Protection of the human gene research literature from contract cheating organizations known as research paper mills

The undeclared use of third-party service providers in academic publishing is unethical: an epistemic reflection and scoping review

There is a substantial body of scientific literature on the use of third-party services (TPS) by academics to assist as "publication consultants" in scholarly publishing. TPS provide a wide range of scholarly services to research teams that lack the equipment, skills, motivation, or time to produce a paper without external assistance. While services such as language editing, statistical support, or graphic design are common and often legitimate, some TPS also provide illegitimate services and send unsolicited e-mails (spam) to academics offering these services. Such illegitimate types of TPS have the potential to threaten the integrity of the peer-reviewed scientific literature. In extreme cases, for-profit agencies known as "paper mills" even offer fake scientific publications or authorship slots for sale. The use of such illegitimate services as well as the failure to acknowledge their use is an ethical violation in academic publishing, while the failure to declare support for a TPS can be considered a form of contract fraud. We discuss some literature on TPS, highlight services currently offered by ten of the largest commercial publishers and expect authors to be transparent about the use of these services in their publications. From an ethical/moral (i.e., non-commercial) point of view, it is the responsibility of editors, journals, and publishers, and it should be in their best interest to ensure that illegitimate TPS are identified and prohibited, while publisher-employed TPS should be properly disclosed in their publications.

Paper mill challenges: past, present, and future

Paper mills are fraudulent organizations that make money by writing fake manuscripts and offering authorship slots for sale to academic customers. Mill activity differs in scale to individual academic misconduct: many thousands of fake paper mill manuscripts have been successfully published in peer-reviewed journals. Despite this, paper mill activity is still relatively unrecognized outside the publishing industry. We discuss what is known about paper mill operations and how publishers, independent organizations, and individuals are working to prevent and detect mill activity. Research readers can also have a part to play in paper mill detection, and we provide detail on what to look out for.

Research culture influences in health and biomedical research: rapid scoping review and content analysis

BACKGROUND

Research culture is strongly influenced by academic incentives and pressures such as the imperative to publish in academic journals, and can influence the nature and quality of the evidence we produce.

OBJECTIVE

The purpose of this rapid scoping review is to capture the breadth of differential pressures and contributors to current research culture, drawing together content from empirical research specific to the health and biomedical sciences.

STUDY DESIGN AND SETTING

PubMed and Web of Science were searched for empirical studies of influences and impacts on health and biomedical research culture, published between January 2012 and April 2024. Data charting extracted the key findings and relationships in research culture from included papers such as workforce composition; equitable access to research; academic journal trends, incentives, and reproducibility; erroneous research; questionable research practices; biases vested interests; and misconduct. A diverse author network was consulted to ensure content validity of the proposed framework of i) inclusivity, ii) transparency, iii) rigor, and iv) objectivity.

RESULTS

A growing field of studies examining research culture exists ranging from the inclusivity of the scientific workforce, the transparency of the data generated, the rigor of the methods used and the objectivity of the researchers involved. Figurative diagrams are presented to storyboard the links between research culture content and findings.

CONCLUSION

The wide range of research culture influences in the recent literature indicates the need for coordinated and sustained research culture conversations. Core principles in effective research environments should include inclusive collaboration and diverse research workforces, rigorous methodological approaches, transparency, data sharing, and reflection on scientific objectivity.

The research literature is an unsafe workplace

Research is conducted in workplaces that can present safety hazards. Where researchers work in laboratories, safety hazards can arise through the need to operate complex equipment that can become unsafe if faulty or broken. The research literature also represents a workplace for millions of scientists and scholars, where publications can be considered as key research equipment. This article compares our current capacity to flag and repair faulty equipment in research laboratories versus the literature. Whereas laboratory researchers can place written notices on faulty and broken equipment to flag problems and the need for repairs, researchers have limited capacity to flag faulty research publications to other users. We argue that our current inability to flag erroneous publications quickly and at scale, combined with the lack of real-world incentives for journals and publishers to direct adequate resources toward post-publication corrections, results in the research literature representing an increasingly unsafe workplace. We describe possible solutions, such as the capacity to transfer signed PubPeer notices describing verifiable errors to relevant publications, and the reactivation of PubMed Commons.

A call for research to address the threat of paper mills

Research paper mills are covert organizations that provide low-quality or fabricated manuscripts to paying clients. As members of the United2Act Research Working Group, we propose 5 key research questions on paper mills that require resourcing and support.

Unveiling scientific articles from paper mills with provenance analysis

The increasing prevalence of fake publications created by paper mills poses a significant challenge to maintaining scientific integrity. While integrity analysts typically rely on textual and visual clues to identify fake articles, determining which papers merit further investigation can be akin to searching for a needle in a haystack, as these fake publications have non-related authors and are published on non-related venues. To address this challenge, we developed a new methodology for provenance analysis, which automatically tracks and groups suspicious figures and documents. Our approach groups manuscripts from the same paper mill by analyzing their figures and identifying duplicated and manipulated regions. These regions are linked and organized in a provenance graph, providing evidence of systematic production. We tested our solution on a paper mill dataset of hundreds of documents and also on a larger version of the dataset that deliberately included thousands of documents intentionally selected to distract our method. Our approach successfully identified and linked systematically produced articles on both datasets by pinpointing the figures they reused and manipulated from one another. The technique herein proposed offers a promising solution to identify fraudulent manuscripts, and it could be a valuable tool for supporting scientific integrity.

Verification of nucleotide sequence reagent identities in original publications in high impact factor cancer research journals

Human gene research studies that describe wrongly identified nucleotide sequence reagents have been mostly identified in journals of low to moderate impact factor, where unreliable findings could be considered to have limited influence on future research. This study examined whether papers describing wrongly identified nucleotide sequences are also published in high-impact-factor cancer research journals. We manually verified nucleotide sequence identities in original Molecular Cancer articles published in 2014, 2016, 2018, and 2020, including nucleotide sequence reagents that were claimed to target circRNAs. Using keywords identified in some 2018 and 2020 Molecular Cancer papers, we also verified nucleotide sequence identities in 2020 Oncogene papers that studied miRNA(s) and/or circRNA(s). Overall, 3.8% (251/6647) and 4.0% (47/1165) nucleotide sequences that were verified in Molecular Cancer and Oncogene papers, respectively, were found to be wrongly identified. Wrongly identified nucleotide sequences were distributed across 18% (91/500) original Molecular Cancer papers, including 38% (31/82) Molecular Cancer papers from 2020, and 40% (21/52) selected Oncogene papers from 2020. Original papers with wrongly identified nucleotide sequences were therefore unexpectedly frequent in two high-impact-factor cancer research journals, highlighting the risks of employing journal impact factors or citations as proxies for research quality.

Meta-Research: Understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results

Present-day publications on human genes primarily feature genes that already appeared in many publications prior to completion of the Human Genome Project in 2003. These patterns persist despite the subsequent adoption of high-throughput technologies, which routinely identify novel genes associated with biological processes and disease. Although several hypotheses for bias in the selection of genes as research targets have been proposed, their explanatory powers have not yet been compared. Our analysis suggests that understudied genes are systematically abandoned in favor of better-studied genes between the completion of -omics experiments and the reporting of results. Understudied genes remain abandoned by studies that cite these -omics experiments. Conversely, we find that publications on understudied genes may even accrue a greater number of citations. Among 45 biological and experimental factors previously proposed to affect which genes are being studied, we find that 33 are significantly associated with the choice of hit genes presented in titles and abstracts of -omics studies. To promote the investigation of understudied genes, we condense our insights into a tool, find my understudied genes (FMUG), that allows scientists to engage with potential bias during the selection of hits. We demonstrate the utility of FMUG through the identification of genes that remain understudied in vertebrate aging. FMUG is developed in Flutter and is available for download at fmug.amaral.northwestern.edu as a MacOS/Windows app.

Meta-Research: understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results

Present-day publications on human genes primarily feature genes that already appeared in many publications prior to completion of the Human Genome Project in 2003. These patterns persist despite the subsequent adoption of high-throughput technologies, which routinely identify novel genes associated with biological processes and disease. Although several hypotheses for bias in the selection of genes as research targets have been proposed, their explanatory powers have not yet been compared. Our analysis suggests that understudied genes are systematically abandoned in favor of better-studied genes between the completion of -omics experiments and the reporting of results. Understudied genes remain abandoned by studies that cite these -omics experiments. Conversely, we find that publications on understudied genes may even accrue a greater number of citations. Among 45 biological and experimental factors previously proposed to affect which genes are being studied, we find that 33 are significantly associated with the choice of hit genes presented in titles and abstracts of - omics studies. To promote the investigation of understudied genes we condense our insights into a tool, find my understudied genes (FMUG), that allows scientists to engage with potential bias during the selection of hits. We demonstrate the utility of FMUG through the identification of genes that remain understudied in vertebrate aging. FMUG is developed in Flutter and is available for download at fmug.amaral.northwestern.edu as a MacOS/Windows app.

Detection of fake papers in the era of artificial intelligence

OBJECTIVES

Paper mills, companies that write scientific papers and gain acceptance for them, then sell authorships of these papers, present a key challenge in medicine and other healthcare fields. This challenge is becoming more acute with artificial intelligence (AI), where AI writes the manuscripts and then the paper mills sell the authorships of these papers. The aim of the current research is to provide a method for detecting fake papers.

METHODS

The method reported in this article uses a machine learning approach to create decision trees to identify fake papers. The data were collected from Web of Science and multiple journals in various fields.

RESULTS

The article presents a method to identify fake papers based on the results of decision trees. Use of this method in a case study indicated its effectiveness in identifying a fake paper.

CONCLUSIONS

This method to identify fake papers is applicable for authors, editors, and publishers across fields to investigate a single paper or to conduct an analysis of a group of manuscripts. Clinicians and others can use this method to evaluate articles they find in a search to ensure they are not fake articles and instead report actual research that was peer reviewed prior to publication in a journal.

Biobanking and research quality: think locally, act globally

Although biobanks can support research across geographic and governance boundaries, biomedical researchers consistently describe preferences for either collaborating with local biobanks or establishing their own biobanks. This article summarizes the potential research impacts of local biobank use and suggests how descriptions of biospecimen provenance can be improved in research publications.