bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long non-coding RNA gene regulation and trait associations across human tissues
Authors: de Goede O. M. , Ferraro N. M. , Nachun D. C. , Rao A. S. , Aguet F. , Barbeira A. N. , Castel S. E. , Kim-Hellmuth S. , Park Y. , Scott A. J. , Strober B. J. ,   GTEx Consortium, Brown C. D. , Wen X. , Hall I. M. , Battle A. , Lappalainen T. , Im H. K. , Ardlie K. G. , Quertermous T. , Kirkegaard K. , Montgomery S. B. 
Published: October 2019

AbstractLong non-coding RNA (lncRNA) genes are known to have diverse impacts on gene regulation. However, it is still a major challenge to distinguish functional lncRNAs from those that are byproducts of surrounding transcriptional activity. To systematically identify hallmarks of biological function, we used the GTEx v8 data to profile the expression, regulation, network relationships and trait associations of lncRNA genes across 49 tissues encompassing 87 distinct traits. In addition to revealing widespread differences in regulatory patterns between lncRNA and protein-coding genes, we identified novel disease-associated lncRNAs, such asC6orf3for psoriasis andLINC01475/RP11-129J12.1for ulcerative colitis. This work provides a comprehensive resource to interrogate lncRNA genes of interest and annotate cell type and human trait relevance.One Sentence SummarylncRNA genes have distinctive regulatory patterns and unique trait associations compared to protein-coding genes.
Minimalin vivorequirements for developmentally regulated cardiac long intergenic non-coding RNAs
Authors: George Matthew R. , Duan Qiming , Nagle Abigail , Kathiriya Irfan S. , Huang Yu , Rao Kavitha , Haldar Saptarsi M. , Bruneau Benoit G. 
Published: October 2019

AbstractLong intergenic non-coding RNAs (lincRNAs) have been implicated in aspects of gene regulation, but their requirement for development needs empirical interrogation. To begin to understand the roles lincRNAs might play in heart development, we computationally identified nine murine lincRNAs that have developmentally regulated transcriptional and epigenomic profiles specific to early heart differentiation. Six of the nine lincRNAs had in vivo expression patterns supporting a potential function in heart development, including a transcript downstream of the cardiac transcription factorHand2that we namedHandlr (Hand2-associated lincRNA),Rubie,andAtcayos. We genetically ablated these six lincRNAs in mouse, which implicated genomic regulatory roles to four of the cohort, However, none of the lincRNA deletions led to severe cardiac phenotypes. Thus, we stressed the hearts of adultHandlrandAtcayosmutant mice by transverse aortic banding and found that absence of these lincRNAs did not affect cardiac hypertrophy or left ventricular function post-stress. Our results support roles for lincRNA transcripts and/or transcription to regulation of topologically associated genes. However, the individual importance of developmentally-specific lincRNAs is yet to be established. Their status as either gene-like entities or epigenetic components of the nucleus should be further considered.
Genome-Wide Classification of Type I, Type II and Type III Interferon-Stimulated Genes in Chicken Fibroblasts
Authors: Santhakumar Diwakar , Rohaim Mohammed A. , Munir Muhammad 
Published: October 2019

AbstractInterferons (IFNs) play central roles in establishing innate immunity and mediating adaptive immunity against multiple pathogens. Three known types of IFNs identify their cognate receptors, initiate cascades of signalling events and eventually result in the induction of myriad of IFN-stimulated genes (ISGs). These ISGs perform multitude of functions and cumulatively corroborate a bespoke antiviral state to safeguard hosts against invading viruses. Owing to unique nature of chicken’s immune system and lack of foundational profiling information on the nature and dynamic expression of IFN-specific ISGs at the genome scale, we performed a systematic and extensive analysis of type I, II and III IFN-induced genes in chicken. Employing pan-IFN responsive chicken fibroblasts coupled with transcriptomics we observed an overwhelming over-representation of up-regulated ISGs by all types of IFNs. Intriguingly, prediction of IFN-stimulated response element (ISRE) and gamma-IFN activation sequence (GAS) revealed a substantial number of GAS motifs in selective significantly induced ISGs in chicken. Extensive comparative, genome-wide and differential expression analysis of ISGs under equivalent signalling input catalogue a set of genes that were either IFN-specific or independent of types of IFNs used to prime fibroblasts. These comprehensive datasets, first of their kinds in chicken, will establish foundations to elucidate the mechanisms of actions and breadth of antiviral action of ISGs which may propose alternative avenues for the targeted antiviral therapy against viruses of poultry and public health importance.
A framework for gene mapping in wheat demonstrated using the Yr7 yellow rust resistance gene
Authors: Gardiner Laura-Jayne , Bansept-Basler Pauline , El-Soda Mohamed , Hall Anthony , O’Sullivan Donal M. 
Published: October 2019

AbstractWe used three approaches to map the yellow rust resistance gene Yr7 and identify associated SNPs in wheat. First, we used a traditional QTL mapping approach using a double haploid (DH) population and mapped Yr7 to a low-recombination region of chromosome 2B. To fine map the QTL, we then used an association mapping panel. Both populations were SNP array genotyped allowing alignment of QTL and genome-wide association scans based on common segregating SNPs. Analysis of the association panel spanning the QTL interval, narrowed the interval down to a single haplotype block. Finally, we used mapping-by-sequencing of resistant and susceptible DH bulks to identify a candidate gene in the interval showing high homology to a previously suggested Yr7 candidate and to populate the Yr7 interval with a higher density of polymorphisms. We highlight the power of combining mapping-by-sequencing, delivering a complete list of gene-based segregating polymorphisms in the interval with the high recombination, low LD precision of the association mapping panel. Our mapping-by-sequencing methodology is applicable to any trait and our results validate the approach in wheat, where with a near complete reference genome sequence, we are able to define a small interval containing the causative gene.HighlightWe show progression from genetic mapping to mapping-by-sequencing and the overlap of defined intervals by each approach culminating with interval refinement and identification of a candidate gene for disease resistance.
Combining free energy simulations and NMR chemical-shift perturbation to identify transient cation-π contacts in proteins
Authors: Reis André A. O. , Sayegh Raphael S. R. , Marana Sandro R. , Arantes Guilherme M. 
Published: October 2019

AbstractFlexible protein regions containing cationic and aromatic side-chains exposed to solvent may form transient cation-π interactions with structural and functional roles. To evaluate their stability and identify important intramolecular cation-π contacts, a combination of free energy profiles estimated from umbrella sampling with molecular dynamics simulations and chemical shift perturbations (CSP) obtained from NMR experiments is applied here to the complete catalytic domain of human phosphatase Cdc25B. This protein is a good model system for transient cation-π interactions as it contains only one Trp residue (W550) in the disordered C-terminal segment and a total of 17 Arg residues, many exposed to solvent. Eight putative Arg-Trp pairs were simulated here. Only R482 and R544 show bound profiles corresponding to important transient cation-π interactions, while the others have dissociative or almost flat profiles. These results are corroborated by CSP analysis of three Cdc25B point mutants (W550A, R482A and R544A) disrupting cation-π contacts. The proposed validation of statistically representative molecular simulations by NMR spectroscopy could be applied to identify transient contacts of proteins in general but carefully, as NMR chemical shifts are sensitive to changes in both molecular contacts and conformational distributions.
The Medicago truncatula DREPP protein triggers microtubule fragmentation in membrane nanodomains during symbiotic infections
Authors: Su Chao , Klein Marie-Luise , Hernández-Reyes Casandra , Batzenschlager Morgane , Ditengou Franck Anicet , Keller Jean , Delaux Pierre-Marc , Ott Thomas 
Published: October 2019

AbstractThe initiation of intracellular host cell colonization by symbiotic rhizobia in Medicago truncatula requires repolarization of root hairs, which includes the re-arrangement of cytoskeletal filaments. The molecular players governing microtubule (MT) re-organization during infection remain to be discovered. Here, we identified the M. truncatula DREPP protein and investigated its functions during rhizobial infections. We show that rhizobial colonization of drepp mutant roots as well as transgenic roots over-expressing DREPP is impaired. DREPP re-localizes into symbiosis-specific membrane nanodomains in a stimulus-dependent manner. This subcellular segregation coincides with DREPP-dependent MT fragmentation and a partial loss of the ability to re-organize the MT cytoskeleton in response to rhizobia, which might relay on an interaction between DREPP and MT organizing protein SPIRAL2 (SPR2). Taken together, our results reveal that establishment of symbiotic associations in M. truncatula require DREPP in order to regulate MT reorganization during initial root hair responses to rhizobia.
Inter-regional innovation correlation effects and influencing factors in China
Authors: Pan Xiongfeng , Ming Yang , Li Mengna , Guo Shucen , Han Cuicui 
Published: October 2019

Purpose
The purpose of this paper is to find out the characteristics and evolutionary trends of China’s inter-regional innovation correlation network, the status and roles of each province in China’s inter-regional innovation correlation network and the influencing factors of China’s inter-regional innovation correlation effect.

Design/methodology/approach
Based on the patent data of 30 provinces (autonomous regions and municipalities) in China from 1991 to 2017, social network analysis was used to find out the characteristics and evolutionary trends of China’s inter-regional innovation correlation network and the status and roles of each province in China’s inter-regional innovation correlation network. Furthermore, the QAP method was used to find out the influencing factors of China’s inter-regional innovation correlation effect.

Findings
China’s inter-regional innovation correlation is becoming increasingly close and inter-regional innovation correlation network is becoming increasingly stable. Jiangsu, Zhejiang, Beijing, Shanghai, Guangdong and other eastern coastal provinces are at the core in the inter-regional innovation correlation network, while the western regions are marginal actors. China’s regional innovation development territory can be divided into four blocks, namely, “bidirectional spillover block,” “net spillover block,” “main beneficial block” and “net beneficial block,” and gradient transfer mechanism is obvious between the blocks. The geographical adjacency and similarity in regional industrial structure, urbanization level and government attention degree have significant positive effect on China’s inter-regional innovation correlation effects.

Research limitations/implications
This paper only uses patent application as a measure of regional innovation level to analyze inter-regional innovation correlation effect. Meanwhile, this paper carries out an empirical study only from the provincial level and not from the city level.

Practical implications
This paper provides the practical basis for further promoting the coordinated development of regional innovation and promoting the construction of regional innovation systems with different characteristics.

Originality/value
This paper contributes to understand the status and role of each province in inter-regional innovation correlation network. Meanwhile, this paper also helps to understand the influence of the proximity and external environmental factors on inter-regional innovation correlation effect.
The impact of high insider ownership on SOX 404 internal controls
Authors: Diala Lucy Uche , Houmes Robert 
Published: October 2019

Purpose
This study aims to investigate the effect of high insider ownership on firms’ internal controls over financial reporting. In particular, it examines how high insider ownership affects the likelihood of an adverse Sarbanes–Oxley Act Section (SOX Section 404) opinion and its subsequent remediation.

Design/methodology/approach
Tests of hypotheses use ineffective controls and remediation models. The initial tests in this study use ineffective internal controls over financial reporting probit regression models to investigate how high insider ownership affects the ex-post likelihood of an adverse 404 opinion. Two remediation models – a multinominal probit regression and probit regression model – are used to investigate the effect of high insider ownership on the likelihood of successfully remediating an adverse 404 opinion.

Findings
Results show that while the ex-ante likelihood of an adverse SOX Section 404 auditor’s internal control opinion increases with high insider ownership, high insider ownership firms are more likely to remediate ineffective 404 controls. This study rationalizes these diverse findings by asserting that prior to an adverse 404 opinion, entrenched managers avoid internal control financial reporting oversight and monitoring. After an adverse opinion, however, and within the context of an imminent and explicit value reducing 404 opinion, powerful high insider owner managers are motivated to remedy ineffective controls.

Originality/value
This research synthesizes existing streams of literature on insider ownership and the effectiveness of internal control over financial reporting quality to provide new information on the effects of high insider ownership on firms’ internal controls.
Crossvergence of socially (ir)responsible employment practices in supplier firms
Authors: Holzberg Britta 
Published: October 2019

PurposeThe purpose of this paper is to introduce the notion of crossvergence from international human resource management (IHRM) as a conceptual lens for understanding and analyzing the formation of socially (ir)responsible employment practices in supplier firms in global production networks (GPNs). The crossvergence perspective can particularly contribute to understanding how the agency of suppliers is influenced by the interaction of global–local dynamics.Design/methodology/approachThe paper illustrates how the formation of socially (ir)responsible employment practices can be understood as a process of crossvergence. Subsequently, it reviews and structures insights from GPN and IHRM literature to detail the process.FindingsThe paper underscores the complicated role of suppliers in ensuring decent work in GPNs. Suppliers face a multitude of global and local interacting, and partially conflicting, demands. They process these demands as active agents and need to develop suitable employment practices in response.Originality/valueThe paper supports the nascent discourse on supplier agency in forming socially responsible employment practices. It connects different streams of literature to illuminate the perspective of suppliers, introduces IHRM insights to the debate and offers conceptual guidance for analyzing interacting global and local pressures on suppliers.
Absorptive capacity, marketing capabilities, and innovation commercialisation in Nigeria
Authors: Medase Kehinde , Barasa Laura 
Published: October 2019

PurposeThe purpose of this paper is to investigate how specialised capabilities including absorptive capacity and marketing capabilities influence innovation commercialisation in manufacturing and service firms in Nigeria. The authors hypothesise that absorptive capacity measures including openness and formal training for innovation, and marketing capabilities encompassing new product marketing and marketing innovation are positively associated with innovation performance.Design/methodology/approachThe authors examine commercialisation of innovation within the profiting from innovation (PFI) and dynamic capabilities (DC) framework and use data from the 2012 Nigeria Innovation Survey to test the hypothesis by means of a Heckman sample selection model.FindingsThe authors find that absorptive capacity measures comprising openness and formal training are positively associated with innovation performance. The authors also find that marketing capabilities as indicated by new product marketing and marketing innovation are positively associated with innovation performance.Research limitations/implicationsThe authors acknowledge that firms undergo continuous changes and that there may be the presence of unobserved or unmeasured heterogeneity. Taking into cognisance that Nigeria is a federal state, cultural diversity and economic factors are likely to differ widely between geographical regions. Also, while the proposed conceptual framework offers a deeper understanding of innovation performance, examining how integrating activities of the R&D department, human resource department and marketing department affect innovation commercialisation is likely to provide more meaningful insights.Practical implicationsThe role that inter-organisational learning and intra-organisational learning play in driving innovation performance provide managers with a basis for incorporating absorptive capacity building programs that boost employees’ ability to recognise and apply valuable external knowledge to commercial ends. Similarly, firms may benefit from offering marketing capabilities development programs. Furthermore, innovation policies in Nigeria are generally designed to focus on fostering innovation activities aimed at developing innovative output. Accordingly, government support explicitly targeting new product marketing and marketing innovation is likely to play a vital role in the successful commercialisation of innovation in Nigeria.Originality/valueThis study fuses the PFI and DC framework to examine why innovating firms may not necessarily succeed. This area of study has received scant attention in sub-Saharan Africa given that extant literature focusses on value creation as opposed to value capture.
The scientific nature of work-based learning and research
Authors: Fergusson Lee , Shallies Bradley , Meijer Gerry 
Published: October 2019

Purpose
The purpose of this paper is to explore the scientific nature of work-based learning (WBL) and research as operationalized in Professional Studies by examining first principles of scientific inquiry.

Design/methodology/approach
This paper introduces a Professional Studies program as it has been implemented at University of Southern Queensland in Australia and examines it from the perspective of five first principles of scientific inquiry: systematic exploration and reporting, use of models, objectivity, testability and applicability. The authors do so not to privilege the meritorious qualities of science or to legitimise WBL or its example in Professional Studies by conferring on them the status of science, but to highlight their systematised approach to learning and research.

Findings
If the authors define Professional Studies to mean the systematic inquiry of work-based people, processes and phenomena, evidence affirmatively suggests that it is scientific “in nature”.

Originality/value
WBL has been well documented, but its orientation to research, particularly mixed methods (MM) research through Professional Studies, and its adherence to first principles of science have never been explored; this paper begins to uncover the value of work-based pedagogical approaches to learning and research.
Response biases in policy compliance research
Authors: Kurowski Sebastian 
Published: October 2019

Purpose
The purpose of this study is to use a developed and pre-tested scenario-based measurement instrument for policy compliance and determine whether policy compliance measurements in the current policy compliance research are biased as has been postulated during a pre-study. The expected biases are because of social desirability and because of biases based on identity theory.

Design/methodology/approach
A survey was conducted (n = 54) that used policy compliance scales from literature and the developed self-reporting policy compliance (SRPC) scale, along with the Marlow–Crowne social desirability (MC-SDB) scale. Differences between the policy compliance scales were assessed. Moreover, a transformation of the SRPC measurements into the literature-based scales was examined using pair-wise t-testing. Finally, correlations between the MC-SDB and the policy compliance scales were examined.

Findings
There are no significant influences on the desire for social approval of the respondents as was exhibited by the MC-SDB values and policy compliance on either scale. However, the SRPC scale measurements show deviations from the literature-based policy compliance scales. Individuals that exhibit secure behaviour, which is not rooted in a policy but rather in anything but the policy, are also captured as being policy compliant in the current scales. This shows that a response bias exists in current scales. Respondents, who perceive to exhibit secure behaviours, may think that they are in compliance with the policy, even when they are not.

Practical implications
These findings mean that several contributions in the field of policy compliance must be questioned and that a revisit of several factors influencing policy compliance may be required.

Originality/value
To the best of the authors’ knowledge, response biases in policy compliance research have not been considered to date.
An overview of strategic responses of Vietnamese higher education institutions
Authors: Do Ngoc Minh 
Published: October 2019

Purpose
The purpose of this paper is to review the strategic management of Vietnamese higher education institutions.

Design/methodology/approach
The paper examined the external environment of the country’s education system based on the five forces framework by Michael Porter and inspected the strategies of universities and colleges.

Findings
It was concluded that lack of environmental analysis from both the government and higher education institutions themselves diminishes the intended effectiveness of the reforms; problems of skill shortage in the labor market, staff insufficiency and poor quality are prevalent; and that strategies developed by the institutions are purely responsive to the State’s direction without considering sustainability.

Research limitations/implications
Lack of literature on Vietnamese higher education limits timely analysis.

Practical implications
Strategic planning based on a thorough investigation of the environment is imperative to enhance the performance of the education system generally as well as of academic institutions individually. The government plays a key role in developing initiatives to enhance staff capabilities and improve quality of educational outputs.

Originality/value
There has not been any paper that approached Vietnam’s higher education management under such an analytical framework.