bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical, Immunological, and Virological Outcomes Among Youths With Perinatal HIV After Transition to Adult Units in Spain From 1997 to 2016
Authors: Aguilera-Alonso David , Sainz Talía , Jimenez de Ory Santiago , Bernardino Ignacio , Díez Cristina , Torres Berta , Merino Dolores , Iribarren José A. , Portilla Irene , Ríos María José , Ibarra Sofía , Sanz José , Bellón José María , Carrasco Itziar , Muñoz-Fernández María Ángeles , Ramos José Tomás , Navarro María Luisa ,   CoRISpe Cohort Working Group and CoRISpe-FARO Cohort Working Group
Published: October 2020

Background:
Children living with HIV are reaching adulthood and transitioning to adult clinics. This study aimed to describe clinical and immunovirological status after transition in patients with perinatal HIV.

Methods:
Patients participating in the Spanish multicenter pediatric HIV cohort (CoRISpe) transferred to adult care (FARO cohort) from 1997 to 2016 were included. Clinical and immunovirological data were collected from 12 years old to the last follow-up moment after transition (up to December 2017). We used mixed-effect models to analyze changes in CD4 counts or viral suppression and multivariate analysis for risk factors for virological failure (VF) and immune status after transition. Transition years were classified into 5-year periods.

Results:
Three hundred thirty-two youths were included. The median age at transition was 18 years (interquartile range: 16.3–18.9) and 58.1% women. The median follow-up time after transition was 6.6 years (interquartile range: 4.6–9.8), and 11 patients (3.3%) died. The immunovirological status at transition improved over the last periods. Globally, VF decreased from 27.7% at transition to 14.4% at 3 years post-transition (P < 0.001), but no changes were observed in the last 2 transition periods. There were no significant differences in CD4 over the transition period. Risk factors for VF after transition were female sex, being born abroad and VF at transition, and for lower CD4 after transition were Romani heritage, younger age at transition, lower CD4 nadir, and CD4 at transition.

Conclusions:
After transition, virological suppression improved in the early transition periods, and immunological status remained stable. Nevertheless, some patients had higher risk of worse outcomes. Identifying these patients may aid during transition.
Brief Report: Drug Overdose Deaths Among People With HIV in New York City, 2007–2017
Authors: Braunstein Sarah L. , Robbins Rebekkah S. , Ramaswamy Chitra , Daskalakis Demetre C. 
Published: October 2020

Background:
Preventable deaths, including those because of drug overdose (OD), are a significant public health concern in New York City (NYC). Trends in drug OD death among people with HIV (PWH) in NYC have not been described.

Methods:
We selected PWH from the NYC HIV Registry who died during 2007–2017, resided in NYC at death, and died because of drug OD. We characterized PWH who died of drug OD and analyzed CD4 and viral load tests from surveillance to evaluate retention in care and viral suppression (viral load < 200 cc/mL) in the 12 months before death as markers of care-seeking.

Results:
From 2007 to 2017, 870 NYC PWH died of drug OD. Of the total OD deaths, 821 (94.4%) were classified as accidental and 49 (5.6%) as intentional. Although the rate of OD deaths among PWH declined during the full period, from 58.5 per 100,000 in 2007 to 47.9 per 100,000 in 2017, it increased from 2014 (30.9/100,000) to 2016 (53.3/100,000) and stayed high through 2017 (47.9/100,000). Decedents during 2007–2017 were predominantly men (70.8%), Black (38.0%) or Latino/Hispanic (38.7%), aged 40–59 years (73.2%), and had a history of injection drug use (43.0%). Over 3-quarters (80.1%) of decedents were retained in HIV care in the 12 months preceding death; 45.4% were viral suppression.

Conclusions:
A sizeable number of PWH died of OD during 2007–2017, and OD death rates in recent years increased. Predeath care patterns reveal frequent interaction with the health care system, underscoring missed opportunities for harm-reduction and suicide prevention interventions for PWH.
How sperm competition shapes the evolution of testes and sperm: a meta-analysis
Authors: Lüpold Stefan , de Boer Raïssa A. , Evans Jonathan P. , Tomkins Joseph L. , Fitzpatrick John L. 
Published: October 2020

Females of many species mate with multiple males, thereby inciting competition among ejaculates from rival males for fertilization. In response to increasing sperm competition, males are predicted to enhance their investment in sperm production. This prediction is so widespread that testes size (correcting for body size) is commonly used as a proxy of sperm competition, even in the absence of any other information about a species' reproductive behaviour. By contrast, a debate about whether sperm competition selects for smaller or larger sperm has persisted for nearly three decades, with empirical studies demonstrating every possible response. Here, we synthesize nearly 40 years of sperm competition research in a meta-analytical framework to determine how the evolution of sperm number (i.e. testes size) and sperm size (i.e. sperm head, midpiece, flagellum and total length) is influenced by varying levels of sperm competition across species. Our findings support the long-held assumption that higher levels of sperm competition are associated with relatively larger testes. We also find clear evidence that sperm competition is associated with increases in all components of sperm length. We discuss these results in the context of different theoretical predictions and general patterns in the breeding biology and selective environment of sperm.This article is part of the theme issue ‘Fifty years of sperm competition’.
Imminent risk of predation reduces the relative strength of postcopulatory sexual selection in the guppy
Authors: Glavaschi Alexandra , Cattelan Silvia , Grapputo Alessandro , Pilastro Andrea 
Published: October 2020

Fifty years of research on sperm competition has led to a very good understanding of the interspecific variation in sperm production traits. The reasons why this variation is often very large within populations have been less investigated. We suggest that the interaction between fluctuating environmental conditions and polyandry is a key phenomenon explaining such variation. We focus here on imminent predation risk (IPR). IPR impacts significantly several aspects of prey behaviour and reproduction, and it is expected to influence the operation of sexual selection before and after mating. We estimated the effect of IPR on the male opportunity for pre- and postcopulatory sexual selection in guppies (Poecilia reticulata), a livebearing fish where females prefer colourful males and mate multiply. We used a repeated-measures design, in which males were allowed to mate with different females either under IPR or in a predator-free condition. We found that IPR increased the total opportunity for sexual selection and reduced the relative contribution of postcopulatory sexual selection to male reproductive success. IPR is inherently variable and our results suggest that interspecific reproductive interference by predators may contribute towards maintaining the variation in sperm production within populations.This article is part of the theme issue ‘Fifty years of sperm competition'.
NHS Hospital ‘Learning from Deaths’ reports: A qualitative and quantitative analysis of the first year of a countrywide patient safety programme
Authors: Brummell Zoe , Vindrola-Padros Cecilia , Braun Dorit , Moonesinghe S. Ramani 
Published: October 2020

ABSTRACTIntroductionPotentially preventable deaths occur worldwide within healthcare organisations. Organisational learning from incidents is essential to improve quality of care. In England, inconsistencies in how NHS secondary care trusts reviewed, investigated and shared learning from deaths, resulted in the introduction of national guidance on ‘Learning from Deaths’ (LfDs) in 2017. This guidance provides a ‘framework for identifying, reporting, investigating and learning from deaths’. Amendments to NHS Quality Account regulations, legally require NHS trusts in England to report quantitative and qualitative information relating to patient deaths annually. The programme intended trusts would share this learning and take measurable action to prevent future deaths.MethodWe undertook qualitative and quantitative secondary data analysis of all NHS secondary care trust LfDs reports within their 2017/18 Quality Accounts, to review how organisations are using the LfDs programme to learn from and prevent, potentially preventable deaths.ResultsAll statutory elements of LfDs reporting were reported by 98 out of 222 (44%) trusts. The percentage of deaths judged more likely than not due to problems in healthcare was between 0% and 13%. The majority of trusts (89%) reported lessons learnt; the most common learning theme was poor communication. 106 out of 222 trusts (48%) have shared or plan to share the learning within their own organisation. The majority of trusts (86%) reported actions taken and 47% discussed or had a plan for assessment of impact. 37 out of 222 trusts (17%) mentioned involvement of bereaved families.ConclusionsThe wide variation in reporting demonstrates that some trusts have engaged fully with LfDs, while other trusts appear to have disengaged with the programme. This may reveal a disparity in organisational learning and patient safety culture which could result in inequity for bereaved families. Many themes identified from the LfD reports have previously been identified in national and international reports and inquiries. Further work is needed to strengthen the LfDs programme.
Role of Professionalism in the Policy Response to COVID-19: Does a Public Health or Medical Background Help?
Authors: Li X. , Lai W. , Wan Q. , Chen X. 
Published: October 2020

AbstractLess than 5 percent of Chinese cities had top-ranked officials with public health or medical backgrounds (PHMBGs). Does professionalism improve their response to a public crisis like the COVID-19 pandemic? Collecting résumés of government and Party officials in almost all prefectural Chinese cities, and matching with other data sources, including weather conditions, city characteristics, COVID-19-related policies, and health outcomes, we demonstrate that cities whose top officials had PHMBGs witnessed significantly lower infection rates, and often lower death rates, than cities whose top officials lacked such backgrounds. Mechanism testing suggests that the effects were at least partially explained by more rapid lockdown or community closure. Our findings offer insights into better preparation for future epidemics via improving leadership team composition, particularly recruiting major officials with PHMBGs.One Sentence SummaryCities whose top officials had PHMBGs saw lower infection and death rates, attributable to more rapid decision to lock down and close communities.
CpelTdm.jl: a Julia package for targeted differential DNA methylation analysis
Authors: Abante Jordi , Goutsias John 
Published: October 2020

AbstractMotivationIdentifying regions of the genome that demonstrate significant differences in DNA methylation between groups of samples is an important problem in computational epigenetics. Available methods assume that methylation occurs in a statistically independent manner at individual cytosine-phosphate-guanine (CpG) sites or perform analysis using empirically estimated joint probability distributions of methylation patterns at no more than 4 contiguous CpG sites. These approaches can lead to poor detection performance and loss of reliability and reproducibility due to reduced specificity and sensitivity in the presence of insufficient data.ResultsTo accommodate data obtained with different bisulfite sequencing technologies, such as RRBS, ERRBS, and WGBS, and improve statistical power, we developed CpelTdm.jl, a Julia package for targeted differential analysis of DNA methylation stochasticity between groups of unmatched or matched samples. This package performs rigorous statistical analysis of methylation patterns within regions of the genome specified by the user that takes into account correlations in methylation and results in robust detection of genomic regions exhibiting statistically significant differences in methylation stochasticity. CpelTdm.jl does not only detect mean methylation differences, as it is commonly done by previous methods, but also differences in methylation entropy and, more generally, between probability distributions of methylation.Availability and ImplementationThis Julia package is supported for Windows, MacOS, and Linux, and can be freely downloaded from GitHub:https://github.com/jordiabante/CpelTdm.jl.Contactsjabante1@jhu.eduorgoutsias@jhu.edu.
Genome-wide identification and transcriptional analyses of the R2R3-MYB gene family in wheat
Authors: Xiao Chunsheng , Jia Yong , Watt Calum , Chen Wenshuai , Zhang Yujuan , Li Chengdao 
Published: October 2020

AbstractMYB transcription factors (TFs) represents one of the largest TF families in plants. In this study, we performed genome-wide MYB-domain screening and identified a total of 997 MYBs in wheat(Triticum aestivum),among which 445 were 2-domain MYBs (R2R3-MYBs) that were clustered into 15 subgroups with varied conservation profiles. Homologous genes were highly conserved across the three subgenomes, with minor variations contributed by segmental duplications. Tandem and proximal gene duplications have contributed significantly to the expansion of the wheatMybgene family. Furthermore, comprehensive transcriptome profiling ofR2R3-Mybgenes in 61 different tissue and time point samples revealed a clear pattern of temporal and spatial variations within six expression groups. The comprehensive genomic and transcriptional analyses provided valuable insights into the evolution and biological functions ofR2R3-Mybgenes in wheat. They would serve as a useful guide to further investigate the potential agronomic traits controlled by this large TF family.
Rejection in early life is associated with high and long-lasting stress and higher incidence of infections in owl monkeys
Authors: Osman Mahdiyah , Olkun Aylin , Maldonado Angela M. , Lopez-Tremoleda Jordi , Sanchez-Perea Nofre , Paredes Ursula M. 
Published: October 2020

1.SUMMARYBackgroundThe mothers of owl monkeys sometimes reject their new-borns. When this occurs in captive colonies, the rejected infants are manually raised by veterinarians, allowing them to survive. However, maternal rejection can induce chronic stress, which in turn is associated with infectious diseases. Rescued, rejected owl monkeys might experience high rates of stress and infections which go undetected.MethodologyTo test this hypothesis, we evaluated the connection between maternal rejection, stress and infections in owl monkeys (Aotus nancymaae) from the IVITA Center for Conservation and Reproduction of Primates (UNMSM, Peru). Specifically, we compared the stress rates and frequency of infection treatment in juveniles (19-24 months) rejected in the first month of life and controls. To assess stress, we compared cortisol levels in hair using a competitive ELISA and recorded behaviours using cameras. We analysed past medical treatments and medication to compare incidence of infection treatment in subjects. We then studied the correlation between the frequency of infection treatments and cortisol using a linear regression.ResultsRejected owl monkeys showed significantly higher cortisol levels (p=0.0123), a higher incidence of stereotypical behaviour and overeating (pacing p=0.0159; head twirling p=0.0476, eating p=0.0238) compared to controls. Rejected owl monkeys also received significantly more treatment for infections than controls per month lived (p=0.0009). Moreover, infection rates observed in this population were positively although weakly associated with concentration of cortisol in hair (R2=0.307, p=0.0075).ConclusionMaternal rejection in the first month of life is associated with high and long-lasting stress levels and infections in the IVITA owl monkey colony. IVITA owl monkeys will be a useful model for studying the long-term effects of early life stress at the population level.
Integrating multimeric threading with high-throughput experiments for structural interactome ofEscherichia coli
Authors: Gong Weikang , Guerler Aysam , Zhang Chengxin , Warner Elisa , Li Chunhua , Zhang Yang 
Published: October 2020

AbstractGenome-wide protein-protein interaction (PPI) determination remains a significant unsolved problem in structural biology. The difficulty is twofold since high-throughput experiments (HTEs) have often a high false-positive rate in assigning PPIs, and PPI quaternary structures are more difficult to solve than tertiary structures using traditional structural biology techniques. We proposed a uniform pipeline to address both problems, which first recognizes PPIs by combining multi-chain threading alignments with HTE results using naïve Bayesian classifiers, where the quaternary complex structures are then constructed by mapping the monomer models with the dimeric threading frameworks through interface-specific structural alignments. The pipeline was applied to theEscherichia coligenome and created 35,125 confident PPIs which is 4.5-fold higher than HTE alone. Graphic analyses of the PPI networks revealed a scale-free cluster size distribution, which was found critical to the robustness of genome evolution and the centrality of functionally important proteins that are essential toE. colisurvival. Furthermore, complex structure models were constructed for all predictedE. coliPPIs based on the quaternary threading alignments, where 6,771 of them were found to have a high confidence score that corresponds to the correct fold of the complexes with a TM-score >0.5 and 93 showed a close consistency with the later released experimental structures with an average TM-score=0.73. These results demonstrated the significant usefulness of threading-based homologous modeling in both genome-wide PPI network detection and complex structural construction.
Dynamic task-linked switching between brain networks - A Tri-Network perspective
Authors: Shaw Saurabh Bhaskar , McKinnon Margaret C. , Heisz Jennifer , Becker Suzanna 
Published: October 2020

AbstractThe highly influential tri-network model proposed by Menon integrates 3 key intrinsic brain networks — the central executive network (CEN), salience network (SN), and the default mode network (DMN), into a single cohesive model underlying normal behaviour and cognition. A large body of evidence suggests that abnormal intra- and inter- network connectivity between these three networks underlies the various behavioural and cognitive dysfunctions observed in patients with neuropsychiatric conditions such as PTSD and depression. An important prediction of the tri-network model is that the DMN and CEN networks are anti-correlated under the control of the SN, such that if a task engages one of the two, the SN inhibits the activation of the other. To date most of the evidence surrounding the functions of these three core networks comes from either resting state analyses or in the context of a single task with respect to rest. Few studies have investigated multiple tasks simultaneously or characterized the dynamics of task switching. Hence, a careful investigation of the temporal dynamics of network activity during task switching is warranted. To accomplish this we collected fMRI data from 14 participants that dynamically switched between a 2-back working memory task and an autobiographical memory retrieval task, designed to activate the CEN, DMN and the SN. The fMRI data were used to 1. identify nodes and sub-networks within the three major networks involved in task-linked dynamic network switching, 2. characterize the temporal pattern of activation of these nodes and sub-networks, and finally 3. investigate the causal influence that these nodes and sub-networks exerted on each other. Using a combination of multivariate neuroimaging analyses, timecourse analyses and multivariate Granger causality measures to study the tri-network dynamics, the current study found that the SN co-activates with the task-relevant network, providing a mechanistic insight into SN-mediated network selection in the context of explicit tasks. Our findings also indicate active involvement of the posterior insula and some medial temporal nodes in task-linked functions of the SN and DMN, warranting their inclusion as network nodes in future studies of the tri-network model. These results add to the growing body of evidence showing the complex interplay of CEN, DMN and SN nodes and sub-networks required for adequate task-switching, and characterizes a normative pattern of task-linked network dynamics within the context of Menon’s tri-network model.
Signatures of Selection in CompositeVrindavaniCattle of India
Authors: Singh Akansha , Mehrotra Arnav , Gondro Cedric , da Silva Romero Andrea Renata , Pandey Ashwni Kumar , Karthikeyan A , Bashir Aamir , Mishra B.P. , Dutt Triveni , Kumar Amit 
Published: October 2020

AbstractVrindavaniis an Indian composite cattle breed developed by crossbreeding taurine dairy breeds with native indicine cattle in the 1960s. About 190,000 semen doses ofVrindavanibulls have been distributed to the farmers till date. The animals are under artificial and natural selection for higher milk production and adaptation to the tropical climate, respectively. However, the selection response for production and adaptation traits in theVrindavanigenome is not explored. In this study, we provide the first overview of the selection signatures in theVrindavanigenome. 96Vrindavanicattle were genotyped using the BovineSNP50 BeadChip and the SNP genotype data of its constituent breeds were collected from a public database. Within-breed selection signatures in Vrindavani were investigated using the integrated haplotype score (iHS). Vrindavani was also compared to each of its parental breeds to discover between-population signatures of selection using two approaches, cross-population extended haplotype homozygosity (XP-EHH) and fixation index (FST). Selection of signature identifies 11 common region identified by more than one harbouring genes such asLRP1B,TNNI3K,APOB,CACNA2D1,FAM110B and SPATA17associated with production and adaptation. Overall, our results suggested stronger selective pressure on regions responsible for adaptation compared to milk yield.
A topic modelling analysis of TCGA breast and lung cancer transcriptomic data
Authors: Valle Filippo , Osella Matteo , Caselle Michele 
Published: October 2020

AbstractTopic modelling is a widely used technique to extract relevant information from large arrays of data. The problem of finding a topic structure in a dataset was recently recognized to be analogous to the community detection problem in network theory. Leveraging on this analogy, a new class of topic modelling strategies has been introduced to overcome some of the limitations of classical methods. This paper applies these recent ideas to TCGA transcriptomic data on breast and lung cancer. The established cancer subtype organization is well reconstructed in the inferred latent topic structure. Moreover, we identify specific topics that are enriched in genes known to play a role in the corresponding disease and are strongly related to the survival probability of patients. Finally, we show that a simple neural network classifier operating in the low dimensional topic space is able to predict with high accuracy the cancer subtype of a test expression sample.