bluuebunny/crossref_metadata_2025_split huggingface dataset:
Homeostasis of columnar synchronization during cortical map formation
Authors: Colonnese Matthew T. , Shen Jing 
Published: September 2016

ABSTRACTSynchronous spontaneous activity is critical for circuit development. A key open question is to what degree is this synchronization models adult activity or is specifically tuned for circuit development. To address this we used multi-electrode array recordings of spontaneous activity in non-anesthetized neonatal mice to quantify firing rates, synchronization, binary spike-vectors and population-coupling of single-units throughout the period of map formation. Consistent with the first hypothesis, adult-like network interactions are established during the period of retinal waves, before the onset of vision and normal inhibition, and are largely conserved throughout juvenile ages. Significant differences from mature properties were limited to initial topographic map formation, when synchronization was lower than expected by chance, suggesting active decoupling in early networks. These findings suggest that developmental activity models adult synchronization, and that there is remarkable homeostasis of network properties throughout development, despite massive changes in the drive and circuit basis of cortical activity.
TheDrosophilaGene Expression Tool (DGET) for expression analyses
Authors: Hu Yanhui , Comjean Aram , Perrimon Norbert , Mohr Stephanie 
Published: September 2016

AbstractBackgroundNext-generation sequencing technologies have greatly increased our ability to identify gene expression levels, including at specific developmental stages and in specific tissues. Gene expression data can help researchers understand the diverse functions of genes and gene networks, as well as help in the design of specific and efficient functional studies, such as by helping researchers choose the most appropriate tissue for a study of a group of genes, or conversely, by limiting a long list of gene candidates to the subset that are normally expressed at a given stage or in a given tissue.ResultsWe report aDrosophilaGene Expression Tool (DGET,www.flyrnai.org/tools/dget/web/), which stores and facilitates search of RNA-Seq based expression profiles available from the modENCODE consortium and other public data sets. Using DGET, researchers are able to look up gene expression profiles, filter results based on threshold expression values, and compare expression data across different developmental stages, tissues and treatments. In addition, at DGET a researcher can analyze tissue or stage-specific enrichment for an inputted list of genes (e.g. ‘hits’ from a screen) and search for additional genes with similar expression patterns. We performed a number of analyses to demonstrate the quality and robustness of the resource. In particular, we show that evolutionary conserved genes expressed at high or moderate levels in both fly and human tend to be expressed in similar tissues. Using DGET, we compared whole tissue profile and sub-region/cell-type specific datasets and estimated the potential cause of false positives in one dataset. We also demonstrated the usefulness of DGET for synexpression studies by querying genes with similar expression profile to the mesodermal master regulator Twist.ConclusionAltogether, DGET provides a flexible tool for expression data retrieval and analysis with short or long lists ofDrosophilagenes, which can help scientists to design stage- or tissue-specificin vivostudies and do other subsequent analyses.
MCbiclust: a novel algorithm to discover large-scale functionally related gene sets from massive transcriptomics data collections
Authors: Bentham Robert B. , Bryson Kevin , Szabadkai Gyorgy 
Published: September 2016

ABSTRACTThe potential to understand fundamental biological processes from gene expression data has grown parallel with the recent explosion of the size of data collections. However, to exploit this potential, novel analytical methods are required, capable of handling massive data matrices. We found current methods limited in the size of correlated gene sets they could discover within biologically heterogeneous data collections, hampering the identification of multi-gene controlled fundamental cellular processes such as energy metabolism, organelle biogenesis and stress responses. Here we describe a novel biclustering algorithm called Massively Correlated Biclustering (MCbiclust) that selects samples and genes from large datasets with maximal correlated gene expression, allowing regulation of complex pathway to be examined. The method has been evaluated using synthetic data and applied to large bacterial and cancer cell datasets. We show that the large biclusters discovered, so far elusive to identification by existing techniques, are biologically relevant and thus MCbiclust has great potential use in the analysis of transcriptomics data to identify large scale unknown effects hidden within the data. The identified massive biclusters can be used to develop improved transcriptomics based diagnosis tools for diseases caused by altered gene expression, or used for further network analysis to understand genotype-phenotype correlations.
A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma
Authors: Way Gregory P. , Allaway Robert J. , Bouley Stephanie J. , Fadul Camilo E. , Sanchez Yolanda , Greene Casey S. 
Published: September 2016

ABSTRACTBackground:We have identified molecules that exhibit synthetic lethality in cells with loss of the neurofibromin 1 (NF1) tumor suppressor gene. However, recognizing tumors that have inactivation of theNF1tumor suppressor function is challenging because the loss may occur via mechanisms that do not involve mutation of the genomic locus. Degradation of the NF1 protein, independent ofNF1mutation status, photocopies inactivating mutations to drive tumors in human glioma cell lines. NF1 inactivation may alter the transcriptional landscape of a tumor and allow a machine learning classifier to detect which tumors will benefit from synthetic lethal molecules.Results:We developed a strategy to predict tumors with low NF1 activity and hence tumors that may respond to treatments that target cells lacking NF1. Using RNAseq data from The Cancer Genome Atlas (TCGA), we trained an ensemble of 500 logistic regression classifiers that integrates mutation status with whole transcriptomes to predict NF1 inactivation in glioblastoma (GBM). On TCGA data, the classifier detectedNF1mutated tumors (test set area under the receiver operating characteristic curve (AUROC) mean = 0.77, 95% quantile = 0.53 – 0.95) over 50 random initializations. On RNA-Seq data transformed into the space of gene expression microarrays, this method produced a classifier with similar performance (test set AUROC mean = 0.77, 95% quantile = 0.53 – 0.96). We applied our ensemble classifier trained on the transformed TCGA data to a microarray validation set of 12 samples with matched RNA and NF1 protein-level measurements. The classifier’s NF1 score was associated with NF1 protein concentration in these samples.Conclusions:We demonstrate that TCGA can be used to train accurate predictors of NF1 inactivation in GBM. The ensemble classifier performed well for samples with very high or very low NF1 protein concentrations but had mixed performance in samples with intermediate NF1 concentrations. Nevertheless, high-performing and validated predictors have the potential to be paired with targeted therapies and personalized medicine.
Identification of misclassified ClinVar variants using disease population prevalence
Authors: Shah Naisha , Claire Hou Ying-Chen , Yu Hung-Chun , Sainger Rachana , Dec Eric , Perkins Brad , Caskey C. Thomas , Venter J. Craig , Telenti Amalio 
Published: September 2016

ABSTRACTThere is a significant interest in the standardized classification of human genetic variants. The availability of new large datasets generated through genome sequencing initiatives provides a ground for the computational evaluation of the supporting evidence. We used whole genome sequence data from 8,102 unrelated individuals to analyze the adequacy of estimated rates of disease on the basis of genetic risk and the expected population prevalence of the disease. Analyses included the ACMG recommended 56 gene-condition sets for incidental findings and 631 genes associated with 348 OrphaNet conditions. A total of 21,004 variants were used to identify patterns of inflation (i.e. excess genetic risk). Inflation, i.e., misclassification, increases as the level of evidence in ClinVar supporting the pathogenic nature of the variant decreases. The burden of rare variants was a main contributing factor of the observed inflation indicating misclassified benign private mutations. We also analyzed the dynamics of re-classification of variant pathogenicity in ClinVar over time. The study strongly suggests that ClinVar includes a significant proportion of wrongly ascertained variants, and underscores the critical role of ClinVar to contrast claims, and foster validation across submitters.
The politics of consent in the casino economy
Authors: Choi Alex H. 
Published: September 2016

Purpose
Accompanying the casino liberalization in Macau has been the massive increase in the importation of migrant workers to drive the labour-intensive, service-oriented economic growth there. Nevertheless, the employment of migrant workers has become an intensely contentious issue. The traditional pluralist approach to migration policy has highlighted a mismatch between restrictive policy pronouncements and actual expansive outcomes. This mismatch has resonated strongly in Macau, where the number of migrant workers skyrocketed in the last decade in spite of repeated guarantees from the government of the adoption of a protectionist labour policy. The pluralist approach has attributed the mismatch to strong constituencies supporting more immigration. The purpose of this paper is to dispute this and maintain that the Macau Government is a capitalist state committed to increasing labour importation to facilitate wealth accumulation.

Design/methodology/approach
The paper uses a qualitative approach based on extensive research of news and media reports, facilitated by a close observation of political developments.

Findings
The Macau Government started, in 2005, to talk about reforming its labour importation programme by adding a migrant worker levy, a ratio mechanism and a six-month waiting period. This paper investigates how the capitalist state navigated the reform process by promising changes and building consent with the working classes. The author maintains that “a game of protection” has been constructed and played to secure the consent of the local working classes for the migrant worker programme.

Originality/value
Very little literature is available that has studied the changes made to the migrant worker system in Macau. This paper will help to close this gap.
The value of the MLS or MLIS degree
Authors: Fraser-Arnott Melissa 
Published: September 2016

Purpose
The purpose of this paper is to examine the competencies, skills and knowledge obtained through a master’s degree in library and information science (LIS) and to identify those competencies that are most valued by graduates who obtained employment in non-library roles. These observations will contribute to an understanding of the transferability of LIS education which will assist LIS professionals and educators to frame LIS competencies in a way that appeals to employers outside of library settings who may not have any knowledge of LIS education or practice.

Design/methodology/approach
The grounded theory methodology was used with data collection taking the form of semi-structured interviews. Interviews were between 30 and 90 min in length and included career narratives, as well as responses to particular questions about different aspects of professional identity. Participants included graduates of master’s level LIS programs employed in a variety of positions including information managers, policy analysts, human resources specialists, marketers, vendors, taxonomists, search engine designers and information consultants. The participants were employed in sectors including government, information technology, aerospace, oil and gas and retail/online sales in both Canada and the USA.

Findings
The participants in this study found that their LIS education was valuable to their success in a number of non-library roles. Although the specific career paths of participants were each unique and the different roles they occupied required different combinations of skills, a list of key transferable LIS competencies could be identified. These included a focus on client service, the ability to identify need, and the ability to search for information and navigate databases. In addition, several participants observed that their coursework and opportunities to participate in internships, co-operative positions or work placements prepared them for such workplace conditions as deadlines and fast-paced environments.

Originality/value
This study involved a population of LIS graduates whose experiences have not been extensively examined in the past. This article helps to fill a gap in the understanding of the professional experiences of LIS graduates who pursue roles outside of libraries. In addition, the semi-structured interview technique allowed for deeper understanding of participants’ perceptions of which of their competencies, skills and knowledge were valuable to employees. This information was gained through answers to specific skills-focused questions intended to identify which competencies developed during their LIS education assisted them most in their careers, as well as larger career narratives. This study will have implications for library practitioners and educators. It will provide insights into valued skills for those who are designing or implementing LIS education programs, as well as LIS graduates who are seeking to market their skills to employers across industry sectors.
Promoting diversity to add value to the LIS profession
Authors: Croxton Rebecca A. , Crumpton Michael A. , Holmes Gerald V. 
Published: September 2016

Purpose
The purpose of this paper is to discuss the impact the University of North Carolina at Greensboro’s (UNCG) Library and Information Studies Academic and Cultural Enrichment (ACE) Scholars Program has had on promoting diversity and adding value to the library and information studies profession.

Design/methodology/approach
This paper is presented as a case study in which three iterations of the ACE Scholars Program are discussed, including program design and suggested impact the program has had on educating and engaging diverse individuals for careers in the library and information studies professions.

Findings
Nearly 50 ACE Scholars program participants, representing ethnically, racially and socioeconomically diverse backgrounds, have graduated from UNCG with their Master of Library and Information Studies degrees since 2011. In the five years since the first ACE cohort graduated, Scholar alums continue to impact the Library and Information Studies (LIS) profession through their professional roles as well as through their community engagement, professional association memberships and leadership roles, professional presentations and numerous publications.

Originality/value
This paper presents a model that has helped to promote diversity in the LIS field in way that can be adapted by other graduate programs that are preparing individuals for successful and engaged careers as library and information studies professionals.
Regulating online erotica – ethnographic observations of a UK-based adult entertainment provider
Authors: Klein Axel 
Published: September 2016

Purpose
The purpose of this paper is to throw a new light on the online adult entertainment industry and help remove the stigma associated with it.

Design/methodology/approach
An ethnographic approach was taken, with participant observation and in-depth interviews with a number of informants.

Findings
This is an environment where female performers can enjoy good income opportunities and work in a safe environment. It also provides a high level of job security for technical support staff.

Research limitations/implications
The study used a sample sample size with no access to clients.

Practical implications
It is important that UK regulation remains light handed to avoid pushing the industry off shore.

Originality/value
The paper provides new data on the working environment in camming studios and positive aspects of job security and the equitable distribution of profits.
The association between alcohol abstinence, drinking or binge drinking and drug use: is alcohol abstinence that safe?
Authors: Dupuis Marc , Baggio Stéphanie , Accard Marion Emilie , Mohler-Kuo Meichun , Gmel Gerhard 
Published: September 2016

Purpose
The purpose of this paper is to investigate the association between alcohol abstinence and illicit drug use during early adulthood, and compares abstinence to moderate drinking and binge drinking, regrouped in different frequencies.

Design/methodology/approach
A total of 5,968 young male adults who completed the questionnaires were selected for the analyses. Alcohol abstinent participants were compared to moderate drinkers (who did not experience binge drinking during the previous 12 months), and casual, monthly, weekly and daily binge drinkers in terms of prevalence of drug use during early adulthood.

Findings
Alcohol abstinence was associated with higher risks of drug use than moderate drinking (odds ratio (OR)>3) for most of drugs, especially last-stage drugs: crystal meth, solvents, spice and heroin (6.50<OR<13.50). Such findings encourage rethinking prevention among alcohol abstainers who were so far considered at low risk of drug use.

Research limitations/implications
The main limitations of the study are the fact that it is cross-sectional, gender-blind and focussing on Swiss native who are less vulnerable than migrants.

Practical implications
High-risk subjects should be identified among young people who do not drink in order to develop specific preventive interventions.

Originality/value
This study is one of the first that compare alcohol abstinence, moderate drinking and binge drinking. Separate results covering 15 different drugs are presented.
The impact of banking concentration on firm leverage in emerging markets
Authors: Abadi Farzin , Bany-Ariffin A.N. , Kokoszczynski Ryszard , Azman-Saini W.N.W. 
Published: September 2016

Purpose
The purpose of this paper is to explore the impact of banking concentration on firm leverage in 21 major emerging countries from different geographical regions, controlling for firm determinant and macroeconomic determinant of firm leverage.

Design/methodology/approach
This study is based on a relatively large sample of 5,779 enterprises with total 48,280 numbers of observations over the period from 2006 to 2013 and the regression model is performed by applying two-step system general method of moment estimator methodology.

Findings
This study finds a positive and significant relationship between banking concentration and firm leverage. Therefore, the overall results follow the information-based theory which indicates lower firms financing obstacles as banks are more concentrated.

Research limitations/implications
Bank-level data of all the countries to measure banking concentration is until 2013, which restrict the empirical analysis until 2013. Also, the study conducts the analysis.

Practical implications
The study enables policymakers, society, and academics to have better understanding on the beneficial effects of alternative banking market structure on firms’ access to credit and therefore, in determining the level of firm leverage in emerging countries.

Originality/value
The study represents one of the limited available empirical researches to examine the beneficial effect of alternative banking market structures of firm leverage in emerging countries.
Matching organizational frame of reference and business strategy with contemporary marketing practices
Authors: Abu Farha Allam 
Published: September 2016

PurposeThe purpose of this paper is to investigate diversity of marketing practices of firms operating in the same environment, by identifying how management perception and business strategy (BS) fits with the choice of the marketing practice.Design/methodology/approachA model was developed and tested using survey methodology based on three well-validated research instruments. Data were analyzed using the partial least square approach.FindingsThe results showed that different marketing practice were coupled with different frame of reference, as well as different BS. These forces were found to be inter related, and internally coherent, resulting in viable configurational profiles.Research limitations/implicationsThe research is unique and exploratory, and was conducted in three Arabic countries with a small sample size. For these reasons, generalizability is somewhat constrained.Practical implicationsThe findings would help managers to carefully examine the internal logic of their marketing-related profiling; it can be used as an assessment tool, where performance should be enhanced if the variables are coherent.Originality/valueTo author’s knowledge this is the first study that inspect three variables that had been associated with decision making, but not integrated together in a holistic framework to explain marketing diversity. Additionally it identified four viable types of marketing practices with its corresponding frame of reference and BS. Therefore, the paper reports a work in an area not previously researched.
Institutional complexity and the strategic behaviors of SMEs in transitional environments
Authors: Ding Yuan , Malleret Véronique , Velamuri S. Ramakrishna 
Published: September 2016

PurposeThe purpose of this paper is to contribute to the literature on institutional complexity by highlighting patterns of strategic behaviors of SMEs in institutional environments undergoing large scale transitions.Design/methodology/approachThe paper uses five in-depth case studies of medium-sized enterprises in the Yangtze River Delta region to study their behaviors over the 2000-2012 period during which the institutional landscape in China underwent major changes.FindingsThe authors find that when institutional complexity is high, i.e., when neither the planned economy nor the market economy logic dominates, the role of organizational filters is more pronounced. In this situation, firm-level characteristics – its revenues and profitability, its competitive position and future prospects – play a dominant role in determining the nature of the strategic decisions and actions the firm undertakes.Research limitations/implicationsThe findings provide a nuanced perspective on strategic behaviors under institutional complexity. The qualitative research design offers rich insights but limited generalizability.Practical implicationsThe findings offer practical insights to SME leaders in terms of exercising caution in undertaking unrelated diversification during periods of transition from planned to market economies.Originality/valueThe authors apply the concepts of institutional complexity and organizational filters in a context of large scale institutional transitions to study the strategic behaviors of SMEs over a 12 year period.