, Visualization and Impact Analysis), to explore and interpret large sets of genomic variations (single nucleotide variations and insertion/deletions) and to help guide and summarize genomic experiments. The annotation, summary plots and tables are packaged and can be downloaded by the user from the email link provided.
Availability and implementation:  http://avia.abcc.ncifcrf.gov.
Contact:  vuonghm@mail.nih.gov
Supplementary information:  Supplementary data are available at Bioinformatics online.
HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences
Authors: Matias Rodrigues João F. , von Mering Christian 
Published: November 2013

Abstract
Motivation: Nucleotide sequence data are being produced at an ever increasing rate. Clustering such sequences by similarity is often an essential first step in their analysis—intended to reduce redundancy, define gene families or suggest taxonomic units. Exact clustering algorithms, such as hierarchical clustering, scale relatively poorly in terms of run time and memory usage, yet they are desirable because heuristic shortcuts taken during clustering might have unintended consequences in later analysis steps.
Results: Here we present HPC-CLUST, a highly optimized software pipeline that can cluster large numbers of pre-aligned DNA sequences by running on distributed computing hardware. It allocates both memory and computing resources efficiently, and can process more than a million sequences in a few hours on a small cluster.
Availability and implementation: Source code and binaries are freely available at http://meringlab.org/software/hpc-clust/; the pipeline is implemented in C++ and uses the Message Passing Interface (MPI) standard for distributed computing.
Contact:  mering@imls.uzh.ch
Supplementary Information:  Supplementary data are available at Bioinformatics online.
Addressing the Mandate for Hand-off Education
Authors: Lane-Fall Meghan B. , Brooks Amber K. , Wilkins Sara A. , Davis Joshua J. , Riesenberg Lee Ann 
Published: November 2013

Abstract
The Accreditation Council for Graduate Medical Education requires that residency programs teach residents about handoffs and ensure their competence in this communication skill. Development of hand-off curricula for anesthesia residency programs is hindered by the paucity of evidence regarding how to conduct, teach, and evaluate handoffs in the various settings where anesthesia practitioners work. This narrative review draws from literature in anesthesia and other disciplines to provide recommendations for anesthesia resident hand-off curriculum development and evaluation.