bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 related messaging, beliefs, information sources, and mitigation behaviors in Virginia: A cross-sectional survey in the summer of 2020
Authors: Silverman Rachel A. , Short Danielle , Wenzel Sophie , Friesen Mary Ann , Cook Natalie E. 
Published: August 2021

AbstractConflicting messages and misinformation related to the coronavirus (COVID-19) pandemic (SARS-CoV-2) have hindered mitigation efforts. To gain insight and inform effective evidence-based public health messaging, we distributed an online cross-sectional survey from May to July, 2020. Among 3,488 respondents, systematic differences were observed in information sources that people trust, events that impacted beliefs and behaviors, and how behaviors changed by socio-demographics, political identity, and geography within Virginia. Characteristics significantly associated (p<0.05) with not wearing a mask in public included identifying as non-Hispanic white, men, Republican, younger age, lower income, not trusting national science and health organizations, believing a non-evidence-based messages, and Southwest Virginia in logistic regression. Similar, lesser in magnitude correlations, were observed for distancing in public. This study can assist decision makers and the public to improve and effectively target public health messaging related to the ongoing COVID-19 pandemic and future public health challenges in Virginia and similar jurisdictions.
Photoreceptor layer thinning is an early biomarker for age-related macular degeneration development: Epidemiological and genetic evidence from UK Biobank optical coherence tomography data
Authors: Zekavat Seyedeh Maryam , Sekimitsu Sayuri , Ye Yixuan , Raghu Vineet , Zhao Hongyu , Elze Tobias , Segrè Ayellet V. , Wiggs Janey L. , Natarajan Pradeep , Priore Lucian Del , Zebardast Nazlee , Wang Jay C. 
Published: August 2021

AbstractIntroductionAge-related macular degeneration (AMD) is a blinding condition for which there is currently no early-stage clinical biomarker. AMD is characterized by thinning of the outer retina and drusen formation leading to thickening of the Bruch’s membrane and RPE complex, but the timing between these two events, as well as the role of genetic variants in these processes, are unclear. Here, we jointly analyzed genomic, electronic health record, and optical coherence tomography (OCT) data across 44,823 individuals from the UK Biobank to characterize the epidemiological and genetic associations between retinal layer thicknesses and AMD.MethodsThe Topcon Advanced Boundary Segmentation algorithm was used for automated retinal layer segmentation. We associated 9 retinal layer thicknesses with prevalent AMD (present at enrollment) in a logistic regression model, and with incident AMD (diagnosed after enrollment) in a Cox proportional hazards model. Next, we tested the association of AMD-associated genetic alleles, individually and as a polygenic risk score (PRS), with retinal layer thicknesses. All analyses were adjusted for age, age2, sex, smoking status, and principal components of ancestry.ResultsPhotoreceptor segment (PS) thinning was observed throughout the lifespan of individuals analyzed and accelerated at age 45, while retinal pigment epithelium and Bruch’s membrane complex (RPE+BM) thickening started after age 57. Each standard deviation (SD) of PS thinning and RPE+BM thickening were associated with prevalent AMD (PS: OR 1.37, 95% CI 1.25-1.49, P=2.5×10−12; RPE+BM: OR=1.34, 95% CI 1.27-1.41, P=8.4×10−28) and incident AMD (PS: HR 1.35, 95% CI 1.23-1.47, P=3.7×10−11; RPE+BM: HR 1.14, 95% CI 1.06-1.22, P=0.00024). An AMD polygenic risk score (PRS) was associated with PS thinning (Beta -0.21 SD per 2-fold genetically increased risk of AMD, 95% CI -0.23 to -0.19, P=2.8×10−74), and its association with RPE+BM was U-shaped (thinning with AMD PRS<92ndpercentile and thickening with AMD PRS>92ndpercentile suggestive of drusen formation). The loci with strongest support were AMD risk-raising variantsCFH:rs570618-T,CFH:10922109-C, andARMS2/HTRA1:rs3750846-C on PS thinning, andSYN3/TIMP3:rs5754227-T on RPE+BM thickening.ConclusionsEpidemiologically, PS thinning precedes RPE+BM thickening by decades, and is the retinal layer most strongly predictive of future AMD risk. Genetically, AMD risk variants are associated with decreased PS thickness. Overall, these findings support PS thinning as an early-stage clinical biomarker for future AMD development.
Early Precursors of Literacy Development in Simultaneous Bilinguals: A Systematic Review and Meta-Analysis
Authors: Bhalloo Insiya , Molnar Monika 
Published: August 2021

AbstractPurposeLiteracy precursors are cognitive, linguistic, and oral-language skills that predict future reading skills in children as young as 4 years. Speech-language pathologists and educators utilize these precursors as assessment tools to identify children at risk for reading difficulties. Most current tools are developed based on monolinguals (predominantly in English), despite the significant percentage of bilinguals globally. As such, bilingual children are typically assessed on tools developed for monolinguals in research and clinical settings. Despite this common practice, there is a lack of comprehensive synthesis on whether these precursors are a reliable indicator of reading skills in bilingual children. Our paper examines whether literacy precursors commonly used with monolinguals are associated with literacy development in simultaneous bilinguals.MethodFollowing PRISMA and Cochrane guidelines, our review includes four databases (LLBA, ERIC, MLA, and PsycINFO), in addition to gray-literature and manual reference-list searches. To control for age of acquisition and language dominance variability, we included typically-developing simultaneous bilinguals exposed to both languages before age 3 (N=5,942). We analyzed reported statistical associations between code-related or oral-language precursors and reading outcome measures, using correlational meta-analyses.ResultsThe 41 reports, that met inclusion/exclusion criteria, were published between 1977-2022. The average age at assessment was 7;5 years (range: 3;0 - 11;0 years), with children speaking over 21 bilingual language combinations. Our meta-analysis demonstrated significant within-language correlations and cross-language transfer effects for code-related (e.g., phonological awareness) and oral-language (e.g., vocabulary, morphological awareness) precursors. Semantic awareness, however, was not a reliable predictor in bilinguals.ConclusionsPhonological awareness and vocabulary measures – even if originally developed for monolingual children - can form a meaningful component of early literacy assessment in simultaneous bilingual children: these precursors may be used as assessment tools across heritage and societal languages in research and clinical practice. Future research suggestions within this domain are also discussed.
CardioVinci: building blocks for virtual cardiac cells using deep learning
Authors: Khadangi Afshin , Boudier Thomas , Rajagopal Vijay 
Published: August 2021

AbstractRecent advances in high-throughput microscopy imaging have made it easier to acquire large volumes of cell images. Thanks to electron microscopy (EM) imaging, they provide a high-resolution and sufficient field of view that suits imaging large cell types, including cardiomyocytes. A significant bottleneck with these large datasets is the time taken to collect, extract and statistically analyse 3D changes in cardiac ultrastructures. We address this bottleneck with CardioVinci.
Multi-omics integration and regulatory inference for unpaired single-cell data with a graph-linked unified embedding framework
Authors: Cao Zhi-Jie , Gao Ge 
Published: August 2021

AbstractWith the ever-increasing amount of single-cell multi-omics data accumulated during the past years, effective and efficient computational integration is becoming a serious challenge. One major obstacle of unpaired multi-omics integration is the feature discrepancies among omics layers. Here, we propose a computational framework called GLUE (graph-linked unified embedding), which utilizes accessible prior knowledge about regulatory interactions to bridge the gaps between feature spaces. Systematic benchmarks demonstrated that GLUE is accurate, robust and scalable. We further employed GLUE for various challenging tasks, including triple-omics integration, model-based regulatory inference and multi-omics human cell atlas construction (over millions of cells) and found that GLUE achieved superior performance for each task. As a generalizable framework, GLUE features a modular design that can be flexibly extended and enhanced for new analysis tasks. The full package is available online athttps://github.com/gao-lab/GLUEfor the community.
Temperature increase affects acetate-derived methane production in Alaskan lake sediments and wetland soils
Authors: Dellagnezze BM , Bovio-Winkler P. , Lavergne C. , Menoni D.A. , Mosquillo F. , Cabrol L , Barret M. , Etchebehere C. 
Published: August 2021

AbstractUnder climate change framework, methanogens activity is expected to be strongly affected, eventually resulting in positive feedback on global climate, with higher greenhouse gas (GHG) emissions in the Arctic. This work aimed to evaluate the effect of increasing temperature on methane production rate and archaeal community of lake sediments and wetland soils from Denali to Toolik regions in Alaska (USA). For that, anaerobic acetate-amended microcosms were incubated at 5, 10, 15 and 20 °C. The acetate-derived methanogenic rate was determined and the methanogenic communities were analyzed by qPCR and 16S rRNA sequencing. Warmer temperatures yielded 4-6 times higher methane production rates and organic matter content (OM) showed significant positive correlation to methane production. Different patterns were observed in the archaeal communities after incubation at higher temperatures, with an increase in Methanosarcina abundance for most of the samples and Methanosaeta in one of the lakes tested, showing the adaptation of key acetoclastic groups among different temperatures. Our results demonstrate the impact of increasing temperature on methane production, bringing insights on key drivers involved in the process of acetoclastic methanogenic potential occurring in these ecosystems in Alaska.
Assessing the use of ellipsoidal microparticles for determining lipid membrane viscosity
Authors: Jahl P. E. , Parthasarathy R. 
Published: August 2021

AbstractThe viscosity of lipid membranes sets the timescales of membrane-associated flows and therefore influences the dynamics of a wide range of cellular processes. Techniques to measure membrane viscosity remain sparse, however, and reported measurements to date, even of similar systems, give viscosity values that span orders of magnitude. To address this, we improve a method based on measuring both the rotational and translational diffusion of membrane-anchored microparticles and apply this approach and one based on tracking the motion of phase-separated lipid domains to the same system of phase-separated giant vesicles. We find good agreement between the two methods, with inferred viscosities within a factor of two of each other. Our technique uses ellipsoidal microparticles, and we show that the extraction of physically meaningful viscosity values from their motion requires consideration of their anisotropic shape. The validation of our method on phase-separated membranes makes possible its application to other systems, which we demonstrate by measuring the viscosity of bilayers composed of lipids with different chain lengths ranging from 14 to 20 carbon atoms, revealing a very weak dependence of two-dimensional viscosity on lipid size. The experimental and analysis methods described here should be generally applicable to a variety of membrane systems, both reconstituted and cellular.Statement of SignificanceThe lipid bilayers that underlie cellular membranes are two-dimensional fluids whose viscosity sets timescales of flow. Lipid membrane viscosity remains poorly quantified, with a paucity of methods and considerable disagreement between values reported using different techniques. We describe a method based on measuring the Brownian diffusion of ellipsoidal microparticles which we apply to phase-separated membranes alongside a previously established method for determining membrane viscosity, finding good agreement between the two techniques. We further examine homogenous membranes composed of lipids with different chain lengths, not amenable to phase-separationbased methods, revealing a very weak dependence of viscosity on lipid size. Our approach should be applicable to a wide range of membrane systems, both in vitro and in living cells.
Genome-wide development of lncRNA-derived-SSR markers for Dongxiang wild rice (Oryza rufipogon Griff.)
Authors: Yang Wanling , Fan Yuanwei , Chen Yong , Ding Gumu , Liu Hu , Xie Jiankun , Zhang Fantao 
Published: August 2021

SummaryDongxiang wild rice (Oryza rufipogon Griff., DXWR) is the northernmost distributed common wild rice found in the world. It contains a large number of agronomically valuable genes, which makes it a natural gene pool for rice breeding. Molecular markers, especially simple repeat sequence (SSR) markers, play important roles in crop breeding. Although a large number of SSR markers have been developed, most of them are derived from the genome coding sequences, rarely from non-coding sequences. Meanwhile, long non-coding RNAs (lncRNAs), which are derived from the transcription of non-coding sequences, play vital roles in plant growth, development and stress responses. In this study, 1878 SSR loci were detected from the lncRNA sequences of DXWR, and 1258 lncRNA-derived-SSR markers were developed on the genome-wide scale. To verify the validity and applicability of these markers, 72 pairs of primers were randomly selected to test 44 rice materials. The results showed that 42 (58.33%) pairs of primers have abundant polymorphism among these rice materials; the polymorphism information content (PIC) values ranged from 0.04 to 0.87 with an average of 0.50; the genetic diversity index of SSR loci varied from 0.04 to 0.88 with an average of 0.56; and the number of alleles per marker ranged from 2 to 11 with an average of 4.36. Thus, we concluded that these lncRNA-derived-SSR markers are a very useful source for future basic and applied research, including genetic diversity analysis, QTL mapping, and molecular breeding programs, to make good use of the elite lncRNA genes from DXWR.
Spontaneous Chiral Symmetry Breaking in a Random Driven Chemical System
Authors: Piñeros William D. , Tlusty Tsvi 
Published: August 2021

AbstractLiving systems have evolved to efficiently consume available energy sources using an elaborate circuitry of chemical reactions which, puzzlingly, bear a strict restriction to asymmetric chiral configurations. While autocatalysis is known to promote such chiral symmetry breaking, whether a similar phenomenon may also be induced in a more general class of configurable chemical systems—via energy exploitation—is a sensible yet underappreciated possibility. This work examines this question within a model of randomly generated complex chemical networks. We show that chiral symmetry breaking may occur spontaneously and generically by harnessing energy sources from external environmental drives. Key to this transition are intrinsic fluctuations of achiral-to-chiral reactions and tight matching of system configurations to the environmental drives, which together amplify and sustain diverged enantiomer distributions. These asymmetric states emerge through steep energetic transitions from the corresponding symmetric states and sharply cluster as highly-dissipating states. The results thus demonstrate a generic mechanism in which energetic drives may give rise to homochirality in an otherwise totally symmetrical environment, and from an early-life perspective, might emerge as a competitive, energy-harvesting advantage.
The crystal structure of the varicella zoster Orf24-Orf27 nuclear egress complex spotlights multiple determinants of herpesvirus subfamily specificity
Authors: Schweininger Johannes , Kriegel Mark , Häge Sigrun , Conrad Marcus , Alkhashrom Sewar , Lösing Josephine , Weiler Sigrid , Tillmanns Julia , Egerer-Sieber Claudia , Decker Andrea , Roviš Tihana Lenac , Eichler Jutta , Sticht Heinrich , Marschall Manfred , Muller Yves A. 
Published: August 2021

ABSTRACTVaricella zoster virus (VZV) is a human pathogen from the α-subfamily of herpesviruses. Here, the crystal structure of the VZV Orf24-Orf27 complex is described, representing the essential viral core nuclear egress complex (NEC) that orchestrates the egress of the preassembled capsids from the nucleus. While previous studies have primarily emphasized the finding that the architecture of core NEC complexes is highly conserved among herpesviruses, the present report focusses on subfamily-specific structural and functional features that help explain the differences in the autologous versus nonautologous interaction patterns observed for NEC formation across herpesviruses. CoIP and confocal imaging data show that Orf24-Orf27 complex formation displays some promiscuity in a herpesvirus subfamily-restricted manner. At the same time, analysis of the NEC formation thermodynamic parameters of three prototypical α-, β- and γ herpesviruses, i.e. VZV, human cytomegalovirus (HCMV) and Epstein-Barr virus (EBV) reveals highly similar binding affinities for the autologous interaction with some specific differences in the enthalpy and entropy terms. Computational alanine scanning and structural comparisons highlight intermolecular interactions shared among α-herpesviruses that are clearly distinct from those seen in β- and γ-herpesviruses. Combined, these data allow to explain the distinct properties of specificity and permissivity so far observed in herpesviral NEC interactions. These findings might prove highly valuable when attempting to target multiple herpesvirus core NECs with selective or broad-acting drug candidates.
Parity-induced changes to mammary epithelial cells control NKT cell expansion and mammary oncogenesis
Authors: Hanasoge Somasundara Amritha V. , Moss Matthew A. , Feigman Mary J. , Chen Chen , Cyrill Samantha L. , Ciccone Michael F. , Trousdell Marygrace C. , Vollbrecht Macy , Li Siran , Kendall Jude , Beyaz Semir , Wilkinson John E. , dos Santos Camila O. 
Published: August 2021

SummaryPregnancy reprograms the epigenome of mammary epithelial cells (MECs) in a manner that control responses to pregnancy hormone re-exposure and the rate of carcinoma progression. However, the influence of pregnancy on the tissue microenvironment of the mammary gland is less clear. Here, we used single-cell RNA sequencing to comparatively profile the composition of epithelial and non-epithelial cells in mammary tissue from nulliparous and parous female mice. Our analysis revealed an expansion of γδ Natural Killer T (NKT) immune cells following pregnancy, in association with upregulation of immune signal molecules in post-pregnancy MECs. We show that expansion of NKT cells following pregnancy is due to elevated expression of the antigen presenting molecule CD1d protein, which is known to induce NKT activation. Accordingly, loss of CD1d expression on post-pregnancy MECs, or overall lack of activated NKT cells, accompanied the development of mammary oncogenesis in response to cMYC overexpression and loss of Brca1 function. Collectively, our findings illustrate how pregnancy-induced epigenetic changes modulate the communication between MECs and the mammary immune microenvironment, and establish a causal link between pregnancy, the immune microenvironment, and mammary oncogenesis.
Recruitment and organization of ESCRT-0 and ubiquitinated cargo via condensation
Authors: Banjade Sudeep , Zhu Lu , Jorgensen Jeffrey R. , Suzuki Sho W. , Emr Scott D. 
Published: August 2021

AbstractThe general mechanisms by which ESCRTs are specifically recruited to various membranes, and how ESCRT subunits are spatially organized remain central questions in cell biology. At the endosome and lysosomes, ubiquitination of membrane proteins triggers ESCRT-mediated substrate recognition and degradation. Using the yeast lysosome/vacuole, we define the principles by which substrate engagement by ESCRTs occurs at this organelle. We find that multivalent interactions between ESCRT-0 and polyubiquitin is critical for substrate recognition at yeast vacuoles, with a lower-valency requirement for cargo engagement at endosomes. Direct recruitment of ESCRT-0 induces dynamic foci on the vacuole membrane, and forms fluid condensates in vitro with polyubiquitin. We propose that self-assembly of early ESCRTs induces condensation, an initial step in ESCRT-assembly/nucleation at membranes. This property can be tuned specifically at various organelles by modulating the number of binding interactions.One-Sentence SummaryCondensation of multivalent ESCRT-0/polyubiquitin assemblies organizes cargo sorting reactions at lysosomes
Prior expectations in visual speed perception predict encoding characteristics of neurons in area MT
Authors: Zhang Ling-Qi , Stocker Alan A. 
Published: August 2021

AbstractBayesian inference provides an elegant theoretical framework for understanding the characteristic biases and discrimination thresholds in visual speed perception. However, the framework is difficult to validate due to its flexibility and the fact that suitable constraints on the structure of the sensory uncertainty have been missing. Here, we demonstrate that a Bayesian observer model constrained by efficient coding not only well explains human visual speed perception but also provides an accurate quantitative account of the tuning characteristics of neurons known for rep-resenting visual speed. Specifically, we found that the population coding accuracy for visual speed in area MT (“neural prior”) is precisely predicted by the power-law, slow-speed prior extracted from fitting the Bayesian model to psychophysical data (“behavioral prior”) to the point that the two priors are indistinguishable in a cross-validation model comparison. Our results demonstrate a quantitative validation of the Bayesian observer model constrained by efficient coding at both the behavioral and neural levels.Significance StatementStatistical regularities of the environment play an important role in shaping both neural representations and perceptual behavior. Most previous works addressed these two aspects independently. Here we present a quantitative validation of a theoretical framework that makes joint predictions for neural coding and behavior, based on the assumption that neural representations of sensory information are efficient but also optimally used in generating a percept. Specifically, we demonstrate that the neural tuning characteristics for visual speed in brain area MT are precisely predicted by the statistical prior expectations extracted from psychophysical data. As such, our results provide a normative link between perceptual behavior and the neural representation of sensory information in the brain.