bluuebunny/crossref_metadata_2025_split huggingface dataset:
A screen of 1,049 schizophrenia and 30 Alzheimer’s-associated variants for regulatory potential
Authors: Myint Leslie , Wang Ruihua , Boukas Leandros , Hansen Kasper D. , Goff Loyal A. , Avramopoulos Dimitrios 
Published: October 2018

AbstractRecent genome-wide association studies (GWAS) identified numerous schizophrenia (SZ) and Alzheimer’s disease (AD) associated loci, most outside protein-coding regions and hypothesized to affect gene transcription. We used a massively parallel reporter assay (MPRA) to screen, 1,049 SZ and 30 AD variants in 64 and 9 loci respectively for allele differences in driving reporter gene expression. A library of synthetic oligonucleotides assaying each allele 5 times was transfected into K562 chronic myelogenous leukemia lymphoblasts and SK-SY5Y human neuroblastoma cells. 148 variants showed allelic differences in K562 and 53 in SK-SY5Y cells, on average 2.6 variants per locus. Nine showed significant differences in both lines, a modest overlap reflecting different regulatory landscapes of these lines that also differ significantly in chromatin marks. Eight of nine were in the same direction. We observe no preference for risk alleles to increase or decrease expression. We find a positive correlation between the number of SNPs in Linkage Disequilibrium (LD) and the proportion of functional SNPs supporting combinatorial effects that may lead to haplotype selection. Our results prioritize future functional follow up of disease associated SNPs to determine the driver GWAS variant(s), at each locus and enhance our understanding of gene regulation dynamics.
Massively scalable genetic analysis of antibody repertoires
Authors: Briney Bryan , Burton Dennis R. 
Published: October 2018

AbstractWith technical breakthroughs in the throughput and read-length of next-generation sequencing platforms, antibody repertoire sequencing is becoming an increasingly important tool for detailed characterization of the immune response. There is a need for open, scalable software for the genetic analysis of repertoire-scale antibody sequence data. To address this gap, we have developed the ab[x] package of software tools. There are three core components of the ab[x] toolkit, all of which are freely available: abcloud (github.com/briney/abcloud) for deployment and management of computational resources on Amazon’s Elastic Compute Cloud; abstar (github.com/briney/abstar) for pre-processing, germline gene assignment and primary annotation of antibody sequence data; and abutils (github.com/briney/abutils), which provides utilities for interactive downstream analysis of antibody repertoire data.
Comparative analysis ofStreptococcusgenomes
Authors: Shelyakin Pavel V , Bochkareva Olga O , Karan Anna A , Gelfand Mikhail S 
Published: October 2018

AbstractBackgroundGenome sequencing of multiple strains demonstrated high variability in gene content even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome, that is, the complete set of genes observed in a given species or a higher level taxon. Here we analysed the pan-genome structure and the genome evolution of 25 strains ofStreptococcus suis, 50 strains ofStreptococcus pyogenesand 28 strains ofStreptococcus pneumoniae.ResultsFractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions. The total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity.About 7% of single-copy periphery genes have been found in different syntenic regions. More than a half of these genes are rare in allStreptococcusspecies; others are rare in at least one species. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are candidates for horizontal transfer between species.An inversion of length 15 kB found in four independent branches ofS. pneumoniaehas breakpoints formed by genes encoding a surface antigen protein (PhtD). The observed parallelism may indicate the action of an antigen variation mechanism.ConclusionsMembers of the genusStreptococcushave a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, understanding of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines.
Quantitative mathematical modeling of clinical brain metastasis dynamics in non-small cell lung cancer
Authors: Bilous M. , Serdjebi C. , Boyer A. , Tomasini P. , Pouypoudat C. , Barbolosi D. , Barlesi F. , Chomy F. , Benzekry S. 
Published: October 2018

AbstractBrain metastases (BMs) are associated with poor prognosis in non-small cell lung cancer (NSCLC), but are only visible when large enough. Therapeutic decisions such as whole brain radiation therapy would benefit from patient-specific predictions of radiologically undetectable BMs. Here, we propose a mathematical modeling approach and use it to analyze clinical data of BM from NSCLC.Primary tumor growth was best described by a gompertzian model for the pre-diagnosis history, followed by a tumor growth inhibition model during treatment. Growth parameters were estimated only from the size at diagnosis and histology, but predicted plausible individual estimates of the tumor age (2.1-5.3 years). Multiple metastatic models were assessed from fitting either literature data of BM probability (n = 183 patients) or longitudinal measurements of visible BMs in two patients. Among the tested models, the one featuring dormancy was best able to describe the data. It predicted latency phases of 4.4 - 5.7 months and onset of BMs 14 - 19 months before diagnosis. This quantitative model paves the way for a computational tool of potential help during therapeutic management.
Development of a functional food bar containing coffee
Authors: Lara Nathália de Souza , de Sousa Maísa Mancini Matioli , Paola de Pádua Gandra Fernanda , de Angelis-Pereira Michel Cardoso , Carneiro João de Deus Souza , Pereira Rosemary Gualberto Fonseca Alvarenga 
Published: October 2018

PurposeThe purpose of this paper is to develop a cereal bar supplemented with coffee beverage that has health benefits.Design/methodology/approachSix types of cereal bars containing raisins or prunes with different concentrations of coffee were developed. Acceptability tests and physicochemical characterizations were performed by analysis of moisture, ash, protein, lipids, fibres and carbohydrates. Moreover, the levels of phenolic compounds, the fatty acid profile and thein vitroantioxidant activity were evaluated by the DPPH free radical scavenging and iron-chelating activity methods. The bars were assessed using the check-all-that-apply (CATA) methodology. The phenolic compound and antioxidant activity data were evaluated by analysis of variance. Averages were compared by the Scott–Knott test. To verify the characteristics of the food bar per the attributes cited in CATA, main component analysis was performed using the SensoMaker software.FindingsThe concentration of coffee did not affect the centesimal composition values. The highest percentage of scavenging activity of free radicals was observed in the food bar containing raisins, with a maximum concentration of coffee beverage equivalent to 10 mL. These values were higher in cereal bars containing raisins than in bars containing prunes with the same concentrations of coffee. The acceptance sensory test showed good acceptability ratios, ranging from 74.33 to 85.22 among different food bar formulations.Practical implicationsThe bar consisting raisins and 100 per cent coffee presented high values of protection against oxidative stress, phenolic content and satisfying acceptability, thereby making it a novel possible alternative as a differentiated product with possible health-beneficial effects.Social implicationsThis paper provides a differentiated product, through healthy ingredients, with convenience of purchase, besides having added value and possible health beneficial effects.Originality/valueThe bar consisting of raisins and 100 per cent coffee presented high values of phenolic content and protection against oxidative stress, as well as satisfying acceptability, thereby making it a novel possible alternative as a differentiated product with possible health-beneficial effects.
Digital Korean studies: recent advances and new frontiers
Authors: Cha Javier 
Published: October 2018

Purpose
This study aims to reflect on the past and prospects of digital Korean studies.

Design/methodology/approach
Discussion includes the remarkably early adoption of computing in the Korean humanities, the astounding pace in which Korean heritage materials have been digitized, and the challenges of balancing artisanal and laboratory approaches to digital research.

Findings
The main takeaway is to reconsider the widespread tendency in the digital humanities to privilege frequentist analysis and macro-level perspectives.

Practical implications
Cha hopes to discover the future of digital Korean studies in semantic networks, graph databases and anthropological inquiries.

Originality/value
Cha reconsiders existing tendencies in the digital humanities and looks to the future of digital Korean studies.
Variable viscosity effects on third-grade liquid flow in post-treatment analysis of wire coating in the presence of nanoparticles
Authors: Mahanthesh B. , Gireesha B.J. , Archana M. , Hayat Tasawar , Alsaedi Ahmed 
Published: October 2018

Purpose
The features of coated wire product are measured by the flow and heat transport occurring in the interior of dies. Therefore, an understanding of characteristics of polymers momentum, heat mass transfer and wall shear stress is of great interest. Enhancement of heat transfer rate is fundamental need of wire coating process. Therefore, this study aims to investigate the effect of suspended nanoparticles in heat and mass transport phenomena of third-grade liquid in post-treatment of wire coating process. Buongiorno model for nanofluid is adopted. Two cases of temperature dependent viscosity are considered.

Design/methodology/approach
The governing equations are modelled with the help of steady-state conservation equations of mass, momentum, energy and nanoparticle concentration. Some appropriate dimensionless variables are introduced. Numerical solutions for the nonlinear problem are developed through Runge–Kutta–Fehlberg technique. The outcome of sundry variables for dimensionless flow, thermal and nanoparticle volume fraction fields are scrutinised through graphical illustrations.

Findings
The study’s numerical results disclose that the force on the total wire surface and shear stress at the surface in case of Reynolds Model dominate Vogel’s Model case. Impact of nanoparticles is constructive for force on the total wire surface and shear stress at the surface. The velocity of the coating material can be enhanced by the non-Newtonian property.

Practical implications
This study may provide useful information to improve the wire coating technology.

Originality/value
Effect of nanoparticles in wire coating analysis by using Brownian motion and thermophoresis slip mechanisms is investigated for the first time. Two different models for variable viscosity are used.
Intersectionality and mixed methods for social context in entrepreneurship
Authors: Dy Angela , Agwunobi Adaku Jennifer 
Published: October 2018

PurposeThis conceptual paper has two central aims: to critically analyse the potential of intersectionality theory as a means by which to understand aspects of context in entrepreneurship studies, and advocate for the value of a realist perspective and mixed methods approaches to produce better intersectional research on entrepreneurship. This paper aims to discuss these issues.Design/methodology/approachHighlighting context as an emerging topic within entrepreneurship literature, the paper examines how drawing upon notions of intersectionality and positionality can help to explain the social context for entrepreneurial activity and outcomes, particularly in terms of agency and resources.FindingsThe paper complements and extends existing intersectional approaches to entrepreneurship studies by introducing Archer’s critical realist philosophical perspective on agency and Anthias’ positional perspective on resource access, considering the usefulness of realism and mixed methods approaches for such work, and outlining a methodologically informed potential research agenda for the area.Originality/valueThe paper offers a theoretical foundation for researchers to begin systematically exploring social entrepreneurial context by accounting for the effects of overarching intersecting structures such as gender, race, and socio-economic class (amongst others), presents empirical methods through which these social-structural influences, and the degree of their impact, can be identified and analysed, and suggests a philosophically robust means of conceptualising how, in combination with agency, they influence essential aspects of entrepreneurial activity.
Influence of religious beliefs and spirituality on decision to insure
Authors: Gill Amarjit , Mand Harvinder S. , Biger Nahum , Mathur Neil 
Published: October 2018

Purpose
The purpose of this paper is to examine the influence of the level of religious beliefs and individual spirituality of small business owners on their decision to insure.

Design/methodology/approach
Small business owners from India were asked about their perceptions regarding the relationship between their level of religious beliefs and spirituality and their decision to insure.

Findings
The results of this study show that the level of religious beliefs and individual spirituality of small business owners positively influence their decisions to purchase commercial insurance and life insurance to manage financial risk in India.

Research limitations/implications
This is a co-relational study that investigated the association between the level of religious beliefs, spirituality, and decision to insure. There is not necessarily a causal relationship between the two. The findings of this study may only be generalized to individuals similar to those that were included in this research.

Originality/value
This study adds to literature on the relationship between the level of religious beliefs, spirituality, and decision to insure. The findings may be useful for financial planners, small business owners and financial management consultants.
Defining potentials and barriers to trade in the Malaysia–Chile partnership
Authors: Devadason Evelyn S. , Govindaraju V.G.R. Chandran , Mubarik Shujaat 
Published: October 2018

Purpose
The purpose of this paper is to investigate the potentials and barriers to trade in the Malaysia–Chile partnership.

Design/methodology/approach
This paper estimates two-way export potentials from an augmented three-dimensional panel gravity model of bilateral trade between Malaysia and the Latin America and the Caribbean (LAC) region, spanning the 1990–2014 period. Utilizing interviews with government officials and industry experts in Malaysia and Chile, this paper also provides insights into market access issues.

Findings
The empirical findings of this study suggest that Malaysia has trade potential in Chile, but Chile is “overtrading” with Malaysia. By major products traded, both countries are found to be “overtrading,” as the export basket remains concentrated in this partnership. Through the interviews, fewer restrictions are reported by the various stakeholders, as the extent of trade engagement remains somewhat low. The main challenge identified within specific sectors in both the countries relates mainly to procedures established to secure compliance with labeling regulations for food products.

Research limitations/implications
The sectoral findings reveal that there is indeed scope for expanding exports beyond the current major products traded, particularly in base metal and scientific and measuring equipment from the Malaysia and Chile perspectives, respectively. Thus, product diversification matters to intensify trade cooperation between the two countries. Non-tariff measures need to be streamlined by both parties to ensure further product diversification to food trade, particularly for Chile.

Originality/value
The limited literature on cross-regional trade within the broader framework of Southeast Asia and LAC only support the fact that potentials do exist but do not appear to provide much research evidence. Empirically, this paper will add to the existing literature on the potentials that hold in the Malaysia–Chile partnership. Further, a lack of adequate information remains on market access and other barriers in both the nations to facilitate decisions on trade opportunities. The findings of the study fill that vacuum of information pertaining to market access and trade facilitation through interviews with various stakeholders in Malaysia and Chile.
A novel care pathway for prisoners with intellectual disability designed through a Delphi process
Authors: Gulati Gautam , Quigley Stephen , Murphy Valerie Elizabeth , Yacoub Evan , Bogue John , Kearns Anthony , O’Neill Conor , Kelly Mary , Morrison Aideen , Griffin Gerard , Blewitt Mary , Fistein Elizabeth , Meagher David , Dunne Colum P. 
Published: October 2018

PurposeIndividuals with an intellectual disability (ID) form a significant minority in the Irish prison population and worldwide prison populations. There is growing recognition that specialist services for such individuals are in need of development. The purpose of this paper is to propose a care pathway for the management of individuals with an ID who present in prison, based on expert elicitation and consensus.Design/methodology/approachA convenience sample of professionals with a special interest in forensic intellectual disabilities was invited to participate in a Delphi exercise. In total, 12 agreed to participation and 10 subsequently completed the study (83.3 per cent). Expert views were elicited using a semi-structured questionnaire. Content analysis was completed using NVivo 11 software. A care pathway was subsequently proposed, based on the outcomes of the analysis, and circulated to participants for debate and consensus. A consensus was reached on management considerations.FindingsTen experts across a range of disciplines with a combined experience of 187 years participated in the study. Current provision of care was seen as limited and geographically variable. The vulnerability of prisoners with ID was highlighted. The need for equivalence of care with the community through multidisciplinary input and development of specialist secure and residential placements to facilitate diversion was identified. Consensus was achieved on a proposed care pathway.Originality/valueThis study proposes a care pathway for the assessment and management of prisoners with an ID and is, therefore, potentially relevant to those interested in this topic internationally who may similarly struggle with the current lack of decision-making tools for this setting. Although written from an Irish perspective, it outlines key considerations for psychiatrists in keeping with international guidance and, therefore, may be generalisable to other jurisdictions.
Impact of a nature-based intervention on incarcerated women
Authors: Toews Barb , Wagenfeld Amy , Stevens Julie 
Published: October 2018

Purpose
The purpose of this paper is to understand the impact of a short-term nature-based intervention on the social-emotional well-being of women incarcerated on a mental health unit in a state prison.

Design/methodology/approach
This research used a mixed method approach with individual interviews, a focus group and a visual analog scale (VAS).

Findings
Qualitative results found that women appreciated the planting party and the way the plants improved the physical environment. Women were also emotionally and relationally impacted by their participation and practiced skills related to planting and working with people. Quantitative results indicate that women were happier, calmer, and more peaceful after the intervention than before.

Research limitations/implications
Study limitations include sample size, self-report data and use of a scale not yet tested for reliability and validity.

Practical implications
Findings suggest that nature-based interventions can serve as an adjunct to traditional mental health therapies in correctional settings. Nature-based interventions can support women’s goals to improve their mental health.

Social implications
Findings suggest that nature-based interventions can serve to improve relationships among incarcerated women, which may make a positive impact on the prison community. Such interventions may also assist them in developing relational and technical skills that are useful upon release.

Originality/value
To date, there is limited knowledge about the impact of nature-based interventions on incarcerated individuals coping with mental health concerns.
Ten propositions about public leadership
Authors: Hartley Jean 
Published: October 2018

PurposeThe purpose of this paper is to provide an overview of some pressing but under-researched aspects of public leadership. Ten propositions about public leadership are set out and these are intended to be thought-provoking and even controversial in order to stimulate researchers to design research which addresses key theoretical and practical questions about leadership in the public sphere. They will also help practitioners navigate an increasingly complex leadership context.Design/methodology/approachThis invited essay uses ten propositions about public leadership, selected from three sources: the leadership literature, the author’s own research and from collaborative research discussions with academics, policy makers and practitioners.FindingsThe first proposition argues for distinguishing public leadership from public service leadership given that the former is about leadership of the public sphere. Other propositions concern context; purpose; conflict and contest at the heart of public leadership; leadership with political astuteness; dual leadership; leadership projections; fostering resilience; leadership, authority and legitimacy; and the challenge to researchers to use research designs which reflect the complexity and dynamism of public leadership.Practical implicationsWhile this essay is primarily addressed to researchers, there are many ideas and concepts which practising leaders will find insightful and useful in their work.Originality/valueThis essay draws on deep experience in undertaking high-quality academic research about public leadership which draws from and feeds into policy and practice. It utilises organisational psychology, public management and political science to create synergies in order to enhance the understanding of public leadership.