bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 aerosol transmission in schools: the effectiveness of different interventions
Authors: Villers Jennifer , Henriques Andre , Calarco Serafina , Rognlien Markus , Mounet Nicolas , Devine James , Azzopardi Gabriella , Elson Philip , Andreini Marco , Tarocco Nicola , Vassella Claudia , Keiser Olivia 
Published: August 2021

AbstractBackgroundIndoor aerosol transmission of SARS-CoV-2 has been widely recognized, especially in schools where children remain in closed indoor spaces and largely unvaccinated. Measures such as strategic natural ventilation and high efficiency particulate air (HEPA) filtration remain poorly implemented and mask mandates are often progressively lifted as vaccination rollout is enhanced.MethodsWe adapted a previously developed aerosol transmission model to study the effect of interventions (natural ventilation, face masks, HEPA filtration, and their combinations) on the concentration of virus particles in a classroom of 160 m3 containing one infectious individual. The cumulative dose of viruses absorbed by exposed occupants was calculated.ResultsThe most effective single intervention was natural ventilation through the full opening of six windows all day during the winter (14-fold decrease in cumulative dose), followed by the universal use of surgical face masks (8-fold decrease). In the spring/summer, natural ventilation was only effective (≥ 2-fold decrease) when windows were fully open all day. In the winter, partly opening two windows all day or fully opening six windows at the end of each class was effective as well (≥ 2-fold decrease). Opening windows during yard and lunch breaks only had minimal effect (≤ 1.2-fold decrease). One HEPA filter was as effective as two windows partly open all day during the winter (2.5-fold decrease) while two filters were more effective (4-fold decrease). Combined interventions (i.e., natural ventilation, masks, and HEPA filtration) were the most effective (≥ 30-fold decrease). Combined interventions remained highly effective in the presence of a super-spreader.ConclusionsNatural ventilation, face masks, and HEPA filtration are effective interventions to reduce SARS-CoV-2 aerosol transmission. These measures should be combined and complemented by additional interventions (e.g., physical distancing, hygiene, testing, contact tracing, and vaccination) to maximize benefit.
Serial interval and transmission dynamics during the SARS-CoV-2 Delta variant predominance in South Korea
Authors: Ryu Sukhyun , Kim Dasom , Lim Jun-Sik , Ali Sheikh Taslim , Cowling Benjamin J. 
Published: August 2021

AbstractWe estimated mean serial interval and superspreading potential for the predominant Delta variant of SARS-CoV-2. Mean serial intervals were similar with 3.7 and 3.5 days during early and latter periods, respectively. Furthermore, the risk of superspreading events was similar with 23% and 25% of cases seeded 80% of all transmissions.
Spinal cord synaptic plasticity by GlyRβ release from receptor fields and syndapin-dependent uptake
Authors: Tröger Jessica , Seemann Eric , Heintzmann Rainer , Kessels Michael M. , Qualmann Britta 
Published: August 2021

AbstractGlycine receptor-mediated inhibitory neurotransmission is key for spinal cord function. Recent observations suggested that by largely elusive mechanisms also glycinergic synapses display synaptic plasticity. We here identify syndapin I as critical player. Interestingly, syndapin I cooperates but in part also competes with gephyrin. Syndapin I deficiency led to fragmentation of glycine receptor fields, more disperse receptors and increased receptor mobility. Kainate treatment highlighted syndapin I’s importance even more. Our analyses unveiled that PKC-mediated S403 phosphorylation-mediated glycine receptor β decoupling from gephyrin scaffolds simultaneously promoted syndapin I association. In line, kainate-treated syndapin I KO spinal cords showed even more severe receptor field fragmentation. Furthermore, syndapin I deficiency completely disrupted kainate-induced glycine receptor internalization. Together, this unveiled important mechanisms controlling the number and organization of glycine receptor fields at inhibitory postsynapses during both steady-state and kainate-induced synaptic rearrangement - principles organizing and fine-tuning synaptic efficacy of inhibitory synapses in the spinal cord.
ReporterSeq reveals genome-wide determinants of proteasome expression
Authors: Work Jeremy J. , Alford Brian D. , Dea Annisa , Ali Asif , Pincus David , Brandman Onn 
Published: August 2021

AbstractThe ubiquitin-proteasome system (UPS) is critical for cellular and organismal health. To uncover mechanisms regulating the UPS in normal and stress conditions, we systematically probed the genome of the eukaryotic model system Saccharomyces cerevisiae for modulators of the UPS master regulator Rpn4 under basal and stress conditions using the reverse genetic method ReporterSeq. The top UPS regulators were the thioredoxin reductase Trr1 and proteins of the large ribosomal subunit, both of which had no previously known role in UPS regulation. Unlike all known mechanisms for Rpn4 regulation which regulate Rpn4 levels, we found that Trr1 modulates the molecular activity of Rpn4 and does so in response to oxidative stress. Our work illuminates the genetic landscape through which cells regulate the UPS, and provides insight into how cells combat proteotoxicity.
The DNA sensors AIM2 and IFI16 are NET-binding SLE autoantigens
Authors: Antiochos Brendan , Fenaroli Paride , Rosenberg Avi , Baer Alan N. , Sohn Jungsan , Li Jessica , Petri Michelle , Goldman Daniel W. , Mecoli Christopher , Casciola-Rosen Livia , Rosen Antony 
Published: August 2021

AbstractNucleic acid binding proteins are frequently targeted as autoantigens in systemic lupus erythematosus (SLE) and other interferon (IFN)-linked rheumatic diseases. The AIM-like receptors (ALRs) are IFN-inducible innate sensors that form supramolecular assemblies along double-stranded DNA of various origins. Here, we identify the ALR Absent in melanoma 2 (AIM2) as a novel autoantigen in SLE, with similar properties to the established ALR autoantigen interferon-inducible protein 16 (IFI16). Our SLE cohort revealed a frequent co-occurrence of anti-AIM2, anti-IFI16 and anti-DNA antibodies, and higher clinical measures of disease activity in patients positive for antibodies against these ALRs. We examined neutrophil extracellular traps (NETs) as DNA scaffolds on which these antigens might interact in a pro-immune context, finding that both ALRs bind NETs in vitro and in SLE renal tissues. We demonstrate that ALR binding causes NETs to resist degradation by DNase I, suggesting a mechanism whereby extracellular ALR-NET interactions may promote sustained IFN signaling. Our work suggests that extracellular ALRs bind NETs, leading to DNase resistant nucleoprotein fibers that are targeted as autoantigens in SLE.
Multi view based imaging genetics analysis on Parkinson disease
Authors: Cerri Guglielmo , Tognon Manuel , Avesani Simone , Oxtoby Neil P. , Altmann Andre , Giugno Rosalba 
Published: August 2021

AbstractLongitudinal studies integrating imaging and genetic data have recently become widespread among bioinformatics researchers. Combining such heterogeneous data allows a better understanding of complex diseases origins and causes. Through a multi-view based workflow proposal, we show the common steps and tools used in imaging genetics analysis, interpolating genotyping, neuroimaging and transcriptomic data. We describe the advantages of existing methods to analyze heterogeneous datasets, using Parkinson’s Disease (PD) as a case study. Parkinson’s disease is associated with both genetic and neuroimaging factors, however such imaging genetics associations are at an early investigation stage. Therefore it is desirable to have a free and open source workflow that integrates different analysis flows in order to recover potential genetic biomarkers in PD, as in other complex diseases.
CNest: A Novel Copy Number Association Discovery Method Uncovers 862 New Associations from 200,629 Whole Exome Sequence Datasets in the UK Biobank
Authors: Fitzgerald Tomas , Birney Ewan 
Published: August 2021

AbstractCopy number variation (CNV) has long been known to influence human traits having a rich history of research into common and rare genetic disease and although CNV is accepted as an important class of genomic variation, progress on copy number (CN) phenotype associations from Next Generation Sequencing data (NGS) has been limited, in part, due to the relative difficulty in CNV detection and an enrichment for large numbers of false positives. To date most successful CN genome wide association studies (CN-GWAS) have focused on using predictive measures of dosage intolerance or gene burden tests to gain sufficient power for detecting CN effects. Here we present a novel method for large scale CN analysis from NGS data generating robust CN estimates and allowing CN-GWAS to be performed genome wide in discovery mode. We provide a detailed analysis in the large scale UK BioBank resource and a specifically designed software package for deriving CN estimates from NGS data that are robust enough to be used for CN-GWAS. We use these methods to perform genome wide CN-GWAS analysis across 78 human traits discovering 862 genetic associations that are likely to contribute strongly to trait distributions based solely on their CN or by acting in concert with other genetic variation. Finally, we undertake an analysis comparing CNV and SNP association signals across the same traits and samples, defining specific CNV association classes based on whether they could be detected using standard SNP-GWAS in the UK Biobank.
Iron oxidation is regulated by the two-component system, RegSR, and plays a role in photolithoheterotrophic growth in Rhodopseudomonas palustris
Authors: Haas Nicholas W. , Jain Abhiney , Hying Zachary , Arif Sabrina J. , Gralnick Jeffrey A. , Fixen Kathryn R. 
Published: August 2021

AbstractPurple nonsulfur bacteria (PNSB) are metabolically versatile organisms generate energy through both aerobic and anaerobic respiration as well as anoxygenic photosynthesis. In many PNSB, the redox-sensing, two-component system RegBA is a global regulator of energy generating and consuming pathways, such as photosynthesis, carbon fixation, and nitrogen fixation, when cells are shifted from an aerobic to an anaerobic environment. However, in the PNSB Rhodopseudomonas palustris, the role of the RegBA homolog, RegSR, was unclear since global regulation of these same pathways involves the oxygen-sensing signal transduction system, FixJL-K, in R. palustris. Using RNA-seq analysis, we found that RegSR plays a role in regulating the operon pioABC, which encodes genes required for Fe(II) oxidation. We found that transcript levels of pioABC under photoheterotrophic conditions was dependent on the oxidation state of the carbon substrate and whether the cells were fixing nitrogen. We also found that R. palustris can carry out photolithoheterotrophic growth using Fe(II) oxidation when grown with the oxidized carbon substrate, malate, requiring regSR and pioABC. We present a model in which RegSR regulates pioABC in response to a cellular redox signal, allowing R. palustris to use Fe(II) oxidation to access more electrons when there is an increased cellular demand for reducing equivalents.SignificanceMixotrophy is thought to be widespread in aquatic environments, yet little is understood about how mixotrophy affects biogeochemical cycles. Fe(II)-oxidizing anoxygenic phototrophs likely play an important role in iron cycling since they are thought to have thrived in the anoxic, iron-rich oceans of early Earth and can be found in both freshwater and marine environments. Although Fe(II) oxidation by anoxygenic phototrophs is largely studied in the context of photoautotrophic growth, these organisms can also grow photoheterotrophically. We present the first evidence linking photolithoheterotrophic growth using Fe(II) to the pathway required for photoautotrophic Fe(II) oxidation in an anoxygenic phototroph. Understanding this metabolism will be important for understanding how mixotrophic metabolism contributes to iron cycling in anoxic environments.
Fatty acid-binding proteins and fatty acid synthase influence glial reactivity and promote the formation of Müller glia-derived progenitor cells in the avian retina
Authors: Campbell Warren A. , Tangeman Allen , El-Hodiri Heithem M. , Hawthorn Evan C. , Hathoot Maddie , Hoang Thanh , Blackshaw Seth , Fischer Andy J. 
Published: August 2021

AbstractThe capacity for retinal regeneration varies greatly across vertebrates species. A recent comparative epigenetic and transcriptomic investigation of Müller glial (MG) in the retinas of fish, birds and mice revealed that Fatty Acid Binding Proteins (FABPs) are among the most highly up-regulated genes in activated chick MG (Hoang et al., 2020). Herein we provide an in-depth follow-up investigation to describe patterns of expression and how FABPs and fatty acid synthase (FASN) influence glial cells in the chick retina. During development, FABP7 is highly expressed by embryonic retinal progenitor cells (eRPCs) and maturing MG, whereas FABP5 is gradually up-regulated in maturing MG and remains elevated in mature glial cells. PMP2 (FABP8) is expressed by oligodendrocytes and FABP5 is expressed by non-astrocytic inner retinal glial cells, and both of these FABPs are significantly up-regulated in activated MG in damaged or growth factor-treated retinas. In addition to suppressing the formation of MGPCs, we find that FABP-inhibition suppressed the accumulation of proliferating microglia, although the microglia appeared highly reactive. scRNA-seq analyses of cells treated with FABP-inhibitor revealed distinct changes in patterns of expression suggesting that FABPs are involved in the transitions of MG from a resting state to a reactive state and conversion from reactive MG to MGPCs. Inhibition of FABPs in undamaged retinas had a significant impact upon the transcriptomic profiles of MG, with up-regulation of genes associated with gliogenesis, decreases in genes associated with neurogenesis, and suppression of the ability of MG to become MGPCs. scRNA-seq analyses of microglia indicated that FABP inhibition enhances gene modules related to reactivity, proliferation and cytokine signaling. We find that the proliferation of retinal progenitors in the circumferential marginal zone (CMZ) is unaffected by FABP-inhibitor. Upstream of FABP activity, we inhibited FASN in damaged retinas, which reduced numbers of dying cells, increased the proliferation of microglia, and potently suppressed the formation MGPCs in damaged retinas. We conclude that the activity of FASN and FABPs are required early during the formation of proliferating MGPCs. Fatty acid metabolism and cell signaling involving fatty acids are important in regulating glial homeostasis in the retina, and the dedifferentiation and proliferation of microglia and MGPCs.
TomatoCRABS CLAWparalogues interact with chromatin remodelling factors to mediate carpel development and floral determinacy
Authors: Castañeda Laura , Giménez Estela , Pineda Benito , García-Sogo Begoña , Ortiz-Atienza Ana , Micol-Ponce Rosa , Angosto Trinidad , Capel Juan , Moreno Vicente , Yuste-Lisbona Fernando J. , Lozano Rafael 
Published: August 2021

AbstractCRABS CLAW(CRC) orthologues play a crucial role in floral meristem (FM) determinacy and gynoecium formation across angiosperms, key developmental processes for ensuring successful plant reproduction and crop production. Here, we revealed that the incomplete penetrance and variable expressivity of the carpel-inside-carpel phenotype observed in flowers of the tomatofruit iterative growth(fig) mutant is due to a lack of function of a homologue of theCRCgene,Solanum lycopersicum CRCa(SlCRCa). Likewise, a comprehensive functional analysis ofSlCRCaandSlCRCbparalogues, including Arabidopsis complementation experiments, allowed us to propose that they operate as positive regulators of FM determinacy by acting in a compensatory and partially redundant manner to safeguard the proper formation of flowers and fruits. Furthermore, we provide the first evidence for the role of putativeCRCorthologues as members of the chromatin remodelling complex that terminates floral stem cell activity by repressingWUSCHELexpression.
Ecological conditions experienced by bat reservoir hosts predict the intensity of Hendra virus excretion over space and time
Authors: Becker Daniel J. , Eby Peggy , Madden Wyatt , Peel Alison J. , Plowright Raina K. 
Published: August 2021

AbstractThe ecological conditions experienced by wildlife reservoir hosts affect the amount of pathogen they excrete into the environment. This then shapes pathogen pressure, the amount of pathogen available to recipient hosts over space and time, which affects spillover risk. Few systems have data on both long-term ecological conditions and pathogen pressure, yet such data are critical for advancing our mechanistic understanding of ecological drivers of spillover risk. To identify these ecological drivers, we here reanalyze shedding data from a spatially replicated, multi-year study of Hendra virus excretion from Australian flying foxes in light of 25 years of long-term data on changing ecology of the bat reservoir hosts. Using generalized additive mixed models, we show that winter virus shedding pulses, previously considered idiosyncratic, are most pronounced after recent food shortages and in bat populations that have been displaced to novel habitats. We next derive the area under each annual shedding curve (representing cumulative virus excretion) and show that pathogen pressure is also affected by the ecological conditions experienced by bat populations. Finally, we illustrate that pathogen pressure positively predicts observed spillover frequency. Our study suggests that recent ecological conditions of flying fox hosts are shifting the timing, magnitude, and cumulative intensity of Hendra virus shedding in ways that shape the landscape of spillover risk. This work provides a mechanistic approach to understanding and estimating risk of spillover from reservoir hosts in complex ecological systems and emphasizes the importance of host ecological context in identifying the determinants of pathogen shedding.
Single-cell transcriptomic assessment of cellular phenotype stability in human precision-cut lung slices
Authors: Winters Nichelle I. , Taylor Chase J. , Jetter Christopher S. , Camarata Jane E. , Gutierrez Austin J. , Bui Linh T. , Gokey Jason J. , Bacchetta Matthew , Banovich Nicholas E. , Sucre Jennifer M.S. , Kropski Jonathan A. 
Published: August 2021

ABSTRACTPrecision-cut lung slices (PCLS) are increasingly utilized for ex vivo disease modeling, but a high-resolution characterization of cellular phenotype stability in PCLS has not been reported. Comparing the single-cell transcriptomic profile of human PCLS after five days of culture to freshly isolated human lung tissue, we found striking changes in endothelial cell and alveolar epithelial cell programs, reflecting both injury and pathways activated in static culture, while immune cell frequencies and programs remained largely intact and similar to the native lung. These cellular dynamics should be considered when utilizing PCLS as a model of the human lung.
Cellulose synthase-like D (CSLD) proteins move in the plasma membrane and their targeting to cell tips, but not cell plates, depends on the actin cytoskeleton
Authors: Wu Shu-Zon , Chaves Arielle M. , Li Rongrong , Bezanilla Magdalena , Roberts Alison W. 
Published: August 2021

AbstractCellulose Synthase-Like D (CSLD) proteins are implicated in cell wall remodeling during tip growth and cell division in plants, and are known to generate β-1,4-glucan. It is unknown whether they form complexes and move in the plasma membrane like members of the Cellulose Synthase (CESA) family. We used the genetically tractable moss Physcomitrium patens, which has a filamentous protonemal stage that undergoes both tip growth and cell division and is amenable to high resolution live cell imaging, to investigate CSLD function and intracellular trafficking. CSLD2 and CSLD6 are highly expressed in gametophores and are redundantly required for gametophore cellular patterning. Live cell imaging revealed that CSLD6 is also expressed in protonemata where it moves in the plasma membrane and localizes to cell plates and cell tips. Notably, delivery to the apical plasma membrane, but not the cell plate, depends on actin. By comparing the behavior of endogenously tagged CSLD6 and CESA10, we discovered that CSLD6 movements in the plasma membrane were significantly faster, shorter in duration and less linear than CESA10 movements and were insensitive to the cellulose synthesis inhibitor isoxaben. These data suggest that CSLD6 and CESA10 function within different structures and may thus produce structurally distinct cellulose microfibrils.
Assessment of Carbon Sequestration Potential of some Selected Urban Tree Species
Authors: Ajayi Ezekiel 
Published: August 2021

AbstractTree species carbon assessment and quantification remain the only opportunity to determine the position of forest in climate change amelioration potentials. Forest biomass constitutes the largest terrestrial carbon sink and accounts for approximately 90% of all living terrestrial biomass. The aim of this study is to assess tree species carbon sequestration potentials of selected urban tree species. The study was carried out in Adekunle Ajasin University Campus, Akungba Akoko, Ondo State, Nigeria. All trees species ≥10 cm Diameter at Breast Height (Dbh) within the area were identified and their Dbh measured as well as other variables for volume computation such as height, diameters at the base, middle and top. Also, for density assessment; stem core samples were collected. Again, the coordinate of individual tree was recorded using a Global Positioning System (GPS) receiver. A total of 124 individual trees were encountered with varying growth variables as well as carbon values. The study area contains some indigenous and exotic tree species such asAcacia auriculiformis, Terminalia mantily, Gmelina arboreaandTectona grandisetc. butAcacia auriculiformishad the highest frequency. The tree species with highest carbon sequestration wasGmelina arboreaas recorded for this study. The total carbon and carbon dioxide sequestered in the study area were reported as 47.94 kg and 176.03 kg respectively.