bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural genomics and interactomics of 2019 Wuhan novel coronavirus, 2019-nCoV, indicate evolutionary conserved functional regions of viral proteins
Authors: Cui Hongzhu , Gao Ziyang , Liu Ming , Lu Senbao , Mo Sun , Mkandawire Winnie , Narykov Oleksandr , Srinivasan Suhas , Korkin Dmitry 
Published: February 2020

AbstractDuring its first month, the recently emerged 2019 Wuhan novel coronavirus (2019-nCoV) has already infected many thousands of people in mainland China and worldwide and took hundreds of lives. However, the swiftly spreading virus also caused an unprecedentedly rapid response from the research community facing the unknown health challenge of potentially enormous proportions. Unfortunately, the experimental research to understand the molecular mechanisms behind the viral infection and to design a vaccine or antivirals is costly and takes months to develop. To expedite the advancement of our knowledge we leverage the data about the related coronaviruses that is readily available in public databases, and integrate these data into a single computational pipeline. As a result, we provide a comprehensive structural genomics and interactomics road-maps of 2019-nCoV and use these information to infer the possible functional differences and similarities with the related SARS coronavirus. All data are made publicly available to the research community athttp://korkinlab.org/wuhan
Abstract neural representations of category membership beyond information coding stimulus or response
Authors: Mok Robert M. , Love Bradley C. 
Published: February 2020

AbstractFor decades, researchers have debated whether mental representations are symbolic or grounded in sensory inputs and motor programs. Certainly, aspects of mental representations are grounded. However, does the brain also contain abstract concept representations that mediate between perception and action in a flexible manner not tied to the details of sensory inputs and motor programs? Such conceptual pointers would be useful when concept remain constant despite changes in appearance and associated actions. We evaluated whether human participants acquire such representations using functional magnetic resonance imaging (fMRI). Participants completed a probabilistic concept learning task in which sensory, motor, and category variables were not perfectly coupled nor entirely independent, making it possible to observe evidence for abstract representations or purely grounded representations. To assess how the learned concept structure is represented in the brain, we examined brain regions implicated in flexible cognition (e.g., prefrontal and parietal cortex) that are most likely to encode an abstract representation removed from sensory-motor details. We also examined sensory-motor regions that might encode grounded sensory-motor based representations tuned for categorization. Using a cognitive model to estimate participants’ category rule and multivariate pattern analysis of fMRI data, we found left prefrontal cortex and MT coded for category in absence of information coding for stimulus or response. Because category was based on the stimulus, finding an abstract representation of category was not inevitable. Our results suggest that certain brain areas support categorization behaviour by constructing concept representations in a format akin to a symbol that differs from stimulus-motor codes.
Exposure to Mites Sensitizes Intestinal Stem Cell Maintenance, Splenic Marginal Zone B Cell Homeostasis, And Heart Development to Notch Dosage and Cooperativity
Authors: Kobia Francis M. , Preusse Kristina , Dai Quanhui , Weaver Nicholas , Chaturvedi Praneet , Stein Sarah J. , Pear Warren S. , Yuan Zhenyu , Kovall Rhett A. , Kuang Yi , Eafergen Natanel , Sprinzak David , Gebelein Brian , Brunskill Eric , Kopan Raphael 
Published: February 2020

AbstractCooperative DNA binding is a key feature of transcriptional regulation. Here we examined the role of cooperativity in Notch signaling by CRISPR-mediated engineering of mice in which neither Notch1 nor Notch2 can homo- or heterodimerize, essential for cooperative binding to sequence paired sites (SPS) located near many Notch-regulated genes. While most known Notch-dependent phenotypes were unaffected in Notch1/2 dimer-deficient mice, a subset of tissues proved highly sensitive to loss of cooperativity. These phenotypes include heart development, compromising viability in combination with low gene dose, and the gut, developing ulcerative colitis in response to 1% DSS. The most striking phenotypes – gender imbalance and splenic marginal zone B cell lymphoma – emerged in combination with dose reduction or when challenged by chronic fur mite infestation. This study highlights the role of the environment in malignancy and colitis, and is consistent with Notch-dependent anti-parasite immune responses being compromised in the dimer deficient animals.HighlightsNotch dimerization has anin vivorole in contributing to intestinal homeostasisLoss of cooperativity can manifest as Notch gain or loss of function phenotypesMite infestation exacerbates all phenotypes, triggers MZB hyperproliferation in mutant animalsMite-infested mutant mice develop SMZL with age
CCR5 deficiency impairs CD4+T cell memory responses and antigenic sensitivity through increased ceramide synthesis
Authors: Martín-Leal Ana , Blanco Raquel , Casas Josefina , Sáez María E. , Rodríguez-Bovolenta Elena , de Rojas Itziar , Drechsler Carina , Real Luis Miguel , Fabrias Gemma , Ruíz Agustín , Castro Mario , Schamel Wolfgang W.A. , Alarcón Balbino , van Santen Hisse M. , Mañes Santos 
Published: February 2020

ABSTRACTIn CD4+T cells, CCR5 is not only a coreceptor for HIV-1 infection, but also contributes to their functional fitness. Here we show that by limiting GATA-1-induced transcription of specific ceramide synthases, CCR5 signaling reduces ceramide levels and thereby increases T cell antigen receptor (TCR) nanoclustering in antigen-experienced mouse and human CD4+T cells. This activity is CCR5-specific and independent of CCR5 costimulatory activity. CCR5-deficient mice showed reduced production of high affinity class-switched antibodies, but only after antigen rechallenge, which implies an impaired memory CD4+T cell response. This study identifies a CCR5 function in the generation of CD4+T cell memory responses, and establishes an antigen-independent mechanism that regulates TCR nanoclustering by altering specific lipid species.
Inferring directional relationships in microbial communities using signed Bayesian networks
Authors: Sazal Musfiqur , Mathee Kalai , Ruiz-Perez Daniel , Cickovski Trevor , Narasimhan Giri 
Published: February 2020

AbstractBackgroundMicrobe-microbe and host-microbe interactions in a microbiome play a vital role in both health and disease. However, the structure of the microbial community and the colonization patterns are highly complex to infer even under controlled wet laboratory conditions. In this study, we investigate what information, if any, can be provided by aBayesian Network(BN) about a microbial community. Unlike the previously proposedCo-occurrence Networks(CoNs), BNs are based on conditional dependencies and can help in revealing complex associations.ResultsIn this paper, we propose a way of combining a BN and a CoN to construct asigned Bayesian Network(sBN). We report a surprising association between directed edges in signed BNs and knowncolonization orders.ConclusionsBNs are powerful tools for community analysis and extracting influences and colonization patterns, even though the analysis only uses an abundance matrix with no temporal information. We conclude that directed edges in sBNs when combined with negative correlations are consistent with and strongly suggestive of colonization order.
Mutation bias interacts with composition bias to influence adaptive evolution
Authors: Cano Alejandro V. , Payne Joshua L. 
Published: February 2020

ABSTRACTMutation is a biased stochastic process, with some types of mutations occurring more frequently than others. Previous work has used synthetic genotype-phenotype landscapes to study how such mutation bias affects adaptive evolution. Here, we consider 746 empirical genotype-phenotype landscapes, each of which describes the binding affinity of target DNA sequences to a transcription factor, to study the influence of mutation bias on adaptive evolution of increased binding affinity. By using empirical genotype-phenotype landscapes, we need to make only few assumptions about landscape topography and about the DNA sequences that each landscape contains. The latter is particularly important because the set of sequences that a landscape contains determines the types of mutations that can occur along a mutational path to an adaptive peak. That is, landscapes can exhibit a composition bias — a statistical enrichment of a particular type of mutation relative to a null expectation, throughout an entire landscape or along particular mutational paths — that is independent of any bias in the mutation process. Our results reveal the way in which composition bias interacts with biases in the mutation process under different population genetic conditions, and how such interaction impacts fundamental properties of adaptive evolution, such as its predictability, as well as the evolution of genetic diversity and mutational robustness.AUTHOR SUMMARYMutation is often depicted as a random process due its unpredictable nature. However, such randomness does not imply uniformly distributed outcomes, because some DNA sequence changes happen more frequently than others. Such mutation bias can be an orienting factor in adaptive evolution, influencing the mutational trajectories populations follow toward higher-fitness genotypes. Because these trajectories are typically just a small subset of all possible mutational trajectories, they can exhibit composition bias – an enrichment of a particular kind of DNA sequence change, such as transition or transversion mutations. Here, we use empirical data from eukaryotic transcriptional regulation to study how mutation bias and composition bias interact to influence adaptive evolution.
Deconvolving nuclesome binding energy from experimental errors
Authors: Heron Mark , Soeding Johannes 
Published: February 2020

1AbstractEukaryotic genomes are compacted into nucleosomes, 147-bp of DNA wrapped around histone proteins. Nucleosomes can hinder transcription factors and other DNA-binding proteins from accessing the genome. This competition at promoters and enhancers regulates gene expression. Therefore, a quantitative understanding of gene regulation requires the quantitative prediction of nucleosome binding affinities. However, little is known for certain about the sequence preference of nucleosomes.Here we develop an integrated model of nucleosome binding and genome-wide measurements thereof. Our model learns similar nucleosome sequence preferences from MNase-Seq and CC-Seq datasets.We find that modelling the positional uncertainty of MNase-Seq deconvolves the commonly described smooth 10-bp-periodic sequence preference into a position-specific pattern more closely resembling the pattern obtained from high-resolution CC-Seq data. By analysing the CC-Seq data we reveal the strong preference of A/T at +/− 3 bp from the dyad as an experimental bias. Our integrated model can separate this bias of CC-Seq from the true nucleosome binding preference.Our results show that nucleosomes have position-specific sequence preferences, which probably play an important role in their competition with transcription factors. Furthermore, our comparison of diverse datasets shows that the experimental biases have a similar strength as the signal of nucleosome-positioning measurements. Validating nucleosome models on experiments with similar biases overestimates their prediction quality of the true nucleosome binding.There are still many open questions about the sequence preference of nucleosomes and our approach will need to be extended to answer them. Only integrated models that combine the thermodynamics of nucleosome binding with experimental errors can deconvolve the two and learn the true preferences of nucleosomes.
Does training adequately equip psychiatrists for intellectual disability?
Authors: Lines Geraldine , Allen Jodie , Marshall Caryl Jane 
Published: February 2020

Purpose
People with intellectual disability (ID) experience significant health and social inequality compared to their non-disabled peers. Individuals with ID who access mental health services can have complex comorbidities and presentations. In the UK, a significant proportion of individuals with ID are supported within general adult mental health services not by specialist ID teams. The purpose of this study is to explore whether psychiatry trainees in the Maudsley Training Programme (MTP) feel adequately skilled to support individuals with ID.

Design/methodology/approach
An online survey of trainee psychiatrists in the MTP was completed to evaluate self-perceived skills and knowledge in the care of individuals with ID in mental health services. Statistical analysis of the results was completed.

Findings
Experience of working in specialist ID teams is positively associated with greater confidence and skills among trainees in the care of people with ID; this is beyond what would be expected based on seniority alone.

Research limitations/implications
The response rate was 16.7 per cent; a larger sample size would add strength to the study. Like all online surveys, there exists the risk of selection bias.

Practical implications
UK Policy states that people with ID should be supported to access mainstream services where possible, including psychiatric care. Practical experience for all psychiatry trainees involving specialist ID services and people with ID could improve the care given to that particularly disadvantaged group.

Originality/value
This is the only paper known to the authors that has focused specifically on the skills and knowledge of psychiatry trainees in the UK with regards to ID.
Advancing organizational corporate social responsibility (CSR) agenda
Authors: Miller Katharine E. , Akdere Mesut 
Published: February 2020

Purpose
Given the growth of demand for companies’ engagement in socially responsible and ethical practices through corporate social responsibility (CSR), this paper aims to expand the literature on such efforts as currently presented in organizational communication, management, Human Resource Development (HRD) literature.

Design/methodology/approach
The authors synthesize the topic of CSR across these various disciplines with a focus on identifying gaps in the literature related to the training and development (T&D) based CSR-related activities. Thus, the authors provide implications for the training of CSR as called for by current literature because today’ corporations appear to lack the proper strategies in the understanding and implementation of such efforts.

Findings
The authors conclude by discussing the pragmatic considerations for this type of T&D and call for further discussion among scholars and professionals in facilitating future work on CSR in a training context.

Originality/value
Exploring CSR within the context of T&D presents critical capacities in enabling organizational CSR agenda across all units.
Twenty years of accreditation in Russian higher education: lessons learnt
Authors: Motova Galina , Navodnov Vladimir 
Published: February 2020

PurposeThe purpose of this article is to analyze main principles, forms and approaches to education quality evaluation in the process of establishment, development and crucial changes in the state accreditation of educational institutions and study programmes in Russian higher education in the last 20 years.Design/methodology/approachThe major research method used in the paper is the qualitative analysis of legal and statistical documents, research papers and accreditation practices, which impacted the development and transformation of accreditation forms in Russia.FindingsThe transformation process of state accreditation during the last 20 years was conditioned by the changes in the state education policy and socio-economic situation. In a short period, under the influence of internal and external factors, Russian higher education has experienced significant changes in the structure of higher education and quality assurance. This resulted in different approaches to accreditation: state and independent, mandatory and voluntary, national and international.Practical implicationsThe research outcomes may be applicable in the countries with developing accreditation systems and comparable scope of education.Social implicationsThe study identifies the tendencies in the development of higher education and quality evaluation.Originality/valueThe paper systematizes the tendencies of development in quality assurance and distinguishes specific features and diversity of forms of the quality assurance in one of the largest systems of higher education.
Teams in new ventures: gender, human capital and motivation
Authors: Cerqueti Roy , Lucarelli Caterina , Marinelli Nicoletta , Micozzi Alessandra 
Published: February 2020

PurposeThis paper aims to dismantle the idea that sexper seexplains entrepreneurial outcomes and demonstrates the influence of a gendered motivation on forging and shaping new venture teams, which is a disruptive choice affecting the future of start-ups.Design/methodology/approachA two-level research model is validated on data from the Panel Study of Entrepreneurial Dynamics II (PSED II), with a system of simultaneous equations. First, if team features affect the performance of new ventures is tested; then, the study investigates determinants of team features with a focus on sex and motivation of nascent entrepreneurs.FindingsHuman capital (HC) in terms of education and experience of team members consistently explains venture evolution only when considering the larger team of affiliates. The HC gathered by nascent entrepreneurs is not because of the simplistic sex condition, but rather to a gendered motivation related to the inferior need of achievement of women.Research limitations/implicationsLimitations of discretionary scoring assigned to items of the PSED II survey are present, but unavoidable when processing qualitative data.Practical implicationsWomen need to be (culturally) educated on how to re-balance their personal motivation towards entrepreneurship by fostering their incentives for achievement. Political and educational programmes could trigger success in the creation of new businesses led by women.Originality/valueThis paper contributes to the literature on nascent entrepreneurship, focusing on the entrepreneurial teams in the initial phase of business creation, and provides the basis for further studies aimed at eradicating the stereotypes of gender roles that lead women to self-exclusion and organizational errors.
Conceptualizing the influence of personality and cognitive traits on project managers’ risk-taking behaviour
Authors: Rashid Ahmad , Boussabiane Halim 
Published: February 2020

PurposeThe purpose of this paper is to analyze the existing project management literature by conceptualizing the influence of personality and cognitive traits on project managers’ risk-taking behaviour.Design/methodology/approachThe paper is based on an in-depth analysis of the existing literature to develop framework for conceptualizing risk propensity in project management.FindingsThe results indicate that the Big Five personality traits cannot capture risk propensity in risk-taking behaviour on their own. Cognitive traits are indispensable components in risk propensity.Research limitations/implicationsThe paper examines the association between risk propensity theories and personality traits. The paper framed project managers’ personality traits that can impact their tendency to take risky decisions, that is risk propensity.Originality/valueThis paper expands literature by increasing our understanding of personality and cognitive traits in risk propensity.
How psychological factors boost compulsive buying behavior in digital era
Authors: Mulyono Kemal Budi , Rusdarti Rusdarti 
Published: February 2020

PurposeTo find the root of the problem for compulsive buying behavior of students in the digital era by exploring psychological factors such as materialism, self-esteem, self-control, narcissism, money attitude and mood as boosters of the effect of income on compulsive buying behavior.Design/methodology/approachThe unit of analysis in this research was a group of students having experience using e-commerce. The data collection method in this study was a closed questionnaire with a scale of 1–5 agree–disagree intervals distributed to 250 students who have shopping experience through e-commerce. WARP-PLS statistics was used.FindingsThe study shows that self-esteem and mood do not moderate the effect of income on compulsive buying behavior. Meanwhile, materialism, narcissism, self-control and money attitude can significantly moderate the effect of income on compulsive buying behavior.Research limitations/implicationsThat the data used is only limited to students in Central Java Province; so for future research, it is necessary to expand data to different provinces or different countries. This research has implications that the synthesis between mainstream conventional economic thought and behavioral economics can be tested well in this model.Originality/valueThis study is proof of the synthesis between conventional and behavioral economic thought, which is a solution to the contradiction of the neoclassical paradigm of thought and behavioral economic thought in understanding consumer behavior, especially in compulsive buying behavior.Peer reviewThe peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-10-2019-0652
Constitutive relation and mechanical mechanism analysis in granular lubrication
Authors: Meng Fanjing , Pang Minghua , Liu Kun 
Published: February 2020

Purpose
Granular lubrication can solve some lubrication problems under many extreme operating conditions. Meanwhile, the flow constitutive relation is one of its unsolved problems in fully understanding its rheological mechanism.

Design/methodology/approach
In this paper, a plane shear cell under granular lubrication is established by the discrete element method to study the flow constitutive relation and its mechanical mechanism of the hard granular lubricants.

Findings
Research results show that the flow regimes in granular flow lubrication strongly rely on the dimensionless parameter I, in which it is called the inertial coefficient. When the inertial coefficient I increase, the flow regimes of the granular lubricants also evolve from a quasi-static state to a collisional state accordingly. Comparing to the influence of the restitution coefficient, the friction coefficient of the hard granular lubricants has a strong influence on its constitutive relation of the granular flow lubrication. Finally, it is shows that the dimensionless parameter I has strong influence on the contacts and flow states of this granular lubrication system than the influence of the dimensionless parameter R.

Originality/value
These findings reveal the constitutive relation and mechanical mechanism of granular lubrication and can also offer the helpful reference for the design of the new granular lubrication bearing.