bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reducing INDEL calling errors in whole-genome and exome sequencing data
Authors: Fang Han , Wu Yiyang , Narzisi Giuseppe , O’Rawe Jason A. , Jimenez Barrón Laura T. , Rosenbaum Julie , Ronemus Michael , Iossifov Ivan , Schatz Michael C. , Lyon Gholson J. 
Published: June 2014

AbstractBackgroundINDELs, especially those disrupting protein-coding regions of the genome, have been strongly associated with human diseases. However, there are still many errors with INDEL variant calling, driven by library preparation, sequencing biases, and algorithm artifacts.MethodsWe characterized whole genome sequencing (WGS), whole exome sequencing (WES), and PCR-free sequencing data from the same samples to investigate the sources of INDEL errors. We also developed a classification scheme based on the coverage and composition to rank high and low quality INDEL calls. We performed a large-scale validation experiment on 600 loci, and find high-quality INDELs to have a substantially lower error rate than low quality INDELs (7% vs. 51%).ResultsSimulation and experimental data show that assembly based callers are significantly more sensitive and robust for detecting large INDELs (>5 bp) than alignment based callers, consistent with published data. The concordance of INDEL detection between WGS and WES is low (52%), and WGS data uniquely identifies 10.8-fold more high-quality INDELs. The validation rate for WGS-specific INDELs is also much higher than that for WES-specific INDELs (85% vs. 54%), and WES misses many large INDELs. In addition, the concordance for INDEL detection between standard WGS and PCR-free sequencing is 71%, and standard WGS data uniquely identifies 6.3-fold more low-quality INDELs. Furthermore, accurate detection with Scalpel of heterozygous INDELs requires 1.2-fold higher coverage than that for homozygous INDELs. Lastly, homopolymer A/T INDELs are a major source of low-quality INDEL calls, and they are highly enriched in the WES data.ConclusionsOverall, we show that accuracy of INDEL detection with WGS is much greater than WES even in the targeted region. We calculated that 60X WGS depth of coverage from the HiSeq platform is needed to recover 95% of INDELs detected by Scalpel. While this is higher than current sequencing practice, the deeper coverage may save total project costs because of the greater accuracy and sensitivity. Finally, we investigate sources of INDEL errors (e.g. capture deficiency, PCR amplification, homopolymers) with various data that will serve as a guideline to effectively reduce INDEL errors in genome sequencing.
Twitter and TV events: an exploration of how to use social media for student-led research
Authors: Bober Magdalena 
Published: June 2014

Purpose
– The purpose of this paper is twofold. First, it investigates the relationship between television, its audiences and Twitter around the creation of social TV events. Here it contributes to knowledge by charting usage in relation to different types of programmes and by comparing Twitter to Facebook data. Second, it evaluates the way in which student-led research can be used to conduct audience studies with the help of Twitter.

Design/methodology/approach
– The research applies a quantitative approach, measuring the volume of Twitter messages before, during and after two different types of television programmes, i.e. Reality TV (The X Factor and The Only Way is Essex) and sports broadcasts (football and Formula One). Brief comparisons are also drawn with data collected from Facebook. The pedagogical evaluation of the research is based on self-reflection by the author/tutor.

Findings
– The research established similar trends and patterns of viewer engagement for both types of television programming, with key activity during and towards the end of a broadcast which points to viewers using Twitter, or Facebook, while watching the event. The findings are compared to previous studies on television programmes and Twitter use. The study also identified that student research using Twitter can lead to a valuable learning experience as it allows students to use their own knowledge of social media to inform the research process.

Originality/value
– This research makes a contribution to the small yet growing body of studies examining Twitter activity in relation to TV events. It also contributes to knowledge on the educational use of social media by providing an account of how Twitter can be applied as a research tool by students.
Psychometric evaluation of the “Men's Polarized Gender Thinking Questionnaire (MPGQ)”
Authors: Bergman Bodil , Larsman Pernilla , Löve Jesper 
Published: June 2014

Purpose– The purpose of this paper is to develop and validate a new measure of gender equality at male-dominated workplaces, allowing quantitative analyses of men's beliefs about gender-based inequality at work.Design/methodology/approach– The present paper examines a questionnaire developed from qualitative interviews based on grounded theory methodology and designed to assess men's beliefs about gender inequality. A 23-item version of the Men's Polarized Gender Thinking Questionnaire (MPGQ) was completed by a sample of 220 men from three different male-dominated organizations in Sweden. Recommended psychometric testing procedures were conducted.Findings– Confirmatory factor analysis supported a six-factor model of male attitudes to gender-based inequality: different views on success, stereotypical gender roles – different jargons, benevolent sexism, conscious of gender order, conscious of the male norm system and strategies for gender equality at work. The final model showed acceptable fit to data. All six factors were positively intercorrelated.Practical implications– It was concluded that the MPGQ provides a useful tool for further studies of men's sometimes polarized views of gender equality in male-dominated workplaces. Hence, MPGQ may allow researchers and practitioners to go deeper in their understanding of persistent and often hidden gender-based inequality at work.Originality/value– Equality plans are difficult to fulfill if people do not know on which subtle mechanisms the concept gender-based inequality is founded. The MPGQ illustrates how they are manifested at a specific workplace. Because of the scarcity of this type of workplace measures, this study may make a contribution of concern to the literature. By measuring these sometimes polarized beliefs, management strategies aiming at decreasing barriers to gender equality at work could become more accurate and efficient.
Performance of microfinance institutions in Muslim countries
Authors: Ashraf Ali , Kabir Hassan M. , J. Hippler III William 
Published: June 2014

Purpose– The aim of the paper is to analyze whether performance measures and their factors for microfinance institutions (MFIs) in Muslim countries are significantly different from those in their non-Muslim counterparts, central to the Islamic scholars' argument that religious and cultural norms in Muslim countries may drive the preference of Islamic microfinance over conventional microfinance.Design/methodology/approach– Using a cross-sectional dataset of 2,138 firm-years for 754 different MFIs across 83 countries, 33 Organization of Islamic Conference (OIC) member Muslim countries and 50 non-member countries, we analyzed the MFI performance based on three sets of measures: outreach, loan recovery and profitability and overall financial performance measures, with respect to two sets of explanatory variables, namely, country-specific and firm-level variables.Findings– Results show that country gross domestic product size is positively related with profitability, and the percentage of women borrowers is also significant in driving loan recovery and firm profitability in the OIC sample, but they are otherwise not significant for the rest of the world sample.Practical implications– This study contributes to the understanding of the core argument in the motivation of Islamic MFIs, which is whether cultural and religious factors are important for MFI success in Muslim countries.Originality/value– This study introduces a variable that measures the difference between a country's independence year and their OIC membership year as a proxy for the “country religious inclination” of a Muslim country. Results suggest that countries with delayed membership in OIC show lower inclination to popular Islamic beliefs and higher market penetration of conventional microfinance outreach. Positive relationships among a country's religious inclination and loan loss ratios and loan provisions are also consistent with the moral hazard hypothesis that few religious communities may be more prone to default.
Detection of drugs in Australian prisons: supply reduction strategies
Authors: Dolan Kate , Rodas Ana 
Published: June 2014

Purpose
– Prisoners have a high level of drug use prior to imprisonment. Many inmates report having injected drugs and using cannabis. Prison authorities employed a range of strategies to detect drugs and drug use in prison. However, it was unclear which supply reduction strategies operated, and the prevalence and types of drugs detected in Australian prisons. The purpose of this paper is to examine supply reduction strategies in Australian prisons. Information on searches for drugs, and from inmate urinalysis was collected. The study focussed on adults in fulltime custody in Australia in 2009.

Design/methodology/approach
– A representative of all corrective services departments and justice health services was asked to complete a questionnaire on supply reduction strategies, including searches for drugs and drug testing of inmates.

Findings
– The two main supply reduction strategies identified in all Australian prisons were the use of drug detection dogs and urinalysis programs. Despite an extensive use of drug searches and urinalysis, the detection of drugs was modest for both strategies. The most commonly used drug was cannabis with the detection of drugs such as amphetamines and heroin being very low.

Research limitations/implications
– Prison inmates have a history of high levels of drug use prior to imprisonment. However, the supply reduction measures of drug detection dogs and urinalysis indicate that drug use was low in Australian prisons.

Practical implications
– The paper recommends that urinalysis comprises targeting testing regimes and that random testing ceases in order to be a more cost effective use of resources for drug detection.

Originality/value
– The study is the first report on the range of supply reduction measures in Australian prisons and, possibly in the world. Both measures were employed extensively across the country and finds of drugs and drug use were relatively low. Two possible conclusions can be drawn; that either drug use was very low in prison or that it was well concealed from the authorities. A comparison of random testing with targeted testing of inmates, where the former yields fewer positive results shows drug use was likely to be low rather than well concealed.
Cycle of coercion: experiences of maltreatment and disciplinary measures in Canadian inmates
Authors: Joubert David , Archambault Kyle , Brown Greg 
Published: June 2014

Purpose– In spite of past and current efforts at implementing effective rehabilitative interventions in carceral settings, institutions of confinement are primarily concerned with the maintenance of order within their walls. The purpose of this paper is to better understand associations between inmates’ developmental background and the experience of institutional discipline, to collect information on childhood maltreatment and disciplinary measures for a sample of Canadian prisoners.Design/methodology/approach– Information relative to socio-economic background, childhood maltreatment and experience of discipline while in custody was obtained using face-to-face interviews and institutional file review for a sample of 416 male and 106 female offenders in Canadian provincial institutions.Findings– Results from logistic regression analyses provided support for the association between childhood maltreatment and the experience of discipline, specifically in the form of increased monitoring from correctional staff. Furthermore, this association was found to be more pronounced for female offenders.Research limitations/implications– The findings highlight the need to incorporate a developmental perspective to current understanding of the use of disciplinary interventions in a prison environment. Such an approach may allow for preventing the enactment of a cycle of coercion, with negative consequences for the inmates.Originality/value– This study is original in its use of latent variable analytic methods to uncover the structure underlying the construct of childhood maltreatment in adult offenders. In addition, it provides valuable data of interest to researchers, corrections personnel and policy makers on the possible links between earlier developmental experiences and adjustment to the prison environment.
Does foreign direct investment affect economic growth? The case of Turkey
Authors: Cambazoglu Birgül , Simay Karaalp Hacer 
Published: June 2014

Purpose– The purpose of this paper is to analyze the impact of inward foreign direct investment (FDI) and international trade on economic growth in Turkey for the post-liberalization period (1980-2010).Design/methodology/approach– The paper employs the vector auto-regression model with four variables: real GDP growth, real inward FDI, the real import volume index and the real export volume index.Findings– Empirical results suggest a relationship between economic growth, inward FDI and exports.Practical implications– The results derived in this paper shed light on the relationship between FDI and international trade on economic growth for Turkey, which has been applying an export-led growth strategy since 1980, and has been implementing many regulations to attract foreign capital. It is evident that although Turkey's efforts and the importance of this issue, new policies and stabilization regulations must be established for the Turkish economy.Originality/value– This study contributes to the literature in at least two aspects. First, a comparative analysis of Turkey's inward and outward FDI with respect to different country groups was analyzed. Second, apart from other studies, the effect of inward FDI and international trade on Turkey's economic growth was tested utilizing an econometric method from 1980 to 2010, which is a relatively long time period for Turkey.
Understanding lesbian, gay, and bisexual worker stigmatization: a review of the literature
Authors: G. Gates Trevor , A. Viggiani Pamela 
Published: June 2014

Purpose– Stigmatization of lesbian, gay, and bisexual (LGB) people at work is an enduring social problem, yet little is known about how those experiences differ. The purpose of this paper is to discuss the above issue.Design/methodology/approach– Using a framework of modified labeling, this conceptual paper addresses that gap by reviewing the literature on differences in LGB worker stigmatization by type of sexual orientation identity, outness, sex and gender identity, and education and social class.Findings– Findings in the literature were that LGB workers are labeled as outsiders, and treated differently in many workplaces. However, there are other distinctions, based upon type of sexual orientation identity (i.e. whether someone is lesbian, gay, or bisexual), sex and gender identity, outness at work, and education and social classes.Originality/value– Moreover, the paper proposes additional aspects of LGB worker stigmatization needing further empirical study.
Workplace health promotion and working conditions as determinants of employee health
Authors: Ljungblad Cecilia , Granström Fredrik , Dellve Lotta , Åkerlind Ingemar 
Published: June 2014

Purpose
– The purpose of this paper is to investigate general psychosocial work conditions and specific workplace health promotion (WHP) measures in relation to employee health and sickness absence in Swedish municipal social care organizations.

Design/methodology/approach
– In a random sample of 60 out of the 290 municipalities in Sweden, 15,871 municipal social care employees working with elderly and disabled clients were sent a questionnaire concerning psychosocial work environment, WHP, and self-rated health. The responses (response rate 58.4 per cent) were complemented by register data on sickness absence (>14 days). All data were aggregated to employer level.

Findings
– A structural equation modelling analysis using employer-level data demonstrated that employers with more favourable employee ratings of the psychosocial work conditions, as well as of specific health-promoting measures, had better self-rated health and lower sickness absence level among employees.

Practical implications
– The results from this representative nationwide sample of employers within one sector indicate that employers can promote employee health both by offering various health-specific programmes and activities, such as work environment education, fitness activities, and lifestyle guidance, as well as by forming a high-quality work environment in general including developmental and supportive leadership styles, prevention of role conflicts, and a supportive and comfortable social climate.

Originality/value
– This study with a representative nationwide sample demonstrates: results in line with earlier studies and explanations to the challenges in comparing effects from specific and general WHP interventions on health.
An evaluation of a comprehensive, incentivized worksite health promotion program with a health coaching component
Authors: M. Merrill Ray , Grant Merrill J. 
Published: June 2014

Purpose– The use of lifestyle coaches in a worksite setting to improve weight, nutrition, physical activity, and smoking behavior among at risk individuals is a relatively new area of research in the field of health promotion. The purpose of this paper is to assess the effectiveness of an accountability-based worksite telephonic health coaching program that incorporates financial incentives, a personal wellness profile (PWP) assessment tool, and biometric testing.Design/methodology/approach– A retrospective cohort study was conducted based on data from four midsize companies in Utah (USA), 2007-2010. Individuals with high-risk biometric scores were required to work with a health coach.Findings– Participants had fewer healthcare claims and lower costs than nonparticipants, which became more pronounced over the study period. Health risks and PWP results significantly improved, more so in those in poorer health at baseline that worked with a health coach. Mean difference between health age and potential achievable age significantly decreased, more so for men than women and among those with the greatest need for improvement.Originality/value– Health coaching effectively improved biometric scores among high-risk individuals and narrowed the difference between current health age and achievable age, more so among those with the greatest health risks at baseline who worked with a health coach.
Diversifying into technical clothing manufacture as entrepreneurial learning
Authors: Theodorakopoulos Nicholas , McGowan Carmel , Bennett David , Kakabadse Nada , Figueira Catarina 
Published: June 2014

Purpose– The purpose of this paper is to demonstrate analytically how entrepreneurial action as learning relating to diversifying into technical clothing – i.e. a high-value manufacturing sector – can take place. This is particularly relevant to recent discussion and debate in academic and policy-making circles concerning the survival of the clothing manufacture industry in developed industrialised countries.Design/methodology/approach– Using situated learning theory (SLT) as the major analytical lens, this case study examines an episode of entrepreneurial action relating to diversification into a high-value manufacturing sector. It is considered on instrumentality grounds, revealing wider tendencies in the management of knowledge and capabilities requisite for effective entrepreneurial action of this kind.Findings– Boundary events, brokers, boundary objects, membership structures and inclusive participation that addresses power asymmetries are found to be crucial organisational design elements, enabling the development of inter- and intracommunal capacities. These together constitute a dynamic learning capability, which underpins entrepreneurial action, such as diversification into high-value manufacturing sectors.Originality/value– Through a refinement of SLT in the context of entrepreneurial action, the paper contributes to an advancement of a substantive theory of managing technological knowledge and capabilities for effective diversification into high-value manufacturing sectors.
International strategy for SMEs: criteria for foreign markets and entry modes selection
Authors: Musso Fabio , Francioni Barbara 
Published: June 2014

Purpose
– The purpose of this paper is to examine the internationalization of small- and medium-sized enterprises (SMEs) in regard to the international market selection (IMS) and entry mode selection (EMS) processes.

Design/methodology/approach
– To achieve this, an examination of the degree of systematic/active behaviour during IMS and EMS on a sample of 221 SMEs was conducted. Moreover, the paper sought to comprehend whether SMEs select foreign market and entry mode in a separate and sequential way, and whether there is a relationship between the sequentiality of IMS and EMS, on one side, and SME behaviour during these two processes, on the other side.

Findings
– Results revealed that SMEs have a non-systematic and passive behaviour during IMS and EMS, respectively. Moreover, a high predilection in performing the two processes contemporaneously or without any logic was found. Finally, a strong relation between sequentiality of IMS and EMS and degree of systematic and active behaviour during the processes existed.

Originality/value
– In this study, using a sample of SMEs located in a region of Italy, SME behaviour in the IMS and entry mode choice processes was tested.
Are growth-oriented SMEs more likely to adopt market and brand orientations?
Authors: Reijonen Helen , Párdányi Szandra , Tuominen Sasu , Laukkanen Tommi , Komppula Raija 
Published: June 2014

Purpose
– The purpose of this paper is to examine how SMEs with varying growth intentions differ from each other with regard to market orientation and brand orientation. Both of these strategic orientations are seen to lead to enhanced market performance. Consequently, the authors investigate whether those small firms that regard growth as an important goal have adopted market or brand orientation.

Design/methodology/approach
– Responses from 492 SMEs were analysed. They were clustered into four groups according to their growth intentions. These groups included firms that have low growth intention, capital adequacy growth intention, expansion growth intention and high growth intention. ANOVA was used to explore whether these groups differed in their market or brand orientation.

Findings
– The results indicate that the higher growth intention group the SME belonged to the more market and brand oriented it is. The biggest differences between the SMEs were found with regards to brand orientation.

Research limitations/implications
– The findings suggest that SMEs have acknowledged the positive effect of market and brand orientations on firm growth, thus highlighting the importance of supporting growth-oriented SMEs in their quest to become more market or brand oriented.

Originality/value
– The study sheds more light on the little researched themes of market and brand orientations in the context of SMEs. It also offers insights into how growth intentions affect the adoption of different strategic orientations.