bluuebunny/crossref_metadata_2025_split huggingface dataset:
Be Clear: A New Intensive Speech Treatment for Adults With Nonprogressive Dysarthria
Authors: Park Stacie , Theodoros Deborah , Finch Emma , Cardell Elizabeth 
Published: February 2016

PurposeThis article describes the effects of a new intensive dysarthria treatment program (Be Clear) on speech intelligibility in adults with dysarthria secondary to stroke and traumatic brain injury.MethodA small group–repeated measures research design was used to examine the effects of treatment on the speech of 8 participants with nonprogressive dysarthria. Treatment consisted of a 1-hr prepractice session followed by 1-hr therapy sessions, 4 times per week, for 4 weeks (16 sessions). Paired-comparison ratings of speech intelligibility served as the primary outcome measure for the study. Perceptual data, quality of life, and communication partner opinion were obtained at 3 time intervals: (a) prior to treatment, (b) immediately posttreatment, and (c) 1–3 months posttreatment.ResultsFollowing treatment, group data demonstrated substantial improvements in speech intelligibility as perceived by naive listeners on a paired-comparison rating task. Word intelligibility was clinically significantly improved posttreatment and sentence intelligibility demonstrated statistically significant improvement. Communication partner ratings of speech intelligibility and overall communicative function were statistically significantly improved posttreatment.ConclusionsThe results of this study suggest that this new intensive treatment may have potential as an effective intervention for nonprogressive dysarthria. However, controlled studies are required to establish treatment efficacy.
„Was ihr wollt“, Ergebnisse einer empirischen Bedarfsanalyse zur Verbesserung der Vereinbarkeit von Familie und Beruf bei Ärztinnen und Ärzten
Authors: Jerg-Bretzke L. , Krüsmann P. , Traue H. , Limbrecht-Ecklundt K. 
Published: February 2016

Zusammenfassung
Ziel der Studie: Kliniken stehen vermehrt der Anforderung gegenüber für Ärztinnen und Ärzte Arbeitsbedingungen zu schaffen, die eine Vereinbarkeit von Familie und Beruf ermöglichen. Dies ist gleichzeitig auch als Chance zu betrachten, sich als Arbeitgeber von anderen Kliniken abzuheben.
Methode: N=120 Ärztinnen und Ärzte der Medizinischen Fakultät sowie N=679 Studierende der Humanmedizin im vorklinischen und klinischen Abschnitt wurden online befragt. Im Fokus dieser Studie stand die Erfassung des Veränderungsbedarfs an Kliniken zur Verbesserung der Vereinbarkeit von Familie und Beruf.
Ergebnisse: Hypothesenkonform zeigte sich in der Work-Family/Family-Work Conflict Scale (WFC/FWC) eine erschwerte Vereinbarkeit von Familie und Tätigkeit nach Eintritt in das Berufsleben – insbesondere mit Kind. Besonders die Arbeitsunterbrechung im Notfall, Teilzeitregelungen oder Notfallbetreuung für Kinder schätzen über 90% Befragten als wichtiges Instrument zur Verbesserung der Vereinbarkeit von Familie und Beruf ein. Zusätzlich wünschen sich Ärztinnen und Ärzte, dass ihre Vorgesetzten Vereinbarkeitsthemen aktiv unterstützen.
Schlussfolgerung: Die Analyse der Vereinbarkeit von Familie und Tätigkeit zeigt Handlungsbedarf in den untersuchten Stichproben. Durch die erfassten Maßnahmen, die als entlastend beurteilt werden, können konkrete Handlungsschritte für Kliniken abgeleitet werden. Die Analyse des WFC/FWC stellt eine Möglichkeit dar, standardisiert die Belastung durch Tätigkeit in der Familie und vice versa zu erfassen.
Integration of string and de Bruijn graphs for genome assembly
Authors: Huang Yao-Ting , Liao Chen-Fu 
Published: February 2016

Abstract
Motivation: String and de Bruijn graphs are two graph models used by most genome assemblers. At present, none of the existing assemblers clearly outperforms the others across all datasets. We found that although a string graph can make use of entire reads for resolving repeats, de Bruijn graphs can naturally assemble through regions that are error-prone due to sequencing bias.
Results: We developed a novel assembler called StriDe that has advantages of both string and de Bruijn graphs. First, the reads are decomposed adaptively only in error-prone regions. Second, each paired-end read is extended into a long read directly using an FM-index. The decomposed and extended reads are used to build an assembly graph. In addition, several essential components of an assembler were designed or improved. The resulting assembler was fully parallelized, tested and compared with state-of-the-art assemblers using benchmark datasets. The results indicate that contiguity of StriDe is comparable with top assemblers on both short-read and long-read datasets, and the assembly accuracy is high in comparison with the others.
Availability and implementation: https://github.com/ythuang0522/StriDe
Contact: ythuang@cs.ccu.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data
Authors: De Sano Luca , Caravagna Giulio , Ramazzotti Daniele , Graudenzi Alex , Mauri Giancarlo , Mishra Bud , Antoniotti Marco 
Published: February 2016

Abstract
Motivation: We introduce TRanslational ONCOlogy (TRONCO), an open-source R package that implements the state-of-the-art algorithms for the inference of cancer progression models from (epi)genomic mutational profiles. TRONCO can be used to extract population-level models describing the trends of accumulation of alterations in a cohort of cross-sectional samples, e.g. retrieved from publicly available databases, and individual-level models that reveal the clonal evolutionary history in single cancer patients, when multiple samples, e.g. multiple biopsies or single-cell sequencing data, are available. The resulting models can provide key hints for uncovering the evolutionary trajectories of cancer, especially for precision medicine or personalized therapy.
Availability and implementation: TRONCO is released under the GPL license, is hosted at http://bimib.disco.unimib.it/ (Software section) and archived also at bioconductor.org.
Contact: tronco@disco.unimib.it
Supplementary information: Supplementary data are available at Bioinformatics online.
ParDRe: faster parallel duplicated reads removal tool for sequencing studies
Authors: González-Domínguez Jorge , Schmidt Bertil 
Published: February 2016

Abstract
Summary: Current next generation sequencing technologies often generate duplicated or near-duplicated reads that (depending on the application scenario) do not provide any interesting biological information but can increase memory requirements and computational time of downstream analysis. In this work we present ParDRe, a de novo parallel tool to remove duplicated and near-duplicated reads through the clustering of Single-End or Paired-End sequences from fasta or fastq files. It uses a novel bitwise approach to compare the suffixes of DNA strings and employs hybrid MPI/multithreading to reduce runtime on multicore systems. We show that ParDRe is up to 27.29 times faster than Fulcrum (a representative state-of-the-art tool) on a platform with two 8-core Sandy-Bridge processors.
Availability and implementation: Source code in C ++ and MPI running on Linux systems as well as a reference manual are available at https://sourceforge.net/projects/pardre/
Contact: jgonzalezd@udc.es
A zero-inflated Poisson model for insertion tolerance analysis of genes based on Tn-seq data
Authors: Liu Fangfang , Wang Chong , Wu Zuowei , Zhang Qijing , Liu Peng 
Published: February 2016

AbstractMotivation: Transposon insertion sequencing (Tn-seq) is an emerging technology that combines transposon mutagenesis with next-generation sequencing technologies for the identification of genes related to bacterial survival. The resulting data from Tn-seq experiments consist of sequence reads mapped to millions of potential transposon insertion sites and a large portion of insertion sites have zero mapped reads. Novel statistical method for Tn-seq data analysis is needed to infer functions of genes on bacterial growth.Results: In this article, we propose a zero-inflated Poisson model for analyzing the Tn-seq data that are high-dimensional and with an excess of zeros. Maximum likelihood estimates of model parameters are obtained using an expectation–maximization (EM) algorithm, and pseudogenes are utilized to construct appropriate statistical tests for the transposon insertion tolerance of normal genes of interest. We propose a multiple testing procedure that categorizes genes into each of the three states, hypo-tolerant, tolerant and hyper-tolerant, while controlling the false discovery rate. We evaluate the proposed method with simulation studies and apply the proposed method to a real Tn-seq data from an experiment that studied the bacterial pathogen, Campylobacter jejuni.Availability and implementation: We provide R code for implementing our proposed method at http://github.com/ffliu/TnSeq. A user’s guide with example data analysis is also available there.Contact: pliu@iastate.eduSupplementary information: Supplementary data are available at Bioinformatics online.
RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data
Authors: Zhan Xiaowei , Hu Youna , Li Bingshan , Abecasis Goncalo R. , Liu Dajiang J. 
Published: February 2016

Abstract
Motivation: Next-generation sequencing technologies have enabled the large-scale assessment of the impact of rare and low-frequency genetic variants for complex human diseases. Gene-level association tests are often performed to analyze rare variants, where multiple rare variants in a gene region are analyzed jointly. Applying gene-level association tests to analyze sequence data often requires integrating multiple heterogeneous sources of information (e.g. annotations, functional prediction scores, allele frequencies, genotypes and phenotypes) to determine the optimal analysis unit and prioritize causal variants. Given the complexity and scale of current sequence datasets and bioinformatics databases, there is a compelling need for more efficient software tools to facilitate these analyses. To answer this challenge, we developed RVTESTS, which implements a broad set of rare variant association statistics and supports the analysis of autosomal and X-linked variants for both unrelated and related individuals. RVTESTS also provides useful companion features for annotating sequence variants, integrating bioinformatics databases, performing data quality control and sample selection. We illustrate the advantages of RVTESTS in functionality and efficiency using the 1000 Genomes Project data.
Availability and implementation: RVTESTS is available on Linux, MacOS and Windows. Source code and executable files can be obtained at https://github.com/zhanxw/rvtests
Contact: zhanxw@gmail.com; goncalo@umich.edu; dajiang.liu@outlook.com
Supplementary information: Supplementary data are available at Bioinformatics online.
solarius: an R interface to SOLAR for variance component analysis in pedigrees
Authors: Ziyatdinov Andrey , Brunel Helena , Martinez-Perez Angel , Buil Alfonso , Perera Alexandre , Soria Jose Manuel 
Published: February 2016

Abstract
Summary: The open source environment R is one of the most widely used software for statistical computing. It provides a variety of applications including statistical genetics. Most of the powerful tools for quantitative genetic analyses are stand-alone free programs developed by researchers in academia. SOLAR is one of the standard software programs to perform linkage and association mappings of the quantitative trait loci (QTLs) in pedigrees of arbitrary size and complexity. solarius allows the user to exploit the variance component methods implemented in SOLAR. It automates such routine operations as formatting pedigree and phenotype data. It parses also the model output and contains summary and plotting functions for exploration of the results. In addition, solarius enables parallel computing of the linkage and association analyses that makes the calculation of genome-wide scans more efficient.
Availability and implementation: solarius is available on CRAN and on GitHub https://github.com/ugcd/solarius.
Contact: aziyatdinov@santpau.cat
Empirical evidence for different cognitive effects in explaining the attribution of marine range shifts to climate change
Authors: van Putten Ingrid E. , Frusher Stewart , Fulton Elizabeth A. , Hobday Alistair J. , Jennings Sarah M. , Metcalf Sarah , Pecl Gretta T. ,   Handling editor: Sarah Kraak
Published: February 2016

AbstractThe changing geographical distribution of species, or range shift, is one of the better documented fingerprints of climate change in the marine environment. Range shifts may also lead to dramatic changes in the distribution of economic, social, and cultural opportunities. These challenge marine resource users' capacity to adapt to a changing climate and managers' ability to implement adaptation plans. In particular, a reluctance to attribute marine range shift to climate change can undermine the effectiveness of climate change communications and pose a potential barrier to successful adaptation. Attribution is a known powerful predictor of behavioural intention. Understanding the cognitive processes that underpin the formation of marine resource users' beliefs about the cause of observed marine range shift phenomena is therefore an important topic for research. An examination of the attribution by marine resource users of three types of range shifts experienced in a marine climate change hotspot in southeast Australia to various climate and non-climate drivers indicates the existence of at least three contributing cognitions. These are: (i) engrained mental representations of environmental phenomena, (ii) scientific complexity in the attribution pathway, and (iii) dissonance from the positive or negative nature of the impact. All three play a part in explaining the complex pattern of attribution of marine climate change range shifts, and should be considered when planning for engagement with stakeholders and managers around adaptation to climate change.
FRB repetition and non-Poissonian statistics
Authors: Connor Liam , Pen Ue-Li , Oppermann Niels 
Published: February 2016

Abstract
We discuss some of the claims that have been made regarding the statistics of fast radio bursts (FRBs). In an earlier Letter, we conjectured that flicker noise associated with FRB repetition could show up in non-cataclysmic neutron star emission models, like supergiant pulses. We show how the current limits of repetition would be significantly weakened if their repeat rate really were non-Poissonian and had a pink or red spectrum. Repetition and its statistics have implications for observing strategy, generally favouring shallow wide-field surveys, since in the non-repeating scenario survey depth is unimportant. We also discuss the statistics of the apparent latitudinal dependence of FRBs, and offer a simple method for calculating the significance of this effect. We provide a generalized Bayesian framework for addressing this problem, which allows for direct model comparison. It is shown how the evidence for a steep latitudinal gradient of the FRB rate is less strong than initially suggested and simple explanations like increased scattering and sky temperature in the plane are sufficient to decrease the low-latitude burst rate, given current data. The reported dearth of bursts near the plane is further complicated if FRBs have non-Poissonian repetition, since in that case the event rate inferred from observation depends on observing strategy.
Genome-wide histone modification patterns inKluyveromyces Lactisreveal evolutionary adaptation of a heterochromatin-associated mark
Authors: Bean Angela , Weiner Assaf , Hughes Amanda , Itskovits Eyal , Friedman Nir , Rando Oliver J. 
Published: February 2016

AbstractThe packaging of eukaryotic genomes into nucleosomes plays critical roles in all DNA-templated processes, and chromatin structure has been implicated as a key factor in the evolution of gene regulatory programs. While the functions of many histone modifications appear to be highly conserved throughout evolution, some well-studied modifications such as H3K9 and H3K27 methylation are not found in major model organisms such asSaccharomyces cerevisiae, while other modifications gain/lose regulatory functions during evolution. To study such a transition we focused on H3K9 methylation, a heterochromatin mark found in metazoans and in the fission yeastS. pombe, but which has been lost in the lineage leading to the model budding yeastS. cerevisiae. We show that this mark is present in the relatively understudied yeastKluyveromyces lactis, a Hemiascomycete that diverged fromS. cerevisiaeprior to the whole-genome duplication event that played a key role in the evolution of a primarily fermentative lifestyle. We mapped genome-wide patterns of H3K9 methylation as well as several conserved modifications. We find that well-studied modifications such as H3K4me3, H3K36me3, and H3S10ph exhibit generally conserved localization patterns. Interestingly, we show H3K9 methylation inK. lactisprimarily occurs over highly-transcribed regions, including both Pol2 and Pol3 transcription units. We identified the H3K9 methylase as the ortholog ofSet6, whose function inS. cerevisiaeis obscure. Functionally, we show that deletion ofKlSet6does not affect highly H3K9me3-marked genes, providing another example of a major disconnect between histone mark localization and function. Together, these results shed light on surprising plasticity in the function of a widespread chromatin mark.
An explanatory model of attitudinal fear of HIV/AIDS testing in the construction industry
Authors: Bowen Paul , Govender Rajen , Edwards Peter , Cattell Keith 
Published: February 2016

Purpose
– Prevalence of HIV/AIDS infection in the South African construction industry exceeds that of most other economic sectors. Voluntary counselling and testing is pivotal in combatting the spread of the disease. Little is known about the attitudinal fear of testing among construction workers, and the determinants thereof. The purpose of this paper is to address these shortcomings.

Design/methodology/approach
– A conceptual integrated model of fear of testing is proposed. Demographic characteristics and behavioural and cognitive factors are posited to explain attitudinal fear of testing. Regression analysis and structural equation modelling are used to test the model, using data gathered from 512 site-based participants in a questionnaire survey.

Findings
– Prejudice and lifestyle risk are the terminal predictors of fear of testing. Prejudice is determined by education level and HIV/AIDS transmission knowledge. Knowledge is predicted by education level and ethnicity. Lifestyle risk is determined by age, gender, harmful substance use, and knowledge. Harmful substance use is determined by age, gender, ethnicity, and employment type. The inter-relationship between knowledge about HIV/AIDS, prejudice towards HIV+ persons, and fear of testing is complex and nuanced.

Practical implications
– Intervention strategies by firms should positively address attitudinal fear of testing. Employers should ensure that effective communication is established with workers. Interventions relating to harmful substance use by employees need particular attention. Awareness campaigns should be sensitive to ethnic and cultural values, and to inter-generational differences.

Originality/value
– Harmful substance use and knowledge about HIV/AIDS transmission are indirect predictors of fear of testing. Education and ethnicity are critical dimensions of knowledge. The complex inter-relationship between knowledge, prejudice, lifestyle risk, and fear of testing is highlighted, providing guidelines for intervention management.
Agile, adaptive leaders
Authors: McPherson Blair 
Published: February 2016

Purpose
– This paper aims to illustrate what agile management looks like, why it is increasingly necessary and how it can be developed and supported.

Design/methodology/approach
– This is a case study from a large complex organization (Lancashire County Council) showing how management restructuring increased managers
'
spans of responsibility, moving them out of their professional comfort zones, and how in response, the organization identified, supported and developed agile leadership.

Findings
– Agile, adaptive leaders are able to move quickly and easily from one area of management to another, able to manage a diverse range of complex services and able to quickly and smoothly adapt to a fast-changing business environment.

Research limitations/implications
– This is a case study from a large complex public sector organization, but the need for agile and adaptive leaders applies equally to the private and not-for-profit sectors.

Originality/value
– This paper offers insights into the changing role of management across a diverse range of services and provides an example of how organizations can successfully respond.
Improving communication among healthcare workers: a controlled study
Authors: Eklof Mats , Ahlborg Jr Gunnar 
Published: February 2016

Purpose
– This paper aims to test the effects on aspects of workplace communication relevant to teamwork, and social support, in hospital units, of a dialog training (DT) intervention based on knowledge of key quality aspects related to interpersonal work-related communication among healthcare workers.

Design/methodology/approach
– A cluster randomized controlled study conducted among approximately 300 Swedish healthcare workers employed at ten hospital units. Workplace communication was measured in the form of participative safety, trust/openness, and social support. Effects were tested at three-month and six-month follow-ups. Repeated measurements were made.

Findings
– The results indicated that DT had a positive influence on participative safety and social support from managers. A positive tendency was observed for trust/openness.

Originality/value
– Developing and practicing good staff communication in hospital units is an important area for interventions designed to improve job performance and health.