bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuromodulation leads to a burst-tonic switch in a subset of VIP neurons in mouse primary somatosensory (barrel) cortex
Authors: Prönneke Alvar , Witte Mirko , Möck Martin , Staiger Jochen F. 
Published: November 2018

AbstractNeocortical GABAergic interneurons expressing vasoactive intestinal polypeptide (VIP) contribute to sensory processing, sensorimotor integration and behavioral control. In contrast to other major subpopulations of GABAergic interneurons, VIP neurons show a remarkable diversity. Studying morphological and electrophysiological properties of VIP cells, we found a peculiar group of neurons in layer II/III of mouse primary somatosensory (barrel) cortex, which showed a highly dynamic burst firing behavior at resting membrane potential that switched to tonic mode at depolarized membrane potentials. Furthermore, we demonstrate that burst firing depends on T-type calcium channels. The burst-tonic switch could be induced by acetylcholine and serotonin. Acetylcholine mediated a depolarization via nicotinic receptors whereas serotonin evoked a biphasic depolarization via ionotropic and metabotropic receptors in 48% of the population and a purely monophasic depolarization via metabotropic receptors in the remaining cells. These data disclose an electrophysiologically-defined subpopulation of VIP neurons that via neuromodulator-induced changes in firing behavior is likely to regulate the state of cortical circuits in a profound manner.
NGOMICS-WF, a Bioinformatic Workflow Tool for Batch Omics Data Analysis
Authors: Li Weizhong 
Published: November 2018

AbstractIn recent years, high throughput next generation omics data have been broadly used in many research fields. However, analyzing omics data is still very challenging, especially for researchers with less experience in bioinformatics, software, and programming. Omics data analysis workflows usually are composed of many processes involving different software tools that demand different compute resources. So, it is often difficult to perform a full workflow in an automated way, despite that many computational tools and resources are available. Here I present NGOMICS-WF, a lightweight workflow tool for batch omics data analysis. This workflow tool has been used in several projects. It can assist researchers to configure and run workflows for various types of omics data on Linux computers or Linux computer clusters. The software package is available from https://github.com/weizhongli/ngomicswf. In addition to the workflow tool, several pre-configured workflows that were tested and published are also available in the package. These pre-configured workflows can be directly used or be used as templates to configure new workflows to analyze metagenomic, metatranscriptomic, RNA-seq and 16S data.
Resistance at No Cost: The Transmissibility and Potential for Disease Progression of Drug-ResistantM. Tuberculosis
Authors: Becerra Mercedes C. , Huang Chuan-Chin , Lecca Leonid , Bayona Jaime , Contreras Carmen , Calderon Roger , Yataco Rosa , Galea Jerome , Zhang Zibiao , Atwood Sidney , Cohen Ted , Mitnick Carole D. , Farmer Paul , Murray Megan 
Published: November 2018

AbstractBackgroundThe future trajectory of drug resistant tuberculosis strongly depends on the fitness costs of drug resistance mutations. Here, we measured the association of phenotypic drug resistance and the risk of TB infection and disease among household contacts (HHCs) of patients with pulmonary TB.MethodsWe evaluated 12767 HHCs of patients with drug sensitive and resistant pulmonary TB at baseline, two, six, and 12 months to ascertain infection status and to determine whether they developed tuberculosis disease. We also assessed the impact of drug resistance phenotype on the likelihood that a TB strain shared a genetic fingerprint with at least one other TB patient in the cohort.FindingsAmong 3339 TB patients for whom were DST available, 1274 (38%) had TB that was resistant to at least one drug and 478 (14⋅3%) had multi-drug resistant (MDR) TB, i.e. TB resistant to both INH and rifampicin. Compared to HHCs of drug sensitive TB patients, those exposed to a patient with MDR-TB had an 8% (95% CI: 4-13%) higher risk of infection by the end of follow up. We found no statistically significant difference in the relative hazard of incident TB disease among HHCs exposed to MDR-TB compared to DS-TB (Adjusted HR 1⋅28 [(95% CI: ⋅9-1⋅83]). Patients with MDR-TB were more likely to be part of a genetic cluster than were DS-TB patients.InterpretationClinical strains of MDR M. tuberculosis are neither less transmissible than drug sensitive strains nor less likely to cause disease. (ClinicalTrials.gov number,NCT00676754)FundingNational Institutes of Health: NIH/NIAID CETR U19AI109755StatementAll authors have seen the manuscript and approved the manuscript.
Identification of single nucleotide variants using position-specific error estimation in deep sequencing data
Authors: Kleftogiannis Dimitrios , Punta Marco , Jayaram Anuradha , Sandhu Shahneen , Wong Stephen Q. , Gasi Tandefelt Delila , Conteduca Vincenza , Wetterskog Daniel , Attard Gerhardt , Lise Stefano 
Published: November 2018

AbstractBackgroundTargeted deep sequencing is a highly effective technology to identify known and novel single nucleotide variants (SNVs) with many applications in translational medicine, disease monitoring and cancer profiling. However, identification of SNVs using deep sequencing data is a challenging computational problem as different sequencing artifacts limit the analytical sensitivity of SNV detection, especially at low variant allele frequencies (VAFs).MethodsTo address the problem of relatively high noise levels in amplicon-based deep sequencing data (e.g. with the Ion AmpliSeq technology) in the context of SNV calling, we have developed a new bioinformatics tool called AmpliSolve. AmpliSolve uses a set of normal samples to model position-specific, strand-specific and nucleotide-specific background artifacts (noise), and deploys a Poisson model-based statistical framework for SNV detection.ResultsOur tests on both synthetic and real data indicate that AmpliSolve achieves a good trade-off between precision and sensitivity, even at VAF below 5% and as low as 1%. We further validate AmpliSolve by applying it to the detection of SNVs in 96 circulating tumor DNA samples at three clinically relevant genomic positions and compare the results to digital droplet PCR experiments.ConclusionsAmpliSolve is a new tool for in-silico estimation of background noise and for detection of low frequency SNVs in targeted deep sequencing data. Although AmpliSolve has been specifically designed for and tested on amplicon-based libraries sequenced with the Ion Torrent platform it can, in principle, be applied to other sequencing platforms as well. AmpliSolve is freely available at https://github.com/dkleftogi/AmpliSolve.
Gentamicin B1 is not a minor gentamicin component with major nonsense mutation suppression activity
Authors: Baradaran-Heravi Alireza , Williams David E. , Powell David A. , Balgi Aruna D. , Andersen Raymond J. , Roberge Michel 
Published: November 2018

AbstractNonsense mutations are single base substitutions that introduce a premature termination codon (PTC) preventing the formation of full-length protein. They are the causative mutations in about 10% of patients in a large number of rare genetic diseases. High concentrations of the antibiotic gentamicin can induce the incorporation of an amino acid at a PTC and formation of full-length protein, a process called PTC readthrough. Gentamicin is composed of several related aminoglycosides. We recently reported (doi/10.1073/pnas.1620982114) that the major gentamicin components that are responsible for its antibacterial activity showed weak to no PTC readthrough activity but that the minor component gentamicin B1 was a potent readthrough inducer. We have now determined that gentamicin B1 acquired from the sole supplier at the time the study was carried out was not gentamicin B1 but instead the closely related aminoglycoside G418. Gentamicin B1 recently became available from a second commercial source. Here, we provide nuclear magnetic resonance (NMR) assignment data for the two commercial compounds and verify only the second is indeed gentamicin B1. We show that gentamicin B1 lacks PTC readthrough activity in HDQ-P1 and DMS-114 cells homozygous for the TP53 R213X nonsense mutation, as well as in a cell-free translation assay.
Watching antibiotics in action: Exploiting time-lapse microfluidic microscopy as a tool for target-drug interaction studies inMycobacterium
Authors: Trojanowski Damian , Kołodziej Marta , Hołówka Joanna , Müller Rolf , Zakrzewska-Czerwińska Jolanta 
Published: November 2018

AbstractSpreading resistance to antibiotics and the emergence of multidrug-resistant strains have become frequent in many bacterial species, including mycobacteria. The genusMycobacteriumencompasses both human and animal pathogens that cause severe diseases and have profound impacts on global health and the world economy. Here, we used a novel system of microfluidics, fluorescence microscopy and target-tagged fluorescent reporter strains ofM.smegmatisto perform real-time monitoring of replisome and chromosome dynamics following the addition of replication-altering drugs (novobiocin, nalidixic acid and griselimycin) at the single-cell level. We found that novobiocin stalled replication forks and caused relaxation of the nucleoid, nalidixic acid triggered rapid replisome collapse and compaction of the nucleoid, and griselimycin caused replisome instability with subsequent over-initiation of chromosome replication and over-relaxation of the nucleoid. This work is an example of using a microscopy-based approach to evaluate the activity of potential replication inhibitors and provides mechanistic insights into their modes of action. Our system also enabled us to observe how the tested antibiotics affected the physiology of mycobacterial cells (i.e., growth, chromosome segregation, etc.). Because proteins involved in the DNA replication are well conserved among bacteria (including mycobacterial species), the properties of various replication inhibitors observed here in fast-growingM. smegmatismay be easily extrapolated to slow-growing pathogenic tubercle bacilli, such asM. tuberculosis.SignificanceThe growing problem of bacterial resistance to antibiotics and the emergence of new strains that are resistant to multiple drugs raise the need to explore new antibiotics and re-evaluate the existing options. Here, we present a system that allows the action of antibiotics to be monitored at the single-cell level. Such studies are important in the light of bacterial heterogeneity, which may be enhanced in unfavorable conditions, such as under antibiotic treatment. Moreover, our studies provide mechanistic insights into the action modes of the tested compounds. As combined therapies have recently gained increased interest, it is also notable that our described system may help researchers identify the best combination of antimicrobials for use against infections caused by a variety of bacteria.
A nonsense mutant of the hepatitis B virus large S protein antagonizes multiple tumor suppressor pathways through c-Jun activation domain-binding protein1
Authors: Chiu Shu-Yi , Chung Hsiang-Ju , Chen Ya-Ting , Huang Min-Syuan , Huang Chien-Chih , Huang Shiu-Feng , Matsuura Isao 
Published: November 2018

AbstractHepatitis B virus (HBV) is a major cause of hepatocellular carcinoma (HCC). Previous studies have identified recurrent nonsense mutations in the HBV large S (LHBs) gene from the liver from HBV core antigen-positive HCC patients. These nonsense mutants have been shown to be oncogenic in mouse xenograft models using a mouse embryonic fibroblast cell line. Here, we expressed in a liver cell line Huh-7 a carboxy terminally truncated protein from a nonsense mutant of the LHBs gene, sW182* (stop codon at tryptophane-182). Although the sW182* protein appeared not to be very stable in the cultured liver cells, we confirmed that the protein can be highly expressed and retained for a prolonged period of time in the hepatocytes in the mouse liver, indicating its stable nature in the physiological condition.In the Huh-7 cells, the sW182* mutant downregulated tumor suppressors p53 and Smad4. This downregulation was reversed by a proteasome inhibitor MG132, implying the involvement of proteasome-based protein degradation in the observed regulation of the tumor suppressors. On the other hand, we found that c-Jun activation domain-binding protein 1 (Jab1) physically interacts with the sW182*, but not wild-type LHBs. RNA interference (RNAi) of Jab1 restored the levels of the downregulated p53 and Smad4. The sW182* mutant inhibited the promoter activity of downstream target genes of the tumor suppressors. Consistently, Jab1 RNAi reversed the inhibition.These results suggest that the LHBs nonsense mutant antagonizes the tumor suppressor pathways through Jab1 in the liver contributing to HCC development.
From information mismanagement to misinformation – the dark side of information management
Authors: Stone Merlin , Aravopoulou Eleni , Evans Geraint , Aldhaen Esra , Parnell Brett David 
Published: November 2018

PurposeThis paper reviews the literature on information mismanagement and constructs a typology of misinformation that can be applied to analyse project planning and strategic planning processes to reduce the chances of failure that results from information mismanagement. This paper aims to summarize the research on information mismanagement and provide guidance to managers concerning how to minimize the negative consequences of information mismanagement and to academics concerning how to research and analyse case studies that might involve information mismanagement.Design/methodology/approachLiterature review accompanied by conceptual analysis.FindingsInformation mismanagement is widespread in organizations, so all those involved in managing and researching them need to be far more aware of the damage that can be done by it.Research limitations/implicationsThe research is based on the Western society (Europe and North America). The same research should be carried out in other parts of the world. Also, all the case studies could usefully be investigated in more depth to apply the taxonomy.Practical implicationsManagers should be much more aware of their own and others’ tendencies to mismanage information to their own benefit.Social implicationsStakeholders in public sector activities, including citizens, should be much more aware of the tendency of the government and the public sector to mismanage information to justify particular policy approaches and to disguise failure.Originality/valueThe taxonomy on information mismanagement is original, as is its application to project planning and strategic decision-making.
Sustainable development concept and creation of innovative business models by retail chains
Authors: Bilińska-Reformat Katarzyna , Kucharska Barbara , Twardzik Malgorzata , Dolega Les 
Published: November 2018

Purpose
The purpose of this paper is to recognise the areas of implementation of the principles of sustainable development (SD) in the model of retail chains activity. In the paper, the assumption was made that nowadays it is necessary to adopt the rules following SD while making strategic decisions by retail chains.

Design/methodology/approach
The study uses secondary data sources, reports, academic literature and the case study research method. A case study research is a multi-method paradigm based on full range of a scientist’s tool-kit: reviewing literature studies, examining secondary documents and comparing the websites of investigated retail chains.

Findings
According to that business model, the authors were recognising selected components of this model, that is to say: recourses and competences of retail chains and value proposition for their customers. The greatest chances of development will be enjoyed by those retail chains that will be able to provide real value to customers. Maintaining a competitive advantage will require constant improvements in the quality of service and innovative business models connected with sustainable elements.

Research limitations/implications
It seems necessary to develop research tools that allow for identification of the level of use of the SD concept in retail chain’s business models in the future.

Practical implications
The paper is of interest to practitioners and students of retail management.

Social implications
The concept of the SD model included in the retailer business models serves to build value for the customer through the care of his quality of life. The vast majority of retailers believe that it is the responsibility of the business sector to respond to social and environmental challenges.

Originality/value
The paper intends to fill the gap in the literature concerning the influence of SD concept on changes in the business models of retail chains. The SD activities can lead to the development of specific capabilities based on intangible recourses that are sources of competitive advantage (SD). That is the main reason of undertaking this subject.
Understanding franchisee performance
Authors: Colla Enrico , Ruiz-Molina Maria Eugenia , Chastenet De Gery Catherine , Schultz Maryline , Deparis Martine , Lemmet Laurence 
Published: November 2018

Purpose
The purpose of this paper is to investigate the impact of participative franchising on performance from the franchisee perspective. In particular, the paper analyses the impact of the franchisee autonomy – in human resource management and marketing decisions – affective commitment to the network and network innovativeness on the franchisee relative performance.

Design/methodology/approach
A survey answered by 226 franchisees in France allowed to estimate a structural equations model through partial least squares regression analysis to test the hypothesised relations between autonomy, affective commitment, innovativeness and performance.

Findings
According to the authors’ findings, franchisee’s autonomy in commercial policies, mediated by to franchisor’s ability to innovate and acknowledge innovations stemming from the franchisees, and the affective commitment to the network, emerge as strong determinants of the franchisee’s performance.

Research limitations/implications
The results confirm the conclusions of other research, but extend and integrate them, providing evidence that the role of participative franchising should not be neglected.

Practical implications
The results obtained provide evidence about the importance of bidirectional communication instruments in the relations between franchisor and franchisee, and participation tools for the identification, recognition and support to the innovative successful practices developed by franchisees to be quickly implemented by other franchisees in the network.

Originality/value
This paper looks at franchisee autonomy, affective commitment and innovativeness as potential determinants of franchisee’s performance, being the latter an underexplored topic.
How perceived social distance and trust influence reciprocity expectations and eWOM sharing intention in social commerce
Authors: Yang Xue 
Published: November 2018

Purpose
Currently, consumers can easily access social media to share information and experiences. How a relationship between these consumers influences their decisions has not been clearly investigated. When consumers participate in information sharing activities, they usually communicate with each other and can perceive their social distance from others. Thus, the purpose of this paper is to explore the direct and indirect effects of perceived social distance on eWOM sharing intentions.

Design/methodology/approach
Specifically, a moderated mediation model was validated, in which the indirect effect of perceived social distance on eWOM sharing intentions through reciprocity expectations was moderated by trust.

Findings
Perceived social distance had a positive indirect effect on eWOM sharing intentions through reciprocity expectations, which was found to be negatively moderated by trust.

Originality/value
This study integrates the concept of perceived social distance into the eWOM research area. Moreover, this result adds to the s-commerce literature by specifying the conditions of the indirect effect of perceived social distance through reciprocity expectations on eWOM sharing intention.
An energy-efficient VM placement method for cloud data centers using a hybrid genetic algorithm
Authors: Kaaouache Mohamed Amine , Bouamama Sadok 
Published: November 2018

Purpose
This purpose of this paper is to propose a novel hybrid genetic algorithm based on a virtual machine (VM) placement method to improve energy efficiency in cloud data centers. How to place VMs on physical machines (PMs) to improve resource utilization and reduce energy consumption is one of the major concerns for cloud providers. Over the past few years, many approaches for VM placement (VMP) have been proposed; however, existing VM placement approaches only consider energy consumption by PMs, and do not consider the energy consumption of the communication network of a data center.

Design/methodology/approach
This paper attempts to solve the energy consumption problem using a VM placement method in cloud data centers. Our approach uses a repairing procedure based on a best-fit decreasing heuristic to resolve violations caused by infeasible solutions that exceed the capacity of the resources during the evolution process.

Findings
In addition, by reducing the energy consumption time with the proposed technique, the number of VM migrations was reduced compared with existing techniques. Moreover, the communication network caused less service level agreement violations (SLAV).

Originality/value
The proposed algorithm aims to minimize energy consumption in both PMs and communication networks of data centers. Our hybrid genetic algorithm is scalable because the computation time increases nearly linearly when the number of VMs increases.
Job autonomy and employee voice: is work-related self-efficacy a missing link?
Authors: Dedahanov Alisher Tohirovich , Rhee Changjoon , Gapurjanova Nazokat 
Published: November 2018

PurposeThe purpose of this paper is twofold: first, this work replicates the existing research by examining the links between job autonomy and work-related self-efficacy; and, second, it extends the literature by investigating the relationships between work-related self-efficacy and two forms of voice such as promotive and prohibitive and by measuring the mediating role of self-efficacy on the link between job autonomy and promotive and prohibitive voice.Design/methodology/approachThe authors used a self-administered instrument to conduct a survey among 1,227 highly skilled employees. The researchers received a total of 904 questionnaires. After disregarding the non-usable questionnaires, the authors retained 813 questionnaires for the study. The overall response rate was 66 percent.FindingsThe results suggest that work-related self-efficacy has a significant relationship with prohibitive voice and mediates the link between job autonomy and prohibitive voice. Meanwhile, the findings of this study indicate that there is no significant association between work-related self-efficacy and promotive voice.Originality/valueThis work is the first to identify the association between work-related self-efficacy and prohibitive voice and the mediating role of work-related self-efficacy on the association between job autonomy and prohibitive voice.