The development of preprints during the COVID-19 pandemic

The promise of community-driven preprints in ecology and evolution

Publishing preprints is quickly becoming commonplace in ecology and evolutionary biology. Preprints can facilitate the rapid sharing of scientific knowledge establishing precedence and enabling feedback from the research community before peer review. Yet, significant barriers to preprint use exist, including language barriers, a lack of understanding about the benefits of preprints and a lack of diversity in the types of research outputs accepted (e.g. reports). Community-driven preprint initiatives can allow a research community to come together to break down these barriers to improve equity and coverage of global knowledge. Here, we explore the first preprints uploaded to EcoEvoRxiv (n = 1216), a community-driven preprint server for ecologists and evolutionary biologists, to characterize preprint use in ecology, evolution and conservation. Our perspective piece highlights some of the unique initiatives that EcoEvoRxiv has taken to break down barriers to scientific publishing by exploring the composition of articles, how gender and career stage influence preprint use, whether preprints are associated with greater open science practices (e.g. code and data sharing) and tracking preprint publication outcomes. Our analysis identifies areas that we still need to improve upon but highlights how community-driven initiatives, such as EcoEvoRxiv, can play a crucial role in shaping publishing practices in biology.

Clinical outcomes and considerations in outpatient with COVID-19 receiving remdesivir therapy

Introduction

This retrospective cross-sectional study aimed to assess the outcomes of Covid-19 patients who received remdesivir therapy at the outpatient department of Ziaian Hospital.

Method

A total of 514 eligible patients were included between May and September 2021. Covid-19 diagnosis was confirmed through positive SARS-COV-2 PCR tests or chest CT scans. Due to limited hospital beds, patients received remdesivir on an outpatient basis.

Results

Patients received six daily doses of remdesivir for 5 days. Those referred to a physician within 7 days of symptom onset had similar hospitalization rates compared to later referrals. Lower blood saturation levels were associated with a higher likelihood of hospital admission, indicating that earlier administration of remdesivir may be more effective. Patients with over 50% lung involvement had higher rates of disease progression despite treatment. Corticosteroids did not significantly improve outcomes in patients with saturation above 90%. Discontinuation of remdesivir due to side effects was rare, with only 1% experiencing increased liver enzymes, 1.2% facial redness and tremors, and 1.5% allergies. After 1 week of treatment, patients commonly reported symptoms such as hair loss, fatigue, body pain, lethargy, and anorexia, particularly among hospitalized patients.

Discussion

Patients generally preferred outpatient treatment over hospitalization. Body mass index (BMI) did not significantly impact hospitalization rates, although average weight tended to be higher among inpatients. The study confirmed the effectiveness of remdesivir therapy with a low occurrence of side effects.

Conclusion

This retrospective study evaluated the outcomes of Covid-19 patients receiving remdesivir at an outpatient department. Early administration of remdesivir showed better outcomes, while corticosteroids had limited benefits. Outpatient treatment was favored, and BMI did not significantly influence hospitalization rates. Remdesivir demonstrated efficacy with a low incidence of side effects.

Exploring the current dynamics of preprints

Preprints are non-peer-reviewed and publicly available articles for open and transparent research communication. Preprint servers host the submission of such manuscripts, and despite the presence of established preprint servers, their numbers have continued to rise in recent times. A steep increasing pattern in posted preprints and their accommodating servers has been observed over the last decade. In this article, we explored the global trends in the preprint adoption and its involvement in promoting open and transparent research findings across various domains. We further emphasized the importance of preprinting, highlighting its significant impact during the pandemic through effective information sharing, and advocating for its broader integration in scholarly communication.

Interventions reducing mortality in COVID-19 patients: a systematic review of randomized evidence

INTRODUCTION

COVID-19 pandemic changed the way medical research is published, possibly forever. As the need for rapidity led to the rise of preprint servers, the undeniable drop in the overall quality of scientific publications requires an in-depth review of all available evidence. The present manuscript aims to identify and summarize all treatments which have been reported to reduce mortality in randomized trials in hospitalized COVID-19 patients.

EVIDENCE ACQUISITION

Independent investigators searched MEDLINE/PubMed, Scopus, and Embase databases to identify all randomized trials of any intervention influencing mortality in hospitalized COVID-19 patients up to August 18th, 2022. Articles were selected only when they fulfilled all the following: randomized trial design; dealing with any kind of interventions in adult hospitalized COVID-19 patients; and statistically significant reduction in mortality.

EVIDENCE SYNTHESIS

We identified 28 interventions (42 manuscripts) reducing mortality in hospitalized COVID-19 patients. About 60% of the studies (26/42) were multicentric, for a total of 1140 centers involved worldwide. Several of these studies were published in high-ranked, peer-reviewed journals. Interventions with randomized evidence of mortality reduction in hospitalized COVID-19 patients belonged to 5 domains: corticosteroids, immunomodulators, antimicrobials, supportive therapies, and other drugs.

CONCLUSIONS

Many interventions have the potential to reduce mortality in COVID-19 hospitalized patients. The correct treatment of future pandemics relies on large, multicentric randomized clinical trials for further evaluation of these promising strategies.

Hindsight2020: Characterizing Uncertainty in the COVID-19 Scientific Literature

Following emerging, re-emerging, and endemic pathogen outbreaks, the rush to publish and the risk of data misrepresentation, misinterpretation, and even misinformation puts an even greater onus on methodological rigor, which includes revisiting initial assumptions as new evidence becomes available. This study sought to understand how and when early evidence emerges and evolves when addressing different types of recurring pathogen-related questions. By applying claim-matching by means of deep learning Natural Language Processing (NLP) of coronavirus disease 2019 (COVID-19) scientific literature against a set of expert-curated evidence, patterns in timing across different COVID-19 questions-and-answers were identified, to build a framework for characterizing uncertainty in emerging infectious disease (EID) research over time. COVID-19 was chosen as a use case for this framework given the large and accessible datasets curated for scientists during the beginning of the pandemic. Timing patterns in reliably answering broad COVID-19 questions often do not align with general publication patterns, but early expert-curated evidence was generally stable. Because instability in answers often occurred within the first 2 to 6 mo for specific COVID-19 topics, public health officials could apply more conservative policies at the start of future pandemics, to be revised as evidence stabilizes.

Publications on COVID-19 in radiology journals in 2020 and 2021: bibliometric citation and co-citation network analysis

OBJECTIVES

The pandemic caused by SARS-CoV-2 has led to the rapid publication of numerous radiology articles, primarily focused on disease diagnosis. The objective of this study is to analyze the intellectual structure of radiology research on COVID-19 using a citation and co-citation analysis.

METHODS

We identified all documents about COVID-19 published in radiology journals included in the Web of Science in the period 2020-2021, conducting a citation analysis. Then we identified all bibliographic references that were cited by these documents, generating a co-citation matrix that was used to perform a co-citation network.

RESULTS

Of the 3418 documents indexed in WoS, 857 were initially "Early Access," 2223 had citations, 393 had more than 20 citations, and 83 had more than 100 citations. The USA had the highest number of publications (32.62%) and China had the highest rate of funded studies (45.38%). The three authors with the most publications were affiliated with Italian institutions, while the five most cited authors were Chinese. A total of 647 publications were co-cited at least 12 times and were published in 206 different journals, with 49% of the documents found in radiology journals. The institutions with the greatest presence among these co-cited articles were Chinese and American.

CONCLUSION

This co-citation analysis is the first to focus exclusively on radiology articles on COVID-19. Our study confirms the existence of interrelated thematic clusters with different specific weights.

KEY POINTS

• As the pandemic caused by SARS-Cov-2 has led to the rapid publication of numerous radiology studies in a short time period, a bibliometric review based on citation and co-citation analysis has been conducted. • The co-citation analysis supported the identification of key themes in the study of COVID-19 in radiology publications. • Many of the most co-cited articles belong to a heterogeneous group of publications, with authors from countries that are far apart and even from different disciplines.

Reliability of citations of medRxiv preprints in articles published on COVID-19 in the world leading medical journals

Introduction

Preprints have been widely cited during the COVID-19 pandemics, even in the major medical journals. However, since subsequent publication of preprint is not always mentioned in preprint repositories, some may be inappropriately cited or quoted. Our objectives were to assess the reliability of preprint citations in articles on COVID-19, to the rate of publication of preprints cited in these articles and to compare, if relevant, the content of the preprints to their published version.

Methods

Articles published on COVID in 2020 in the BMJ, The Lancet, the JAMA and the NEJM were manually screened to identify all articles citing at least one preprint from medRxiv. We searched PubMed, Google and Google Scholar to assess if the preprint had been published in a peer-reviewed journal, and when. Published articles were screened to assess if the title, data or conclusions were identical to the preprint version.

Results

Among the 205 research articles on COVID published by the four major medical journals in 2020, 60 (29.3%) cited at least one medRxiv preprint. Among the 182 preprints cited, 124 were published in a peer-reviewed journal, with 51 (41.1%) before the citing article was published online and 73 (58.9%) later. There were differences in the title, the data or the conclusion between the preprint cited and the published version for nearly half of them. MedRxiv did not mentioned the publication for 53 (42.7%) of preprints.

Conclusions

More than a quarter of preprints citations were inappropriate since preprints were in fact already published at the time of publication of the citing article, often with a different content. Authors and editors should check the accuracy of the citations and of the quotations of preprints before publishing manuscripts that cite them.

Need for universal acceptance of preprinting by editors of journals of health professional education

None