bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating the impact of interventions against COVID-19: from lockdown to vaccination
Authors: Thompson James , Wattam Stephen 
Published: March 2021

AbstractCoronavirus disease 2019 (COVID-19) is an infectious disease of humans caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the first case was identified in China in December 2019 the disease has spread worldwide, leading to an ongoing pandemic. In this article, we present a detailed agent-based model of COVID-19 in Luxembourg, and use it to estimate the impact, on cases and deaths, of interventions including testing, contact tracing, lockdown, curfew and vaccination.Our model is based on collation, with agents performing activities and moving between locations accordingly. The model is highly heterogeneous, featuring spatial clustering, over 2000 behavioural types and a 10 minute time resolution. The model is validated against COVID-19 clinical monitoring data collected in Luxembourg in 2020.Our model predicts far fewer cases and deaths than the equivalent equation-based SEIR model. In particular, withR0= 2.45, the SEIR model infects 87% of the resident population while our agent-based model infects only around 23% of the resident population. Our simulations suggest that testing and contract tracing reduce cases substantially, but are less effective at reducing deaths. Lockdowns are very effective although costly, while the impact of an 11pm-6am curfew is relatively small. When vaccinating against a future outbreak, our results suggest that herd immunity can be achieved at relatively low levels, with substantial levels of protection achieved with only 30% of the population immune. When vaccinating in the midst of an outbreak, the challenge is more difficult. In this context, we investigate the impact of vaccine efficacy, capacity, hesitancy and strategy.We conclude that, short of a permanent lockdown, vaccination is by far the most effective way to suppress and ultimately control the spread of COVID-19.
Socioeconomic and geographic correlates of intimate partner violence in Sri Lanka: Analysis of the 2016 Demographic and Health Survey
Authors: Bandara Piumee , Knipe Duleeka , Munasinghe Sithum , Rajapakse Thilini , Page Andrew 
Published: March 2021

AbstractIntimate partner violence (IPV) is a serious public health issue and violation of human rights. The prevalence of IPV in South Asia is especially pronounced. This is the first study in Sri Lanka to examine the associations between socioeconomic position (SEP), geographical factors and IPV using nationally representative data. Data collected from Sri Lanka’s 2016 Demographic and Health Survey were analysed using multilevel logistic regression techniques. A total 16,390 eligible ever-partnered women aged 15-49 years were included in the analysis. Analyses were also stratified by ethnicity, type of violence, neighbourhood poverty and post-conflict residential status for selected variables. Consistent associations were found for low SEP and IPV. Lower educational attainment among women (OR 2.46 95% CI 1.83-3.30) and their partners (OR 2.87 95% CI 2.06-4.00), financial insecurity (OR 2.17 95% CI 1.92-2.45) and poor household wealth (OR 2.64 95% CI 2.22-3.13) were the socioeconomic factors that showed the strongest association with any IPV, after adjusting for age and religion. These associations predominately related to physical and/or sexual violence, with weak associations for psychological violence. Women living in a post-conflict environment had a higher risk (OR 2.96 95% CI 2.51-3.49) of IPV compared to other areas. Ethnic minority women (Tamil and Moor) were more likely to reside in post-conflict areas and experience poverty more acutely compared to the majority Sinhala women, which may explain the stronger associations for low SEP, post-conflict residence and IPV found among Tamil and Moor women. We found IPV is more likely to occur in the context of socioeconomic disadvantage and post-conflict regions. Further exploratory studies investigating the complex interplay of individual, household and community-level factors occurring in this context is required.
Rescaling and Small Area Estimation of Health Survey Data as applied to Smoking Rates in Allegheny County, Pennsylvania
Authors: Stacy Shaina L. , Chandra Hukum , Gurewitsch Raanan , Brink LuAnn L. , Robertson Linda B. , Wilson David O. , Yuan Jian-Min , Pyne Saumyadipta 
Published: March 2021

AbstractWe propose a novel, two-step method for rescaling health survey data and creating small area estimates of smoking rates using a Behavioral Risk Factor Surveillance System (BRFSS) survey administered in 2015 to participants living in Allegheny County, in the state of Pennsylvania, USA. The first step consisted of a spatial microsimulation to rescale location of survey respondents from zip codes to tracts based on census population distributions by age, sex, race, and education. The rescaling allowed us, in the second step, to utilize and select from available census tract specific ancillary data on social vulnerability for small area estimation (SAE) of local health risk using an area level version of a logistic linear mixed model. To demonstrate this new two-step algorithm, we estimated the ever-smoking rate for the census tracts of Allegheny County. The ever-smoking rate was slightly above 70% for two census tracts to the southeast of the city of Pittsburgh. Several tracts in the southern and eastern sections of Pittsburgh also had relatively high (>65%) ever-smoking rates. These small area estimates may be used in local public health efforts to target interventions and educational resources aimed at reducing cigarette smoking. Further, our new two-step methodology may be extended to small area estimation for other locations, and other health-related behaviors and outcomes.
Viability RT-PCR for SARS-CoV-2: a step forward to solve the infectivity quandary
Authors: Cuevas-Ferrando Enric , Randazzo Walter , Pérez-Cataluña Alba , Falcó Irene , Navarro David , Martin-Latin Sandra , Díaz-Reolid Azahara , Girón-Guzmán Inés , Allende Ana , Sánchez Gloria 
Published: March 2021

SummaryBackgroundIsolation, contact tracing and restrictions on social movement are being globally implemented to prevent and control onward spread of SARS-CoV-2, even though the infection risk modelled on RNA detection by RT-qPCR remains biased as viral shedding and infectivity are not discerned. Thus, we aimed to develop a rapid viability RT-qPCR procedure to infer SARS-CoV-2 infectivity in clinical specimens and environmental samples.MethodsWe screened monoazide dyes and platinum compounds as viability molecular markers on five SARS-CoV-2 RNA targets. A platinum chloride-based viability RT-qPCR was then optimized using genomic RNA, and inactivated SARS-CoV-2 particles inoculated in buffer, stool, and urine. Our results were finally validated in nasopharyngeal swabs from persons who tested positive for COVID-19 and in wastewater samples positive for SARS-CoV-2 RNA.FindingsWe established a rapid viability RT-qPCR that selectively detects potentially infectious SARS-CoV-2 particles in complex matrices. In particular, the confirmed positivity of nasopharyngeal swabs following the viability procedure suggests their potential infectivity, while the complete prevention of amplification in wastewater indicated either non-infectious particles or free RNA.InterpretationThe viability RT-qPCR approach provides a more accurate ascertainment of the infectious viruses detection and it may complement analyses to foster risk-based investigations for the prevention and control of new or re-occurring outbreaks with a broad application spectrum.FundingsThis work was supported by Spanish Scientific Research Council (CSIC), Generalitat Valenciana, and MICINN co-founded by AEI/FEDER, UE.
The vaccine-elicited immunoglobulin profile in milk after COVID-19 mRNA-based vaccination is IgG-dominant and lacks secretory antibodies
Authors: Fox Alisa , Norris Caroline , Amanat Fatima , Zolla-Pazner Susan , Powell Rebecca L. 
Published: March 2021

AbstractThe Pfizer/BioNTech and Moderna mRNA-based COVID-19 vaccines are licensed under emergency use authorization, with millions of doses already administered globally [1]. No COVID-19 vaccines are yet under investigation for use in infants or young children. As such, the passive immunity of the antibodies (Abs) provided through milk from a vaccinated person may be one of the only ways to protect this population until pediatric COVID-19 vaccines are licensed. Our early work (as well as an expanded study being published concurrently with this report) examining the milk Ab response after SARS-CoV-2 infection demonstrated that Spike-specific IgA in milk after infection is dominant and highly correlated with a secretory Ab response [2]. Determining if secretory Abs are elicited in milk is critical, as this Ab class is highly stable and resistant to enzymatic degradation in all mucosae - not only in the infant oral/nasal cavity and gut, but in the airways and GI tract as well [3, 4]. Presently, we describe our analysis of the milk Ab response 14 days after completion of an mRNA-based COVID-19 vaccine regimen among 10 individuals. It was evident that unlike the post-infection milk Ab profile, IgG dominates after COVID-19 vaccination. One hundred percent of post-vaccine milk contained significant levels of Spike-specific IgG, with 8/10 samples exhibiting high IgG endpoint titers. Conversely, 6/10 (60%) of post-vaccine samples were positive for Spike specific IgA, with only 1 (10%) exhibiting high IgA endpoint titer. Furthermore, 5/10 (50%) post-vaccine milk samples contained Spike-specific secretory Ab, none of which were found to be high-titer. As our analyses of the immune response in milk to COVID-19 vaccination continues, it will provide a critical opportunity to address huge knowledge gaps, inform the field as to which COVID-19 vaccine, if any, is likely to provide the best milk Ab response, and highlight the need to design improved vaccines with protection of the breastfeeding infant in mind.
Hemodynamic Differences Between Women and Men with Elevated Blood Pressure in China: A Non-Invasive Assessment of 45,082 Adults Using Impedance Cardiography
Authors: Caraballo César , Mahajan Shiwani , Gu Jianlei , Lu Yuan , Spatz Erica S. , Dreyer Rachel P. , Zhang MaoZhen , Sun NingLing , Ren Yihong , Zheng Xin , Zhao Hongyu , Lu Hui , Ma Zheng J. , Krumholz Harlan M. 
Published: March 2021

AbstractBackgroundWhether there are sex differences in hemodynamic profiles among people with elevated blood pressure is not well understood and could guide personalization of treatment.Methods and resultsWe described the clinical and hemodynamic characteristics of adults with elevated blood pressure in China using impedance cardiography. We included 45,082 individuals with elevated blood pressure (defined as systolic blood pressure of ≥130 mmHg or a diastolic blood pressure of ≥80 mmHg), of which 35.2% were women. Overall, women had a higher mean systolic blood pressure than men (139.0 [±15.7] mmHg vs 136.8 [±13.8] mmHg, P<0.001), but a lower mean diastolic blood pressure (82.6 [±9.0] mmHg vs 85.6 [±8.9] mmHg, P<0.001). After adjusting for age, region, and body mass index, women <50 years old had lower systemic vascular resistance index (beta-coefficient [β] -31.7; 95% CI: -51.2, -12.2) and higher cardiac index (β 0.07; 95% CI: 0.04, 0.09) than men of their same age group, whereas among those ≥50 years old women had higher systemic vascular resistance index (β 120.4; 95% CI: 102.4, 138.5) but lower cardiac index (β -0.15; 95% CI: -0.16, -0.13). Results were consistent with a propensity score matching sensitivity analysis, although the magnitude of the SVRI difference was lower and non-significant. However, there was substantial overlap between women and men in the distribution plots of these variables, with overlapping areas ranging from 78% to 88%.ConclusionsOur findings indicate that there are sex differences in hypertension phenotype, but that sex alone is insufficient to infer an individual’s profile.
Vitamin D-related polymorphisms and vitamin D levels as risk biomarkers of COVID-19 infection severity
Authors: Freitas Ana Teresa , Calhau Conceição , Antunes Gonçalo , Araújo Beatriz , Bandeira Matilde , Barreira Sofia , Bazenga Filipa , Braz Sandra , Caldeira Daniel , Santos Susana Constantino Rosa , Faria Ana , Faria Daniel , Fraga Marta , Nogueira-Garcia Beatriz , Gonçalves Lúcia , Kovalchuk Pavlo , Lacerda Luísa , Lopes Hugo , Luís Daniel , Medeiros Fábio , Melo Ana M. P. , Melo-Cristino José , Miranda Ana , Pereira Clara , Pinto Ana Teresa , Pinto João , Proença Helena , Ramos Angélica , P. R. Rato João , Rocha Filipe , César Rocha Júlio , Moreira-Rosário André , Vazão Helena , Volovetska Yuliya , Guimarães João-Tiago , Pinto Fausto 
Published: March 2021

AbstractBackgroundVitamin D is a fundamental regulator of host defences by activating genes related to innate and adaptive immunity. Previous research shows a correlation between the levels of vitamin D in patients infected with SARS-CoV-2 and the degree of disease severity. This work investigates the impact of the genetic background related to vitamin D pathways on COVID-19 severity. For the first time, the Portuguese population was characterized regarding the prevalence of high impact variants in genes associated with the vitamin D pathways.MethodsThis study enrolled 517 patients admitted to two tertiary Portuguese hospitals. The serum concentration of 25 (OH)D, was measured in the hospital at the time of patient admission. Genetic variants, 18 variants, in the genes AMDHD1, CYP2R1, CYP24A1, DHCR7, GC, SEC23A, and VDR were analysed.ResultsThe results show that polymorphisms in the vitamin D binding protein encoded by the GC gene are related to the infection severity (p = 0.005). There is an association between vitamin D polygenic risk score and the serum concentration of 25 (OH)D (p = 0.042). There is an association between 25 (OH)D levels and the survival and fatal outcomes (p = 1.5e-4). The Portuguese population has a higher prevalence of the DHCR7 RS12785878 variant when compared with its prevalence in the European population (19% versus 10%).ConclusionThis study shows a genetic susceptibility for vitamin D deficiency that might explain higher severity degrees in COVID-19 patients. These results reinforce the relevance of personalized strategies in the context of viral diseases.Trial registrationNCT04370808
Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19
Authors: Tsitsiklis Alexandra , Zha Beth Shoshana , Byrne Ashley , DeVoe Catherine , Rackaityte Elze , Levan Sophia , Sunshine Sara , Mick Eran , Ghale Rajani , Love Christina , Tarashansky Alexander J. , Pisco Angela , Albright Jack , Jauregui Alejandra , Sarma Aartik , Neff Norma , Serpa Paula Hayakawa , Deiss Thomas J. , Kistler Amy , Carrillo Sidney , Ansel K. Mark , Leligdowicz Aleksandra , Christenson Stephanie , Detweiler Angela , Jones Norman G. , Wu Bing , Darmanis Spyros , Lynch Susan V. , DeRisi Joseph L. ,   COMET Consortium, Matthay Michael A. , Hendrickson Carolyn M. , Kangelaris Kirsten N. , Krummel Matthew F. , Woodruff Prescott G. , Erle David J. , Rosenberg Oren , Calfee Carolyn S. , Langelier Charles R. 
Published: March 2021

AbstractSecondary bacterial infections, including ventilator-associated pneumonia (VAP), lead to worse clinical outcomes and increased mortality following viral respiratory infections including in patients with coronavirus disease 2019 (COVID-19). Using a combination of tracheal aspirate bulk and single-cell RNA sequencing we assessed lower respiratory tract immune responses and microbiome dynamics in 23 COVID-19 patients, 10 of whom developed VAP, and eight critically ill uninfected controls. At a median of three days (range: 2-4 days) before VAP onset we observed a transcriptional signature of bacterial infection. At a median of 15 days prior to VAP onset (range: 8-38 days), we observed a striking impairment in immune signaling in COVID-19 patients who developed VAP. Longitudinal metatranscriptomic analysis revealed disruption of lung microbiome community composition in patients with VAP, providing a connection between dysregulated immune signaling and outgrowth of opportunistic pathogens. These findings suggest that COVID-19 patients who develop VAP have impaired antibacterial immune defense detectable weeks before secondary infection onset.
Optimizing SARS-CoV-2 Variant of Concern Screening: Experience from British Columbia, Canada, Early 2021
Authors: Hogan Catherine A. , Sbihi Hind , Jassem Agatha , Prystajecky Natalie , Tyson John R. , Lee Tracy D. , Tsang Frankie , Ng Corrinne , Janz Loretta , Romney Marc G. , Hoang Linda 
Published: March 2021

AbstractComprehensive and timely testing is required for SARS-CoV-2 variant of concern (VoC) screening. Whole genome sequencing (WGS) provides the broadest means to detect circulating VoCs, but requires longer turnaround time than targeted molecular testing by quantitative polymerase chain reaction (qPCR). We demonstrated the feasibility of a combined testing approach for VoC prevalence assessment in British Columbia, and showed high concordance between qPCR testing and WGS. This directly informed wider VoC screening strategy implementation, and public health efforts.
High-dimensional analysis reveals abnormal B cell subsets associated with specific changes to circulating T and myeloid cell populations in patients with idiopathic inflammatory myopathies
Authors: Wilfong Erin M. , Bartkowiak Todd , Vowell Katherine N. , Westlake Camille S. , Irish Jonathan M. , Kendall Peggy L. , Crofford Leslie J. , Bonami Rachel H. 
Published: March 2021

AbstractObjectivesThe idiopathic inflammatory myopathies (IIM) are a clinically heterogeneous group of conditions affecting the skin, muscle, joint, and lung in various combinations. This study aims to investigate the immunologic heterogeneity through detailed immunophenotyping of peripheral blood mononuclear cells (PBMCs) in IIM patients and healthy controls.MethodsWe collected PBMCs from 17 patients with a clinical diagnosis of inflammatory myositis in the inpatient or outpatient setting and performed immunophenotyping using mass cytometry by time of flight (CyTOF) to simultaneously characterize B, T, and myeloid cell subsets. Data were analyzed using a combination of supervised biaxial gating and unsupervised clustering algorithms including t-distributed stochastic neighbor embedding (tSNE), cluster identification, characterization, and regression (CITRUS), and marker enrichment modeling (MEM).ResultsWe identified two distinct immune signatures amongst IIM patients. In one signature, increased CD19+CXCR4hiCCR7hi cells correlated with increased CD3+CXCR4hiCD38hi (r=0.62, p=0.009) and CD14+CD16-CXCR4+CD38+HLADR-(r=0.61, p=0.01) populations. In the second signature, increased CD19+CD21loCD11c+ cells correlated with an increased CD3+CD4+PD1+ (r=0.60, p=0.01) population. Other shared immunologic features amongst IIM patients compared to healthy controls included decreased surface expression of RP105/CD180 on B cells (median mass intensity 39.9 ± 16.0 v. 60.9 ± 20.1, p=0.002). In the T cell compartment, all circulating CD3+CXCR3+ subsets (2.7 ± 2.4 v. 9.6 ± 8.1% of all PBMCs, p=0.0004) were reduced.ConclusionBased on circulating B cell phenotype, we identified two distinct immunologic signatures in IIM patients. Future work is needed to determine the significance of these immune signatures for clinical manifestations and treatment responses.
Seroprevalence of antibodies against SARS-CoV-2 virus in the adult Norwegian population, winter 2020/2021: pre-vaccination period
Authors: Anda Erik Eik , Braaten Tonje , Borch Kristin B. , Nøst Therese H. , Chen Sairah L. F. , Lukic Marko , Lund Eiliv , Forland Frode , Leon David , Winje Brita Askeland , Kran Anne-Marte Bakken , Kalager Mette , Johansen Fridtjof Lund , Sandanger Torkjel M. 
Published: March 2021

AbstractSince early 2020, over 123 million people worldwide have been diagnosed with coronavirus disease (Covid-19), but the true number of infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is undoubtedly higher. The seroprevalence of antibodies against SARS-CoV-2 can provide crucial epidemiological information about the extent of infections independent of virologically detected case numbers. There is no large population-based SARS-CoV-2 seroprevalence survey from Norway; thus we estimated SARS-CoV-2 seroprevalence in Norway before the introduction of vaccines and described its distribution across demographic groups. In November-December 2020, a total of 110,000 people aged 16 years or older were randomly selected from the National Population Register and invited to complete a questionnaire and provide a dried blood spot (DBS) sample. The response rate was 30%; compliance rate for return of DBS samples was 88%. The national weighted and adjusted seroprevalence was 0.9% (confidence interval 0.7-1.0).Seroprevalence was highest among those aged 16-19 years (1.9%, 0.9-2.9), those born outside the Nordic countries 1.4% (1.0-1.9), and in the counties of Oslo 1.7 % (1.2-2.2) and Vestland 1.4% (0.9-1.8). The ratio of SARS-CoV-2 seroprevalence (0.9) to the cumulative incidence of virologically detected cases by mid-December 2020 (0.8%) was slightly above one. SARS-CoV-2 seroprevalence was low before the introduction of vaccines in Norway and was comparable to virologically detected cases, indicating that most cases in the first 10 months of the pandemic were detected. Preventive measures including contact tracing have been effective, people are complying with social distancing recommendations, and local efforts to contain outbreaks have been essential.