bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of Sept4 expression in fibrotic livers of mice infected with Schistosoma japonicum
Authors: DUAN Y. N. , QIAN H. Y. , QIN Y. W. , ZHU D. D. , HE X. X. , ZHOU Q. , YANG Y. N. , BAO J. , FENG J. R. , SUN W. , CHEN J. L. 
Published: June 2011

SUMMARYIn order to investigate the dynamics of Septin4 (Sept4) expression and its function in the formation of fibrotic livers in mice infected with Schistosoma japonicum, we constructed the mouse model of S. japonicum egg-induced liver fibrosis for 24 weeks. Immunohistochemical staining, qRT-PCR and Western blot were used to detect the expression of Sept4 and α-smooth muscle actin (α-SMA). We found Sept4 localized in the perisinusoidal space where hepatic stellate cells (HSCs) distribute in the periphery of circumoval granulomas and the portal venule. The expression of Sept4 and α-SMA had a similar significant tendency of an up-regulation to a peak at 12 weeks post-infection (p.i.) followed by a down-regulation. At 24 weeks p.i. both were at a low level. These results suggest that Sept4 and α-SMA may interact together in HSCs. Based on this evidence, we hypothesize that Sept4 seems to be involved in the formation of inflammatory granulomata and subsequent liver fibrosis by regulating HSCs activation.
Rational Feelings and Moral Agency
Authors: Geiger Ido 
Published: June 2011

AbstractKant's conception of moral agency is often charged with attributing no role to feelings. I suggest that respect is the effective force driving moral action. I then argue that four additional types of rational feelings are necessary conditions of moral agency: (1) The affective inner life of moral agents deliberating how to act and reflecting on their deeds is rich and complex (conscience). To act morally we must turn our affective moral perception towards the ends of moral action: (2) the welfare of others (love of others); and (3) our own moral being (self-respect). (4) Feelings shape our particular moral acts (moral feeling). I tentatively suggest that the diversity of moral feelings might be as great as the range of our duties.
Quest for the descent of the Escherichia coli outbreak strain TY2482 – out of Germany?
Authors: Avasthi Tiruvayipati , Kumar Narender , Baddam Ramani , Ahmed Niyaz 
Published: June 2011

AbstractThe recent outbreak of the Escherichia coli infection in north Germany reportedly has killed 35 people and sickened about 4000. Infections were reported in 2001 and 2002 in Germany and Central Africa respectively. In order to dissect all possible connections among the three infection/outbreak strains and to extract the most virulent genes responsible for the augmented pathogenicity of the present German strain (2011), whole genome sequence data of the two isolates (E. coli TY_2482 & LB226692) were analyzed. We report that the German outbreak strain isolated in 2011 is a seasoned clone of the 2002 isolate sequenced from Central Africa (55989) and perhaps a direct descendent of the German EAEC strain reported in 2001 infection cases.
PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions
Authors: Lin Michael F. , Jungreis Irwin , Kellis Manolis 
Published: June 2011

Abstract
Motivation: As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multispecies nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models.
Results: We show that PhyloCSF's classification performance in 12-species Drosophila genome alignments exceeds all other methods we compared in a previous study. We anticipate that this method will be widely applicable as the transcriptomes of many additional species, tissues and subcellular compartments are sequenced, particularly in the context of ENCODE and modENCODE, and as interest grows in long non-coding RNAs, often initially recognized by their lack of protein coding potential rather than conserved RNA secondary structures.
Availability and Implementation: The Objective Caml source code and executables for GNU/Linux and Mac OS X are freely available at http://compbio.mit.edu/PhyloCSF
Contact: mlin@mit.edu; manoli@mit.edu
Tanglegrams for rooted phylogenetic trees and networks
Authors: Scornavacca Celine , Zickmann Franziska , Huson Daniel H. 
Published: June 2011

Abstract
Motivation: In systematic biology, one is often faced with the task of comparing different phylogenetic trees, in particular in multi-gene analysis or cospeciation studies. One approach is to use a tanglegram in which two rooted phylogenetic trees are drawn opposite each other, using auxiliary lines to connect matching taxa. There is an increasing interest in using rooted phylogenetic networks to represent evolutionary history, so as to explicitly represent reticulate events, such as horizontal gene transfer, hybridization or reassortment. Thus, the question arises how to define and compute a tanglegram for such networks.
Results: In this article, we present the first formal definition of a tanglegram for rooted phylogenetic networks and present a heuristic approach for computing one, called the NN-tanglegram method. We compare the performance of our method with existing tree tanglegram algorithms and also show a typical application to real biological datasets. For maximum usability, the algorithm does not require that the trees or networks are bifurcating or bicombining, or that they are on identical taxon sets.
Availability: The algorithm is implemented in our program Dendroscope 3, which is freely available from www.dendroscope.org.
Contact: scornava@informatik.uni-tuebingen.de; huson@informatik.uni-tuebingen.de
Meta-IDBA: a de Novo assembler for metagenomic data
Authors: Peng Yu , Leung Henry C. M. , Yiu S. M. , Chin Francis Y. L. 
Published: June 2011

Abstract
Motivation: Next-generation sequencing techniques allow us to generate reads from a microbial environment in order to analyze the microbial community. However, assembling of a set of mixed reads from different species to form contigs is a bottleneck of metagenomic research. Although there are many assemblers for assembling reads from a single genome, there are no assemblers for assembling reads in metagenomic data without reference genome sequences. Moreover, the performances of these assemblers on metagenomic data are far from satisfactory, because of the existence of common regions in the genomes of subspecies and species, which make the assembly problem much more complicated.
Results: We introduce the Meta-IDBA algorithm for assembling reads in metagenomic data, which contain multiple genomes from different species. There are two core steps in Meta-IDBA. It first tries to partition the de Bruijn graph into isolated components of different species based on an important observation. Then, for each component, it captures the slight variants of the genomes of subspecies from the same species by multiple alignments and represents the genome of one species, using a consensus sequence. Comparison of the performances of Meta-IDBA and existing assemblers, such as Velvet and Abyss for different metagenomic datasets shows that Meta-IDBA can reconstruct longer contigs with similar accuracy.
Availability: Meta-IDBA toolkit is available at our website http://www.cs.hku.hk/~alse/metaidba.
Contact: chin@cs.hku.hk
A folding algorithm for extended RNA secondary structures
Authors: zu Siederdissen Christian Höner , Bernhart Stephan H. , Stadler Peter F. , Hofacker Ivo L. 
Published: June 2011

Abstract
Motivation: RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment.
Results: We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for parameter optimization and structure prediction.
Availability: All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at/software/rnawolf/.
Contact: choener@tbi.univie.ac.at
Detecting epistatic effects in association studies at a genomic level based on an ensemble approach
Authors: Li Jing , Horstman Benjamin , Chen Yixuan 
Published: June 2011

Abstract
Motivation: Most complex diseases involve multiple genes and their interactions. Although genome-wide association studies (GWAS) have shown some success for identifying genetic variants underlying complex diseases, most existing studies are based on limited single-locus approaches, which detect single nucleotide polymorphisms (SNPs) essentially based on their marginal associations with phenotypes.
Results: In this article, we propose an ensemble approach based on boosting to study gene–gene interactions. We extend the basic AdaBoost algorithm by incorporating an intuitive importance score based on Gini impurity to select candidate SNPs. Permutation tests are used to control the statistical significance. We have performed extensive simulation studies using three interaction models to evaluate the efficacy of our approach at realistic GWAS sizes, and have compared it with existing epistatic detection algorithms. Our results indicate that our approach is valid, efficient for GWAS and on disease models with epistasis has more power than existing programs.
Contact: jingli@case.edu
Detection and interpretation of metabolite–transcript coresponses using combined profiling data
Authors: Redestig Henning , Costa Ivan G. 
Published: June 2011

Abstract
Motivation: Studying the interplay between gene expression and metabolite levels can yield important information on the physiology of stress responses and adaptation strategies. Performing transcriptomics and metabolomics in parallel during time-series experiments represents a systematic way to gain such information. Several combined profiling datasets have been added to the public domain and they form a valuable resource for hypothesis generating studies. Unfortunately, detecting coresponses between transcript levels and metabolite abundances is non-trivial: they cannot be assumed to overlap directly with underlying biochemical pathways and they may be subject to time delays and obscured by considerable noise.
Results: Our aim was to predict pathway comemberships between metabolites and genes based on their coresponses to applied stress. We found that in the presence of strong noise and time-shifted responses, a hidden Markov model-based similarity outperforms the simpler Pearson correlation but performs comparably or worse in their absence. Therefore, we propose a supervised method that applies pathway information to summarize similarity statistics to a consensus statistic that is more informative than any of the single measures. Using four combined profiling datasets, we show that comembership between metabolites and genes can be predicted for numerous KEGG pathways; this opens opportunities for the detection of transcriptionally regulated pathways and novel metabolically related genes.
Availability: A command-line software tool is available at http://www.cin.ufpe.br/~igcf/Metabolites.
Contact: henning@psc.riken.jp; igcf@cin.ufpe.br
Supplementary information: Supplementary data are available at Bioinformatics online.
StructHDP: automatic inference of number of clusters and population structure from admixed genotype data
Authors: Shringarpure Suyash , Won Daegun , Xing Eric P. 
Published: June 2011

Abstract
Motivation: Clustering of genotype data is an important way of understanding similarities and differences between populations. A summary of populations through clustering allows us to make inferences about the evolutionary history of the populations. Many methods have been proposed to perform clustering on multilocus genotype data. However, most of these methods do not directly address the question of how many clusters the data should be divided into and leave that choice to the user.
Methods: We present StructHDP, which is a method for automatically inferring the number of clusters from genotype data in the presence of admixture. Our method is an extension of two existing methods, Structure and Structurama. Using a Hierarchical Dirichlet Process (HDP), we model the presence of admixture of an unknown number of ancestral populations in a given sample of genotype data. We use a Gibbs sampler to perform inference on the resulting model and infer the ancestry proportions and the number of clusters that best explain the data.
Results: To demonstrate our method, we simulated data from an island model using the neutral coalescent. Comparing the results of StructHDP with Structurama shows the utility of combining HDPs with the Structure model. We used StructHDP to analyze a dataset of 155 Taita thrush, Turdus helleri, which has been previously analyzed using Structure and Structurama. StructHDP correctly picks the optimal number of populations to cluster the data. The clustering based on the inferred ancestry proportions also agrees with that inferred using Structure for the optimal number of populations. We also analyzed data from 1048 individuals from the Human Genome Diversity project from 53 world populations. We found that the clusters obtained correspond with major geographical divisions of the world, which is in agreement with previous analyses of the dataset.
Availability: StructHDP is written in C++. The code will be available for download at http://www.sailing.cs.cmu.edu/structhdp.
Contact: suyash@cs.cmu.edu; epxing@cs.cmu.edu
An integrative clustering and modeling algorithm for dynamical gene expression data
Authors: Sivriver Julia , Habib Naomi , Friedman Nir 
Published: June 2011

AbstractMotivation: The precise dynamics of gene expression is often crucial for proper response to stimuli. Time-course gene-expression profiles can provide insights about the dynamics of many cellular responses, but are often noisy and measured at arbitrary intervals, posing a major analysis challenge.Results: We developed an algorithm that interleaves clustering time-course gene-expression data with estimation of dynamic models of their response by biologically meaningful parameters. In combining these two tasks we overcome obstacles posed in each one. Moreover, our approach provides an easy way to compare between responses to different stimuli at the dynamical level. We use our approach to analyze the dynamical transcriptional responses to inflammation and anti-viral stimuli in mice primary dendritic cells, and extract a concise representation of the different dynamical response types. We analyze the similarities and differences between the two stimuli and identify potential regulators of this complex transcriptional response.Availability: The code to our method is freely available http://www.compbio.cs.huji.ac.il/DynaMiteC.Contact: nir@cs.huji.ac.il
Systematic exploration of error sources in pyrosequencing flowgram data
Authors: Balzer Susanne , Malde Ketil , Jonassen Inge 
Published: June 2011

Abstract
Motivation: 454 pyrosequencing, by Roche Diagnostics, has emerged as an alternative to Sanger sequencing when it comes to read lengths, performance and cost, but shows higher per-base error rates. Although there are several tools available for noise removal, targeting different application fields, data interpretation would benefit from a better understanding of the different error types.
Results: By exploring 454 raw data, we quantify to what extent different factors account for sequencing errors. In addition to the well-known homopolymer length inaccuracies, we have identified errors likely to originate from other stages of the sequencing process. We use our findings to extend the flowsim pipeline with functionalities to simulate these errors, and thus enable a more realistic simulation of 454 pyrosequencing data with flowsim.
Availability: The flowsim pipeline is freely available under the General Public License from http://biohaskell.org/Applications/FlowSim.
Contact: susanne.balzer@imr.no
The effect of an educational programme on attitudes of nurses and medical residents towards the benefits of positive communication and collaboration
Authors: McCaffrey Ruth , Hayes Rose Marie , Cassell Asenath , Miller‐Reyes Sharmin , Donaldson Audeane , Ferrell Cheryl 
Published: June 2011

mccaffrey r., hayes r.m., cassell a., miller‐reyes s., donaldson a. & ferrell c. (2012) The effect of an educational programme on attitudes of nurses and medical residents towards the benefits of positive communication and collaboration. Journal of Advanced Nursing 68(2), 293–301.AbstractAims.  This article is a report of a study to determine the effect of an educational programme and to follow up weekly meetings on nurses and medical resident’s attitudes towards positive communication and collaboration.Background.  Clear and appropriate communication and interdisciplinary collaboration is critical to the delivery of quality care. Collaborative practice among all healthcare professionals creates a positive work environment, decreases costs, improves job satisfaction among nurses and improves patient care, as well as decreasing patient morbidity and mortality. Poor communication and lack of teamwork or collaboration have been cited as persistent problems in healthcare.Method.  The study was conducted in 2008 ‐ 2009 at a hospital where a new medical residency programme was beginning and nurses had no prior experience working with medical residents. A quasi‐experimental pre test, post‐test design was used. The Jefferson Scale of Attitudes towards Physician‐Nurse Collaboration and the Communication, Collaboration and Critical Thinking for Quality Patient Outcomes Survey tool measured the attitudes of 68 nurses and 47 medical residents in the areas of positive communication and collaboration.Results/Findings.  The study demonstrates that a formal educational programme and follow‐up discussions improved the attitudes of both nurses and medical residents on the Jefferson scale (medical residents t = 4·68, P = 0·001, nurses t = 4·37, P = 0·001) and on the communication scale (medical residents t = 4·23, P = 0·001, nurses t = 4·13, P = 0·001).Conclusion.  Continuing education for nurses, medical residents and other healthcare providers may assist in developing positive communication styles and promote collegiality and team work.
Is the Community Attitudes towards the Mentally Ill scale valid for use in the investigation of European nurses’ attitudes towards the mentally ill? A confirmatory factor analytic approach
Authors: Morris Roisin , Scott Philomena Anne , Cocoman Angela , Chambers Mary , Guise Veslemøy , Välimäki Maritta , Clinton Gerard 
Published: June 2011

morris r., scott p.a., cocoman a., chambers m., guise v., välimäki m. & clinton g. (2012) Is the Community Attitudes towards the Mentally Ill scale valid for use in the investigation of European nurses’ attitudes towards the mentally ill? A confirmatory factor analytic approach. Journal of Advanced Nursing 68(2), 460–470.AbstractAim.  This study aimed to assess the construct validity of the Community Attitudes towards the Mentally Ill scale in the investigation of European nurses’ attitudes towards mental illness and mental health patients.Background.  The harbouring of negative attitudes by nurses towards any patient can have implications for recovery. To gather robust evidence upon which to base information and education aimed at fostering acceptance, support and general positivity towards people with mental health illness, a valid and reliable system of data collection is required.Method.  A confirmatory factor analysis of both the original Community Attitudes towards the Mentally Ill scale and two modified versions of the scale were carried out during May ‐ June 2007 using a data set representing the responses of 858 European nurses to the scale. Data were subjected to three different confirmatory factor analyses using Maximum Likelihood estimation in the software package, Analysis of Moment Structures 7. A number of absolute, relative and incremental fit statistics were used to assess the fit of the original Community Attitudes towards the Mentally Ill scale and two modified versions to the European nursing data.Findings.  A modification of the scale was found to be most suitable for use in the investigation of European nurses’ attitudes towards mental illness and people with mental illness.Conclusion.  Further research is recommended to develop a valid and reliable research tool to specifically measure the attitudes of ‘nurses’ working across different mental healthcare facilities towards this vulnerable patient group.
A structure and process evaluation of an Australian hospital admission avoidance programme for aged care facility residents
Authors: Crilly Julia , Chaboyer Wendy , Wallis Marianne 
Published: June 2011

crilly j., chaboyer w. & wallis m. (2012) A structure and process evaluation of an Australian hospital admission avoidance programme for aged care facility residents. Journal of Advanced Nursing 68(2), 322–334.AbstractAim.  To describe and evaluate the structures and processes involved in a hospital in the Nursing Home programme.Background.  Older Australians are the largest consumers of healthcare, and as a result of the ageing process are at risk of developing hospital acquired iatrogenic complications. Hospital admission avoidance programmes that aim to provide care for patients in their own environment include Hospital in the Home and, more recently, Hospital in the Nursing Home.Methods.  In 2006, a qualitative evaluation of a nurse‐led Hospital in the Nursing Home programme using semi‐structured interviews with 19 stakeholders was undertaken. Data analysis involved using start codes and content analysis.Findings.  Effective referral and communication strategies were important for Hospital in the Nursing Home implementation. Furthermore, the Hospital in the Nursing Home programme manager had acute care and community experience and worked in an advanced practice role. These elements were integral to the programme’s operation.Conclusion.  As the population ages, reducing hospital admissions for aged‐care facility residents has the potential to improve patient outcomes. A structurally and procedurally sound programme is a key element in achieving this aim.
Assessing the effects of interactive blogging on student attitudes towards peer interaction, learning motivation, and academic achievements
Authors: Yang C. , Chang Y.‐S. 
Published: June 2011

AbstractBlogs have been increasingly used to supplement traditional classroom lectures in higher education. This paper explores the use of blogs, and how student attitudes towards online peer interaction and peer learning, as well as motivation to learn from peers, may differ when using the blog comments feature, and when students are encouraged to read and comment on each other's work. We contrast two ways blogs affect learning engagement: (1) solitary blogs as personal digital portfolios for writers; or (2) blogs used interactively to facilitate peer interaction by exposing blogging content and comments to peers. A quasi‐experiment was conducted across two semesters, involving 154 graduate and undergraduate students. The result suggests that interactive blogs, compared with isolated blogs, are associated with positive attitudes towards academic achievement in course subjects and in online peer interaction. Students showed positive motivation to learn from peer work, regardless of whether blogs were interactive or solitary.