bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between rRT-PCR test results upon admission and outcome in hospitalized chest CT-Positive COVID-19 patients; a provincial retrospective cohort with active follow-up
Authors: Nemati Saeed , Najari Hamid Reza , Eftekharzadeh Anita , Kazemifar Amir Mohammad , Qandian Ali , Fattahi Pedram , Nikoo Maedeh Zokaei , Leghaei Shiva , Rouhollahi Mohammad Reza 
Published: April 2020

AbstractBackgroundThe Covid-19 pandemic imposed the most devastating challenge on healthcare systems worldwide. Iran was among the first countries that had to confront serious shortages in RT-PCR testing for SARS-CoV-2 and ventilators availabilities throughout the COVID-19 outbreak. This study aimed to investigate the clinical course of hospitalized COVID-19 patients with different rRT-PCR test results during the first 3 weeks of the outbreak in Qazvin province, Iran.MethodsFor this retrospective cohort study, data of hospitalized patients primarily diagnosed as having COVID-19 in all 12 centers across the whole Qazvin province during Feb 20-Mar 11, 2020 was analyzed. A multivariate logistic regression model was applied to assess the independent associates of death among COVID-19 patients.Results998 patients (57% male, median age 54 years) with positive chest CT-scan changes were included in this study. Among them, 558 patients were examined with rRT-PCR test and 73·8% tested positive. Case fatality rate was 20·68% and 7·53% among test-positive and test negative hospitalized patients, respectively. While only 5·2% of patients were ICU admitted, case fatality rates outside ICU were 17·70% and 4·65% in test-positive and test-negative non-ICU admitted patients, correspondingly. The independent associates of death were age ≥ 70 years, testing positive with rRT-PCR test, having immunodeficiency disorders and ICU admission.ConclusionsHospitalized COVID-19 patients with mild symptoms despite positive chest CT changes and major comorbidities were more probable to have negative rRT-PCR test result, hence lower case fatality rate and a more favorable outcome.
COMPENSATED HYPOGONADISM IN MEN WITH SICKLE CELL DISEASE
Authors: Ribeiro Anna Paloma Martins Rocha , Silva Carolina Santos , Zambrano Jean Carlos , de Oliveira Freitas Miranda Juliana , Molina Carlos Augusto Fernandes , Gomes Cristiano Mendes , de Paula Miranda Eduardo , de Bessa Júnior José 
Published: April 2020

ABSTRACTIntroductionSickle cell disease (SCD) is associated with the development of hypogonadism, but there is still controversy regarding its etiology and clinical implications.ObjectiveTo evaluate the prevalence of hypogonadism in a population of men with SCD and characterize its etiology.MethodsWe performed a cross-sectional study of 34 men with SCD aged > 18 years. Sociodemographic and clinical data, including anthropometric measurements (weight, height, and BMI), were obtained. Early morning blood samples were collected and total testosterone (TT), free testosterone (FT), luteinizing hormone (LH), follicle-stimulating hormone (FSH), a complete blood count, and hemoglobin electrophoresis were measured.ResultsMedian age was 33 [26-41] years, and SS genotype was the most frequent (73.5%). The prevalence of eugonadism, compensated, and secondary hypogonadism was 67.5%, 26.4%, and 5.88%, respectively. No men with primary hypogonadism were identified in our sample. Those with compensated hypogonadism had also higher FSH levels than individuals with eugonadism; p < 0.001).ConclusionIn our study population of men with SCD a high prevalence of compensated hypogonadism was identified, which is a controversial and distinct clinical entity that warrants monitoring and further research.
VERSO: a comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples
Authors: Ramazzotti Daniele , Angaroni Fabrizio , Maspero Davide , Gambacorti-Passerini Carlo , Antoniotti Marco , Graudenzi Alex , Piazza Rocco 
Published: April 2020

SummaryWe introduce VERSO, a two-step framework for the characterization of viral evolution from sequencing data of viral genomes, which improves over phylogenomic approaches for consensus sequences. VERSO exploits an efficient algorithmic strategy to return robust phylogenies from clonal variant profiles, also in conditions of sampling limitations. It then leverages variant frequency patterns to characterize the intra-host genomic diversity of samples, revealing undetected infection chains and pinpointing variants likely involved in homoplasies. On simulations, VERSO outperforms state-of-the-art tools for phylogenetic inference. Notably, the application to 6726 Amplicon and RNA-seq samples refines the estimation of SARS-CoV-2 evolution, while co-occurrence patterns of minor variants unveil undetected infection paths, which are validated with contact tracing data. Finally, the analysis of SARS-CoV-2 mutational landscape uncovers a temporal increase of overall genomic diversity, and highlights variants transiting from minor to clonal state and homoplastic variants, some of which falling on the spike gene. Available at:https://github.com/BIMIB-DISCo/VERSO.
Comparison of Cepheid Xpert Xpress and Abbott ID Now to Roche cobas for the Rapid Detection of SARS-CoV-2
Authors: Smithgall Marie C. , Scherberkova Ioana , Whittier Susan , Green Daniel A. 
Published: April 2020

AbstractThe SARS-CoV-2 pandemic has created an urgent and unprecedented need for rapid large-scale diagnostic testing to inform timely patient management. This study compared two recently-authorized rapid tests, Cepheid Xpert Xpress SARS-CoV-2 and Abbott ID Now SARS-CoV-2 to the Roche cobas SARS-CoV-2 assay. A total of 113 nasopharyngeal swabs were tested, including 88 positives spanning the full range of observed Ctvalues on the cobas assay. Compared to cobas, the overall positive agreement was 73.9% with ID Now and 98.9% with Xpert. Negative agreement was 100% and 92.0% for ID Now and Xpert, respectively. Both ID Now and Xpert showed 100% positive agreement for medium and high viral concentrations (Ctvalue <30). However, for Ctvalues >30, positive agreement was 34.3% for ID Now and 97.1% for Xpert. These findings highlight an important limitation of ID Now for specimens collected in viral or universal transport media with low viral concentrations. Further studies are needed to evaluate the performance of ID Now for direct swabs.
Self-amplifying RNA SARS-CoV-2 lipid nanoparticle vaccine induces equivalent preclinical antibody titers and viral neutralization to recovered COVID-19 patients
Authors: McKay Paul F. , Hu Kai , Blakney Anna K. , Samnuan Karnyart , Bouton Clément R. , Rogers Paul , Polra Krunal , Lin Paulo J.C. , Barbosa Christopher , Tam Ying , Shattock Robin J. 
Published: April 2020

ABSTRACTThe spread of the SARS-CoV-2 into a global pandemic within a few months of onset motivates the development of a rapidly scalable vaccine. Here, we present a self-amplifying RNA encoding the SARS-CoV-2 spike protein encapsulated within a lipid nanoparticle as a vaccine and demonstrate induction of robust neutralization of a pseudo-virus, proportional to quantity of specific IgG and of higher quantities than recovered COVID-19 patients. These data provide insight into the vaccine design and evaluation of immunogenicity to enable rapid translation to the clinic.
rdmc: an open source R package implementing convergent adaptation models of Lee and Coop (2017)
Authors: Tittes Silas 
Published: April 2020

ABSTRACTThe availability of whole genome sequencing data from multiple related populations creates opportunities to test sophisticated population genetic models of convergent adaptation. Recent work by Lee and Coop (2017) developed models to infer modes of convergent adaption at local genomic scales, providing a rich framework for assessing how selection has acted across multiple populations at the tested locus. Here I present,rdmc, an R package that builds on the existing software implementation of Lee and Coop (2017) that prioritizes ease of use, portability, and scalability. I demonstrate installation and comprehensive overview of the package’s current utilities.
Inequality in acute respiratory infection outcomes in the United States: A review of the literature and its implications for public health policy and practice
Authors: Moran Elizabeth , Kubale John , Noppert Grace , Malosh Ryan , Zelner Jon 
Published: April 2020

AbstractSeasonal and pandemic respiratory viruses such as influenza and the novel coronavirus (SARS-COV-2) currently sweeping the globe have often been described as ‘equal opportunity infectors’, implying little socioeconomic disparity in susceptibility. However, early data from the COVID-19 pandemic has underscored that the burden of respiratory viruses actually reflect and magnify existing socioeconomic inequalities. We review the literature on socioeconomic and racial disparities in acute respiratory infection (ARI), as well as ARI-associated hospitalization and mortality. Our goal is to identify key principles of the relationship between socioeconomic inequality and ARI outcomes, as well as highlighting poorly understood areas that need to be addressed by research and policy in the wake of the COVID-19 pandemic. We find that there has been descriptive work in this area, but that there is a distinct lack of cohesive methodology in the literature exploring social determinants and ARI. We propose the fundamental cause theory is a useful framework for guiding future research of disparities in ARI and for the design of interventions to alleviate these disparities.
Taking Account of Asymptomatic Infections – A Modeling Study on the COVID-19 Outbreak on the Diamond Princess Cruise Ship
Authors: Huang Li-Shan , Li Li , Dunn Lucia , He Mai 
Published: April 2020

AbstractBackgroundThe COVID-19 outbreak on the Diamond Princess (DP) cruise ship provided empirical data to study the transmission potential of COVID-19 under quarantine with the presence of asymptomatic cases.MethodsWe studied the changes in R0 on the DP from January 21 to February 19, 2020 based on chain-binomial models under two scenarios: no quarantine assuming a random mixing condition, and quarantine of passengers in cabins — passengers may get infected either by an infectious case in a shared cabin or by asymptomatic crew who continued to work.ResultsEstimates of R0 at the beginning of the epidemic were 3.27 (95% CI, 3.02-3.54) and 3.78 (95% CI, 3.49-4.09) respectively for serial intervals of 5 and 6 days; and when quarantine started, with the reported asymptomatic ratio 0.505, R0 rose to 4.18 (95%CI, 3.86-4.52) and 4.73 (95%CI, 4.37-5.12) respectively for passengers who might be exposed to the virus due to contacts with asymptomatic crew. The overall R0 for both crew and passengers was decreased to 2.55 (95%CI, 2.36-2.76) and 2.90 (95% CI, 2.67-3.13). Results show that the higher the asymptomatic ratio is, the more infectious contacts would happen.ConclusionsWe find evidence to support a US CDC report that “a high proportion of asymptomatic infections could partially explain the high attack rate among cruise ship passengers and crew.” Our study suggests that the effects of quarantine may be limited if the asymptomatic ratio is high, implying that a combination of preventive measures is needed to stop the spread of virus.
Clinical utility of genetic and genomic testing in the precision diagnosis and management of pediatric patients with kidney and urinary tract diseases
Authors: Bekheirnia Nasim , Glinton Kevin E. , Rossetti Linda , Manor Joshua , Chen Wuyan , Lamb Dolores J. , Braun Michael C. , Bekheirnia Mir Reza 
Published: April 2020

AbstractAs genetic and genomic testing increasingly integrates into the practice of nephrology, our understanding of the basis of many kidney disorders has exponentially increased. Given this, we recently initiated a Renal Genetics Clinic (RGC) at our large, urban children’s hospital for patients with either a personal or strong family history of renal disorders. Genetic testing was performed in Clinical Laboratory Improvement Amendments (CLIA) certified laboratories using single gene testing, multi-gene panels, chromosomal microarray (CMA), or exome sequencing (ES). A total of 192 patients (185 probands) were evaluated in this clinic, with cystic kidney disease (49/192) being the most common reason for referral followed by Congenital Anomalies of the Kidney and Urinary Tract (CAKUT: 41/192) and hematuria (38/192). Genetic testing was performed for 153 probands with an overall diagnostic yield of 75/153 (49%). In the patients who reached a molecular diagnosis, 13/75 (17.3%), medical or surgical treatment of the patients were impacted, and in 12/75 (16%), previous clinical diagnoses were changed to more accurate molecular diagnoses. Such testing provided an accurate diagnosis for children and in some cases led to further diagnosis in seemingly asymptomatic family members and changes to overall medical management. Molecular testing, as facilitated by such a specialized clinical setting, thus appears to have clear utility in the diagnosis and counseling of patients with a wide range of renal manifestations.
Non-Linear Fitting of Sigmoidal Growth Curves to predict a maximum limit to the total number of COVID-19 cases in the United States
Authors: Dutra Carlos Maximiliano 
Published: April 2020

AbstractIn the present work is used non-linear fitting of the “Gompert” and “Logistic” growth models to the number of total COVID-19 cases from the United States as a country and individually by states. The methodology allowed us to estimate that the maximum limit for the total number of cases of COVID-19 patients such as those registered with the World Health Organization will be approximately one million and one hundred thousand cases to the United States. Up to 04/19/20 the models indicate that United States reached 70% of this maximum number of “total cases” and the United States will reach 95% of this limit by 05/14/2020. The application of the nonlinear fitting of growth curves to the individual data of each American state showed that only 25% of them did not reach, on 04/19/20, the percentage of 59% of the maximum limit of “total cases” and that 17 of the 50 states still will not have reached 95% of that limit on 05/14/20.
Antibody tests in detecting SARS-CoV-2 infection: a meta-analysis
Authors: Kontou Panagiota I , Braliou Georgia G , Dimou Niki L , Nikolopoulos Georgios , Bagos Pantelis G 
Published: April 2020

SummaryBackgroundWith the emergence of SARS-CoV-2 and the associated Coronavirus disease 2019 (COVID-19), there is an imperative need for diagnostic tests that can identify the infection. Although Nucleic Acid Test (NAT) is considered to be the gold standard, serological tests based on antibodies could be very helpful. However, individual studies measuring the accuracy of the various tests are usually underpowered and inconsistent, thus, a comparison of different tests is needed.MethodsWe performed a systematic review and meta-analysis following the PRISMA guidelines. We conducted the literature search in PubMed, medRxiv and bioRxiv. For the statistical analysis we used the bivariate method for meta-analysis of diagnostic tests pooling sensitivities and specificities. We evaluated IgM and IgG tests based on Enzyme-linked immunosorbent assay (ELISA), Chemiluminescence Enzyme Immunoassays (CLIA), Fluorescence Immunoassays (FIA) and the point-of-care (POC) Lateral Flow Immunoassays (LFIA) that are based on immunochromatography.FindingsIn total, we identified 38 eligible studies that include data from 7,848 individuals. The analyses showed that tests using the S antigen are more sensitive than N antigen-based tests. IgG tests perform better compared to IgM ones, and show better sensitivity when the samples were taken longer after the onset of symptoms. Moreover, irrespective of the method, a combined IgG/IgM test seems to be a better choice in terms of sensitivity than measuring either antibody type alone. All methods yielded high specificity with some of them (ELISA and LFIA) reaching levels around 99%. ELISA- and CLIA-based methods performed better in terms of sensitivity (90-94%) followed by LFIA and FIA with sensitivities ranging from 80% to 86%.InterpretationELISA tests could be a safer choice at this stage of the pandemic. POC tests (LFIA), that are more attractive for large seroprevalence studies show high specificity but lower sensitivity and this should be taken into account when designing and performing seroprevalence studies.FundingNone
Machine learning algorithm for early mortality prediction in patients with advanced penile cancer
Authors: Chen Robert , Kudelka Matthew R , Rosado Aaron M , Zhang James 
Published: April 2020

ABSTRACTPenile cancer remains a rare cancer with an annual incidence of 1 in 100,000 men in the United States, accounting for 0.4-0.6% of all malignancies. Furthermore, to date there are no predictive models of early mortality in penile cancer. Meanwhile, machine learning has potential to serve as a prognostic tool for patients with advanced disease.We developed a machine learning model for predicting early mortality in penile cancer (survival less than 11 months after initial diagnosis. A cohort of 88 patients with advanced penile cancer was extracted from the Surveillance, Epidemiology and End Results (SEER) program. In the cohort, patients with advanced penile cancer exhibited a median overall survival of 21 months, with the 25th percentile of overall survival being 11 months. We constructed predictive features based on patient demographics, staging, metastasis, lymph node biopsy criteria, and metastatic sites. We trained a multivariate logistic regression model, tuning parameters with respect to regularization, and feature selection criteria.Upon evaluation with 5-fold cross validation, our model achieved 68.2% accuracy with AUC 0.696. Criteria for advanced staging (T4, group stage IV), as well as higher age, white race and squamous cell histology, were the most predictive of early mortality. Tumor size was the strongest negative predictor of early mortality.Our study showcases the first known predictive model for early mortality in patients with advanced penile cancer and should serve as a framework for approaching the clinical problem in future studies. Future work should aim to incorporate other data sources such as genomic and metabolomic data, increase patient counts, incorporate clinical characteristics such as ECOG and RECIST criteria, and assess the performance of the model in a prospective fashion.
Lack of association between genetic variants at ACE2 and TMPRSS2 genes involved in SARS-CoV-2 infection and human quantitative phenotypes
Authors: Lopera Esteban , van der Graaf Adriaan , Lanting Pauline , van der Geest Marije ,   Lifelines Cohort Study, Fu Jingyuan , Swertz Morris , Franke Lude , Wijmenga Cisca , Deelen Patrick , Zhernakova Alexandra , Sanna Serena 
Published: April 2020

AbstractCoronavirus disease 2019 (COVID-19) shows a wide variation in expression and severity of symptoms, from very mild or no symptomes, to flu-like symptoms, and in more severe cases, to pneumonia, acute respiratory distress syndrome and even death. Large differences in outcome have also been observed between males and females. The causes for this variability are likely to be multifactorial, and to include genetics. The SARS-CoV-2 virus responsible for the infection uses the human receptor angiotensin converting enzyme 2 (ACE2) for cell invasion, and the serine protease TMPRSS2 for S protein priming. Genetic variation in these two genes may thus modulate an individual’s genetic predisposition to infection and virus clearance. While genetic data on COVID-19 patients is being gathered, we carried out a phenome-wide association scan (PheWAS) to investigate the role of these genes in other human phenotypes in the general population. We examined 178 quantitative phenotypes including cytokines and cardio-metabolic biomarkers, as well as 58 medications in 36,339 volunteers from the Lifelines population biobank, in relation to 1,273 genetic variants located in or near ACE2 and TMPRSS2. While none reached our threshold for significance, we observed a suggestive association of polymorphisms within the ACE2 gene with (1) the use of angiotensin II receptor blockers (ARBs) combination therapies (p=5.7×10−4), an association that is significantly stronger in females (pdiff=0.01), and (2) with the use of non-steroid anti-inflammatory and antirheumatic products (p=5.5×10−4). While these associations need to be confirmed in larger sample sizes, they suggest that these variants play a role in diseases such as hypertension and chronic inflammation that are often observed in the more severe COVID-19 cases. Further investigation of these genetic variants in the context of COVID-19 is thus promising for better understanding of disease variability. Full results are available at https://covid19research.nl.
Heat treatment for reuse of disposable respirators during Covid-19 pandemic: Is filtration and fit adversely affected?
Authors: Loh Miranda , Clark Ross , Cherrie John 
Published: April 2020

AbstractA number of methods for decontaminating disposable filtering face piece respirators have been explored for use in health care settings during epidemics where respirators are in short supply, such as the current Covid-19 pandemic. Heating to temperatures above 65°C has been shown to successfully inactivate the SARS-CoV-2 virus on various surfaces. Ovens or similar heating devices are likely already widely available in hospitals globally. We did a quantitative fit test on nine models of FFP2 and FFP3 respirators before and after heat treatment in an oven. These included both flat fold and moulded cup styles. All passed the initial fit test, and all but two passed the post-treatment fit test. This study demonstrates that FFP respirators can still retain both filtration efficiency and fit after wear and heat treatment, but that it is necessary to understand the probability for failure of fit after decontamination. Heat shows promise as a simple and effective way of treating FFP respirators. Further evaluation of longer-term wear and disinfection effectiveness of heat treatment should be done before widespread use.
White matter variability, cognition, and disorders: a systematic review
Authors: Forkel Stephanie J. , Friedrich Patrick , de Schotten Michel Thiebaut , Howells Henrietta 
Published: April 2020

AbstractInter-individual differences can inform treatment procedures and - if accounted for - have the potential to significantly improve patient outcomes. However, when studying brain anatomy, these inter-individual variations are commonly unaccounted for, despite reports of differences in gross anatomical features, cross-sectional and connectional anatomy. Brain connections are essential to facilitate functional organisation and, when severed, cause impairments or complete loss of function. Hence the study of cerebral white matter may be an ideal compromise to capture inter-individual variability in structure and function. We reviewed the wealth of studies that associate functions and clinical symptoms with individual tracts using diffusion tractography. Our systematic review indicates that tractography has proven to be a sensitive method in neurology, psychiatry, and healthy populations to identify variability and its functional correlates. However, the literature may be biased, as we determined that the most commonly studied tracts are not necessarily those with the highest sensitivity to cognitive functions and pathologies. Additionally, the hemisphere of the studied tract is often unreported, thus neglecting functional laterality and asymmetries. Finally, we demonstrate that tracts, as we define them, are not usually correlated with only one, but rather multiple cognitive domains or pathologies. While our systematic review identified some methodological caveats, it also suggests that tract-function correlations might be a promising biomarker for precision medicine. It characterises variations in brain anatomy, differences in functional organisation, and predicts resilience and recovery in patients.