bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Longitudinal Model for Functional Connectivity Networks Using Resting-State fMRI
Authors: Hart Brian , Cribben Ivor , Fiecas Mark ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: June 2017

AbstractMany neuroimaging studies collect functional magnetic resonance imaging (fMRI) data in a longitudinal manner. However, the current network modeling literature lacks a general framework for analyzing functional connectivity (FC) networks in fMRI data obtained from a longitudinal study. In this work, we build a novel longitudinal FC network model using a variance components approach. First, for all subjects’ visits, we account for the autocorrelation inherent in the fMRI time series data using a non-parametric technique. Second, we use a generalized least squares approach to estimate 1) the within-subject variance component shared across the population, 2) the FC network, and 3) the FC network’s longitudinal trend. Our novel method for longitudinal FC networks seeks to account for the within-subject dependence across multiple visits, the variability due to the subjects being sampled from a population, and the autocorrelation present in fMRI data, while restricting the number of parameters in order to make the method computationally feasible and stable. We develop a permutation testing procedure to draw valid inference on group differences in baseline FC and change in FC over time between a set of patients and a comparable set of controls. To examine performance, we run a series of simulations and apply the model to longitudinal fMRI data collected from the Alzheimer’s Disease Neuroimaging Initiative database.
Project MinE: study design and pilot analyses of a large-scale whole genome sequencing study in amyotrophic lateral sclerosis
Authors:   Project MinE ALS Sequencing Consortium, Rheenen Wouter Van , Pulit Sara L. , Dekker Annelot M. , Khleifat Ahmad Al , Brands William J. , Iacoangeli Alfredo , Kenna Kevin P. , Kooyman Maarten , McLaughlin Russell L. , Middelkoop Bas , Moisse Matthieu , Schellevis Raymond D. , Shatunov Aleksey , Sproviero William , Tazelaar Gijs H.P. , Van der Spek Rick A.A. , Van Doormaal Perry T.C. , Van Eijk Kristel R. , van Vugt Joke J.F.A. , Basak A. Nazli , Glass Jonathan D. , Hardiman Orla , Hide Winston , Landers John E , Mora Jesus S. , Morrison Karen E. , Robberecht Wim , Newhouse Stephen , Shaw Christopher E. , Shaw Pamela J. , Van Damme Philip , Van Es Michael A. , Al-Chalabi Ammar , Van den Berg Leonard H. , Veldink Jan H. 
Published: June 2017

AbstractThe most recent genome-wide association study in amyotrophic lateral sclerosis (ALS) demonstrates a disproportionate contribution from low-frequency variants to genetic susceptibility of disease. We have therefore begun Project MinE, an international collaboration that seeks to analyse whole-genome sequence data of at least 15,000 ALS patients and 7,500 controls. Here, we report on the design of Project MinE and pilot analyses of newly whole-genome sequenced 1,264 ALS patients and 611 controls drawn from the Netherlands. As has become characteristic of sequencing studies, we find an abundance of rare genetic variation (minor allele frequency < 0.1 %), the vast majority of which is absent in public data sets. Principal component analysis reveals local geographical clustering of these variants within The Netherlands. We use the whole-genome sequence data to explore the implications of poor geographical matching of cases and controls in a sequence-based disease study and to investigate how ancestry-matched, externally sequenced controls can induce false positive associations. Also, we have publicly released genome-wide minor allele counts in cases and controls, as well as results from genic burden tests.
Molecular insights into conformational dynamics associated with the open-closed-phosphorylated states of PITPα
Authors: Kotyada Chaithanya 
Published: June 2017

AbstractPhosphatidylinositol transfer proteins (PITPα) are lipid carrier proteins that are involved in replenishing the phosphatidylinositol lipid molecules on the plasma membranes. Transitions between the open and closed state conformations are necessary steps in the mechanism of lipid transfer by PITPα. The apo (open state) conformation is assumed to occur at the membrane surface during the lipid exchange while the lipid bound (closed state) conformation is required for transfer activity. The transfer of phosphatidylinositol by PITPα is controlled by the phosphorylation of S166 in its regulatory region. We wanted to decipher the molecular basis for structure-function relationship between the open-closed-phosphorylated states of PITPα. We used all-atom Molecular Dynamics Simulations to study the conformational dynamics in each of these states. Our study shows that the open state is highly dynamic and its transition to closed state would stabilize PITPα. We observed restricted conformational sampling of the phosphorylated state which provide basis for its decreased lipid transfer activity. Further, using analysis of residue-residue contact maps and hydrogen bond interactions we discuss the impact of phosphorylation on the global conformation of PITPα. Overall, our work provides insights into the structural dynamics in each state and their functional significance.
Copy Number Variation Analysis of 100 Twin Pairs Enriched for Neurodevelopmental Disorders
Authors: Stamouli Sofia , Anderlid Britt-Marie , Willfors Charlotte , Thiruvahindrapuram Bhooma , Wei John , Berggren Steve , Nordgren Ann , Scherer Stephen W , Lichtenstein Paul , Tammimies Kristiina , Bölte Sven 
Published: June 2017

AbstractHundreds of penetrant risk loci have been identified across different neurodevelopmental disorders (NDDs), and these often involve rare (<1% frequency) copy number variations (CNVs), which can involve one or more genes. Monozygotic (MZ) twin pairs are long thought to share 100% of their genomic information. However, genetic differences in the form of postzygotic somatic variants have been reported recently both in typically developing (TD) and in clinically discordant MZ pairs. Here, we sought to investigate the contribution of CNVs in 100 twin pairs enriched for NDD phenotypes with a particular focus on MZ pairs discordant for autism spectrum disorder (ASD) using the PsychChip array. In our collection, no postzygoticde novoCNVs were found in 55 MZ twin pairs, including the 13 pairs discordant for ASD. When analyzing the burden of rare CNVs among pairs concordant and discordant for ASD/NDD in comparison with typically developed (TD) pairs, no differences were found. However, we did detect a higher rate of CNVs overlapping genes involved in disorders of the nervous system in MZ pairs discordant and concordant for ASD in comparison with TD pairs (p=0.02). Our results are in concordance with earlier findings that postzygoticde novoCNV events are typically rare in genomic DNA derived from saliva or blood and, in the majority of MZ twins, do not explain the discordance of NDDs. Still, studies investigating postzygotic variation in MZ discordant twins using DNA from different tissues and single cells and higher resolution genomics are needed in the future.
The evolutionary history of Nebraska deer mice: local adaptation in the face of strong gene flow
Authors: Pfeifer Susanne P. , Laurent Stefan , Sousa Vitor C. , Linnen Catherine R. , Foll Matthieu , Excoffier Laurent , Hoekstra Hopi E. , Jensen Jeffrey D. 
Published: June 2017

ABSTRACTThe interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective over the last century. Wright and Haldane laid the foundation for expectations under an island-continent model, demonstrating that an island-specific beneficial allele may be maintained locally if the selection coefficient is larger than the rate of migration of the ancestral allele from the continent. Subsequent extensions of this model have provided considerably more insight. Yet, connecting theoretical results with empirical data has proven challenging, owing to a lack of information on the relationship between genotype, phenotype, and fitness. Here, we examine the demographic and selective history of deer mice in and around the Nebraska Sand Hills, a system in which variation at theAgoutilocus affects cryptic coloration that in turn affects the survival of mice in their local habitat. We first genotyped 250 individuals from eleven sites along a transect spanning the Sand Hills at 660,000 SNPs across the genome. Using these genomic data, we found that deer mice first colonized the Sand Hills following the last glacial period. Subsequent high rates of gene flow have served to homogenize the majority of the genome between populations on and off the Sand Hills, with the exception of theAgoutipigmentation locus. Furthermore, mutations at this locus are strongly associated with the pigment traits that are strongly correlated with local soil coloration and thus responsible for cryptic coloration.
Reference Quality Assembly of the 3.5 Gb genome ofCapsicum annuumfrom a Single Linked-Read Library
Authors: Hulse-Kemp Amanda M. , Maheshwari Shamoni , Stoffel Kevin , Hill Theresa A. , Jaffe David , Williams Stephen , Weisenfeld Neil , Ramakrishnan Srividya , Kumar Vijay , Shah Preyas , Schatz Michael C. , Church Deanna M. , Deynze Allen Van 
Published: June 2017

AbstractBackgroundLinked-Read sequencing technology has recently been employed successfully forde novoassembly of multiple human genomes, however the utility of this technology for complex plant genomes is unproven. We evaluated the technology for this purpose by sequencing the 3.5 gigabase (Gb) diploid pepper(Capsicum annuum)genome with a single Linked-Read library. Plant genomes, including pepper, are characterized by long, highly similar repetitive sequences. Accordingly, significant effort is used to ensure the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus. With a phased assembly approach, we targeted a heterozygous F1derived from a wide cross to assess the ability to derive both haplotypes for a pungency gene characterized by a large insertion/deletion.ResultsThe Supernova software generated a highly ordered, more contiguous sequence assembly than all currently availableC. annuumreference genomes. Eighty-four percent of the final assembly was anchored and oriented using fourde novolinkage maps. A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly. The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5 kb insertion/deletion haplotypes of thePUN1locus in the F1sample that represents pungent and non-pungent peppers.ConclusionsThe most contiguous pepper genome assembly to date has been generated through this work which demonstrates that Linked-Read library technology provides a rapid tool to assemblede novocomplex highly repetitive heterozygous plant genomes. This technology can provide an opportunity to cost-effectively develop high-quality reference genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction.
Sex-biased transcriptomic response of the reproductive axis to stress
Authors: Calisi Rebecca , Austin Suzanne H. , Lang Andrew S. , MacManes Matthew D. 
Published: June 2017

ABSTRACTStress is a well-known cause of reproductive dysfunction in many species, including birds, rodents, and humans. However, little is known of the genomic basis for this dysfunction and how it may differ between the sexes. Using the classic reproductive model of the rock dove (Columba livia), we conducted the most in-depth investigation to date of how stress affects all gene transcription of a biological system essential for facilitating reproduction - the hypothalamic-pituitary-gonadal (HPG) axis. The HPG transcriptome responded to stress in both sexes, but females exhibited more differential expression than males, and these stress responsive genes were mostly unique to females. This result may be due to 1) fluctuations in the female endocrine environment to facilitate ovulation and follicle maturation, and 2) their evolutionary history. We offer a vital genomic foundation on which sex-specific reproductive dysfunction can be studied, as well as novel gene targets for genetic intervention and therapy investigations.
Unravelling the participation of stakeholders in the governance models of social enterprises in Greece
Authors: Argyrou Aikaterini , Blomme Robert J. , Lambooy Tineke , Kievit Henk 
Published: June 2017

Purpose
This paper aims to examine the concept of participatory governance through membership in the context of the tailor-made legal form for social enterprises in Greece, i.e. the social cooperative enterprise (Koinsep). As such, the paper aims to contribute to the theoretical discussion regarding the participation of stakeholders in the governance of social enterprises not only as a theoretical construct prescribed by law but also by examining its implementation in practice.

Design/methodology/approach
The development of two in-depth case studies demonstrate whether and how the application and implementation of legal requirements regarding governance and membership permit and encourage stakeholders to participate in the decision-making processes of social enterprises. The study accordingly showcases the influence exerted by the legal regime over the social enterprise.

Findings
The case studies demonstrate how participatory governance is not realised in a formal manner in the organisational set-up of two social enterprises. It thereby shows how stakeholders and employees participate informally in the decision-making processes of Greek social enterprises, although legislation is conducive to formal means of participation.

Research limitations/implications
This study is part of a larger project involving a comparative research of tailor-made legal forms of social enterprises and corresponding organisations in three jurisdictions, i.e. Greece, Belgium, and the UK. In this study, the research was limited to the legal form of Koinsep.

Practical implications
This paper also contributes to the development of a better understanding of the Koinsep as a new tailor-made legal form for social enterprises in Greece. It therefore, sheds light in its function and its participatory governance structure.

Originality/value
The study is an original attempt to theoretically and practically examine the subject of participatory governance in the Greek social enterprises context.
Fast multipole cell-based domain integration method for treatment of volume potentials in 3D elasticity problems
Authors: Wang Qiao , Zhou Wei , Cheng Yonggang , Ma Gang , Chang Xiaolin 
Published: June 2017

Purpose
Domain integrals, known as volume potentials in 3D elasticity problems, exist in many boundary-type methods, such as the boundary element method (BEM) for inhomogeneous partial differential equations. The purpose of this paper is to develop an accurate and reliable technique to effectively evaluate the volume potentials in 3D elasticity problems.

Design/methodology/approach
An adaptive background cell-based domain integration method is proposed for treatment of volume potentials in 3D elasticity problems. The background cells are constructed from the information of the boundary elements based on an oct-tree structure, and the domain integrals are evaluated over the cells rather than volume elements. The cells that contain the boundary elements can be subdivided into smaller sub-cells adaptively according to the sizes and levels of the boundary elements. The fast multipole method (FMM) is further applied in the proposed method to reduce the time complexity of large-scale computation.

Findings
The method is a boundary-only discretization method, and it can be applied in the BEM easily. Much computational time is saved by coupling with the FMM. Numerical examples demonstrate the accuracy and efficiency of the proposed method..

Originality/value
Boundary elements are used to create adaptive background cells, and domain integrals are evaluated over the cells rather than volume elements. Large-scale computation is made possible by coupling with the FMM.
An appraisal of the barriers to client involvement in health and safety in Nigeria’s construction industry
Authors: Umeokafor Nnedinma 
Published: June 2017

Purpose
The purpose of this paper is to present the findings of a study that identified and assessed the barriers to client involvement in health and safety (H&S) in the Nigerian construction industry.

Design/methodology/approach
On the basis of literature review and a pilot study, structured questionnaires were designed and administered to clients and their representatives in ongoing construction projects in Nigeria. Descriptive and inferential statistics were then adopted while analysing the data.

Findings
The research reveals that the major barriers to client involvement in H&S in Nigeria’s construction industry focus on the gaps created by lack of H&S legislation in specifying client roles and responsibilities in H&S, trust and confidence in the supply chain, low levels of awareness at various levels, procurement issues, the attitudes of the various members of the project team and resource-related issues. In total, 20 barriers to client involvement in H&S were identified and assessed.

Practical implications
Policy makers will find the study beneficial as it provides a good understanding of the issues to address while making policies that seek to involve the client in H&S in Nigeria.

Originality/value
While the findings offer insight on the barriers to client involvement in H&S in Nigeria’s construction industry, the study also contributes to the discourse in developing countries. The paper recommends transparent steps in procurement, H&S legislation that factors in economic incentives and community and financial institutions contributions to involving clients in H&S. The study is the first attempt to investigate the barriers to client involvement in construction H&S in Nigeria, contributing to the dearth of H&S literature in Nigeria.
Building an implicit change leadership theory
Authors: Magsaysay Jowett F. , Hechanova Ma. Regina M. 
Published: June 2017

Purpose
The purpose of this paper is to propose a model for implicit change leadership theory (ICLT) and to explore its relationship with perceived effectiveness of change management (CM).

Design/methodology/approach
The study employed a mixed-methods design. It used a qualitative approach to identify schemas on the traits and behaviors of an ideal leader and schemas on what constitute effective CM. A quantitative approach was followed to test the conceptual model.

Findings
The study suggests five competencies of ideal change leaders: strategic and technical competencies, execution competencies, social competencies, character, and resilience. Together, these five competencies comprise an ICLT. Moreover, schema congruence correlates with perceived effectiveness of CM. The closer the congruence between subordinates’ ideal change leader and their actual change leader, the greater the perceived effectiveness of CM.

Research limitations/implications
The study was limited to employees in the Philippines. It is thus suggested that data gathering in other populations be conducted to allow for generalizability of results. The research was cross-sectional in design, that limits causal explanations. Longitudinal studies examining perceptions and attitudes during and after the implementation of change could provide more robust evidence of the relationships between schemas and perceptions of change.

Practical implications
The results suggest that to increase the chances of success of their change initiatives, organizations could consider leadership development interventions that could enhance the competencies of their leaders in the implicit change leadership constructs. Organizations also need to consider employee schemas of effective CM when implementing change.

Originality/value
The main contribution of this paper is to expand implicit leadership theory by applying it to a specific leadership context, that of organizational change, and to derive an ICLT.
Leader-member exchange and the transfer of knowledge from Taiwanese managers to their Chinese subordinates
Authors: Cheng Shih Yu (Cheryl) 
Published: June 2017

PurposeThe purpose of this paper is to investigate the relationships among leader-member exchange (LMX) quality, social interaction, and the effectiveness of knowledge transfer.Design/methodology/approachThis study used a paired questionnaire to collect 209 valid sets of paired data, consisting of responses from 37 Taiwanese supervisors and their 209 Chinese subordinates at 35 Taiwanese manufacturing firms located in Mainland China. The proposed hypotheses were tested with the application of a two-step approach of PLS-SEM analysis.FindingsThe results of this study showed that LMX quality and social interaction are positively associated with effective knowledge transfer, and most importantly, it found that social interaction between Taiwanese managers and their subordinates has a full mediating effect on this relationship.Research limitations/implicationsThe data were collected from a dyad supervisor-subordinate relationship; thus, future research is encouraged to collect data from peer co-worker relationships. The findings, however, suggested that organizations should provide a supportive environment where a good supervisor-subordinate relationship can be created for the enhancement of knowledge transfer.Practical implicationsThe study suggested that managers should work to develop high-quality LMX relationships with their subordinates, as this can enhance social interaction among employees and facilitate more effective knowledge transfer.Originality/valueThe paper applied a four-level training evaluation model to assess the effectiveness of knowledge transfer which has never been done before, and found that both LMX quality and social interaction affect how well individuals can acquire knowledge.