bluuebunny/crossref_metadata_2025_split huggingface dataset:
Health-related quality of life of female sex workers living with HIV in South Africa: a cross-sectional study
Authors: Wang Linwei , Dowdy David W. , Comins Carly A. , Young Katherine , Mcingana Mfezi , Mulumba Ntambue , Mhlophe Hlengiwe , Chen Claire , Hausler Harry , Schwartz Sheree R. , Baral Stefan , Mishra Sharmistha 
Published: June 2021

ABSTRACTIntroductionHealth-related quality of life (HRQoL) is an important HIV outcome beyond viral suppression. However, there are limited data characterizing HRQoL of key populations including female sex workers (FSW) living with HIV.MethodsWe used baseline data (June 22, 2018-March 23, 2020) of FSW who were diagnosed with HIV and enrolled into a randomized trial in Durban, South Africa. HRQoL information was collected by a generic preference-accompanied tool with five domains (EQ-5D), and summarized into a single score (range 0-1) which represents health utility. We employed multivariable beta regression models to identify determinants of HRQoL and to estimate subgroup-specific HRQoL score. Using external estimates of life expectancy and population size, we estimated the number of quality adjusted life years reduced among FSW living with HIV in South Africa associated with violence and drug use.ResultsOf 1363 individuals (mean age: 32.4 years; mean HRQoL score: 0.857) in our analysis, 62.6% used drugs, 61.3% experienced physical or sexual violence, and 64.6% self-reported taking antiretroviral treatment (ART). The following were associated with a reduction in the average marginal HRQoL score: older age (per decade: 0.018 [95% confidence interval (CI): 0.008, 0.027]), drug use (0.022 [0.007, 0.036]), experience of violence (0.024 [0.010, 0.038]), and moderate (vs. no) level of internalized stigma (0.023 [0.004, 0.041]). Current ART use was associated with a 0.015-point (−0.001, 0.031) increase in the HRQoL score. The estimated mean (95%CI) HRQoL scores ranged from 0.838 (0.816, 0.860) for FSW who used drugs, experienced violence, and were not on ART; to 0.899 (0.883, 0.916) for FSW who did not use drugs nor experience violence and were on ART. Our results can be translated into a reduction in 37,184 and 39,722 quality adjusted life years related to drug use and experience of violence, respectively in South Africa.ConclusionsThese results demonstrate the association of ART with higher HRQoL among FSW and the need to further address structural risks including drug use, violence, and stigma. Population-specific estimates of HRQoL score can be further used to calculate quality-adjusted life years in economic evaluations of individual and structural interventions addressing the needs of FSW living with HIV.Clinical Trial RegistrationNCT03500172 (April 17, 2018)
Prevalence of dysphagia in patients with multiple sclerosis; a systematic review and meta-analysis
Authors: Mirmosayyeb Omid , Ebrahimi Narges , Shekarian Arman , Bagherieh Sara , Afshari-Safavi Alireza , Shaygannejad Vahid , Barzegar Mahdi 
Published: June 2021

AbstractObjectivesDysphagia is a major comorbidity observed in patients with multiple sclerosis, yet different prevalence rates are reported for it. Therefore, we have designed this systematic review to estimate the pooled prevalence of dysphagia in patients with MS.MethodWe searched PubMed, Scopus, EMBASE, Web of Science, and gray literature including references from the identified studies, reviews studies, and conference abstracts which were published up to February 2021. Articles that were relevant to our topic and could provide information regarding the prevalence of dysphagia among MS patients were included; however, articles with self-report screening strategies were excluded.ResultsThe literature search found 1993 articles. After eliminating duplicates, 1272 articles remained. Sixteen abstract conference papers were included for final analysis. A total of 10846 MS cases and 4913 MS patients with dysphagia included in the analysis. The pooled prevalence of dysphagia in the included studies was 45.3% (95% CI: [40.7%-50%])ConclusionThe results of this systematic review shows that the prevalence of dysphagia in MS patients is 45% which is greatly higher compared to the general population.
Mapping Potential Antigenic Drift Sites (PADS) on SARS-CoV-2 Spike in Continuous Epitope-Paratope Space
Authors: Miller Nathaniel L. , Clark Thomas , Raman Rahul , Sasisekharan Ram 
Published: June 2021

AbstractSARS-CoV-2 mutations with antigenic effects pose a risk to immunity developed through vaccination and natural infection. While vaccine updates for current variants of concern (VOCs) are underway, it is likewise important to prepare for further antigenic mutations as the virus navigates the heterogeneous global landscape of host immunity. Toward this end, a wealth of data and tools exist that can augment existing genetic surveillance of VOC evolution. In this study, we integrate published datasets describing genetic, structural, and functional constraints on mutation along with computational analyses of antibody-spike co-crystal structures to identify a set of potential antigenic drift sites (PADS) within the receptor binding domain (RBD) and N-terminal domain (NTD) of SARS-CoV-2 spike protein. Further, we project the PADS set into a continuous epitope-paratope space to facilitate interpretation of the degree to which newly observed mutations might be antigenically synergistic with existing VOC mutations, and this representation suggests that functionally convergent and synergistic antigenic mutations are accruing across VOC NTDs. The PADS set and synergy visualization serve as a reference as new mutations are detected on VOCs, enable proactive investigation of potentially synergistic mutations, and offer guidance to antibody and vaccine design efforts.Graphical Abstract
Conservation and diversity in transcriptional responses among host plants forming distinct arbuscular mycorrhizal morphotypes
Authors: Tominaga Takaya , Miura Chihiro , Sumigawa Yuuka , Hirose Yukine , Yamaguchi Katsushi , Shigenobu Shuji , Mine Akira , Kaminaka Hironori 
Published: June 2021

SummaryThe morphotype of arbuscular mycorrhizal (AM) roots is distinct mostly depending on AM host species:Arum,Paris, and Intermediate types. We previously reported that gibberellin (GA) promotes the establishment ofParis-type AM symbiosis inEustoma grandiflorumdespite its negative effects onArum-type AM symbiosis in model plants. However, the molecular mechanisms underlying the differential effects of GA on different morphotypes, including Intermediate-type AM symbiosis, remain elusive.Comparative transcriptomics revealed that several symbiosis-related genes were transcriptionally promoted upon AM fungal colonization inLotus japonicus(Arum-type),Daucus carota(Intermediate-type), andE. grandiflorum(Paris-type). Interestingly, upon GA treatment, the fungal colonization levels and expression of symbiosis-related genes were suppressed inL. japonicusandD. carotabut were promoted inE. grandiflorum.Exogenous GA transcriptionally inhibited the biosynthetic process of a host-derived signal molecule involved in AM symbiosis, strigolactone, inL. japonicusandE. grandiflorum. Additionally, disaccharides mainly metabolized in AM roots would be different betweenL. japonicusandD. carota/E. grandiflorum.This study uncovered the conserved transcriptional responses during mycorrhization and diverse responses to GA in AM roots with distinct morphotypes among phylogenetically distant host plants.
NanoDam identifies novel temporal transcription factors conserved between the Drosophila central brain and visual system
Authors: Tang Jocelyn L.Y. , Hakes Anna E. , Krautz Robert , Suzuki Takumi , Contreras Esteban G. , Fox Paul M. , Brand Andrea H. 
Published: June 2021

SummaryTemporal patterning of neural progenitors is an evolutionarily conserved strategy for generating neuronal diversity. Type II neural stem cells in the Drosophila central brain produce transit-amplifying intermediate neural progenitors (INPs) that exhibit temporal patterning. However, the known temporal factors cannot account for the neuronal diversity in the adult brain. To search for new temporal factors, we developed NanoDam, which enables rapid genome-wide profiling of endogenously-tagged proteins in vivo with a single genetic cross. Mapping the targets of known temporal transcription factors with NanoDam identified Homeobrain and Scarecrow (ARX and NKX2.1 orthologues) as novel temporal factors. We show that Homeobrain and Scarecrow define middle-aged and late INP temporal windows and play a role in cellular longevity. Strikingly, Homeobrain and Scarecrow have conserved functions as temporal factors in the developing visual system. NanoDam enables rapid cell type-specific genome-wide profiling with temporal resolution and can be easily adapted for use in higher organisms.
Core and indicative bacterial and fungal taxa define characteristic soil communities of arable land, grassland, and forest
Authors: Florian Gschwend , Martin Hartmann , Johanna Mayerhofer , Anna Hug , Jürg Enkerli , Andreas Gubler , Meuli Reto G. , Beat Frey , Franco Widmer 
Published: June 2021

AbstractSoil microbial diversity has major influences on ecosystem functions and services. However, due to its complexity and uneven distribution of abundant and rare taxa, quantification of soil microbial diversity remains challenging and thereby impeding its integration into long-term monitoring programs. Using metabarcoding, we analyzed soil bacterial and fungal communities over five years at thirty long-term soil monitoring sites from the three land-use types, arable land, permanent grassland, and forest. Unlike soil microbial biomass and alpha-diversity, microbial community compositions and structures were site- and land-use-specific with CAP reclassification success rates of 100%. The temporally stable site core communities included 38.5% of bacterial and 33.1% of fungal OTUs covering 95.9% and 93.2% of relative abundances. We characterized bacterial and fungal core communities and their land-use associations at the family-level. In general, fungal families revealed stronger land-use type associations as compared to bacteria. This is likely due to a stronger vegetation effect on fungal core taxa, while bacterial core taxa were stronger related to soil properties. The assessment of core communities can be used to form cultivation-independent reference lists of microbial taxa, which may facilitate the development of microbial indicators for soil quality and the use of soil microbiota for long-term soil biomonitoring.
Bidirectional cooperation between Ubtf1 and SL1 determines RNA Polymerase I promoter recognition in cell and is negatively affected in the UBTF-E210K neuroregression syndrome
Authors: Tremblay Michel G. , Sibai Dany S. , Valère Melissa , Mars Jean-Clément , Lessard Frédéric , Hori Roderick T. , Khan Mohammad M. , Stefanovsky Victor Y. , Ledoux Mark S. , Moss Tom 
Published: June 2021

ABSTRACTTranscription of the ∼200 mouse and human ribosomal RNA genes (rDNA) by RNA Polymerase I (RPI/PolR1) accounts for 80% of total cellular RNA, around 35% of all nuclear RNA synthesis, and determines the cytoplasmic ribosome complement. It is therefore a major factor controlling cell growth and its misfunction has been implicated in hypertrophic and developmental disorders. Activation of each rDNA repeat requires nucleosome replacement by the architectural multi-HMGbox factor UBTF to create a 15kbp nucleosome free region (NFR). Formation of this NFR is also essential for recruitment of the TBP-TAFI factor SL1 and for preinitiation complex (PIC) formation at the gene and enhancer-associated promoters of the rDNA. However, these promoters show little sequence commonality and neither UBTF nor SL1 display significant DNA sequence binding specificity, making what drives PIC formation a mystery. Here we show that cooperation between SL1 and the longer UBTF1 splice variant generates the specificity required for rDNA promoter recognition in cell. We find that conditional deletion of the Taf1b subunit of SL1 causes a striking depletion UBTF at both rDNA promoters but not elsewhere across the rDNA. We also find that while both UBTF1 and −2 variants bind throughout the rDNA NFR, only UBTF1 is present with SL1 at the promoters. The data strongly suggest an induced-fit model of RPI promoter recognition in which UBTF1 plays an architectural role. Interestingly, a recurrent UBTF-E210K mutation and the cause of a pediatric neurodegeneration syndrome provides indirect support for this model. E210K knock-in cells show enhanced levels of the UBTF1 splice variant and a concomitant increase in active rDNA copies. In contrast, they also display reduced rDNA transcription and promoter recruitment of SL1. We suggest the underlying cause of the UBTF-E210K syndrome is therefore a reduction in cooperative UBTF1-SL1 promoter recruitment that may be partially compensated by enhanced rDNA activation.
Loss of SET1/COMPASS methyltransferase activity reduces lifespan and fertility in Caenorhabditis elegans
Authors: Caron Matthieu , Gely Loïc , Garvis Steven , Adrait Annie , Couté Yohann , Palladino Francesca , Fabrizio Paola 
Published: June 2021

AbstractPost-translational modification of histones, particularly lysine methylation, are thought to play a crucial role in the aging process. Histone 3 lysine 4 (H3K4) methylation, a modification associated with active chromatin, is mediated by a family of SET1 methyltransferases acting within conserved multiprotein complexes known as COMPASS. Previous work in model organisms with partial or complete deletion of COMPASS subunits has yielded conflicting results about the requirement for H3K4 methylation during aging. Here, we reassessed the role of SET1/COMPASS-dependent H3K4 methylation in Caenorhabditis elegans lifespan regulation and fertility by generating set-2(syb2085) mutant animals that express a catalytically inactive form of SET-2, the C. elegans homolog of SET1. We show that animals bearing catalytically inactive SET-2 retain the ability to form COMPASS complexes but have a marked global loss of H3K4 dimethylation and trimethylation. Consistent with previous work, reduced H3K4 methylation was accompanied by loss of fertility; however, in striking contrast to earlier studies, set-2(syb2085) mutants displayed a significantly shortened, not extended, lifespan and had normal intestinal fat stores. Furthermore, other commonly used set-2 mutants were also short-lived, as was a cfp-1 mutant that lacks a non-catalytic SET1/COMPASS component and displays reduced H3K4 methylation. These results challenge previously held views and establish that wild-type H3K4 methylation levels are necessary to achieve a normal lifespan in C. elegans.
The payoffs and tradeoffs of hygienic behavior: A large-scale field study on a local population of honey bees
Authors: Seltzer Rya , Kahanov Paz , Kamer Yosef , Hetzroni Amots , Bieńkowska Małgorzata , Hefetz Abraham , Soroker Victoria 
Published: June 2021

AbstractHoney bees (Apis mellifera) are exposed to a variety of risk factors, but the ectoparasitic mite Varroa destructor and its associated viruses are considered to be the most significant problem worldwide. It has been widely recognized that honey bee stocks resistant to the mites are an essential part of any sustainable long-term management of Varroa. The aim of this study was to evaluate the efficacy of hygienic behavior in a local population of honey bees in order to reduce Varroa infestation. A bi-directional selection for high and low rates of hygienic behavior was carried out in Israel using either queen artificially inseminated or naturally mated. Colonies were screened for performance: population size, honey production, control of Varroa infestation, and the level of hygienic behavior. Furthermore, we examined the costs and benefits of selection using measurements of colony performance. Either way, selected lines should be tested for trade-offs and benefits to ensure their productivity. The selection process revealed that the trait is heritable. Maternal phenotype has a significant effect on Varroa load, as colonies founded by hygienic daughter queens showed a significantly lower parasite load. No major trade-offs were found between the rate of hygienic behavior, honey yield, and population size. Measuring the direct benefits of hygienic behavior through colony performance suggests that breeding for this trait makes bees more resistant to Varroa destructor. These results are promising for our successful local bee breeding programs in a Mediterranean climate.
Structural Variation and Polysaccharide Profiling of Intervessel Pit Membranes
Authors: Sun Qiang 
Published: June 2021

AbstractFunctional roles of intervessel pit membrane (PM) depend on its structure and polysaccharide composition, which are mostly unknown or lack of accurate information. This study uses grapevine as a model plant and an immunogold-scanning electron microscopy technique to simultaneously analyze structures and polysaccharide compositions of intervessel PMs in relation to their functions. Intervessel PMs with different structural integrity were found in functional xylem with about 90 % of them being intact with a smooth or relatively smooth surface and the rest 10 % with progressively degraded structures. The results also elucidated details of the removal process of wall materials from surface toward its depth during the natural intervessel PM degradation. Four groups of pectic and hemicellulosic polysaccharides were present in intervessel PMs but displayed differential spatial distributions and quantities: weakly methyl-esterified homogalacturonans abundant in the surficial layers, heavily methyl-esterified homogalacturonans and xylans mostly in deep layers, and fucosylated xyloglucans relatively uniform in presence at different depths of an intervessel PM. This information is crucial to reveal the polysaccharide profiling of primary cell wall and to understand intervessel PM’s roles in the safety and regulation of water transport as well as the plant susceptibility to vascular diseases.
Myofibroblast differentiation is governed by adhesion mechanics, and inhibition of Talin2 reverses lung and kidney fibrosis
Authors: White Michael JV , Ozkan Melis , Gomez Medellin Jorge Emiliano , Solanki Ani , Hubbell Jeffrey A 
Published: June 2021

AbstractFibrosis is involved in 45% of deaths in the United States, and no treatment exists to reverse progression of the disease. In order to find novel targets for fibrosis therapeutics, we developed a model for the differentiation of monocytes to myofibroblasts that allowed us to screen for proteins involved in myofibroblast differentiation. Inhibition of a novel protein target generated by our model, talin2, reduces myofibroblast morphology, α-smooth muscle actin content, collagen I content, and lowers the pro-fibrotic secretome of myofibroblasts. We find that knockdown of talin2 de-differentiates myofibroblasts, talin2 knockdown reverses bleomycin-induced lung fibrosis in mice, and Tln2 -/-mice are resistant to unilateral ureteral obstruction-induced kidney fibrosis and are resistant to bleomycin-induced lung fibrosis. Talin2 inhibition is a potential treatment for reversing lung and kidney fibroses.One Sentence SummarySilencing the stress sensor Talin2 reverses myofibroblast differentiation and existing fibrosis.
Hippocampal ripples signal contextually-mediated episodic recall
Authors: Sakon John J. , Kahana Michael J. 
Published: June 2021

High-frequency oscillatory events, termed ripples, represent synchrony of neural activity in the brain. Recent evidence suggests medial temporal lobe (MTL) ripples support memory retrieval. However, it is unclear if ripples signal the reinstatement of episodic memories. Analyzing electrophysiological MTL recordings from 219 neurosurgical participants performing episodic recall tasks, we find that the rate of hippocampal ripples rises just prior to the free recall of recently-formed memories. This pre-recall ripple effect (PRE) is stronger in the CA1 and dentate gyrus (DG) subfields of hippocampus than neighboring MTL regions entorhinal and parahippocampal cortex. The PRE is also stronger prior to the retrieval of temporally and semantically clustered as compared with unclustered recalls, indicating the involvement of ripples in contextual reinstatement, which is a hallmark of episodic memory.One sentence summaryHigh frequency human hippocampal ripples occur prior to those memories most likely retrieved via episodic mechanisms.
Bacterial gasdermins reveal an ancient mechanism of cell death
Authors: Johnson Alex G. , Wein Tanita , Mayer Megan L. , Duncan-Lowey Brianna , Yirmiya Erez , Oppenheimer-Shaanan Yaara , Amitai Gil , Sorek Rotem , Kranzusch Philip J. 
Published: June 2021

AbstractGasdermin proteins form large membrane pores in human cells that release immune cytokines and induce lytic cell death. Gasdermin pore formation is triggered by caspase-mediated cleavage during inflammasome signaling and is critical for defense against pathogens and cancer. Here we discover gasdermin homologs encoded in bacteria that execute prokaryotic cell death. Structures of bacterial gasdermins reveal a conserved pore-forming domain that is stabilized in the inactive state with a buried lipid modification. We demonstrate that bacterial gasdermins are activated by dedicated caspase-like proteases that catalyze site-specific cleavage and removal of an inhibitory C-terminal peptide. Release of autoinhibition induces the assembly of >200 Å pores that form a mesh-like structure and disrupt membrane integrity. These results demonstrate that caspase-mediated activation of gasdermins is an ancient form of regulated cell death shared between bacteria and animals.
Assessing student success in a Peer Assisted Learning program using propensity score matching
Authors: Shanbrom Corey , Norris Michelle , Esgana Caitlin , Krauel Matthew , Pigno Vincent , Lundmark Jennifer 
Published: June 2021

AbstractThe Peer Assisted Learning program at Sacramento State University (PAL) was established in 2012 with one section supporting introductory chemistry. It now serves 17 gatekeeper courses in Biology, Chemistry, Mathematics, Physics, and Statistics, enrolling approximately 1,400 students annually. Adapting the Peer-Led Team Learning model, PAL Facilitators do not teach, tutor, or even confirm answers; they do ask scaffolding questions, provide encouragement, and ensure that all group members participate in problem-solving. Here we assess the efficacy of the program in terms of student success in the parent course. As PAL is an opt-in program, we employ propensity score matching techniques to account for confounding factors. Our analysis of 11 classes shows that PAL provides an average course GPA bump ranging from .23 to .71 grade points (mean .42). Compared to the non-PAL baseline course GPA, this amounts to an increase of 9% to 51% (mean 23%). We consider data from over 25,000 students, and our propensity score analysis uses over 10,000 students (4,519 PAL, 5,814 non-PAL) for whom appropriate matches could be found.