bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional classes of SNPs related to psychiatric disorders and behavioral traits contrast with those related to neurological disorders
Authors: Reimers Mark A. , Kendler Kenneth S. 
Published: February 2021

AbstractWe investigated the functional classes of genomic regions containing SNPS contributing most to the SNP-heritability of important psychiatric and neurological disorders and behavioral traits, as determined from recent genome-wide association studies. We employed linkage-disequilibrium score regression with several brain-specific genomic annotations not previously used. The classes of genomic annotations conferring substantial SNP-heritability for the psychiatric disorders and behavioral traits differed systematically from the classes associated with neurological disorders, and both differed from the classes enriched for height, a biometric trait used here as a control outgroup. The SNPs implicated in these psychiatric disorders and behavioral traits were highly enriched in CTCF binding sites, in conserved regions likely to be enhancers, and in brain-specific promoters, regulatory sites likely to affect dynamic responses. The SNPs relevant for neurological disorders were highly enriched in constitutive coding regions and splice regulatory sites. We suggest that our results provide a bridge between genetics and the well-known effects of life history and recent stressful experiences on risk of psychiatric illness.
CVTree: A Parallel Alignment-free Phylogeny and Taxonomy Tool based on Composition Vectors of Genomes
Authors: Zuo Guanghong 
Published: February 2021

ABSTRACTCVTree is an alignment-free algorithm to infer phylogenetic relationships from genome sequences. It had been successfully applied to study phylogeny and taxonomy of viruses, prokaryotes, and fungi based on the whole genomes, as well as chloroplasts, mitochondria, and metagenomes. Here we presented the standalone software for the CVTree algorithm. In the software, a parallel workflow for the CVTree algorithm was designed. Based on the workflow, new alignment-free methods were also implemented. And by examining the phylogeny and taxonomy of 13903 prokaryotes based on 16S rRNA sequences, we showed that CVTree software is an efficient and effective tool for the studying of phylogeny and taxonomy based on genome sequences.Availabilityhttps://github.com/ghzuo/cvtree
An extracellular redox signal triggers calcium release and impacts the asexual development ofToxoplasma gondii
Authors: Alves Eduardo , Benns Henry J. , Magnus Lilian , Dominicus Caia , Dobai Tamás , Blight Joshua , Wincott Ceire J. , Child Matthew A. 
Published: February 2021

AbstractThe ability of an organism to sense and respond to environmental redox fluctuations relies on a signaling network that is incompletely understood in apicomplexan parasites such asToxoplasma gondii. The impact of changes in redox upon the development of this intracellular parasite is not known. Here, we provide a revised collection of 58 genes containing domains related to canonical antioxidant function, with their encoded proteins widely dispersed throughout different cellular compartments. We demonstrate that addition of exogenous H2O2to human fibroblasts infected withT. gondiitriggers a Ca2+flux in the cytosol of intracellular parasites that can induce egress. In line with existing models, egress triggered by exogenous H2O2is reliant upon both Calcium-Dependent Protein Kinase 3 and diacylglycerol kinases. Finally, we show that the overexpression a glutaredoxin-roGFP2 redox sensor fusion protein in the parasitophorous vacuole severely impacts parasite replication. These data highlight the rich redox network that exists inT. gondii, evidencing a link between extracellular redox and intracellular Ca2+signaling that can culminate in parasite egress. Our findings also indicate that the redox potential of the intracellular environment contributes to normal parasite growth. Combined, our findings highlight the important role of redox as an unexplored regulator of parasite biology.
Substantial somatic genomic variation and selection for BCOR mutations in human induced pluripotent stem cells
Authors: Rouhani Foad J , Zou Xueqing , Danecek Petr , Dias Amarante Tauanne , Koh Gene , Wu Qianxin , Memari Yasin , Durbin Richard , Martincorena Inigo , Bassett Andrew R , Gaffney Daniel , Nik-Zainal Serena 
Published: February 2021

SummaryHuman Induced Pluripotent Stem Cells (hiPSC) are an established patient-specific model system where opportunities are emerging for cell-based therapies. We contrast hiPSCs derived from different tissues, skin and blood, in the same individual. We show extensive single-nucleotide mutagenesis in all hiPSC lines, although fibroblast-derived hiPSCs (F-hiPSCs) are particularly heavily mutagenized by ultraviolet(UV)-related damage. We utilize genome sequencing data on 454 F-hiPSCs and 44 blood-derived hiPSCs (B-hiPSCs) to gain further insights. Across 324 whole genome sequenced(WGS) F-hiPSCs derived by the Human Induced Pluripotent Stem Cell Initiative (HipSci), UV-related damage is present in ~72% of cell lines, sometimes causing substantial mutagenesis (range 0.25-15 per Mb). Furthermore, we find remarkable genomic heterogeneity between independent F-hiPSC clones derived from the same reprogramming process in the same donor, due to oligoclonal populations within fibroblasts. Combining WGS and exome-sequencing data of 452 HipSci F-hiPSCs, we identify 272 predicted pathogenic mutations in cancer-related genes, of which 21 genes were hit recurrently three or more times, involving 77 (17%) lines. Notably, 151 of 272 mutations were present in starting fibroblast populations suggesting that more than half of putative driver events in F-hiPSCs were acquired in vivo. In contrast, B-hiPSCs reprogrammed from erythroblasts show lower levels of genome-wide mutations (range 0.28-1.4 per Mb), no UV damage, but a strikingly high prevalence of acquired BCOR mutations of ~57%, indicative of strong selection pressure. All hiPSCs had otherwise stable, diploid genomes on karyotypic pre-screening, highlighting how copy-number-based approaches do not have the required resolution to detect widespread nucleotide mutagenesis. This work strongly suggests that models for cell-based therapies require detailed nucleotide-resolution characterization prior to clinical application.
Large-scale analysis of SARS-CoV-2 spike-glycoprotein mutants demonstrates the need for continuous screening of virus isolates
Authors: Schrörs Barbara , Gudimella Ranganath , Bukur Thomas , Rösler Thomas , Löwer Martin , Sahin Ugur 
Published: February 2021

AbstractDue to the widespread of the COVID-19 pandemic, the SARS-CoV-2 genome is evolving in diverse human populations. Several studies already reported different strains and an increase in the mutation rate. Particularly, mutations in SARS-CoV-2 spike-glycoprotein are of great interest as it mediates infection in human and recently approved mRNA vaccines are designed to induce immune responses against it.We analyzed 146,917 SARS-CoV-2 genome assemblies and 2,393 NGS datasets from GISAID, NCBI Virus and NCBI SRA archives focusing on non-synonymous mutations in the spike protein.Only around 13.8% of the samples contained the wild-type spike protein with no variation from the reference. Among the spike protein mutants, we confirmed a low mutation rate exhibiting less than 10 non-synonymous mutations in 99.98% of the analyzed sequences, but the mean and median number of spike protein mutations per sample increased over time. 2,592 distinct variants were found in total. The majority of the observed variants were recurrent, but only nine and 23 recurrent variants were found in at least 0.5% of the mutant genome assemblies and NGS samples, respectively. Further, we found high-confidence subclonal variants in about 15.1% of the NGS data sets with mutant spike protein, which might indicate co-infection with various SARS-CoV-2 strains and/or intra-host evolution. Lastly, some variants might have an effect on antibody binding or T-cell recognition.These findings demonstrate the increasing importance of monitoring SARS-CoV-2 sequences for an early detection of variants that require adaptations in preventive and therapeutic strategies.
Sensory cilia act as a specialized venue for regulated EV biogenesis and signaling
Authors: Wang Juan , Nikonorova Inna A. , Silva Malan , Walsh Jonathon D. , Tilton Peter , Gu Amanda , Barr Maureen M. 
Published: February 2021

AbstractExtracellular vesicles play major roles in intercellular signaling, yet fundamental aspects of their biology remain poorly understood. Ciliary EV shedding is evolutionary conserved. Here we use super resolution, real time imaging of fluorescent-protein tagged EV cargo combined within vivobioassays to study signaling EVs inC. elegans. We find that neuronal sensory cilia shed the TRP polycystin-2 channel PKD-2::GFP-carrying EVs from two distinct sites - the ciliary tip and the ciliary base. Ciliary tip shedding requires distal ciliary enrichment of PKD-2 by the myristoylated coiled-coil protein CIL-7. Kinesin-3 KLP-6 and intraflagellar transport (IFT) kinesin-2 motors are also required for ciliary tip EV shedding. Blocking ciliary tip shedding results in excessive EV shedding from the base. Finally, we demonstrate thatC. elegansmale ciliated neurons modulate EV cargo composition in response to sensory stimulation by hermaphrodite mating partners. Overall, our study indicates that the cilium and its trafficking machinery act as a specialized venue for regulated EV biogenesis and signaling.
Convalescent Plasma and Improved Survival in Patients with Hematologic Malignancies and COVID-19
Authors: Thompson Michael A. , Henderson Jeffrey P. , Shah Pankil K. , Rubinstein Samuel M. , Joyner Michael J. , Choueiri Toni K. , Flora Daniel B. , Griffiths Elizabeth A. , Gulati Anthony P. , Hwang Clara , Koshkin Vadim S. , Papadopoulos Esperanza B. , Robilotti Elizabeth V. , Su Christopher T. , Wulff-Burchfield Elizabeth M. , Xie Zhuoer , Yu Peter Paul , Mishra Sanjay , Senefeld Jonathon W. , Shah Dimpy P. , Warner Jeremy L. 
Published: February 2021

SummaryConvalescent plasma may benefit immunocompromised individuals with COVID-19, including those with hematologic malignancy. We evaluated the association of convalescent plasma treatment with 30-day mortality in hospitalized adults with hematologic malignancy and COVID-19 from a multi-institutional cohort. 143 treated patients were compared to 823 untreated controls. After adjustment for potential confounding factors, convalescent plasma treatment was associated with improved 30-day mortality (hazard ratio, 0.60; 95% CI, 0.37-0.97). This association remained significant after propensity-score matching (hazard ratio, 0.52; 95% CI, 0.29-0.92). These findings suggest a potential survival benefit in the administration of convalescent plasma to patients with hematologic malignancy and COVID-19.
The chameleonic garment integrated POF fabric with a tricolour LED and wearable device technology
Authors: Lin Miao-Tzu 
Published: February 2021

PurposeThe purpose of this article is to develop a smart illuminated polymeric optical fibre (POF) chameleonic garment, using a wearable device technology for camouflage or safety warnings based on user needs.Design/methodology/approachThis study integrates the theory of the optical foundation, control system, wireless communication, program development and apparel design into a chameleonic garment, displaying some vests, bags and shoes.FindingsAfter selecting a pixel in the photo taken by the smart phone, the four modes of the application developed in this study are used to change the POF colour of the garment.Originality/valueThis study develops four modes of smart phone application; picked mode: picks a pixel colour on a smart phone canvas, contrastive mode: transfers to contrastive colour of the picked pixel, customized mode – gives input colour number manual and random mode – it based on a system random number. When users have different functional requirements, the four modes provide various choices.
Structural design of high-speed rolling bearing test rig spindle with cantilever
Authors: Li Hui , Li Hao , Zhang Rongfeng , Liu Yi , Qi Shemiao , Liu Heng 
Published: February 2021

Purpose
The purpose of this paper is to introduce the structure design process of the cantilever spindle with limited installation space and wishing to increase its critical speed.

Design/methodology/approach
In this paper, the finite element method was used to analyze the influence of the supporting stiffness and the structure of the spindle on the critical speed, and then the structure of the spindle was designed; moreover, the experiment was accomplished and the experiment results show that the spindle can work stably.

Findings
Through analyzing the influence of the supporting stiffness and the structure of the spindle on the critical speed, the following conclusions could be obtained: the shape of the first-mode is the bend vibration of the cantilever of the spindle; the first-order critical speed of the spindle gradually decreases with the diameter and length of the cantilever increasing; the first-order critical speed of the spindle increases with the depth and diameter of the blind hole increasing; and the experiment was accomplished and the experiment results show that the spindle can work stably.

Originality/value
In this paper, the finite element method was used to design the spindle of the testing machine, and satisfactory results were obtained. It can provide a theoretical reference for the design of a similar spindle.
Effect of supplier supply network resources on buyer–supplier collaborative product innovation: a contingency perspective
Authors: Li Yuzhong , Li Suicheng , Cui Hecheng 
Published: February 2021

Purpose
This study aims to examine the effect of supplier supply network (SSN) resources on buyer–supplier collaborative product innovation. The existing relevant studies from the network perspective are focused more horizontally on the mobilization of the firm’s entire supplier network resources and less vertically on the utilization of the individual supplier's supply network resources. Therefore, this paper takes a contingency perspective, regards the buyer as the receiver of a supplier’s supply network resources and, based on the theoretical motivation–opportunity–ability framework, explores the important motivation and ability factors that may weaken or enhance the product innovation value of the network resources.

Design/methodology/approach
This paper develops a new research model that assesses how the innovation utilization effectiveness of SSN resources is contingent on a buyer’s perception of the SSN effects and relative absorptive capacity on the SSN. A large sample questionnaire is designed and collected from 300 Chinese high-tech manufacturing firms and their suppliers. An empirical test is carried out in which multiple regression analysis is applied to 246 valid sample data.

Findings
The results show that SSN resources can significantly enhance buyer–supplier collaborative product innovation; however, the innovation utilization effectiveness is limited by the buyer’s relative absorptive capacity for the SSN and perception of the SSN effects. Specifically, if a buyer perceives that a greater innovation effect of a supplier’s supply network is correlated with an improved relative position in the SSN or with higher network structural equivalence and network cognitive congruence between the buyer and the supplier on the SSN, then the buyer will be more motivated and capable of transforming the SSN resources into actual product innovation value.

Practical implications
The research results provide useful guidance for firms to effectively mobilize their SSN resources to tap into the supplier innovation value for a sustainable competitive advantage.

Originality/value
This paper extends the research on supplier innovation value to the SSN field. Through linking dyadic and network levels of analysis, this paper reveals the value and uniqueness of product innovation utilization of a specific supplier’s supply network resources in the buyer–supplier relationship and provides a new research perspective for future studies on related issues.
Predicting the effect of decompression sickness on survival following submarine tower escape
Authors: Loveman Geoff A.M. , Edney Joel J.E. 
Published: February 2021

Purpose
The purpose of the present study was the development of a methodology for translating predicted rates of decompression sickness (DCS), following tower escape from a sunken submarine, into predicted probability of survival, a more useful statistic for making operational decisions.

Design/methodology/approach
Predictions were made, using existing models, for the probabilities of a range of DCS symptoms following submarine tower escape. Subject matter expert estimates of the effect of these symptoms on a submariner’s ability to survive in benign weather conditions on the sea surface until rescued were combined with the likelihoods of the different symptoms occurring using standard probability theory. Plots were generated showing the dependence of predicted probability of survival following escape on the escape depth and the pressure within the stricken submarine.

Findings
Current advice on whether to attempt tower escape is based on avoiding rates of DCS above approximately 5%–10%. Consideration of predicted survival rates, based on subject matter expert opinion, suggests that the current advice might be considered as conservative in the distressed submarine scenario, as DCS rates of 10% are not anticipated to markedly affect survival rates.

Originality/value
According to the authors’ knowledge, this study represents the first attempt to quantify the effect of different DCS symptoms on the probability of survival in submarine tower escape.
Perpetrators of corporate crimes in commercial organizations in Italy and Russia
Authors: Rusanov Georgy 
Published: February 2021

Purpose
The purpose of this paper is dedicated to the features of subjects of official crimes in commercial organizations in accordance with the laws of Italy and Russia.

Design/methodology/approach
Based on the study of Russian and Italian legislation, it was revealed that the Italian criminal law provides for a more extensive system of the criminal law provisions on liability for corporate economic crimes.

Findings
These norms are in various normative legal acts (civil legislation, separate legislative acts). In the Russian criminal legislation, the norms in the sphere of corporate crimes in the sphere of economy are systematized and are located in a separate chapter of the Criminal Code of the Russian Federation. At the same time, the list of acts for which liability is provided is significantly narrower than in the Italian criminal law.

Originality/value
In general, the institute of criminal liability for subjects of economic crimes with special features is adopted and developed as in the Russian criminal law as in the Italian criminal law. The existence of this institution shows the awareness by legislators of the increased danger to the society of such persons’ actions owing to the fact that the existence of the official status, special powers of certain duties or the lack of an appropriate indication on the contrary allows such a person to commit an act that is not available to other persons.
The Gender Dynamics of Dress Gifts from Elizabethan Men at the Court of Elizabeth I
Authors: Gomulkiewicz Abigail 
Published: February 2021

AbstractThis article explores the gender dynamics of giving dress gifts at the Elizabethan court (1558–1603). Current scholarship considers the role of elite women and the ‘favourite’ in giving dress gifts. In contrast, this article seeks to understand the significant but largely overlooked role of merchant and courtier men as both givers of dress to Elizabeth I and holders of vital information that others relied upon in giving dress gifts to her. Drawing on New Year's gift lists, correspondence and records of progresses this article shows how an approach informed by material culture and situated in a gendered framework actually complicates our understanding of the Elizabethan court's culture of dress gifts. A gendered analysis highlights that merchant and courtier male subjects, sometimes in tandem with their wives, played a vital role in shaping the fashion and economy of early modern England by providing innovative and tasteful offerings to their queen. Dress gifts from male subjects strongly influenced Elizabeth's image of magnificence and made the English court one of the most fashionable in Europe.
Including intraspecific trait variability to avoid distortion of functional diversity and ecological inference: Lessons from natural assemblages
Authors: Wong Mark K. L. , Carmona Carlos P. 
Published: February 2021

Abstract

Functional diversity assessments are crucial and increasingly used for understanding ecological processes and managing ecosystems. The functional diversity of a community is assessed by sampling traits at one or more scales (individuals, populations and species) and calculating a summary index of the variation in trait values. However, it remains unclear how the scales at which traits are sampled and the indices used to estimate functional diversity may alter the patterns observed and inferences about ecological processes.

For 40 plant and 61 ant communities, we assess functional diversity using six methods—spanning various mean‐based and probabilistic methods—that reflect common scenarios where different levels of detail are available in trait data. We test whether including trait variability at different scales (from individuals to species) alters functional diversity values calculated using the volume‐based and dissimilarity‐based indices, Functional Richness (FRic) and Rao, respectively. We further test whether such effects alter functional diversity patterns observed across communities and their relationships with environmental drivers such as abiotic gradients and occurrences of invasive species.

Intraspecific trait variability strongly determined FRic and Rao. Methods using only species' mean trait values to calculate FRic (convex hulls) and Rao (Gower‐based dissimilarity) distorted the patterns observed when intraspecific trait variability was considered. These distortions generated Type I and Type II errors for the effects of environmental factors structuring the plant and ant communities. A high sensitivity of FRic to individuals with extreme trait values was revealed in comparisons of different probabilistic methods including among‐individual and among‐population trait variability in functional diversity. In contrast, values of and ecological patterns in Rao were consistent among methods including different scales of intraspecific trait variability.

Our results show empirically that decisions about where traits are sampled and how trait variability is included in functional diversity can drastically change the patterns observed and conclusions about ecological processes. We recommend sampling the traits of multiple individuals per species and capturing their intraspecific trait variability using probabilistic methods. We discuss how intraspecific trait variability can be reasonably estimated and included in functional diversity in the common circumstance where only limited trait data are available.