bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene co-expression network analysis identifies BEH3 as a stabilizer of secondary vascular development in Arabidopsis
Authors: Furuya Tomoyuki , Saito Masato , Uchimura Haruka , Satake Akiko , Nosaki Shohei , Miyakawa Takuya , Shimadzu Shunji , Yamori Wataru , Tanokura Masaru , Fukuda Hiroo , Kondo Yuki 
Published: May 2021

Abstract
In plants, vascular stem cells located in the cambium continuously undergo self-renewal and differentiation during secondary growth. Recent advancements in cell sorting techniques have enabled access to the transcriptional regulatory framework of cambial cells. However, mechanisms underlying the robust control of vascular stem cells remain unclear. Here, we identified a new cambium-related regulatory module through co-expression network analysis using multiple transcriptome datasets obtained from an ectopic vascular cell transdifferentiation system using Arabidopsis cotyledons, Vascular cell Induction culture System Using Arabidopsis Leaves (VISUAL). The cambium gene list included a gene encoding the transcription factor BES1/BZR1 Homolog 3 (BEH3), whose homolog BES1 negatively affects vascular stem cell maintenance. Interestingly, null beh3 mutant alleles showed a large variation in their vascular size, indicating that BEH3 functions as a stabilizer of vascular stem cells. Genetic analysis revealed that BEH3 and BES1 perform opposite functions in the regulation of vascular stem cells and the differentiation of vascular cells in the context of the VISUAL system. At the biochemical level, BEH3 showed weak transcriptional repressor activity and functioned antagonistically to other BES/BZR members by competing for binding to the brassinosteroid response element. Furthermore, mathematical modeling suggested that the competitive relationship between BES/BZR homologs leads to the robust regulation of vascular stem cells.
Phosphorylation of WRKY16 by MPK3-1 is essential for its transcriptional activity during fiber initiation and elongation in cotton (Gossypium hirsutum)
Authors: Wang Na-Na , Li Yang , Chen Yi-Hao , Lu Rui , Zhou Li , Wang Yao , Zheng Yong , Li Xue-Bao 
Published: May 2021

Abstract
Cotton, one of the most important crops in the world, produces natural fiber materials for the textile industry. WRKY transcription factors play important roles in plant development and stress responses. However, little is known about whether and how WRKY transcription factors regulate fiber development of cotton so far. In this study, we show that a fiber-preferential WRKY transcription factor, GhWRKY16, positively regulates fiber initiation and elongation. GhWRKY16-silenced transgenic cotton displayed a remarkably reduced number of fiber protrusions on the ovule and shorter fibers compared to the wild-type. During early fiber development, GhWRKY16 directly binds to the promoters of GhHOX3, GhMYB109, GhCesA6D-D11, and GhMYB25 to induce their expression, thereby promoting fiber initiation and elongation. Moreover, GhWRKY16 is phosphorylated by the mitogen-activated protein kinase GhMPK3-1 at residues T-130 and S-260. Phosphorylated GhWRKY16 directly activates the transcription of GhMYB25, GhHOX3, GhMYB109, and GhCesA6D-D11 for early fiber development. Thus, our data demonstrate that GhWRKY16 plays a crucial role in fiber initiation and elongation, and that GhWRKY16 phosphorylation by GhMPK3-1 is essential for the transcriptional activation on downstream genes during the fiber development of cotton.
How Much Does Size Erode Mutual Fund Performance? A Regression Discontinuity Approach
Authors: Reuter Jonathan , Zitzewitz Eric 
Published: May 2021

Abstract
The level of diseconomies of scale in asset management has important implications for tests of manager skill and the expected level of performance persistence. To identify the causal impact of fund size on future returns, we exploit the fact that small differences in returns can cause discrete changes in Morningstar ratings that, in turn, generate discrete differences in fund size. Using our regression discontinuity approach, we find that ratings significantly increase fund size, but that fund size has a negligible effect on fund returns. Within Berk and Green’s (2004) model, the absence of meaningful fund-level diseconomies of scale implies that the lack of performance persistence arises from a lack of fund manager skill. Alternatively, the lack of performance persistence may arise from competitive pressures outside of their model.
Changes of evening exposure to electronic devices during the COVID-19 lockdown affect the time course of sleep disturbances
Authors: Salfi Federico , Amicucci Giulia , Corigliano Domenico , D’Atri Aurora , Viselli Lorenzo , Tempesta Daniela , Ferrara Michele 
Published: May 2021

AbstractStudy ObjectivesDuring the coronavirus disease 2019 (COVID-19) lockdown, there was a worldwide increase in electronic devices’ daily usage. Prolonged exposure to backlit screens before sleep influences the circadian system leading to negative consequences on sleep health. We investigated the relationship between changes in evening screen exposure and the time course of sleep disturbances during the home confinement period due to COVID-19.Methods2,123 Italians (mean age ± standard deviation, 33.1 ± 11.6) were tested longitudinally during the third and the seventh week of lockdown. The web-based survey evaluated sleep quality and insomnia symptoms through the Pittsburgh Sleep Quality Index and the Insomnia Severity Index. The second assessment survey inquired about intervening changes in backlit screen exposure in the two hours before falling asleep.ResultsParticipants who increased electronic device usage showed decreased sleep quality, exacerbated insomnia symptoms, reduced sleep duration, prolonged sleep onset latency, and delayed bedtime and rising time. In this subgroup, the prevalence of poor sleepers and individuals reporting moderate/severe insomnia symptoms increased. Conversely, respondents reporting decreased screen exposure exhibited improved sleep quality and insomnia symptoms. In this subgroup, the prevalence of poor sleepers and moderate/severe insomniacs decreased. Respondents preserving screen time habits did not show variations of the sleep parameters.ConclusionsOur investigation demonstrated a strong relationship between modifications of evening electronic device usage and time course of sleep disturbances during the lockdown period. Monitoring the potential impact of excessive evening exposure to backlit screens on sleep health is recommendable during the current period of restraining measures due to COVID-19.
A systematic review of psychosocial interventions for Latinx and American Indian patient-family caregiver dyads coping with chronic health conditions
Authors: McCarthy Michael J , Sanchez Angelica , Garcia Y Evie , Bakas Tamilyn 
Published: May 2021

Abstract
Latinx and American Indians experience high rates of chronic health conditions. Family members play a significant role as informal caregivers for loved ones with chronic conditions and both patients and family caregivers report poor psychosocial outcomes. This systematic review synthesizes published studies about psychosocial interventions for Latinx and American Indian care dyads to determine: (i) the benefits of these interventions; (ii) their distinguishing features or adaptations, and; (iii) recommendations for future intervention development. Out of 366 records identified, seven studies met inclusion criteria. Interventions demonstrated benefits to outcomes such as disease knowledge, caregiver self-efficacy and burden, patient and caregiver well-being, symptom distress, anxiety and depression, and dyadic communication. Distinguishing features included tailoring to cultural values, beliefs, and delivery preferences, participants’ level of acculturation, and population-specific issues such as migratory stressors and support networks. Based upon this review, six recommendations for future intervention development are put forth.
COVID-19 exposure and diagnosis among college student drinkers: links to alcohol use behavior, motives, and context
Authors: Allen Hannah K , Cohen-Winans Samantha , Armstrong Kaitlyn , Clark Nash C , Ford M Allison 
Published: May 2021

Abstract
The COVID-19 pandemic is a public health crisis. College student alcohol use is highly prevalent and primarily occurs in social settings where risk for COVID-19 transmission is heightened. This study explored the associations between alcohol use frequency, quantity, motives, and context with: (i) quarantine due to COVID-19 exposure and (ii) a positive diagnosis for COVID-19. A sample of n = 409 college student drinkers completed an online survey about their health and behaviors during the Fall 2020 semester. Since the start of the semester, 36% of students quarantined and 13% of students received a COVID-19 diagnosis. More frequent alcohol use was associated with increased odds of both quarantine and COVID-19 diagnosis. More frequent drinking for social motives was associated with increased likelihood of quarantine, and more frequent drinking for conformity motives was associated with increased likelihood of COVID-19 diagnosis. Participants who often drank alone or with a small group of friends were about half as likely to have quarantined, while those who often drank with a large group of friends were almost twice as likely to have quarantined. Participants who often drank in a bar or nightclub had almost three times the odds of a COVID-19 diagnosis. Frequent alcohol use and drinking for social and conformity motives and in certain contexts are linked to increased likelihood of COVID-19 exposure and diagnosis. Alcohol use prevention efforts, coupled with messaging to discourage large social gatherings in public places, might help to mitigate the spread of COVID-19 among college students.
Novel next-generation sequencing-based methodologies to characterize the mutational consequences of (prenatal) chemotherapy exposure in noncancerous tissue
Authors: Struys Ilana , Lenaerts Liesbeth , Thienpont Bernard , Amant Frédéric 
Published: May 2021

Purpose of review
Although chemotherapeutics are considered as genotoxins for decades, their exact mutagenic impact on the genome of cancerous and normal cells of cancer patients was unknown for a long time. However, this knowledge is necessary to understand the long-term side effects of chemotherapy. A particular condition represents pregnant cancer patients being treated with chemotherapy. Since certain chemotherapeutics can cross the placenta, concerns exist about possible mutational effects on the fetus’ genome with potential long-term health consequences.

Recent findings
Recent advances of next-generation sequencing (NGS) techniques have opened possibilities to explore the exact mutational footprint of chemotherapies in healthy tissue from treated cancer patients. However, the ultra-low frequency of chemotherapy-induced mutations, introduction of technical artefacts, and inaccessibility of normal tissue has posed important limitations. This review discusses five state-of-the-art approaches that were recently designed to overcome these drawbacks.

Summary
Results of the latest investigations give valuable insights into the genome-wide genotoxicity profile of frequently applied chemotherapies, with most of these drugs being associated with a signature of random base substitutions and small indels. Though these findings still might be limited to extrapolate to healthy tissue, they pave the way for studies on the origin of long-term chemotherapy-related adverse health effects.
Emergence of a new SARS-CoV-2 variant from GR clade with a novel S glycoprotein mutation V1230L in West Bengal, India
Authors: Sarkar Rakesh , Saha Ritubrita , Mallick Pratik , Sharma Ranjana , Kaur Amandeep , Dutta Shanta , Chawla-Sarkar Mamta 
Published: May 2021

AbstractIndia is currently facing the devastating second wave of COVID-19 pandemic resulting in approximately 4000 deaths per day. To control this pandemic continuous mutational surveillance and genomic epidemiology of circulating strains is very important. In this study, we performed mutational analysis of the protein coding genes of SARS-CoV-2 strains (n=2000) collected during January 2021 to March 2021. Our data revealed the emergence of a new variant in West Bengal, India, which is characterized by the presence of 11 co-existing mutations including D614G, P681H and V1230L in S-glycoprotein. This new variant was identified in 70 out of 412 sequences submitted from West Bengal. Interestingly, among these 70 sequences, 16 sequences also harbored E484K in the S glycoprotein. Phylogenetic analysis revealed strains of this new variant emerged from GR clade (B.1.1) and formed a new cluster. We propose to name this variant as GRL or lineage B.1.1/S:V1230L due to the presence of V1230L in S glycoprotein along with GR clade specific mutations. Co-occurrence of P681H, previously observed in UK variant, and E484K, previously observed in South African variant and California variant, demonstrates the convergent evolution of SARS-CoV-2 mutation. V1230L, present within the transmembrane domain of S2 subunit of S glycoprotein, has not yet been reported from any country. Substitution of valine with more hydrophobic amino acid leucine at position 1230 of the transmembrane domain, having role in S protein binding to the viral envelope, could strengthen the interaction of S protein with the viral envelope and also increase the deposition of S protein to the viral envelope, and thus positively regulate virus infection. P618H and E484K mutation have already been demonstrated in favor of increased infectivity and immune invasion respectively. Therefore, the new variant having G614G, P618H, P1230L and E484K is expected to have better infectivity, transmissibility and immune invasion characteristics, which may pose additional threat along with B.1.617 in the ongoing COVID-19 pandemic in India.
Does immune recognition of SARS-CoV2 epitopes vary between different ethnic groups?
Authors: Bose Tungadri , Pant Namrata , Pinna Nishal Kumar , Bhar Subhrajit , Dutta Anirban , Mande Sharmila S. 
Published: May 2021

AbstractThe SARS-CoV2 mediated Covid-19 pandemic has impacted humankind at an unprecedented scale. While substantial research efforts have focused towards understand the mechanisms of viral infection and developing vaccines/ therapeutics, factors affecting the susceptibility to SARS-CoV2 infection and manifestation of Covid-19 remain less explored. Given that the Human Leukocyte Antigen (HLA) system is known to vary among ethnic populations, it is likely to affect the recognition of the virus, and in turn, the susceptibility to Covid-19. To understand this, we used bioinformatic tools to probe all SARS-CoV2 peptides which could elicit T-cell response in humans. We also tried to answer the intriguing question of whether these potential epitopes were equally immunogenic across ethnicities, by studying the distribution of HLA alleles among different populations and their share of cognate epitopes. We provide evidence that the newer mutations in SARS-CoV2 are unlikely to alter the T-cell mediated immunogenic responses among the studied ethnic populations. The work presented herein is expected to bolster our understanding of the pandemic, by providing insights into differential immunological response of ethnic populations to the virus as well as by gauging the possible effects of mutations in SARS-CoV2 on efficacy of potential epitope-based vaccines through evaluating ∼40000 viral genomes.
Feasibility and utility of rapid antigen testing for COVID-19 in a university residence: a cross sectional study
Authors: Wong Sabrina T. , Romney Marc , Matic Nancy , Haase Kristen , Ranger Manon , Dhari Ranjit , Affleck Frances , Tan Elsie , Ndateba Innocent , Tobias Erica , Saewyc Elizabeth , Schwandt Michael , Sin Don 
Published: May 2021

AbstractImportanceUnderstanding feasibility of rapid testing in congregate living setting provides critical data to reduce the risk of outbreaks in these settings.ObjectiveUse rapid antigen screening to detect SARS-CoV-2 in an asymptomatic group of university students and staff.DesignCross-sectionalSettingUniversity of British Columbia, Vancouver, Canada.ParticipantsStudents and staff living or working in congregate housing.InterventionHealth care professional administered rapid antigen testMain Outcomes and measuresUse of BD Veritor rapid antigen testing and asymptomatic participants’ experiences with rapid testingResultsA total of 3536 BD Veritor tests were completed in 1141 unique individuals. One third of participants completed between two to four tests and 21% were screened five or more times. The mean number of tests completed per person was three. The mean length of time between those who had more than one test was seven days. There were eight false positives and 25 PCR confirmed COVID-19 positive individuals identified through this work. All individuals reported having no symptoms that they attributed to COVID-19. Almost all (n=22, 88%) COVID-19 positive cases were found in male participants. A total of 86 additional students from multiple different student residences (n=9) were asked to self-isolate while they waited for their COVID-19 diagnostic test results. An average of seven additional students positive for COVID-19 living in congregate housing were identified through contact tracing by finding one positive case.Conclusions and relevanceRapid testing is a relatively inexpensive and operationally easy method of identifying asymptomatic individuals with COVID-19.
Identification of evolutionary trajectories shared across human betacoronaviruses
Authors: Escalera-Zamudio Marina , Kosakovsky Pond Sergei L. , de la Viña Natalia Martínez , Gutiérrez Bernardo , Inward Rhys P. D. , Thézé Julien , van Dorp Lucy , Castelán-Sánchez Hugo G. , Bowden Thomas A. , Pybus Oliver G. , Hulswit Ruben J.G. 
Published: May 2021

ABSTRACTComparing the evolution of distantly related viruses can provide insights into common adaptive processes related to shared ecological niches. Phylogenetic approaches, coupled with other molecular evolution tools, can help identify mutations informative on adaptation, whilst the structural contextualization of these to functional sites of proteins may help gain insight into their biological properties. Two zoonotic betacoronaviruses capable of sustained human-to-human transmission have caused pandemics in recent times (SARS-CoV-1 and SARS-CoV-2), whilst a third virus (MERS-CoV) is responsible for sporadic outbreaks linked to animal infections. Moreover, two other betacoronaviruses have circulated endemically in humans for decades (HKU1 and OC43). To search for evidence of adaptive convergence between established and emerging betacoronaviruses capable of sustained human-to-human transmission (HKU1, OC43, SARS-CoV-1 and SARS-CoV-2), we developed a methodological pipeline to classify shared non-synonymous mutations as putatively denoting homoplasy (repeated mutations that do not share direct common ancestry) or stepwise evolution (sequential mutations leading towards a novel genotype). In parallel, we look for evidence of positive selection, and draw upon protein structure data to identify potential biological implications. We find 30 mutations, with four of these [codon sites 18121 (nsp14/residue 28), 21623 (spike/21), 21635 (spike/25) and 23948 (spike/796); SARS-CoV-2 genome numbering] displaying evolution under positive selection and proximity to functional protein regions. Our findings shed light on potential mechanisms underlying betacoronavirus adaptation to the human host and pinpoint common mutational pathways that may occur during establishment of human endemicity.
Species-specific deployment of Runx2 isoforms and differential regulation of target genes during avian jaw development and evolution
Authors: Smith Spenser S. , Chu Daniel B. , Qu Tiange , Huang Tiffany , Lucena Austen J. , Krish Goutam , Schneider Richard A. 
Published: May 2021

ABSTRACTDevelopmental regulation of bone formation in the jaw skeleton is essential to species-specific adaptation. The jaws are derived from neural crest mesenchyme (NCM), a progenitor population that directs skeletal patterning by exerting temporal and spatial control over molecular and cellular programs for osteogenesis. One important NCM-mediated gene isRunx2, which is a transcription factor required for osteoblast differentiation. RUNX2 protein binds many target genes involved in the deposition and resorption of bone. To determine the extent to which changes inRunx2structure, function, and expression underlie the evolution of the jaw skeleton, we compareRunx2across vertebrates and within birds.Runx2contains two alternative promoters, tandem repeats of glutamine and alanine with variable lengths in different species, a conserved DNA-binding domain, an exon that is alternatively spliced, as well as two possible C-termini. Such alternative splicing produces eight potential isoforms that show distinct stage- and species-specific patterns in the jaw primordia of chick, quail and duck embryos. We also find that certain isoforms are strongly induced by TGFβ signaling whereas others are not. OverexpressingRunx2isoforms in NCM reveals that some are transcriptionally activating, while others are repressive. But context appears to be relevant since species-specific polymorphisms in the promoter of target genes likeMmp13, can modulate the effects of different isoforms. Overall, our study indicates that the structure and species-specific deployment ofRunx2isoforms affect the transcriptional activity of target genes in ways that may have played a generative and regulatory role in the evolution of the avian jaw skeleton.
Rhizobiales commensal bacteria promoteArabidopsis thalianaroot growth via host sulfated peptide pathway
Authors: Hucklenbroich Jana , Gigolashvili Tamara , Koprivova Anna , Spohr Philipp , Chegini Mahnaz Nezamivand , Klau Gunnar W. , Kopriva Stanislav , Nakano Ryohei Thomas 
Published: May 2021

AbstractRoot-associated commensal bacteria that belong to the order Rhizobiales, which also contains symbiotic and pathogenic bacteria, promote primary root growth ofArabidopsis thaliana.However, the molecular mechanism underlying this root growth promotion (RGP) activity remained unclear. Here, we conducted a transcriptomic analysis ofA. thalianaroots inoculated with root-associated commensal bacteria of Rhizobiales and sister lineages and revealed common and strain/lineage-specific transcriptional response, possibly mediated by WRKY and ANAC family of transcription factors. We showed that the observed common response was also partly triggered by a wide range of non-pathogenic bacteria, fungi, and a multikingdom synthetic community (SynCom). This response was characterized by a down-regulation of genes related to intracellular redox regulation, suggesting distinctive redox status between pathogenic and non-pathogenic interactions. By integrating with developmental and cell biological experiments, we identified a crucial role of TYROSYLPROTEIN SULFOTRANSFERASE (TPST) in Rhizobiales RGP. Conversely, none of the known TPST-dependent sulfated peptide pathways appeared to be required for this activity, suggesting an unidentified component in the protein sulfation pathway targeted by Rhizobiales RGP. Finally, we show that TPST is needed for RGP exerted by Rhizobiales but not Pseudomonadales isolates, delineating lineage-specific mechanisms to manipulate host root development.