bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coupled Co-clustering-based Unsupervised Transfer Learning for the Integrative Analysis of Single-Cell Genomic Data
Authors: Zeng Pengcheng , WangWu Jiaxuan , Lin Zhixiang 
Published: March 2020

AbstractUnsupervised methods, such as clustering methods, are essential to the analysis of single-cell genomic data. Most current clustering methods are designed for one data type only, such as scRNA-seq, scATAC-seq or sc-methylation data alone, and a few are developed for the integrative analysis of multiple data types. Integrative analysis of multimodal single-cell genomic data sets leverages the power in multiple data sets and can deepen the biological insight. We propose a coupled co-clustering-based unsupervised transfer learning algorithm (coupleCoC) for the integrative analysis of multimodal single-cell data. Our proposedcoupleCoC builds upon the information theoretic co-clustering framework. We appliedcoupleCoC for the integrative analysis of scATAC-seq and scRNA-seq data, sc-methylation and scRNA-seq data, and scRNA-seq data from mouse and human. We demonstrate thatcoupleCoC improves the overall clustering performance and matches the cell subpopulations across multimodal single-cell genomic data sets. The software and data sets are available athttps://github.com/cuhklinlab/coupleCoC.
TDP-43 and HSP70 phase separate into anisotropic, intranuclear liquid spherical annuli
Authors: Yu Haiyang , Lu Shan , Gasior Kelsey , Singh Digvijay , Tapia Olga , Vazquez-Sanchez Sonia , Toprani Divek , Beccari Melinda S. , Yates John R. , Da Cruz Sandrine , Newby Jay M. , Larfaga Miguel , Gladfelter Amy S. , Villa Elizabeth , Cleveland Don W. 
Published: March 2020

AbstractThe RNA binding protein TDP-43 naturally phase separates within cell nuclei and forms cytoplasmic aggregates in age-related neurodegenerative diseases. Here we show that acetylation-mediated inhibition of TDP-43 binding to RNA produces co-de-mixing of acetylated and unmodified TDP-43 into symmetrical, intranuclear spherical annuli whose shells and cores have liquid properties. Shells are anisotropic, like liquid crystals. Consistent with our modelling predictions that annulus formation is driven by components with strong self-interactions but weak interaction with TDP-43, the major components of annuli cores are identified to be HSP70 family proteins, whose chaperone activity is required to maintain liquidity of the core. Proteasome inhibition, mimicking reduction in proteasome activity during aging, induces TDP-43-containing annuli in neurons in rodents. Thus, we identify that TDP-43 phase separation is regulated by acetylation, proteolysis, and ATPase-dependent chaperone activity of HSP70.One Sentence SummaryAcetylation of TDP-43 drives its phase separation into spherical annuli that form a liquid-inside-a-liquid-inside-a-liquid.
Factors influencing swift and effective resolution of supplier problems
Authors: Clemons Rebecca , Baddam Swathi Reddy , Henry Raymond M. 
Published: March 2020

PurposeHow might an organization swiftly resolve supplier problems such that the issue does not reoccur? The purpose of this study seeks to understand the impact of different knowledge-sharing routines on measures of effective problem resolution.Design/methodology/approachData are collected from an automotive manufacturer's (buyer) database. A hierarchical linear model analyzes dyadic data collected from 155 problems across 24 suppliers.FindingsThis study reveals that different ways of communicating have differing impact on measures of effective problem-solving. Communication involving face-to-face interaction slows the process, whereas frequent communication can lead to swift resolution. Furthermore, management teams are more likely to lead to a “better” fix in that these teams are more likely to implement changes in the process or product.Research limitations/implicationsThe data are for a tier-one automotive supplier. Hence, the findings are limited by the extent to which other organizations may differ.Practical implicationsThe results provide insights for managers experiencing supply issues. Some forms of communication should be encouraged as they enhance the process. Moreover, the findings suggest there are consequences to pressuring a supplier to resolve a complaint quickly.Originality/valueVery few researchers can claim to have investigated observed collaborative mechanisms that occur between a buyer and its suppliers when resolving a problem. This research adds to the literature on the relational view theory as it applies to supply chain management and problem resolution.
Transforming growth factor‐β promotes the function of HIV‐specific CXCR5+CD8 T cells
Authors: Yang Hong‐Ge , Jiao Yan‐Mei , Huang Hui‐Huang , Zhang Chao , Zhang Ji‐Yuan , Xu Ruo‐Nan , Song Jin‐Wen , Fan Xing , Jin Lei , Shi Ming , Wang Fu‐Sheng 
Published: March 2020

AbstractHIV replication can be inhibited by CXCR5+CD8 T cells (follicular cytotoxic T cell [TFC]) which transfer into B‐cell follicles where latent HIV infection persists. However, how cytokines affect TFC remain unclear. Understanding which cytokines show the ability to affect TFC could be a key strategy toward curing HIV. Similar mechanisms could be used for the growth and transfer of TFCs and follicular helper T (TFH) cells; as a result, we hypothesized that cytokines IL‐6, IL‐21, and transforming growth factor‐β (TGF‐β), which are necessary for the differentiation of TFH cells, could also dictate the development of TFCs. In this work, lymph node mononuclear cells and peripheral blood mononuclear cells from HIV‐infected individuals were cocultured with IL‐6, IL‐21, and TGF‐β. We then carried out T‐cell receptor (TCR) repertoire analysis to compare the differences between CXCR5– and CXCR5+CD8 T cells. Our results showed that the percentage and function of TFC can be enhanced by stimulation with TGF‐β. Besides, TGF‐β stimulation enhanced the diversity of TCR and complementarity‐determining region 3 sequences. HIV DNA showed a negative correlation with TFC. The use of TGF‐β to promote the expression of CXCR5+CD8 T cells could become a new treatment approach for curing HIV.
Genomic characterization of antibiotic resistance‐encoding genes in clinical isolates of Vibrio cholerae non‐O1/non‐O139 strains from Kolkata, India: generation of novel types of genomic islands containing plural antibiotic resistance genes
Authors: Morita Daichi , Takahashi Eizo , Morita Masatomo , Ohnishi Makoto , Mizuno Tamaki , Miyoshi Shin‐ichi , Dutta Devarati , Ramamurthy Thandavarayan , Chowdhury Goutam , Mukhopadhyay Asish K. , Okamoto Keinosuke 
Published: March 2020

AbstractNon‐O1/non‐O139 nontoxigenic Vibrio cholerae associated with cholera‐like diarrhea has been reported in Kolkata, India. However, the property involved in the pathogenicity of these strains has remained unclear. The character of 25 non‐O1/non‐O139 nontoxigenic V. cholerae isolated during 8 years from 2007 to 2014 in Kolkata was examined. Determination of the serogroup showed that the serogroups O6, O10, O35, O36, O39, and O70 were represented by two strains in each serogroup, and the remaining isolates belonged to different serogroups. To clarify the character of antibiotic resistance of these isolates, an antibiotic resistance test and the gene analysis were performed. According to antimicrobial drug susceptibility testing, 13 strains were classified as drug resistant. Among them, 10 strains were quinolone resistant and 6 of the 13 strains were resistant to more than three antibiotics. To define the genetic background of the antibiotic character of these strains, whole‐genome sequences of these strains were determined. From the analysis of these sequences, it becomes clear that all quinolone resistance isolates have mutations in quinolone resistance‐determining regions. Further research on the genome sequence showed that four strains possess Class 1 integrons in their genomes, and that three of the four integrons are found to be located in their genomic islands. These genomic islands are novel types. This indicates that various integrons containing drug resistance genes are spreading among V. cholerae non‐O1/non‐O139 strains through the action of newly generated genomic islands.
Consistent metacommunity structure despite inconsistent drivers of assembly at the continental scale
Authors: Murray‐Stoker David , Murray‐Stoker Kelly M. 
Published: March 2020

Abstract

A fundamental goal of community ecology is to understand the drivers of community assembly and diversity. Local factors acting on community assembly are typically related to environmental conditions while regional factors are typically related to dispersal. Previous research has not consistently demonstrated the importance of local or regional factors, but this is likely because these factors act in concert and not in isolation. Studies that simultaneously integrate local and regional factors into analyses of community assembly can be a useful avenue to further our understanding of this core concept in community ecology.

Here, we aimed to identify metacommunity structure and diversity and the local and regional drivers of community assembly at the continental scale.

We evaluated metacommunity structure and drivers of assembly of macroinvertebrate communities in 941 rivers and streams nested within nine ecoregions distributed across the conterminous United States. Pattern‐based metacommunity analyses and boosted regression tree techniques were used to (a) assign metacommunity structures and (b) identify the environmental, landscape and network drivers of assembly. We also evaluated how biodiversity scaled across hierarchical levels and varied among ecoregions.

Metacommunity structures were consistent for the conterminous United States and each of the nine ecoregion subsets, with each ecoregional metacommunity displaying a Clementsian structure. Environmental variables were the predominant drivers of assembly, suggesting the importance of species sorting and environmental filtering on community structure; however, the identity of the most influential environmental variables differed among ecoregions and suggested hierarchical filtering on assembly. Partitioned diversity was found to be lower at the local and ecoregional levels, but turnover in diversity among ecoregions was higher than expected.

Our results demonstrate contingencies in community assembly, notwithstanding consistency in metacommunity structure and support the importance of environmental control over community assembly and biodiversity. Moreover, biodiversity at the continental scale is likely maintained through this inherent variation in the drivers of assembly and concomitant changes in community composition among ecoregions. We suggest that further work should evaluate the assembly of other facets of community structure and the underlying mechanisms of the contingency in assembly drivers.
Recent biological invasion shapes species recognition and aggressive behaviour in a native species: A behavioural experiment using robots in the field
Authors: Dufour Claire M. S. , Clark David L. , Herrel Anthony , Losos Jonathan B. 
Published: March 2020

Abstract

Invasive species are a world‐wide threat to biodiversity. Yet, our understanding of biological invasions remains incomplete, partly due to the difficulty of tracking and studying behavioural interactions in recently created species interactions.

We tested whether the interactions between the recently introduced invasive lizard Anolis cristatellus and the native Anolis oculatus in Dominica have led to changes in species recognition and aggressive behaviour of the native species.

The use of realistic robots allowed us to test the behavioural response of 131 A. oculatus males towards relevant and controlled conspecific versus heterospecific stimuli, directly in the field and in two contexts (allopatry vs. sympatry).

Our results show that species recognition evolved prior to sympatry in A. oculatus. Moreover, interspecific competition resulted in an increase in the time spent displaying and a divergence in the aggressive behaviour of the native species towards conspecifics versus heterospecifics. Inherent species recognition and higher aggressive behaviour may limit species coexistence as they are expected to favour A. oculatus during territorial interactions with A. cristatellus.

While more studies are needed to understand the causes of these behavioural shifts and their consequences on long‐term species coexistence, the present study highlights the role of behaviour as a first response to interspecific interactions.
Tryptophan 387 and 390 residues in ADAMTS13 are crucial to the ability of vascular tube formation and cell migration of endothelial cells
Authors: Liu Ling , Ma Zhenni , Zhou Xuemei , Yin Jie , Lu Jun , Su Jian , Shen Fei , Xie Liqian , Hu Shaoyan , Ling Jing 
Published: March 2020

AbstractA disintegrin and metalloproteinase with thrombospondin motifs 13 (ADAMTS13) was mainly generated and secreted from endothelial cells (ECs). Our previous study showed that tryptophan (Trp) residues at 387 and 390 in ADAMTS13 are required for its secretion and enzymatic activity. However, the effects on its host cell as well as the potential mechanism have not been clear. The aim of the study was to examine the effects of Trp residues 387 and 390 of ADAMTS13 on the biological processes of ECs. Herein, Trp was substituted with alanine in ADAMTS13 to generate ADAMTS13 mutants at 387 (W387A), 390 (W390A), and double mutants at 387 and 390 (2WA), respectively. We found that substitution mutation impaired vascular endothelial growth factor (VEGF) secretion and the downstream JAK1/STAT3 activation, the binding ability to Von Willebrand factor, cell proliferation, migration, and vascular tube formation. Overall, our study concluded that Trp387 and Trp390 of ADAMTS13 play vital roles in the biological function of ECs.
Changes in the community structure of anurans in the Coastal plain forest, southeastern Brazil
Authors: Pereira‐Ribeiro Juliane , Ferreguetti Átilla C. , Bergallo Helena G. , Rocha Carlos Frederico D. 
Published: March 2020

AbstractIn this study, we analyzed how variations in species richness, composition and abundance of anurans in a community could be explained by temporal environmental factors such as temperature and precipitation and spatially between different vegetation types. The study was carried out in Vale Natural Reserve, state of Espírito Santo, Brazil, from June 2015 to October 2016. We sampled the anuran community in 21 plots of 250 m in length, with 10 m of width. We recorded a total of 326 individuals of anurans, corresponding to 23 species in six families. We concluded that the anurans community of the Vale Natural Reserve remained relatively stable throughout the seasons and along vegetation types in terms of richness but differed in composition and abundance. The anurans were more abundant in the rainy season, with precipitation being the most important factor for anuran density in the area. Anuran community composition varied among vegetation types due to differences in complexity and structure of each vegetation type. Our study showed that different factors were determinant for the variation in species abundance and composition in the area. Therefore, the conservation of fragments and their associated habitat and the monitoring of environmental changes is of fundamental importance in anuran conservation in the area.
Effect of high hydrostatic pressure challenge on biogenic amines, microbiota, and sensory profile in traditional poultry‐ and pork‐based semidried fermented sausage
Authors: Borges Ana F. , Cózar Almudena , Patarata Luís , Gama Luis T. , Alfaia Cristina M. , Fernandes Maria J. , Fernandes Maria H. , Pérez Herminia Vergara , Fraqueza Maria J. 
Published: March 2020

AbstractThe processing of traditional poultry‐ and pork‐based semidried fermented smoked sausages needs to be modernized to improve product quality and further extend its shelf life. The aim of the present study was to apply different combinations of high pressure (300 to 600 MPa) and time (154 to 1,800 s) on the sausages using an experimental design based on response surface methodology. The chemical, microbial, and sensory characteristics of sausages treated with high‐pressure processing (HPP) were investigated. HPP application to semidried fermented sausages resulted in color changes, which could be dependent on the ingredients, formulation, and smoking conditions used. Nevertheless, none of the HPP treatments applied resulted in detectable changes in sensory properties, as tested in a triangle test and confirmed by the analysis of focus groups assessment. Significant differences were detected for lactic acid bacteria (LAB) counts from 344 MPa and 1,530 s onward, with a marked decrease for the combination of 600 MPa and 960 s (P < 0.05). Coagulase‐negative staphylococci showed higher tolerance to the increase in pressure than LAB. HPP induced a microbial reduction on Enterobacteriaceae, molds, and yeasts, minimizing the production of the main biogenic amines. However, the polyamines (spermine and spermidine) increased since their metabolic use by microorganisms did not occur. Given the reduction of the main spoilage microbial indicators with no detectable sensory changes observed with the binomial condition of 600 MPa and 960 s, this was chosen as the optimal combination to be further applied.Practical ApplicationThe results from sensory analysis revealed that any of the HPP treatments applied resulted in detectable changes in sensory properties, as tested in a triangle test and confirmed by the analysis of the focus groups speeches.
SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets
Authors: Portik Daniel M. , Wiens John J. 
Published: March 2020

Abstract

Phylogenies with extensive taxon sampling have become indispensable for many types of ecological and evolutionary studies. Many large‐scale trees are based on a ‘supermatrix’ approach, which involves amalgamating thousands of published sequences for a group. Constructing up‐to‐date supermatrices can be challenging, especially as new sequences may become available almost constantly. Additionally, genomic datasets (composed of thousands of loci) are becoming common in phylogenetics and phylogeography, and present novel challenges for constructing such datasets.

Here we present SuperCRUNCH, a Python toolkit for assembling large phylogenetic datasets. It can be applied to GenBank sequences, unpublished sequences or combinations of GenBank and unpublished data. SuperCRUNCH constructs local databases and uses them to conduct rapid searches for user‐specified sets of taxa and loci. Sequences are parsed into putative loci and passed through rigorous filtering steps. A post‐filtering step allows for selection of one sequence per taxon (i.e. species‐level supermatrix) or retention of all sequences per taxon (i.e. population‐level dataset). Importantly, SuperCRUNCH can generate ‘vouchered’ population‐level datasets, in which voucher information is used to generate multi‐locus phylogeographic datasets. SuperCRUNCH offers many options for taxonomy resolution, similarity filtering, sequence selection, alignment and file manipulation.

We demonstrate the range of features available in SuperCRUNCH by generating a variety of phylogenetic datasets. Output datasets include traditional species‐level supermatrices, large‐scale phylogenomic matrices and phylogeographic datasets. Finally, we briefly compare the ability of SuperCRUNCH to construct species‐level supermatrices relative to alternative approaches. SuperCRUNCH generated a large‐scale supermatrix (1,400 taxa and 66 loci) from 16 GB of GenBank data in ~1.5 hr, and generated population‐level datasets (<350 samples, <10 loci) in <1 min. It outperformed alternative methods for supermatrix construction in terms of taxa, loci and sequences recovered.

SuperCRUNCH is a modular bioinformatics toolkit that can be used to assemble datasets for any taxonomic group and scale (kingdoms to individuals). It allows rapid construction of supermatrices, greatly simplifying the process of updating large phylogenies with new data. It is also designed to produce population‐level datasets. SuperCRUNCH streamlines the major tasks required to process phylogenetic data, including filtering, alignment, trimming and formatting. SuperCRUNCH is open‐source, documented and available at https://github.com/dportik/SuperCRUNCH.
Mossy cell synaptic dysfunction causes memory imprecision via miR‐128 inhibition of STIM2 in Alzheimer's disease mouse model
Authors: Deng Manfei , Zhang Qingping , Wu Zhuoze , Ma Tian , He Aodi , Zhang Tongmei , Ke Xiao , Yu Quntao , Han Yunyun , Lu Youming 
Published: March 2020

AbstractRecently, we have reported that dentate mossy cells (MCs) control memory precision via directly and functionally innervating local somatostatin (SST) inhibitory interneurons. Here, we report a discovery that dysfunction of synaptic transmission between MCs and SST cells causes memory imprecision in a mouse model of early Alzheimer's disease (AD). Single‐cell RNA sequencing reveals that miR‐128 that binds to a 3′UTR of STIM2 and inhibits STIM2 translation is increasingly expressed in MCs from AD mice. Silencing miR‐128 or disrupting miR‐128 binding to STIM2 evokes STIM2 expression, restores synaptic function, and rescues memory imprecision in AD mice. Comparable findings are achieved by directly engineering MCs with the expression of STIM2. This study unveils a key synaptic and molecular mechanism that dictates how memory maintains or losses its details and warrants a promising target for therapeutic intervention of memory decays in the early stage of AD.
Brief Report: Opioid‐Involved Overdose Mortality in United States Veterans
Authors: Peltzman Talya , Ravindran Chandru , Schoen Patrick M. , Morley Sybil W. , Drexler Karen , Katz Ira R. , McCarthy John F. 
Published: March 2020

Background and ObjectivesThe purpose of this study is to assess trends in opioid‐involved overdose mortality among US Veterans.MethodsAge‐adjusted drug overdose mortality rates, overall and by opioid subtype, were assessed from National Death Index data for US Veterans; statistical significance of trends was assessed for 2010 to 2015 and 2015 to 2016.ResultsVeteran age‐adjusted overdose mortality rates increased 23.7% from 2010 to 2015 (19.7‐24.4 of 100 000) and a further 20.4% through 2016 (29.3 of 100 000). Opioid involvement increased from 51.3% in 2010 to 62.1% in 2016, as opioid overdose rates increased from 10.9 to 19.5 of 100 000. Overdose mortality varied substantially by opioid subtype and demographics.Conclusions and scientific significanceThis report provides the first‐ever description of trends and characteristics of overdose mortality and opioid‐involved deaths among US Veterans of military service for the period 2010 to 2016. With the exception of female Veterans and Veterans in Western States, it has been found that trends in Veteran overdose mortality paralleled rising rates of drug overdose observed in the United States more broadly. Published 2020. This article is a U.S. Government work and is in the public domain in the USA. (Am J Addict 2020;00:00–00)