bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-Wide Search for Candidate Drivers of Adaptation Reveals Genes Enriched for Shifts in Purifying Selection (SPurS)
Authors: Popejoy AB , Domanska DE , Thomas JH 
Published: January 2020

AbstractAn open question in comparative evolutionary genomics is whether or not certain loci are the primary drivers of divergence between taxonomic lineages or species groups. Alternatively, genetic drivers of species divergence may be evenly distributed across the genome. The increasing availability of genome sequences from diverse taxa has enabled the development of novel methods to address this question. Genomes of many highly diverged species may now be compared in order to tease apart genetic differences that drive adaptive or functional divergence, and genetic differences that are observed by chance and are not causally linked to traits that differ between species or lineages. In order to test the hypothesis that a particular subset of loci or genes is responsible for driving adaptive changes between mammals and non-mammals, we developed a novel comparative approach to identify sites that are highly conserved within lineages or species groups and diverge between them. Loci with a high concentration of these sites may be called Shifts in Purifying Selection (SPurS) because a change has occurred between two groups of species at some point in the past, and the shift is conserved (via purifying selection) over a long period of time. Evaluating 7484 orthologous gene copies from 76 vertebrate species, we developed an empirical distribution of SPurS across the genome between Synapsida (placental and non-placental mammals) and Sauropsida (birds, crocodilians, squamates, and turtles), and compared this distribution to the expected null distribution of SPurS using matched simulated data. We then identified a subset of genes that is enriched for SPurS, relative to the full set of genes and to their matched simulated alignments. These SPurS-enriched genes are thus likely candidate drivers of functional divergence or adaptation between the mammalian and non-mammalian species groups in our analysis. Investigators seeking to identify genetic drivers of inter-species evolution may find this method useful, and we provide a web-based software interface to facilitate its use.
Deep transfer learning for reducing health care disparities arising from biomedical data inequality
Authors: Gao Yan , Cui Yan 
Published: January 2020

AbstractAs artificial intelligence (AI) is increasingly applied to biomedical research and clinical decisions, developing unbiased AI models that work equally well for all racial and ethnic groups is of crucial importance to health disparity prevention and reduction. However, the biomedical data inequality between different racial and ethnic groups is set to generate new health care disparities through data-driven, algorithm-based biomedical research and clinical decisions. Using an extensive set of machine learning experiments on cancer omics data, we found that current prevalent schemes of multiethnic machine learning are prone to generating significant model performance disparities between racial groups. We showed that these performance disparities are caused by data inequality and data distribution discrepancies between racial groups. We also found that transfer learning can improve machine learning model performance for data-disadvantaged racial groups, and thus provides a novel approach to reduce health care disparities arising from data inequality among racial groups.
An Oncometabolite Isomer Rapidly Induces A Pathophysiological Protein Modification
Authors: Bergholtz Sarah E. , Briney Chloe A. , Najera Susana S. , Perez Minervo , Linehan W. Marston , Meier Jordan L. 
Published: January 2020

ABSTRACTMetabolites regulate protein function via covalent and non-covalent interactions. However, manipulating these interactions in living cells remains a major challenge. Here we report a chemical strategy for inducing cysteine S-succination, a non-enzymatic posttranslational modification derived from the oncometabolite fumarate. Using a combination of antibody-based detection and kinetic assays we benchmark the in vitro and cellular reactivity of two novel S-succination “agonists,” maleate and 2-bromosuccinate. Cellular assays reveal maleate to be a more potent and less toxic inducer of S-succination which can activate KEAP1-NRF2 signaling in living cells. By enabling the cellular reconstitution of an oncometabolite-protein interaction with physiochemical accuracy and minimal toxicity, this study provides a methodological basis for better understanding the signaling role of metabolites in disease.
Modeling human age-associated increase in Gadd45γ expression leads to spatial recognition memory impairments in young adult mice
Authors: Brito David V.C. , Karaca Kubra Gulmez , Kupke Janina , Mudlaff Franziska , Zeuch Benjamin , Gomes Rui , Lopes Luísa V. , Oliveira Ana M.M. 
Published: January 2020

AbstractAging is associated with the progressive decay of cognitive function. Hippocampus-dependent processes, such as the formation of spatial memory, are particularly vulnerable to aging. Currently, the molecular mechanisms responsible for age-dependent cognitive decline are largely unknown. Here, we investigated the expression and function of the growth arrest DNA damage gamma (Gadd45γ) during aging and cognition. We report that Gadd45γ expression is increased in the hippocampus of aged humans and that Gadd45γ overexpression in the young adult mouse hippocampus compromises cognition. Moreover, Gadd45γ overexpression in hippocampal neurons disrupted CREB signaling and the expression of well-established activity-regulated genes. This work shows that Gadd45γ expression is tightly controlled in the hippocampus and its disruption may be a mechanism contributing to age-related cognitive impairments observed in humans.
More motivated but equally good: no effect of gamification on visual working memory performance
Authors: Mystakidou Maria , van den Berg Ronald 
Published: January 2020

ABSTRACTGamification refers to the introduction of gaming elements such as scores and leaderboards in non-gaming contexts. While there is growing evidence that gamification has positive effects on intrinsic motivation and engagement, it is largely unknown whether these effects translate to improved cognitive performance. Here, we examine whether gamification affects performance on a visual working memory (VWM) task. In Experiment 1, we gamified a standard delayed-estimation task by introducing scores and a leveling system. On each trial, the subject’s estimation error was mapped to a score between −100 and +100 and added to their total score. Subjects started at a set size of 1 and “leveled up” to the next set size each time they had accumulated 1,500 points. Post-experiment questionnaire data confirmed that subjects who performed the gamified version of the task were more motivated than control subjects. However, we found no difference in VWM performance between these two groups, nor between below-median and above-median motivated subjects. In Experiment 2, we tested for effects of trial-by-trial manipulations of motivation on VWM performance, by varying the scoring function across trials. Three scoring functions were used, with maxima of 7, 21, and 101 points. At the beginning of each trial, the subject was informed whether the potential reward was “low”, “medium”, or “high”. Post-questionnaire data showed that subjects were more motivated on high-reward trials. However, we found no evidence for a difference in performance between the three reward levels. Our results suggest that gamification increases people’s motivation to carry out visual working memory tasks, but it does not necessarily increase their performance.
Small-scale field assessment of efficacy of the autodissemination approach against Aedes sp. in an urban area
Authors: Mohd Ngesom Ahmad Mohiddin , Othman Hidayatulfathi , Bahauddin Rawaida , Ahmad Nazni Wasi , Lim Lee Han , Lasim Asmalia Md , Liang Yanfeng , Greenhalgh David , Min Jasmine Chia Siew , Sahani Mazrura , Hod Rozita , Omar Topek 
Published: January 2020

AbstractThis is the first study to evaluate the efficacy of an autodissemination approach, as suggested by WHO. Therefore, the efficacy of an autodissemination approach in small-scale field trials against wildAedessp. population was evaluated in an urbanized setting, Malaysia. Lethal ovitraps enhanced with pyriproxyfen were used to controlAedessp. populations at treatment sites, with the autodissemination activity was assessed using the WHO larval bioassays. Lethal ovitraps enhanced with pyriproxyfen effectively reduced ofAedessp. population. All autodissemination stations were shown to be visited byAedessp. mosquitoes with 100% complete inhibition against eggs and larvae development. In the larvae bioassay, pupae mortality ranged from 14 to 40%. Statistically, a significant reduction ofAedessp. population in the treatment sites compared to the untreated areas. The study proved for the autodissemination of pyriproxyfen to breeding habitats by wildAedessp. This technique is highly potentially for vector control activities. Future evaluation should focus on large-scale field trials.Author SummarySince 2012, Dataran Automobil, Seksyen 15, Shah Alam, was declared as one of the dengue hotspot areas. Major vector control activities were conducted by government, NGOs, social communities, and local authorities, but the number still rising. We conducted a new invention of autodissemination concepts in this area by an entomological study on mosquito populations reduction and dispersal abilities of the technique. We found that the technique has proven to control mosquito populations, but the other factors such as epidemiology link still unclear and need further clarification. Our finding highlighted the effectiveness of autodissemination strategies that can be considered as one of the alternative tools in vector control programme.
Multiple retrospective analysis of survival and evaluation of cardiac death predictors in a population of dogs affected by degenerative mitral valve disease in ACVIM class C treated with different therapeutic protocols
Authors: Bagardi Mara , Locatelli Chiara , Zanaboni Annamaria , Galizzi Alberto , Malchiodi Dario , Brambilla Paola G. 
Published: January 2020

AbstractClinical records of dogs with spontaneous degenerative mitral valve disease (DMVD) with clinical signs related to congestive heart failure (CHF) that had been recruited during routine clinical practice, between 2001 and 2018 at the Cardiology Unit of the Veterinary Teaching Hospital (University of Milan) were included in this retrospective cohort study. Baseline echocardiographic data were evaluated. Median survival times (MSTs) were calculated. Data on therapeutic treatment, ISACHC or ACVIM classes were reviewed based on the inclusion period and type of endpoint (i.e. cardiac death or death for other causes). The main goal of this data review was to retrospectively evaluate 259 clinical records of subjects belonging to ACVIM C class examined between 2001 to 2018 together with the 202 examined between 2010 to 2018. The MSTs of these subjects was 531 d (2001-2018) and 335.5 d (2010-2018), respectively. Univariate survival regression analysis for subjects included from 2010 to 2018 showed the following variables as being significantly related to cardiac death (CD): LA/Ao ratio (HR 2.754, p=0.000), E wave (HR 2.961, p=0.000), E/A ratio (HR 1.372, p=0.000), EDVI (HR 1.007, p=0.000), ESVI (HR 1.012, p=0.026), Allo(d) (HR 4.018, p=0.000) and Allo(s) (HR 2.674, p=0.049), age (HR 1.006, p=0.009) and PH severity (HR=1.309, p=0.012). Multivariate analysis, adjusted for age, showed that the only variable that determined a statistically significant difference in MST was PH severity (HR 1.334, p=0.033). The type of therapeutic treatment within this class was not significant for the MST of the subjects.
CRISPR-Cas13d induces efficient mRNA knock-down in animal embryos
Authors: Kushawah Gopal , Abugattas-Nuñez del Prado Joaquin , Martinez-Morales Juan R. , DeVore Michelle , Guelfo Javier R. , Brannan Emry O. , Wang Wei , Corbin Timothy J. , Moran Andrea M. , Alvarado Alejandro Sánchez , Málaga-Trillo Edward , Takacs Carter M. , Bazzini Ariel A. , Moreno-Mateos Miguel A. 
Published: January 2020

AbstractEarly embryonic development is driven exclusively by maternal gene products deposited into the oocyte. Although critical in establishing early developmental programs, maternal gene functions have remained elusive due to a paucity of techniques for their systematic disruption and assessment. CRISPR-Cas13 systems have recently been employed to induce RNA degradation in yeast, plants and mammalian cell lines. However, no systematic study of the potential of Cas13 has been carried out in an animal system. Here, we show that CRISPR-Cas13d is an effective and precise system to deplete specific mRNA transcripts in zebrafish embryos. We demonstrate that both zygotically-expressed and maternally-provided transcripts are efficiently targeted, resulting in an 80% average decrease in transcript level and the recapitulation of well-known embryonic phenotypes. Moreover, we show that this system can be used in medaka, killifish and mouse embryos. Altogether our results demonstrate that CRISPR-Cas13d is an efficient knock-down platform to interrogate gene function in animal embryos.
A phylogenetic analysis of MCTP proteins: from amino acid sequence to function
Authors: Téllez Arreola José Luis , Estrada-Mondragón Argel , Martínez Torres Ataúlfo 
Published: January 2020

AbstractMCTPs (Multiple C2 domain proteins with two transmembrane regions) are evolutionarily and structurally related to other C2 proteins which play fundamental roles in exocytosis and membrane trafficking, however their specific role has been little studied. This work points out possible functional implications of MCTPs by comparing their primary amino acid sequence and functional domains. MCTP amino acid sequences were identified in non-chordates and chordates. The primary sequences grouped in three classes: MCTP, MCTP-1 and MCTP-2. MCTP is present only in non-chordates, while MCTP-1 and MCTP-2 are present in chordates. MCTP genes emerged early in metazoan evolution and are well conserved across species including humans. Genomic analysis of diverse species of representative phyla showed that the three C2 domains (C2A-C2C) and transmembrane regions (TMR) are well conserved. The C2 domains have eight β strands as well as aspartate residues known to bind calcium. Interestingly, we identified a lysine-rich cluster, also known as polybasic cluster in C2A and C2B, which is known to bind lipids in other proteins. We also describe the phylogenetic distribution of MCTPs and analyze conserved domains and their predicted secondary structure in metazoans. We highlight important motifs that have not been previously described in MCTPs C2A and C2B domains that suggest MCTPs potentially bind phospholipids. Our observations show MCTPs are proteins widely distributed in eukaryotic organisms and may play an important role in membrane fusion or exocytosis.
Benchmarking joint multi-omics dimensionality reduction approaches for cancer study
Authors: Cantini Laura , Zakeri Pooya , Hernandez Celine , Naldi Aurelien , Thieffry Denis , Remy Elisabeth , Baudot Anaïs 
Published: January 2020

AbstractHigh-dimensional multi-omics data are now standard in biology. They can greatly enhance our understanding of biological systems when effectively integrated. To achieve this multi-omics data integration, Joint Dimensionality Reduction (jDR) methods are among the most efficient approaches. However, several jDR methods are available, urging the need for a comprehensive benchmark with practical guidelines.We performed a systematic evaluation of nine representative jDR methods using three complementary benchmarks. First, we evaluated their performances in retrieving ground-truth sample clustering from simulated multi-omics datasets. Second, we used TCGA cancer data to assess their strengths in predicting survival, clinical annotations and known pathways/biological processes. Finally, we assessed their classification of multi-omics single-cell data.From these in-depth comparisons, we observed that intNMF performs best in clustering, while MCIA offers a consistent and effective behavior across many contexts. The full code of this benchmark is implemented in a Jupyter notebook - multi-omics mix (momix) - to foster reproducibility, and support data producers, users and future developers.
The more you value, the less you practice: a study on culture and managerial discretion
Authors: Haj Youssef Moustafa Salman , Hussein Hiba Maher , Awada Hoda 
Published: January 2020

PurposeThe purpose of this paper is to examine cross-cultural differences in managerial discretion and the extent to which variations and interaction of cultural practices and values affect the degree of freedom in decision making that is accorded to executives. This paper offers a holistic approach to investigating culture in addition to acknowledging its paradoxical nature.Design/methodology/approachUsing a panel of prominent management consultants to rate discretion across 18 countries, the authors further develop the national-level construct of managerial discretion by empirically investigating the influence of cultural practices and values on CEOs’ discretion.FindingsThe study reveals that cultural values moderate the relationship between cultural practices and managerial discretion for three cultural dimensions: individualism, uncertainty tolerance and power distance (PD). By adopting the logic of marginal utility, the authors also show that the more a society values individualism, uncertainty tolerance and PD, the weaker the effect of their practices on managerial discretion.Originality/valueFew research has attempted to assess both cultural values and practices in relation to managerial discretion. By showing the mechanism in which culture affects the level of managerial discretion, the authors offer new theoretical insights and practical implications, overall contributing to the field of cross-cultural and strategic management. Finally, this will offer CEO’s a new perspective of leveraging culture as a tool, enhancing their decision-making capabilities in the aim of improving organizational performance.
SME network relationships and competitive strategies in the agri-food sector
Authors: Camanzi Luca , Giua Carlo 
Published: January 2020

Purpose
The purpose of this paper is to identify the main factors influencing agri-food small and medium enterprises (SMEs) participation in business networks and to evaluate the impacts of these factors on network structure and the ensuing competitive strategy.

Design/methodology/approach
The study is articulated in four main steps. First, a critical literature review is conducted concerning the main approaches to firm competitive advantage and the role of stakeholder relationships. Then, three research questions are formulated and discussed in the light of two case studies describing the implementation of an innovative contractual solution in Italy (i.e. business network contracts). Finally, based on these findings, a set of more general “propositions” are stated and included in a provisional conceptual model that schematically depicts an integrated vision of the antecedents and mechanisms influencing SMEs business network structure and competitive strategy.

Findings
The study results pointed out the opportunity to adopt an integrated approach, combining resource-based view and stakeholder causal scope approaches. The provisional conceptual model proposed illustrates the role of both external and internal resources and relational constructs to shaping network structure and competitive strategy.

Originality/value
The study’s contribution is twofold. First, the empirical study shed light on opportunities and limits of two business networks with different backgrounds, approaches and outcomes towards value creation. Second, the conceptual framework proposed advances our understanding and knowledge of the factors and mechanisms influencing SMEs business network structure and competitive strategy.
Value of supply chain resilience: roles of culture, flexibility, and integration
Authors: Chunsheng Li , Wong Christina W.Y. , Yang Ching-Chiao , Shang Kuo-Chung , Lirn Taih-cherng 
Published: January 2020

PurposeBuilding supply chain (SC) resilience is crucial for business continuity given the ever-changing environmental conditions. Based on the resource orchestration and organizational culture theories, the purpose of this paper is to investigate the business value of SC resilience with the consideration of the roles of internal integration (II) and external integration (EI), risk management culture (RMC) and SC flexibility (SCF).Design/methodology/approachThis study investigates how RMC, SCF and intra and interorganizational integration affect the performance of SC resilience. It collects primary and secondary data from 194 manufacturing firms listed in the Taiwan Stock Exchange and Taipei Exchange.FindingsResults validate the authors’ hypothesis that RMC, SCF and II improve the financial performance of firms through SC resilience efforts.Research limitations/implicationsThis study uses firms from Taiwan manufacturing industry, which might introduce country and industry bias.Practical implicationsThis study helps managers improve the financial performance of their SC resilience efforts by developing RMC, SCF, II and IE across functions and partner firms.Originality/valueThis study contributes to the literature by empirically testing the relationship between SC resilience and financial performance, and how the relationship is moderated by RMC, SCF, II and EI based on the theories of organizational culture and resource orchestration.
Study on friction behavior of SiC-B4C composite ceramics after annealing
Authors: Zhang Wei , Yamashita Seiji , Kumazawa Takeshi , Ozeki Fumihito , Hyuga Hideki , Kita Hideki 
Published: January 2020

Purpose
This study aims to investigate the friction behavior of SiC-B4C composite ceramics treated by annealing in air sliding against SiC balls.

Design/methodology/approach
The dry sliding tests were performed with a ball-on-disk tribometer in ambient air condition. Analysis of friction coefficient, phase compositions of the surfaces, morphologies of worn surfaces of disks and wear scars of balls and surface profiles of wear tracks for disks were carried out using Raman spectroscope, microscope and surface profilometer.

Findings
The results show that a self-lubricating layer with the main composition of H3BO3 was successfully fabricated on the surface of SiC-B4C composite ceramics by the annealing treatment in air. When the mass fraction of SiC is more than that of B4C, SiC-B4C composite ceramics show higher friction coefficients, the values of which are 0.38 for 80 Wt.%SiC-20 Wt.%B4C and 0.72 for 60 Wt.%SiC-40 Wt.%B4C, respectively. SiC-B4C composite ceramics show lower friction coefficients when the mass fraction of B4C is more than that of SiC. The low friction coefficients of 40 Wt.%SiC-60 Wt.% B4C composite ceramics (0.16) and 20 Wt.%SiC-80 Wt.% B4C composite ceramics (0.20) are attributed to the formation of a sufficient amount of H3BO3 layer, rather than the layer of silicon oxides.

Originality/value
This study will help to understand the friction behavior of SiC-B4C composite ceramics with different ratios of SiC to B4C treated by annealing in air.