Raising concerns on questionable ethics approvals - a case study of 456 trials from the Institut Hospitalo-Universitaire Méditerranée Infection

BACKGROUND

The practice of clinical research is strictly regulated by law. During submission and review processes, compliance of such research with the laws enforced in the country where it was conducted is not always correctly filled in by the authors or verified by the editors. Here, we report a case of a single institution for which one may find hundreds of publications with seemingly relevant ethical concerns, along with 10 months of follow-up through contacts with the editors of these articles. We thus argue for a stricter control of ethical authorization by scientific editors and we call on publishers to cooperate to this end.

METHODS

We present an investigation of the ethics and legal aspects of 456 studies published by the IHU-MI (Institut Hospitalo-Universitaire Méditerranée Infection) in Marseille, France.

RESULTS

We identified a wide range of issues with the stated research authorization and ethics of the published studies with respect to the Institutional Review Board and the approval presented. Among the studies investigated, 248 were conducted with the same ethics approval number, even though the subjects, samples, and countries of investigation were different. Thirty-nine (39) did not even contain a reference to the ethics approval number while they present research on human beings. We thus contacted the journals that published these articles and provide their responses to our concerns. It should be noted that, since our investigation and reporting to journals, PLOS has issued expressions of concerns for several publications we analyze here.

CONCLUSION

This case presents an investigation of the veracity of ethical approval, and more than 10 months of follow-up by independent researchers. We call for stricter control and cooperation in handling of these cases, including editorial requirement to upload ethical approval documents, guidelines from COPE to address such ethical concerns, and transparent editorial policies and timelines to answer such concerns. All supplementary materials are available.

An analysis of reporting practices in the top 100 cited health and medicine-related bibliometric studies from 2019 to 2021 based on a proposed guidelines

Bibliometric analysis has gained popularity as a quantitative research methodology to evaluate scholarly productivity and identify trends within specific research areas. However, there are currently no established reporting guidelines for bibliometric studies. The present study aimed to investigate the reporting practices of bibliometric research related to health and medicine based on a guidelines "Preferred Reporting Items for Bibliometric Analysis (PRIBA)" proposed in this study. The Science Citation Index, Expanded of the Web of Science was used to identify the top 100 articles with the highest normalized citation counts per year. The search was conducted on April 9, 2022, using the search topic "bibliometric" and including publications from 2019 to 2021. The results substantiated the need for a standardized reporting guideline for bibliometric research. Specifically, among the 25 proposed items in the PRIBA, only five were consistently reported across all articles examined. Further, 11 items were reported by at least 80% of the articles, while nine items were reported by less than 80% of the articles. In conclusion, our findings suggest that the reporting practices of bibliometric studies in the field of health and medicine are in need of improvement. Future research should be conducted to refine the PRIBA guidelines.

Bibliometric analysis of original articles of journal Enfermería Intensiva in the period 2001-2020

INTRODUCTION

Bibliometric analysis allow the quantitative evaluation of the characteristics of a scientific publication.

OBJECTIVE

To perform a bibliometric analysis of original articles in the journal Enfermería Intensiva from 2001 to 2020.

RESULTS

The journal Enfermería Intensiva has published, between 2001 and 2020, 438 works, of which 259 are original articles (59.1%). These original articles are mostly quantitative studies (76.1%), with an average of 30.5 bibliographic references (SD 13.9), 4.9 citations (SD 1.7) in the Web of Science and Scopus repertoires, and 15,489.5 visits/downloads (median 9090 and interquartile range 4567-15,260) according to information on the magazine's website. These originals have been signed by 1345 authors, which represents a collaboration index of 5.2. 78.0% of the authors are sporadic, having published only one work. Most of the articles come from authors who work in institutionally located in hospitals and university centers, and geographically in the Communities of Madrid, Cataluña, Navarra and Andalucía.

CONCLUSIONS

There is little international, regional and institutional collaboration, producing the highest level of collaboration between authors from the same center. The journal has established itself in the panorama of scientific nursing research in Spain and shows bibliometric indicators similar or even superior to other publications in its environment.

Scientific Publications and Subject Clusters in the Field of Glaucoma: A Scientometric Analysis

Purpose

To analyze the glaucoma research in the Web of Science (WoS) and Scopus to determine the top features, trends, and subject clusters.

Methods

In this scientometric study, all glaucoma publications in Scopus and WoS were analyzed based on various characteristics such as authors, journals, and co-word analysis. Data analysis was conducted using both Excel and VOSviewer.

Results

A gradual increase in the publication rate was found for articles in the field of glaucoma in both Scopus and WoS databases. In this regard, most publications were conducted in the USA and the University of California System. The co-word network was constituted of five clusters, including glaucoma, intraocular pressure, open-angle glaucoma, visual acuity, and optic disc. It showed that the top 10 highly cited articles were more addressed by epidemiologic studies.

Conclusions

The findings of this study had a more precise vision of the previous research on the field of glaucoma. It also provided the possibility to discover hidden patterns and emerging events of a subject by explaining the most essential aspects of research and identifying the areas that need more research. The findings could be useful for authors and health policymakers in academia and countries.

A Systematic Review and Meta-analysis of Antibiotic Resistance of Foodborne Pathogenic Bacteria in West Africa Between 2010 and 2020

OBJECTIVE

In the past, studies on antimicrobial resistance were carried out on pathogens in the clinical areas. However, since then, this phenomenon has become a general case both in the environment and in the food sector. This systematic review aimed to review the various scientific publications on the resistance of bacteria to antibiotics in foods in West Africa.

METHODS

An extensive literature search was carried out through an electronic database including PubMed, Google Scholar, Research Gate, and African Journals Online (AJOL). Articles published from fifteen countries of the Economic Community of West African States (ECOWAS) between 2010 and 2020 on antibiotic resistance of foodborne pathogens were included in the study. The titles and abstracts of the retrieved articles and then the full texts of the selected articles were reviewed.

RESULTS

Out of the 565 articles found in our initial research, 149 publications (26.55%) were considered suitable for inclusion in this review. Globally, 2018, 2019, and 2020 had more included papers (n = 21 to 25) than the other years. Of the 149 publications analyzed, four types of food commodities were identified as products of high consumption based on the number of publications in the field such as poultry (39/149), read-to-eat food (22/149), meat, and animal products (20/149). Most studies have shown that E. coli has the highest prevalence followed by Salmonella and Staphylococcus. Only 33 (22.14%) of the 149 publications were based on further molecular characterization of the isolates. Publications analyzed showed that the most prevalent detected genes were tet(A), tet(B), tet(C), tet(K) blaTEM, catA1, catA2, cmlA, blaCTXM and qnrA, qnrB, qnrS, parC, and qepA4.

CONCLUSION

From these results, antibiotic use in the food areas must be strongly regulated, especially in developing countries, particularly in Africa. This highlights the need to implement suitable and appropriate control strategies to reduce complications and prevent the dissemination of resistant bacteria isolates in foods. One health antimicrobial resistance surveillance system in the region must be a great concern.

Scientific publications and data evaluation in the digital age (a perspective of a thermodynamics researcher)

The state of scientific publications, problems, possible solutions, and underutilized opportunities are discussed on the basis of author's experience as a reader, author, reviewer, and editor. The author feels that significant improvement can be made, which will increase the efficiency of communication and quality of information. The focused area is thermophysical properties related to chemical engineering, but the concerns and conclusions can be applied to a wider scope.

COVID-19 and the scientific publishing system: growth, open access and scientific fields

We model the growth of scientific literature related to COVID-19 and forecast the expected growth from 1 June 2021. Considering the significant scientific and financial efforts made by the research community to find solutions to end the COVID-19 pandemic, an unprecedented volume of scientific outputs is being produced. This questions the capacity of scientists, politicians and citizens to maintain infrastructure, digest content and take scientifically informed decisions. A crucial aspect is to make predictions to prepare for such a large corpus of scientific literature. Here we base our predictions on the Autoregressive Integrated Moving Average (ARIMA) and exponential smoothing models using the Dimensions database. This source has the particularity of including in the metadata information on the date in which papers were indexed. We present global predictions, plus predictions in three specific settings: by type of access (Open Access), by domain-specific repository (SSRN and MedRxiv) and by several research fields. We conclude by discussing our findings.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11192-022-04536-x.

Scientometric evaluation of trends and global characteristics of published research on occupational public health

The objective of this scientometric study was to assess the global trends and characteristics of published occupational health research from 2016 to 2020. The SciVal tool (Elsevier) was used to perform the corresponding bibliometric analyses such as the Field-Weighted Citation Impact (FWCI), Source Normalized Impact per Paper (SNIP), CiteScore, and SCImago Journal Rank (SJR). Most of the manuscripts (46.5%) had national collaboration, with an average of 6.1 citations per paper. However, only 71 manuscripts (5.4%) presented single authorship (without collaboration). It was found that 486 manuscripts related to occupational health were published in Q2 journals (top 26-50%). Scientific publications on occupational health have increased remarkably worldwide, especially in Europe, and have mainly been published in Q1 and Q2 journals with a total of 292 and 289 scientific manuscripts in 2019 and 2020, respectively.

Using Artificial Intelligence to extract information on pathogen characteristics from scientific publications

Health risk assessment of environmental exposure to pathogens requires complete and up to date knowledge. With the rapid growth of scientific publications and the protocolization of literature reviews, an automated approach based on Artificial Intelligence (AI) techniques could help extract meaningful information from the literature and make literature reviews more efficient. The objective of this research was to determine whether it is feasible to extract both qualitative and quantitative information from scientific publications about the waterborne pathogen Legionella on PubMed, using Deep Learning and Natural Language Processing techniques. The model effectively extracted the qualitative and quantitative characteristics with high precision, recall and F-score of 0.91, 0.80, and 0.85 respectively. The AI extraction yielded results that were comparable to manual information extraction. Overall, AI could reliably extract both qualitative and quantitative information about Legionella from scientific literature. Our study paved the way for a better understanding of the information extraction processes and is a first step towards harnessing AI to collect meaningful information on pathogen characteristics from environmental microbiology publications.

The scientific publications of AIFM members in 2015-2019: A survey of the FutuRuS working group

PURPOSE

Within the Italian Association of Medical Physics and Health Physics (AIFM) working group "FutuRuS" we carried out a survey regarding the number of the peer-reviewed articles by AIFM members.

METHODS

We surveyed papers published in the years 2015-2019. Data extracted from Scopus included information regarding authors, title, journal, impact factor (IF), leading or standard authorship by AIFM members, keywords, type of collaboration (monocentric/multicentric/international), area of interest [radiation oncology (RO), radiology (RAD), nuclear medicine (NM), radioprotection (RP) and professional issue (PI)] and topics.

RESULTS

We found 1210 papers published in peer-reviewed journals: 48%, 22%, 16%, 6%, 2 and 6% in RO, RAD, NM, RP, PI and other topics, respectively. Forty-seven percent of the papers involved monocentric teams, 31% multicentric and 22% international collaborations. Leading authorship of AIFM members was in 56% of papers, with a corresponding IF equal to 52% of the total IF (3342, IF_mean = 2.8, IF_max = 35.4). The most represented journal was Physica Medica, with 15% of papers, while a relevant fraction of IF (54%) appeared in clinically oriented journals. The number of papers increased significantly between 2015 and 2016 and remained almost constant in 2017-2019.

CONCLUSIONS

This survey led to the first quantitative assessment of the number and theme distribution of peer-reviewed scientific articles contributed by AIFM members. It constitutes a ground basis to support future AIFM strategies and promote working groups on scientific activity of medical physicists, and to build the basis for rational comparison with other countries, first of all within Europe.

Analyzing knowledge entities about COVID-19 using entitymetrics

COVID-19 cases have surpassed the 109 + million markers, with deaths tallying up to 2.4 million. Tens of thousands of papers regarding COVID-19 have been published along with countless bibliometric analyses done on COVID-19 literature. Despite this, none of the analyses have focused on domain entities occurring in scientific publications. However, analysis of these bio-entities and the relations among them, a strategy called entity metrics, could offer more insights into knowledge usage and diffusion in specific cases. Thus, this paper presents an entitymetric analysis on COVID-19 literature. We construct an entity–entity co-occurrence network and employ network indicators to analyze the extracted entities. We find that ACE-2 and C-reactive protein are two very important genes and that lopinavir and ritonavir are two very important chemicals, regardless of the results from either ranking.

Orthopedics and COVID-19: Scientific Publications Rush

BACKGROUND

The purpose of this literature review is to analyze all the articles related to COVID-19 and orthopedics and to shed light on the scientific evidence that has actually been found.

METHODS

A systematic review of the existing literature was performed to identify all studies dealing with COVID-19 and orthopedics. The guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) were followed for the identification of the articles. On April 19 2020, a search was performed using MEDLINE and PubMed Central. For the research, the following terms were used: "COVID-19" OR "SARS-CoV-2" OR "Coronavirus" AND "orthopaedic" OR "orthopedic" OR "traumatology".

RESULTS

A total of 23 studies were included in the review, of which 19 (82.6%) were editorials, letters to editors, orthopedic forums or expert opinions, 3 (13.0%) studies were level IV of evidence and 1 (4.4%) was a literature review. Articles have been divided into the follow categories: guidelines, traumatology, pediatric, spine surgery, telemedicine, sports medicine, bioethical, educational, rehabilitation, survey and hand surgery.

CONCLUSIONS

Although scientific production is very active on the topic of COVID-19 and orthopedics, the scientific evidence is practically nil, mainly dealing with editorials, letters to editors or expert opinions. Therefore, future studies should focus on clinical outcomes and treatments in COVID-19-positive orthopedic patients and prevention strategies. Additionally, international guidelines and consensus statements must be developed to standardize procedures as much as possible in this pandemic scenario.

Broad-coverage biomedical relation extraction with SemRep

BACKGROUND

In the era of information overload, natural language processing (NLP) techniques are increasingly needed to support advanced biomedical information management and discovery applications. In this paper, we present an in-depth description of SemRep, an NLP system that extracts semantic relations from PubMed abstracts using linguistic principles and UMLS domain knowledge. We also evaluate SemRep on two datasets. In one evaluation, we use a manually annotated test collection and perform a comprehensive error analysis. In another evaluation, we assess SemRep's performance on the CDR dataset, a standard benchmark corpus annotated with causal chemical-disease relationships.

RESULTS

A strict evaluation of SemRep on our manually annotated dataset yields 0.55 precision, 0.34 recall, and 0.42 F 1 score. A relaxed evaluation, which more accurately characterizes SemRep performance, yields 0.69 precision, 0.42 recall, and 0.52 F 1 score. An error analysis reveals named entity recognition/normalization as the largest source of errors (26.9%), followed by argument identification (14%) and trigger detection errors (12.5%). The evaluation on the CDR corpus yields 0.90 precision, 0.24 recall, and 0.38 F 1 score. The recall and the F 1 score increase to 0.35 and 0.50, respectively, when the evaluation on this corpus is limited to sentence-bound relationships, which represents a fairer evaluation, as SemRep operates at the sentence level.

CONCLUSIONS

SemRep is a broad-coverage, interpretable, strong baseline system for extracting semantic relations from biomedical text. It also underpins SemMedDB, a literature-scale knowledge graph based on semantic relations. Through SemMedDB, SemRep has had significant impact in the scientific community, supporting a variety of clinical and translational applications, including clinical decision making, medical diagnosis, drug repurposing, literature-based discovery and hypothesis generation, and contributing to improved health outcomes. In ongoing development, we are redesigning SemRep to increase its modularity and flexibility, and addressing weaknesses identified in the error analysis.

Dataset of the frequency patterns of publications annotated to human protein-coding genes, their protein products and genetic relevance

We present data concerning the distribution of scientific publications for human protein-coding genes together with their protein products and genetic relevance. We annotated the gene2pubmed dataset Maglott et al., 2007 provided by the NCBI (National Center for Biotechnology Information) with publication years, genetic metadata corresponding to Online Mendelian Inheritance in Man (OMIM) Hamosh et al., 2005 entries and the frequency of their appearance in Genome-Wide Association Studies (GWAS) Buniello et al., 2019 provided by the European Bioinformatics Institute (EBI) using the KNIME^® Analytics Platform Berthold et al., 2008. The results of this data integration process comprise two datasets: 1) A dataset containing information on all human protein-coding genes that can be used to analyse the number of scientific publications in context of the potential disease relevance of the individual genes. 2) A table with the annual and cumulated number of PubMed entries. For further interpretation of the data presented in this article, please see the research article 'Target 2035 - probing the human proteome' by Carter et al. https://doi.org/10.1016/j.drudis.2019.06.020 Carter et al., 2019.

The Impact of Electronic Obstetric Records Using the ObsCare Software on Scientific Production

AIMS

To compare the characteristics of scientific publications performed in hospitals that used with those that didn't use an obstetric electronic health record (EHR).

METHODS

This study included two reviews (A and B). Review A was an exploratory analysis of all 100 abstracts presented at the Scientific Meeting of the Portuguese Society of Obstetrics and Maternal-Fetal Medicine, in November 2017. Review B was a systematic review of studies in obstetrics, performed in Portugal and published between 2016-18 and indexed in PubMed. In both reviews, the included papers/abstracts were divided into two groups: from hospitals that used ObsCare^® (ObsCare group) and from hospitals without a specific obstetric EHR or that didn't use ObsCare (sObsCare group).

RESULTS

In both reviews, the sample size was significantly higher in hospitals from the ObsCare group. In review B, the length of the study period was also significantly longer in ObsCare group; no significant difference was found in review A.

CONCLUSION

Publications from hospitals that used an obstetric specific EHR (ObsCare), included a higher number of patients and longer study periods.

Publish and flourish: Take the road less travelled!

Scientific research and publications are essential for advancement of medical knowledge. The perceived need for 'publications' in medical journals, has increased substantially in view of the recently mandated requirement of original research publications in indexed journals to ensure career progression in academic institutions. There has been an unprecedented rise in the number of standalone journals and publishers, ready to process manuscripts on priority with almost guaranteed publication, at a cost. Many of these publishers have questionable credibility and could be regarded as 'predatory'. It is imperative for a concerted and broad based initiative to foster awareness creation among students at the post-graduate level and for faculty of medical colleges and research institutions. We need to adopt stringent measures to curtail this scourge of predatory publishing. It is advisable for researchers to take the road less travelled, and publish in 'reputed' and 'accepted' journals to flourish. This article aims to bring focus on to the present situation in the scientific publication arena in the Indian context, highlight emerging threats and suggest possible remedies.

Visibility of healthcare research institutes through the Web of Science database

OBJECTIVES

The strategic importance of healthcare research institutes (HRIs) in health sciences research in Spain has motivated this analysis of the feasibility of studing their contribution to the Spanish scientific output through their presence as a signatory institution in the publications.

MATERIAL AND METHODS

We identified the output of the HRIs in the Web of Science database, comparing their observed output (the institutes are explicitly listed in the authors' workplace) and potential output (estimated based on the linked hospitals).

RESULTS AND CONCLUSIONS

The studies based on scientific publications do not help us reliably identify the contribution of the HRIs because their observed production is much lower than the potential output, although their visibility tends to increase over time. This article highlights the importance of HRI members including the institute among their work addresses to increase the visibility of these organisations and to facilitate studies aimed at assessing their activity in the national and international context.

Bibliometric Indices of Scientific Journals: Time to overcome the obsession and think beyond the Impact Factor

Journal Impact Factor (JIF) has been widely used for a long time as a proxy marker of journal prestige. However, off late, accuracy and reliability of JIF for evaluation of scientific journals has been increasingly questioned by numerous stakeholders in the field of scholarly publications. Having realized the perils and pitfalls of JIF, there is an increasing understanding among academia to develop and consider alternatives to the traditional JIF. It is possibly time for all concerned to understand the pros and cons of JIF to overcome this obsession. Limitations of JIF and possible alternative and emerging bibliometric indicators are being discussed in this article for the benefit of the readers of MJAFI.

A Simple Framework for Evaluating Authorial Contributions for Scientific Publications

A simple tool is provided to assist researchers in assessing contributions to a scientific publication, for ease in evaluating which contributors qualify for authorship, and in what order the authors should be listed. The tool identifies four phases of activity leading to a publication-Conception and Design, Data Acquisition, Analysis and Interpretation, and Manuscript Preparation. By comparing a project participant's contribution in a given phase to several specified thresholds, a score of up to five points can be assigned; the contributor's scores in all four phases are summed to yield a total "contribution score", which is compared to a threshold to determine which contributors merit authorship. This tool may be useful in a variety of contexts in which a systematic approach to authorial credit is desired.

Scientometric analysis: A technical need for medical science researchers either as authors or as peer reviewers

The nature of performing a scientific research is a process that has several different components which consist of identifying the key research question(s), choices of scientific approach for the study and data collection, data analysis, and finally reporting on results. Generally, peer review is a series of procedures in the evaluation of a creative work or performance by other people, who work in the same or related field, with the aim of maintaining and improving the quality of work or performance in that field. The assessment of the achievement of every scientist, and thus indirectly determining his reputation in the scientific community of these publications, especially journals, is done through the so-called impact factor index. The impact factor predicts or estimates that how many annual citations article may receive after its publication. Evaluation of scientific productivity and assessment of the published articles of researchers and scientists can be made through the so-called H-index. The quality of published results of scientific work largely depends on knowledge sources that are used in the preparation, which means that it should be considered to serve the purpose and the very relevance of the information used. Scientometrics as a field of science covers all aforementioned issues, and scientometric analysis is obligatory for quality assessment of the scientific validity of published articles and other type of publications.