bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative effectiveness of ChAdOx1 versus BNT162b2 COVID-19 vaccines in Health and Social Care workers in England: a cohort study using OpenSAFELY
Authors: Hulme William J , Williamson Elizabeth J , Green Amelia , Bhaskaran Krishnan , McDonald Helen I , Rentsch Christopher T , Schultze Anna , Tazare John , Curtis Helen J , Walker Alex J , Tomlinson Laurie , Palmer Tom , Horne Elsie , MacKenna Brian , Morton Caroline E , Mehrkar Amir , Fisher Louis , Bacon Seb , Evans Dave , Inglesby Peter , Hickman George , Davy Simon , Ward Tom , Croker Richard , Eggo Rosalind M , Wong Angel YS , Mathur Rohini , Wing Kevin , Forbes Harriet , Grint Daniel , Douglas Ian J , Evans Stephen JW , Smeeth Liam , Bates Chris , Cockburn Jonathan , Parry John , Hester Frank , Harper Sam , Sterne Jonathan AC , Hernán Miguel , Goldacre Ben 
Published: October 2021

AbstractObjectivesTo compare the effectiveness of the BNT162b2 mRNA (Pfizer-BioNTech) and the ChAdOx1 (Oxford-AstraZeneca) COVID-19 vaccines against infection and COVID-19 disease in health and social care workers.DesignCohort study, emulating a comparative effectiveness trial.SettingLinked primary care, hospital, and COVID-19 surveillance records available within the OpenSAFELY-TPP research platform.Participants317,341 health and social care workers vaccinated between 4 January and 28 February 2021, registered with a GP practice using the TPP SystmOne clinical information system in England, and not clinically extremely vulnerable.InterventionsVaccination with either BNT162b2 or ChAdOx1 administered as part of the national COVID-19 vaccine roll-out.Main outcome measuresRecorded SARS-CoV-2 positive test, or COVID-19 related Accident and Emergency attendance or hospital admission occurring within 20 weeks of vaccination.ResultsThe cumulative incidence of each outcome was similar for both vaccines during the first 20 weeks post-vaccination. The cumulative incidence of recorded SARS-CoV-2 infection 6 weeks after vaccination with BNT162b2 was 19.2 per 1000 people (95%CI 18.6 to 19.7) and with ChAdOx1 was 18.9 (95%CI 17.6 to 20.3), representing a difference of -0.24 per 1000 people (95%CI -1.71 to 1.22). The difference in the cumulative incidence per 1000 people of COVID-19 accident and emergency attendance at 6 weeks was 0.01 per 1000 people (95%CI -0.27 to 0.28). For COVID-19 hospital admission, this difference was 0.03 per 1000 people (95%CI -0.22 to 0.27).ConclusionsIn this cohort of healthcare workers where we would not anticipate vaccine type to be related to health status, we found no substantial differences in the incidence of SARS-CoV-2 infection or COVID-19 disease up to 20 weeks after vaccination. Incidence dropped sharply after 3-4 weeks and there were very few COVID-19 hospital attendance and admission events after this period. This is in line with expected onset of vaccine-induced immunity, and suggests strong protection against COVID-19 disease for both vaccines.
Differentiating COVID-19 and dengue from other febrile illnesses in co-epidemics: Development and internal validation of COVIDENGUE scores
Authors: Gérardin Patrick , Maillard Olivier , Bruneau Léa , Accot Frédéric , Legrand Florian , Poubeau Patrice , Manaquin Rodolphe , Andry Fanny , Bertolotti Antoine , Levin Cécile 
Published: October 2021

AbstractBackgroundFrom a cohort study, we developed two scores to discriminate coronavirus 2019 (COVID-19) from dengue and other febrile illnesses (OFIs).MethodsAll subjects suspected of COVID-19 who attended the SARS-CoV-2 testing center of Saint-Pierre hospital, Reunion, between March 23 and May 10, 2020, were assessed for identifying predictors of both infectious diseases from a multinomial logistic regression model. Two scores were developed after weighting the odd ratios then validated by bootstrapping.ResultsOver 49 days, 80 COVID-19, 60 non-severe dengue and 872 OFIs were diagnosed. The translation of the best fit model yielded two scores composed of 11 criteria: contact with a COVID-19 positive case (+3 points for COVID-19; 0 point for dengue), return from travel abroad within 15 days (+3/-1), previous individual episode of dengue (+1/+3), active smoking (−3/0), body ache (0/+5), cough (0/-2), upper respiratory tract infection symptoms (−1/-1), anosmia (+7/-1), headache (0/+5), retro-orbital pain (−1/+5), and delayed presentation (>3 days) to hospital (+1/0). The area under the receiver operating characteristic curve was 0.79 (95%CI 0.76-0.82) for COVID-19 score and 0.88 (95%CI 0.85-0.90) for dengue score. Calibration was satisfactory for COVID-19 score and excellent for dengue score. For predicting COVID-19, sensitivity was 97% at the 0-point cut-off and specificity 99% at the 10-point cut-off. For predicting dengue, sensitivity was 97% at the 3-point cut-off and specificity 98% at the 11-point cut-off.ConclusionsThe COVIDENGUE scores proved discriminant to differentiate COVID-19 and dengue from OFIs in the context of SARS-CoV-2 testing center during a co-epidemic.
Medical genetics workforce in Brazil: practitioners, services, and disease distribution
Authors: Bonilla Carolina , Sortica Vinicius Albuquerque , Schuler-Faccini Lavinia , Matijasevich Alicia , Scheffer Mário C. 
Published: October 2021

AbstractPurposeIn anticipation of the implementation of personalized medicine (PM) in Brazil we assessed the demographic characteristics of its medical genetics workforce together with the distribution of rare genetic diseases (RGD) and hereditary cancer syndromes (HCS) across municipalities in the country.MethodsWe used demographic data from an earlier report on medical specialties, and open databases providing summarized data on the public and private healthcare systems, for the years 2019 and 2020. In the public system we considered RGD live births and hospitalizations, and HCS mortality. In the private system we obtained data on RGD, HCS and genetic counselling appointments.ResultsThe 332 registered medical geneticists (MGs) were mostly female, attended a public medical school, and were predominantly registered in the Southeast. The distribution of MGs overlapped the country-wise distribution of all types of genetic disease and service examined, indicating that ∼30% of the patient population has access to a MG specialist.ConclusionThe Brazilian MG workforce is concentrated in the richest and most populated areas and while it covers a significant proportion of the population there are vast regions with very limited services. The public health system should address these inequalities for a successful transition to PM.
Persistence of antibody and T cell responses to the Sinopharm/BBIBP-CorV vaccine in Sri Lankan individuals
Authors: Jeewandara Chandima , Aberathna Inoka Sepali , Pushpakumara Pradeep Darshana , Kamaladasa Achala , Guruge Dinuka , Wijesinghe Ayesha , Gunasekera Banuri , Tanussiya Shyrar , Kuruppu Heshan , Ranasinghe Thushali , Dayarathne Shashika , Dissanayake Osanda , Gamalath Nayanathara , Ekanayake Dinithi , Jayamali Jeewantha , Jayathilaka Deshni , Dissanayake Madushika , Jayadas Tibutius Thanesh , Mudunkotuwa Anushika , Somathilake Gayasha , Harvie Michael , Nimasha Thashmi , Danasekara Saubhagya , Wijayamuni Ruwan , Schimanski Lisa , Rijal Pramila , Tan Tiong K. , Dong Tao , Townsend Alain , Ogg Graham S. , Malavige Gathsaurie Neelika 
Published: October 2021

AbstractBackgroundTo determine the kinetics and persistence of immune responses following the Sinopharm/BBIBP-CorV, we investigated immune responses in a cohort of Sri Lankan individuals.MethodsSARS-CoV-2 specific total antibodies were measured in 20-to-39 year (n=61), 40-to-59-year and those >60 years of age (n=22) by ELISA, 12 weeks after the second dose of the vaccine. ACE2 receptor blocking antibodies (ACE2R-Ab), antibodies to the receptor binding domain (RBD) of the ancestral virus (WT) and variants of concern, were measured in a sub cohort. T cell responses and memory B cell responses were assessed by ELISpot assays.Results193/203 (95.07%) of individuals had detectable SARS-CoV-2 specific total antibodies, while 67/110 (60.9%) had ACE2R-Ab. 14.3% to 16.7% individuals in the 20 to 39 age groups had detectable antibodies to the RBD of the WT and VOC, while the positivity rates of those >60 years of age was <10%. 14/49 (28.6%) had IFNγ ELISpot responses to overlapping peptides of the spike protein, while memory B cell responses were detected in 9/20 to the S1 recombinant protein. The total antibody levels and ACE2R-Ab declined after 2 to 12 weeks from the second dose, while ex vivo T cell responses remained unchanged. The decline in ACE2R-Ab levels was significant among the 40 to 59 (p=0.0007) and ≥60 (p=0.005) age groups.ConclusionsAntibody responses declined in all age groups, especially in those >60 years, while T cell responses persisted. The effect of waning of immunity on hospitalization and severe disease should be assessed by long term efficacy studies.
Applying Behavioral Nudges in a Dietary Comparator for Surgical Trials: Developing the MediDiet
Authors: Zhang Irene Y. , Norwitz Daniel , Drewnowski Adam , Agrawal Nidhi , Flum David R. , Liao Joshua M. 
Published: October 2021

AbstractIntroductionThe Mediterranean diet is being studied as an alternative to surgery for common gastrointestinal conditions. However, dietary change can be challenging. “Nudges” – behavioral science strategies seeking to influence cognitive processes to promote good behaviors – may help. We conducted a pilot study evaluating the acceptability of the MediDiet, a behaviorally designed dietary intervention incorporating nudges and recommendations based on the Mediterranean Diet.MethodsWe conducted a three-phase pilot study involving parallel randomized surveys of U.S. adults. After completing a validated questionnaire assessing dietary consistency with a Mediterranean diet, participants were randomized to feedback containing no nudge versus nudge: peer comparison; peer comparison + positive affect induction; or default. Participants then rated their positive and negative emotions, motivation for dietary change, and interest in recipes. Responses were analyzed using baseline covariate-adjusted regression.ResultsAmong 1,709 participants, 56% were men, 73% were White, and the mean age was 38. In response to dietary feedback, participants reported low negative emotions, high positive emotions, moderate motivation for dietary change and high interest in recipes. Nudges did not affect the extent of negative (p=0.104) or positive (p=0.34) emotions, motivation (p=0.139), or interest (p=0.86). In exploratory analyses, those with moderate and high consistency with the Mediterranean diet, with or without nudges, reported lower negative affect, greater positive affect, greater motivation, and greater interest in recipes, than the minimally consistent, no nudge group.ConclusionDelivering dietary feedback based on the Mediterranean diet using behavioral nudges was acceptable among U.S. adults, rousing positive reactions without triggering negative ones. As early evidence, this pilot study provides the basis for testing nudge-based dietary guidance among individuals with symptomatic gallstones, diverticulitis, and other gastrointestinal diseases.HighlightsThe MediDiet is being developed as a novel, behaviorally designed dietary intervention for the non-operative management of common gastrointestinal conditions including symptomatic gallstones and diverticulitis, classically managed with surgery.In this exploratory pilot study, delivering dietary feedback based on the Mediterranean diet using behavioral nudges was acceptable among U.S. adults.This foundational work will help serve as the basis for testing nudge-based dietary guidance among individuals with symptomatic gallstones, diverticulitis, and other gastrointestinal diseases, and ultimately conducting clinical trials to compare dietary interventions to surgical management for these conditions.
Fetal brain growth and infant autistic traits
Authors: Aydin Ezra , Tsompanidis Alex , Chaplin Daren , Hawkes Rebecca , Allison Carrie , Hackett Gerald , Austin Topun , Padaigaitė Eglė , Gabis Lidia V. , Sucking John , Holt Rosemary , Baron-Cohen Simon 
Published: October 2021

AbstractBackgroundResearch indicates that structural differences exist in the brains of individuals who later display developmental conditions (e.g., autism). To date only a handful of studies have explored the relationship between fetal brain growth and later infant outcomes, with a particular focus on fetal head circumference (HC) as a proxy for brain development. These findings have been inconsistent. We investigate whether fetal brain measurements correlate with the emergence of autistic traits in toddlers.Method219 singleton pregnancies (104 males and 115 females) were recruited at the Rosie Hospital, Cambridge, UK. A 2D ultrasound was performed at 12-, 20- and between 26-30-weeks of pregnancy, measuring head circumference (HC), ventricular atrium (VA) and transcerebellar diameter (TCD). 178 infants were subsequently followed up at 18-20 months of age and completed the Quantitative Checklist for Autism in Toddlers (Q-CHAT) to observe early autistic traits.ResultsHC was larger in males than in females in both the second and third trimester. There was a significant positive association between TCD size at 20 weeks and Q-CHAT scores at 18-20 months of age, found in both univariate and multivariate analyses, and this remained significant after controlling for sex.ConclusionThere is a positive relationship between cerebellar (TCD) development at 20 weeks’ gestation and the later emergence of autistic traits (at 18-20 months of age). Atypical neurodevelopment may start prenatally. If replicated these findings could facilities early diagnosis and improved outcomes.
Factors associated with severity of COVID-19 disease in a multicenter cohort of people with HIV in the United States, March-December 2020
Authors: Shapiro Adrienne E. , Bender Ignacio Rachel A. , Whitney Bridget M. , Delaney Joseph A. , Nance Robin M. , Bamford Laura , Wooten Darcy , Keruly Jeanne C. , Burkholder Greer , Napravnik Sonia , Mayer Kenneth H. , Webel Allison R. , Kim H. Nina , Van Rompaey Stephen E. , Christopoulos Katerina , Jacobson Jeffrey , Karris Maile , Smith Davey , Johnson Mallory O. , Willig Amanda , Eron Joseph J. , Hunt Peter , Moore Richard D. , Saag Michael S. , Mathews W. Christopher , Crane Heidi M. , Cachay Edward R. , Kitahata Mari M. ,   for the CFAR Network of Integrated Clinical Systems
Published: October 2021

AbstractBackgroundUnderstanding the spectrum of SARS-CoV-2 infection and COVID-19 disease in people with HIV (PWH) is critical to provide clinical guidance and implement risk-reduction strategies.ObjectiveTo characterize COVID-19 in PWH in the United States and identify predictors of disease severity.DesignObservational cohort study.SettingGeographically diverse clinical sites in the CFAR Network of Integrated Clinical Systems (CNICS)ParticipantsAdults receiving HIV care through December 31, 2020.MeasurementsCOVID-19 cases and severity (hospitalization, intensive care, death).ResultsOf 16,056 PWH in care, 649 were diagnosed with COVID-19 between March-December 2020. Case fatality was 2%; 106 (16.3%) were hospitalized and 12 died. PWH with current CD4 count <350 cells/mm3(aRR 2.68; 95%CI 1.93-3.71; P<.001) or lowest recorded CD4 count <200 (aRR 1.67; 95%CI 1.18-2.36; P<.005) had greater risk of hospitalization. HIV viral load suppression and antiretroviral therapy (ART) status were not associated with hospitalization, although the majority of PWH were suppressed (86%). Black PWH were 51% more likely to be hospitalized with COVID-19 compared to other racial/ethnic groups (aRR 1.51; 95%CI 1.04-2.19, P=.03). Chronic kidney disease (CKD), chronic obstructive pulmonary disease, diabetes, hypertension, obesity, and increased cardiovascular and hepatic fibrosis risk scores were associated with higher risk of hospitalization. PWH who were older, not on ART, with current CD4 <350, diabetes, and CKD were overrepresented amongst PWH who required intubation or died.LimitationsUnable to compare directly to persons without HIV; underestimate of total COVID-19 cases.ConclusionsPWH with CD4 <350 cells/mm3, low CD4/CD8 ratio, and history of CD4 <200, have a clear excess risk of severe COVID-19, after accounting for comorbidities also associated with severe outcomes. PWH with these risk factors should be prioritized for COVID-19 vaccination, early treatment, and monitored closely for worsening illness.
SVRare: discovering disease-causing structural variants in the 100K Genomes Project
Authors: Yu Jing , Szabo Anita , Pagnamenta Alistair T , Shalaby Ahmed , Giacopuzzi Edoardo , Taylor Jenny , Shears Deborah , Pontikos Nikolas , Wright Genevieve , Michaelides Michel , Halford Stephanie , Downes Susan ,   Genomics England Research Consortium
Published: October 2021

AbstractDiscovery of disease-causing structural variants (dcSV) from whole genome sequencing data is difficult due to high number of false positives and a lack of efficient way to estimate allele frequency. Here we introduce SVRare, an application that aggregates structural variants (SV) called by other tools, and efficiently annotates rare SVs to aid dcSVs discovery.Applied in the Genomics England (GEL) research environment to data from the 100K Genomes Project, SVRare aggregated 554,060,126 SVs called by Manta and Canvas in all the 71,408 participants in the rare-disease arm. From a pilot study of 4313 families, SVRare identified 36 novel protein-coding disrupting SVs on diagnostic grade genes that may explain proband’s phenotype. It is estimated that SVRare can increase SV-based diagnosis yield by at least 4-fold. We also performed a genome-wide association study, and uncovered clusters of dcSVs in genes with known pathogenicity, such as PKD1/2 - cystic kidney diseases and LDLR - familial hypercholesterolaemia.
The usefulness of antigen testing in predicting contagiousness in COVID-19
Authors: Lopera Tulio J. , Alzate-Ángel Juan Carlos , Díaz Francisco J , Rugeles María T. , Aguilar-Jiménez Wbeimar 
Published: October 2021

AbstractIncreasing the diagnostic capacity of COVID-19 (SARS-CoV-2 infection) is required to improve case detection, reduce COVID-19 expansion, and boost the world economy. Rapid antigen detection tests are cheaper and easier to implement, but their diagnostic performance has been questioned compared to RT-PCR. Here, we evaluate the performance of the Standard Q COVID-19 antigen test for diagnosing SARS-CoV-2 infection and predicting contagiousness compared to RT-PCR and viral culture, respectively. The antigen test was 100.0% specific but only 40.9% sensitive for diagnosing infection compared to RT-PCR. Interestingly, SARS-CoV-2 contagiousness is highly unlikely with a negative antigen test since it exhibited a negative predictive value of 99.9% than viral culture. Furthermore, a cycle threshold (Ct) value of 18.1 in RT-PCR was shown to be the one that best predicts contagiousness (AUC 97.6%). Thus, screening people with antigen testing is a good approach to prevent SARS-CoV-2 contagion and allow returning to daily activities.
BugSplit: highly accurate taxonomic binning of metagenomic assemblies enables genome-resolved metagenomics
Authors: Chandrakumar Induja , Gauthier Nick P.G. , Nelson Cassidy , Bonsall Michael B. , Locher Kerstin , Charles Marthe , MacDonald Clayton , Krajden Mel , Manges Amee R. , Chorlton Samuel D. 
Published: October 2021

AbstractA large gap remains between sequencing a microbial community and characterizing all of the organisms inside of it. Here we develop a novel method to taxonomically bin metagenomic assemblies through alignment of contigs against a reference database. We show that this workflow, BugSplit, bins metagenome-assembled contigs to species with a 33% absolute improvement in F1-score when compared to alternative tools. We perform nanopore mNGS on patients with COVID-19, and using a reference database predating COVID-19, demonstrate that BugSplit’s taxonomic binning enables sensitive and specific detection of a novel coronavirus not possible with other approaches. When applied to nanopore mNGS data from cases ofKlebsiella pneumoniaeandNeisseria gonorrhoeaeinfection, BugSplit’s taxonomic binning accurately separates pathogen sequences from those of the host and microbiota, and unlocks the possibility of sequence typing,in silicoserotyping, and antimicrobial resistance prediction of each organism within a sample. BugSplit is available athttps://bugseq.com/academic.
The power of peer networking for improving STEM faculty job applications: a successful pilot program
Authors: Guardia Carlos M. , Kane Erin , Tebo Alison G. , Sanders Anna A.W.M. , Kaya Devrim , Grogan Kathleen E. 
Published: October 2021

AbstractIn order to successfully obtain a faculty position, postdoctoral fellows or ‘postdocs’, must submit an application which requires considerable time and effort to produce. These job applications are often reviewed by mentors and colleagues, but rarely are postdocs offered the opportunity to solicit feedback multiple times from reviewers with the same breadth of expertise often found on an academic search committee. To address this gap, this manuscript describes an international peer reviewing program for small groups of postdocs with a broad range of expertise to reciprocally and iteratively provide feedback to each other on their application materials. Over 145 postdocs have participated, often multiple times, over three years. A survey of participants in this program revealed that nearly all participants would recommend participation in such a program to other faculty applicants. Furthermore, this program was more likely to attract participants who struggled to find mentoring and support elsewhere, either because they changed fields or because of their identity as a woman or member of an underrepresented population in STEM. Participation in programs like this one could provide early career academics like postdocs with a diverse and supportive community of peer mentors during the difficult search for a faculty position. Such psychosocial support and encouragement has been shown to prevent attrition of individuals from these populations and programs like this one target the largest ‘leak’ in the pipeline, that of postdoc to faculty. Implementation of similar peer reviewing programs by universities or professional scientific societies could provide a valuable mechanism of support and increased chances of success for early-career academics in their search for independence.