bluuebunny/crossref_metadata_2025_split huggingface dataset:
CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data
Authors: Packer Jonathan S. , Maxwell Evan K. , O’Dushlaine Colm , Lopez Alexander E. , Dewey Frederick E. , Chernomorsky Rostislav , Baras Aris , Overton John D. , Habegger Lukas , Reid Jeffrey G. 
Published: September 2015

Abstract
Motivation: Several algorithms exist for detecting copy number variants (CNVs) from human exome sequencing read depth, but previous tools have not been well suited for large population studies on the order of tens or hundreds of thousands of exomes. Their limitations include being difficult to integrate into automated variant-calling pipelines and being ill-suited for detecting common variants. To address these issues, we developed a new algorithm—Copy number estimation using Lattice-Aligned Mixture Models (CLAMMS)—which is highly scalable and suitable for detecting CNVs across the whole allele frequency spectrum.
Results: In this note, we summarize the methods and intended use-case of CLAMMS, compare it to previous algorithms and briefly describe results of validation experiments. We evaluate the adherence of CNV calls from CLAMMS and four other algorithms to Mendelian inheritance patterns on a pedigree; we compare calls from CLAMMS and other algorithms to calls from SNP genotyping arrays for a set of 3164 samples; and we use TaqMan quantitative polymerase chain reaction to validate CNVs predicted by CLAMMS at 39 loci (95% of rare variants validate; across 19 common variant loci, the mean precision and recall are 99% and 94%, respectively). In the Supplementary Materials (available at the CLAMMS Github repository), we present our methods and validation results in greater detail.
Availability and implementation: https://github.com/rgcgithub/clamms (implemented in C).
Contact: jeffrey.reid@regeneron.com
Supplementary information: Supplementary data are available at Bioinformatics online.
ScaffoldScaffolder: solving contig orientation via bidirected to directed graph reduction
Authors: Bodily Paul M. , Fujimoto M. Stanley , Snell Quinn , Ventura Dan , Clement Mark J. 
Published: September 2015

Abstract
Motivation: The contig orientation problem, which we formally define as the MAX-DIR problem, has at times been addressed cursorily and at times using various heuristics. In setting forth a linear-time reduction from the MAX-CUT problem to the MAX-DIR problem, we prove the latter is NP-complete. We compare the relative performance of a novel greedy approach with several other heuristic solutions.
Results: Our results suggest that our greedy heuristic algorithm not only works well but also outperforms the other algorithms due to the nature of scaffold graphs. Our results also demonstrate a novel method for identifying inverted repeats and inversion variants, both of which contradict the basic single-orientation assumption. Such inversions have previously been noted as being difficult to detect and are directly involved in the genetic mechanisms of several diseases.
Availability and implementation: http://bioresearch.byu.edu/scaffoldscaffolder.
Contact: paulmbodily@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Transjugular Intrahepatic Portosystemic Shunt for Extrahepatic Portal Venous Obstruction in Children
Authors: Lv Yong , He Chuangye , Guo Wengang , Yin Zhanxin , Wang Jianhong , Zhang Bojing , Meng Xiangchen , Cai Jingzhi , Luo Bohan , Wu Feifei , Niu Jing , Fan Daiming , Han Guohong 
Published: September 2015

ABSTRACTObjectives:To evaluate the feasibility and efficacy of transjugular intrahepatic portosystemic shunt (TIPS) for extrahepatic portal venous obstruction with recurrent variceal bleeding in children.Methods:From November 2005 to December 2013, 28 consecutive paediatric patients with extrahepatic portal venous obstruction treated with TIPS for recurrent variceal bleeding refractory to medical/endoscopic therapy and/or surgical treatment in a tertiary‐care centre were followed until last clinical evaluation or death. The median follow‐up time was 36.0 months (range 4.0–106.0 months).Results:Seventeen boys and 11 girls of ages 7.1 to 17.9 years (median 12.3 years) weighing 19.0 to 62.0 kg (median 33.5 kg) were treated. TIPS was successfully placed in 17 of 28 (60.7%) patients via a transjugular approach alone (n = 4), a combined transjugular/transhepatic approach (n = 9), or a combined transjugular/transsplenic approach (n = 4). Shunt dysfunction occurred in 6 of 17 (35.3%) patients. The cumulative 1‐ and 3‐year free‐from‐variceal‐rebleeding rates in TIPS success group were higher than those in TIPS failure group (75.0% and 67.5% vs 45.5% and 18.2%, respectively, P = 0.0075). Compared with the TIPS failure group, the improvements in the height‐for‐age z scores were greater in the TIPS success group (P = 0.017). Procedure‐related complication occurred in 1 patient (3.6%), and no episode of post‐TIPS hepatic encephalopathy occurred in any patient. Except 1 patient in the TIPS success group died at 115 postoperative days, all patients were alive.Conclusions:TIPS is feasible and effective in children with extrahepatic portal venous obstruction and recurrent variceal bleeding. TIPS could represent a less‐invasive alternative to traditional surgical portosystemic shunting or a valuable treatment option if surgery and endoscopic treatment failed.
High frequency RNA recombination in porcine reproductive and respiratory syndrome virus occurs preferentially between parental sequences with high similarity
Authors: van Vugt Joke J. F. A. , Storgaard Torben , Oleksiewicz Martin B. , Bøtner Anette 
Published: September 2015

Two types of porcine reproductive and respiratory syndrome virus (PRRSV) exist, a North American type and a European type. The co-existence of both types in some countries, such as Denmark, Slovakia and Canada, creates a risk of inter-type recombination. To evaluate this risk, cell cultures were co-infected with either a North American and a European type of PRRSV or two diverse types of European isolate. Subsequently, an approximately 600 bp region of the PRRSV genome was tested for recombination by quantitative real-time RT–PCR. Between 0·1 and 2·5% RNA recombination was found between the European isolates, but no recombination was detected between the European and North American types. Calculation of the maximum theoretical risk of European–American recombination, based on the sensitivity of the RT–PCR system, revealed that RNA recombination between the European and North American types of PRRSV is at least 10000 times less likely to occur than RNA recombination between diverse European isolates.
Diverse phenotypic and genetic responses to short-term selection in evolvingEscherichia colipopulations
Authors: Dillon Marcus M. , Rouillard Nicholas P. , Dam Brian Van , Gallet Romain , Cooper Vaughn S. 
Published: September 2015

AbstractBeneficial mutations fuel adaptation by altering phenotypes that enhance the fit of organisms to their environment. However, the phenotypic effects of mutations often depend on ecological context, making the distribution of effects across multiple environments essential to understanding the true nature of beneficial mutations. Studies that address both the genetic basis and ecological consequences of adaptive mutations remain rare. Here, we characterize the direct and pleiotropic fitness effects of a collection of 21 first-step beneficial mutants derived from naïve and adapted genotypes used in a long-term experimental evolution ofEscherichia coli. Whole-genome sequencing was used to identify most beneficial mutations. In contrast to previous studies, we find diverse fitness effects of mutations selected in a simple environment and few cases of genetic parallelism. The pleiotropic effects of these mutations were predominantly positive but some mutants were highly antagonistic in alternative environments. Further, the fitness effects of mutations derived from the adapted genotypes were dramatically reduced in nearly all environments. These findings suggest that many beneficial variants are accessible from a single point on the fitness landscape, and the fixation of alternative beneficial mutations may have dramatic consequences for niche breadth reduction via metabolic erosion.
Are women better leaders than men?
Authors: De Mascia Sharon 
Published: September 2015

Purpose– Examines some of the reasons women remain under-represented at the top of organizations, despite developments in management thinking that appear to reward areas where women traditionally excel.Design/methodology/approach– Looks at some of the research into leadership skills and draws conclusions regarding the paucity of women in management.Findings– Considers some of the obstacles to women becoming managers to be: the attitudes of male managers, the lack of suitable role models for women, women’s reticence to network, and lack of confidence.Practical implications– Urges organizations to work harder to reduce the significance of these obstacles.Social implications– Shows how organizations – and through them society as a whole – would benefit from having more women in top jobs.Originality/value– Argues that having more women in leadership positions – that is, more positive role models – would help to give women more confidence in their ability to be great leaders and would encourage more women to push themselves forward for leadership opportunities.
Step-by-step to stopping the cyber-bully
Authors: Sarkar Anita 
Published: September 2015

Purpose
– Describes the role of HR in addressing traditional bullying and cyber-bullying at the workplace.

Design/methodology/approach
– Explains how organizations can design policy guidelines to tackle the issue of bullying and, thereby, help every employee to contribute to his or her best ability.

Findings
– Argues that the proliferation of electronic communication has made cyber-bullying rampant in workplaces and has devastating effects on some employees.

Practical implications
– Advances the view that creating a zero-tolerance policy against bullying, using technological help, conducting structured interviews, providing an employee-sensitization program, crafting effective job design and, from time to time, taking employees’ opinion can go a long way in ensuring a safe workplace for all.

Social implications
– Shows that bullying in any form is a social menace both for employees and the organization, and it needs to be nipped in the bud.

Originality/value
– Provides insights into how organizations can effectively address the issue of bullying at the workplace.
Study on work-life balance of women entrepreneurs – review and research agenda
Authors: Agarwal Sucheta , Lenka Usha 
Published: September 2015

Purpose
– The purpose of this paper is to review and conceptually explain the work-life balance of women entrepreneurs.

Design/methodology/approach
– Through the secondary data, selected papers have analysed to prepare a conceptual framework depicting the work-life balance of women entrepreneurs.

Findings
– Entrepreneurship has emerged as a global concept and contributed for economic development of the country. It utilizes competencies of entrepreneurs for success of their enterprises. Working women executives suffers the problem of work-life balance. Developing family responsibilities as well as their potential roles, generate the issue of role conflict. In order to overcome role conflict, they need to balance between work and personal life style. To gain more flexibility and control on their work and personal obligations, women start up their own business. They contribute in job creation, innovation, and economic development of nation through their entrepreneurial activities.

Originality/value
– It provides future direction to various researchers, academicians and policy makers in this field.
Authenticity matters more than intelligence and personality in predicting metacognition
Authors: Chiaburu Dan S. , Cho Inchul , Gardner Richard 
Published: September 2015

Purpose– Metacognition – or learning how to learn – is an important competence in business and academic settings. The purpose of this paper is to examine individual difference predictors of metacognition, including two traditional (general mental ability (GMA), five-factor model (FFM) personality traits) ones, and a novel one, individual authenticity.Design/methodology/approach– Volunteers (n=243) were asked to rate the extent to which they agreed with the respective statements on a seven-point Likert-type scale for GMA, FFM personality traits, and authenticity measures. Data were collected at different points in time to introduce psychological separation among the study measures.Findings– The authors found that while metacognition is not predicted by GMA, it is positively predicted by two of the five-factor model personality traits, conscientiousness, and extraversion. More importantly, the authors examined that individuals’ authenticity – in the form of (low) self-alienation – will enhance metacognition, over-and-above the previously mentioned predictors.Originality/value– The authors attempt to broaden the understanding of authenticity and its relationship with another important outcome construct, metacognition along with GMA and personality traits, in academic settings.
Star talent: investing in high-potential employees for organizational success
Authors: Downs Lisa 
Published: September 2015

Purpose
– The purpose of this paper is to provide practical how-to information for those looking to develop high-potential employees within their organizations or for their clients.

Design/methodology/approach
– The paper is based on a combination of recent surveys and studies of what is happening with the development (or lack thereof) of high-potential employees as well as recommendations of key components for high-potential programs based on the author’s direct experience.

Findings
– Though not a research paper, this work finds that while some organizations have programs in place to develop high potentials, many still do not, despite it being viewed as helpful in recruiting and retaining top talent.

Practical implications
– The information provided can be used by both internal practitioners and external consultants to implement high-potential employee development programs for any size of organization.

Social implications
– High-potential employees represent future leaders. Without developing them, organizations run the risk of high attrition costs along with a lack of qualified talent to fill leadership pipelines.

Originality/value
– The value of this paper is twofold: it offers detailed information to set the tone with stakeholders when it comes to talking about and developing high-potential talent, and it provides a starting point with first steps for successful program implementation.
Emotional intelligence, conflict management styles, and innovation performance
Authors: Zhang Su Juan , Chen Yong Qiang , Sun Hui 
Published: September 2015

Purpose– This paper aims to investigate the relationship among emotional intelligence (EI), conflict management styles (CMSs) and innovation performance, and test the mediating effects of various types of CMSs. Innovation is playing a more and more critical role in the survival and development of companies. EI is assumed to be an antecedent of employees’ innovation performance. Conflict is an inevitable phenomenon in organizations, and different CMSs have different impacts on individual performance.Design/methodology/approach– Research data were obtained from 159 employees in the construction industry in China. SPSS 19.0 was used to test and verify the hypotheses concerning the relationship among EI, CMSs and innovation performance. The authors also conducted a 500-times bootstrapping to verify the mediating roles of different CMSs.Findings– Results indicate that EI is positively and significantly associated with integrating, compromising and dominating styles, as well as innovation performance in the construction industry. In addition, the integrating style has a significantly positive relationship with innovation performance. This research also confirms the mediating effect of integrating style on the relationship between EI and innovation performance.Practical implications– The authors recommend that managers, especially in the construction industry, who are willing to maintain high levels of innovation performance of employees can provide EI training programs. In addition, to improve innovation performance, companies should provide employees with appropriate training emphasizing the importance of conflict management strategies, especially the integrating style.Originality/value– Limited research has focused on the antecedents of conflict management strategies or the relationship between EI and innovation performance. A framework integrating EI, CMSs and innovation performance is put forward and empirical evidence of the relationship between EI and employees’ innovation performance is provided. This research helps to have a better understanding of the relationship between EI and innovation performance by introducing the integrating style as a mediating variable.
The role of affects in conflict frames and conflict management
Authors: Yang Mei-Yu , Cheng Fei-Chun , Chuang Aichia 
Published: September 2015

Purpose– The purpose of this paper is to identify the roles of trait affectivity and momentary moods in conflict frames and conflict management. This paper goes beyond affect induction and focuses on the affective – rather than rational – antecedents of the choice of conflict management strategy.Design/methodology/approach– This paper adopts a within- and between-person approach and uses hierarchical linear modeling to test the hypotheses with group-mean centering. Over the course of 12 days within a three-week period, the authors collected participants’ momentary moods and how they thought about and would respond to conflict scenarios. Data were gathered from 1,545 observations, involving 180 individuals.Findings– After controlling for anger raised from the conflict scenario, both positive trait affectivity and positive momentary moods were found to be positively related to a compromise frame. Surprisingly, neither negative trait affectivity nor momentary mood was related to the win frame. A compromise frame predicted a cooperative strategy, and a win frame predicted a competitive strategy. The relationships between trait and momentary affects and conflict management strategy were partially mediated by conflict frame, but only for positive affects.Practical implications– If seeking a constructive resolution, choose the right person (i.e. an individual with positive trait affectivity) and the right moment (i.e. the individual is in a positive mood state) to communicate disagreements.Originality/value– This paper sheds light on the prediction of conflict frame and conflict management behavior by testing trait affectivity and momentary mood simultaneously.
The impact of interpersonal conflict on construction project performance
Authors: Zhang Lianying , Huo Xiaoyan 
Published: September 2015

Purpose– The purpose of this paper is to examine the relationship between interpersonal conflict and construction project performance. The authors test the proposition that this relationship is mediated by negative emotions and moderated by political skill.Design/methodology/approach– This study used a structured questionnaire survey and gathered 266 completed data from 45 construction project teams in mainland China. To test the hypotheses, bootstrapping procedures were used.Findings– The results show that interpersonal conflict and negative emotions all have inverse relationships with project performance. Additionally, negative emotions mediated the relationship between interpersonal conflict and project performance, and this indirect relationship will be mitigated when team members have a high level of political skill.Research limitations/implications– These findings indicate that interpersonal conflict has a detrimental influence on project performance and should attract broad attention for future empirical literature. Furthermore, political skill is an effective contingent factor to suppress the detrimental influence of interpersonal conflict.Practical implications– The findings imply that managers should highlight the importance of interpersonal conflict in construction projects.Originality/value– This paper addresses a moderated mediation model to examine the relationship among interpersonal conflict, negative emotions and construction project performance, and it takes into account the moderating role of political skill. The paper also offers practical assistance to construction project managers in managing interpersonal conflict.
Effects of gender, rape myth acceptance, and perpetrator occupation on perceptions of rape
Authors: Duff Simon , Tostevin Amy 
Published: September 2015

Purpose– The purpose of this paper is to assess the impact of gender-stereotypical beliefs and associated factors (gender, level of rape myth acceptance (RMA), and occupation) on public attitudes towards rape victims with the aim of establishing whether participant and perpetrator characteristics have effects on individuals’ attitudes towards rape victims. With regards to participants, gender, age, occupation, and the extent to which an individual endorses rape myths were investigated. The authors also considered whether participants’ attitudes were influenced by the occupation of a rapist as described in a vignette looking at occupations deemed to be stereotypically male or female.Design/methodology/approach– In total, 185 individuals participated in the study and were randomly assigned to one of three conditions based on the rapist’s occupation (stereotypically male occupation, gender-neutral occupation or stereotypically female occupation). Participants completed an online survey consisting of a RMA questionnaire, read a short vignette depicting a rape scenario (where they were also informed of the perpetrator’s occupation) and completed a further questionnaire on their attitudes towards rape victims. Results were examined by regression.Findings– The results indicate that both participant occupation and level of RMA significantly contributed to attitudes towards rape victims, however, a statistically significant effect for rapist occupation was not found.Originality/value– Findings are discussed in terms of implications for individuals working within services supporting victims of rape and the potential consequences of holding stereotypical beliefs for rape victims and perpetrators. It is important that research identifies those factors that might bias decision making in the legal system and thus impact upon outcomes for victims and offenders.