bluuebunny/crossref_metadata_2025_split huggingface dataset:
Educational attainment as a modifier of the effect of polygenic scores for cardiovascular risk factors: cross-sectional and prospective analysis of UK Biobank
Authors: Carter Alice R , Harrison Sean , Gill Dipender , Smith George Davey , Taylor Amy E , Howe Laura D , Davies Neil M 
Published: March 2021

AbstractBackgroundUnderstanding the interplay between educational attainment and genetic predictors of cardiovascular risk may improve our understanding of mechanisms relating educational attainment to cardiovascular disease.MethodsIn up to 320 120 UK Biobank participants of White British ancestry (mean age = 57, female 54%), we created polygenic scores for nine cardiovascular risk factors or diseases: alcohol consumption, body mass index, low-density lipoprotein cholesterol, lifetime smoking behaviour, systolic blood pressure, atrial fibrillation, coronary heart disease, type 2 diabetes and stroke. We estimated whether educational attainment modified genetic susceptibility to these risk factors and diseases.ResultsOn the additive scale, higher educational attainment reduced genetic susceptibility to higher BMI, smoking, atrial fibrillation and type 2 diabetes, but increased genetic susceptibility to higher LDL-C and higher systolic blood pressure.On the multiplicative scale, there was evidence that higher educational attainment increased genetic susceptibility to atrial fibrillation and coronary heart disease, but no evidence of effect modification was found for all other considered traits.ConclusionsEducational attainment modifies the genetic susceptibility to some cardiovascular risk factors and diseases. The direction of this effect was mixed across traits considered and differences in associations between the effect of the polygenic score across strata of educational attainment was uniformly small. Therefore, any effect modification by education of genetic susceptibility to cardiovascular risk factors or diseases is unlikely to contribute substantially to the mechanisms driving inequalities in cardiovascular risk.Key MessagesThe role of educational attainment in modifying the effect of polygenic scores for a wide range of cardiovascular risk factors or diseases has not previously been studiedWe explore whether educational attainment modifies the effects of polygenic susceptibility to alcohol consumption, body mass index, low-density lipoprotein cholesterol, lifetime smoking behaviour, systolic blood pressure, atrial fibrillation, coronary heart disease, type 2 diabetes and strokeEffect modification by education was observed for some cardiovascular polygenic scores, but not all.Effects were not always in the hypothesised direction and were dependent on the scale of analysis.Modification of the effect of genetic susceptibility to cardiovascular risk factors or cardiovascular disease by educational attainment is unlikely to contribute substantially to the mechanisms driving inequalities in cardiovascular risk.
Head-to-head performance comparison of self-collected nasal versus professional-collected nasopharyngeal swab for a WHO-listed SARS-CoV-2 antigen-detecting rapid diagnostic test
Authors: Klein Julian A.F. , Krüger Lisa J. , Tobian Frank , Gaeddert Mary , Lainati Federica , Schnitzler Paul , Lindner Andreas K. , Nikolai Olga , Knorr B. , Welker A. , de Vos Margaretha , Sacks Jilian A. , Escadafal Camille , Denkinger Claudia M. ,   for the study team
Published: March 2021

BackgroundIn 2020, the World Health Organization (WHO) recommended two SARS-CoV-2 lateral flow antigen detecting rapid diagnostics tests (Ag-RDTs), both initially with nasopharyngeal (NP) sample collection. Independent head-to-head studies demonstrated for SARS-CoV-2 Ag-RDTs nasal sampling to be a comparable and reliable alternative for nasopharyngeal (NP) sampling.MethodsWe conducted a head-to-head comparison study of a supervised, self-collected nasal mid-turbinate (NMT) swab and a professional-collected NP swab, using the Panbio Ag-RDT (the second WHO-listed SARS-CoV-2 Ag-RDT, distributed by Abbott). We calculated positive and negative percent agreement and, compared to the reference standard reverse transcription polymerase chain reaction (RT-PCR), sensitivity and specificity for both sampling techniques.ResultsA SARS-CoV-2 infection could be diagnosed by RT-PCR in 45 of 290 participants (15.5%). Comparing the NMT and NP sampling the positive percent agreement of the Ag-RDT was 88.1% (37/42 PCR positives detected; CI 75.0% - 94.8%). The negative percent agreement was 98.8% (245/248; CI 96.5% - 99.6%). The overall sensitivity of Panbio with NMT sampling was 84.4% (38/45; CI 71.2% - 92.3%) and 88.9% (40/45; CI 76.5% - 95.5%) with NP sampling. Specificity was 99.2% (243/245; CI 97.1% - 99.8%) for both, NP and NMT sampling. The sensitivity of the Panbio test in participants with high viral load (> 7 log10 SARS-CoV-2 RNA copies/mL) was 96.3% (CI 81.7% - 99.8%) for both, NMT and NP sampling.ConclusionFor the Panbio Ag-RDT supervised NMT self-sampling yields to results comparable to NP sampling. This suggests that nasal self-sampling could be used for scale-up population testing.
COVID-19 in Children with Brain-Based Developmental Disabilities: A Rapid Review Update
Authors: Dugas Michèle , Stéfan Théo , Lépine Johanie , Blouin Patrick , Poirier Andrée-Anne , Carnovale Valérie , Mailhot Benoit , Skidmore Becky , Faust Lena , Costello Carrie , Thomson Donna , Majnemer Annette , Goldowitz Dan , Miller Steven P. , LeBlanc Annie 
Published: March 2021

AbstractObjectiveInformation regarding the impact of COVID-19 in children with brain-based disabilities, or those at risk of developing such conditions, remains scarce. The objective was to evaluate if children with brain-based disabilities are more likely to (1) develop COVID-19, (2) develop complications from the disease, and (3) to have a poorer prognosis.Study designWe conducted a rapid review using search strategies iteratively developed and tested by an experienced medical information specialist in consultation with the review team and a panel of knowledge users. Searches were initially performed on April 18th, 2021, and updated on October 31st, 2020. Four reviewers individually performed study selection using pilot-tested standardized forms. Single reviewers extracted the data using a standardized extraction form that included study characteristics, patients’ characteristics, and outcomes reported.ResultsWe identified 1448 publications, of which 29 were included. Studies reported data on 2288 COVID-19 positive children, including 462 with a brain-based disability, and 72 at risk of developing such disability. Overall, the included studies showed a greater risk to develop severe COVID-19 disease in children with brain-based disabilities. Although mortality is very low, the case-fatality rate appeared to be higher in children with disabilities compared to children without disabilities.ConclusionsOur review shows that children with brain-based disabilities are overrepresented in hospitalization numbers compared to children without disabilities. However, most studies included children that were hospitalized from COVID-19 in secondary and tertiary care centers. Results of this review should therefore be interpreted with caution.
Background rates of all-cause mortality, hospitalizations, and emergency department visits among nursing home residents in Ontario, Canada to inform COVID-19 vaccine safety assessments
Authors: Sundaram Maria , Nasreen Sharifa , Calzavara Andrew , He Siyi , Chung Hannah , Bronskill Susan E. , Buchan Sarah A. , Tadrous Mina , Tanuseputro Peter , Wilson Kumanan , Wilson Sarah , Kwong Jeffrey C. 
Published: March 2021

AbstractBackgroundNursing home (NH) residents are prioritized for COVID-19 vaccination. We report monthly mortality, hospitalizations, and emergency department (ED) visit incidence rates (IRs) during 2010-2020 to provide context for COVID-19 vaccine safety assessments.MethodsWe observed outcomes among NH residents using administrative databases. IRs were calculated by month, sex, and age group. Comparisons between months were assessed using one-sample t-tests; comparisons by age and sex were assessed using chi-squared tests.ResultsFrom 2010-2019, there were 83,453 (SD: 652.4) NH residents per month, with an average of 2.3 (SD: 0.28) deaths, 3.1 (SD: 0.16) hospitalizations, and 3.6 (SD: 0.17) ED visits per 100 residents per month. From March to December 2020, mortality IRs were increased, but hospitalization and ED visit IRs were reduced (p<0.05).ConclusionWe identified consistent monthly mortality, hospitalization, and ED visit IRs during 2010-2019. Marked differences in these rates were observed during 2020, coinciding with the COVID-19 pandemic.
Enhancing Histopathological Colorectal Cancer Image Classification by using Convolutional Neural Network
Authors: Al.Shawesh Radwan , Chen Yi Xiang 
Published: March 2021

AbstractColorectal cancer (CRC) also known as bowl cancer is one of the leading death causes worldwide. Early diagnosis has become vital for a successful treatment. Now days with the new advancements in Convolutional Neural networks (CNNs) it’s possible to classify different images of CRC into different classes. Today It is crucial for physician to take advantage of the new advancement’s in deep learning, since classification methods are becoming more and more accurate and efficient. In this study, we introduce a method to improve the classification accuracy from previous studies that used the National Center for Tumor diseases (NCT) data sets. We adapt the ResNet-50 model in our experiment to classify the CRC histopathological images. Furthermore, we utilize transfer learning and fine-tunning techniques to improve the accuracy. Our Experiment results show that ResNet_50 network is the best CNN architecture so far for classifying CRC histopathological images on the NCT Biobank open source dataset. In addition to that using transfer learning allow us to obtain 97.7% accuracy on the validation dataset, which is better than all previous results we found in literature.
The tumor burden of metastatic colorectal cancer patients at initial diagnosis, pre- versus post-Covid-19 lockdown
Authors: Thierry AR , Pastor B , Pisareva E , Ghiringhelli F , Bouche O , De La Fouchardière C , Vanbockstael J , Smith D , François E , Dos Santos M , Botsen D , Ellis S , Fonck M , Andre T , Guardiola E , Khemissa F , Linot B , Martin-Babau J , Rinaldi Y , Assenat E , Clavel L , Dominguez S , Gavoille C , Sefrioui D , Pezzella V , Mollevi C , Ychou M , Mazard T 
Published: March 2021

AbstractBackgroundThe COVID-19 pandemic led to a significant reduction in the provision of screening, case identification and hospital referrals to cancer patients. To our knowledge, no study has yet correlated quantitatively the consequences of these limitations for cancer patient management. This study evaluates the implications of such reductions for patients newly diagnosed with metastatic colorectal cancer (mCRC) in both the pre- and post-lockdown periods.MethodsWe examined 80 newly identified mCRC patients from 18 different clinical centers. These cases come from the screening procedure of a clinical trial which is using circulating DNA (cirDNA) analysis to determine their RAS and BRAF status.ResultsThe tumor burden as evaluated by the median total plasma cirDNA concentration showed a statistically higher level in patients diagnosed post-lockdown compared to those diagnosed pre-lockdown (119.2 versus 17.3 ng/mL; p<0.0001). In order to link tumor burden to survival, we compared the survival of these mCRC patients with previous studies in which cirDNA was examined in the same way (median survival, 16.2 months; median follow up, 48.7 months, N=135). Given the poor survival rate of mCRC patients with high cirDNA levels (14.7 vs 20.0 and 8.8 vs 19.3 months median survival when dichotomizing the cohort by the median cirDNA concentration 24.4 and 100 ng/mL, respectively), our study points to the potential deleterious consequences of the COVID-19 pandemic.ConclusionsRecognizing that our exploratory study offers a snapshot of an evolving situation, our observations nonetheless clearly highlight the need to determine actions which would minimize delays in diagnosis during the ongoing and future waves of COVID-19.
A SIRD model applied to COVID-19 dynamics and intervention strategies during the first wave in Kenya
Authors: Ogana Wandera , Juma Victor Ogesa , Bulimo Wallace D. 
Published: March 2021

AbstractThe first case of COVID-19 was reported in Kenya in March 2020 and soon after non-pharmaceutical interventions (NPIs) were established to control the spread of the disease. The NPIs consisted, and continue to consist, of mitigation measures followed by a period of relaxation of some of the measures. In this paper, we use a deterministic mathematical model to analyze the dynamics of the disease, during the first wave, and relate it to the intervention measures. In the process, we develop a new method for estimating the disease parameters. Our solutions yield a basic reproduction number, R0 = 2.76, which is consistent with other solutions. The results further show that the initial mitigation reduced disease transmission by 40% while the subsequent relaxation increased transmission by 25%. We also propose a mathematical model on how interventions of known magnitudes collectively affect disease transmission rates. The modelled positivity rate curve compares well with observations. If interventions of unknown magnitudes have occurred, and data is available on the positivity rate, we use the method of planar envelopes around a curve to deduce the modelled positivity rate and the magnitudes of the interventions. Our solutions deduce mitigation and relaxation effects of 42.5% and 26%, respectively; these percentages are close to values obtained by the solution of the SIRD system. Our methods so far apply to a single wave; there is a need to investigate the possibility of extending them to handle multiple waves.
COVID-19 risk perception and vaccine acceptance in individuals with chronic disease
Authors: Smith Brianna A. , Ricotta Emily E. , Kwan Jennifer L. , Evans Nicholas G. 
Published: March 2021

AbstractBackgroundCOVID-19 disproportionately affects those with preexisting conditions, but little research has determined whether those with chronic diseases view the pandemic itself differently - and whether there are differences between chronic diseases. We theorized that while individuals with respiratory disease or autoimmune disorders would perceive greater threat from COVID-19 and be more supportive of non-pharmaceutical interventions (NPIs), those with autoimmune disorders would be less likely to support vaccination-based interventions.MethodsWe conducted a two-wave online survey conducted in February and November 2021 asking respondents their beliefs about COVID-19 risk perception, adoption and support of interventions, willingness to be vaccinated against COVID-19, and reasons for vaccination. Regression analysis was conducted to assess the relationship of respondents reporting a chronic disease and COVID-19 behaviors and attitudes, compared to healthy respondents adjusting for demographic and political factors.ResultsIn the initial survey, individuals reporting a chronic disease had stronger both stronger feelings of risk from COVID-19 as well as preferences for NPIs than healthy controls. The only NPI that was still practiced significantly more compared to healthy controls in the resample was limiting trips outside of the home. Support for community-level NPIs was higher among individuals reporting a chronic disease than healthy controls and remained high among those with respiratory diseases in sample 2. Vaccine acceptance produced more divergent results: those reporting chronic respiratory diseases were 6% more willing to be vaccinated than healthy controls, while we found no significant difference between individuals with autoimmune diseases and healthy controls. Respondents with chronic respiratory disease and those with autoimmune diseases were more likely to want to be vaccinated to protect themselves from COVID-19, and those with an autoimmune disease were more likely to report fear of a bad vaccine reaction as the reason for vaccine hesitancy. In the resample, neither those with respiratory diseases nor autoimmune diseases reported being more willing to receive a booster vaccine than healthy controls.ConclusionsIt is not enough to recognize the importance of health in determining attitudes: nuanced differences between conditions must also be recognized.
A scalable EHR-based approach for phenotype discovery and variant interpretation for hereditary cancer genes
Authors: Zeng Chenjie , Bastarache Lisa A. , Tao Ran , Venner Eric , Hebbring Scott , Andujar Justin D. , Bland Sarah T. , Crosslin David R. , Pratap Siddharth , Cooley Ayorinde , Pacheco Jennifer A. , Christensen Kurt D. , Perez Emma , Zawatsky Carrie L. Blout , Witkowski Leora , Zouk Hana , Weng Chunhua , Leppig Kathleen A. , Sleiman Patrick M. A. , Hakonarson Hakon , Williams Marc. S. , Luo Yuan , Jarvik Gail P. , Green Robert C. , Chung Wendy K. , Gharavi Ali G. , Lennon Niall J. , Rehm Heidi L. , Gibbs Richard A. , Peterson Josh F. , Roden Dan M. , Wiesner Georgia L. , Denny Joshua C. 
Published: March 2021

AbstractKnowledge of the clinical spectrum of rare genetic disorders helps in disease management and variant pathogenicity interpretation. Leveraging electronic health record (EHR)-linked genetic testing data from the eMERGE network, we determined the associations between a set of 23 hereditary cancer genes and 3017 phenotypes in 23544 individuals. This phenome-wide association study replicated 45% (184/406) of known gene-phenotype associations (P = 5.1×10−125). Meta-analysis with an independent EHR-derived cohort of 3242 patients confirmed 14 novel associations with phenotypes in the neoplastic, genitourinary, digestive, congenital, metabolic, mental and neurologic categories. Phenotype risk scores (PheRS) based on weighted aggregations of EHR phenotypes accurately predicted variant pathogenicity for at least 50% of pathogenic variants for 8/23 genes. We generated a catalog of PheRS for 7800 variants, including 5217 variants of uncertain significance, to provide empirical evidence of potential pathogenicity. This study highlights the potential of EHR data in genomic medicine.
SARS-CoV-2 Seroprevalence in 12 Cities of India from July-December 2020
Authors: Velumani Arokiaswamy , Nikam Chaitali , Suraweera Wilson , Fu Sze Hang , Gelband Hellen , Brown Patrick , Bogoch Isaac , Nagelkerke Nico , Jha Prabhat 
Published: March 2021

SUMMARYObjectivesWe sought to understand the spread of SARS-CoV-2 infection in urban India, which has surprisingly low COVID-19 deaths.DesignCross-sectional and trend analyses of seroprevalence in self-referred test populations, and of reported cases and COVID mortality data.Participants448,518 self-referred individuals using a nationwide chain of private laboratories with central testing of SARS-CoV-2 antibodies and publicly available case and mortality data.Setting12 populous cities with nearly 92 million total population.Main outcome measuresSeropositivity trends and predictors (using a Bayesian geospatial model) and prevalence derived from mortality data and infection fatality rates (IFR).ResultsFor the whole of India, 31% of the self-referred individuals undergoing antibody testing were seropositive for SARS-CoV-2 antibodies. Seropositivity was higher in females (35%) than in males (30%) overall and in nearly every age group. In these 12 cities, seroprevalence rose from about 18% in July to 41% by December, with steeper increases at ages <20 and 20-44 years than at older ages. The “M-shaped” age pattern is consistent with intergenerational transmission. Areas of higher childhood measles vaccination in earlier years had lower seropositivity. The patterns of increase in seropositivity and in peak cases and deaths varied substantially across cities. In Delhi, death rates and cases first peaked in June and again in November; Chennai had a single peak in July. Based local IFRs and COVID deaths (adjusted for undercounts), we estimate that 43%-65% of adults above age 20 had been infected (range of mid-estimates of 12%-77%) corresponding 26 to 36 million infected adults in these cities, or an average of 9-12 infected adults per confirmed case.ConclusionEven with relatively low death rates, the large cities of India had remarkably high levels of SARS-CoV-2 infection. Vaccination strategies need to consider widespread intergenerational transmission.
Argentine Registry of neurological manifestations due to coronavirus-19 (COVID-19)
Authors: Alessandro Lucas , Appiani Franco , Bendersky Mariana , Borrego Guerrero Brenda , Bruera Guadalupe , Cairola Patricia , Calandri Ismael , Cardozo Oliver Juan Martín , Clément María Emilia , Di Egidio Marianna , Di Pace José Luis , Diaconchuk Melina , Esliman Celeste , Esnaola y Rojas Ma Martha , Fernández Boccazzi Julián , Franco Andrea Fabiana , Gargiulo Gisella , Giardino Daniela Laura , Gómez César , Guevara Ana Karina , Gutierrez Natalia , Hryb Javier , Viviana Ibarra , Janota Franco , Laserna Mabel , Larcher Luis Alfredo , Leone Fernando , Luetic Geraldine , Medina Claudia Andrea , Menichini María Laura , Nieto Gonzalo , Páez María Fernanda , Peñalver Francisco , Perassolo Mónica , Persi Gabriel , Pestchanker Claudia , Porta Oscar , Rey Roberto Daniel , Rodríguez Gabriel Eduardo , Romano Marina , Rugiero Marcelo , Saidón Patricia , Sica María Florencia , Stankievich Erica , Tarulla Adriana , Zalazar Guillermo 
Published: March 2021

AbstractCOVID-19 disease has spread around the world since December 2019. Neurological symptoms are part of its clinical spectrum.ObjectiveTo know the neurological manifestations in patients infected by COVID-19 in Argentina.MethodsMulticenter study conducted in adults, from May 2020 to January 2021, with confirmed COVID-19 and neurological symptoms. Demographic variables, existence of systemic or neurological comorbidities, the form of onset of the infection, alteration in complementary studies and the degree of severity of neurological symptoms were recorded.Results817 patients from all over the country were included, 52% male, mean age 38 years, most of them without comorbidities or previous neurological pathology. The first symptom of the infection was neurological in 56.2% of the cases, predominantly headache (69%), then anosmia / ageusia (66%). Myalgias (52%), allodynia / hyperalgesia (18%), and asthenia (6%) were also reported. 3.2% showed diffuse CNS involvement such as encephalopathy or seizures. 1.7% had cerebrovascular complications. Sleep disorders were observed in 3.2%. 6 patients were reported with Guillain Barré (GBS), peripheral neuropathy (3.4%), tongue paresthesia (0.6%), hearing loss (0.4%), plexopathy (0.3%). The severity of neurological symptoms was correlated with age and the existence of comorbidities.ConclusionsOur results, similar to those of other countries, show two types of neurological symptoms associated with COVID-19: some potentially disabling or fatal such as GBS or encephalitis, and others less devastating, but more frequent such as headache or anosmia that demand increasingly long-term care.