bluuebunny/crossref_metadata_2025_split huggingface dataset:
NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts
Authors: Kurs Jason P. , Simi Manuele , Campagne Fabien 
Published: February 2016

ABSTRACTComputational workflows and pipelines are often created to automate series of processing steps. For instance, workflows enable one to standardize analysis for large projects or core facilities, but are also useful for individual biologists who need to perform repetitive data processing. Some workflow systems, designed for beginners, offer a graphical user interface and have been very popular with biologists. In practice, these tools are infrequently used by more experienced bioinformaticians, who may require more flexibility or performance than afforded by the user interfaces, and seem to prefer developing workflows with scripting or command line tools. Here, we present a workflow system, the NextflowWorkbench (NW), which was designed for both beginners and experts, and blends the distinction between user interface and scripting language. This system extends and reuses the popular Nextflow workflow description language and shares its advantages. In contrast to Nextflow, NextflowWorkbench offers an integrated development environment that helps complete beginners get started with workflow development. Auto-completion helps beginners who do not know the syntax of the Nextflow language. Reusable processes provide modular workflows. Programmers will benefit from unique interactive features that help users work more productively with docker containers. We illustrate this tool with a workflow to estimate RNA-Seq counts using Kallisto. We found that beginners can be taught how to assemble this workflow in a two hours training session. NW workflows are portable and can execute on laptop/desktop computers with docker, on a lab cluster, or in the cloud to facilitate training. NextflowWorkbench is open-source and available athttp://workflow.campagnelab.org.
Security behaviors of smartphone users
Authors: Das Amit , Khan Habib Ullah 
Published: February 2016

Purpose
– This paper aims to report on the information security behaviors of smartphone users in an affluent economy of the Middle East.

Design/methodology/approach
– A model based on prior research, synthesized from a thorough literature review, is tested using survey data from 500 smartphone users representing three major mobile operating systems.

Findings
– The overall level of security behaviors is low. Regression coefficients indicate that the efficacy of security measures and the cost of adopting them are the main factors influencing smartphone security behaviors. At present, smartphone users are more worried about malware and data leakage than targeted information theft.

Research limitations/implications
– Threats and counter-measures co-evolve over time, and our findings, which describe the state of smartphone security at the current time, will need to be updated in the future.

Practical implications
– Measures to improve security practices of smartphone users are needed urgently. The findings indicate that such measures should be broadly effective and relatively costless for users to implement.

Social implications
– Personal smartphones are joining enterprise networks through the acceptance of Bring-Your-Own-Device computing. Users’ laxity about smartphone security thus puts organizations at risk.

Originality/value
– The paper highlights the key factors influencing smartphone security and compares the situation for the three leading operating systems in the smartphone market.
Private label brands in an emerging economy: an exploratory study in India
Authors: Sarkar Siddhartha , Sharma Dinesh , Kalro Arti D. 
Published: February 2016

Purpose
– The purpose of this paper is to present different naming, packaging, and pricing strategies adopted by private label (PL) retailers in India. This study also aims to identify preferred private label brand (PLB) categories, factors influencing their selection, and the importance of cues in evaluation of PLBs. The overall purpose is to identify important areas for future research of PLBs in the wake of organized retail growth in an emerging economy (India is the context here).

Design/methodology/approach
– This study is based on in-store observations of major Indian retail chains, longitudinal analyses of customers’ shopping bills, qualitative analyses of consumer interviews, and focus group discussions.

Findings
– The results indicate that retailers primarily adopt “Sub-branding” (using the store name along with a separate brand name) and “House of Brands” (using a separate brand name only) strategies to sell PLBs in the Indian market. Groceries, food and beverages, and apparel are the preferred categories in PLB. Price, quality, and convenience are the major factors influencing PLB. Taste, ingredients, packaging, price, brand name, and store name are the main factors that are used to evaluate PLBs.

Research limitations/implications
– Due to the qualitative analyses and interpretation, there are limitations to this study which need to be empirically validated.

Practical implications
– This research has implications for organized retailers in understanding the various strategies used for PLBs in India.

Originality/value
– This study is a novel study for documenting the PLB strategies adopted by organized retailers in India. It also uses a longitudinal exploratory approach to further understanding the consumption of PLBs in India.
Interest, views and perceived barriers to bariatric surgery in patients with morbid obesity
Authors: Wharton S. , Serodio K. J. , Kuk J. L. , Sivapalan N. , Craik A. , Aarts M.‐A. 
Published: February 2016

SummaryThe objective of the study was to assess the interest, views and patient‐perceived barriers to bariatric surgery among surgery‐eligible patients. Surveys were completed at a weight management clinic and local hospital in Ontario, Canada. Patients were ≥18 years of age with a body mass index (BMI) >40 kg m−2 or BMI > 35 kg m−2 with ≥1 comorbidity. The sample included 105 participants, 73.3% female, with a mean BMI of 46.6 ± 7.1 kg m−2. Only 33.3% of participants were interested in surgery; 50.5% of participants were not interested and 16.2% had mixed feelings. Participants identified risks (69.5%) and side effects (57.1%) as significant surgical barriers. Interested participants were more likely to perceive themselves as obese, were unhappy with their current weight loss method and were less likely to fear surgery (P < 0.05). The prevalence of comorbidities was not different by surgical interest (P = 0.17). Despite the effectiveness of bariatric surgery, the majority of qualified patients are not interested in surgery mainly due to the perceived risk of surgery in general and satisfaction with current non‐surgical weight loss efforts. The self‐perception of obesity, as opposed to medical comorbidities, may be a stronger driver of the decision to have bariatric surgery. It is unclear if patients are aware of the effectiveness of bariatric surgery to help improve comorbidities or if bariatric surgery is perceived as being more cosmetic in nature.
Photosensitivity of murine skin greatly depends on the genetic background: clinically relevant dose as a new measure to replace minimal erythema dose in mouse studies
Authors: Gyöngyösi Nóra , Lőrincz Kende , Keszeg András , Haluszka Dóra , Bánvölgyi András , Tátrai Erika , Kárpáti Sarolta , Wikonkál Norbert M. 
Published: February 2016

AbstractArtificial UV irradiation of murine skin is a frequently used method for testing photosensitivity, study carcinogenesis and photoprotective effects of different compounds. However, doses of UV radiation and mouse strains used in experiments vary greatly. The genetic background of mice may influence the photosensitivity as melanin content, pigmentation and hair cycle parameters are dissimilar. Doses of UV are often expressed in relation to the minimal erythema dose (MED) that was not necessarily determined for the given strain. We set out to standardize the method of measuring photosensitivity in three commonly used mouse strains, C57BL/6N, Balb/c and SKH‐1. We found that MED may not be determined for some strains as erythema development in mice with diverse genotypes differs greatly. We measured the oedema response in vivo and ex vivo by using OCT. Given the strain‐specific variability of erythema, we introduced Clinically Relevant Dose (CRD) as a new term to replace MED in experiments, to describe the lowest dose that triggers a perceptible skin reaction in mice. Not only the CRD but the proportion of erythema and oedema were different in strains examined. C57BL/6N mice display skin reactions at the lowest UVB dose, while SKH‐1 hairless mice show changes, mostly oedema, after higher doses of UVB. The cellular composition and skin thickness were examined by histopathology. IL‐1beta and IL‐6 levels in skin correlated with the increasing doses of UVB. Despite the variations in the degree of erythema and oedema, no major differences in cytokine expressions were seen among various strains of mice.
Mast cell histamine‐mediated transient inflammation following exposure to nickel promotes nickel allergy in mice
Authors: Kinbara Masayuki , Bando Kanan , Shiraishi Daisuke , Kuroishi Toshinobu , Nagai Yasuhiro , Ohtsu Hiroshi , Takano‐Yamamoto Teruko , Sugawara Shunji , Endo Yasuo 
Published: February 2016

AbstractWe previously reported that allergic responses to nickel (Ni) were minimal in mice deficient in the histamine‐forming enzyme histidine decarboxylase (HDC‐KO), suggesting an involvement of histamine in allergic responses to Ni. However, it remains unclear how histamine is involved in the process of Ni allergy. Here, we examined the role of histamine in Ni allergy using a murine model previously established by us. Mice were sensitized to Ni by intraperitoneal injection of a NiCl2‐lipopolysaccharide (LPS) mixture. Ten days later, allergic inflammation was elicited by challenging ear‐pinnas intradermally with NiCl2. Then, ear‐swelling was measured. Pyrilamine (histamine H1‐receptor antagonist) or cromoglicate (mast cell stabilizer) was intravenously injected 1 h before the sensitization or the challenge. In cell‐transfer experiments, spleen cells from Ni‐sensitized donor mice were intravenously transferred into non‐sensitized recipient mice. In both sensitized and non‐sensitized mice, 1 mm or more NiCl2 (injected into ear‐pinnas) induced transient non‐allergic inflammation (Ni‐TI) with accompanying mast cell degranulation. LPS did not affect the magnitude of this Ni‐TI. Pyrilamine and cromoglicate reduced either the Ni‐TI or the ensuing allergic inflammation when administered before Ni‐TI (at either the sensitization or elicitation step), but not if administered when the Ni‐TI had subsided. Experiments on HDC‐KO and H1‐receptor‐KO mice, and also cell‐transfer experiments using these mice, demonstrated histamine's involvement in both the sensitization and elicitation steps. These results suggest that mast cell histamine‐mediated Ni‐TI promotes subsequent allergic inflammatory responses to Ni, raising the possibility that control of Ni‐TI by drugs may be effective at preventing or reducing Ni allergy.
Associations between adiposity and indicators of thyroid status in children and adolescents
Authors: Krause A. J. , Cines B. , Pogrebniak E. , Sherafat‐Kazemzadeh R. , Demidowich A. P. , Galescu O. A. , Brady S. M. , Reynolds J. C. , Hubbard V. S. , Yanovski J. A. 
Published: February 2016

SummaryBackgroundIn adults, obesity is associated with abnormalities of thyroid function; there are fewer studies in paediatric cohorts.ObjectivesTo examine associations of weight and adiposity with indices of thyroid function and thyroid‐related metabolic factors in children.Design/MethodsA sample of 1203 children without obesity (body mass index [BMI] < 95th percentile; N = 631) and with obesity (BMI ≥ 95th percentile; N = 572), age 5–18 years, had height and weight measured (to calculate BMI‐Z score for age and sex) and had blood collected in the morning for thyroid‐stimulating hormone (TSH), free thyroxine (FT4) and leptin. A subset (N = 829) also underwent measurement of fat mass by dual‐energy X‐ray absorptiometry. Analyses examined associations of TSH and FT4 with adiposity and obesity‐related conditions accounting for sociodemographic factors.ResultsThyroid‐stimulating hormone was positively related to BMIz and fat mass (both p‐values < 0.001). FT4 was negatively related to BMIz and fat mass (both p‐values < 0.001). TSH was positively correlated to leptin (p = 0.001) even after accounting for fat mass.ConclusionsPaediatric obesity is associated with higher TSH and lower FT4 concentrations and with a greater prevalence of abnormally high TSH. Leptin concentrations may in part explain obesity's effects on thyroid status, perhaps through leptin's effects on TSH secretion.
Clopidogrel, prasugrel or ticagrelor in patients with acute coronary syndromes undergoing percutaneous coronary intervention
Authors: Yudi M. B. , Clark D. J. , Farouque O. , Eccleston D. , Andrianopoulos N. , Duffy S. J. , Brennan A. , Lefkovits J. , Ramchand J. , Yip T. , Oqueli E. , Reid C. M. , Ajani A. E. ,   Melbourne Interventional Group
Published: February 2016

BackgroundGuidelines recommend prasugrel or ticagrelor instead of clopidogrel in patients with acute coronary syndromes (ACS) undergoing percutaneous coronary interventions (PCI).AimWe sought to describe the trends in uptake of the newer agents and analyse the clinical characteristics and short‐term outcomes of patients treated with clopidogrel, prasugrel or ticagrelor.MethodsWe analysed the temporal trends of antiplatelet use since the availability of prasugrel (2009–2013) in patients with ACS from the Melbourne Interventional Group registry. To assess clinical characteristics and outcomes, we included 1850 patients from 2012 to 2013, corresponding to the time all three agents were available. The primary outcome was major adverse cardiovascular events (MACE). The safety end‐point was in‐hospital bleeding.ResultsFor the period of 2009–2013, the majority of patients were treated with clopidogrel (72%) compared with prasugrel (14%) or ticagrelor (14%). There was a clear trend towards ticagrelor by the end of 2013. Patients treated with clopidogrel were more likely to present with non‐ST‐elevation ACS, be older, and have more comorbidities. There was no difference in unadjusted 30‐day mortality (0.9 vs 0.5 vs 1.0%, P = 0.76), myocardial infarction (2 vs 1 vs 2%, P = 0.52) or MACE (3 vs 3 vs 4%, P = 0.57) between the three agents. There was no difference in in‐hospital bleeding (3 vs 2 vs 2%, P = 0.64).ConclusionPrasugrel and ticagrelor are increasingly used in ACS patients treated with PCI, predominantly in a younger cohort with less comorbidity. Although antiplatelet therapy should still be individualised based on the thrombotic and bleeding risk, our study highlights the safety of the new P2Y12
inhibitors in contemporary Australian practice.
Neutronic Design Features of a Transportable Fluoride-Salt-Cooled High-Temperature Reactor
Authors: Sun Kaichao , Hu Lin-Wen , Forsberg Charles 
Published: February 2016

The fluoride-salt-cooled high-temperature reactor (FHR) is a new reactor concept, which combines low-pressure liquid salt coolant and high-temperature tristructural isotropic (TRISO) particle fuel. The refractory TRISO particle coating system and the dispersion in graphite matrix enhance safeguards (nuclear proliferation resistance) and security. Compared to the conventional high-temperature reactor (HTR) cooled by helium gas, the liquid salt system features significantly lower pressure, larger volumetric heat capacity, and higher thermal conductivity. The salt coolant enables coupling to a nuclear air-Brayton combined cycle (NACC) that provides base-load and peak-power capabilities. Added peak power is produced using jet fuel or locally produced hydrogen. The FHR is, therefore, considered as an ideal candidate for the transportable reactor concept to provide power to remote sites. In this context, a 20-MW (thermal power) compact core aiming at an 18-month once-through fuel cycle is currently under design at Massachusetts Institute of Technology (MIT). One of the key challenges of the core design is to minimize the reactivity swing induced by fuel depletion, since excessive reactivity will increase the complexity in control rod design and also result in criticality risk during the transportation process. In this study, burnable poison particles (BPPs) made of B4C with natural boron (i.e., 20% B10 content) are adopted as the key measure for fuel cycle optimization. It was found that the overall inventory and the individual size of BPPs are the two most important parameters that determine the evolution path of the multiplication factor over time. The packing fraction (PF) in the fuel compact and the height of active zone are of secondary importance. The neutronic effect of Li6 depletion was also quantified. The 18-month once-through fuel cycle is optimized, and the depletion reactivity swing is reduced to 1 beta. The reactivity control system, which consists of six control rods and 12 safety rods, has been implemented in the proposed FHR core configuration. It fully satisfies the design goal of limiting the maximum reactivity worth for single control rod ejection within 0.8 beta and ensuring shutdown margin with the most valuable safety rod fully withdrawn. The core power distribution including the control rod’s effect is also demonstrated in this paper.
Identification and Characterization of a Novel Broad-Spectrum Virus Entry Inhibitor
Authors: Chou Yi-ying , Cuevas Christian , Carocci Margot , Stubbs Sarah H. , Ma Minghe , Cureton David K. , Chao Luke , Evesson Frances , He Kangmin , Yang Priscilla L. , Whelan Sean P. , Ross Susan R. , Kirchhausen Tom , Gaudin Raphaël 
Published: February 2016

ABSTRACT
Virus entry into cells is a multistep process that often requires the subversion of subcellular machineries. A more complete understanding of these steps is necessary to develop new antiviral strategies. While studying the potential role of the actin network and one of its master regulators, the small GTPase Cdc42, during Junin virus (JUNV) entry, we serendipitously uncovered the small molecule ZCL278, reported to inhibit Cdc42 function as an entry inhibitor for JUNV and for vesicular stomatitis virus, lymphocytic choriomeningitis virus, and dengue virus but not for the nonenveloped poliovirus. Although ZCL278 did not interfere with JUNV attachment to the cell surface or virus particle internalization into host cells, it prevented the release of JUNV ribonucleoprotein cores into the cytosol and decreased pH-mediated viral fusion with host membranes. We also identified SVG-A astroglial cell-derived cells to be highly permissive for JUNV infection and generated new cell lines expressing fluorescently tagged Rab5c or Rab7a or lacking Cdc42 using clustered regularly interspaced short palindromic repeat (CRISPR)-caspase 9 (Cas9) gene-editing strategies. Aided by these tools, we uncovered that perturbations in the actin cytoskeleton or Cdc42 activity minimally affect JUNV entry, suggesting that the inhibitory effect of ZCL278 is not mediated by ZCL278 interfering with the activity of Cdc42. Instead, ZCL278 appears to redistribute viral particles from endosomal to lysosomal compartments. ZCL278 also inhibited JUNV replication in a mouse model, and no toxicity was detected. Together, our data suggest the unexpected antiviral activity of ZCL278 and highlight its potential for use in the development of valuable new tools to study the intracellular trafficking of pathogens.

IMPORTANCE
The Junin virus is responsible for outbreaks of Argentine hemorrhagic fever in South America, where 5 million people are at risk. Limited options are currently available to treat infections by Junin virus or other viruses of the
Arenaviridae
, making the identification of additional tools, including small-molecule inhibitors, of great importance. How Junin virus enters cells is not yet fully understood. Here we describe new cell culture models in which the cells are susceptible to Junin virus infection and to which we applied CRISPR-Cas9 genome engineering strategies to help characterize early steps during virus entry. We also uncovered ZCL278 to be a new antiviral small molecule that potently inhibits the cellular entry of the Junin virus and other enveloped viruses. Moreover, we show that ZCL278 also functions
in vivo
, thereby preventing Junin virus replication in a mouse model, opening the possibility for the discovery of ZCL278 derivatives of therapeutic potential.
Functional Dissection of an Alternatively Spliced Herpesvirus Gene by Splice Site Mutagenesis
Authors: Schommartz Tim , Loroch Stefan , Alawi Malik , Grundhoff Adam , Sickmann Albert , Brune Wolfram 
Published: February 2016

ABSTRACT
Herpesviruses have large and complex DNA genomes. The largest among the herpesviruses, those of the cytomegaloviruses, include over 170 genes. Although most herpesvirus gene products are expressed from unspliced transcripts, a substantial number of viral transcripts are spliced. Some viral transcripts are subject to alternative splicing, which leads to the expression of several proteins from a single gene. Functional analysis of individual proteins derived from an alternatively spliced gene is difficult, as deletion and nonsense mutagenesis, both common methods used in the generation of viral gene knockout mutants, affect several or all gene products at the same time. Here, we show that individual gene products of an alternatively spliced herpesvirus gene can be inactivated selectively by mutagenesis of the splice donor or acceptor site and by intron deletion or substitution mutagenesis. We used this strategy to dissect the essential M112/113 gene of murine cytomegalovirus (MCMV), which encodes the MCMV Early 1 (E1) proteins. The expression of each of the four E1 protein isoforms was inactivated individually, and the requirement for each isoform in MCMV replication was analyzed in fibroblasts, endothelial cells, and macrophages. We show that the E1 p87 isoform, but not the p33, p36, and p38 isoforms, is essential for viral replication in cell culture. Moreover, the presence of one of the two medium-size isoforms (p36 or p38) and the presence of intron 1, but not its specific sequence, are required for viral replication. This study demonstrates the usefulness of splice site mutagenesis for the functional analysis of alternatively spliced herpesvirus genes.

IMPORTANCE
Herpesviruses include up to 170 genes in their DNA genomes. The functions of most viral gene products remain poorly defined. The construction of viral gene knockout mutants has thus been an important tool for functional analysis of viral proteins. However, this strategy is of limited use when viral gene transcripts are alternatively spliced, leading to the expression of several proteins from a single gene. In this study, we showed, as a proof of principle, that each protein product of an alternatively spliced gene can be eliminated individually by splice site mutagenesis. Mutant viruses lacking individual protein products displayed different phenotypes, demonstrating that the products of alternatively spliced genes have nonredundant functions.