bluuebunny/crossref_metadata_2025_split huggingface dataset:
DIVAS: a centralized genetic variant repository representing 150 000 individuals from multiple disease cohorts
Authors: Cheng Wei-Yi , Hakenberg Jörg , Li Shuyu Dan , Chen Rong 
Published: September 2015

Abstract
Motivation: A plethora of sequenced and genotyped disease cohorts is available to the biomedical research community, spread across many portals and represented in various formats.
Results: We have gathered several large studies, including GERA and GRU, and computed population- and disease-specific genetic variant frequencies. In total, our portal provides fast access to genetic variants observed in 84 928 individuals from 39 disease populations. We also include 66 335 controls, such as the 1000 Genomes and Scripps Wellderly.
Conclusion: Combining multiple studies helps validate disease-associated variants in each underlying data set, detect potential false positives using frequencies of control populations, and identify novel candidate disease-causing alterations in known or suspected genes.
Availability and implementation: https://rvs.u.hpc.mssm.edu/divas
Contact: rong.chen@mssm.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
markophylo: Markov chain analysis on phylogenetic trees
Authors: Dang Utkarsh J. , Golding G. Brian 
Published: September 2015

Abstract
Summary: Continuous-time Markov chain models with finite state space are routinely used for analysis of discrete character data on phylogenetic trees. Examples of such discrete character data include restriction sites, gene family presence/absence, intron presence/absence and gene family size data. While models with constrained substitution rate matrices have been used to good effect, more biologically realistic models have been increasingly implemented in the recent literature combining, e.g., site rate variation, site partitioning, branch-specific rates, allowing for non-stationary prior root probabilities, correcting for sampling bias, etc. to name a few. Here, a flexible and fast R package is introduced that infers evolutionary rates of discrete characters on a tree within a probabilistic framework. The package, markophylo, fits maximum-likelihood models using Markov chains on phylogenetic trees. The package is efficient, with the workhorse functions written in C++ and the interface in user-friendly R.
Availability and implementation: markophylo is available as a platform-independent R package from the Comprehensive R Archive Network at https://cran.r-project.org/web/packages/markophylo/. A vignette with numerous examples is also provided with the R package.
Contact: udang@mcmaster.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Prioritization of sites for plant species restoration in the Chilean Biodiversity Hotspot: A spatial multi-criteria decision analysis approach
Authors: Fernández Ignacio C. , Morales Narkis S. 
Published: September 2015

AbstractVarious initiatives to identify global priority areas for conservation have been developed over the last 20 years (e.g. Biodiversity Hotspots). However, translating this information to actionable local scales has proven to be a major task, highlighting the necessity of efforts to bridge the global-scale priority areas with local-based conservation actions. Furthermore, as these global priority areas are increasingly threatened by climate change and by the loss and alteration of their natural habitats, developing additional efforts to identify priority areas for restoration activities is becoming an urgent task. In this study we used a Spatial Multi-Criteria Decision Analysis (SMCDA) approach to help optimize the selection of sites for restoration initiatives of two endemic threatened flora species of the “Chilean Winter Rainfall-Valdivian Forest” Hotspot. Our approach takes advantage of freely GIS software, niche modeling tools, and available geospatial databases, in an effort to provide an affordable methodology to bridge global-scale priority areas with local actionable restoration scales. We used a set of weighting scenarios to evaluate the potential effects of short-termvslong-term planning perspective in prioritization results. The generated SMCDA was helpful for evaluating, identifying and prioritizing best suitable areas for restoration of the assessed species. The method proved to be simple, transparent, cost effective and flexible enough to be easily replicable on different ecosystems. This approach could be useful for prioritizing regional-scale areas for species restoration in Chile, as well as in other countries with restricted budgets for conservation efforts.
French supervisory board gender composition and quota threat: changes from 2008 to 2010
Authors: Singh Val , Point Sébastien , Moulin Yves 
Published: September 2015

Purpose– The purpose of this paper is to explore how an environmental threat (possible quotas for female supervisory directors) might change supervisory board gender composition in SBF120 French company boards between 2008 and 2010.Design/methodology/approach– From a census of supervisory board membership of SBF120 companies in France in January 2008 and December 2010, data were obtained to test hypotheses relating to changes in gender composition of boards and demographic differences between new and earlier director appointees. The authors drew on institutional theory to inform the discussion of this paper’s findings.Findings– The authors reveal significant increases over 2008-2010 in SBF120 board female representation and significant cohort differences between recent and earlier appointees. Newer female appointees differed from male peers and from earlier appointed females and males, bringing youth and international experience. New females were more likely to gain CAC40 seats than their male peers. There was an increase in boards with multiple female directors.Research limitations/implications– Actual motivations for increase in female appointments are unknown, but institutional theory provides possible explanations, as suggestion of coercive forces loomed. Chairmen of larger firms may have made strategic choices to attract younger and English-speaking foreign women, before the rush. Limitations include the descriptive nature of the paper, but it sets a benchmark for later studies to monitor progress in depth.Practical implications– The talent pool for female directors has widened to include foreign English-speaking women, bringing a range of new insights and experience of international governance practice to traditional French boardrooms. However, this could be seen as further discriminatory practice that requires female appointees to bring more human and social capital than that required of their male peers.Originality/value– This is the first paper charting the changes in supervisory board composition during the three-year period of environmental unrest as quotas were proposed and legislated in France and comparing new and existing cohort French director demographics.
Focus of tricholemmal differentiation (tricholemmal carcinoma) within Bowen's disease/carcinoma
Authors: Misago Noriyuki , Toda Shuji , Nakao Tomokazu 
Published: September 2015

AbstractBowen's disease (BD)/carcinoma is a type of squamous cell carcinoma of the skin, however, the possibility of adnexal differentiation (the development of sebaceous carcinoma or porocarcinoma) occurring in BD/carcinoma has been suggested. We herein describe a case of BD with superficial invasive carcinoma, which showed a clear cell focus, demonstrating tricholemmal differentiation. This clear cell focus showed the following findings: primarily composed of clear cells, somewhat columnar clear cells aligned in a palisade along a discernible basement membrane, tricholemmal keratinization and glycogen contained within the cells. In addition, the immunohistochemical profile in this clear cell focus, namely, negative staining for cytokeratin (CK)1 and positive staining for CK17 and calretinin in the inner cells of the neoplastic lobule, corresponded to that of the outer root sheath cells. This case suggested that adnexal differentiation can rarely occur within true BD/carcinoma, although adnexal carcinomas are commonly associated with a simple bowenoid change.
Policy Mobilities and Interdisciplinary Engagement
Authors: Cook Ian R. 
Published: September 2015

AbstractThis essay explores the nature and potential of interdisciplinarity in the expanding body of research on the circulation of policies between places. It focuses on the policy mobilities literature, highlighting its geographical underpinnings as well as its links to, and divergences from, literature beyond geography, in particular the political science‐led work on policy transfer. Acknowledging the potential downfalls of interdisciplinarity, it calls for increased conversations and co‐working between geographers, political scientists and other social scientists to explore the topic further.
Increasing inter‐generational social mobility: is educational expansion the answer?
Authors: Sturgis Patrick , Buscha Franz 
Published: September 2015

AbstractReforms which increase the stock of education in a society have long been held by policy‐makers as key to improving rates of intergenerational social mobility. Yet, despite the intuitive plausibility of this idea, the empirical evidence in support of an effect of educational expansion on social fluidity is both indirect and weak. In this paper we use the raising of the minimum school leaving age from 15 to 16 years in England and Wales in 1972 to estimate the effect of educational participation and qualification attainment on rates of intergenerational social class mobility. Because, in expectation, children born immediately before and after the policy was implemented are statistically exchangeable, the difference in the amount of education they received may be treated as exogenously determined. The exogenous nature of the additional education gain means that differences in rates of social mobility between cohorts affected by the reform can be treated as having been caused by the additional education. The data for the analysis come from the ONS Longitudinal Study, which links individual records from successive decennial censuses between 1971 and 2001. Our findings show that, although the reform resulted in an increase in educational attainment in the population as a whole and a weakening of the association between attainment and class origin, there was no reliably discernible increase in the rate of intergenerational social mobility.
BiMat: a MATLAB package to facilitate the analysis of bipartite networks
Authors: Flores Cesar O. , Poisot Timothée , Valverde Sergi , Weitz Joshua S. 
Published: September 2015

Summary

Bipartite networks are ubiquitous in community ecology, including examples of facilitative interactions, such as plant‐pollinator networks, and antagonistic interactions, such as virus–host infection networks. Statistical network analysis is increasingly used to identify emergent, nonrandom patterns of interaction and the effect of interaction patterns on ecological and evolutionary dynamics. Two recurring patterns are that of modularity and nestedness. Modularity is a feature of networks in which there are densely interacting subgroups. Nestedness is a feature of networks in which the interactions form ordered subsets.

Here we describe BiMat, an open‐source MATLAB package for the study of the structure of bipartite ecological networks. Unlike alternative tools, BiMat enables both multiscale analysis of the structure of a bipartite ecological network – spanning global (i.e. entire network) to local (i.e. module‐level) scales – and meta‐analyses of many bipartite networks simultaneously. In common with other tools, BiMat calculates the degree to which a bipartite network is modular and/or nested, the statistical significance of these patterns, and enables visualization of latent structures in the network.

BiMat is available as an open‐source MATLAB package, with a quick‐start guide and worked examples at: http://bimat.github.io/.
Fear and overprotection in Australian residential aged‐care facilities: The inadvertent impact of regulation on quality continence care
Authors: Ostaszkiewicz Joan , O'Connell Beverly , Dunning Trisha 
Published: September 2015

AimMost residents in residential aged‐care facilities are incontinent. This study explored how continence care was provided in residential aged‐care facilities, and describes a subset of data about staffs' beliefs and experiences of the quality framework and the funding model on residents' continence care.MethodsUsing grounded theory methodology, 18 residential aged‐care staff members were interviewed and 88 hours of field observations conducted in two facilities. Data were analysed using a combination of inductive and deductive analytic procedures.ResultsStaffs' beliefs and experiences about the requirements of the quality framework and the funding model fostered a climate of fear and risk adversity that had multiple unintended effects on residents' continence care, incentivising dependence on continence management, and equating effective continence care with effective pad use.ConclusionThere is a need to rethink the quality of continence care and its measurement in Australian residential aged‐care facilities.
Neonatal oesophageal and axilla temperatures in the neonatal intensive care unit care
Authors: Hoffman Laurie , Santos Mary Ann , Tucker Richard , Laptook Abbot 
Published: September 2015

AbstractAimTo compare oesophageal and axilla temperatures in routine neonatal intensive care unit (NICU) care.MethodsProspective observational study of NICU infants with indwelling oral/nasogastric tubes. Three simultaneous temperature measurements were taken: Physitemp axilla, digital Premie Faichney axilla in predictive mode and Physitemp oesophageal. Temperatures were measured on two separate days.ResultsFifty infants were studied over a range of gestational ages (median 28.9 weeks, IQR 25.8–30.6 weeks) and birthweights (median 1140 g, IQR 742–1498 g). Mean Physitemp oesophageal temperatures were 0.3 ± 0.1°C (range 0.1–0.6°C) higher than Physitemp axilla temperatures. After adjustment for weight, the Physitemp oesophageal–Physitemp axilla difference remained constant over the average oesophageal–axilla temperature range studied (p = 0.07). Physitemp oesophageal temperatures were not affected by weight (p = 0.2) or postmenstrual age (p = 0.51). Physitemp axilla temperatures decreased with increasing weight (p = 0.03) and postmenstrual age (p = 0.048). The Physitemp oesophageal–Physitemp axilla difference was greater for infants in cribs (mean ± SD = 0.4 ± 0.1°C) than in incubators (mean ± SD = 0.3 ± 0.1°C, p < 0.001). The relationship between oesophageal and digital Premie Faichney axilla temperature was similar to oesophageal and axilla Physitemp temperatures.ConclusionOver a range of infant temperatures encountered in routine NICU care, oesophageal temperature is higher than axilla temperature, although the difference is small. Axillary temperatures measured by digital thermometers in predictive mode are comparable to core oesophageal temperatures.
Comparing Treatment Policies with Assistance from the Structural Nested Mean Model
Authors: Lu Xi , Lynch Kevin G. , Oslin David W. , Murphy Susan 
Published: September 2015

Summary
Treatment policies, also known as dynamic treatment regimes, are sequences of decision rules that link the observed patient history with treatment recommendations. Multiple, plausible, treatment policies are frequently constructed by researchers using expert opinion, theories, and reviews of the literature. Often these different policies represent competing approaches to managing an illness. Here, we develop an “assisted estimator” that can be used to compare the mean outcome of competing treatment policies. The term “assisted” refers to the fact estimators from the Structural Nested Mean Model, a parametric model for the causal effect of treatment at each time point, are used in the process of estimating the mean outcome. This work is motivated by our work on comparing the mean outcome of two competing treatment policies using data from the ExTENd study in alcohol dependence.
From ‘Entering into a Firm’ to ‘Entering into a Profession’: An Anthropological Approach to Changing Personhood in Japan
Authors: Fu Huiyan 
Published: September 2015

AbstractDrawing on extensive ethnographic fieldwork, the article uses discourse analysis to examine the social dynamics involved in the construction of personhood in Japan. While the gap between powerful discourse and lived reality is a well‐documented phenomenon, there is little systematic empirical research on how to integrate individual and social levels of analysis in this process. By contrasting discourse from above and from below, the article illuminates power asymmetry and the resulting tension between discursive freedom and social exclusion among disadvantaged groups.
Greenfield FDI and skill upgrading: A polarized issue
Authors: Davies Ronald B. , Desbordes Rodolphe 
Published: September 2015

AbstractOutbound FDI is often accused of increasing income inequality in developed countries by shifting labour demand from low‐skilled towards high‐skilled workers (wage polarization). In response, we employ data on greenfield FDI that, in contrast to M&As, may be more clearly linked to skill upgrading. Our data also delineate greenfield FDI by sector, function and destination, allowing us to control for different motives and skill intensities for 17 developed countries for 2003–2005. We find that greenfield FDI in support services, e.g., back and front office services, induces polarized skill upgrading, benefitting high‐skilled workers at the expense of medium‐skilled workers, thereby polarizing wages.
Effect of glove occlusion on the skin barrier
Authors: Tiedemann Daniel , Clausen Maja Lisa , John Swen Malthe , Angelova‐Fischer Irena , Kezic Sanja , Agner Tove 
Published: September 2015

SummaryWet work tasks are the most common exposures leading to occupational irritant contact dermatitis. Use of liquid‐proof gloves is recommended when performing wet work, however, gloves may also contribute to impairment of the skin barrier and development of irritant contact dermatitis. The aim of this study is to review the literature on the effects of glove occlusion on skin barrier function. The PubMed database was searched up to 1 February 2015 for articles on the association between glove occlusion and skin barrier function, including human studies only and in English. Only experimental studies including assessment of the skin barrier function were included in the data analysis. Thirteen articles were identified, 8 with focus on occlusion alone, 7 with focus on occlusion in combination with irritant exposure (some overlapping), and 2 field studies. In conclusion, data from the literature showed that the negative effect of occlusion in itself is limited, and that only extensive and long‐term occlusion will cause barrier impairment. However, studies investigating combined effect of occlusion and exposure to soaps/detergents indicate that occlusion significantly enhances the skin barrier damage caused by detergents/soaps in a dose‐response fashion.
Accurate Response with Refurbished Consumer Returns
Authors: Reimann Marc 
Published: September 2015

ABSTRACTCentering around anticipative and reactive capabilities of firms, accurate response is an important supply‐side strategy to deal with demand uncertainty. Clearly, the structure of the possible reaction will crucially influence the optimal anticipative decision making. In this article, we extend the existing literature in this area by including a new reactive capability, namely the utilization of refurbished consumer returns from early sales to react to demand later in the selling season. Because consumer returns depend on previous sales, there is also a direct link to the anticipative supply decision. We capture this effect in a newsvendor‐type model and provide both analytical and numerical insights into the optimal anticipative and reactive decisions as well as the value of refurbishing in terms of the retailer's expected profitability.
The Dynamics of Pre‐ and Post‐purchase Service and Consumer Evaluation of Online Retailers: A Comparative Analysis of Dissonance and Disconfirmation Models*
Authors: Park Insu , Cho Jeewon , Rao H. Raghav 
Published: September 2015

ABSTRACTThis article explores the theoretical underpinnings of the dissonance framework in online consumer satisfaction formation process. Specifically, we suggest that any discrepancy between pre‐ and post‐purchase service performance would help determine consumers’ evaluations of online vendors. Drawing upon cognitive dissonance theory, a conceptual model is developed and tested in two different studies (preliminary and main studies). Using data from 191 college students collected longitudinally, the preliminary study demonstrates the validity and reliability of the measurements. Using a comparative analysis, the main study then tests our conceptual model as well as various competing models, including the expectation–confirmation model, with a sample of 292 online consumers. The results in both studies support our main prediction that the service encountered in different stages establishes dissonance. Specifically, we find that dissonance explains online consumers’ satisfaction process to a substantial extent, as compared with disconfirmation under the same conditions in online retailers. This study contributes to providing an alternative yet substantial approach for expectation–confirmation theory, reflecting the overarching nature of online shopping.
Seasonal variation in the diet of Tetrix tenuicornis (Orthoptera: Tetrigidae)
Authors: Kuřavová Kateřina , Kočárek Petr 
Published: September 2015

AbstractMany animals change their diet during the season according to food availability. The current field study determined whether the groundhopper Tetrix tenuicornis (Orthoptera: Tetrigidae), which specializes on moss and detritus, changes its diet during the season under conditions in which food components are constantly available. Dietary differences of T. tenuicornis were studied through the season, from May to October, by alimentary tract analyses. Detritus and moss (phylloids) dominated the alimentary tract contents, and other components were found in only minor amounts. The diversity of moss species in the alimentary tract varied during the season, and more moss species were consumed in spring and summer than in autumn. Diet was affected by developmental stage, sex (females consumed more food than males), population and abiotic factors. The rate at which detritus was consumed was significantly affected by the ambient temperature but the rate at which moss was consumed was mainly affected by relative humidity. Later instars consumed greater amounts of detritus than younger instars, and this difference corresponded to body size.