bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 antibody prevalence and determinants of six ethnic groups living in Amsterdam, the Netherlands: a population-based cross-sectional study, June-October 2020
Authors: Coyer Liza , Boyd Anders , Schinkel Janke , Agyemang Charles , Galenkamp Henrike , Koopman Anitra D M , Leenstra Tjalling , van Charante Eric P Moll , van den Born Bert-Jan H , Lok Anja , Verhoeff Arnoud , Zwinderman Aeilko H , Jurriaans Suzanne , van Vught Lonneke A , Stronks Karien , Prins Maria 
Published: March 2021

AbstractBackgroundEthnic minorities have higher rates of SARS-CoV-2 diagnoses, but little is known about ethnic differences in past exposure. We aimed to determine whether prevalence and determinants of SARS-CoV-2 exposure varied between six ethnic groups in Amsterdam, the Netherlands.MethodsParticipants aged 25-79 years enrolled in a population-based prospective cohort were randomly selected within ethnic groups and invited to test for SARS-CoV-2-specific antibodies and answer COVID-19 related questions. We estimated prevalence and determinants of SARS-CoV-2 exposure within ethnic groups using survey-weighted logistic regression adjusting for age, sex and calendar time.ResultsBetween June 24-October 9, 2020, we included 2497 participants. Adjusted SARS-CoV-2 seroprevalence was comparable between ethnic-Dutch (25/498; 5.5%, 95%CI=3.2-7.9), South-Asian Surinamese (22/451; 4.8%, 95%CI=2.1-7.5), African Surinamese (22/400; 8.2%, 95%CI=3.0-13.4), Turkish (30/408; 7.8%, 95%CI=4.3-11.2) and Moroccan (32/391; 7.0%, 95%CI=4.0-9.9) participants, but higher among Ghanaians (95/327; 26.5%, 95%CI=18.7-34.4). 57.1% of SARS-CoV-2-positive participants did not suspect or were unsure of being infected, which was lowest in African Surinamese (18.2%) and highest in Ghanaians (90.5%). Determinants of SARS-CoV-2 exposure varied across ethnic groups, while the most common determinant was having a household member suspected of infection. In Ghanaians, seropositivity was associated with older age, larger household sizes, living with small children, leaving home to work and attending religious services.ConclusionsNo remarkable differences in SARS-CoV-2 seroprevalence were observed between the largest ethnic groups in Amsterdam after the first wave of infections. The higher infection seroprevalence observed among Ghanaians, which passed mostly unnoticed, warrants wider prevention efforts and opportunities for non-symptom-based testing.
A human multisystem disorder with autoinflammation, leukoencephalopathy and hepatopathy is caused by mutations in C2orf69
Authors: Lausberg Eva , Gießelmann Sebastian , Dewulf Joseph P , Wiame Elsa , Holz Anja , Salvarinova Ramona , Karnebeek Clara Van , Klemm Patricia , Ohl Kim , Mull Michael , Braunschweig Till , Weis Joachim , Sommer Clemens , Demuth Stephanie , Haase Claudia , Debray François-Guillaume , Libioulle Cecile , Choukair Daniela , Oommen Prasad T. , Borkhardt Arndt , Surowy Harald , Wieczorek Dagmar , Meyer Robert , Eggermann Thomas , Begemann Matthias , Schaftingen Emile Van , Häusler Martin , Tenbrock Klaus , den Heuvel Lambert van , Elbracht Miriam , Kurth Ingo , Kraft Florian 
Published: March 2021

AbstractBackgroundDeciphering the function of the many genes previously classified as uncharacterized “open reading frame” (orf) completes our understanding of cell function and its pathophysiology.MethodsWhole-exome sequencing, yeast 2-hybrid and transcriptome analyses together with molecular characterization are used here to uncover the function of the C2orf69 gene.ResultsWe identify loss-of-function mutations in the uncharacterized C2orf69 gene in eight individuals with brain abnormalities involving hypomyelination and microcephaly, liver dysfunction and recurrent autoinflammation. C2orf69 contains an N-terminal signal peptide that is required and sufficient for mitochondrial localization. Consistent with mitochondrial dysfunction, patients show signs of respiratory chain defect and a CRISPR-Cas9 knockout cell model of C2orf69 shows comparable respiratory chain defects. Patient-derived cells reveal alterations in immunological signaling pathways. Deposits of PAS-positive material in tissues from affected individuals together with decreased glycogen branching enzyme 1 (GBE1) activity indicate an additional impact of C2orf69 on glycogen metabolism.ConclusionOur study identifies C2orf69 as an important regulator of human mitochondrial function and suggests an additional influence on other metabolic pathways.Graphical Abstract
Evolutionary and phenotypic characterization of spike mutations in a new SARS-CoV-2 Lineage reveals two Variants of Interest
Authors: Ruiz-Rodriguez Paula , Francés-Gómez Clara , Chiner-Oms Álvaro , López Mariana G. , Jiménez-Serrano Santiago , Cancino-Muñoz Irving , Ruiz-Hueso Paula , Torres-Puente Manuela , Bracho Maria Alma , D’Auria Giuseppe , Martinez-Priego Llúcia , Guerreiro Manuel , Montero-Alonso Marta , Gómez María Dolores , Piñana José Luis ,   SeqCOVID-SPAIN consortium, González-Candelas Fernando , Comas Iñaki , Marina Alberto , Geller Ron , Coscolla Mireia 
Published: March 2021

AbstractMolecular epidemiology of SARS-CoV-2 aims to monitor the appearance of new variants with the potential to change the virulence or transmissibility of the virus. During the first year of SARS-CoV-2 evolution, numerous variants with possible public health impact have emerged. We have detected two mutations in the Spike protein at amino acid positions 1163 and 1167 that have appeared independently multiple times in different genetic backgrounds, indicating they may increase viral fitness. Interestingly, the majority of these sequences appear in transmission clusters, with the genotype encoding mutations at both positions increasing in frequency more than single-site mutants. This genetic outcome that we denote as Lineage B.1.177.637, belongs to clade 20E and includes 12 additional single nucleotide polymorphisms but no deletions with respect to the reference genome (first sequence in Wuhan). B.1.177.637 appeared after the first wave of the epidemic in Spain, and subsequently spread to eight additional countries, increasing in frequency among sequences in public databases. Positions 1163 and 1167 of the Spike protein are situated in the HR2 domain, which is implicated in the fusion of the host and viral membranes. To better understand the effect of these mutations on the virus, we examined whether B.1.177.637 altered infectivity, thermal stability, or antibody sensitivity. Unexpectedly, we observed reduced infectivity of this variant relative to the ancestral 20E variantin vitrowhile the levels of viral RNA in nasopharyngeal swabs did not vary significantly. In addition, we found the mutations do not impact thermal stability or antibody susceptibility in vaccinated individuals but display a moderate reduction in sensitivity to neutralization by convalescent sera from early stages of the pandemic. Altogether, this lineage could be considered a Variant of Interest (VOI), we denote VOI1163.7. Finally, we detected a sub-cluster of sequences within VOI1163.7 that have acquired two additional changes previously associated with antibody escape and it could be identified as VOI1163.7.V2. Overall, we have detected the spread of a new Spike variant that may be advantageous to the virus and whose continuous transmission poses risks by the acquisition of additional mutations that could affect pre-existing immunity.
Ensemble Forecasts of Seasonal Dengue Epidemics
Authors: Chen Yuliang , Liu Tao , Pei Sen , Yu Xiaolin , Zeng Qinghui , Wu Haisheng , Xiao Jianpeng , Ma Wenjun , Guo Pi 
Published: March 2021

AbstractAs a common vector-borne disease, dengue fever still remains a lot of challenges to forecast for which the significant distinction of epidemic scale is affected by multiple factors, such as mosquito density, meteorological conditions, geographical environment, travel and so on. To track down the epidemic scale and forecast the remaining time of epidemic season, the population size affected by the epidemic is evaluated before the compartmental model is optimized by assimilation observation with filtering method. In retrospective forecast of dengue pandemic for Guangzhou from 2014-2015 seasons, accurate forecast of dengue cases is generated with an accurate prediction of peak time in all time periods. The real-time forecast system shows a good performance on capturing the trajectory of dengue transmission and scale of epidemic.
Cumulative incidence of SARS-CoV-2 infection and associated risk factors among frontline health care workers in Paris, France: the SEROCOV prospective cohort study
Authors: Hausfater Pierre , Boutolleau David , Lacombe Karine , Beurton Alexandra , Dumont Margaux , Constantin Jean-Michel , Ghosn Jade , Combes Alain , Cury Nicolas , Guedj Romain , Djibré Michel , Bompard Rudy , Mazerand Sandie , Pourcher Valérie , Gimeno Linda , Marois Clemence , Teyssou Elisa , Marcelin Anne-Geneviève , Hajage David , Tubach Florence 
Published: March 2021

AbstractBackgroundWith the COVID-19 pandemic, documenting whether health care workers (HCWs) are at increased risk of SARS-CoV-2 contamination and identifying risk factors is of major concern.MethodsIn this multicenter prospective cohort study, HCWs from frontline departments were included in March and April 2020 and followed for 3 months. SARS-CoV-2 serology was performed at month 0 (M0), M1, and M3 and RT-PCR in case of symptoms. The primary outcome was laboratory-confirmed SARS-CoV-2 infection at M3. Risk factors of laboratory-confirmed SARS-CoV-2 infection at M3 were identified by multivariate logistic regression.ResultsAmong 1,062 HCWs (median [interquartile range] age, 33 [28-42] years; 758 [71.4%] women; 321 [30.2%] physicians), the cumulative incidence of SARS-CoV-2 infection at M3 was 14.6% (95% confidence interval [CI] [12.5; 16.9]). Risk factors were the working department specialty, with increased risk for intensive care units (odds ratio 1.80, 95%CI [0.38; 8.58]), emergency departments (3.91 [0.83; 18.43]) and infectious diseases departments (4.22 [0.92; 18.28]); active smoking was associated with reduced risk (0.36 [0.21; 0.63]). Age, sex, professional category, number of years of experience in the job or department, and public transportation use were not significantly associated with laboratory-confirmed SARS-CoV-2 infection at M3.ConclusionThe rate of SARS-CoV-2 infection in frontline HCWs was 14.6% at the end of the first COVID-19 wave in Paris and occurred mainly early. The study argues for an origin of professional in addition to private life contamination and therefore including HCWs in the first-line vaccination target population. It also highlights that smokers were at lower risk.Key messagesDuring the first epidemic wave, 14.6% of 1,062 first-line Health Care Workers had a positive serology and/or RT-PCR test for SARS-CoV-2.Most infections occurred earlyRisk was increased by working in infectious diseases (OR 4.22, 95% confidence interval [0.92; 18.28]), emergency (3.91 [0.83; 18.43]) and intensive care units (1.80, [0.38; 8.58])Being an active smoker was protective (0.36 [0.21; 0.3]).
Antibody response to SARS-CoV-2 vaccination is extremely vivacious in subjects with previous SARS-CoV-2 infection
Authors: Callegaro Annapaola , Borleri Daniela , Farina Claudio , Napolitano Gavino , Valenti Daniela , Rizzi Marco , Maggiolo Franco 
Published: March 2021

AbstractBackgroundThe SARS-CoV-2 pandemic calls for rapid actions, now principally oriented to a world-wide vaccination campaign.In this study we verified if, in individuals with a previous SARS-CoV-2 infection, a single dose of mRNA vaccine would be immunologically equivalent to a full vaccine schedule in naïve individuals.MethodsHealth care workers (184) with a previous SARS-CoV-2 infection were sampled soon before the second dose of vaccine and between 7 and 10 days after the second dose, the last sampling time was applied to SARS-CoV-2 naïve individuals, too.Antibodies against SARS-CoV-2 were measured using Elecsys® Anti-SARS-CoV-2 S immunoassay.The study was powered for non-inferiority. We used non parametric tests and Pearson correlation test to perform inferential analysis.ResultsAfter a single vaccine injection, the median titer of specific antibodies in individuals with previous COVID-19 was 30,527 U/ml (IQR 19,992-39,288) and in subjects with previous SARS-CoV-2 asymptomatic infection was 19,367.5 U/ml (IQR 14,688-31,353) (P=0.032). Both results were far above the median titer in naïve individuals after a full vaccination schedule: 1,974.5 U/ml (IQR 895-3,455) (P<0.0001). Adverse events after vaccine injection were more frequent after the second dose of vaccine (mean 0.95, 95%CI from 0.75 to 1.14 versus mean 1.91, 95%CI from 1.63 to 2.19)(P<0.0001) and in exposed compared to naïve (mean 1.63; 95%CI from 1.28 to 1.98 versus mean 2.35; 95%CI from 1.87 to 2.82)(P=0.015).ConclusionIn SARS-CoV-2 naturally infected individuals a single mRNA vaccine dose seems sufficient to reach immunity. Modifying current dosing schedules would speed-up vaccination campaigns.
Global association of obesity and COVID-19 death rates
Authors: Adams Mary L. 
Published: March 2021

AbstractImportanceCOVID-19 was responsible for an enormous global death toll with large variation among countries.ObjectiveTo examine the possible impact of obesity on COVID-19 death rates.DesignMeasure associations between obesity rates in 2016 and COVID-19 deaths/million population through 2/25/2021, across countries.SettingGlobalParticipants167 countries for which obesity and death data were available, grouped by population size, with multiples of 10 countries in each of 8 groups plus a group including all 57 countries with obesity rates <15%.Outcome and measuresUsing Excel, COVID-19 deaths/million were regressed on the obesity rate for each country, based on obesity being a key factor in COVID hospitalizations and deaths. Using the least squares formula for the best fit for each model, R2, components of the formula, and the percentage of world population represented, were recorded for each group.ResultsObesity rates ranged from 2.1% to 37.9% and death rates ranged from 0.4/million to 1,892/million for groups representing up to 91% of global population. Results for the 8 population groups had R2 from 0.30 to 0.90 with slopes of the fitted line ranging from 27.9-51.0. Countries with obesity rates <15% had consistently low death rates (≤233/million), R2 of 0.003 and slope of the line=1.01.ConclusionsFor most countries about one-third of the difference in COVID death rates was due to obesity while in countries with obesity <15%, consistently low death rates were not associated with obesity. Reduced obesity rates could potentially have lowered the COVID death toll.
What role for asbestos in idiopathic pulmonary fibrosis? Findings from the IPF job exposures study
Authors: Reynolds Carl J , Sisodia Rupa , Barber Chris , Minelli Cosetta , Matteis Sara De , Moffatt Miriam , Cherrie John , Taylor Anthony Newman , Cullinan Paul , Fletcher Sophie , Walters Gareth , Spenser Lisa , Parfrey Helen , Saini Gauri , Chaudhuri Nazia , West Alex , Adamali Huzaifa , Beirne Paul , Forrest Ian , Gibbons Michael , Pepperell Justin , Hirani Nik , Harrison Kim , Dempsey Owen , O’Hickey Steve , Thickett David , Parekh Dhruv , Babu Suresh , Wilson Andrew , Chalmers George , Wickremasinghe Melissa , Coker Robina 
Published: March 2021

AbstractRationaleAsbestos is posited to cause otherwise ‘idiopathic’ pulmonary fibrosis (IPF); establishing this has important diagnostic and therapeutic implications.ObjectivesTo determine the association between occupational asbestos exposure and IPF; to investigate interaction with MUC5B rs35705950 genotype.MethodsMulti-centre, incident case-control study. Cases (n=494) were men diagnosed with IPF at 21 United Kingdom hospitals. Controls (n=466) were age-matched men who attended a hospital clinic in the same period. Asbestos exposure was measured using a validated job exposure matrix and a source-receptor model. The primary outcome was the association between asbestos exposure and IPF, estimated using logistic regression adjusted for age, smoking and centre. Interaction with MUC5B rs3570950 was investigated using a genetic dominant model.Measurements and Main Results327 (66%) cases and 293 (63%) controls ever had a high or medium asbestos exposure risk job; 8% of both cases and controls, had cumulative exposure estimates ≥ 25 fibre.ml−1.years. Occupational asbestos exposure was not associated with IPF, adjusted OR 1.1(95%CI 0.8-1.4; p=0.6) and there was no gene-environment interaction (p=0.2). Ever smoking was associated with IPF, OR 1.4 (95%CI 1-1.9; p=0.04). When stratifying for genotype there was significant interaction between smoking and work in an exposed job (p<0.01) for carriers of the minor allele of MUC5B rs3570950.ConclusionsOccupational asbestos exposure alone, or through interaction with MUC5B rs35705950 genotype, was not associated with IPF. However, exposure to asbestos and smoking interact to increase IPF risk in carriers of the minor allele of MUC5B rs3570950.Clinical trial registered with www.clinicaltrials.gov (NCT03211507).
A Data-driven Framework for Learning and Visualizing Characteristics of Thrombotic Event Phenotypes from Clinical Texts
Authors: Davoudi Anahita , Yang Audrey , Hwang Sy , Mowery Danielle L. 
Published: March 2021

AbstractAutomatically identifying thrombotic phenotypes based on clinical data, particularly clinical texts, can be challenging. Although many investigators have developed targeted information extraction methods for identifying thrombotic phenotypes from radiology notes, these methods can be time consuming to train, require large amounts of training data, and may miss subtle textual clues predictive of a thrombotic phenotype from notes beyond the radiology note. We developed a generalizable, data-driven framework for learning, characterizing, and visualizing clinical concepts from both radiology and discharge summaries predictive of thrombotic phenotypes.
Environmental drivers of SARS-CoV-2 lineage B.1.1.7 transmission intensity
Authors: Smith Thomas P. , Dorigatti Ilaria , Mishra Swapnil , Volz Erik , Walker Patrick G. T. , Ragonnet-Cronin Manon , Tristem Michael , Pearse William D. 
Published: March 2021

AbstractPrevious work has shown that environment affects SARS-CoV-2 transmission, but it is unclear whether emerging strains show similar responses. Here we show that, like other SARS-CoV-2 strains, lineage B.1.1.7 spread with greater transmission in colder and more densely populated parts of England. However, we also find evidence of B.1.1.7 having a transmission advantage at warmer temperatures compared to other strains. This implies that spring and summer conditions are unlikely to slow B.1.1.7’s invasion in Europe and across the Northern hemisphere - an important consideration for public health interventions.
The fast-slow continuum is not the end-game of life history evolution, human or otherwise
Authors: Salguero-Gómez Roberto 
Published: March 2021

AbstractLife history human evolution places a strong emphasis on the fast-slow continuum and pace-of-life continuum. Papers in this area frequently make a call for more integrative research to explore the relationships between the fast-slow continuum (population-level variation in traits) and pace-of-life continuum (ditto at the individual level). Here, using high-resolution demographic models from natural populations of 41 modern human populations, and hundreds of non-human animal populations and plant populations, I show that the fast-slow continuum, while of interest to explore variation in human strategies, should not be the sole focus of attention. Using a phylogenetically corrected principal component analysis, I show that other axes of life history variation show great promise. Specifically, understanding of the mechanisms of inter-specific and intra-specific differences in senescence rates in reproduction and survival, and how species respond to stochastic variation, I argue, should become the focus of my interdisciplinary research. The proposed new axis of demographic buffering-lability emerges as an important one to explain over 20% of variation in human and non-human populations. I show that these axes help predict demographic resilience, and also correlates with human nation per capita GDP and population growth rates.
Contribution of SARS-CoV-2 accessory proteins to viral pathogenicity in K18 hACE2 transgenic mice
Authors: Silvas Jesus , Morales-Vasquez Desarey , Park Jun-Gyu , Chiem Kevin , Torrelles Jordi B. , Platt Roy Neal , Anderson Tim , Ye Chengjin , Martinez-Sobrido Luis 
Published: March 2021

ABSTRACTSevere Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is the viral pathogen responsible for the current coronavirus disease 2019 (COVID-19) pandemic. To date, it is estimated that over 113 million individuals have been infected with SARS-CoV-2 and over 2.5 million human deaths have been recorded worldwide. Currently, three vaccines have been approved by the Food and Drug Administration for emergency use only. However much of the pathogenesis observed during SARS-CoV-2 infection remains elusive. To gain insight into the contribution of individual accessory open reading frame (ORF) proteins in SARS-CoV-2 pathogenesis, we used our recently described reverse genetics system approach to successfully engineer recombinant (r)SARS-CoV-2, where we individually removed viral 3a, 6, 7a, 7b, and 8 ORF proteins, and characterized these recombinant virusesin vitroandin vivo. Our results indicate differences in plaque morphology, with ORF deficient (ΔORF) viruses producing smaller plaques than those of the wild-type (rSARS-CoV-2/WT). However, growth kinetics of ΔORF viruses were like those of rSARS-CoV-2/WT. Interestingly, infection of K18 human angiotensin converting enzyme 2 (hACE2) transgenic mice with the ΔORF rSARS-CoV-2 identified ORF3a and ORF6 as the major contributors of viral pathogenesis, while ΔORF7a, ΔORF7b and ΔORF8 rSARS-CoV-2 induced comparable pathology to rSARS-CoV-2/WT. This study demonstrates the robustness of our reverse genetics system to generate rSARS-CoV-2 and the major role for ORF3a and ORF6 in viral pathogenesis, providing important information for the generation of attenuated forms of SARS-CoV-2 for their implementation as live-attenuated vaccines for the treatment of SARS-CoV-2 infection and associated COVID-19.IMPORTANCEDespite great efforts put forward worldwide to combat the current coronavirus disease 2019 (COVID-19) pandemic, Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) continues to be a human health and socioeconomic threat. Insights into the pathogenesis of SARS-CoV-2 and contribution of viral proteins to disease outcome remains elusive. Our study aims to determine the contribution of SARS-CoV-2 accessory open reading frame (ORF) proteins in viral pathogenesis and disease outcome, and develop a synergistic platform combining our robust reverse genetics system to generate recombinant (r)SARS-CoV-2 with a validated rodent model of infection and disease. We demonstrated that SARS-CoV-2 ORF3a and ORF6 contribute to lung pathology and ultimately disease outcome in K18 hACE2 transgenic mice, while ORF7a, ORF7b, and ORF8 have little impact on disease outcome. Moreover, our combinatory platform serves as the foundation to generate attenuated forms of the virus to develop live-attenuated vaccines for the treatment of SARS-CoV-2.