bluuebunny/crossref_metadata_2025_split huggingface dataset:
Studying models of balancing selection using phase-type theory
Authors: Zeng Kai , Charlesworth Brian , Hobolth Asger 
Published: April 2021

AbstractBalancing selection (BLS) is the evolutionary force that maintains high levels of genetic variability in many important genes. To further our understanding of its evolutionary significance, we analyze models with BLS acting on a biallelic locus: an equilibrium model with long-term BLS, a model with long-term BLS and recent changes in population size, and a model of recent BLS. Using phase-type theory, a mathematical tool for analyzing continuous time Markov chains with an absorbing state, we examine how BLS affects polymorphism patterns in linked neutral regions, as summarized by nucleotide diversity, the expected number of segregating sites, the site frequency spectrum, and the level of linkage disequilibrium (LD). Long-term BLS affects polymorphism patterns in a relatively small genomic neighborhood, and such selection targets are easier to detect when the equilibrium frequencies of the selected variants are close to 50%, or when there has been a population size reduction. For a new mutation subject to BLS, its initial increase in frequency in the population causes linked neutral regions to have reduced diversity, an excess of both high and low frequency derived variants, and elevated LD with the selected locus. These patterns are similar to those produced by selective sweeps, but the effects of recent BLS are weaker. Nonetheless, compared to selective sweeps, nonequilibrium polymorphism and LD patterns persist for a much longer period under recent BLS, which may increase the chance of detecting such selection targets. An R package for analyzing these models, among others (e.g., isolation with migration), is available.
Social Participation in Widowhood: Evidence From a 12-Year Panel
Authors: Lim-Soh Jeremy W 
Published: April 2021

Abstract

Objectives
Social participation is important to the quality of life of older adults, especially widows. This is the first study to test whether older widows’ formal and informal social participation rises or declines using multiple panel observations pre- and postbereavement. This article also tests the moderating effects of economic and marital satisfaction, depression, and husband’s illness before death on these trends.

Methods
Seven waves of the Korean Longitudinal Study of Ageing are used to track changes in 4 measures of social participation—meeting and contacting a child, meeting friends, and attending a formal group. A comparison group of married individuals, weighted with coarsened exact matching, controls for age and time trends. Mixed model regressions estimate the effects of widowhood over time.

Results
Social participation shows little change before bereavement and rises significantly after bereavement for all measures. However, frequencies of meeting and contacting a child peak and decline early postbereavement, while meeting friends and attending a group show delayed but long-lasting effects. With regard to moderators, economic and marital satisfaction are positively associated with overall social participation levels but negatively associated with social participation postbereavement.

Discussion
Increased social participation after bereavement underscores the resilience of widows and the social support they receive. However, differences in timing suggest that contact with children is gradually substituted with extrafamilial relationships in the long run. The negative moderating roles of economic and marital satisfaction point to a paradox where seemingly well-off individuals may be more vulnerable to widowhood.
Women as ‘new security actors’ in preventing and countering violent extremism in Mali
Authors: Lorentzen Jenny 
Published: April 2021

Abstract
The frames of counterterrorism and countering violent extremism are increasingly shaping much international engagement in Mali. In this environment, women's contributions are often reduced to their peacemaking potential. This article studies how the UN policy agendas on Women, Peace and Security (WPS) and Preventing and Countering Violent Extremism (P/CVE) are translated in discourses on P/CVE in Mali. It draws on feminist and postcolonial scholarship to develop a framework for analysing how local intermediaries in norm translation engage in ‘discursive practices of re-presentation’ and conducts a discourse analysis of interviews with Malian civil society and government representatives. The analysis finds that a re-presentation of women as security actors, constructed as an extension of their roles as peacemakers, dominates the discourse. I use the term ‘new security actors’ to describe the dominant re-presentation of women that emerges in this context: a woman who will contribute to preventing radicalization and violent extremism by influencing, counselling, and/or informing on her family or community members. ‘New security actors’, however, emerges as a problematic re-presentation of women which emphasizes traditional gender roles and potentially exposes women to risks, and in many ways seem to contradict much of the normative aspirations of the WPS agenda.
How the clinical research community responded to the COVID-19 pandemic: an analysis of the COVID-19 clinical studies in ClinicalTrials.gov
Authors: He Zhe , Erdengasileng Arslan , Luo Xiao , Xing Aiwen , Charness Neil , Bian Jiang 
Published: April 2021

Abstract

Objective
In the past few months, a large number of clinical studies on the novel coronavirus disease (COVID-19) have been initiated worldwide to find effective therapeutics, vaccines, and preventive strategies for COVID-19. In this study, we aim to understand the landscape of COVID-19 clinical research and identify the issues that may cause recruitment difficulty or reduce study generalizability.

Methods
We analyzed 3765 COVID-19 studies registered in the largest public registry—ClinicalTrials.gov, leveraging natural language processing (NLP) and using descriptive, association, and clustering analyses. We first characterized COVID-19 studies by study features such as phase and tested intervention. We then took a deep dive and analyzed their eligibility criteria to understand whether these studies: (1) considered the reported underlying health conditions that may lead to severe illnesses, and (2) excluded older adults, either explicitly or implicitly, which may reduce the generalizability of these studies to the older adults population.

Results
Our analysis included 2295 interventional studies and 1470 observational studies. Most trials did not explicitly exclude older adults with common chronic conditions. However, known risk factors such as diabetes and hypertension were considered by less than 5% of trials based on their trial description. Pregnant women were excluded by 34.9% of the studies.

Conclusions
Most COVID-19 clinical studies included both genders and older adults. However, risk factors such as diabetes, hypertension, and pregnancy were under-represented, likely skewing the population that was sampled. A careful examination of existing COVID-19 studies can inform future COVID-19 trial design towards balanced internal validity and generalizability.
Dietary fiber in a low-protein diet during gestation affects nitrogen excretion in primiparous gilts, with possible influences from the gut microbiota
Authors: Yang Min , Mao Zhengyu , Jiang Xuemei , Cozannet Pierre , Che Lianqiang , Xu Shengyu , Lin Yan , Fang Zhengfeng , Feng Bin , Wang Jianping , Li Jian , Wu De , Zhuo Yong 
Published: April 2021

AbstractWe investigated the effects of dietary fiber (DF) supplementation in normal or low crude protein (CP) diets on reproductive performance and nitrogen (N) utilization in primiparous gilts. In total, 77 Landrace × Yorkshire pregnant gilts were randomly allocated to four dietary treatments in a 2 × 2 factorial design. The groups comprised 1) equal intake of normal CP (12.82% and 0.61% total lysine), 2) low CP (LP) (10.53% and 0.61% total lysine), and 3) with or 4) without DF supplementation (cellulose, inulin, and pectin in a 34:10:1 ratio). A low-protein diet during gestation significantly reduced daily weight gain from days 91 to 110 of pregnancy (−162.5 g/d, P = 0.004). From N balance trials conducted at days 35 to 38, 65 to 68, and 95 to 98 of pregnancy, DF addition increased fecal N excretion at days 65 to 68 (+24.1%) and 95 to 98 (+13.8%) of pregnancy (P &lt; 0.05) but reduced urinary N excretion (P &lt; 0.05), resulting in greater N retention at each gestational stage. DF increased fecal microbial protein levels and excretion during gestation. An LP diet also reduced urinary N excretion at different gestational stages. An in vitro fermentation trial on culture media with nonprotein N urea and ammonium bicarbonate (NH4HCO3) as the only N sources revealed that microbiota derived from feces of gestating gilts fed the high DF diet exhibited a greater capacity to convert nonprotein N to microbial protein. Microbial fecal diversity, as measured by 16S rRNA sequencing, revealed significant changes from DF but not CP diets. Gilts fed an LP diet had a higher number of stillbirths (+0.83 per litter, P = 0.046) and a lower piglet birth weight (1.52 vs. 1.37 kg, P = 0.006), regardless of DF levels. Collectively, DF supplementation to gestation diets shifted N excretion from urine to feces in the form of microbial protein, suggesting that the microbiota had a putative role in controlling N utilization from DF. Additionally, a low-protein diet during gestation negatively affected the litter performance of gilts.
What Causes the Most Stress in Breast Radiology Practice? A Survey of Members of the Society of Breast Imaging
Authors: Parikh Jay R , Sun Jia , Mainiero Martha B 
Published: April 2021

Abstract

Objective
The objective of this study is to determine the major stressors affecting practicing breast radiologists.

Methods
All members of the Society of Breast Imaging within the United States received an email invitation to complete an anonymous survey evaluating stressors that may contribute to physician burnout. Stressors evaluated included pace at work, work–life balance, care of dependents, job security, financial strain, decreasing reimbursement, new regulations, delivering bad news, fear of getting sued, and dealing with difficult patients, radiologists, and administrators.

Results
The overall response rate was 13.5% (312/2308). For those who opened the email, response rate was 24.6% (312/1269). The most prevalent stressors reported were working too fast (222/312, 71.2%), balancing demands of work with personal life (209/312, 70.0%), fear of getting sued (164/312, 52.6%), and dealing with difficult administrators (156/312, 50%). Prevalence of stress related to new regulation requirements, job security, financial strain, decreased reimbursement, dependent care, call, delivering bad news, and dealing with difficult patients, difficult referrers, and difficult radiologists were present in fewer than 50% of respondents.

Conclusion
The most prevalent sources of stress in breast imaging radiologists relate to working too fast and balancing demands of work with time needed for personal life.
ParapanopeDe Man, 1895 (Decapoda: Brachyura: Pilumnoidea: Galenidae): revisited and revised, with descriptions of two new species
Authors: Ng Peter K L , Guinot Danièle 
Published: April 2021

AbstractThe taxonomy of the pilumnoid genus ParapanopeDe Man, 1895 is revisited and two new species are recognised. With a better series of specimens, more differences between the type species, P. euagoraDe Man, 1895 (from Java), and the morphologically similar P. hextii (Alcock, 1898) (from India) are documented. Specimens previously identified as P. euagora from China, Japan, and Korea are here referred to a new species, P. orientalisn. sp.; while others from Malaysia previously assigned to P. cultripes (Alcock, 1898) are here regarded as P. parvan. sp.Parapanope hextii is recorded from Malaysia, Singapore, and Brunei for the first time, while P. siamensis is a new record for China. The identity of the poorly known P. pagenstecheri (Neumann, 1878) from India and its possible conspecificity with P. hextii also discussed. A key to the eight species of Parapanope now recognised is also presented.
Insecticide Resistance Patterns and Mechanisms in Aedes aegypti (Diptera: Culicidae) Populations Across Abidjan, Côte d’Ivoire Reveal Emergent Pyrethroid Resistance
Authors: Konan Lucien Yao , Oumbouke Welbeck Achille , Silué Urbain Garhapié , Coulibaly Ibrahima Zanakoungo , Ziogba Jean-Claude Tokou , N’Guessan Raphael Kouassi , Coulibaly Daouda , Bénié Joseph Bi Vroh , Lenhart Audrey 
Published: April 2021

Abstract
From 2008 to 2017, the city of Abidjan, Côte d’Ivoire experienced several Aedes-borne disease epidemics which required control of the vector mosquito population based on the reduction of larval habitats and insecticidal sprays for adult mosquitoes. This study was undertaken to assess the insecticide susceptibility status of Aedes aegypti (Linnaeus) in the city of Abidjan. Immature Ae. aegypti were sampled from several larval habitats within seven communes of Abidjan and reared to adults. Three to five days old F1 emerged adults were tested for susceptibility using insecticide-impregnated papers and the synergist piperonyl butoxide (PBO) following WHO bioassay guidelines. The results showed that Ae. aegypti populations from Abidjan were resistant to 0.1% propoxur, and 1% fenitrothion, with mortality rates ranging from 0% to 54.2%. Reduced susceptibility (93.4–97.5% mortality) was observed to 0.05% deltamethrin, 0.75% permethrin, 0.05% lambda-cyhalothrin, 5% malathion, and 0.8% chlorpyrifos-methyl. This reduced susceptibility varied depending on the insecticide and the collection site. The restoration of mortality when the mosquitoes were pre-exposed to the synergist PBO suggests that increased activity of oxidases could be contributing to resistance. Three kdr mutations (V410L, V1016I, and F1534C) were present in populations tested, with low frequencies for the Leu410 (0.28) and Ile1016 (0.32) alleles and high frequencies for the Cys1534 allele (0.96). These findings will be used to inform future arbovirus vector control activities in Abidjan.
LipidSuite: interactive web server for lipidomics differential and enrichment analysis
Authors: Mohamed Ahmed , Hill Michelle M 
Published: April 2021

Abstract
Advances in mass spectrometry enabled high throughput profiling of lipids but differential analysis and biological interpretation of lipidomics datasets remains challenging. To overcome this barrier, we present LipidSuite, an end-to-end differential lipidomics data analysis server. LipidSuite offers a step-by-step workflow for preprocessing, exploration, differential analysis and enrichment analysis of untargeted and targeted lipidomics. Three lipidomics data formats are accepted for upload: mwTab file from Metabolomics Workbench, Skyline CSV Export, and a numerical matrix. Experimental variables to be used in analysis are uploaded in a separate file. Conventional lipid names are automatically parsed to enable lipid class and chain length analyses. Users can interactively explore data, choose subsets based on sample types or lipid classes or characteristics, and conduct univariate, multivariate and unsupervised analyses. For complex experimental designs and clinical cohorts, LipidSuite offers confounding variables adjustment. Finally, data tables and plots can be both interactively viewed or downloaded for publication or reports. Overall, we anticipate this free, user-friendly webserver to facilitate differential lipidomics data analysis and re-analysis, and fully harness biological interpretation from lipidomics datasets. LipidSuite is freely available at http://suite.lipidr.org.
OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions
Authors: Chen Shengquan , Liu Qiao , Cui Xuejian , Feng Zhanying , Li Chunquan , Wang Xiaowo , Zhang Xuegong , Wang Yong , Jiang Rui 
Published: April 2021

Abstract
Chromatin accessibility, as a powerful marker of active DNA regulatory elements, provides valuable information for understanding regulatory mechanisms. The revolution in high-throughput methods has accumulated massive chromatin accessibility profiles in public repositories. Nevertheless, utilization of these data is hampered by cumbersome collection, time-consuming processing, and manual chromatin accessibility (openness) annotation of genomic regions. To fill this gap, we developed OpenAnnotate (http://health.tsinghua.edu.cn/openannotate/) as the first web server for efficiently annotating openness of massive genomic regions across various biosample types, tissues, and biological systems. In addition to the annotation resource from 2729 comprehensive profiles of 614 biosample types of human and mouse, OpenAnnotate provides user-friendly functionalities, ultra-efficient calculation, real-time browsing, intuitive visualization, and elaborate application notebooks. We show its unique advantages compared to existing databases and toolkits by effectively revealing cell type-specificity, identifying regulatory elements and 3D chromatin contacts, deciphering gene functional relationships, inferring functions of transcription factors, and unprecedentedly promoting single-cell data analyses. We anticipate OpenAnnotate will provide a promising avenue for researchers to construct a more holistic perspective to understand regulatory mechanisms.
A termination-independent role of Rat1 in cotranscriptional splicing
Authors: Dhoondia Zuzer , Elewa Hesham , Malik Marva , Arif Zahidur , Pique-Regi Roger , Ansari Athar 
Published: April 2021

Abstract
Rat1 is a 5′→3′ exoribonuclease in budding yeast. It is a highly conserved protein with homologs being present in fission yeast, flies, worms, mice and humans. Rat1 and its human homolog Xrn2 have been implicated in multiple nuclear processes. Here we report a novel role of Rat1 in mRNA splicing. We observed an increase in the level of unspliced transcripts in mutants of Rat1. Accumulation of unspliced transcripts was not due to the surveillance role of Rat1 in degrading unspliced mRNA, or an indirect effect of Rat1 function in termination of transcription or on the level of splicing factors in the cell, or due to an increased elongation rate in Rat1 mutants. ChIP-Seq analysis revealed Rat1 crosslinking to the introns of a subset of yeast genes. Mass spectrometry and coimmunoprecipitation revealed an interaction of Rat1 with the Clf1, Isy1, Yju2, Prp43 and Sub2 splicing factors. Furthermore, recruitment of splicing factors on the intron was compromised in the Rat1 mutant. Based on these findings we propose that Rat1 has a novel role in splicing of mRNA in budding yeast. Rat1, however, is not a general splicing factor as it crosslinks to only long introns with an average length of 400 nucleotides.
The N
6-methyladenosine RNA-binding protein YTHDF1 modulates the translation of TRAF6 to mediate the intestinal immune response
Authors: Zong Xin , Xiao Xiao , Shen Bin , Jiang Qin , Wang Hong , Lu Zeqing , Wang Fengqin , Jin Mingliang , Min Junxia , Wang Fudi , Wang Yizhen 
Published: April 2021

Abstract
The intestinal invasion of pathogenic microorganisms can have serious health consequences. Recent evidence has shown that the N6-methyladenosine (m6A) mRNA modification is closely associated with innate immunity; however, the underlying mechanism is poorly understood. Here, we examined the function and mechanism of m6A mRNA modification and the YTH domain-containing protein YTHDF1 (YTH N6-methyladenosine RNA-binding protein 1) in the innate immune response against bacterial pathogens in the intestine. Ribo-seq and m6A-seq analyses revealed that YTHDF1 directs the translation of Traf6 mRNA, which encodes tumor necrosis factor receptor-associated factor 6, thereby regulating the immune response via the m6A modification near the transcript's stop codon. Furthermore, we identified a unique mechanism by which the P/Q/N-rich domain in YTHDF1 interacts with the DEAD domain in the host factor DDX60, thereby regulating the intestinal immune response to bacterial infection by recognizing the target Traf6 transcript. These results provide novel insights into the mechanism by which YTHDF1 recognizes its target and reveal YTHDF1 as an important driver of the intestinal immune response, opening new avenues for developing therapeutic strategies designed to modulate the intestinal immune response to bacterial infection.
Future climate change will impact the size and location of breeding and wintering areas of migratory thrushes in South America
Authors: Da Silveira Natália Stefanini , Vancine Maurício Humberto , Jahn Alex E , Pizo Marco Aurélio , Sobral-Souza Thadeu 
Published: April 2021

AbstractBird migration patterns are changing worldwide due to current global climate changes. Addressing the effects of such changes on the migration of birds in South America is particularly challenging because the details about how birds migrate within the Neotropics are generally not well understood. Here, we aim to infer the potential effects of future climate change on breeding and wintering areas of birds that migrate within South America by estimating the size and elevations of their future breeding and wintering areas. We used occurrence data from species distribution databases (VertNet and GBIF), published studies, and eBird for 3 thrush species (Turdidae; Turdus nigriceps, T. subalaris, and T. flavipes) that breed and winter in different regions of South America and built ecological niche models using ensemble forecasting approaches to infer current and future potential distributions throughout the breeding and wintering periods of each species. Our findings point to future shifts in wintering and breeding areas, mainly through elevational and longitudinal changes. Future breeding areas for T. nigriceps, which migrates along the Andes Mountains, will be displaced to the west, while breeding displacements to the east are expected for the other 2 species. An overall loss in the size of future wintering areas was also supported for 2 of the species, especially for T. subalaris, but an increase is anticipated for T. flavipes. Our results suggest that future climate change in South America will require that species shift their breeding and wintering areas to higher elevations in addition to changes in their latitudes and longitude. Our findings are the first to show how future climate change may affect migratory birds in South America throughout the year and suggest that even closely related migratory birds in South America will be affected in different ways, depending on the regions where they breed and overwinter.
Vaccine responses in ageing and chronic viral infection
Authors: Rees-Spear Chloe , McCoy Laura E 
Published: April 2021

Abstract
Over the last few decades, changing population demographics have shown that there are a growing number of individuals living past the age of 60. With this expanding older population comes an increase in individuals that are more susceptible to chronic illness and disease. An important part of maintaining health in this population is through prophylactic vaccination, however, there is growing evidence that vaccines may be less effective in the elderly. Furthermore, with the success of anti-viral therapies, chronic infections such as HIV are becoming increasingly prevalent in older populations and present a relatively unstudied population with respect to the efficacy of vaccination. Here we will examine the evidence for age-associated reduction in antibody and cellular responsiveness to a variety of common vaccines and investigate the underlying causes attributed to this phenomenon, such as inflammation and senescence. We will also discuss the impact of chronic viral infections on immune responses in both young and elderly patients, particularly those living with HIV, and how this affects vaccinations in these populations.