bluuebunny/crossref_metadata_2025_split huggingface dataset:
An atlas of human viruses provides new insights into diversity and tissue tropism of human viruses
Authors: Ye Sifan , Lu Congyu , Qiu Ye , Zheng Heping , Ge Xingyi , Wu Aiping , Xia Zanxian , Jiang Taijiao , Zhu Haizhen , Peng Yousong 
Published: November 2021

AbstractViruses continue to threaten human health. Yet, the complete viral species carried by humans and their infection characteristics have not been fully revealed. This study curated an atlas of human viruses from public databases and literatures, and built the Human Virus Database (HVD) available at http://computationalbiology.cn/humanVirusBase/#/. The HVD contains 1,131 virus species of 54 viral families which were more than twice the number of the human-infecting virus species reported in previous studies. These viruses were identified in human samples including 68 human tissues, the excreta and body fluid. The viral diversity in humans was age-dependent with a peak in the infant and a valley in the teenager. The tissue range of viruses was found to be associated with several factors including the viral group (DNA, RNA or reverse-transcribing viruses), enveloped or not, viral genome length and GC content, viral receptors and the virus-interacting proteins. Finally, the tissue range of DNA viruses was predicted using a random-forest algorithm with a medium performance. Overall, the study not only provides a valuable resource for further studies of human viruses, but also deepens our understanding towards the diversity and tissue tropism of human viruses.
Yersinia pseudotuberculosis doxycycline tolerance strategies include modulating expression of genes involved in cell permeability and tRNA modifications
Authors: Alvarez-Manzo Hector S. , Davidson Robert K. , de Wyels Jasper Van Cauwelaert , Cotten Katherine L. , Nguyen Benjamin , Zhu Zeyu , Anthony Jon , van Opijnen Tim , Davis Kimberly M. 
Published: November 2021

AbstractAntibiotic tolerance is typically associated with a phenotypic change within a bacterial population, resulting in a transient decrease in antibiotic susceptibility that can contribute to treatment failure and recurrent infections. Although tolerant cells may emerge prior to treatment, the stress of prolonged antibiotic exposure can also promote tolerance. Here, we sought to determine how Yersinia pseudotuberculosis responds to doxycycline exposure, to then verify if these gene expression changes could promote doxycycline tolerance in culture and in our mouse model of infection. Only four genes were differentially regulated in response to a physiologically-relevant dose of doxycycline: osmB and ompF were upregulated, tusB and cnfy were downregulated; differential expression also occurred during doxycycline treatment in the mouse. ompF, tusB and cnfy were also differentially regulated in response to chloramphenicol, indicating these could be general responses to ribosomal inhibition. cnfy has previously been associated with persistence and was not a major focus here. We found deletion of the OmpF porin resulted in increased antibiotic accumulation, suggesting expression may promote diffusion of doxycycline out of the cell, while OsmB lipoprotein had a minor impact on antibiotic permeability. Overexpression of tusB significantly impaired bacterial survival in culture and in the mouse, suggesting that tRNA modification by tusB, and the resulting impacts on translational machinery, may play an important role in promoting tolerance. We believe this is the first observation of bactericidal activity of doxycycline, which was revealed by reversing tusB downregulation.
Conservation and divergence in cortical cellular organization between human and mouse revealed by single-cell transcriptome imaging
Authors: Fang Rongxin , Xia Chenglong , Zhang Meng , He Jiang , Close Jennie , Long Brian , Miller Jeremy , Lein Ed , Zhuang Xiaowei 
Published: November 2021

AbstractThe human cerebral cortex has tremendous cellular diversity and complex cellular organization that are essential for brain function. How different types of cells are organized and interact with each other in the human cortex, and how cellular organizations and interaction patterns vary across species are, however, unclear. Here, we performed spatially resolved single-cell expression profiling of 4,000 genes in human middle and superior temporal gyrus using multiplexed error-robust fluorescence in situ hybridization (MERFISH). We identified >100 neuronal and non-neuronal cell populations with distinct transcriptional signatures, generated a molecularly defined and spatially resolved cell atlas of these brain regions, and analyzed cell-cell interactions in a cell-type-specific manner. Comparison with the mouse cortex showed conservation in the laminar organization of cells and substantial divergence in cell-cell interactions between human and mouse. Notably, our data revealed a drastic increase in interactions between neurons and non-neuronal cells in the human cortex, uncovered human-specific cell-cell interaction patterns, and identified potential ligand-receptor basis of microglia-neuron interactions.
Separable mechanisms drive local and global polarity establishment in the C. elegans intestinal epithelium
Authors: Pickett Melissa A. , Sallee Maria D. , Naturale Victor F. , Akpinaroglu Deniz , Lee Joo , Shen Kang , Feldman Jessica L. 
Published: November 2021

ABSTRACTApico-basolateral polarization is essential for epithelial cells to function as selective barriers and transporters, and to provide mechanical resiliency to organs. Epithelial polarity is established locally, within individual cells to establish distinct apical, junctional, and basolateral domains, and globally, within a tissue where cells coordinately orient their apico-basolateral axes. Using live imaging of endogenously tagged proteins and tissue specific protein depletion in the C. elegans embryonic intestine, we found that local and global polarity establishment are temporally and genetically separable. Local polarity is initiated prior to global polarity and is robust to perturbation. PAR-3 is required for global polarization across the intestine but is not required for local polarity establishment as small groups of cells are able to correctly establish polarized domains in PAR-3 depleted intestines in an HMR-1/E-cadherin dependent manner. Despite belonging to the same apical protein complex, we additionally find that PAR-3 and PKC-3/aPKC have distinct roles in the establishment and maintenance of local and global polarity. Together, our results indicate that different mechanisms are required for local and global polarity establishment in vivo.SUMMARY STATEMENTLive-imaging and intestine specific protein depletion reveal that apico-basolateral polarity establishment can be temporally and genetically separated at the local level of individual cells and globally, across a tissue.
Soil microbes mediate the effects of environmental variability on plant invasion
Authors: Zhang Xue , van Kleunen Mark , Chang Chunling , Liu Yanjie 
Published: November 2021

AbstractMany studies indicate that increases in resource variability promote plant invasion. However, it remains unknown to what extent these effects might indirectly be mediated by other organisms. To test this, we grew eight alien species in pot-mesocosms with five different native communities under eight combinations of two nutrient-availability, two nutrient-fluctuation and two soil-microbe treatments. We found that when plants grew in sterilized soil, nutrient fluctuation promoted the dominance of alien plants under low nutrient availability, whereas its effect was minimal under high nutrient availability. However, the opposite pattern was found when plants grew in living soil. Analysis of the soil microbial community suggests that this might reflect that nutrient fluctuation strongly increased the soil fungal pathogen diversity under high nutrient availability, but slightly decreased it under low nutrient availability. Our findings indicate that besides its direct influence, environmental variability could also indirectly affect plant invasion via changes in soil-microbial communities.
Genetic control of rhizosheath formation in pearl millet
Authors: De la Fuente Cantó C. , Diouf M.N. , Ndour P.M.S. , Debieu M. , Grondin A. , Passot S. , Champion A. , Barrachina C. , Pratlong M. , Gantet P. , Assigbetsé K. , Kane N. , Cubry P. , Diedhiou A.G. , Heulin T. , Achouak W. , Vigouroux Y. , Cournac L. , Laplaze L. 
Published: November 2021

AbstractThe rhizosheath, the layer of soil that adheres strongly to roots, influences water and nutrients acquisition. Pearl millet is a cereal crop that plays a major role for food security in arid regions of sub Saharan Africa and India. We previously showed that root-adhering soil mass is a heritable trait in pearl millet and that it correlates with changes in rhizosphere microbiota structure and functions. Here, we studied the correlation between root-adhering soil mass and root hair development, root architecture, and symbiosis with arbuscular mycorrhizal fungi and we analysed the genetic control of this trait using genome wide association (GWAS) combined with bulk segregant analysis and gene expression studies. Root-adhering soil mass was weakly correlated only to root hairs traits in pearl millet. Twelve QTLs for rhizosheath formation were identified by GWAS. Bulk segregant analysis on a biparental population validated five of these QTLs. Combining genetics with a comparison of global gene expression in the root tip of contrasted inbred lines revealed candidate genes that might control rhizosheath formation in pearl millet. Our study indicates that rhizosheath formation is under complex genetic control in pearl millet and suggests that it is mainly regulated by root exudation.HighlightFormation of the rhizosheath, a layer of soil adhering to the root, is under complex genetic control in pearl millet and is mainly regulated by root exudation.
DNA-free CRISPR-Cas9 gene editing of tetraploid tomatoes using protoplast regeneration
Authors: Hsu Chen-Tran , Yuan Yu-Hsuan , Zheng Po-Xing , Wu Fu-Hui , Cheng Qiao-Wei , Wu Yu-Lin , Lin Steven , Yue Jin-Jun , Cheng Ying-Huey , Lin Shu-I , Shih Ming-Che , Sheen Jen , Lin Yao-Cheng , Lin Choun-Sea 
Published: November 2021

AbstractWild tomatoes are important genomic resources for tomato research and breeding. Development of a foreign DNA-free CRISPR-Cas delivery system has potential to mitigate public concern about genetically modified organisms. Here, we established a DNA-free protoplast regeneration and CRISPR-Cas9 genome editing system for Solanum peruvianum, an important resource for tomato introgression breeding. We generated mutants for genes involved in small interfering RNAs (siRNA) biogenesis, RNA-DEPENDENT RNA POLYMERASE 6 (SpRDR6) and SUPPRESSOR OF GENE SILENCING 3 (SpSGS3); pathogen-related peptide precursors, PATHOGENESIS-RELATED PROTEIN-1 (SpPR-1) and PROSYSTEMIN (SpProsys); and fungal resistance (MILDEW RESISTANT LOCUS O, SpMlo1) using diploid or tetraploid protoplasts derived from in vitro-grown shoots. The ploidy level of these regenerants was not affected by PEG-calcium-mediated transfection, CRISPR reagents, or the target genes. By karyotyping and whole genome sequencing analysis, we confirmed that CRISPR-Cas9 editing did not introduce chromosomal changes or unintended genome editing sites. All mutated genes in both diploid and tetraploid regenerants were heritable in the next generation. spsgs3 null T0 regenerants and sprdr6 null T1 progeny had wiry, sterile phenotypes in both diploid and tetraploid lines. The sterility of the spsgs3 null mutant was partially rescued, and fruits were obtained by grafting to wild-type stock and pollination with wild-type pollen. The resulting seeds contained the mutated alleles. Tomato yellow leaf curl virus proliferated at higher levels in spsgs3 and sprdr6 mutants than in the wild type. Therefore, this protoplast regeneration technique should greatly facilitate tomato polyploidization and enable the use of CRISPR-Cas for S. peruvianum domestication and tomato breeding.One-sentence summaryDNA-free CRISPR-Cas9 genome editing in wild tomatoes creates stable and inheritable diploid and tetraploid regenerants.
Plasmotype condition nuclear pleiotropic effects on clock and fitness in barley
Authors: Bdolach Eyal , Prusty Manas Ranjan , Tiwari Lalit Dev , Kashkush Khalil , Fridman Eyal 
Published: November 2021

ABSTRACTIn plants, the role of chloroplasts and mitochondria (plasmotype) in controlling circadian clock plasticity and overall plant robustness has not been elucidated. In this study, we investigated the rhythmicity of chlorophyll fluorescence (Chl F) clock output, and fitness in the field at optimal and elevated temperatures, in three different barley populations. First, we examined a reciprocal DH population between two wild barley (Hordeum vulgare ssp. spontaneum), in which we identified two pleiotropic QTLs (frp2.1 and amp7.1) that modulate clock and fitness including conditioning of these effects by plasmotype diversity. In the second population, a complete diallel consisting of 11 genotypes (reciprocal hybrids differing in plasmotype), we observed a gradual reduction in plasmotype, ranging from 26% and 15% for Chl F and clock measurements to 5.3% and 3.7% for growth and reproductive traits, respectively. The third population studied was a collection of cytolines in which nine different wild plasmotypes replaced the cultivated Noga (H. vulgare) plasmotype. Here, the order and magnitude of the effects of the plasmotypes differed from what we observed in the diallel population, with the greatest effect of plasmotype diversity observed for clock period and amplitude. Comparison of the chloroplast sequences suggests several candidate genes in the plastid-encoded RNA polymerase (PEP) complex that may be responsible for the observed plasmotype effects. Overall, our results unravel previously unknown cytonuclear epistatic interactions that controls clock performance while also having pleiotropic effects on a plant field characteristics.
Chemiluminescence analysis of saliva for the assessment of emotional stress in autistic children undergoing a medical examination
Authors: Proskurnina Elena , Portnova Galina , Ivanova Maria , Sokolova Svetlana 
Published: November 2021

Purpose
An electroencephalography (EEG) examination may cause psychological stress in children with autism that can interfere with the examination results. The objective information on the presence or absence of psycho-emotional stress in patients can help interpret electroencephalograms. This paper aimed to demonstrate the potential of noninvasive objective diagnostics of emotional stress in autistic children undergoing an EEG examination based on analysis of saliva.

Design/methodology/approach
This study involved 19 children with autism spectrum disorder (ASD) (ICD-10 F84.0); the mean age was seven years. During EEG examination of the children, behavioral parameters were assessed. The activity of cytochrome P450 reductase (CYPOR) in saliva was measured before and after the EEG procedure using lucigenin-enhanced nicotinamide adenine dinucleotide phosphate-stimulated chemiluminescence assay.

Findings
Significant differences in CYPOR activity were found between the children who were distressed during an EEG examination and the children without behavioral disturbances (Mann–Whitney test, p = 0.002). Thus, the EEG examination resulted in an increase in CYPOR activity in saliva cells, which may prove the stressful effect of this procedure on autistic children.

Originality/value
The chemiluminescent indices reflecting the activity of microsomal CYPOR in cells presenting in saliva correlate with the absence or presence of psychological stress in children; this phenomenon can be explained by an increased metabolism of the stress hormone, cortisol, by the cytochrome P450 microsomal system. Furthermore, the proposed method is completely safe, noninvasive, rapid (recording time is 20 min), inexpensive and promising for an objective assessment of psycho-emotional stress in autistic children undergoing medical examinations.
Forced online experiment and its acceptance among the University students during pandemic in Pakistan
Authors: Abdullah Iqra , Parveen Shazia , Haq Saif Ul 
Published: November 2021

Purpose
This study aims to assess the acceptability of online classes among university students of Pakistan through the extension of the unified theory of acceptance and use of technology (UTAUT) model.

Design/methodology/approach
This study follows a quantitative research approach and data were collected from 662 university students of 10 different universities of Pakistan through a self-administrative Web survey. Structural equation modeling through SmartPLS was used to analyze the data.

Findings
Findings of the research show that performance expectancy, effort expectancy, social influence and facilitating conditions play a significant role in developing the intention to adopt online classes. Furthermore, facilitating conditions and intention to adopt online classes have further resulted in frequent use behavior. The authors also investigated the moderating role effect of active learning in relationship behavioral intention and use behavior. Findings show that active learning is an important component of online classes that interacts with the behavioral intention to develop the behavior of attending the online mode of learning by students. However, no significant moderation of uncertainty was found in the relationship between four components of acceptance of technology and behavioral intention to adopt the technology.

Originality/value
The authors have extended the UTUAT model by establishing the relationship between facilitating conditions and behavioral intention that supports e-learning. Furthermore, this study tests the moderating role of uncertainty and active learning on the UTUAT model.
The impact of trade openness on the cost of financial intermediation and bank performance: evidence from BRICS countries
Authors: Rahman Mohammed Mizanur , Rahman Md. Mominur , Rahman Mahfuzur , Masud Md. Abdul Kaium 
Published: November 2021

PurposeThe purpose of this paper is to examine the impact of trade openness on the cost of financial intermediation and bank performance. Developed and developing countries are currently pursuing trade openness to achieve higher bank performance with less intermediation costs.Design/methodology/approachIn attaining the study's objectives, several regression methodologies were employed (i.e. system generalized method of moments (GMM), fixed effect, pooled ordinary least squares (OLS) and vector error correction model (VECM)). The authors tested the hypothesis on data of 885 banks from BRICS countries, which span 18 years (2000–2017).FindingsThe results from this robust study showed that embedding higher trade openness reduces financial intermediation costs and improves banks' performance. The results remain robust following the use of different estimation methods and alternative variables as proxies. In addition, results were still valid upon considering bank level, industry level and country level as control variables. It was also observed that the relation pattern holds its rigidity during “good” and “bad” times (i.e. the global financial crisis).Originality/valueThe results provide better references for bank regulators, academics and policymakers to take advantage of the low financial intermediation costs resulting from trade openness.
Enhancing the tensile strength of SiC reinforced aluminium-based functionally graded structure through the mixture design approach
Authors: Poornesh M. , Bhat Shreeranga , Gijo E.V. , Bellairu Pavana Kumara 
Published: November 2021

PurposeThis article aims to study the tensile properties of a functionally graded composite structure with Al–18wt%Si alloy as the matrix material and silicon carbide (SiC) particles as the reinforcing element. More specifically, the study's primary objective is to optimize the composition of the material elements using a robust statistical approach.Design/methodology/approachIn this research, the composite material is fabricated using a combination of stir casting and the centrifugal casting technique. Moreover, the test specimen required to study the tensile strength are prepared according to the ASTM (American Society for Testing and Materials) standards. Eventually, optimal composition to maximize the tensile property of the material is determined using the mixture design approach.FindingsThe investigation results imply that the addition of the SiC plays a crucial role in increasing the tensile strength of the composite. The optical microstructural images of the composite show the adequate distribution of the reinforcing particles with the matrix. The proposed regression model shows better predictability of tensile strength. In addition, the methodology aids in optimizing the mixture component values to maximize the tensile strength of the produced functionally graded composite structure.Originality/valueLittle work has been reported so far where a hypereutectic Al–Si alloy is considered the matrix material to produce the composite structure. The article attempts to make a composite structure by using a combination of stir casting and centrifugal casting. Furthermore, it employs the mixture design to optimize the composition and predict the model of the study, which is one of a kind in the field of material science.
An automated mobile app labeling framework based on primary motivations for smartphone use
Authors: Ayanso Anteneh , Han Mingshan , Zihayat Morteza 
Published: November 2021

PurposeThis paper aims to propose an automated mobile app labeling framework based on a novel app classification scheme that is aligned with users’ primary motivations for using smartphones. The study addresses the gaps in incorporating the needs of users and other context information in app classification as well as recommendation systems.Design/methodology/approachBased on a corpus of mobile app descriptions collected from Google Play store, this study applies extensive text analytics and topic modeling procedures to profile mobile apps within the categories of the classification scheme. Sufficient number of representative and labeled app descriptions are then used to train a classifier using machine learning algorithms, such as rule-based, decision tree and artificial neural network.FindingsExperimental results of the classifiers show high accuracy in automatically labeling new apps based on their descriptions. The accuracy of the classification results suggests a feasible direction in facilitating app searching and retrieval in different Web-based usage environments.Research limitations/implicationsAs a common challenge in textual data projects, the problem of data size and data quality issues exists throughout the multiple phases of experiments. Future research will extend the data collection scope in many aspects to address the issues that constrained the current experiments.Practical implicationsThese empirical experiments demonstrate the feasibility of textual data analysis in profiling apps and user context information. This study also benefits app developers by improving app descriptions through a better understanding of user needs and context information. Finally, the classification framework can also guide practitioners in customizing products and services beyond mobile apps where context information and user needs play an important role.Social implicationsGiven the widespread usage and applications of smartphones today, the proposed app classification framework will have broader implications to different Web-based application environments.Originality/valueWhile there have been other classification approaches in the literature, to the best of the authors’ knowledge, this framework is the first study on building an automated app labeling framework based on primary motivations of smartphone usage.