bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fundamentally different repetitive element composition of sex chromosomes in Rumex acetosa
Authors: Jesionek Wojciech , Bodláková Markéta , Kubát Zdeněk , Čegan Radim , Vyskot Boris , Vrána Jan , Šafář Jan , Puterova Janka , Hobza Roman 
Published: September 2020

Abstract

Background and Aims
Dioecious species with well-established sex chromosomes are rare in the plant kingdom. Most sex chromosomes increase in size but no comprehensive analysis of the kind of sequences that drive this expansion has been presented. Here we analyse sex chromosome structure in common sorrel (Rumex acetosa), a dioecious plant with XY1Y2 sex determination, and we provide the first chromosome-specific repeatome analysis for a plant species possessing sex chromosomes.

Methods
We flow-sorted and separately sequenced sex chromosomes and autosomes in R. acetosa using the two-dimensional fluorescence in situ hybridization in suspension (FISHIS) method and Illumina sequencing. We identified and quantified individual repeats using RepeatExplorer, Tandem Repeat Finder and the Tandem Repeats Analysis Program. We employed fluorescence in situ hybridization (FISH) to analyse the chromosomal localization of satellites and transposons.

Key Results
We identified a number of novel satellites, which have, in a fashion similar to previously known satellites, significantly expanded on the Y chromosome but not as much on the X or on autosomes. Additionally, the size increase of Y chromosomes is caused by non-long terminal repeat (LTR) and LTR retrotransposons, while only the latter contribute to the enlargement of the X chromosome. However, the X chromosome is populated by different LTR retrotransposon lineages than those on Y chromosomes.

Conclusions
The X and Y chromosomes have significantly diverged in terms of repeat composition. The lack of recombination probably contributed to the expansion of diverse satellites and microsatellites and faster fixation of newly inserted transposable elements (TEs) on the Y chromosomes. In addition, the X and Y chromosomes, despite similar total counts of TEs, differ significantly in the representation of individual TE lineages, which indicates that transposons proliferate preferentially in either the paternal or the maternal lineage.
A practical guide to mechanistic systems modeling in biology using a logic-based approach
Authors: Niarakis Anna , Helikar Tomáš 
Published: September 2020

Abstract
Mechanistic computational models enable the study of regulatory mechanisms implicated in various biological processes. These models provide a means to analyze the dynamics of the systems they describe, and to study and interrogate their properties, and provide insights about the emerging behavior of the system in the presence of single or combined perturbations. Aimed at those who are new to computational modeling, we present here a practical hands-on protocol breaking down the process of mechanistic modeling of biological systems in a succession of precise steps. The protocol provides a framework that includes defining the model scope, choosing validation criteria, selecting the appropriate modeling approach, constructing a model and simulating the model. To ensure broad accessibility of the protocol, we use a logical modeling framework, which presents a lower mathematical barrier of entry, and two easy-to-use and popular modeling software tools: Cell Collective and GINsim. The complete modeling workflow is applied to a well-studied and familiar biological process—the lac operon regulatory system. The protocol can be completed by users with little to no prior computational modeling experience approximately within 3 h.
DeepHPV: a deep learning model to predict human papillomavirus integration sites
Authors: Tian Rui , Zhou Ping , Li Mengyuan , Tan Jinfeng , Cui Zifeng , Xu Wei , Wei Jingyue , Zhu Jingjing , Jin Zhuang , Cao Chen , Fan Weiwen , Xie Weiling , Huang Zhaoyue , Xie Hongxian , You Zeshan , Niu Gang , Wu Canbiao , Guo Xiaofang , Weng Xuchu , Tian Xun , Yu Fubing , Yu Zhiying , Liang Jiuxing , Hu Zheng 
Published: September 2020

Abstract
Human papillomavirus (HPV) integrating into human genome is the main cause of cervical carcinogenesis. HPV integration selection preference shows strong dependence on local genomic environment. Due to this theory, it is possible to predict HPV integration sites. However, a published bioinformatic tool is not available to date. Thus, we developed an attention-based deep learning model DeepHPV to predict HPV integration sites by learning environment features automatically. In total, 3608 known HPV integration sites were applied to train the model, and 584 reviewed HPV integration sites were used as the testing dataset. DeepHPV showed an area under the receiver-operating characteristic (AUROC) of 0.6336 and an area under the precision recall (AUPR) of 0.5670. Adding RepeatMasker and TCGA Pan Cancer peaks improved the model performance to 0.8464 and 0.8501 in AUROC and 0.7985 and 0.8106 in AUPR, respectively. Next, we tested these trained models on independent database VISDB and found the model adding TCGA Pan Cancer performed better (AUROC: 0.7175, AUPR: 0.6284) than the model adding RepeatMasker peaks (AUROC: 0.6102, AUPR: 0.5577). Moreover, we introduced attention mechanism in DeepHPV and enriched the transcription factor binding sites including BHLHA15, CHR, COUP-TFII, DMRTA2, E2A, HIC1, INR, NPAS, Nr5a2, RARa, SCL, Snail1, Sox10, Sox3, Sox4, Sox6, STAT6, Tbet, Tbx5, TEAD, Tgif2, ZNF189, ZNF416 near attention intensive sites. Together, DeepHPV is a robust and explainable deep learning model, providing new insights into HPV integration preference and mechanism.
Availability: DeepHPV is available as an open-source software and can be downloaded from https://github.com/JiuxingLiang/DeepHPV.git, Contact: huzheng1998@163.com, liangjiuxing@m.scnu.edu.cn, lizheyzy@163.com
Predicting drug–disease associations through layer attention graph convolutional network
Authors: Yu Zhouxin , Huang Feng , Zhao Xiaohan , Xiao Wenjie , Zhang Wen 
Published: September 2020

AbstractBackground: Determining drug–disease associations is an integral part in the process of drug development. However, the identification of drug–disease associations through wet experiments is costly and inefficient. Hence, the development of efficient and high-accuracy computational methods for predicting drug–disease associations is of great significance.Results: In this paper, we propose a novel computational method named as layer attention graph convolutional network (LAGCN) for the drug–disease association prediction. Specifically, LAGCN first integrates the known drug–disease associations, drug–drug similarities and disease–disease similarities into a heterogeneous network, and applies the graph convolution operation to the network to learn the embeddings of drugs and diseases. Second, LAGCN combines the embeddings from multiple graph convolution layers using an attention mechanism. Third, the unobserved drug–disease associations are scored based on the integrated embeddings. Evaluated by 5-fold cross-validations, LAGCN achieves an area under the precision–recall curve of 0.3168 and an area under the receiver–operating characteristic curve of 0.8750, which are better than the results of existing state-of-the-art prediction methods and baseline methods. The case study shows that LAGCN can discover novel associations that are not curated in our dataset.Conclusion: LAGCN is a useful tool for predicting drug–disease associations. This study reveals that embeddings from different convolution layers can reflect the proximities of different orders, and combining the embeddings by the attention mechanism can improve the prediction performances.
The VEGA suite of programs: an versatile platform for cheminformatics and drug design projects
Authors: Pedretti Alessandro , Mazzolari Angelica , Gervasoni Silvia , Fumagalli Laura , Vistoli Giulio 
Published: September 2020

Abstract

The purpose of the article is to offer an overview of the latest release of the VEGA suite of programs. This software has been constantly developed and freely released during the last 20 years and has now reached a significant diffusion and technology level as confirmed by the about 22 500 registered users. While being primarily developed for drug design studies, the VEGA package includes cheminformatics and modeling features, which can be fruitfully utilized in various contexts of the computational chemistry. To offer a glimpse of the remarkable potentials of the software, some examples of the implemented features in the cheminformatics field and for structure-based studies are discussed. Finally, the flexible architecture of the VEGA program which can be expanded and customized by plug-in technology or scripting languages will be described focusing attention on the HyperDrive library including highly optimized functions.

Availability and implementation
The VEGA suite of programs and the source code of the VEGA command-line version are available free of charge for non-profit organizations at http://www.vegazz.net.
Severity of prepregnancy diabetes on the fetal malformations and viability associated with early embryos in rats†
Authors: Bueno Aline , Sinzato Yuri Karen , Volpato Gustavo Tadeu , Gallego Franciane Quintanilha , Perecin Felipe , Rodrigues Tiago , Damasceno Débora Cristina 
Published: September 2020

AbstractPreexisting/pregestational diabetes enhances the risk of birth defects. Several factors have been involved during the implantation process, such as cytokines (granulocyte-macrophage–colony-stimulating factor [GM-CSF]). The objective was to evaluate the effects of two levels of diabetes on the redox status of preimplantation embryos during the implantation process to comprehend how both are involved in embryo and fetal viability against maternal diabetes. Female Sprague–Dawley rats received streptozotocin at birth (mild diabetes [MD]) or at adulthood (severe diabetes [SD]) to obtain two experimental diabetes intensities. After confirming the diabetic status, the nondiabetic and diabetic groups were mated around day 110 of life. At gestational day (GD) 21, fetuses were assessed for viability and malformations and ovaries for embryo loss before implantation. Other pregnant nondiabetic and diabetic rats were sacrificed at GD2–4 for maternal and preimplantation embryo oxidative stress markers, maternal serum insulin, uterine fluid GM-CSF, and preimplantation embryo morphological analysis. MD and SD caused abnormal redox levels, lower GM-CSF and insulin levels during the preimplantation period, and embryonic loss before implantation. SD caused lower fetal viability and higher fetal malformation percentages at GD21. The SD dam-derived preimplantation embryos presented lower glutathione levels and higher thiobarbituric acid reactive substances concentration at GD3 and an increased frequency of abnormal preimplantation embryos at GD4. In conclusion, preexisting diabetes leads to complications in the implantation process. Furthermore, maternal oxidative stress and other metabolic changes alter the redox state and morphological structure of preimplantation embryos, contributing to damaged growth and development in late pregnancy.
Specification tests for covariance structures in high-dimensional statistical models
Authors: Guo X , Tang C Y 
Published: September 2020

SummaryWe consider testing the covariance structure in statistical models. We focus on developing such tests when the random vectors of interest are not directly observable and have to be derived via estimated models. Additionally, the covariance specification may involve extra nuisance parameters which also need to be estimated. In a generic additive model setting, we develop and investigate test statistics based on the maximum discrepancy measure calculated from the residuals. To approximate the distributions of the test statistics under the null hypothesis, new multiplier bootstrap procedures with dedicated adjustments that incorporate the model and nuisance parameter estimation errors are proposed. Our theoretical development elucidates the impact due to the estimation errors with high-dimensional data and demonstrates the validity of our tests. Simulations and real data examples confirm our theory and demonstrate the performance of the proposed tests.
Posterior contraction in sparse generalized linear models
Authors: Jeong Seonghyun , Ghosal Subhashis 
Published: September 2020

Summary
We study posterior contraction rates in sparse high-dimensional generalized linear models using priors incorporating sparsity. A mixture of a point mass at zero and a continuous distribution is used as the prior distribution on regression coefficients. In addition to the usual posterior, the fractional posterior, which is obtained by applying Bayes theorem with a fractional power of the likelihood, is also considered. The latter allows uniformity in posterior contraction over a larger subset of the parameter space. In our set-up, the link function of the generalized linear model need not be canonical. We show that Bayesian methods achieve convergence properties analogous to lasso-type procedures. Our results can be used to derive posterior contraction rates in many generalized linear models including logistic, Poisson regression and others.
The Implementation of Connecting People in Community Mental Health Teams in England: A Quasi-Experimental Study
Authors: Webber M , Ngamaba K , Moran N , Pinfold V , Boehnke J R , Knapp M , Henderson C , Rehill A , Morris D 
Published: September 2020

Abstract
Loneliness and social isolation have become significant concerns in many countries, particularly amongst people experiencing mental health problems. A social intervention—Connecting People—has been found to increase their access to social capital, though it has been difficult to implement with high fidelity in community mental health teams (CMHTs) in England. This study aimed to evaluate outcomes for mental health service users of a practitioner-led implementation of Connecting People in CMHTs. It used a pragmatic non-randomised two-group pre-post study to evaluate the implementation process in CMHTs. Implementation materials co-produced with service users were provided to the intervention teams for practitioners to use with the support of a senior social worker in each mental health National Health Service Trust (n = 5). Service users were interviewed at baseline (n = 151) and at six-month follow-up (n = 127), and their outcome and cost data were analysed on an intention-to-treat basis. Analysis of primary and secondary outcome variables found no differences between the intervention and control groups. The economic evaluation found no significant differences between groups in mean costs or outcomes. The findings suggest that it could be difficult for social workers to implement Connecting People in CMHTs or that it does not improve outcomes for CMHT users.
Media, Affect, and Authoritarian Futures in “New Turkey:” Spectacular Confessions on Television in the Post-Coup Era
Authors: Bulut Ergin , Can Başak 
Published: September 2020

AbstractA spectacular shock doctrine is reformatting Turkey since the failed coup in July 2016. We examine how the television economy transformed the organization behind the coup (FETÖ) from a public secret into a spectacle. We investigate the televised confessions of former Gulenists, who revealed the scandalous FETÖ’s inner workings live on television. We argue that former Gulenists’ media performances based on confession, apology, and spectacular secrecy captured public affect to justify their complicity with the putschists rather than bringing political justice. The government capitalized on these confessions as part of its strategic information warfare to tame the opposition after the coup, while reconstructing Gulenists as a weird cult rather than a political network. As the citizens were bombarded with affective televisual confessions, politicians secured authoritarian futures without a glimpse of justice, because these shows spectacularly erased the networks behind the coup.
Color Naming and Categorization Depend on Distinct Functional Brain Networks
Authors: Siuda-Krzywicka Katarzyna , Witzel Christoph , Bartolomeo Paolo , Cohen Laurent 
Published: September 2020

Abstract
Naming a color can be understood as an act of categorization, that is, identifying it as a member of a category of colors that are referred to by the same name. But are naming and categorization equivalent cognitive processes and consequently rely on same neural substrates? Here, we used task and resting-state functional magnetic resonance imaging as well as behavioral measures to identify functional brain networks that modulated naming and categorization of colors. We first identified three bilateral color-sensitive regions in the ventro-occipital cortex. We then showed that, across participants, color naming and categorization response times (RTs) were correlated with different resting state connectivity networks seeded from the color-sensitive regions. Color naming RTs correlated with the connectivity between the left posterior color region, the left middle temporal gyrus, and the left angular gyrus. In contrast, color categorization RTs correlated with the connectivity between the bilateral posterior color regions, and left frontal, right temporal and bilateral parietal areas. The networks supporting naming and categorization had a minimal overlap, indicating that the 2 processes rely on different neural mechanisms.
MEG Theta during Lexico-Semantic and Executive Processing Is Altered in High-Functioning Adolescents with Autism
Authors: You Yuqi , Correas Angeles , Jao Keehn R Joanne , Wagner Laura C , Rosen Burke Q , Beaton Lauren E , Gao Yangfeifei , Brocklehurst William T , Fishman Inna , Müller Ralph-Axel , Marinkovic Ksenija 
Published: September 2020

AbstractNeuroimaging studies have revealed atypical activation during language and executive tasks in individuals with autism spectrum disorders (ASD). However, the spatiotemporal stages of processing associated with these dysfunctions remain poorly understood. Using an anatomically constrained magnetoencephalography approach, we examined event-related theta oscillations during a double-duty lexical decision task that combined demands on lexico-semantic processing and executive functions. Relative to typically developing peers, high-functioning adolescents with ASD had lower performance accuracy on trials engaging selective semantic retrieval and cognitive control. They showed an early overall theta increase in the left fusiform cortex followed by greater activity in the left-lateralized temporal (starting at ~250 ms) and frontal cortical areas (after ~450 ms) known to contribute to language processing. During response preparation and execution, the ASD group exhibited elevated theta in the anterior cingulate cortex, indicative of greater engagement of cognitive control. Simultaneously increased activity in the ipsilateral motor cortex may reflect a less lateralized and suboptimally organized motor circuitry. Spanning early sensory-specific and late response selection stages, the higher event-related theta responsivity in ASD may indicate compensatory recruitment to offset inefficient lexico-semantic retrieval under cognitively demanding conditions. Together, these findings provide further support for atypical language and executive functions in high-functioning ASD.
Health-care Professionals’ Perceptions of Critical Care Resource Availability and Factors Associated With Mental Well-being During Coronavirus Disease 2019 (COVID-19): Results from a US Survey
Authors: Sharma Monisha , Creutzfeldt Claire J , Lewis Ariane , Patel Pratik V , Hartog Christiane , Jannotta Gemi E , Blissitt Patricia , Kross Erin K , Kassebaum Nicholas , Greer David M , Curtis J Randall , Wahlster Sarah 
Published: September 2020

Abstract

Background
Assessing the impact of coronavirus disease 2019 (COVID-19) on intensive care unit (ICU) providers’ perceptions of resource availability and evaluating the factors associated with emotional distress/burnout can inform interventions to promote provider well-being.

Methods
Between 23 April and 7 May 2020, we electronically administered a survey to physicians, nurses, respiratory therapists (RTs), and advanced practice providers (APPs) caring for COVID-19 patients in the United States. We conducted a multivariate regression to assess associations between concerns, a reported lack of resources, and 3 outcomes: a primary outcome of emotional distress/burnout and 2 secondary outcomes of (1) fear that the hospital is unable to keep providers safe; and (2) concern about transmitting COVID-19 to their families/communities.

Results
We included 1651 respondents from all 50 states: 47% were nurses, 25% physicians, 17% RTs, and 11% APPs. Shortages of intensivists and ICU nurses were reported by 12% and 28% of providers, respectively. The largest supply restrictions reported were for powered air purifying respirators (56% reporting restricted availability). Provider concerns included worries about transmitting COVID-19 to their families/communities (66%), emotional distress/burnout (58%), and insufficient personal protective equipment (PPE; 40%). After adjustment, emotional distress/burnout was significantly associated with insufficient PPE access (adjusted relative risk [aRR], 1.43; 95% confidence interval [CI], 1.32–1.55), stigma from community (aRR, 1.32; 95% CI, 1.24–1.41), and poor communication with supervisors (aRR, 1.13; 95% CI, 1.06–1.21). Insufficient PPE access was the strongest predictor of feeling that the hospital is unable to keep providers safe and worries about transmitting infection to their families/communities.

Conclusions
Addressing insufficient PPE access, poor communication from supervisors, and community stigma may improve provider mental well-being during the COVID-19 pandemic.
Utilization of Blood Culture in South Asia for the Diagnosis and Treatment of Febrile Illness
Authors: Hemlock Caitlin , Luby Stephen P , Saha Shampa , Qamar Farah , Andrews Jason R , Saha Samir K , Tamrakar Dipesh , Date Kashmira , Longley Ashley T , Garrett Denise O , Bogoch Isaac I 
Published: September 2020

Abstract

Background
Blood culture is the current standard for diagnosing bacteremic illnesses, yet it is not clear how physicians in many low- and middle-income countries utilize blood culture for diagnostic purposes and to inform treatment decisions.

Methods
We screened suspected enteric fever cases from 6 hospitals in Bangladesh, Nepal, and Pakistan, and enrolled patients if blood culture was prescribed by the treating physician. We used generalized additive regression models to analyze the probability of receiving blood culture by age, and linear regression models to analyze changes by month to the proportion of febrile cases prescribed a blood culture compared with the burden of febrile illness, stratified by hospital. We used logistic regression to analyze predictors for receiving antibiotics empirically. We descriptively reviewed changes in antibiotic therapy by susceptibility patterns and coverage, stratified by country.

Results
We screened 30 809 outpatients resulting in 1819 enteric fever cases; 1935 additional cases were enrolled from other hospital locations. Younger outpatients were less likely to receive a blood culture. The association between the number of febrile outpatients and the proportion prescribed blood culture varied by hospital. Antibiotics prescribed empirically were associated with severity and provisional diagnoses, but 31% (1147/3754) of enteric fever cases were not covered by initial therapy; this was highest in Pakistan (50%) as many isolates were resistant to cephalosporins, which were commonly prescribed empirically.

Conclusions
Understanding hospital-level communication between laboratories and physicians may improve patient care and timeliness of appropriate antibiotics, which is important considering the rise of antimicrobial resistance.