Transparency assessment of COVID-19 models.
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ABSTRACT:
SUBMITTER: Jalali MS
PROVIDER: S-EPMC7833180 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Mathematical models have become very influential, especially during the COVID-19 pandemic. Data and code sharing are indispensable for reproducing them, protocol registration may be useful sometimes, and declarations of conflicts of interest (COIs) and of funding are quintessential for transparency. Here, we evaluated these features in publications of infectious disease-related models and assessed whether there were differences before and during the COVID-19 pandemic and for COVID-19 models versus models for other diseases. We analysed all PubMed Central open access publications of infectious disease models published in 2019 and 2021 using previously validated text mining algorithms of transparency indicators. We evaluated 1338 articles: 216 from 2019 and 1122 from 2021 (of which 818 were on COVID-19); almost a six-fold increase in publications within the field. 511 (39.2%) were compartmental models, 337 (25.2%) were time series, 279 (20.9%) were spatiotemporal, 186 (13.9%) were agent-based and 25 (1.9%) contained multiple model types. 288 (21.5%) articles shared code, 332 (24.8%) shared data, 6 (0.4%) were registered, and 1197 (89.5%) and 1109 (82.9%) contained COI and funding statements, respectively. There was no major changes in transparency indicators between 2019 and 2021. COVID-19 articles were less likely to have funding statements and more likely to share code. Further validation was performed by manual assessment of 10% of the articles identified by text mining as fulfilling transparency indicators and of 10% of the articles lacking them. Correcting estimates for validation performance, 26.0% of papers shared code and 41.1% shared data. On manual assessment, 5/6 articles identified as registered had indeed been registered. Of articles containing COI and funding statements, 95.8% disclosed no conflict and 11.7% reported no funding. Transparency in infectious disease modelling is relatively low, especially for data and code sharing. This is concerning, considering the nature of this research and the heightened influence it has acquired.
| S-EPMC9543956 | biostudies-literature
Project description:The COVID-19-the worst pandemic since the Spanish flu-has dramatically changed the world, with a significant number of people suffering from and dying of the disease. Some scholars argue that democratic governments are disadvantaged in coping with the current pandemic mainly because they cannot intervene in their citizens' lives as aggressively as their authoritarian counterparts. Other scholars, however, suggest that possible data manipulation may account for the apparent advantage of authoritarian countries. Taking such a possibility seriously, this paper analyzes the relationship between political regimes, data transparency, and COVID-19 deaths using cross-national data for over 108 countries, obtained from Worldometer COVID-19 Data, Polity V Project, Variety of Democracy (V-Dem) Project, HRV Transparency Project among other sources. Regression analyses indicate that authoritarian countries do not necessarily tend to have fewer COVID-19 deaths than their democratic counterparts after controlling for other factors, especially data transparency. The transparency variable itself, on the other hand, is positively correlated with the number of death cases more consistently (P <0.05). Overall, the estimation results point to the possible data manipulation, not the nature of regime characteristics itself, as a more significant source for the seemingly low casualty rates in authoritarian countries.
| S-EPMC8219996 | biostudies-literature
Project description:ObjectiveWe aimed to assess the adherence to transparency practices (data availability, code availability, statements of protocol registration and conflicts of interest and funding disclosures) and FAIRness (Findable, Accessible, Interoperable, and Reusable) of shared data from open access COVID-19-related articles published in dental journals available from the Europe PubMed Central (PMC) database.MethodsWe searched and exported all COVID-19-related open-access articles from PubMed-indexed dental journals available in the Europe PMC database in 2020 and 2021. We detected transparency indicators with a validated and automated tool developed to extract the indicators from the downloaded articles. Basic journal- and article-related information was retrieved from the PMC database. Then, from those which had shared data, we assessed their accordance with FAIR data principles using the F-UJI online tool (f-uji.net).ResultsOf 650 available articles published in 59 dental journals, 74% provided conflicts of interest disclosure and 40% funding disclosure and 4% were preregistered. One study shared raw data (0.15%) and no study shared code. Transparent practices were more common in articles published in journals with higher impact factors, and in 2020 than in 2021. Adherence to the FAIR principles in the only paper that shared data was moderate.ConclusionWhile the majority of the papers had a COI disclosure, the prevalence of the other transparency practices was far from the acceptable level. A much stronger commitment to open science practices, particularly to preregistration, data and code sharing, is needed from all stakeholders.
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Project description:To understand how COVID-19 alters the platelet transcriptome.
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Project description:The recent emergence of COVID-19 presents a major global crisis. Profound knowledge gaps remain about the interaction between the virus and the immune system. Here, we used a systems biology approach to analyze immune responses in 76 COVID-19 patients and 69 age and sex- matched controls, from Hong Kong and Atlanta. Mass cytometry revealed prolonged plasmablast and effector T cell responses, reduced myeloid expression of HLA-DR and inhibition of mTOR signaling in plasmacytoid DCs (pDCs) during infection. Production of pro-inflammatory cytokines plasma levels of inflammatory mediators, including EN-RAGE, TNFSF14, and Oncostatin-M, which correlated with disease severity, and increased bacterial DNA and endotoxin in plasma in and reduced HLA-DR and CD86 but enhanced EN-RAGE expression in myeloid cells in severe transient expression of IFN stimulated genes in moderate infections, consistent with transcriptomic analysis of bulk PBMCs, that correlated with transient and low levels of plasma COVID-19.
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Project description:Bat sarbecovirus BANAL-236 is highly related to SARS-CoV-2 and infects human cells, albeit lacking the furin cleavage site in its spike protein. BANAL-236 replicates efficiently and pauci-symptomatically in humanized mice and in macaques, where its tropism is enteric, strongly differing from that of SARS-CoV-2. BANAL-236 infection leads to protection against superinfection by a virulent strain. We find no evidence of antibodies recognizing bat sarbecoviruses in populations in close contact with bats in which the virus was identified, indicating that such spillover infections, if they occur, are rare. Six passages in humanized mice or in human intestinal cells, mimicking putative early spillover events, select adaptive mutations without appearance of a furin cleavage site and no change in virulence. Therefore, acquisition of a furin site in the spike protein is likely a pre-spillover event that did not occur upon replication of a SARS-CoV-2-like bat virus in humans or other animals. Other hypotheses regarding the origin of the SARS-CoV-2 should therefore be evaluated, including the presence of sarbecoviruses carrying a spike with a furin cleavage site in bats.
| S-SCDT-10_15252-EMBR_202256055 | biostudies-other