bluuebunny/crossref_metadata_2025_split huggingface dataset:
The cohesin ring uses its hinge to organize DNA using non-topological as well as topological mechanisms
Authors: Srinivasan Madhusudhan , Scheinost Johanna C. , Petela Naomi J. , Gligoris Thomas G. , Wissler Maria , Ogushi Sugako , Collier James , Voulgaris Menelaos , Kurze Alexander , Chan Kok-Lung , Hu Bin , Costanzo Vincenzo , Nasmyth Kim A. 
Published: October 2017

SummaryAs predicted by the notion that sister chromatid cohesion is mediated by entrapment of sister DNAs inside cohesin rings, there is a perfect correlation between co-entrapment of circular minichromosomes and sister chromatid cohesion in a large variety of mutants. In most cells where cohesin loads onto chromosomes but fails to form cohesion, loading is accompanied by entrapment of individual DNAs. However, cohesin with a hinge domain whose positively charged lumen has been neutralized not only loads onto and translocates along chromatin but also organizes it into chromatid-like threads, despite largely failing to entrap DNAs inside its ring. Thus, cohesin engages chromatin in a non-topological as well as a topological manner. Our finding that hinge mutations, but not fusions between Smc and kleisin subunits, abolish entrapment suggests that DNAs may enter cohesin rings through hinge opening. Lastly, mutation of three highly conserved lysine residues inside the Smc1 moiety of Smc1/3 hinges abolishes all loading without affecting cohesin’s initial recruitment toCENloading sites or its ability to hydrolyze ATP. We suggest that loading and translocation are mediated by conformational changes in cohesin’s hinge driven by cycles of ATP hydrolysis.
Profiling and leveraging relatedness in a precision medicine cohort of 92,455 exomes
Authors: Staples Jeffrey , Maxwell Evan K. , Gosalia Nehal , Gonzaga-Jauregui Claudia , Snyder Christopher , Hawes Alicia , Penn John , Ulloa Ricardo , Bai Xiadong , Lopez Alexander E. , Van Hout Cristopher V. , O’Dushlaine Colm , Teslovich Tanya M. , McCarthy Shane E. , Balasubramanian Suganthi , Kirchner H. Lester , Leader Joseph B. , Murray Michael F. , Ledbetter David H. , Shuldiner Alan R. , Yancoupolos George , Dewey Frederick E. , Carey David J. , Overton John D. , Baras Aris , Habegger Lukas , Reid Jeffrey G. 
Published: October 2017

AbstractLarge-scale human genetics studies are ascertaining increasing proportions of populations as they continue growing in both number and scale. As a result, the amount of cryptic relatedness within these study cohorts is growing rapidly and has significant implications on downstream analyses. We demonstrate this growth empirically among the first 92,455 exomes from the DiscovEHR cohort and, via a custom simulation framework we developed called SimProgeny, show that these measures are in-line with expectations given the underlying population and ascertainment approach. For example, we identified ∼66,000 close (first- and second-degree) relationships within DiscovEHR involving 55.6% of study participants. Our simulation results project that >70% of the cohort will be involved in these close relationships as DiscovEHR scales to 250,000 recruited individuals. We reconstructed 12,574 pedigrees using these relationships (including 2,192 nuclear families) and leveraged them for multiple applications. The pedigrees substantially improved the phasing accuracy of 20,947 rare, deleterious compound heterozygous mutations. Reconstructed nuclear families were critical for identifying 3,415de novomutations in ∼1,783 genes. Finally, we demonstrate the segregation of known and suspected disease-causing mutations through reconstructed pedigrees, including a tandem duplication inLDLRcausing familial hypercholesterolemia. In summary, this work highlights the prevalence of cryptic relatedness expected among large healthcare population genomic studies and demonstrates several analyses that are uniquely enabled by large amounts of cryptic relatedness.
Association Analysis and Meta-Analysis of Multi-allelic Variants for Large Scale Sequence Data
Authors: Zhan Xiaowei , Chen Sai , Jiang Yu , Liu Mengzhen , Iacono William G. , Hewitt John K. , Hokanson John E , Krauter Kenneth , Laakso Markku , Li Kevin W. , Lutz Sharon M , McGue Matthew , Pandit Anita , Zajac Gregory JM , Boehnke Michael , Abecasis Goncalo R. , Jiang Bibo , Vrieze Scott I. , Liu Dajiang J. 
Published: October 2017

AbstractMotivation:There is great interest to understand the impact of rare variants in human diseases using large sequence datasets. In deep sequences datasets of >10,000 samples, ∼10% of the variant sites are observed to be multi-allelic. Many of the multi-allelic variants have been shown to be functional and disease relevant. Proper analysis of multi-allelic variants is critical to the success of a sequencing study, but existing methods do not properly handle multi-allelic variants and can produce highly misleading association results.Results:We propose novel methods to encode multi-allelic sites, conduct single variant and gene-level association analyses, and perform meta-analysis for multi-allelic variants. We evaluated these methods through extensive simulations and the study of a large meta-analysis of ∼18,000 samples on the cigarettes-per-day phenotype. We showed that our joint modeling approach provided an unbiased estimate of genetic effects, greatly improved the power of single variant association tests, and enhanced gene-level tests over existing approaches.Availability:Software packages implementing these methods are available at (https://github.com/zhanxw/rvtestshttp://genome.sph.umich.edu/wiki/RareMETAL).Contact:xiaowei.zhan@utsouthwestem.edu; dajiang.liu@psu.edu
RES complex is associated with intron definition and required for zebrafish early embryogenesis
Authors: Fernandez Juan P. , Moreno-Mateos Miguel A. , Gohr Andre , Chan Shun Hang , Irimia Manuel , Giraldez Antonio J. 
Published: October 2017

AbstractPre-mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome-wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA-binding proteins. The retention and splicing (RES) complex is formed by three different proteins (Bud13p, Pml1p and Snu17p) and is involved in splicing in yeast. However, the importance of the RES complex for vertebrate splicing, the intronic features associated with its activity, and its role in development are unknown. In this study, we have generated loss-of-function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis ofbud13,snip1(pml1) andrbmx2(snu17) mutants revealed a global defect in intron splicing, with strong mis-splicing of a subset of introns. We found these RES-dependent introns were short, rich in GC and flanked by GC depleted exons, all of which are features associated with intron definition. Using these features we developed a predictive model that classifies RES dependent introns. Altogether, our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.
Networks of genetic similarity reveal non-neutral processes shape strain structure inPlasmodium falciparum
Authors: He Qixin , Pilosof Shai , Tiedje Kathryn E. , Ruybal-Pesántez Shazia , Artzy-Randrup Yael , Baskerville Edward B. , Day Karen P. , Pascual Mercedes 
Published: October 2017

AbstractPathogens compete for hosts through patterns of cross-protection conferred by immune responses to antigens. InPlasmodium falciparummalaria, thevarmultigene family encoding for the major blood-stage antigenPfEMP1 has evolved enormous genetic diversity through ectopic recombination and mutation. With 50-60vargenes per genome, it is unclear whether immune selection can act as a dominant force in structuringvarrepertoires of local populations. The combinatorial complexity of thevarsystem remains beyond the reach of existing strain theory, and previous evidence for non-random structure cannot demonstrate immune selection without comparison to neutral models. We develop two neutral models that encompass malaria epidemiology but exclude competitive interactions between parasites. These models, combined with networks of genetic similarity, reveal non-neutral strain structure in both simulated systems and an extensively sampled population in Ghana. The unique population structure we identify underlies the large transmission reservoir characteristic of highly endemic regions in Africa.
A feed-forward relay between Bicoid and Orthodenticle regulates the timing of embryonic patterning inDrosophila
Authors: Datta Rhea R. , Ling Jia , Kurland Jesse , Ren Xiaotong , Xu Zhe , Yucel Gozde , Moore Jackie , Shokri Leila , Baker Isabel , Bishop Timothy , Struffi Paolo , Levina Rimma , Bulyk Martha L. , Johnston Robert J. , Small Stephen 
Published: October 2017

AbstractThe K50 homeodomain (K50HD) protein Orthodenticle (Otd) is critical for anterior patterning and brain and eye development in most metazoans. InDrosophila melanogaster, another K50HD protein, Bicoid (Bcd), has evolved to replace Otd’s ancestral function in embryo patterning. Bcd is distributed as a long-range maternal gradient and activates transcription of a large number of target genes includingotd. Otd and Bcd bind similar DNA sequencesin vitro, but how their transcriptional activities are integrated to pattern anterior regions of the embryo is unknown. Here we define three major classes of enhancers that are differentially sensitive to binding and transcriptional activation by Bcd and Otd. Class 1 enhancers are initially activated by Bcd, and activation is transferred to Otd via a feed-forward relay (FFR) that involves sequential binding of the two proteins to the same DNA motif. Class 2 enhancers are activated by Bcd, and maintained by an Otd-independent mechanism. Class 3 enhancers are never bound by Bcd, but Otd binds and activates them in a second wave of zygotic transcription. The specific activities of enhancers in each class are mediated by DNA motif variants preferentially bound by Bcd or Otd, and the presence or absence of sites for cofactors that interact with these proteins. Our results define specific patterning roles for Bcd and Otd, and provide mechanisms for coordinating the precise timing of gene expression patterns during embryonic development.
Anger following provocation in individuals with psychopathic traits
Authors: Steuerwald Brian L. , Brown Allison R. , Mneimne Malek , Kosson David 
Published: October 2017

Purpose
The purpose of this paper is to test the attenuated-anger and heightened-anger hypotheses of psychopathy by assessing the physiological, behavioral, and subjective measures of anger in individuals with and without psychopathic traits.

Design/methodology/approach
In all, 62 male college students were assigned to one of three groups based on evidence of elevated affective-interpersonal (Factor 1) and antisocial lifestyle (Factor 2) traits associated with psychopathy (the IF1+F2 group), evidence of only Factor 2 traits (the F2 only group), or based on the absence of psychopathic traits (the control group), using Gough’s (1957) Socialization scale and a modified, interview only form of Hare’s (1991) Psychopathy Checklist-Revised. To induce anger, participants received unjust criticism about their performance on a computer-based affective lexical decision task and were denied a performance bonus they had reason to expect.

Findings
Following provocation, the three groups displayed similar increases in blood pressure, pulse, and self-reported anger. The control and IF1+F2 groups also displayed similar retaliation toward the confederate. However, the IF1+F2 group displayed smaller increases on two of three measures of facial muscle activity associated with anger.

Originality/value
This study is one of the first to assess anger responsiveness in individuals with psychopathic traits using a powerful anger induction and using physiological, behavioral, and subjective indices of anger. It is also the first to assess both the attenuated-anger and the heightened-anger hypotheses of psychopathy. The findings appear largely inconsistent with both perspectives.
Understanding researchers’ intention to publish in open access journals
Authors: Moksness Lars , Olsen Svein Ottar 
Published: October 2017

PurposeThe purpose of this paper is to understand how attitudes, norms (injunctive and descriptive) and perceived behavioral control (PBC) (capacity and autonomy) influence the intention to publish open access (OA), and how personal innovativeness in information technology affects attitude and PBC.Design/methodology/approachThis study employs an integrated and extended theory of planned behavior (TPB) framework within a cross-sectional survey design. The sample consists of researchers at a Norwegian university, and data are collected digitally via e-mail invitation and analyzed using structural equation modeling.FindingsThis study determines that attitude is the strongest predictor of the intention to publish OA, followed by injunctive and descriptive social norms, and PBC capacity and autonomy. All factors positively influence intention apart from PBC autonomy, which has a negative effect.Research limitations/implicationsPotential limitations include: a relatively small sample size, self-reported data and employing intention, not behavior, as the ultimate dependent variable.Practical implicationsThis research contributes with a deeper understanding of what drives the intention to publish OA research articles, and how innovativeness affects attitudes and PBC autonomy. Support is found for an extended TPB model with decomposed normative and PBC components. This knowledge is essential in creating an impetus for systematic research on OA publishing behavior.Originality/valueTheory-driven research into understanding OA publishing behavior is rare. Decomposing the normative and PBC constructs is uncommon in TPB research, and a novel approach in OA research. Personal innovativeness has not been explored previously in relation to OA publishing.
Music questions in social Q&A: an analysis of Yahoo! Answers
Authors: Hertzum Morten , Borlund Pia 
Published: October 2017

Purpose
Social question and answer (social Q&A) sites have become a popular tool for obtaining music information. The purpose of this paper is to investigate what users ask about, what experience the questions convey, and how users specify their questions.

Design/methodology/approach
A total of 3,897 music questions from the social Q&A site Yahoo! Answers were categorized according to their question type, user experience, and question specification.

Findings
The music questions were diverse with (dis)approval (42 percent), factual (21 percent), and advice (15 percent) questions as the most frequent types. Advice questions were the longest and roughly twice as long as (dis)approval and factual questions. The user experience associated with the questions was most often pragmatic (24 percent) or senso-emotional (12 percent). Pragmatic questions were typically about the user’s own performance of music, while senso-emotional questions were about finding music for listening. Notably, half of the questions did not convey information about the user experience but the absence of such information did not reduce the number of answers. In specifying the questions, the most frequent information was about the music context and the user context.

Research limitations/implications
This study suggests a division of labor between social Q&A sites and search engines for music information retrieval. It should be noted that the study is restricted to one social Q&A site.

Originality/value
Social Q&A sites provide an opportunity for studying what information real users seek about music and what information they specify to retrieve it, thereby elucidating the role of social Q&A in music information seeking.
Whenguanximeets connectivity
Authors: Lin Xun , Huang Hua 
Published: October 2017

PurposeThe purpose of this paper is to reveal the underlying mechanisms that drive young adults’ participation in micro-charity.Design/methodology/approachA case study, which formed a large online ethnographic project, was conducted in which the twin methods of participatory observation and in-depth interviews were used to access the experience of a selected group (n= 60) of college students.FindingsThe present paper identifies that young adults’ participation in micro-charity is mainly driven by three underlying mechanisms: the formation of a powerful environment for the distribution of awareness of obligation, creation of trust towards others in distant or weak ties and symbolic construction of collective identity with a shared commitment.Originality/valueThis paper is an exploratory work which sheds new light on charity or other social entrepreneurship development in the social media era. Specifically, the connectivity of social media and the pre-existing relationships may work well together and lead to many positive outputs, including distributing awareness of social obligation, instilling social trust and strengthening social coherence.
Mediators of ethical leadership and group performance outcomes
Authors: Peng J.C. , Lin Julian 
Published: October 2017

PurposeThe purpose of this paper is to examine the relationship between ethical leadership and group-level performance outcomes and show that group value congruence and group trust play pivotal mediating roles in the relationship between ethical leadership and work group performance outcomes.Design/methodology/approachTo examine the proposed model, survey data from 116 branches of a baked goods and beverages chain located in Northern Taiwan were analyzed.FindingsThe results revealed that ethical leadership was positively and significantly related to group in-role performance and group helping behavior; the relationship was fully mediated by group value congruence and group trust after controlling for idealized influence leadership.Research limitations/implicationsThis study features a cross-sectional study design, thus limiting the accuracy of inferences about causality.Practical implicationsThe results of the current study revealed that ethical leadership behaviors enhance group trust. Hence, these leadership behaviors could be among the best and most appropriate practices to be implemented in China and Taiwan.Originality/valueThe data suggested that ethical leadership was associated with not only individual-level behavior but also group-level performance. Furthermore, this paper also uncovered the mediation mechanism through which ethical leadership enhances group performance.
Incidence of predatory journals in computer science literature
Authors: Ibba Simona , Pani Filippo Eros , Stockton John Gregory , Barabino Giulio , Marchesi Michele , Tigano Danilo 
Published: October 2017

Purpose
One of the main tasks of a researcher is to properly communicate the results he obtained. The choice of the journal in which to publish the work is therefore very important. However, not all journals have suitable characteristics for a correct dissemination of scientific knowledge. Some publishers turn out to be unreliable and, against a payment, they publish whatever researchers propose. The authors call “predatory journals” these untrustworthy journals. The purpose of this paper is to analyse the incidence of predatory journals in computer science literature and present a tool that was developed for this purpose.

Design/methodology/approach
The authors focused their attention on editors, universities and publishers that are involved in this kind of publishing process. The starting point of their research is the list of scholarly open-access publishers and open-access stand-alone journals created by Jeffrey Beall. Specifically, they analysed the presence of predatory journals in the search results obtained from Google Scholar in the engineering and computer science fields. They also studied the change over time of such incidence in the articles published between 2011 and 2015.

Findings
The analysis shows that the phenomenon of predatory journals somehow decreased in 2015, probably due to a greater awareness of the risks related to the reputation of the authors.

Originality/value
We focused on computer science field, using a specific sample of queries. We developed a software to automatically make queries to the search engine, and to detect predatory journals, using Beall’s list.
An analytical technique for solving quadratic nonlinear oscillator
Authors: Molla Md. Helal Uddin , Razzak Md. Abdur , Alam M.S. 
Published: October 2017

Purpose
The purpose of this paper is to present an analytical technique, based on the He’s energy balance method (an improved version recently presented by Khan et al.), to obtain the approximate solution of quadratic nonlinear oscillator (QNO).

Design/methodology/approach
This oscillator (QNO) is used as a mathematical model of the human eardrum oscillation.

Findings
It has been shown that the results by the present technique are very close to the numerical solution.

Originality/value
The results obtained in this paper are compared with those obtained by Hu (harmonic balance method) and Khan et al. The result shows that the method is more accurate and effective than harmonic balance as well as improved energy balance methods.
Finite element analysis of aircraft tire for safety assessment with CV and CPM methods
Authors: Yao Shile , Feng Yue Zhu , Geng Xiaoliang , Wang Peiyan 
Published: October 2017

Purpose
The purpose of this paper is to present a study of radial aircraft tire for safety assessment during various scenarios.

Design/methodology/approach
A detailed finite element (FE) model of aircraft tire was established based on the actual geometry of the target tire for numerical simulations. As the major component of this tire, rubber material usually presents a complicated mechanical behavior. To obtain the reliable hyperelastic properties of rubber, a series of material tests have been processed. Moreover, in order to validate the proposed model, the simulations results of inflation and static load scenarios were compared with the experimental results. Both of the control volume and corpuscular particle method methods were used in the numerical simulations of aircraft tire.

Findings
The comparisons of the two methods exhibit close agreement with the experimental results. To assess the safety of aircraft tire during the landing scenario, the dynamic simulations were processed with different landing weights and vertical landing speeds. According to the relevant airworthiness regulations and technical documents, the tire pressure, deflection and load have been chosen as the safety criteria. Subsequently, the analysis, results and comments have been discussed in detail.

Originality/value
The validated FE model proposed in present study can be effectively used in tire modeling in static and dynamic problems, and also in the design process of aircraft tire.