bluuebunny/crossref_metadata_2025_split huggingface dataset:
Social Media Study of Public Opinions on Potential COVID-19 Vaccines: Informing Dissent, Disparities, and Dissemination
Authors: Lyu Hanjia , Wang Junda , Wu Wei , Duong Viet , Zhang Xiyang , Dye Timothy D. , Luo Jiebo 
Published: December 2020

AbstractThe current development of vaccines for SARS-CoV-2 is unprecedented. Little is known, however, about the nuanced public opinions on the coming vaccines. We adopt a human-guided machine learning framework (using more than 40,000 rigorously selected tweets from more than 20,000 distinct Twitter users) to capture public opinions on the potential vaccines for SARS-CoV-2, classifying them into three groups: pro-vaccine, vaccine-hesitant, and anti-vaccine. We aggregate opinions at the state and country levels, and find that the major changes in the percentages of different opinion groups roughly correspond to the major pandemic-related events. Interestingly, the percentage of the pro-vaccine group is lower in the Southeast part of the United States. Using multinomial logistic regression, we compare demographics, social capital, income, religious status, political affiliations, geo-locations, sentiment of personal pandemic experience and non-pandemic experience, and county-level pandemic severity perception of these three groups to investigate the scope and causes of public opinions on vaccines. We find that socioeconomically disadvantaged groups are more likely to hold polarized opinions on potential COVID-19 vaccines. The anti-vaccine opinion is the strongest among the people who have the worst personal pandemic experience. Next, by conducting counterfactual analyses, we find that the U.S. public is most concerned about the safety, effectiveness, and political issues regarding potential vaccines for COVID-19, and improving personal pandemic experience increases the vaccine acceptance level. We believe this is the first large-scale social media-based study to analyze public opinions on potential COVID-19 vaccines that can inform more effective vaccine distribution policies and strategies.
Screening for high amounts of SARS-CoV-2 identifies pre-symptomatic subjects among healthy healthcare workers
Authors: Dillner Joakim , Elfström K. Miriam , Blomqvist Jonas , Engstrand Lars , Uhlén Mathias , Eklund Carina , Boulund Fredrik , Lagheden Camilla , Hamsten Marica , Nordqvist-Kleppe Sara , Seifert Maike , Hellström Cecilia , Olofsson Jennie , Andersson Eni , Falk August Jernbom , Bergström Sofia , Hultin Emilie , Pin Elisa , Pimenoff Ville N. , Hassan Sadaf , Månberg Anna , Nilsson Peter , Hedhammar My , Hober Sophia , Mattsson Johan , Mühr Laila Sara Arroyo , Lundgren Kalle Conneryd 
Published: December 2020

AbstractBackgroundPre-symptomatic subjects are spreaders of SARS-CoV-2 infection, and strategies that could identify these subjects, particularly in hospital settings, are needed.MethodsWe tested a cohort of 9449 employees at work at the Karolinska University Hospital, Stockholm, Sweden for SARS-CoV-2 RNA and antibodies, linked the screening results to sick leave records and examined the association between screening results and past or future sick leave using multinomial logistic regression.ResultsWe found that healthcare workers with high amounts of SARS-CoV-2 virus, as indicated by the Cycle threshold (Ct) value in the PCR, had the highest risk for sick leave in the two weeks after testing (OR 11·97 (CI 95% 6·29-22·80)) whereas subjects with low amounts of virus had the highest risk for sick leave in the past three weeks before testing (OR 6·31 (4·38-9·08)). Only 2·5% of employees were SARS-CoV-2 positive while 10·5% were positive by serology and 1·2% were positive in both tests. Serology-positive subjects were not at excess risk for future sick leave (OR 1·06 (95% CI, 0·71-1·57)), but virus-positive subjects had a 7·23 fold (95% CI, 4·52-11·57)) increased risk for sick leave within two weeks post testing.ConclusionsScreening of asymptomatic healthcare workers for high amounts of SARS-CoV-2 virus using Ct values will identify pre-symptomatic subjects who will develop disease in the next few weeks. Identification of potentially contagious, pre-symptomatic subjects is likely critical for protecting patients and healthcare workers.Main pointHealthy healthcare workers with low amounts of SARS-CoV-2 nucleic acids will previously have had the disease. Presence of a high amount of SARS-CoV-2 nucleic acids predicts future symptomatic disease.
The seroprevalence and trends of SARS-CoV-2 in Delhi, India: A repeated population-based seroepidemiological study
Authors: Sharma Nandini , Sharma Pragya , Basu Saurav , Saxena Sonal , Chawla Rohit , Dushyant Kumar , Mundeja Nutan , Marak Z SK , Singh Sanjay , Singh Gautam Kumar , Rustagi Ruchir 
Published: December 2020

ABSTRACTBackgroundThree rounds of a repeated cross-sectional serosurvey to estimate the seroprevalence and trends of SARS-CoV-2 were conducted from August-October’ 2020 in the state of Delhi in India in the general population aged ≥5 years.MethodsThe selection of participants was through a multi-stage sampling design from all the 11 districts and 280 wards of the city-state, with two-stage allocation proportional to population- size. Household selected was via systematic random sampling, and individual participant selection through the age-order procedure. The blood samples were screened using the IgG ELISA COVID-Kawach kit (August Round), and the ERBALISA COVID-19 IgG (September and October) rounds. The seroprevalence was estimated by applying the sampling weights based on age and sex with further adjustment for the assay-kit characteristics.ResultsA total of 4267 (n=15046), 4311 (n=17409), and 3829 (n=15015) positive tests indicative of the presence of IgG antibody to SARS-CoV-2 were observed during the August, September, and October 2020 serosurvey rounds, respectively. The adjusted seroprevalence declined from 28.39% (95% CI 27.65-29.14) (August) to 24.08% (95% CI 23.43-24.74) (September), and 24.71% (95% CI 24.01, 25.42%) (October). The antibody positivity was highest in the ≥50 and female age-group during all rounds of the serosurvey, while the decline was maximum among the younger age-group (5-17 years). On adjusted analysis, participants with lower per capita income, living in slums or overcrowded households, and those with diabetes comorbidity had significantly higher statistical odds of antibody positivity.ConclusionsDespite high IgG seroprevalence, there was evidence for waning of antibody positivity with the progression of the COVID-19 epidemic, implying a potential reduction in population immunity, especially if also associated with the lack of trained T cell immunity.
Transcription factor network analysis identifies REST/NRSF as an intrinsic regulator of CNS regeneration
Authors: Cheng Yuyan , Yin Yuqin , Zhang Alice , Bernstein Alexander M. , Kawaguchi Riki , Gao Kun , Potter Kyra , Gilbert Hui-Ya , Ao Yan , Ou Jing , Fricano-Kugler Catherine J. , Goldberg Jeffrey L. , Woolf Clifford J. , Sofroniew Michael V. , Benowitz Larry I. , Geschwind Daniel H. 
Published: December 2020

SUMMARYThe inability of neurons to regenerate long axons within the CNS is a major impediment to improving outcome after spinal cord injury, stroke, and other CNS insults. Recent advances have uncovered an intrinsic program that involves coordinate regulation by multiple transcription factors that can be manipulated to enhance growth in the peripheral nervous system. Here, we used a system-genomics approach to characterize regulatory relationships of regeneration-associated transcription factors, identifying RE1-Silencing Transcription Factor (REST; Neuron-Restrictive Silencer Factor, NRSF) as a predicted upstream suppressor of a pro-regenerative gene program associated with axon regeneration in the CNS. We validate our predictions using multiple paradigms, showing that mature mice bearing cell type-specific deletions of REST or expressing dominant-negative mutant REST showed improved regeneration of the corticospinal tract and optic nerve, accompanied by upregulation of regeneration-associated genes in cortical motor neurons and retinal ganglion cells, respectively. These analyses identify a novel role for REST as an upstream suppressor of the intrinsic regenerative program in the CNS and demonstrate the power of a systems biology approach involving integrative genomics and bio-informatics to predict key regulators of CNS repair.
SARS-CoV-2 among migrants and forcibly displaced populations: a rapid systematic review
Authors: Hintermeier Maren , Gencer Hande , Kajikhina Katja , Rohleder Sven , Santos-Hövener Claudia , Tallarek Marie , Spallek Jacob , Bozorgmehr Kayvan 
Published: December 2020

AbstractThe economic and health consequences of the COVID-19 pandemic pose a particular threat to vulnerable groups, such as migrants, particularly forcibly displaced populations. The aim of this review is (i) to synthesise the evidence on risk of infection and transmission among migrants, refugees, asylum seekers and internally displaced populations, and (ii) the effect of lockdown measures on these populations. We searched MEDLINE and WOS, preprint servers, and pertinent websites between 1st December 2019 and 26th June 2020. The included studies showed a high heterogeneity in study design, population, outcome and quality. The incidence risk of SARS-CoV-2 varied from 0·12% to 2·08% in non-outbreak settings and from 5·64% to 21·15% in outbreak settings. Migrants showed a lower hospitalisation rate compared to non-migrants. Negative impacts on mental health due to lockdown measures were found across respective studies. However, findings show a tenuous and heterogeneous data situation, showing the need for more robust and comparative study designs.
The SEQC2 Epigenomics Quality Control (EpiQC) Study: Comprehensive Characterization of Epigenetic Methods, Reproducibility, and Quantification
Authors: Foox Jonathan , Nordlund Jessica , Lalancette Claudia , Gong Ting , Lacey Michelle , Lent Samantha , Langhorst Bradley W. , Ponnaluri V K Chaithanya , Williams Louise , Padmanabhan Karthik Ramaswamy , Cavalcante Raymond , Lundmark Anders , Butler Daniel , Mozsary Chris , Gurvitch Justin , Greally John M. , Suzuki Masako , Menor Mark , Nasu Masaki , Alonso Alicia , Sheridan Caroline , Scherer Andreas , Bruinsma Stephen , Golda Gosia , Muszynska Agata , Łabaj Paweł P. , Campbell Matthew A. , Wos Frank , Raine Amanda , Liljedahl Ulrika , Axelsson Tomas , Wang Charles , Chen Zhong , Yang Zhaowei , Li Jing , Yang Xiaopeng , Wang Hongwei , Melnick Ari , Guo Shang , Blume Alexander , Franke Vedran , de Caceres Inmaculada Ibanez , Rodriguez-Antolin Carlos , Rosas Rocio , Davis Justin Wade , Ishii Jennifer , Megherbi Dalila B. , Xiao Wenming , Liao Will , Xu Joshua , Hong Huixiao , Ning Baitang , Tong Weida , Akalin Altuna , Wang Yunliang , Deng Youping , Mason Christopher E. 
Published: December 2020

AbstractCytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and a global resource for epigenetics research from the FDA’s Epigenomics Quality Control (EpiQC) Group. The study design leverages seven human cell lines that are designated as reference materials and publicly available from the National Institute of Standards and Technology (NIST) and Genome in a Bottle (GIAB) consortium. These samples were subject to a variety of genome-wide methylation interrogation approaches across six independent laboratories, with a primary focus was on 5-methylcytosine modifications. Each sample was processed in two or more technical replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), one enzymatic deamination method (EMseq), targeted methylation sequencing (Illumina Methyl Capture EPIC), and single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, BWAMeth, and GemBS), we found overall high concordance between assays (R=0.87-R0.93), differences in efficency of read mapping and CpG capture and coverage, and platform performance. The data provided herein can guide continued used of these reference materials in epigenomics assays, as well as provide best practices for epigenomics research and experimental design in future studies.
Sex difference in hip adduction during the stance phase of running: A swing phase problem?
Authors: Liu Jia , Salem George J , Powers Christopher M 
Published: December 2020

ABSTRACTPurposeThe purpose of the current study was to: 1) evaluate sex differences in peak hip adduction during the late swing and stance phases of running and 2) determine if peak hip adduction during late swing is predictive of peak hip adduction during stance.Methods15 female and 16 male heel strike runners ran over ground at a speed of 4 m/s. Hip joint kinematics during running were quantified using a 3D motion capture system. Sex differences in peak hip adduction during the late swing and stance phases were compared using independent sample t-tests. Linear regression analysis was used to determine the relationship between late swing and stance phase hip adduction.ResultsCompared to males, females exhibited significantly greater peak hip adduction during both the late swing (8.5 ± 2.6 vs 6.1 ± 2.8°, p = 0.019) and stance phases of running (13.3 ± 4.2 vs 9.6 ± 3.4°, p = 0.011). Furthermore, late swing peak hip adduction was predictive of subsequent stance phase peak hip adduction (r = 0.63, p < 0.001).ConclusionSex differences in hip adduction during stance are influenced in part by late swing phase hip adduction. Further studies are needed to identify potential causes of excessive hip adduction during the late swing phase of running.
Genetic and Epigenetic Regulation of Skeletal Muscle Ribosome Biogenesis with Exercise
Authors: Figueiredo Vandré C. , Wen Yuan , Alkner Björn , Fernandez-Gonzalo Rodrigo , Norrbom Jessica , Vechetti Ivan J. , Valentino Taylor , Mobley C. Brooks , Zentner Gabriel E. , Peterson Charlotte A. , McCarthy John J. , Murach Kevin A. , von Walden Ferdinand 
Published: December 2020

ABSTRACTRibosomes are the macromolecular engines of protein synthesis. Skeletal muscle ribosome biogenesis is stimulated by exercise, but the contribution of ribosomal DNA (rDNA) copy number and methylation to exercise-induced rDNA transcription is unclear. To investigate the genetic and epigenetic regulation of ribosome biogenesis with exercise, a time course of skeletal muscle biopsies was obtained from 30 participants (18 men and 12 women; 31 ±8 yrs, 25 ±4 kg/m2) at rest and 30 min, 3h, 8h, and 24h after acute endurance (n=10, 45 min cycling, 70% VO2max) or resistance exercise (n=10, 4 x 7 x 2 exercises); 10 control participants underwent biopsies without exercise. rDNA transcription and dosage were assessed using qPCR and whole genome sequencing. rDNA promoter methylation was investigated using massARRAY EpiTYPER, and global rDNA CpG methylation was assessed using reduced-representation bisulfite sequencing. Ribosome biogenesis andMYCtranscription were associated with resistance but not endurance exercise, indicating preferential up-regulation during hypertrophic processes. With resistance exercise, ribosome biogenesis was associated with rDNA gene dosage as well as epigenetic changes in enhancer and non-canonical MYC-associated areas in rDNA, but not the promoter. A mouse model ofin vivometabolic RNA labeling and genetic myonuclear fluorescent labeling validated the effects of an acute hypertrophic stimulus on ribosome biogenesis andMyctranscription, and corroborated rDNA enhancer and Myc-associated methylation alterations specifically in myonuclei. This study provides the first information on skeletal muscle genetic and rDNA gene-wide epigenetic regulation of ribosome biogenesis in response to exercise, revealing novel roles for rDNA dosage and CpG methylation.GRAPHICAL ABSTRACT
Imaging of native transcription and transcriptional dynamicsin vivousing a tagged Argonaute protein
Authors: Toudji-Zouaz Amel , Bertrand Vincent , Barrière Antoine 
Published: December 2020

AbstractA flexible method to image unmodified transcripts and transcriptionin vivowould be a valuable tool to understand the regulation and dynamics of transcription. Here, we present a novel approach to follow native transcription, with fluorescence microscopy, in liveC. elegans. By using the fluorescently tagged Argonaute protein NRDE-3, programmed by exposure to defined dsRNA to bind to nascent transcripts of the gene of interest, we demonstrate transcript labelling of multiple genes, at the transcription site and in the cytoplasm. This flexible approach does not require genetic manipulation, and can be easily scaled up by relying on whole-genome dsRNA libraries. We apply this method to image the transcriptional dynamics of two transcription factors:ttx-3(a LHX2/9 orthologue) in embryos, andhlh-1(a MyoD orthologue) in larvae, respectively involved in neuronal and muscle development.
GSTZ1 sensitizes hepatocellular carcinoma cells to sorafenib-induced ferroptosis via inhibition of NRF2/GPX4 axis
Authors: Wang Qiujie , Cheng Bin , Xue Qiang , Gao Qingzhu , Huang Ailong , Wang Kai , Tang Ni 
Published: December 2020

AbstractIncreasing evidence supports that ferroptosis plays an important role in tumor growth inhibition. Sorafenib, originally identified as an inhibitor of multiple oncogenic kinases, has been shown to induce ferroptosis in hepatocellular carcinoma (HCC). However, some hepatoma cell lines are less sensitive to sorafenib-induced ferroptotic cell death. Glutathione S-transferase zeta 1 (GSTZ1), an enzyme in the catabolism of phenylalanine, has been found to negatively regulate the master regulator of cellular redox homeostasis nuclear factor erythroid 2-related factor 2 (NRF2). This study aimed to investigate the role of GSTZ1 in sorafenib-induced ferroptosis in HCC cell lines and determine the involved molecular mechanisms. Mechanistically, GSTZ1 depletion enhanced the activation of the NRF2 pathway and increased the glutathione peroxidase 4 (GPX4) level, thereby suppressing sorafenib-induced ferroptosis. The combination of sorafenib and RSL3, a GPX4 inhibitor, significantly inhibited GSTZ1 deficient cell viability and promoted ferroptosis, accompanied with ectopic increases of iron and lipid peroxides. Anin vivoexperiment showed that the combination of sorafenib and RSL3 had a synergic therapeutic effect on HCC progression inGstz1−/−mice. In conclusion, GSTZ1 was significantly downregulated in sorafenib resistant hepatoma cells. GSTZ1 enhanced sorafenib-induced ferroptosis by inhibiting the NRF2/GPX4 axis in HCC cells. GSTZ1 deficiency was resistant to sorafenib-induced ferroptosis and is, therefore, a potential therapeutic approach for treating HCC by synergizing sorafenib and RSL3 to induce ferroptosis.
A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs
Authors: Nguyen Thu , Phan Kim L , Kreitler Dale F , Andrews Lawrence C , Gabelli Sandra B , Kozakov Dima , Jakoncic Jean , Sweet Robert M , Soares Alexei S , Bernstein Herbert J 
Published: December 2020

AbstractOne often observes small but measurable differences in diffraction data measured from different crystals of a single protein. These differences might reflect structural differences in the protein and potentially reflect the natural dynamism of the molecule in solution. Partitioning these mixed-state data into single-state clusters is a critical step to extract information about the dynamic behavior of proteins from hundreds or thousands of single-crystal data sets. Mixed-state data can be obtained deliberately (through intentional perturbation) or inadvertently (while attempting to measure highly redundant single-crystal data). State changes may be expressed as changes in morphology, so that a subset of the polystates may be observed as polymorphs. After mixed-state data are deliberately or inadvertently measured, the challenge is to sort the data into clusters that may represent relevant biological polystates. Here we address this problem using a simple multi-factor clustering approach that classifies each data set using independent observables in order to assign each data set to the correct location in conformation space. We illustrate this method using two independent observables (unit cell constants and intensities) to cluster mixed-state data from chymotrypsinogen (ChTg) crystals. We observe that the data populate an arc of the reaction trajectory as ChTg is converted into chymotrypsin.
Neuroinvasion and encephalitis following intranasal inoculation of SARS-CoV-2 in K18-hACE2 mice
Authors: Kumari Pratima , Rothan Hussin A. , Natekar Janhavi P. , Stone Shannon , Pathak Heather , Strate Philip G. , Arora Komal , Brinton Margo A. , Kumar Mukesh 
Published: December 2020

AbstractSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection can cause neurological disease in humans, but little is known about the pathogenesis of SARS-CoV-2 infection in the central nervous system. Herein, using K18-hACE2 mice, we demonstrate that SARS-CoV-2 neuroinvasion and encephalitis is associated with mortality in these mice. Intranasal infection of K18-hACE2 mice with 105plaque-forming units of SARS-CoV-2 resulted in 100% mortality by day 6 after infection. The highest virus titers in the lungs were observed at day 3 and declined at days 5 and 6 after infection. In contrast, very high levels of infectious virus were uniformly detected in the brains of all the animals at days 5 and 6. Onset of severe disease in infected mice correlated with peak viral levels in the brain. SARS-CoV-2-infected mice exhibited encephalitis hallmarks characterized by production of cytokines and chemokines, leukocyte infiltration, hemorrhage and neuronal cell death. SARS-CoV-2 was also found to productively infect cells within the nasal turbinate, eye and olfactory bulb, suggesting SARS-CoV-2 entry into the brain by this route after intranasal infection. Our data indicate that direct infection of CNS cells together with the induced inflammatory response in the brain resulted in the severe disease observed in SARS-CoV-2-infected K18-hACE2 mice.
The Covid-19 containment effects of public health measures - A spatial difference-in-differences approach
Authors: Kosfeld Reinhold , Mitze Timo , Rode Johannes , Wälde Klaus 
Published: December 2020

AbstractSince mid-March 2020 the Federal and state governments in Germany agreed on comprehensive public health measures to curb the spread of SARS-CoV-2 infections leading to the Covid-19 disease. We study the containment effects of these policy interventions on the progression of the pandemic in the first containment phase in spring 2020 before the easing of restrictions may become effective by the end of April. To exploit both the temporal and spatial dimension in the dissemination of the virus, we conduct a spatial panel data analysis for German NUTS-3 regions. Specifically, we employ a spatial difference-in-differences approach to identify the effects of six compound sets of public health measures. We find that contact restrictions and closure of schools substantially contributed to flattening the infection curve. Additionally, a strong treatment effect of mandatory wearing of face masks is established for the few treated regions during this containment phase. No incremental effect is evidenced for closure of establishments, such as museums, theaters, cinemas and parks, and the shutdown of shopping malls and other non-essential retail stores. These findings prove to be robust to changes in model specification. By contrast, the dampening effect of restaurant closure is sensitive to model variation.