bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depression, Anxiety and Depression-anxiety comorbidity amid COVID-19 Pandemic: An online survey conducted during lockdown in Nepal
Authors: Sigdel Anil , Bista Anu , Bhattarai Navaraj , Pun Bimal Chandra , Giri Govind , Marqusee Hannah , Thapa Subash 
Published: May 2020

AbstractBackgroundLittle is known about the effect of the COVID-19 pandemic on mental health status during the lockdown period. Therefore, this study was conducted to assess prevalence of depression, anxiety and depression-anxiety comorbidity, and associated factors during the COVID-19 lockdown in Nepal.MethodsA quantitative cross-sectional study was conducted among the general population of Nepal. Data was collected from April 9 to April 16, 2020 using an e-questionnaire which was shared through different popular social media. A total of 349 participants were included. Self-reported depression and anxiety were assessed using the Patient Health Questionnaire and Generalized Anxiety tools respectively. Logistic regression analysis was conducted to identify the factors associated with depression, anxiety and depression and anxiety co-morbidity.ResultsThe prevalence rates of depression, anxiety and depression-anxiety co-morbidity were found to be 34.0%, 31.0% and 23.2% respectively. The multi-variate analysis showed that females, those living alone, health professionals and those who spent more time in accessing information about COVID-19 were significantly more likely to have depression, anxiety and depression-anxiety co-morbidity.ConclusionsHigh rates of depression and anxiety and co-morbidity were found to be prevailing among the general population during the COVID-19 pandemic lockdown in Nepal. The results suggest that only the scientific, but contextually appropriate messages about the disease should be disseminated to reduce unnecessary fears and anxiety. Awareness interventions to promote mental wellbeing need to be integrated into the response interventions. Community mental health care should be made accessible to at-risk groups.
Effect of Alert Level 4 on Reff: review of international COVID-19 cases
Authors: Binny Rachelle N. , Hendy Shaun C. , James Alex , Lustig Audrey , Plank Michael J. , Steyn Nicholas 
Published: May 2020

AbstractThe effective reproduction number, Reff, is an important measure of transmission potential in the modelling of epidemics. It measures the average number of people that will be infected by a single contagious individual. A value of Reff > 1 suggests that an outbreak will occur, while Reff < 1 suggests the virus will die out. In response to the COVID-19 pandemic, countries worldwide are implementing a range of intervention measures, such as population-wide social distancing and case isolation, with the goal of reducing Reff to values below one, to slow or eliminate transmission. We analyse case data from 25 international locations to estimate their Reff values over time and to assess the effectiveness of interventions, equivalent to New Zealand’s Alert Levels 1-4, for reducing transmission. Our results show that strong interventions, equivalent to NZ’s Alert Level 3 or 4, have been successful at reducing Reff below the threshold for outbreak. In general, countries that implemented strong interventions earlier in their outbreak have managed to maintain case numbers at lower levels. These estimates provide indicative ranges of Reff for each Alert Level, to inform parameters in models of COVID-19 spread under different intervention scenarios in New Zealand and worldwide. Predictions from such models are important for informing policy and decisions on intervention timing and stringency during the pandemic.Executive SummaryIn response to the COVID-19 pandemic, countries around the world are implementing a range of intervention measures, such as population-wide social distancing and case isolation, with the goal of reducing the spread of the virus.Reff, the effective reproduction number, measures the average number of people that will be infected by a single contagious individual. A value of Reff > 1 suggests that an outbreak will occur, while Reff < 1 suggests the virus will die out.Comparing Reff in an early outbreak phase (no or low-level interventions implemented) with a later phase (moderate to high interventions) indicates how effective these measures are for reducing Reff.We estimate early-phase and late-phase Reff values for COVID-19 outbreaks in 25 countries (or provinces/states). Results suggest interventions equivalent to NZ’s Alert Level 3-4 can successfully reduce Reff below the threshold for outbreak.
Frequency of routine testing for COVID-19 in high-risk healthcare environments to reduce outbreaks
Authors: Chin Elizabeth T , Huynh Benjamin Q , Chapman Lloyd A. C. , Murrill Matthew , Basu Sanjay , Lo Nathan C 
Published: May 2020

AbstractRoutine asymptomatic testing strategies for COVID-19 have been proposed to prevent outbreaks in high-risk healthcare environments. We used simulation modeling to evaluate the optimal frequency of viral testing. We found that routine testing substantially reduces risk of outbreaks, but may need to be as frequent as twice weekly.
Using viral load and epidemic dynamics to optimize pooled testing in resource constrained settings
Authors: Cleary Brian , Hay James A. , Blumenstiel Brendan , Harden Maegan , Cipicchio Michelle , Bezney Jon , Simonton Brooke , Hong David , Senghore Madikay , Sesay Abdul K. , Gabriel Stacey , Regev Aviv , Mina Michael J. 
Published: May 2020

AbstractExtensive virological testing is central to SARS-CoV-2 containment, but many settings face severe limitations on testing. Group testing offers a way to increase throughput by testing pools of combined samples; however, most proposed designs have not yet addressed key concerns over sensitivity loss and implementation feasibility. Here, we combine a mathematical model of epidemic spread and empirically derived viral kinetics for SARS-CoV-2 infections to identify pooling designs that are robust to changes in prevalence, and to ratify losses in sensitivity against the time course of individual infections. Using this framework, we show that prevalence can be accurately estimated across four orders of magnitude using only a few dozen pooled tests without the need for individual identification. We then exhaustively evaluate the ability of different pooling designs to maximize the number of detected infections under various resource constraints, finding that simple pooling designs can identify up to 20 times as many positives compared to individual testing with a given budget. We illustrate how pooling affects sensitivity and overall detection capacity during an epidemic and on each day post infection, finding that sensitivity loss is mainly attributed to individuals sampled at the end of infection when detection for public health containment has minimal benefit. Crucially, we confirm that our theoretical results can be accurately translated into practice using pooled human nasopharyngeal specimens. Our results show that accounting for variation in sampled viral loads provides a nuanced picture of how pooling affects sensitivity to detect epidemiologically relevant infections. Using simple, practical group testing designs can vastly increase surveillance capabilities in resource-limited settings.
Objective extraction of movement features prompting expert identification of dystonia in ambulatory children with cerebral palsy
Authors: Aravamuthan Bhooma R. , Ueda Keisuke , Miao Hanyang , Gilbert Laura , Smith Sarah , Pearson Toni 
Published: May 2020

AbstractAimTo determine the specific movement features in children with cerebral palsy (CP) that prompt expert identification of dystoniaMethodsDystonia identification in CP, particularly when co-morbid with spasticity, can be difficult. For this retrospective case-control study, we conducted a qualitative thematic analysis of consensus-building discussions between three pediatric movement disorders physicians as they attempted to identify the presence or absence of dystonia in gait videos of 40 subjects with spastic CP and periventricular leukomalacia.ResultsInitial unanimous consensus regarding the presence or absence of dystonia was achieved in 12 videos (30%). Following consensus building discussion, 22 additional videos (55%) yielded unanimous consensus. Two main themes were generated: 1) Unilateral leg or foot adduction that was variable over time, and 2) Difficulty in identifying dystonia. Codes contributing to Theme 1 were more likely to appear when a discussant was favoring the presence of dystonia in a video (Chi-square, p=0.004).DiscussionThese results provide specific movement features that could aid dystonia diagnosis in ambulatory children with CP. However, these results also suggest that, even amongst putative motor phenotyping experts, visual dystonia diagnosis in CP remains difficult, highlighting the need for developing and using objective dystonia diagnosis measures.What this paper adds-Dystonia identification is visually difficult, even for experts-Unilateral lower extremity variable adduction could represent gait dystonia in cerebral palsy-Qualitative thematic analysis objectively identifies expert-cited dystonia features in cerebral palsy
Causal associations between salt intake with body mass, shape and composition: A two-sample Mendelian randomization study
Authors: Feng Qi , Yuan Shuai , Yang Qian , Lu Yingchang , Loos Ruth J.F. , Li Gloria H.Y. , Fei Yue , Tsoi Man Fung , Cheung Ching Lung , Cheung Bernard M.Y. 
Published: May 2020

AbstractBackgroundObservational studies have found associations between salt intake with obesity, body shape and composition; but the findings may be biased by residual confounding.ObjectiveTo analyze the causal associations between salt intake and obesity measures in both sex-combined and sex-specific models.DesignsThis was a two-sample Mendelian randomization study. Genome-wide association (GWA) studies of urinary sodium secretion (UNa, a surrogate for salt intake), body mass index (BMI), BMI-adjusted waist-to-hip ratio (WHR), body fat (BF) percentage and estimated glomerular filtration rate (eGFR) were identified. We initially extracted fifty SNPs associated with UNa at GWA significance level of 5 × 10−8, but further removed those SNPs with potential horizontal pleiotropy. Univariable MR and multivariable MR with adjustment for eGFR were performed. Inverse-variance weighted MR was performed as the primary analysis, with MR-Egger methods as sensitivity analysis. The potential bidirectional association between BMI and UNa was investigated. All exposure and outcomes were continuous, and the effect measure was linear regression coefficients (beta) and their 95% confidence intervals (95%CI).ResultsUNa was causally associated with increased BMI in both men (eGFR-adjusted beta 0.443 (0.163 to 0.724)) and women (0.594 (0.333 to 0.855)). UNa caused BF percentage increase in men (0.622 (0.268 to 0.976)) and women (0.334 (0.007 to 0.662)). UNa significantly elevated BMI-adjusted WHR in men (0.321 (0.094 to 0.548)), but not in women (0.170 (−0.052 to 0.391)). Additionally, we found that BMI causally increased UNa (0.043 (0.023 to 0.063)).ConclusionsSalt intake increased BMI and BF percentage. Salt intake affects male body shape by increasing BMI-adjusted WHR, but showed no effects on female body shape. The bidirectional association between BMI and UNa suggested that salt reduction measures and weight reduction measures should be implemented simultaneously to break the vicious cycle and gain more health benefits.AbbreviationsALM: appendicular lean massBF: body fatBMI: body mass indexeGFR: estimated glomerular filtration rateGWA: genome-wide associationHC: hip circumferenceMR: Mendelian randomizationPRESSO test: Pleiotropy RESidual Sum and Outlier testSNP: single nucleotide polymorphismUNa: urinary sodium secretionWC: waist circumferenceWHR: waist-to-hip ratioWLM: whole body lean mass
Robust estimation of diagnostic rate and real incidence of COVID-19 for European policymakers
Authors: Català M. , Pino D. , Marchena M. , Palacios P. , Urdiales T. , Cardona P.J. , Alonso S. , López-Codina D. , Prats C. , Alvarez-Lacalle E. 
Published: May 2020

AbstractPolicymakers need a clear and fast assessment of the real spread of the epidemic of COVID-19 in each of their respective countries. Standard measures of the situation provided by the governments include reported positive cases and total deaths. While total deaths immediately indicate that countries like Italy and Spain have the worst situation as of mid April 2020, on its own, reported cases do not provide a correct picture of the situation. The reason is that different countries diagnose diversely and present very distinctive reported case fatality rate (CFR). The same levels of reported incidence and mortality might hide a very different underlying picture. Here we present a straightforward and robust estimation of the diagnostic rate in each European country. From that estimation we obtain an uniform unbiased incidence of the epidemic. The method to obtain the diagnostic rate is transparent and empiric. The key assumption of the method is that the real CFR in Europe of COVID-19 is not strongly country-dependent. We show that this number is not expected to be biased due to demography nor the way total deaths are reported. The estimation protocol has a dynamic nature, and it has been giving converging numbers for diagnostic rates in all European countries as of mid April 2020. From this diagnostic rate, policy makers can obtain an Effective Potential Growth (EPG) updated everyday providing an unbiased assessment of the countries with more potential to have an uncontrolled situation. The method developed will be used to track possible improvements on the diagnostic rate in European countries as the epidemic evolves.
The use of facemasks by the general population to prevent transmission of Covid 19 infection: A systematic review
Authors: Gupta Madhu , Gupta Khushi , Gupta Sarika 
Published: May 2020

AbstractBackgroundThe pandemic of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a serious worldwide public health emergency. This systematic review aims to summarize the available evidence regarding the role of face mask in community settings in slowing the spread of respiratory viruses such as SARS-CoV-2.MethodsThe preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines were used for this review. Literature search using PUBMED, Google Scholar and Cochrane database was performed using Medical subject heading (MeSH) words from the year 2000-2020. The articles focused on the use of masks and N95 respirators in healthcare workers were excluded.ResultsA total of 305 records were identified, out of which 14 articles were included in the review based upon quality and eligibility criteria. All the articles mentioned about role of face masks in preventing the spread of respiratory viruses like influenza, SARS and SARS-CoV-2, in the community or experimental setting. Studies also suggested that early initiation of face mask usage was more effective. Masks were also reported to be more effective in viruses which transmit easily from asymptomatic individuals, as is now known in SARS-CoV-2.ConclusionTheoretical, experimental and clinical evidence suggested that usage of face masks in general population offered significant benefit in preventing the spread of respiratory viruses especially in the pandemic situation, but it’s utility is limited by inconsistent adherence to mask usage.
Early phases of COVID-19 are characterized by a reduction of lymphocyte populations and the presence of atypical monocytes
Authors: Lombardi Andrea , Trombetta Elena , Cattaneo Alessandra , Castelli Valeria , Palomba Emanuele , Tirone Mario , Mangioni Davide , Lamorte Giuseppe , Manunta Maria , Prati Daniele , Ceriotti Ferruccio , Gualtierotti Roberta , Costantino Giorgio , Aliberti Stefano , Scaravilli Vittorio , Grasselli Giacomo , Gori Andrea , Porretti Laura , Bandera Alessandra ,   for the COVID-19 Network
Published: May 2020

AbstractBackgroundSevere acute respiratory syndrome coronavirus 2 is a recently discovered pathogen responsible of coronavirus disease 2019 (COVID-19). The immunological changes associated with this infection are largely unknown.MethodsWe evaluated the peripheral blood mononuclear cells profile of 63 patients with COVID-19 at diagnosis and the presence of association with inflammatory biomarkers and 28-days mortality.ResultsLymphocytopenia was present in 51 of 63 (80.9%) patients. This reduction was mirrored also on CD8+ lymphocytes (128 cells/μL), natural killer cells (67 cells/μL) and natural killer T cells (31 cells/μL). Monocytes were preserved in total number but displayed a subpopulation composed mainly of cells with a reduced expression of both CD14 and HLA-DR. A direct correlation was found between serum values of IL-6 and the frequency of Th2 lymphocytes (R=0.17; p=0.04) but not with the monocytes count (R=0.01; p=0.60). Patients who died in the 28 days from admission (N=10, 15.9%), when compared to those who did not, displayed lower mean values of CD3+ (p=0.028) and CD4+ cells (p=0.042) and higher mean percentages of CD8+/CD38+/HLA-DR+ lymphocytes (p=0.026).ConclusionsThe early phases of COVID-19 are characterized by lymphocytopenia, predominance of Th2 lymphocytes and less immunocompetent monocytes, which include atypical mononuclear cells.eTOC-At diagnosis patients with COVID-19 have lymphocytopenia-Monocytes with both normal or altered scatter properties display a reduced expression of CD14 and HLA-DR in most of COVID-19 patients-Patients who die in the 28 days from admission have lower values of CD3+ and CD4+ cells and higher percentages of activated CTL cells compared to those who survive
Fully automatic deep convolutional approaches for the analysis of Covid-19 using chest X-ray images
Authors: de Moura Joaquim , Novo Jorge , Ortega Marcos 
Published: May 2020

AbstractCovid-19 is a new infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Given the seriousness of the situation, the World Health Organization declared a global pandemic as the Covid-19 rapidly around the world. Among its applications, chest X-ray images are frequently used for an early diagnostic/screening of Covid-19 disease, given the frequent pulmonary impact in the patients, critical issue to prevent further complications caused by this highly infectious disease.In this work, we propose complementary fully automatic approaches for the classification of chest X-ray images under the analysis of 3 different categories: Covid-19, pneumonia and healthy cases. Given the similarity between the pathological impact in the lungs between Covid-19 and pneumonia, mainly during the initial stages of both lung diseases, we performed an exhaustive study of differentiation considering different pathological scenarios. To face these classification tasks, we exploited and adapted to this topic a densely convolutional network architecture, which connects each layer to every other layer in a feed-forward fashion. To validate the designed approaches, several representative experiments were performed using images retrieved from different public chest X-ray images datasets. overall, satisfactory results were obtained from the designed experiments, facilitating the doctors’ work and allowing better an early diagnostic/screening and treatment of this relevant pandemic pathology.
Monitoring of circulating monocyte HLA-DR expression in a large cohort of intensive care patients: relation with outcome and secondary infections
Authors: de Roquetaillade C. , Dupuis C. , Faivre V. , Lukaszewicz AC. , Brumpt C. , Payen D. 
Published: May 2020

ABSTRACTBackgroundpost-injury acquired immunodepression (AID) is frequently assessed by the diminished expression of Human Leukocyte Antigen-D Related on circulating monocytes (mHLA-DR). The relation with mortality and the occurrence of ICU-acquired infections (IAI) requires confirmation in large cohorts of patients. This study tested in a large number of ICU patients from a single center the association of mHLA-DR with mortality and secondary infections.MethodsThis prospective, observational study in a surgical ICU of a French tertiary hospital reports mHLA-DR measurements (fixed flow cytometry protocol) done 1st within the 3 days post-admission and 2nd after the 7th day. The other collected parameters were: the SAPS II and SOFA scores, sex, age, comorbidity, mortality and ICU-acquired infections. The associations between mHLA-DR and outcomes were tested by adjusted Fine and Gray sub-distribution competing risk models.Findings1053 patients were subdivided into 4 subgroups depending on the main motif for admission. Overall, 151 patients (14.3%) died in the ICU with an independent association with the amplitude of the first mHLA-DR decrease (HR = 0.71 [0.57; 0.95], p < 0.01); 592 patients had a 2nd mHLA-DR measurement of whom 223 patients (37.7%) complicated by IAI. These patients had a lower mHLA-DR than other patients (mHLA-DR = 9.0 log vs. 9.3 log, p < 0.01). IAI occurrence was independently associated with first, the 2nd mHLA-DR level regardless the initial severity (HR = 0.66 [0.51; 0.84], p = 0.001) and second, with the slope between the 1st and 2nd values (HR = 0.62 [0.43; 0.89], p = 0.009).Interpretationthe association between the early mHLA-DR expression and ICU mortality does not improve the prediction given by the severity scores. The persistence or a decrease of low mHLA-DR expression are independent and reliable predictors of ICU-acquired infection.Fundingno financial interest
Statistical Properties of Stepped Wedge Cluster-Randomized Trials in Infectious Disease Outbreaks
Authors: Kennedy-Shaffer Lee , Lipsitch Marc 
Published: May 2020

ABSTRACTRandomized controlled trials are crucial for the evaluation of interventions such as vaccinations, but the design and analysis of these studies during infectious disease outbreaks is complicated by statistical, ethical, and logistical factors. Attempts to resolve these complexities have led to the proposal of a variety of trial designs, including individual randomization and several types of cluster randomization designs: parallel-arm, ring vaccination, and stepped wedge designs. Because of the strong time trends present in infectious disease incidence, however, methods generally used to analyze stepped wedge trials may not perform well in these settings. Using simulated outbreaks, we evaluate various designs and analysis methods, including recently proposed methods for analyzing stepped wedge trials, to determine the statistical properties of these methods. While new methods for analyzing stepped wedge trials can provide some improvement over previous methods, we find that they still lag behind parallel-arm cluster-randomized trials and individually-randomized trials in achieving adequate power to detect intervention effects. We also find that these methods are highly sensitive to the weighting of effect estimates across time periods. Despite the value of new methods, stepped wedge trials still have statistical disadvantages compared to other trial designs in epidemic settings.