bluuebunny/crossref_metadata_2025_split huggingface dataset:
Near- and forecasting the SARS-COV-2 epidemic requires a global view and multiple methods
Authors: Austin Daren 
Published: April 2020

AbstractConventional epidemiological models require estimates of important parameters including incubation time and case fatality rate that may be unavailable in the early stage of an epidemic. For the ongoing SARS-COV-2 epidemic, with no previous population exposure, alternative prediction methods less reliant on assumptions may prove more effective in the near-term. We present three methods used to provide early estimates of likely SARS-COV-2 epidemic progression. During the first stage of the epidemic, growth rate charts revealed the UK, Italy and Spain as outliers, with differentially increasing growth of deaths over cases. A novel data-driven time-series model was then used to near-cast 7-day future cases and deaths with much greater precision. Finally, an epidemio-statistical model was used to bridge from near-casting to forecasting the future course of the global epidemic. By applying multiple approaches to global SARS-COV-2 data, coupled with mixed-effects methods, countries further ahead in the epidemic provide valuable information for those behind. Using current daily global data, we note convergence in near-term predictions for Italy signifying an appropriate call on the future course of the global epidemic. For the UK and elsewhere, prediction of peak and eventual time to resolution is now possible.
How do environmental, economic and health factors influence regional vulnerability to COVID-19?
Authors: Tahmasebi Pejman , Shokri-Kuehni Salome M.S. , Sahimi Muhammad , Shokri Nima 
Published: April 2020

AbstractWe have studied the correlations between twelve environmental, economic and health variables, by carrying out a statistical analysis of the fatality rate of COVID-19 in 14 countries. Our statistical analysis indicates that, among the 12 variables, the diabetes percentage of the total population and the extent of the population ages 65 and older in each country are correlated most strongly with the total number of deaths in them. Although the strength of the correlations between the variables and the total ND may change as the ongoing pandemic evolves, the study highlights the importance of integrating regional-specific variables in the modelling efforts aimed at projecting how the spread of the virus may influence different parts of the world.
Case- fatality rate in COVID- 19 patients: A meta- analysis of publicly accessible database
Authors: Maitra Souvik , Biswas Mansij , Bhattacharjee Sulagna 
Published: April 2020

AbstractA novel coronavirus was reported in Wuhan, China in December 2019 to cause severe acute respiratory symptoms (COVID-19). In this meta-analysis, we estimated case fatality rate from COVID-19 infection by random effect meta-analysis model with country level data. Publicly accessible web database WorldOMeter (https://www.worldometers.info/coronavirus/) was accessed on 24th March 2020 GMT and reported total number of cases, total death, active cases and seriously ill/ critically ill patients were retrieved. Primary outcome of this meta-analysis was case fatality rate defined by total number of deaths divided by total number of diagnosed cases. Pooled case fatality rate (95% CI) was 1.78 (1.34-2.22) %. Between country heterogeneity was 0.018 (p<0.0001). Pooled estimate of composite poor outcome (95% CI) was 4.06 (3.24-4.88) % at that point of time after exclusion of countries reported small number of cases. Pooled mortality rate (95% CI) was 33.97 (27.44-40.49) % amongst closed cases (where patients have recovered or died) with. Meta regression analysis identified statistically significant association between health expenditure and case fatality rate (p=0.0017).
Cardiac imaging of aortic valve area from 26,142 UK Biobank participants reveal novel genetic associations and shared genetic comorbidity with multiple disease phenotypes
Authors: Córdova-Palomera Aldo , Tcheandjieu Catherine , Fries Jason , Varma Paroma , Chen Vincent S. , Fiterau Madalina , Xiao Ke , Tejeda Heliodoro , Keavney Bernard , Cordell Heather J. , Tanigawa Yosuke , Venkataraman Guhan , Rivas Manuel , Ré Christopher , Ashley Euan , Priest James R. 
Published: April 2020

ABSTRACTThe aortic valve is an important determinant of cardiovascular physiology and anatomic location of common human diseases. From a sample of 26,142 European-ancestry participants, we estimated functional aortic valve area by planimetry from prospectively obtained cardiac MRI sequences of the aortic valve. A genome-wide association study of aortic valve area in these UK Biobank participants showed two significant associations indexed by rs71190365 (chr13:50764607,DLEU1, p=1.8×10−9) and rs35991305 (chr12:94191968,CRADD, p=3.4×10−8). From the GWAS findings we constructed a polygenic risk score for aortic valve area, which in a separate cohort of 311,728 individuals without imaging demonstrated that smaller aortic valve area is predictive of increased risk for aortic valve disease (Odds Ratio 0.88,p=2.3×10−6). After excluding subjects with a medical diagnosis of aortic valve stenosis (remaining n=310,546 individuals), phenome-wide association of >10,000 traits showed multiple links between the polygenic score for aortic valve disease and key health-related comorbidities involving the cardiovascular system and autoimmune disease. Genetic correlation analysis supports a shared genetic etiology with between aortic valve size and birthweight along with other cardiovascular conditions. These results illustrate the use of automated phenotyping of cardiac imaging data from the general population to investigate the genetic etiology of aortic valve disease, perform clinical prediction, and uncover new clinical and genetic correlates of cardiac anatomy.
COVID-19 Global Pandemic Planning: Decontamination and Reuse Processes for N95 Respirators
Authors: Perkins Douglas J , Villescas Steven , Wu Terry H. , Muller Timothy , Bradfute Steven , Hurwitz Ivy , Cheng Qiuying , Wilcox Hannah , Weiss Myissa , Bartlett Chris , Langsjoen Jens , Seidenberg Phil 
Published: April 2020

ABSTRACTCoronavirus disease 2019 (COVID-19) is an illness caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease was first identified as a cluster of respiratory illness in Wuhan City, Hubei Province, China in December 2019, and has rapidly spread across the globe to greater than 200 countries. Healthcare providers are at an increased risk for contracting the disease due to occupational exposure and require appropriate personal protective equipment (PPE), including N95 respirators. The rapid worldwide spread of high numbers of COVID-19 cases has facilitated the need for a substantial supply of PPE that is largely unavailable in many settings, thereby creating critical shortages. Creative solutions for the decontamination and safe reuse of PPE to protect our frontline healthcare personnel are essential. Here, we describe the development of a process that began in late February 2020 for selecting and implementing the use of hydrogen peroxide vapor (HPV) as viable method to reprocess N95 respirators. Since pre-existing HPV decontamination chambers were not available, we optimized the sterilization process in an operating room after experiencing initial challenges in other environments. Details are provided about the prioritization and implementation of processes for collection and storage, pre-processing, HPV decontamination, and post-processing of filtering facepiece respirators (FFRs). Important lessons learned from this experience include, developing an adequate reserve of PPE for effective reprocessing and distribution, and identifying a suitable location with optimal environmental controls (i.e., operating room). Collectively, information presented here provides a framework for other institutions considering decontamination procedures for N95 respirators.
Sphingolipid Biosynthesis Inhibition As A Host Strategy Against Diverse Pathogens
Authors: Kumar Sandeep , Li Jinmei , Park Jiwoong , Hart Sydney K. , Song Niki J. , Burrow Damon T. , Bean Nicholas L. , Jacobs Nicholas C. , Coler-Reilly Ariella , Pendergrass Anastasiia Onyshchenko , Pierre Tanya H. , Bradley India C. , Carette Jan E. , Varadarajan Malini , Brummelkamp Thijn R. , Dolle Roland , Peterson Tim R. 
Published: April 2020

ABSTRACTChloroquine is an anti-malarial and immunosuppressant drug that has cationic amphipathic chemical properties. We performed genome-wide screens in human cells with chloroquine and several other widely used cationic amphipathic drugs (CADs) including the anti-depressants, sertraline (Zoloft) and fluoxetine (Prozac), the analgesic nortriptyline (Pamelor), the anti-arrhythmic amiodarone (Cordarone), and the anti-hypertensive verapamil (Calan) to characterize their molecular similarities and differences. Despite CADs having different disease indications but consistent with them sharing key chemical properties, we found CADs to have remarkably similar phenotypic profiles compared with non-CADs we and others have previously screened (1–5). The most significant genetic interaction for all CADs was the initiating step in sphingolipid biosynthesis catalyzed by serine palmitoyltransferase (SPT). A comparison of genome-wide screens performed with diverse pathogens from viruses, bacteria, plants, and parasites including Ebola (6), adeno-associated virus AAV2 (7), HIV (8), Rotavirus (9), Influenza A (10), Zika virus (11), Picornavirus (12), Exotoxin A (13), Cholera toxin (14), Type III secretion system and Shiga toxin (15, 16), Ricin toxin (17), and Toxoplasma gondii (18) showed SPT as a top common host factor and 80% overlap overall in top hits specifically with CADs. Potential sphingolipid-mediated mechanisms for the host response- and virulence-modulating effects of CADs involve autophagy and SERPINE1/PAI-1 (plasminogen activator inhibitor-1). Chloroquine has recently shown potential as an anti-viral agent for the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease (19, 20). Our study demonstrates that numerous readily available drugs molecularly function highly similar to chloroquine, which suggests they might be considered for further pre-clinical investigation in the context of SARS-CoV-2. More generally, our work suggests the diverse pathogen mitigating potential of drugs that inhibit host sphingolipid biosynthesis such as CADs.Brief SummaryOur study demonstrates that numerous readily available drugs molecularly function highly similar to chloroquine, which suggests they might be considered for further pre-clinical investigation in the context of SARS-CoV-2.
Relationship between Average Daily Temperature and Average Cumulative Daily Rate of Confirmed Cases of COVID-19
Authors: Pirouz Behzad , Golmohammadi Amirsina , SaeidpourMasouleh Hasti , Violini Galileo , Pirouz Behrouz 
Published: April 2020

AbstractAIMSThe main purpose of this study is to investigate the correlation between the average daily temperature and the rate of coronavirus epidemic growth in the infected regions.BACKGROUNDThe rapid outbreak of the new Coronavirus (COVID-19) pandemic and the spread of the virus worldwide, especially in the Northern Hemisphere, have prompted various investigations about the impact of environmental factors on the rate of development of this epidemic. Different studies have called attention to various parameters that may have influenced the spread of the virus, and in particular, the impact of climatic parameters has been emphasized.OBJECTIVEThe main hypothesis object of our research is that between regions exhibiting a significant difference in the mean daily temperature, a significant difference is also observed in the average cumulative daily rate of confirmed cases and that this does not happen if there is no significant difference in mean daily temperature.METHODThe research hypothesis was investigated through statistical analysis. The F-test was used to test whether there is significant equality of variances for each pair of case studies, and then, by the T- Test, the existence of a significant difference was investigated. In all statistical tests, the confidence level of 95% is considered. In order to minimize the impact on the results of factors like the policy of the government or cultural differences among countries (food, exercise, weight, etc.), three case studies within five countries, namely Iran, Italy, Germany, Spain, and United States were compared separately.RESULTThis statistical analysis shows that there is a correlation between the average temperature and the epidemic rate, and this is especially evident when differences in average daily temperature are significantly larger, as it happens for Bandar Abbas in Iran, Milan in Italy, Santa Cruz in Spain, and Los Angeles in the US. Besides, the analysis of the average air temperatures shows that the epidemic rates of COVID-19 were higher in the case studies with a lower average temperature. Instead, when no significant differences exist in the average daily temperature of two cities in the same country, there is no significant difference in the average cumulative daily rate of confirmed cases.CONCLUSIONIn all five selected countries, we found that when there is a significant difference in the daily mean temperature between two regions of a country, a significant difference also exists in the average cumulative daily rate of confirmed cases. Conversely, if there are no significant differences in the mean daily temperature of two regions in the same country, no significant difference is observed in the average cumulative daily rate of confirmed cases for these regions. In conclusion, the results of this study support the research hypothesis and confirm the effectiveness of the proposed method for analysis of the epidemic rates.
Molecular Mechanism of Action of Repurposed Drugs and Traditional Chinese Medicine Used for the Treatment of Patients Infected With COVID-19: A Systematic Scoping Review
Authors: Lem Fui Fui , Opook Fernandes , Lee Dexter Jiunn Herng , Chee Fong Tyng , Lawson Fahcina P. , Chin Su Na 
Published: April 2020

AbstractBackgroundThe emergence of COVID-19 as a pandemic has resulted in the need for urgent development of vaccines and drugs and the conduction of clinical trials to fight the outbreak. Because of the time constraints associated with the development of vaccines and effective drugs, drug repurposing and other alternative treatment methods have been used to treat patients that have been infected by the SARS-CoV-2 virus and have acquired COVID-19.ObjectiveThe objective of this systematic scoping review is to provide an overview of the molecular mechanism of action of repurposed drugs or alternative treatment medicines used to attenuate COVID-19 disease.Data SourcesThe research articles or grey literature, including theses, government reports, and official news online, were identified from 4 databases and 1 search engine. The full content of a total of 160 articles that fulfilled our inclusion criteria was analyzed and information about 6 drugs (ritonavir, lopinavir, oseltamivir, remdesivir, favipiravir, and chloroquine) and 4 traditional Chinese medicines (Shuang Huang Lian Kou Fu Ye, TCM combination of Bu Huan Jin Zheng Qi San and Da Yuan Yin, Xue Bi Jing Injection and Qing Fei Pai Du Tang) were extracted.ConclusionsAll of the repurposed drugs that have been used for the treatment of COVID-19 depend on the ability of the drug to inhibit the proliferation of the SARS-CoV-2 virus by binding to enzyme active sites, viral chain termination, or triggering of the molecular pathway, whereas traditional Chinese medicine has a pivotal role in triggering the inflammation pathway, such as the neuraminidase blocker, to fight the SARS-CoV-2 virus. This review provides an insight to experimental validation of drugs and alternative medicine used for the treatment and control of COVID-19.
Protecting our health care workers while protecting our communities during the COVID-19 pandemic: a comparison of approaches and early outcomes in two Italian regions, 2020
Authors: Binkin Nancy , Michieletto Federica , Salmaso Stefania , Russo Francesca 
Published: April 2020

AbstractIntroductionItaly, which has been hard-hit by the COVID-19 pandemic, has an overriding national strategy, but its 21 regions have adapted their response based on the organization of their curative and public health services. In this paper, we compare short-term outcomes for two northern Italian regions which had almost simultaneous initial outbreaks: Lombardy, which had a patient-centered approach that relied on primary care physicians and hospital care, and Veneto, which focused on community-based diagnosis and care.MethodsWe used numerator and denominator data from public Italian government sources to calculate reported rates of COVID-19 testing/1000, COVID-19 cases/100,000 overall and for health care workers (HCWs) and non-HCWs, deaths per 100,000, and the percent of cases admitted to hospitals and ICUs for February 24-April 1, 2020.ResultsAs of April 1, 2020, Lombardy experienced 44,733 cases and 7,539 deaths; for Veneto, the corresponding values were 9,625 and 499. The cumulative case rate was 445/100,000 for Lombardy and 196/100,000 for Veneto, a 2.3-fold difference. Mortality rates were 7.5 times higher in Lombardy than in Veneto (75/100,000 and 10/100,000, respectively). Cumulative rates of testing were nearly twice as high in Veneto and were 2.7 times higher in the first week of the epidemic. In Lombardy, 51.5% of patients were admitted, including, 5.2% to intensive care units; for Veneto, the corresponding figures were 25.1% and 4.3%, respectively. HCWs account for 14.3% of all cases in Lombardy compared with 4.4% in Veneto. In Lombardy, the rate among HCWs was 19.1 times higher than in the general population (6,924/100,000 versus 362/100,000), while in Veneto it was 3.9 times higher (676/100,000 versus 172/100,000).DiscussionThe community-based approach in Veneto appears to be associated with substantially reduced rates of cases, hospitalizations, deaths, and infection in HCWs compared with the patient-centered approach in Lombardy. Our findings suggest that the impact of COVID-19 can be reduced through strong and aggressive public health efforts to confirm and isolate initial cases and contacts in a timely way and to minimize unnecessary contact between HCWs and cases through home-based testing and pro-active home follow-up.
Immunological assays for SARS-CoV-2: an analysis of available commercial tests to measure antigen and antibodies
Authors: González John M. , Shelton William J. , Díaz-Vallejo Manuel , Rodriguez-Castellanos Victoria E. , Zuluaga Juan Diego H. , Chamorro Diego F. , Arroyo-Ariza Daniel 
Published: April 2020

AbstractThe rapid spread of SARS-CoV-2 coronavirus infection has led to the development of molecular and serologic tests in a short period of time. While tests such as RT-PCR have applications in the immediate diagnosis revealing the presence of the virus, serological tests can be used to determine previous exposure to the virus and complement acute diagnosis. Antibody production can occur as early as 5 days post-infection. Both IgM and IgG specific anti-SARS-COV-2 antibodies can be a useful tool to test faster and larger groups of individuals. The objective of this study was to carry out a review of the different serological tests offered to detect antigen or antibodies against SARS-CoV-2. This information should be useful for decision takers in different countries to choose a test according to their needs. Based on web pages that listed serological assays, we found 226 coming from 20 countries, the majority are indirect tests for specific antibodies detection (n 180) and use immunochromatography methods (n 110) with samples coming from blood-derived products (n 105). Measuring IgM/IgG at the same time (n 112) and a procedure time of <20 min (n 83) are the most common. The overall average sensitivity was 91.8% and specificity was 97%. Most of the tests are currently for in vitro diagnosis (IVD). This information gathered could change day by day due to the expedite process of production and emergency of authorization use.
Multi-Stage Group Testing Improves Efficiency of Large-Scale COVID-19 Screening
Authors: Eberhardt JN , Breuckmann NP , Eberhardt CS 
Published: April 2020

AbstractBackgroundSARS-CoV-2 test kits are in critical shortage in many countries. This limits large-scale population testing and hinders the effort to identify and isolate infected individuals.ObjectivesHerein, we developed and evaluated multi-stage group testing schemes that test samples in groups of various pool sizes in multiple stages. Through this approach, groups of negative samples can be eliminated with a single test, avoiding the need for individual testing and achieving considerable savings of resources.Study designWe designed and parameterized various multi-stage testing schemes and compared their efficiency at different prevalence rates using computer simulations.ResultsWe found that three-stage testing schemes with pool sizes of maximum 16 samples can test up to three and seven times as many individuals with the same number of test kits for prevalence rates of around 5% and 1%, respectively. We propose an adaptive approach, where the optimal testing scheme is selected based on the expected prevalence rate.ConclusionThese group testing schemes could lead to a major reduction in the number of testing kits required and help improve large-scale population testing in general and in the context of the current COVID-19 pandemic.
Neuropsychiatric adverse events of chloroquine: A real-world pharmacovigilance study using the FAERS database
Authors: Sato Kenichiro , Mano Tatsuo , Iwata Atsushi , Toda Tatsushi 
Published: April 2020

AbstractObjectivesAs of the early April 2020, the antimalarial drug, chloroquine, has been approved as an emergency treatment for the coronavirus disease 2019 (COVID-19) in the United States and in Europe. Although infrequent, neuropsychiatric symptoms have been reported in patients who received chloroquine for the treatment of malaria or autoimmune diseases. In this study, we investigated these adverse events (AEs) using a large self-reporting database.Materials and MethodsWe conducted a disproportionality analysis for the detection of neuropsychiatric AE signals associated with the use of chloroquine (or hydroxychloroquine), reported to FAERS database between the fourth quarter of 2012 and the fourth quarter of 2019. Adjusted reporting odds ratio (ROR) for the development of each of the neuropsychiatric AEs following the use of chloroquine was calculated using a multilevel model.ResultsWe included 2,389,474 AE cases, among which 520 cases developed neuropsychiatric AE following the use of chloroquine. Exposure to chloroquine was associated with a statistically significant high reporting of amnesia, delirium, hallucinations, depression, and loss of consciousness, (lower 95% confidence interval of the adjusted ROR > 1), although the degree of increase in their ROR was limited. There was no statistically significant high reporting of any other neuropsychiatric AE, including suicide, psychosis, confusion, and agitation.ConclusionCurrent pharmacovigilance study results did not suggest any potential link between the use of chloroquine and an increased risk of suicide, psychosis, confusion, and agitation, which would be informative during the emergency use of chloroquine for the treatment of COVID-19.