bluuebunny/crossref_metadata_2025_split huggingface dataset:
Episignatures stratifying ADNP syndrome show modest correlation with phenotype
Authors: Breen Michael S. , Garg Paras , Tang Lara , Mendonca Danielle , Levy Tess , Barbosa Mafalda , Arnett Anne B , Kurtz-Nelson Evangeline , Agolini Emanuele , Battaglia Agatino , Chiocchetti Andreas G , Freitag Christine M , Garcia-Alcon Alicia , Grammatico Paola , Hertz-Picciotto Irva , Ludena-Rodriguez Yunin , Moreno Carmen , Novelli Antonio , Parellada Mara , Pascolini Giulia , Tassone Flora , Grice Dorothy E , Bernier Raphael A , Kolevzon Alexander , Sharp Andrew , Buxbaum Joseph D , Siper Paige M , De Rubeis Silvia 
Published: April 2020

AbstractADNP syndrome, also known as Helsmoortel-van Der Aa syndrome, is a neurodevelopmental condition associated with intellectual disability/developmental delay, autism spectrum disorder, and multiple medical comorbidities. ADNP syndrome is caused by mutations in the activity-dependent neuroprotective protein (ADNP). A recent study identified genome-wide DNA methylation changes in 22 individuals with ADNP syndrome, adding to the group of neurodevelopmental disorders with an epigenetic signature. This methylation signature segregated those with ADNP syndrome into two groups, based on the location of the mutations. Here, we conducted an independent study on 24 individuals with ADNP syndrome and replicated the existence of the two, mutation-dependent ADNP episignatures. To probe whether the two distinct episignatures correlate with clinical outcomes, we used deep behavioral and neurobiological data from two prospective cohorts of individuals with a genetic diagnosis of ADNP syndrome. We found limited phenotypic differences between the two ADNP groups, and no evidence that individuals with more widespread methylation changes are more severely affected. Also, in spite of the methylation changes, we observed no profound alterations in the blood transcriptome of individuals with ADNP syndrome. Our data warrant caution in harnessing methylation signatures in ADNP syndrome as a tool for clinical stratification, at least with regards to behavioral phenotypes.
Constructing and Optimizing 3D Atlases From 2D Data With Application to the Developing Mouse Brain
Authors: Young David M , Darbandi Siavash Fazel , Schwartz Grace , Bonzell Zachary , Yuruk Deniz , Nojima Mai , Gole Laurent , Rubenstein John , Yu Weimiao , Sanders Stephan J 
Published: April 2020

Abstract3D imaging data necessitate 3D reference atlases for accurate quantitative interpretation. Existing computational methods to generate 3D atlases from 2D-derived atlases result in extensive artifacts, while manual curation approaches are labor-intensive. We present a computational approach for 3D atlas construction that substantially reduces artifacts by identifying anatomical boundaries in the underlying imaging data and using these to guide 3D transformation. Anatomical boundaries also allow extension of atlases to complete edge regions. Applying these methods to the eight developmental stages in the Allen Developing Mouse Brain Atlas (ADMBA) led to more comprehensive and accurate atlases. We generated imaging data from fifteen whole mouse brains to validate atlas performance and observed qualitative and quantitative improvement (37% greater alignment between atlas and anatomical boundaries). We provide the methods as the MagellanMapper software and the eight 3D reconstructed ADMBA atlases. These resources facilitate whole-organ quantitative analysis between samples and across development.
Distinct Vegfa isoforms control endothelial cell proliferation through PI3 kinase signalling mediated regulation of cdkn1a/p21
Authors: Lange Martin , Leonard Elvin , Ohnesorge Nils , Hoffmann Dennis , Rocha Susana F. , Benedito Rui , Siekmann Arndt F. 
Published: April 2020

SUMMARYThe formation of appropriately patterned blood vessel networks requires endothelial cell migration and proliferation. Signaling through the Vascular Endothelial Growth Factor A (VEGFA) pathway is instrumental in coordinating these processes. mRNA splicing generates short (diffusible) and long (extracellular matrix bound) Vegfa isoforms. The differences between these isoforms in controlling cellular functions are not understood. In zebrafish,vegfaagenerates short and long isoforms, whilevegfabonly generates long isoforms. We found that mutations invegfaaaffected endothelial cell migration and proliferation. Surprisingly, mutations invegfabspecifically reduced endothelial cell proliferation. Analysis of downstream signaling revealed no change in MAPK (ERK) activation, while inhibiting PI3 kinase signaling phenocopiedvegfabmutants. The cell cycle inhibitorcdkn1a/p21was upregulated invegfabdeficient embryos. Accordingly, reducingcdkn1a/p21restored endothelial cell proliferation. Together, these results suggest that extracellular matrix bound Vegfa acts through PI3K signaling to specifically control endothelial cell proliferation during angiogenesis independently of MAPK (ERK) regulation.
Bayesian genome scale modelling identifies thermal determinants of yeast metabolism
Authors: Li Gang , Hu Yating , Wang Hao , Zelezniak Aleksej , Ji Boyang , Zrimec Jan , Nielsen Jens 
Published: April 2020

AbstractThe molecular basis of how temperature affects cell metabolism has been a long-standing question in biology, where the main obstacles are the lack of high-quality data and methods to associate temperature effects on the function of individual proteins as well as to combine them at a systems level. Here we develop and apply a Bayesian modeling approach to resolve the temperature effects in genome scale metabolic models (GEM). The approach minimizes uncertainties in enzymatic thermal parameters and greatly improves the predictive strength of the GEMs. The resulting temperature constrained yeast GEM uncovered enzymes that limit growth at superoptimal temperatures, and squalene epoxidase (ERG1) was predicted to be the most rate limiting. By replacing this single key enzyme with an ortholog from a thermotolerant yeast strain, we obtained a thermotolerant strain that outgrew the wild type, demonstrating the critical role of sterol metabolism in yeast thermosensitivity. Therefore, apart from identifying thermal determinants of cell metabolism and enabling the design of thermotolerant strains, our Bayesian GEM approach facilitates modelling of complex biological systems in the absence of high-quality data and therefore shows promise for becoming a standard tool for genome scale modeling.
Genome-wide bisulfite sequencing data of normal andAscosphaera apis-infected larval guts of eastern honeybee
Authors: Du Yu , Zhu Zhiwei , Chen Huazhi , Fan Yuanchan , Wang Jie , Fan Xiaoxue , Jiang Haibin , Xiong Cuiling , Zheng Yanzhen , Chen Dafu , Guo Rui 
Published: April 2020

ABSTRACTApis cerana cerana, a subspecies of eastern honey,Apis cerana, plays a specific role in beekeeping industry and ecosystem in China and other Asian countries. Larvae ofA. c. ceranacan be infected byAscosphaera apis, the fungal pathogen of chalkbrood. In this article, normal 4-, 5-, and 6-day-old larval guts (AcCK1, AcCK2, AcCK3) andA. apis-infected 4-, 5- and 6-day-old larval guts (AcT1, AcT2, AcT3) ofA. c. ceranaworkers were respectively harvested followed by DNA isolation, bisulfite conversion, cDNA library construction and Illumina sequencing. Based on genome-wide bisulfite sequencing, 79167210, 82175052, 79331489, 81051009, 74742842 and 74849091 raw reads were generated from AcCK1, AcCK2, AcCK3, AcT1, AcT2 and AcT3, and after quality control, 73417030 (92.73%), 76660370 (93.27%), 71804727 (90.44%), 75046507 (92.82%), 67487782 (90.30%) and 67367023 (90.04%) clean reads were obtained, respectively. Additionally, 73333333, 76533333, 71466667, 75066667, 67590965 and 67200000 clean reads were mapped to the reference genome ofA. cerana, including 54656767, 58583415, 54127407, 57943220, 52547867 and 51295824 unique mapped clean reads, and 8624392, 8789458, 7531333, 7747337, 6249679 and 5394174 multiple mapped clean reads. The genome-wide bisulfite sequencing data reported here can be used for genome-wide identification of 5mC methylation sites in eastern honeybee larval guts and systematic investigation of DNA methylation-mediated host response toA. apisinfection.Value of the dataThe current dataset contributes to genome-wide identification of 5mC methylation sites in normal andA. apis-infected larval guts of eastern honeybee.The reported data could be used for systematic investigation of DNA methylation-mediated response of eastern honeybee larvae toA. apisinfection.Our data offers a valuable genetic resource for better understanding epigenetic regulation mechanism involved in eastern honeybee larvae-A. apisinteraction.
A rapid, super-selective method for detection of single nucleotide variants inC. elegans
Authors: Touroutine Denis , Tanis Jessica E. 
Published: April 2020

ABSTRACTWith the widespread use of single nucleotide variants generated through mutagenesis screens, the million mutation project, and genome editing technologies, there is pressing need for an efficient and low-cost strategy to genotype single nucleotide substitutions. We have developed a rapid and inexpensive method for detection of point mutants through optimization of SuperSelective (SS) primers for end point PCR inCaenorhabditis elegans. Each SS primer consists of a 5’ “anchor” that hybridizes to the template, followed by a non-complementary “bridge,” and a “foot” corresponding to the target allele. The foot sequence is short, such that a single mismatch at the terminal 3’ nucleotide destabilizes primer binding and prevents extension, enabling discrimination of different alleles. We explored how length, stability, and sequence composition of each SS primer segment affected selectivity and efficiency in order to develop simple rules for primer design that allow for distinction between any mismatches in various genetic contexts over a broad range of annealing temperatures. Manipulating bridge length affects amplification efficiency, while modifying the foot sequence can increase discriminatory power. Flexibility in the positioning of the anchor enables SS primers to be used for genotyping in regions with sequences that are challenging for standard primer design. In summary, we have demonstrated flexibility in design of SS primers and their utility for genotyping inC. elegans. Since SS primers reliably detect single nucleotide variants, we propose that this method could have broad application for SNP mapping, screening of CRISPR mutants, and colony PCR to identify successful site-directed mutagenesis constructs.
Functional diversification of Ser-Arg rich protein kinases to control ubiquitin-dependent neurodevelopmental signalling
Authors: Bustos Francisco , Segarra-Fas Anna , Nardocci Gino , Cassidy Andrew , Antico Odetta , Brandenburg Lennart , Macartney Thomas , Toth Rachel , Hastie C. James , Gourlay Robert , Vargese Joby , Soares Renata , Montecino Martin , Findlay Greg M. 
Published: April 2020

SUMMARYConserved protein kinases with core cellular functions have been frequently redeployed during metazoan evolution to regulate specialized developmental processes. Ser-Arg Repeat Protein Kinase (SRPK) is one such conserved eukaryotic kinase, which controls mRNA splicing. Surprisingly, we show that SRPK has acquired a novel function in regulating a neurodevelopmental ubiquitin signalling pathway. In mammalian embryonic stem cells, SRPK phosphorylates Ser-Arg motifs in RNF12/RLIM, a key developmental E3 ubiquitin ligase that is mutated in an intellectual disability syndrome. Processive phosphorylation by SRPK stimulates RNF12-dependent ubiquitylation of transcription factor substrates, thereby acting to restrain a neural gene expression programme that is aberrantly expressed in intellectual disability. SRPK family genes are also mutated in intellectual disability disorders, and patient-derived SRPK point mutations impair RNF12 phosphorylation. Our data reveal unappreciated functional diversification of SRPK to regulate ubiquitin signalling that ensures correct regulation of neurodevelopmental gene expression.
Psychodynamic psychotherapy in severe and profound intellectual disability
Authors: Himmerich Julian 
Published: April 2020

PurposePsychodynamic psychotherapy is increasingly adapted and used with individuals with intellectual disability (ID) and mental health difficulties. However, the evidence base is still small and largely based on case studies and small trials whose participants mainly have mild to moderate ID. This paper aims to review and critique the literature in regards to the adaptations; and the effectiveness of psychodynamic psychotherapy for those with severe and profound ID.Design/methodology/approachA systematic literature search of PsycINFO, Social Policy and Practice, Medline, Cumulative Index to nursing and allied health literature and applied social sciences index and abstracts was conducted. Six studies met inclusion criteria and underwent a quality evaluation and critical review.FindingsSix papers (all case studies) met inclusion criteria and underwent a quality evaluation and critical review. Some adaptations to therapy were reported, such as a more flexible therapeutic frame and increased use of the physical environment as a therapeutic tool. Due to significant methodological weaknesses of the included studies, it is yet unclear whether psychodynamic psychotherapy is an effective intervention for individuals with severe and profound ID.Research limitations/implicationsOnly a small number of case studies met the inclusion criteria. Further research should use more robust outcome measures, larger samples and compare psychodynamic psychotherapy to alternative interventions.Originality/valueThis paper is the first to review the psychodynamic psychotherapy literature with regard to its effectiveness as a treatment specifically for individuals with severe and profound ID and mental health difficulties.
Motives to engage with sports brands on Facebook and Instagram–The case of a Portuguese football club
Authors: Machado Joana César , Martins Carla Carvalho , Ferreira Frederico Correia , Silva Susana C. , Duarte Paulo Alexandre 
Published: April 2020

PurposeSocial network sites are key marketing tools that allow brands to connect and engage with consumers. However, there is still a lack of evidence of their value for football brands. This research aims to understand the motivations for fans to engage with their favourite football brands on Facebook and Instagram.Design/methodology/approachAn online survey was performed, resulting in 214 valid responses. As the social media strategy followed by the football brand analysed was built around games, the authors divided fans into two groups based on the main method in which the club's games are watched: in stadium versus mediated. Multiple linear regression analysis was used to explore the relationship between motivations and fans' engagement, through content consumption and contribution, on Facebook and Instagram. Analysis was performed first with the whole sample and then by group (stadium attendance vs mediated attendance fans).FindingsThe findings show that social influence, entertainment, searching for information and rewards are the most relevant motivations for consumers to engage with brand-related content on Facebook. Entertainment, rewards and social influence are the main motivations influencing consumer interactions on Instagram. Group moderation was only confirmed in the impact of social influence on Facebook page content consumption.Originality/valueThe results provide valuable insights into the social media marketing activities of sports brands, which will assist brand managers to develop strategies for effectively stimulating engagement with the different groups of fans.
Social inequality and access to social capital in microfinance interventions
Authors: Singh Mudit Kumar , Lee Jaemin 
Published: April 2020

PurposeThe purpose of this paper is to empirically examine the inequality perpetuated through social categories in accessing the social capital generated through the microfinance interventions in India as the country has pronounced economic inequality by social categories like many developing stratified societies.Design/methodology/approachThe study uses survey data collected from 75 villages in rural India and tests whether the formation and maximization of social capital through self-help groups (SHGs) is dominated by social categories, e.g. high-caste groups, males and superior occupation classes. Using logistic regression framework, the study assesses the formation and maximization of social capital through multiple SHG membership.FindingsThe paper finds that the microfinance approach of empowering weaker sections is considerably limited in its success, in the sense that it provides them with the opportunity to the credit access and support through SHGs. But, the empirical model further indicates that social capital in form of these SHGs may fall prey to the dominant social categories, and thus, these institutions may potentially enhance inequality.Research limitations/implicationsThe paper is derived from the secondary data set, so it is unable to comment field reality qualitatively.Practical implicationsMicrofinance policy makers will have an improved understanding of inherent social inequalities while implementing group-based programs in socially stratified societies.Originality/valueSocial capital, if treated as an outcome accumulated in form of groups, provides with an important framework to assess the unequal access through the microfinance interventions. Overlooking the inherent unequal access will deceive the purpose of social justice in the group-based interventions. The microfinance and other welfare policies engaged in group formation and generating the social capital need to be more sensitive to the disadvantageous sections while focusing on multiple group access by disadvantaged social groups.
Let's ask our students what really matters to them
Authors: Cladera Magdalena 
Published: April 2020

PurposeStudents' feedback is of great importance to the development of knowledge about teaching in higher education. One of the main purposes for which this feedback is collected is teaching quality assessment, usually conducted through course and teacher evaluations completed at the end of the course. However, for improving students' perceptions of teaching quality, their prior expectations should be identified first and the aspects that they consider relevant for a “good teaching” should be found out. Moreover, obtaining feedback at the end of a course could not benefit the respondents themselves. This work analyses students' opinions about the importance of several aspects related to the quality of teaching in an undergraduate course.Design/methodology/approachA questionnaire was administered to gather students' opinions about the importance of several aspects related to the quality of teaching in an undergraduate course. Differences in the mean score of each aspect depending on students' characteristics were also analyzed.FindingsThe teaching characteristics that students considered more important were lecturer enthusiasm, the organization of the lectures and materials, the examination methods and feedbacks, the interest and intellectual challenge of the course and the friendliness, interest and accessibility of the lecturer. Differences in the importance of the different aspects exist depending on gender, expected grade and prior interest in the subject.Originality/valueResults could help lecturers to do a better programming of the different features of the course and prepare the subject more effectively, which is likely to positively impact student satisfaction; student satisfaction, in turn, has been related to an improvement in students' performance.
A review of inter-firm relationship quality in supply chains
Authors: Qian Chen , Seuring Stefan , Wagner Ralf 
Published: April 2020

Purpose
This paper aims to conduct a review of the recent literature on inter-firm relationship quality (RQ) in the supply chain (SC) settings.

Design/methodology/approach
100 English-language scientific publications on inter-firm RQ, published from 2006 to 2015 were selected and analyzed by using a content analysis approach.

Findings
The results of the frequency analysis map the antecedents, dimensions and consequences – particularly the performance and behavioral intentions of collaborating partners – of buyer–seller RQ presented in the current literature. The contingency analysis offers insights into the use of relevant constructs of inter-firm RQ in SCs in the individual papers. A range of research gaps is uncovered.

Research limitations/implications
The category building for the content analysis was based on an RQ framework that focuses on the mediator structure and neglects the effects of moderators.

Practical implications
The developed framework of inter-firm RQ in SCs provides managers with a guide to the relevant influencing factors, evaluation indicators and consequences of the quality of their relationships with SC partners.

Originality/value
This paper provides the first literature review at the intersection of RQ and SC. The research framework developed specifies the use of the previous RQ framework in the business-to-business and SC context. A critique of the existing studies is discussed and the agenda for future research are suggested.
Leadership style effect on virtual team efficiency: trust, operational cohesion and media richness roles
Authors: Ben Sedrine Sinda , Bouderbala Amel , Nasraoui Hamza 
Published: April 2020

PurposeThe purpose of this article is to explain the effect of leadership styles on a virtual team efficiency, assuming the existence of mediating variables (media richness) influencing this relationship.Design/methodology/approachThe data were collected within the framework of an online survey based on a sample of 300 observations (MENA region) with respondents from the IT sector. These results were generated by SPSS and AMOS 23 software and treated using an exploratory factor analysis and modeling by structural equation.FindingsThe results of the research attest that trust and operational cohesion play a mediating role between leadership styles and team performance. They also confirm that leadership styles impact operational cohesion and group trust according to different levels of media richness, thus creating different situations fluctuating according to its level.Research limitations/implicationsFrom a methodological point of view, the sample choice was not diversified. Only the IT companies are concerned with this study. Therefore, the generalization of obtained results can be questioned. The research results could be refined by trying to highlight trust mediating variable through antecedents evoked by Mayer et al. (1995) or Williams (2001), namely, competence, benevolence or even integrity. Competence and benevolence deserve, on the conceptual plan, to be fully integrated to the definition itself of trust under penalty of see the concept itself of trust impoverish considerably (Mayeret al., 1995).Practical implicationsOn a practical level, the optimal efficiency of a virtual team depends on a high level of media richness with a transformational leadership mobilized by the managers that would favor a good operational cohesion of the group. Various techniques could be employed to improve a social dynamic of the group (periodic conference calls, face to face meetings, team building).Originality/valueThis research clarifies how leadership styles influence virtual team efficiency through operational cohesion and trust. Furthermore, this research reaffirms, in addition from previous works, that the communication means to which virtual teams recur influence the degree of operating cohesion and increase that of performance.