bluuebunny/crossref_metadata_2025_split huggingface dataset:
Galaxy Portal: interacting with the galaxy platform through mobile devices
Authors: Børnich Claus , Grytten Ivar , Hovig Eivind , Paulsen Jonas , Čech Martin , Sandve Geir Kjetil 
Published: February 2016

Abstract
Summary: We present Galaxy Portal app, an open source interface to the Galaxy system through smart phones and tablets. The Galaxy Portal provides convenient and efficient monitoring of job completion, as well as opportunities for inspection of results and execution history. In addition to being useful to the Galaxy community, we believe that the app also exemplifies a useful way of exploiting mobile interfaces for research/high-performance computing resources in general.
Availability and implementation: The source is freely available under a GPL license on GitHub, along with user documentation and pre-compiled binaries and instructions for several platforms: https://github.com/Tarostar/QMLGalaxyPortal. It is available for iOS version 7 (and newer) through the Apple App Store, and for Android through Google Play for version 4.1 (API 16) or newer.
Contact: geirksa@ifi.uio.no
FILTUS: a desktop GUI for fast and efficient detection of disease-causing variants, including a novel autozygosity detector
Authors: Vigeland Magnus D. , Gjøtterud Kristina S. , Selmer Kaja K. 
Published: February 2016

Abstract
Summary: FILTUS is a stand-alone tool for working with annotated variant files, e.g. when searching for variants causing Mendelian disease. Very flexible in terms of input file formats, FILTUS offers efficient filtering and a range of downstream utilities, including statistical analysis of gene sharing patterns, detection of de novo mutations in trios, quality control plots and autozygosity mapping. The autozygosity mapping is based on a hidden Markov model and enables accurate detection of autozygous regions directly from exome-scale variant files.
Availability and implementation: FILTUS is written in Python and runs on Windows, Mac and Linux. Binaries and source code are freely available at http://folk.uio.no/magnusv/filtus.html and on GitHub: https://github.com/magnusdv/filtus. Automatic installation is available via PyPI (e.g. pip install filtus).
Contact: magnusdv@medisin.uio.no
Supplementary information: Supplementary data are available at Bioinformatics online.
Sprites: detection of deletions from sequencing data by re-aligning split reads
Authors: Zhang Zhen , Wang Jianxin , Luo Junwei , Ding Xiaojun , Zhong Jiancheng , Wang Jun , Wu Fang-Xiang , Pan Yi 
Published: February 2016

AbstractMotivation: Advances of next generation sequencing technologies and availability of short read data enable the detection of structural variations (SVs). Deletions, an important type of SVs, have been suggested in association with genetic diseases. There are three types of deletions: blunt deletions, deletions with microhomologies and deletions with microsinsertions. The last two types are very common in the human genome, but they pose difficulty for the detection. Furthermore, finding deletions from sequencing data remains challenging. It is highly appealing to develop sensitive and accurate methods to detect deletions from sequencing data, especially deletions with microhomology and deletions with microinsertion.Results: We present a novel method called Sprites (SPlit Read re-alIgnment To dEtect Structural variants) which finds deletions from sequencing data. It aligns a whole soft-clipping read rather than its clipped part to the target sequence, a segment of the reference which is determined by spanning reads, in order to find the longest prefix or suffix of the read that has a match in the target sequence. This alignment aims to solve the problem of deletions with microhomologies and deletions with microinsertions. Using both simulated and real data we show that Sprites performs better on detecting deletions compared with other current methods in terms of F-score.Availability and implementation: Sprites is open source software and freely available at https://github.com/zhangzhen/sprites.Contact: jxwang@mail.csu.edu.cnSupplementary data: Supplementary data are available at Bioinformatics online.
The geospatial data quality REST API for primary biodiversity data
Authors: Otegui Javier , Guralnick Robert P. 
Published: February 2016

Abstract
Summary: We present a REST web service to assess the geospatial quality of primary biodiversity data. It enables access to basic and advanced functions to detect completeness and consistency issues as well as general errors in the provided record or set of records. The API uses JSON for data interchange and efficient parallelization techniques for fast assessments of large datasets.
Availability and implementation: The Geospatial Data Quality API is part of the VertNet set of APIs. It can be accessed at http://api-geospatial.vertnet-portal.appspot.com/geospatial and is already implemented in the VertNet data portal for quality reporting. Source code is freely available under GPL license from http://www.github.com/vertnet/api-geospatial.
Contact: javier.otegui@gmail.com or rguralnick@flmnh.ufl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Model-based media selection to minimize the cost of metabolic cooperation in microbial ecosystems
Authors: Zampieri Mattia , Sauer Uwe 
Published: February 2016

Abstract
Motivation: Simple forms of mutualism between microorganisms are widespread in nature. Nevertheless, the role played by the environmental nutrient composition in mediating cross-feeding in microbial ecosystems is still poorly understood.
Results: Here, we use mixed-integer bilevel linear programming to investigate the cost of sharing metabolic resources in microbial communities. The algorithm infers an optimal combination of nutrients that can selectively sustain synergistic growth for a pair of species and guarantees minimum cost of cross-fed metabolites. To test model-based predictions, we selected a pair of Escherichia coli single gene knockouts auxotrophic, respectively, for arginine and leucine: ΔargB and ΔleuB and we experimentally verified that model-predicted medium composition significantly favors mutualism. Moreover, mass spectrometry profiling of exchanged metabolites confirmed the predicted cross-fed metabolites, supporting our constraint based modeling approach as a promising tool for engineering microbial consortia.
Availability and implementation: The software is freely available as a matlab script in the Supplementary materials.
Contact: zampieri@imsb.biol.ethz.ch.
Supplementary information: Supplementary data are available at Bioinformatics online.
Privacy-preserving microbiome analysis using secure computation
Authors: Wagner Justin , Paulson Joseph N. , Wang Xiao , Bhattacharjee Bobby , Corrada Bravo Héctor 
Published: February 2016

Abstract
Motivation: Developing targeted therapeutics and identifying biomarkers relies on large amounts of research participant data. Beyond human DNA, scientists now investigate the DNA of micro-organisms inhabiting the human body. Recent work shows that an individual’s collection of microbial DNA consistently identifies that person and could be used to link a real-world identity to a sensitive attribute in a research dataset. Unfortunately, the current suite of DNA-specific privacy-preserving analysis tools does not meet the requirements for microbiome sequencing studies.
Results: To address privacy concerns around microbiome sequencing, we implement metagenomic analyses using secure computation. Our implementation allows comparative analysis over combined data without revealing the feature counts for any individual sample. We focus on three analyses and perform an evaluation on datasets currently used by the microbiome research community. We use our implementation to simulate sharing data between four policy-domains. Additionally, we describe an application of our implementation for patients to combine data that allows drug developers to query against and compensate patients for the analysis.
Availability and implementation: The software is freely available for download at: http://cbcb.umd.edu/∼hcorrada/projects/secureseq.html
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: hcorrada@umiacs.umd.edu
Trinculo: Bayesian and frequentist multinomial logistic regression for genome-wide association studies of multi-category phenotypes
Authors: Jostins Luke , McVean Gilean 
Published: February 2016

Abstract
Motivation: For many classes of disease the same genetic risk variants underly many related phenotypes or disease subtypes. Multinomial logistic regression provides an attractive framework to analyze multi-category phenotypes, and explore the genetic relationships between these phenotype categories. We introduce Trinculo, a program that implements a wide range of multinomial analyses in a single fast package that is designed to be easy to use by users of standard genome-wide association study software.
Availability and implementation: An open source C implementation, with code and binaries for Linux and Mac OSX, is available for download at http://sourceforge.net/projects/trinculo
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: lj4@well.ox.ac.uk
Adding value to education for sustainability in Africa with inquiry-based approaches in open and distance learning
Authors: Pretorius Rudi , Lombard Andrea , Khotoo Anisa 
Published: February 2016

Purpose
– Inquiry-based approaches can potentially enrich sustainability learning in any educational context, more so in open and distance learning (ODL – perceived as theoretically inclined) and in regions of educational need (such as the Global South, of which Africa forms part). The purpose of this paper is to map the benefits and challenges of using inquiry-based learning (IBL), with reference to ODL and the value added by IBL in terms of education for sustainability (EfS) in Africa.

Design/methodology/approach
– Evidence-based reflection is used to provide a narrative assessment of the experience gained with IBL in two undergraduate sustainability-focussed modules in the Department of Geography at the University of South Africa (Unisa), an ODL provider in Africa and the Global South.

Findings
– Consideration of enabling and limiting factors indicates that although constraints are experienced, adoption of IBL approaches holds potential as pedagogic for EfS in Africa, due to grounding of learning in theory and applied to local places/contexts. This indicates a role for IBL to change perceptions regarding the lack of practical utility of ODL.

Originality/value
– Implementing place-based and contextual IBL is innovative in ODL. It adds value to learning experiences and supports transformative learning, both important components of EfS and addressing a need in the African context. Practitioners will find the experience gained with implementation of IBL, coupled with possibilities associated with information and communication technologies, of value.
On display in East and West
Authors: Gatejel Luminita 
Published: February 2016

Purpose– The purpose of this paper is to show how state socialist countries used soft power to improve their image in the West and advocate “the socialist way of life” in the context of the Cold War.Design/methodology/approach– The author argues from a cultural history perspective that underlines transfers and entanglements among the two camps during the Cold War. The study is based on primary and secondary sources such as automotive periodicals and archival material from the German Bundesarchiv.Findings– International fairs turned in the late 1950s into a new “battlefield” of the Cold War. The Soviet Union and its allies were celebrating at these meetings, important medial victories, laying the grounds for a state socialist consumer society. For the first time, Western audiences were realizing that irrespective of certain stylistic differences, consumer goods and particularly cars were not that different on the other side of the Iron Curtain. However, ideological bias and manufacturing flaws prevented them from being fully acknowledged by the Western side.Originality/value– Cold War research mainly focused on bipolar confrontation and the high-level decision-making process. This study is part of a recent trend in historiography to reassess the history of the Cold War, focusing on the multi-layered interactions between the two camps. It also shows that consumption and material well-being were important topics for understanding the dynamics and the flow of ideas through the Iron Curtain.
Cold War consumption and the marketing of childhood in the Soviet Union and the United States, 1950-1960
Authors: Peacock Margaret 
Published: February 2016

Purpose– This paper aims to explore the relationship between childhood, consumption and the Cold War in 1950s America and the Soviet Union. The author argues that Soviet and American leaders, businessmen, and politicians worked hard to convince parents that buying things for their children offered the easiest way to raise good American and Soviet kids and to do their part in waging the economic battles of the Cold War. The author explores how consumption became a Cold War battleground in the late 1950s and suggests that the history of childhood and Cold War consumption alters the way we understand the conflict itself.Design/Methodology/Approach– Archival research in the USA and the Russian Federation along with close readings of Soviet and American advertisements offer sources for understanding the global discourse of consumption in the 1950s and 1960s.Findings– Leaders, advertisers, and propagandists in the Soviet Union and the USA used the same images in the same ways to sell the ethos of consumption to their populations. They did this to sell the Cold War, to bolster the status quo, and to make profits.Originality/Value– This paper offers a previously unexplored, transnational perspective on the role that consumption and the image of the child played in shaping the Cold War both domestically and abroad.
Cold War binaries and the culture of consumption in the late Soviet home
Authors: Reid Susan E. 
Published: February 2016

Purpose– The purpose of this paper is to challenge Cold War binaries, seeking a more nuanced understanding of popular experience of change in the Soviet Union’s last decades. This was a period of intensive modernization and rapid transformation in Soviet citizens’ everyday material environment, marked by the mass move to newly constructed housing and by changing relations with goods.Design/methodology/approach– To probe popular experience and changing meanings, the paper turns to qualitative, subjective sources, drawing on oral history interviews (Everyday Aesthetics in the Modern Soviet Flat, 2004-2007).Findings– The paper finds that qualitative changes took place in Soviet popular consumer culture during the 1960s-1970s, as millions of people made home in new housing amid the widespread media circulation of authoritative images representing a desirable modern lifestyle and modernist aesthetic. Soviet people began to make aesthetic or semiotic distinctions between functionally identical goods and were concerned to find the right furniture to fit a desired lifestyle, aesthetic ideal and sense of self.Research limitations/implications– The problem is how to conceptualize the trajectory of change in ways that do justice to historical subjects’ experience and narratives, while avoiding uncritically reproducing Cold War binaries or perpetuating the normative status claimed by the postwar West in defining modernity and consumer culture.Originality/value– The paper challenges dominant Cold War narratives, according to which Soviet popular relations with goods were encompassed by shortage and necessity. It advances understanding of the specific form of modern consumer culture, which, it argues, took shape in the USSR after Stalin.
Oral tofacitinib efficacy, safety and tolerability in Japanese patients with moderate to severe plaque psoriasis and psoriatic arthritis: A randomized, double‐blind, phase 3 study
Authors: Asahina Akihiko , Etoh Takafumi , Igarashi Atsuyuki , Imafuku Shinichi , Saeki Hidehisa , Shibasaki Yoshiyuki , Tomochika Yukiko , Toyoizumi Shigeyuki , Nagaoka Makoto , Ohtsuki Mamitaro ,   the study investigators
Published: February 2016

AbstractTofacitinib is an oral Janus kinase inhibitor that is being investigated for psoriasis and psoriatic arthritis. Japanese patients aged 20 years or more with moderate to severe plaque psoriasis and/or psoriatic arthritis were double‐blindly randomized 1:1 to tofacitinib 5 or 10 mg b.i.d. for 16 weeks, open‐label 10 mg b.i.d. for 4 weeks, then variable 5 or 10 mg b.i.d. to Week 52. Primary end‐points at Week 16 were the proportion of patients achieving at least a 75% reduction in Psoriasis Area and Severity Index (PASI75) and Physician's Global Assessment of “clear” or “almost clear” (PGA response) for psoriasis, and 20% or more improvement in American College of Rheumatology criteria (ACR20) for patients with psoriatic arthritis. Safety was assessed throughout. Eighty‐seven patients met eligibility criteria for moderate to severe plaque psoriasis (5 mg b.i.d., n = 43; 10 mg b.i.d., n = 44), 12 met eligibility criteria for psoriatic arthritis (5 mg b.i.d., n = 4; 10 mg b.i.d., n = 8) including five who met both criteria (10 mg b.i.d.). At Week 16, 62.8% and 72.7% of patients achieved PASI75 with tofacitinib 5 and 10 mg b.i.d., respectively; 67.4% and 68.2% achieved PGA responses; all patients with psoriatic arthritis achieved ACR20. Responses were maintained through Week 52. Adverse events occurred in 83% of patients through Week 52, including four (4.3%) serious adverse events and three (3.2%) serious infections (all herpes zoster). No malignancies, cardiovascular events or deaths occurred. Tofacitinib (both doses) demonstrated efficacy in patients with moderate to severe plaque psoriasis and/or psoriatic arthritis through 52 weeks; safety findings were generally consistent with prior studies.
Primary hyperhidrosis: Implications on symptoms, daily life, health and alcohol consumption when treated with botulinum toxin
Authors: Shayesteh Alexander , Boman Jens , Janlert Urban , Brulin Christine , Nylander Elisabet 
Published: February 2016

AbstractPrimary hyperhidrosis affects approximately 3% of the population and reduces quality of life in affected persons. Few studies have investigated the symptoms of anxiety, depression and hazardous alcohol consumption among those with hyperhidrosis and the effect of treatment with botulinum toxin. The first aim of this study was to investigate the effect of primary hyperhidrosis on mental and physical health, and alcohol consumption. Our second aim was to study whether and how treatment with botulinum toxin changed these effects. One hundred and fourteen patients answered questionnaires regarding hyperhidrosis and symptoms, including hyperhidrosis disease severity scale (HDSS), visual analog scale (VAS) 10‐point scale for hyperhidrosis symptoms, hospital anxiety and depression scale (HADS), alcohol use disorder identification test (AUDIT) and short‐form health survey (SF‐36) before treatment with botulinum toxin and 2 weeks after. The age of onset of hyperhidrosis was on average 13.4 years and 48% described heredity for hyperhidrosis. Significant improvements were noted in patients with axillary and palmar hyperhidrosis regarding mean HDSS, VAS 10‐point scale, HADS, SF‐36 and sweat‐related health problems 2 weeks after treatment with botulinum toxin. Changes in mean AUDIT for all participants were not significant. Primary hyperhidrosis mainly impairs mental rather than physical aspects of life and also interferes with specific daily activities of the affected individuals. Despite this, our patients did not show signs of anxiety, depression or hazardous alcohol consumption. Treatment with botulinum toxin reduced sweat‐related problems and led to significant improvements in HDSS, VAS, HADS and SF‐36 in our patients.
Neutrophil extracellular Taps play an important role in clearance of Streptococcus suis in vivo
Authors: Zhao Jianqing , Lin Lan , Fu Lei , Han Li , Zhang Anding 
Published: February 2016

ABSTRACTStreptococcus suis infection induces formation of neutrophil extracellular traps (NETs) in vitro; however, the contribution of NETs‐mediated killing to the pathogenesis of S. suis in vivo is yet to be elicited. The findings of the present study indicated that extracellular DNA fiber can be induced in a murine model in response to S. suis infection. A nuclease that destroys their structure was used to evaluate the role of NETs on S. suis infection. Treatment with nuclease resulted in a greater bacteria load and higher serum TNF‐α concentrations in response to S. suis infection, indicating that NETs structure played an essential role in S. suis clearance and inflammation. Furthermore, nuclease treatment resulted in more severe clinical signs during and higher mortality from S. suis infection. These findings indicated that NETs structure contributes to protection against S. suis infection.
The Economics of Disclosure and Financial Reporting Regulation: Evidence and Suggestions for Future Research
Authors: LEUZ CHRISTIAN , WYSOCKI PETER D. 
Published: February 2016

ABSTRACTThis paper discusses the empirical literature on the economic consequences of disclosure and financial reporting regulation, drawing on U.S. and international evidence. Given the policy relevance of research on regulation, we highlight the challenges with (1) quantifying regulatory costs and benefits, (2) measuring disclosure and reporting outcomes, and (3) drawing causal inferences from regulatory studies. Next, we discuss empirical studies that link disclosure and reporting activities to firm‐specific and market‐wide economic outcomes. Understanding these links is important when evaluating regulation. We then synthesize the empirical evidence on the economic effects of disclosure regulation and reporting standards, including the evidence on International Financial Reporting Standards (IFRS) adoption. Several important conclusions emerge. We generally lack evidence on market‐wide effects and externalities from regulation, yet such evidence is central to the economic justification of regulation. Moreover, evidence on causal effects of disclosure and reporting regulation is still relatively rare. We also lack evidence on the real effects of such regulation. These limitations provide many research opportunities. We conclude with several specific suggestions for future research.
What Works?
Authors: Schell‐Busey Natalie , Simpson Sally S. , Rorie Melissa , Alper Mariel 
Published: February 2016

Research SummaryWe conducted a meta‐analysis of corporate crime deterrence strategies by using 80 effect sizes calculated from 58 studies in four treatment areas—Law, Punitive Sanctions, Regulatory Policy, and Multiple Treatments. Of the single‐treatment strategies, only Regulatory Policy produced a significant deterrent impact at the company level, but the results were not consistent across all study and effect size types. Studies examining multiple treatments, though, produced a consistent, significant deterrent effect on offending at both the individual and company levels.Policy ImplicationsOur results suggest that regulatory policies that involve consistent inspections and include a cooperative or educational component aimed at the industry may have a substantial impact on corporate offending. However, a mixture of agency interventions will likely have the biggest impact on broadly defined corporate crime. The variety of offenders and behaviors included in corporate crime and its relative complexity likely necessitate multiple intervention strategies, which is similar to the “pulling levers” approach developed to deter gang violence and the responsive regulation strategy advocated by Braithwaite (2011). However, given some of the shortcomings in the literature, we also recommend that scholars and practitioners more clearly and consistently define the phenomenon of “corporate crime” and target evaluation research toward specific programs and interventions.