bluuebunny/crossref_metadata_2025_split huggingface dataset:
A statistical approach for inferring the 3D structure of the genome
Authors: Varoquaux Nelle , Ay Ferhat , Noble William Stafford , Vert Jean-Philippe 
Published: June 2014

Abstract
Motivation: Recent technological advances allow the measurement, in a single Hi-C experiment, of the frequencies of physical contacts among pairs of genomic loci at a genome-wide scale. The next challenge is to infer, from the resulting DNA–DNA contact maps, accurate 3D models of how chromosomes fold and fit into the nucleus. Many existing inference methods rely on multidimensional scaling (MDS), in which the pairwise distances of the inferred model are optimized to resemble pairwise distances derived directly from the contact counts. These approaches, however, often optimize a heuristic objective function and require strong assumptions about the biophysics of DNA to transform interaction frequencies to spatial distance, and thereby may lead to incorrect structure reconstruction.
Methods: We propose a novel approach to infer a consensus 3D structure of a genome from Hi-C data. The method incorporates a statistical model of the contact counts, assuming that the counts between two loci follow a Poisson distribution whose intensity decreases with the physical distances between the loci. The method can automatically adjust the transfer function relating the spatial distance to the Poisson intensity and infer a genome structure that best explains the observed data.
Results: We compare two variants of our Poisson method, with or without optimization of the transfer function, to four different MDS-based algorithms—two metric MDS methods using different stress functions, a non-metric version of MDS and ChromSDE, a recently described, advanced MDS method—on a wide range of simulated datasets. We demonstrate that the Poisson models reconstruct better structures than all MDS-based methods, particularly at low coverage and high resolution, and we highlight the importance of optimizing the transfer function. On publicly available Hi-C data from mouse embryonic stem cells, we show that the Poisson methods lead to more reproducible structures than MDS-based methods when we use data generated using different restriction enzymes, and when we reconstruct structures at different resolutions.
Availability and implementation: A Python implementation of the proposed method is available at http://cbio.ensmp.fr/pastis.
Contact: william-noble@uw.edu or jean-philippe.vert@mines.org
Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation
Authors: Äijö Tarmo , Butty Vincent , Chen Zhi , Salo Verna , Tripathi Subhash , Burge Christopher B. , Lahesmaa Riitta , Lähdesmäki Harri 
Published: June 2014

AbstractMotivation: Gene expression profiling using RNA-seq is a powerful technique for screening RNA species’ landscapes and their dynamics in an unbiased way. While several advanced methods exist for differential expression analysis of RNA-seq data, proper tools to anal.yze RNA-seq time-course have not been proposed.Results: In this study, we use RNA-seq to measure gene expression during the early human T helper 17 (Th17) cell differentiation and T-cell activation (Th0). To quantify Th17-specific gene expression dynamics, we present a novel statistical methodology, DyNB, for analyzing time-course RNA-seq data. We use non-parametric Gaussian processes to model temporal correlation in gene expression and combine that with negative binomial likelihood for the count data. To account for experiment-specific biases in gene expression dynamics, such as differences in cell differentiation efficiencies, we propose a method to rescale the dynamics between replicated measurements. We develop an MCMC sampling method to make inference of differential expression dynamics between conditions. DyNB identifies several known and novel genes involved in Th17 differentiation. Analysis of differentiation efficiencies revealed consistent patterns in gene expression dynamics between different cultures. We use qRT-PCR to validate differential expression and differentiation efficiencies for selected genes. Comparison of the results with those obtained via traditional timepoint-wise analysis shows that time-course analysis together with time rescaling between cultures identifies differentially expressed genes which would not otherwise be detected.Availability: An implementation of the proposed computational methods will be available at http://research.ics.aalto.fi/csb/software/Contact: tarmo.aijo@aalto.fi or harri.lahdesmaki@aalto.fiSupplementary information: Supplementary data are available at Bioinformatics online.
Detecting differential protein expression in large-scale population proteomics
Authors: Ryu So Young , Qian Wei-Jun , Camp David G. , Smith Richard D. , Tompkins Ronald G. , Davis Ronald W. , Xiao Wenzhong 
Published: June 2014

AbstractMotivation: Mass spectrometry (MS)-based high-throughput quantitative proteomics shows great potential in large-scale clinical biomarker studies, identifying and quantifying thousands of proteins in biological samples. However, there are unique challenges in analyzing the quantitative proteomics data. One issue is that the quantification of a given peptide is often missing in a subset of the experiments, especially for less abundant peptides. Another issue is that different MS experiments of the same study have significantly varying numbers of peptides quantified, which can result in more missing peptide abundances in an experiment that has a smaller total number of quantified peptides. To detect as many biomarker proteins as possible, it is necessary to develop bioinformatics methods that appropriately handle these challenges.Results: We propose a Significance Analysis for Large-scale Proteomics Studies (SALPS) that handles missing peptide intensity values caused by the two mechanisms mentioned above. Our model has a robust performance in both simulated data and proteomics data from a large clinical study. Because varying patients’ sample qualities and deviating instrument performances are not avoidable for clinical studies performed over the course of several years, we believe that our approach will be useful to analyze large-scale clinical proteomics data.Availability and Implementation: R codes for SALPS are available at http://www.stanford.edu/%7eclairesr/software.html .Contact: wenzhong.xiao@mgh.harvard.eduSupplementary information: Supplementary materials are available at Bioinformatics online.
NetBioV: an R package for visualizing large network data in biology and medicine
Authors: Tripathi Shailesh , Dehmer Matthias , Emmert-Streib Frank 
Published: June 2014

AbstractSummary: NetBioV (Network Biology Visualization) is an R package that allows the visualization of large network data in biology and medicine. The purpose of NetBioV is to enable an organized and reproducible visualization of networks by emphasizing or highlighting specific structural properties that are of biological relevance.Availability and implementation: NetBioV is freely available for academic use. The package has been tested for R 2.14.2 under Linux, Windows and Mac OS X. It is available from Bioconductor.Contact: v@bio-complexity.comSupplementary information: Supplementary data are available at Bioinformatics online.
BioBlend.objects: metacomputing with Galaxy
Authors: Leo Simone , Pireddu Luca , Cuccuru Gianmauro , Lianas Luca , Soranzo Nicola , Afgan Enis , Zanetti Gianluigi 
Published: June 2014

AbstractSummary: BioBlend.objects is a new component of the BioBlend package, adding an object-oriented interface for the Galaxy REST-based application programming interface. It improves support for metacomputing on Galaxy entities by providing higher-level functionality and allowing users to more easily create programs to explore, query and create Galaxy datasets and workflows.Availability and implementation: BioBlend.objects is available online at https://github.com/afgane/bioblend . The new object-oriented API is implemented by the galaxy/objects subpackage.Contact: simone.leo@crs4.it
Incidence of Herpes Simplex Virus Type 2 Infections in Africa: A Systematic Review
Authors: Rajagopal Sharanya , Magaret Amalia , Mugo Nelly , Wald Anna 
Published: June 2014

AbstractThe burden of HSV type 2 varies substantially by region, with the highest incidence and prevalence in sub-Saharan Africa. We undertook a systematic review to identify studies reporting prospective data on incidence rates in men and women in Africa. Of 18 eligible studies, 7 were conducted in high-risk populations. Among women, incidence rates appeared to be higher in those with high-risk sexual behavior, with rates ranging from 3 to 23 per 100 person-years. In contrast, incidence rates in men appeared to be lower, ranging from 1 to 12 per 100 person-years. Risk factors for HSV-2 in women included prevalent human immunodeficiency virus (HIV) infection, younger age at sexual initiation, and sexual activity. Among men, condom use and circumcision had a protective effect, whereas prevalent HIV increased the risk of HSV-2 acquisition. This review draws attention to the high HSV-2 acquisition rates reported in Africa, thereby identifying an efficient setting for preventative HSV-2 vaccine trials.
Invasive Haemophilus influenzae Disease in Adults ≥65 Years, United States, 2011
Authors: Blain Amy , MacNeil Jessica , Wang Xin , Bennett Nancy , Farley Monica M. , Harrison Lee H. , Lexau Catherine , Miller Lisa , Nichols Megin , Petit Susan , Reingold Arthur , Schaffner William , Thomas Ann , Clark Thomas , Cohn Amanda , Briere Elizabeth 
Published: June 2014

Abstract
Background.  Since the introduction of the Haemophilus influenzae serotype b vaccine, H influenzae epidemiology has shifted. In the United States, the largest burden of disease is now in adults aged ≥65 years. However, few data exist on risk factors for disease severity and outcome in this age group.
Methods.  A retrospective case-series review of invasive H influenzae infections in patients aged ≥65 years was conducted for hospitalized cases reported to Active Bacterial Core surveillance in 2011.
Results.  There were 299 hospitalized cases included in the analysis. The majority of cases were caused by nontypeable H influenzae, and the overall case fatality ratio (CFR) was 19.5%. Three or more underlying conditions were present in 63% of cases; 94% of cases had at least 1. Patients with chronic heart conditions (congestive heart failure, coronary artery disease, and/or atrial fibrillation) (odds ratio [OR], 3.27; 95% confidence interval [CI], 1.65–6.46), patients from private residences (OR, 8.75; 95% CI, 2.13–35.95), and patients who were not resuscitate status (OR, 2.72; 95% CI, 1.31–5.66) were more likely to be admitted to the intensive care unit (ICU). Intensive care unit admission (OR, 3.75; 95% CI, 1.71–8.22) and do not resuscitate status (OR, 12.94; 95% CI, 4.84–34.55) were significantly associated with death.
Conclusions.  Within this age group, burden of disease and CFR both increased significantly as age increased. Using ICU admission as a proxy for disease severity, our findings suggest several conditions increased risk of disease severity and patients with severe disease were more likely to die. Further research is needed to determine the most effective approach to prevent H influenzae disease and mortality in older adults.
Down-regulation of MicroRNA-21 Is Involved in the Propofol-induced Neurotoxicity Observed in Human Stem Cell–derived Neurons
Authors: Twaroski Danielle M. , Yan Yasheng , Olson Jessica M. , Bosnjak Zeljko J. , Bai Xiaowen 
Published: June 2014

Abstract

Background:
Recent studies in various animal models have suggested that anesthetics such as propofol, when administered early in life, can lead to neurotoxicity. These studies have raised significant safety concerns regarding the use of anesthetics in the pediatric population and highlight the need for a better model to study anesthetic-induced neurotoxicity in humans. Human embryonic stem cells are capable of differentiating into any cell type and represent a promising model to study mechanisms governing anesthetic-induced neurotoxicity.

Methods:
Cell death in human embryonic stem cell–derived neurons was assessed using terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate in situ nick end labeling staining, and microRNA expression was assessed using quantitative reverse transcription polymerase chain reaction. miR-21 was overexpressed and knocked down using an miR-21 mimic and antagomir, respectively. Sprouty 2 was knocked down using a small interfering RNA, and the expression of the miR-21 targets of interest was assessed by Western blot.

Results:
Propofol dose and exposure time dependently induced significant cell death (n = 3) in the neurons and down-regulated several microRNAs, including miR-21. Overexpression of miR-21 and knockdown of Sprouty 2 attenuated the increase in terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate in situ nick end labeling–positive cells following propofol exposure. In addition, miR-21 knockdown increased the number of terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate in situ nick end labeling–positive cells by 30% (n = 5). Finally, activated signal transducer and activator of transcription 3 and protein kinase B (Akt) were down-regulated, and Sprouty 2 was up-regulated following propofol exposure (n = 3).

Conclusions:
These data suggest that (1) human embryonic stem cell–derived neurons represent a promising in vitro human model for studying anesthetic-induced neurotoxicity, (2) propofol induces cell death in human embryonic stem cell–derived neurons, and (3) the propofol-induced cell death may occur via a signal transducer and activator of transcription 3/miR-21/Sprouty 2–dependent mechanism.
Analysis of new product development research: 1998-2009
Authors: Kalluri Vinayak , Kodali Rambabu 
Published: June 2014

Purpose
– The purpose of this paper is to present a systematic review and analysis of existing research articles on new product development (NPD) published in the 12-year period starting from 1998 to 2009.

Design/methodology/approach
– To explore the articles related to NPD, four key words namely new product, product design, product development and product innovation were used in combination of title or abstract or keyword of the articles through several knowledge databases. The abstracts of journal papers were read and a decision as to whether article belongs to any NPD research issue or not was made. In total, 1,127 research articles were categorized systematically and then analyzed on various principal NPD information groups.

Findings
– Analysis of selected articles led to a certain level of dispersion in the publication of NPD research in different journals. It is found that more attention needs to be on knowledge and creativity management, communication and information transfer in any NPD process.

Originality/value
– By observing extended literature from authors reviewing articles from various journals, growth in research, and variety of topics covered in NPD, a broad systematic multi journal review of NPD literature is clearly overdue. The authors have developed a comprehensive listing of publications on NPD where they have classified the surveyed papers according to various principal NPD information groups like: published year, NPD research stream, type of organization studied (industrial/consumer/service), level of innovation (high/moderate/low), NPD focus on frameworks, performance perspective (success, failure or both), NPD research design (conceptual/empirical and qualitative/quantitative) and NPD relevant best practice element. Based on the classification scheme, the issues were analyzed from the system's perspective and their implications to NPD research.
Relative leader-member exchange and employee voice
Authors: Zhao Hongdan 
Published: June 2014

Purpose– This study aims to examine the effect of relative leader-member exchange (RLMX) on employee voice by developing a moderated mediation model. The model focuses on the mediating role of affective commitment underpinning the relationship between RLMX and employee voice, and the moderating role of Chinese traditionality in influencing the mediation.Design/methodology/approach– We tested the model with data from 358 supervisor-subordinate dyads in a large Chinese company. Employees and their immediate supervisors provided data on separate questionnaires and on different occasions. And then, we used an identification number to match each employee questionnaire with the response of his/her immediate supervisor.Findings– Results indicated that affective commitment fully mediated the positive relationship between RLMX and employee voice, even after controlling for personal leader-member exchange (LMX) quality. We also found that Chinese traditionality moderated the mediated relationship between RLMX and employee voice via affective commitment, such that the mediation was stronger for people lower, rather than higher, in Chinese traditionality.Research limitations/implications– Testing the moderated mediation model helps to advance our theoretical understanding of the psychological mechanisms that underlie the effect of RLMX on employees’ behaviour.Originality/value– This empirical study provides preliminary evidence of the mediating role of affective commitment in the positive relationship between RLMX and employee voice. Our moderated mediation model also extends the existing finding by adding substantive moderators (Chinese traditionality) to explain how the effect of RLMX on employees’ behaviours unfolds.
Psychological ownership, organization-based self-esteem and positive organizational behaviors
Authors: Pan Xiao-Fu , Qin Qiwen , Gao Fei 
Published: June 2014

Purpose– The purpose of this paper is to explore the effect of organizational psychological ownership (OPO) and organization-based self-esteem (OBSE) on positive organizational behaviors (POBs).Design/methodology/approach– Based on empirical survey, 2,566 employees from 45 production enterprises in China were surveyed by a self-designed questionnaire on OPO, OBSE and POB. Then, the methods of correlation analysis, multiple regressions, impact effect and path analysis were used to verify the research hypothesis.Findings– The results showed that POB is positively related to OPO and OBSE, and that OPO and OBSE are positive predictors of POBs. The results also demonstrated that OBSE has partial mediating effects on OPO and POB. In particular, psychological ownership has a significant impact on each sub-factor of POB, while OBSE has a remarkable effect on the behavior of devotion and interpersonal harmony.Research limitations/implications– This is a non-experimental field study and as such inferences about causality are limited, and there is a possibility that the results may be influenced by common method variance.Practical implications– The findings of the present study reveal that to strengthen employees’ POBs, manager should enhance employees’ OPO and OBSE, and therefore the organizational performance and the individual efficacy will be improved.Originality/value– This is the first research which studies the relationship among OPO, POB and OBSE under the background of China.
Exploring the direct and indirect effects of CSR on organizational commitment
Authors: Anthony Wong IpKin , Hong Gao Jennifer 
Published: June 2014

Purpose– The purpose of this study is to investigate the effect of perceived corporate social responsibility (CSR) on employees’ affective commitment through the mediating role of perceived corporate culture.Design/methodology/approach– Data were collected by means of self-administered survey. A total of 379 complete responses were obtained from tourism and hospitality organizations in China. The proposed relationships were tested using structural equation modeling in four nested models.Findings– Results show that CSR to employees and CSR to customers are fully mediated by employee development, harmony and customer orientation of the corporate culture, while CSR to stakeholders is partially mediated.Practical implications– The findings also suggest that the literature should reconsider how CSR initiatives could pinpoint a specific dimension in developing loyal employees. This study also shows that employees are social actors who seek a corporate culture that best suits their self-interest; hence, they are more committed to an organization particularly in respect to employee development and social harmony.Originality/value– This study adds to the literature by showing that not all CSR efforts would directly lead to employee commitment. It shows that the CSR-to-employee and CSR-to-customer dimensions play the most salient roles in nurturing a corporate culture that is perceived to focus on employee development, harmony, customers and innovation.
Vulnerability assessment of earthquake prone communities in Baluchistan
Authors: Syed Ainuddin , Kumar Routray Jayant 
Published: June 2014

Purpose
– The purpose of this paper is to assess the vulnerability of communities prone to earthquake hazards in Baluchistan at the community and household levels and identify the determinants accounting for the vulnerability of the communities. Baluchistan is vulnerable to potential seismic risk and has recently suffered huge economic and property losses due to the October 2008 earthquake.

Design/methodology/approach
– The study is based on household surveys, field observations, key informant interviews and focus-group discussions for the assessment of community vulnerability to earthquakes.

Findings
– The analysis revealed that the community is vulnerable to earthquake hazards both at the community and household levels. The logistic regression model identified three variables, namely, ownership of residential unit, family size and household income, as the most important factors in influencing community vulnerability to earthquake hazards.

Practical implications
– The paper may help emergency managers, policymakers and local government authorities to implement building codes, urban planning by-laws and projects and activities to empower communities for disaster preparedness and disaster risk reduction.

Originality/value
– The paper concludes that for earthquake safety, building regulations and spatial planning by-laws should be implemented and monitored rigorously. Community preparedness is essential for enhancing people’s awareness against future earthquake hazards in the area.
Designing small-scale sport events in the countryside
Authors: Bertella Giovanna 
Published: June 2014

Purpose– The purpose of this paper is to develop and illustrate a conceptual tool for the planning of rural sport events.Design/methodology/approach– The proposed model is elaborated based on theoretical contributions from the tourism and event literature, and illustrated with an empirical case concerning a sport and cultural event arranged in the Chianti countryside in Italy.Findings– The results suggest that a form of professionalization of the event design process, understood as the search of high-quality experience for the local population and the tourists, is feasible within the socialization style of model typical of small events.Research limitations/implications– This study is based on selected theoretical contributions, and on a limited empirical investigation. Further research is needed in order to better understand the event design process, and in particular the processes of communication and involvement among the different community members.Practical implications– The practical implications are related to the possible use of the developed model.Originality/value– The theoretical contribution of this study is relative to the use of the concept of tourism experience, and more specifically of the embodied tourism experience, within the context of event design.