bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between use of the progestin Depot Medroxyprogesterone Acetate and Cervicovaginal Lavage Proinflammatory Cytokines among HIV-1 and HSV-2 co-infected African women: a case control study
Authors: Walong Edwin , Gontier Christopher , Jaoko Walter , Bukusi Elizabeth 
Published: March 2016

ABSTRACTBackgroundUse of the progestin contraceptive Depot Medroxyprogesterone Acetate (DMPA) by HIV 1 infected women is associated with increased female to male transmission of HIV. Mucosal innate immune activation has been proposed as a likely mechanism. To establish the effect of DMPA upon mucosal immune activation, this study sought to evaluate the concentrations of 5 proinflammatory and the regulatory cytokine IL 10 in cervicovaginal lavage fluid.MethodsThis was a case control study, 70 participants were recruited, comprising of 35 asymptomatic ART naïve HIV positive women on DMPA recruited as cases and 35 age matched asymptomatic ART naive HIV positive women not on contraceptives recruited as controls. Peripheral blood CD4 and total lymphocyte counts, High vaginal swab microscopy, endocervical smears and cervical cytology were performed for each participant. Concentrations of six proinflammatory cytokines were measured on cervicovaginal lavage by multiplex cytometric bead array.ResultsThe mean age of cases was 26.8 years and 30 years for controls. Total lymphocyte counts and CD4 cell counts were significantly higher among cases (p=0.02 and 0.004 respectively). HSV 2 prevalence as determined by ELISA was higher (p=0.034 among cases. The concentrations of the cytokines IL 1β, IL 6, IL 8, IL 12p70 and TNF α were lower among cases, with IL 1β being statistically significant (p=0.046). Concentrations of IL 10 was higher among cases (p=0.022). On multivariate analysis, reduction in IL 1β and IL 8 were associated with the duration of DMPA use (p=0.015 and 0.041 respectively). Inclusion of HSV 2 into the multivariate models showed elevation of all cytokines measured (p=<0.001).ConclusionDMPA use is associated with reduction of proinflammatory cytokines and elevation of the regulatory cytokine IL 10. This may explain increased female to male transmission of HIV infection by modulation of male genital tract mucosa in the absence of increased HIV 1 genital shedding.
An algebraic approach to parameter optimization in biomolecular bistable systems
Authors: Mardanlou Vahid , Franco Elisa 
Published: March 2016

AbstractIn a synthetic biological network it may often be desirable to maximize or minimize parameters such as reaction rates, fluxes and total concentrations of reagents, while preserving a given dynamic behavior. We consider the problem of parameter optimization in biomolecular bistable circuits. We show that, under some assumptions often satisfied by bistable biological networks, it is possible to derive algebraic conditions on the parameters that determine when bistability occurs. These (global) algebraic conditions can be included as nonlinear constraints in a parameter optimization problem. We derive bistability conditions using Sturm's theorem for Gardner and Collins toggle switch. Then we optimize its nominal parameters to improve switching speed and robustness to a subset of uncertain parameters.
fluff: exploratory analysis and visualization of high-throughput sequencing data
Authors: Georgiou Georgios , van Heeringen Simon J. 
Published: March 2016

AbstractSummaryIn this application note we describe fluff, a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data mapped to a reference genome. The package contains three command-line tools to generate publication-quality figures in an uncomplicated manner using sensible defaults. Genome-wide data can be aggregated, clustered and visualized in a heatmap, according to different clustering methods. This includes a predefined setting to identify dynamic clusters between different conditions or developmental stages. Alternatively, clustered data can be visualized in a bandplot. Finally, fluff includes a tool to generate genomic profiles. As command-line tools, the fluff programs can easily be integrated into standard analysis pipelines. The installation is straightforward and documentation is available at http://fluff.readthedocs.org.Availabilityfluff is implemented in Python and runs on Linux. The source code is freely available for download at http://github.com/simonvh/fluff.Contacts.vanheeringen@science.ru.nl
On the Origin and Evolutionary Consequences of Gene Body DNA Methylation
Authors: Bewick Adam J. , Ji Lexiang , Niederhuth Chad E. , Willing Eva-Maria , Hofmeister Brigitte T. , Shi Xiuling , Wang Li , Lu Zefu , Rohr Nicholas A. , Hartwig Benjamin , Kiefer Christiane , Deal Roger B. , Schmutz Jeremy , Grimwood Jane , Stroud Hume , Jacobsen Steven E. , Schneeberger Korbinian , Zhang Xiaoyu , Schmitz Robert J. 
Published: March 2016

AbstractIn plants, CG DNA methylation is prevalent in the transcribed regions of many constitutively expressed genes (“gene body methylation; gbM”), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum has lost gbM from its genome, the first known instance for an angiosperm. Of all known DNA methyltransferases, only CHROMOMETHYLASE 3 (CMT3) is missing from E. salsugineum. Identification of an additional angiosperm, Conringia planisiliqua, which independently lost CMT3 and gbM supports that CMT3 is required for the establishment of gbM. Detailed analyses of gene expression, the histone variant H2A.Z and various histone modifications in E. salsugineum and in Arabidopsis thaliana epiRILs found no evidence in support of any role for gbM in regulating transcription or affecting the composition and modifications of chromatin over evolutionary time scales.
Empirical modelling of trait selection by partitioning selection into direct selection and selection that is mediated by interspecific interactions
Authors: Damgaard Christian 
Published: March 2016

AbstractTrait selection has received considerable attention in the pursuit to understand niche-based community assembly processes and to generate ecological predictions. To further advance the study of trait selection, a conceptual statistical model is presented that outlines and discuss the possibilities of i) estimating the effect of interspecific interactions on traits rather than just testing weather selection has had an effect on the observed trait distributions, ii) discriminating between environmental filtering and niche partitioning processes and estimate the characteristic features and importance of both processes, and iii) predicting the effect of environmental changes and gradients on trait selection. To achieve these goals a number of necessary assumptions have to be specified and these assumptions are discussed and assessed. Simulated plant cover data from a simple uniform environment was successfully fitted to the model and the results indicates that it is possible to partition direct population growth and population growth that is mediated by interspecific interaction. The data requirements of the model are modest, i.e. time series data on plant species abundance and a species trait matrix. Consequently, the model concept may be used to model trait selection, including the effect of interspecific interactions, in many existing plant ecological datasets.
Relative contributions of conformational selection and induced fit
Authors: Michel Denis 
Published: March 2016

ABSTRACTA long standing debate in biochemistry is to determine whether the conformational changes observed during biomolecular interactions proceed through conformational selection (of preexisting isoforms) or induced fit (ligand-induced 3D reshaping). The latter mechanism had been invoked in certain circumstances, for example to explain the non-Michaelian activity of monomeric enzymes like glucokinase. But the relative importance of induced fit has been recently depreciated in favor of conformational selection, assumed to be always sufficient, predominant in general and in particular for glucokinase. The relative contributions of conformational selection and induced fit are reconsidered here in and out of equilibrium, in the light of earlier concepts such as the cyclic equilibrium rule and the turning wheel of Wyman, using single molecule state probability, one way fluxes and net fluxes. The conditions for a switch from conformational selection to induced fit at a given ligand concentration are explicitly determined. Out of equilibrium, the inspection of the enzyme states circuit shows that conformational selection alone would give a Michaelian reaction rate but not the established nonlinear behavior of glucokinase. Moreover, when induced fit and conformational selection coexist and allow kinetic cooperativity, the net flux emerging in the linkage cycle necessarily corresponds to the induced fit path.
Genotype-specific developmental plasticity shapes the timing and robustness of reproductive capacity inCaenorhabditis elegans
Authors: Alicea Bradly 
Published: March 2016

AbstractThe effects of environmental stress on developmental phenotypes allows us to observe the adaptive capacity of various genotypes. In single-genotype populations, this allows for observing the effects of standing variation on the process of developmental plasticity. Typically, such efforts do not allow us to distinguish the effect of genotype from the effects of environment. In the NematodeCaenorhabditis elegans, however, the L1 stage of development allows for precise and controlled imposition of starvation on a synchronized population of individuals. This allows for systematic comparisons within and between defined genotypes.This study provides a number of innovations in the study of Nematode developmental plasticity. The first is to demonstrate systems-level mechanisms of adaptive response for various genetic mutant phenotypes to extended L1 arrest. The effects of developmental deprivation are quantifiable by applying statistical modeling techniques to reproductive time-series. This is characterized for both a wildtype strain (N2) and a host of genetic mutant strains. A further contribution is investigating the effects of starvation at multi-generational timescales. This includes both two generations post-starvation and multiple starvation experiences with selection for fecundity over 11 generations.Statistical techniques such as Kernel Density Estimation (KDE), fold-change analysis, and Area Under the Curve (AUC) analysis reveal differences from baseline in the form of shifts in reproductive timing and kurtosis in peak reproductive capacity characterize adaptive responses that are semi-independent of environment. Extending these patterns of response toad hoccomparisons with multi-generational contexts reveals that different genotypes characterized by mutations of specific genetic loci lead to vastly different outcomes.
Early developmental pathways to autism spectrum disorder in tuberous sclerosis complex
Authors: Tye Charlotte , Varcin Kandice , Bolton Patrick , Jeste Shafali Spurling 
Published: March 2016

Purpose
– Tuberous sclerosis complex (TSC) is a genetic disorder with a high prevalence of autism spectrum disorder (ASD), yet no single genetic, neurological or neurophysiological risk marker is necessary or sufficient to increase risk for ASD. This paper aims to discuss the utility of adopting a developmental perspective.

Design/methodology/approach
– The increasing number of TSC infants presenting with abnormalities prenatally provides a unique opportunity to study risk pathways to ASD from birth. Here, the authors review findings to date that support the investigation of infants with TSC to further our understanding of typical and atypical development.

Findings
– Evidence has accumulated from studies of infants at familial risk for ASD (“baby siblings”) to suggest that early markers of ASD are present in the first year of life. The early waves of prospective studies of infants with TSC indicate dynamic changes in developmental trajectories to ASD and are likely to provide insight into cascading effects of brain “insult” early in development. Emerging evidence of phenotypic and biological homology between syndromic and idiopathic cases of ASD supports the notion of a convergence of risk factors on a final common pathway in ASD.

Originality/value
– The delineation of brain-based biomarkers of risk, prediction and treatment response in TSC will be critical in aiding the development of targeted intervention and prevention strategies for those infants at high risk of poorer developmental outcomes.
Divorce in the family business: unfolding the legal problems by learning from practice
Authors: Haag Kajsa , Sund Lars-Göran 
Published: March 2016

Purpose
Our purpose is to explore the case of divorce in family business from a legal perspective and highlight the problems of applying family law in the family business context.

Design/methodology/approach
We rely on legal analysis and interviews with estate distribution executors to discuss problems with the legal rules and how they are practiced.

Findings
Our findings show that the law is ill fitted to the situation where there is a family business included in the division of marital property. In divorce, family law dictates the division of marital property and the family business is reduced to an asset to be divided like any other. Critical issues are identified and elaborated.

Research limitations/implications
Divorce and other disruptions to the family system should be considered in family business consultancy among other threats to the business. The legal perspective on divorce in the family business offered here primarily concerns ownership issues. The impact of divorce on management is equally in need of exploration, which is our suggestion for further studies.

Practical implications
Our paper illuminates in which ways the business is hampered from divorcing owners and discuss critical issues with applying family law in a family business context.

Originality/value
New light is shed on the practical problems of interpreting family law in a family business context advancing our understanding of family aspects in family business management.
An examination of the associations among cultural dimensions, relational silence and stress
Authors: Dedahanov Alisher Tohirovich , Lee Dohyung , Rhee Jaehoon , Yusupov Sardorbek 
Published: March 2016

Purpose– The purpose of this paper is to examine the relationship between power distance, collectivism and relational silence; the associations between relational silence and stress; and the mediating role of relational silence in the link between power distance, collectivism and stress.Design/methodology/approach– The authors conducted a survey among 1,153 highly skilled employees using a self-administered questionnaire. The authors received 813 responses from a total of 1,153 individuals. Among the 813 responses, the authors excluded 81 due to incomplete data, and thus analyzed a total of 732 responses. The overall response rate was 63.4 percent. Confirmatory factor analysis and structural equation modeling were utilized for the analyses.Findings– The findings suggest that power distance and collectivism induce relational silence; relational silence increases stress and mediates the associations between power distance, collectivism and stress.Originality/value– The present study is the first to provide empirical evidence of a link between power distance, collectivism and relational silence; the relationship between relational silence and stress; and the role of relational silence in mediating the associations between power distance, collectivism and stress.
How to make a knowledge-sharing group: a group social capital perspective
Authors: Wu Wei-Li , Lee Yi-Chih 
Published: March 2016

Purpose– Although the work group is the main context for knowledge exchange and combination in today’s organizations, few knowledge-sharing studies have been conducted at the group level. The purpose of this paper is to apply the concept of group social capital to determine how to promote knowledge sharing at the group level. The authors divided group social capital into two segments, conduits and resources, and argue that different group social capital conduits (i.e. work design in this study) lead to varied resources, which subsequently influence group knowledge sharing.Design/methodology/approach– In this study, group social capital conduits included social interaction and task interdependence, and group social capital resources included group trust and a supportive climate for knowledge sharing. The authors conducted a survey on work groups in the high-tech industry using a sample of 86 work groups.Findings– The results indicated that social interaction in a work group was positively related to group trust and that task interdependence was positively related to group trust and a supportive climate for knowledge sharing. Furthermore, group trust and a supportive climate for knowledge sharing were both found to have an influence on knowledge sharing.Originality/value– Applying the concept of group social capital, this paper is the first research to discuss how group social capital conduits and resources influence knowledge sharing. The results of this study lead us to a better understand the relationship between group social capital and knowledge sharing.
Current status of nanotechnology in Jordan
Authors: Alshamaileh Ehab , Al-Sulaibi Mazen , Al-Khawaldeh Ahmad , Almatarneh Mansour H. , El-Sabawi Dina , Al-Rawajfeh Aiman 
Published: March 2016

Purpose– The current status of nanotechnology research and development in Jordan is analyzed. In recent years, Jordanian institutions demonstrated considerable interest in the development and production of nanotechnology. Here the purpose of this paper is to provide detailed information about the status of nanotechnology in Jordan in terms of several factors that influence selectivity in nanotechnology and the number of published peer-reviewed research articles.Design/methodology/approach– Several factors that influence selectivity in nanotechnology and the number of published peer-reviewed research articles were analyzed. A detailed analysis of the collected data reveals that the number of publications, citations, and patents is highly dependent on the amount of research fund.Findings– The development in nanotechnology is associated with presence and accessibility of sensitive laboratory equipment. The nanotechnology research output in Jordan is still lower than it should be due to the lack of necessary laboratory infrastructure. This is due to the insufficient funds allocated to scientific research, the restrictive access to available instruments and the bureaucracy of some governmental departments. Compared to some developed countries, Jordan is noticeably behind in developing a nanotechnology system of research and industry. It will take time as well as technical and financial resources in order to achieve an advanced level in the field of nanotechnology in Jordan. Nevertheless, many Jordanian researchers are doing their best and are producing some good research articles.Research limitations/implications– The many applications to the same approach.Practical implications– Time and publications’ resources.Social implications– Peer cooperation.Originality/value– First comprehensive review ever. A base for researchers and decision makers.
Towards sustainable indicators of food and nutritional outcomes in India
Authors: Reddy A. Amarender , Rani Ch. Radhika , Cadman Timothy , Kumar Soora Naresh , Reddy Anugula N 
Published: March 2016

Purpose
– The purpose of this paper is to measure performance of India in food and nutrition security relative to other Asian countries like Bangladesh, China, Africa and also developed countries from 1991 to 2016.

Design/methodology/approach
– The study is based on FAO food security indicators under four dimensions, namely, food availability, access, stability and utilization. These indicators are further categorized into determinants and outcome indicators of food security. A comprehensive fifteen indicators are examined in depth.

Findings
– Food availability in terms of dietary calories and protein per capita was less in India compared to even Africa and Bangladesh. However, food access indicators like road density is better, food prices remain low and stable, which improved food access and stability. However, in utilization indicators, access to water and sanitation remained low, anaemia among pregnant women and undernourishment was relatively higher when even compared to least developed countries like Africa and Bangladesh. Depth of food deficit (an indicator of severity of food deficit) was higher in India except Africa.

Research limitations/implications
– Future research should focus on policies for decreasing undernourishment and anaemia and severity in depth of food deficit with focus on India.

Practical implications
– The results highlight the severity of food deficit and anaemia among women, undernourishment and provide benchmark to monitor sustainable development goals in zero hunger goal.

Originality/value
– This study examined the relative performance of India in various food and nutrition security indicators in comparison to other countries.
Author‐suggested reviewers: gender differences and influences on the peer review process at an ecology journal
Authors: Fox Charles W. , Burns C. Sean , Muncy Anna D. , Meyer Jennifer A. 
Published: March 2016

Summary

Peer review is the primary method by which journals evaluate the quality and importance of scientific papers. To help editors find suitable reviewers, many journals allow or require authors to suggest names of preferred and nonpreferred reviewers. Though authors should know best who is qualified to review their papers, they also have a strong incentive to suggest reviewers that they expect to review their paper positively.

In this study, we examine the reviewers that are suggested as preferred and nonpreferred by authors, the use of these author suggestions by editors, and the influence of author suggestions on the peer review process and outcomes at the journal Functional Ecology. In particular, we examined how gender of the participants (author, editor and reviewer) influences the role of preferred reviewers in the peer review process.

Even when not required by the journal, most authors suggest preferred reviewers, but few suggest nonpreferred reviewers. Most author‐preferred reviewers are male, but the proportion of women among author suggestions increased over the 11 years, from a low of 15% in 2004 to a high of 25% in 2014.

Male and female authors did not differ in how likely they were to suggest preferred reviewers, but the proportion of women among author suggestions was higher for female authors (~28%, averaged across years) than for male authors (~21%). Women that were suggested as author‐preferred reviewers were more likely to be selected by editors than were men suggested by authors.

There was no evidence that editor gender, seniority or length of service as an editor for Functional Ecology affected the probability that they used author suggestions. Of reviewers invited to review, those that were author‐suggested were more likely to respond to the editors' review invitations but were not more likely to agree to review.

Most strikingly, author‐preferred reviewers rated papers more positively than did editor‐selected reviewers, and papers reviewed by author‐preferred reviewers were much more likely to be invited for revision than were papers reviewed by editor‐selected reviewers. This difference was not influenced by the gender of the participants in the process.

Suggesting preferred reviewers benefits authors because preferred reviewers rate papers significantly more positively than do editor‐selected reviewers, improving the chances that a paper will be published. Journals and journal editors should recognize that preferred reviewers rate manuscripts differently than do editor‐selected reviewers, and be aware that this difference can have large effects on editor decisions.

A Lay Summary is available for this article.