[The year 2022 placed in perspective by hospital internists]. / Année 2022 mise en perspective par les internistes hospitaliers.

According to PubMed statistics when writing this review, the year 2022 is expected to mark the first dip in the number of articles published in relation to the Covid-19 pandemic. This review, without any mention to Sars-CoV-2, highlight this transition and addresses many topics in internal medicine: gastroenterology, cardiology, endocrinology, respiratory medicine, infectious diseases and venous access. Each year, the chief residents of the internal medicine ward in Lausanne university hospital (CHUV) in Switzerland meet up to share their readings: here is a selection of ten articles that have caught our attention, summarized and commented for you, which should change our daily practice.

D'après les statistiques PubMed au moment de la rédaction de cette revue, l'année 2022 devrait marquer le premier infléchissement du nombre d'articles publiés en relation avec la pandémie de Covid-19. Cette revue d'articles, sans écho au Sars-CoV-2, souligne cette transition et aborde de nombreux sujets de la médecine interne : gastroentérologie, cardiologie, endocrinologie, pneumologie, infectiologie et accès veineux. Chaque année, les cheffes et chefs de clinique du Service de médecine interne du CHUV se réunissent pour partager leurs lectures : voici une sélection de dix articles ayant retenu notre attention, revus et commentés pour vous, et qui devraient faire évoluer notre pratique quotidienne.

Systematic comparison of published host gene expression signatures for bacterial/viral discrimination.

BACKGROUND: Measuring host gene expression is a promising diagnostic strategy to discriminate bacterial and viral infections. Multiple signatures of varying size, complexity, and target populations have been described. However, there is little information to indicate how the performance of various published signatures compare to one another. METHODS: This systematic comparison of host gene expression signatures evaluated the performance of 28 signatures, validating them in 4589 subjects from 51 publicly available datasets. Thirteen COVID-specific datasets with 1416 subjects were included in a separate analysis. Individual signature performance was evaluated using the area under the receiving operating characteristic curve (AUC) value. Overall signature performance was evaluated using median AUCs and accuracies. RESULTS: Signature performance varied widely, with median AUCs ranging from 0.55 to 0.96 for bacterial classification and 0.69-0.97 for viral classification. Signature size varied (1-398 genes), with smaller signatures generally performing more poorly (P < 0.04). Viral infection was easier to diagnose than bacterial infection (84% vs. 79% overall accuracy, respectively; P < .001). Host gene expression classifiers performed more poorly in some pediatric populations (3 months-1 year and 2-11 years) compared to the adult population for both bacterial infection (73% and 70% vs. 82%, respectively; P < .001) and viral infection (80% and 79% vs. 88%, respectively; P < .001). We did not observe classification differences based on illness severity as defined by ICU admission for bacterial or viral infections. The median AUC across all signatures for COVID-19 classification was 0.80 compared to 0.83 for viral classification in the same datasets. CONCLUSIONS: In this systematic comparison of 28 host gene expression signatures, we observed differences based on a signature's size and characteristics of the validation population, including age and infection type. However, populations used for signature discovery did not impact performance, underscoring the redundancy among many of these signatures. Furthermore, differential performance in specific populations may only be observable through this type of large-scale validation.

Mind the gender gap: COVID-19 lockdown effects on gender differences in preprint submissions.

The gender gap is a well-known problem in academia and, despite its gradual narrowing, recent estimations indicate that it will persist for decades. Short-term descriptive studies suggest that this gap may have actually worsened during the months of confinement following the start of the COVID-19 pandemic in 2020. In this work, we evaluate the impact of the COVID-19 lockdown on female and male academics' research productivity using preprint drop-off data. We examine a total of 307,902 unique research articles deposited in 5 major preprint repositories during the period between January and May each year from 2017 to 2020. We find that the proportion of female authors in online repositories steadily increased over time; however, the trend reversed during the confinement and gender parity worsened in two respects. First, the proportion of male authors in preprints increased significantly during lockdown. Second, the proportion of male authors in COVID-19-related articles was significantly higher than that of women. Overall, our results imply that the gender gap in academia suffered an approximately 1-year setback during the strict lockdown months of 2020, and COVID-related research areas suffered an additional 1.5-year setback.

Comparison of COVID-19 and non-COVID-19 papers.

OBJECTIVE: The need to generate evidence related to COVID-19, the acceleration of publication and peer-review process and the competition between journals may have influenced the quality of COVID-19 papers. Our objective was to compare the characteristics of COVID-19 papers against those of non-COVID-19 papers and identify the variables in which they differ. METHOD: We conducted a journal-matched case-control study. Cases were COVID-19 papers and controls were non-COVID-19 papers published between March 2020 and January 2021. Journals belonging to five different Journal Citations Reports categories were selected. Within each selected journal, a COVID-19 paper (where there was one) and another non-COVID-19 paper were selected. Conditional logistic regression models were fitted. RESULTS: We included 81 COVID-19 and 143 non-COVID-19 papers. Descriptive observational studies and analytical observational studies had, respectively, a 55-fold (odds ratio [OR]: 55.12; 95% confidence interval [95%CI]: 7.41-409.84) and 19-fold (OR: 19.28; 95%CI: 3.09-120.31) higher likelihood of being COVID-19 papers, respectively, and also a higher probability of having a smaller sample size (OR: 7.15; 95%CI: 2.33-21.94). COVID-19 papers had a higher probability of being cited since their publication (OR: 4.97; 95%CI: 1.63-15.10). CONCLUSIONS: The characteristics of COVID-19 papers differed from those of non-COVID-19 papers published in the first months of the pandemic. In order to ensure the publication of good scientific evidence the quality of COVID-19-papers should be preserved.

Tracking changes between preprint posting and journal publication during a pandemic.

Amid the Coronavirus Disease 2019 (COVID-19) pandemic, preprints in the biomedical sciences are being posted and accessed at unprecedented rates, drawing widespread attention from the general public, press, and policymakers for the first time. This phenomenon has sharpened long-standing questions about the reliability of information shared prior to journal peer review. Does the information shared in preprints typically withstand the scrutiny of peer review, or are conclusions likely to change in the version of record? We assessed preprints from bioRxiv and medRxiv that had been posted and subsequently published in a journal through April 30, 2020, representing the initial phase of the pandemic response. We utilised a combination of automatic and manual annotations to quantify how an article changed between the preprinted and published version. We found that the total number of figure panels and tables changed little between preprint and published articles. Moreover, the conclusions of 7.2% of non-COVID-19-related and 17.2% of COVID-19-related abstracts undergo a discrete change by the time of publication, but the majority of these changes do not qualitatively change the conclusions of the paper.

The 2020 research pandemic: A bibliometric analysis of publications on COVID-19 and their scientific impact during the first months.

BACKGROUND: The outbreak of COVID-19 has created a landslide of publications, from different sources and unequal impact. We considered that the first 3 months are crucial to understand how knowledge has been generated by performing a bibliometric analysis, including the citations to these articles to guide researchers in exploring this field, and to evaluate the relationship between confirmed COVID-19 cases and deaths with the number of papers per country. METHODS: Scientific publications were obtained from PubMed (January-March 2020) and their citations during the first 6 months retrieved from the Scopus database. An analysis of the number of papers by country, approach (type and category of publication), and impact was made. A multiple linear regression model was implemented to analyze the correlation between the number of publications and confirmed cases and deaths. RESULTS: A total of 2,530 publications were analyzed with 59,104 citations (23.4 citations/article), written by authors from 67 countries. China was the country with more publications (988, 39%) and more citations (36,416, 63%) followed by the United States with 423 articles (16.7%) and 7,458 citations (12.6%). The coauthorship network identified 10,756 authors. According to the multivariate analysis, both confirmed cases and deaths were significantly correlated with the number of publications per country (corrected by population size and gross domestic product). CONCLUSION: The correlation with the number of publications suggests that cases and deaths had some impact on the medical literature, reflecting how rapidly the scientific community has been on the frontline in the fight against COVID-19.

Characteristics of published/registered clinical trials on COVID-19 treatment: A systematic review.

OBJECTIVES: Due to the rapid spread of COVID-19 worldwide, many countries have designed clinical trials to find efficient treatments. We aimed to critically report the characteristics of all the registered and published randomized clinical trials (RCTs) conducted on COVID-19, and summarize the evaluation of potential therapies developed in various regions. EVIDENCE ACQUISITION: We comprehensively searched PubMed, Cochrane Library, Web of Science, Scopus, and Clinicaltrial.gov databases to retrieve all the relevant studies up to July 19, 2021, in conformity with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) flowchart. We included all English-language published/registered RCTs on COVID-19, and excluded non-RCT, in-vitro/in-vivo, editorials, and review studies. Two reviewers independently evaluated all the records, and then analyzed by using SPSS 17. RESULTS: Within 3018 included studies, 2801 (92.8%) and 217 (7.2%) were registered or published RCTs consisting of about 600 synthetic drugs. Herbal medicines have been studied in 23 trials (10.6%) among the published RCTs and in 357 registered RCTs (12.7%). Hydroxychloroquine 23 (10.6%) and convalescent plasma 194 (6.9%) alone or in combination with other agents were the most frequently used interventions in published and registered RCTs, respectively. Most published RCTs have been conducted in Western Pacific Region (WPRO) (50 trials, 23.0%) including 45 trials from China. Also, a greater proportion of registered RCTs have been conducted in the Region of the Americas (PAHO) (885 trials, 31.6%) including 596 RCTs from the United States (U.S). Globally, 283 registered trials have been conducted to assess new developed vaccines for COVID or previously established for other disorders. CONCLUSION: The present study highlighted the wide range of potential therapeutic agents in published and registered COVID-19 clinical trials across a wide range of regions. However, it is urgently required to global coordination in order to conduct more well-designed trials and progress in discovering safe and effective treatments.

Hand hygiene in health care: 20 years of ongoing advances and perspectives.

Health-care-associated infections are the most prevalent adverse events of hospital care, posing a substantial threat to patient safety and burden on society. Hand hygiene with alcohol-based hand rub is the most effective preventive strategy to reduce health-care-associated infections. Over the past two decades, various interventions have been introduced and studied to improve hand hygiene compliance among health-care workers. The global implementation of the WHO multimodal hand hygiene improvement strategy and constant efforts to replace the use of soap and water with alcohol-based hand rub have led to a faster and more efficient hand cleaning method. These strategies have strongly contributed to the success of behaviour change and a subsequent decrease in health-care-associated infections and cross-transmission of multidrug-resistant organisms worldwide. The WHO multimodal behaviour change strategy requires a series of elements including system change as a prerequisite for behaviour, change, education, monitoring and performance feedback, reminders in the workplace, and an institutional safety climate. Successful adoption of the promotion strategy requires adaptation to available resources and sociocultural contexts. This Review focuses on the major advances and challenges in hand hygiene research and practices in the past 20 years and sets out various ways forward for improving this lifesaving action.

[COVID-19 and medical publications: How three articles have influenced the media and public decisions in France]. / Littérature médicale et COVID-19 : comment trois articles ont influencé les médias et la décision publique en France.

The present article details the publication process and the vicissitudes of three articles about SARS-CoV-2 and its related disease (COVID-19). The three articles were published one month apart between March and May 2020. Their mediatization led French health authorities to intervene. Our article does not focus on and does not assess the scientific quality of the articles presented, but only aims to open the reflection on medical publication. Beyond the description of these three specific cases, this article raises issues about article retraction, peer-reviewing, preprints, authorship and the dissemination of scientific medical information, including through the mass media. It discusses new publishing modes and the dissemination of published information in clinical research.

Top 50 cited articles on Covid-19 after the first year of the pandemic: A bibliometric analysis.

BACKGROUND & AIMS: It has been just over a year since the Covid-19 pandemic started. The top 50 cited articles on this subject would help identify trends and focus on the research efforts. METHODS: We utilised e-utilities in PubMed to find publications on Covid-19 until the date of search on 7/2/21. The iCite website was used to find the top 50 citations of the output from the search strategy. We looked into their full text for the editorial dates, type of study, level of evidence, focus of the article and country of origin. We also counted the errata and comments on each of them. RESULTS: The total number of citations of all 50 articles was 123,960, the highest being 10, 754 for a single article. Huang C was the most cited first author. They were published from week 4-17, with February being the month with most citations. Lancet was the most cited journal, having published 9 of the 50 articles. Majority belonged to level 3 of the evidence ladder and were retrospective studies. Thirty percent of them had an errata published and an average of 7 comments per article. CONCLUSION: The top 50 most cited articles identify the most impactful studies on Covid-19, providing a resource to educators while identifying trends to guide research and publishing efforts. There has been an explosion of publications and an unprecedented rate and number of citations within the first year for any single condition in the literature.

Investigating the Scientific 'Infodemic' Phenomenon Related to the COVID-19 Pandemic.

OBJECTIVES: The study aims at understanding the structural characteristics and content features of COVID-19 literature and public health data from the perspective of the 'Language and Meaning in Biomedicine' Working Group (LaMB WG) of IMIA. The LaMB WG has interest in conceptual characteristics, transparency, comparability, and reusability of medical information, both in science and practice. METHODS: A set of methods were used (i) investigating the overall speed and dynamics of COVID-19 publications; (ii) characterizing the concepts of COVID-19 (text mining, visualizing a semantic map of related concepts); (iii) assessing (re)usability and combinability of data sets and paper collections (as textual data sets), and checking if information is Findable, Accessible, Interoperable, and Reusable (FAIR). A further method tested practical usability of FAIR requirements by setting up a common data space of epidemiological, virus genetics and governmental public health measures' stringency data of various origin, where complex data points were visualized as scatter plots. RESULTS: Never before were that many papers and data sources dedicated to one pandemic. Worldwide research shows a plateau at ∼ 2,200 papers per week - the dynamics of areas of studies being slightly different. Ratio of epidemic modelling is rather low (∼1%). A few 'language and meaning' methods, such as using integrated terminologies, applying data and metadata standards for processing epidemiological and case-related clinical information and in general, principles of FAIR data handling could contribute to better results, such as improved interoperability and meaningful knowledge sharing in a virtuous cycle of continuous improvements.

Longitudinal analyses of gender differences in first authorship publications related to COVID-19.

OBJECTIVE: Concerns have been raised that the COVID-19 pandemic has shifted research productivity to the disadvantage of women in academia, particularly in early career stages. In this study, we aimed to assess the pandemic's effect on women's COVID-19-related publishing over the first year of the pandemic. METHODS AND RESULTS: We compared the gender distribution of first authorships for 42 898 publications on COVID-19 from 1 February 2020 to 31 January 2021 to 483 232 publications appearing in the same journals during the same period the year prior. We found that the gender gap-the percentage of articles on which men versus women were first authors-widened by 14 percentage points during the COVID-19 pandemic, despite many pertinent research fields showing near equal proportions of men and women first authors publishing in the same fields before the pandemic. Longitudinal analyses revealed that the significant initial expansions of the gender gap began to trend backwards to expected values over time in many fields. As women may have been differentially affected depending on their geography, we also assessed the gender distribution of first authorships grouped by countries and geographical areas. While we observed a significant reduction of the shares of women first authors in almost all countries, longitudinal analyses confirmed a resolving trend over time. CONCLUSION: The reduction in women's COVID-19-related research output appears particularly concerning as many disciplines informing the response to the pandemic had near equal gender shares of first authorship in the year prior to the pandemic. The acute productivity drain with the onset of the pandemic magnifies deep-rooted obstacles on the way to gender equity in scientific contribution.

Outbreaks of publications about emerging infectious diseases: the case of SARS-CoV-2 and Zika virus.

BACKGROUND: Outbreaks of infectious diseases generate outbreaks of scientific evidence. In 2016 epidemics of Zika virus emerged, and in 2020, a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a pandemic of coronavirus disease 2019 (COVID-19). We compared patterns of scientific publications for the two infections to analyse the evolution of the evidence. METHODS: We annotated publications on Zika virus and SARS-CoV-2 that we collected using living evidence databases according to study design. We used descriptive statistics to categorise and compare study designs over time. RESULTS: We found 2286 publications about Zika virus in 2016 and 21,990 about SARS-CoV-2 up to 24 May 2020, of which we analysed a random sample of 5294 (24%). For both infections, there were more epidemiological than laboratory science studies. Amongst epidemiological studies for both infections, case reports, case series and cross-sectional studies emerged first, cohort and case-control studies were published later. Trials were the last to emerge. The number of preprints was much higher for SARS-CoV-2 than for Zika virus. CONCLUSIONS: Similarities in the overall pattern of publications might be generalizable, whereas differences are compatible with differences in the characteristics of a disease. Understanding how evidence accumulates during disease outbreaks helps us understand which types of public health questions we can answer and when.

The Covid-19 pandemic in low- and middle-income countries, who carries the burden? Review of mass media and publications from six countries.

During the Covid-19 pandemic, rich countries employed lockdown and physical distancing policies for transmission control. However, the question still remains whether these measures are also suitable in countries with a fragile economy, which rests mainly on the informal sector. The impacts of lockdown measures in disadvantaged population strata in six low- and middle-income countries (LMICs) were reviewed using i) 93 media reports and ii) 17 published scientific papers. This review showed that those who suffered the most from the lockdown were migrants, workers in the large informal sector, small businesses, slum dwellers, women and elderly, revealing the social, cultural and economic inequalities of societies. Financial and food support for the poor was inadequate and sometimes mismanaged. In the better organized societies, the resilience was stronger (South Korea, Kerala/India) but here also the poor had to suffer the most. It is strongly recommended that outbreak response strategies should particularly focus on the poor and vulnerable population.

LitCovid: an open database of COVID-19 literature.

Since the outbreak of the current pandemic in 2020, there has been a rapid growth of published articles on COVID-19 and SARS-CoV-2, with about 10,000 new articles added each month. This is causing an increasingly serious information overload, making it difficult for scientists, healthcare professionals and the general public to remain up to date on the latest SARS-CoV-2 and COVID-19 research. Hence, we developed LitCovid (https://www.ncbi.nlm.nih.gov/research/coronavirus/), a curated literature hub, to track up-to-date scientific information in PubMed. LitCovid is updated daily with newly identified relevant articles organized into curated categories. To support manual curation, advanced machine-learning and deep-learning algorithms have been developed, evaluated and integrated into the curation workflow. To the best of our knowledge, LitCovid is the first-of-its-kind COVID-19-specific literature resource, with all of its collected articles and curated data freely available. Since its release, LitCovid has been widely used, with millions of accesses by users worldwide for various information needs, such as evidence synthesis, drug discovery and text and data mining, among others.

COVID-19 trials: declarations of data sharing intentions at trial registration and at publication.

BACKGROUND: The sharing of individual participant-level data from COVID-19 trials would allow re-use and secondary analysis that can help accelerate the identification of effective treatments. The sharing of trial data is not the norm, but the unprecedented pandemic caused by SARS-CoV-2 may serve as an impetus for greater data sharing. We sought to assess the data sharing intentions of interventional COVID-19 trials as declared in trial registrations and publications. METHODS: We searched ClinicalTrials.gov and PubMed for COVID-19 interventional trials. We analyzed responses to ClinicalTrials.gov fields regarding intent to share individual participant level data and analyzed the data sharing statements in eligible publications. RESULTS: Nine hundred twenty-four trial registrations were analyzed. 15.7% were willing to share, of which 38.6% were willing to share immediately upon publication of results. 47.6% declared they were not willing to share. Twenty-eight publications were analyzed representing 26 unique COVID-19 trials. Only seven publications contained data sharing statements; six indicated a willingness to share data whereas one indicated that data was not available for sharing. CONCLUSIONS: At a time of pressing need for researchers to work together to combat a global pandemic, intent to share individual participant-level data from COVID-19 interventional trials is limited.

The impact of COVID-19 on academic productivity by female physicians and researchers in transfusion medicine.

BACKGROUND: Several studies have highlighted the disparities in gender equity that exist in different medical specialties. The COVID-19 pandemic has further heightened the inequity faced by female physicians as they are challenged by increasing household and childcare duties in addition to their professional responsibilities. Given these hurdles, fewer women than men have published in various medical disciplines. In this brief report, we wanted to determine the impact of the COVID-19 pandemic on the academic output of female physicians and researchers in transfusion medicine. STUDY DESIGN AND METHODS: We compared all articles in four transfusion medicine journals published from January 1 to July 31, 2019 with the same time period in 2020. Overall, 1024 articles were reviewed for whether they included women as first or senior authors. RESULTS: Overall, women were first authors in 45.9% (n = 458) of all publications and senior authors in 35% (n = 356) of all publications. There was a statistically significant decrease in the percentage of women as first authors between 2019 (49.1%) and 2020 (42.7%) (p = .04). There was no significant change in the percentage of women as senior authors between 2019 (35.4%) and 2020 (35.5%) (p = 0.99). CONCLUSIONS: Similar to other medical specialties, the COVID-19 pandemic has further increased the disparities faced by female researchers in transfusion medicine as evidenced by a decrease in publications with women as first authors.

Contradictions in the promotion of publishing academic and scientific journal articles, and the inability to cope with the new coronavirus (COVID-19).

BACKGROUND: Translating research into practice is a central priority within the National Institutes of Health (NIH) Roadmap. The underlying aim of the NIH Roadmap is to accelerate the movement of scientific findings into practical health care provisions through translational research. MAIN TEXT: Despite the advances in health sciences, emerging infectious diseases have become more frequent in recent decades. Furthermore, emerging and reemerging pathogens have led to several global public health challenges. A question, and to an extent a concern, arises from this: Why our health care system is experiencing several challenges in encountering the coronavirus outbreak, despite the ever-growing advances in sciences, and the exponential rise in the number of published articles in the first quartile journals and even the ones among the top 1%? CONCLUSION: Two responses could be potentially provided to the above question: First, there seems to be a significant gap between our theoretical knowledge and practice. And second that many scholars and scientists publish papers only to have a longer list of publications, and therefore publishing is viewed as a personal objective, rather than for improving communities' public health.