Identification of human gene research articles with wrongly identified nucleotide sequences

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.

Metadata analysis of retracted fake papers in Naunyn-Schmiedeberg's Archives of Pharmacology

An increasing fake paper problem is a cause for concern in the scientific community. These papers look scientific but contain manipulated data or are completely fictitious. So-called paper mills produce fake papers on a large scale and publish them in the name of people who buy authorship. The aim of this study was to learn more about the characteristics of fake papers at the metadata level. We also investigated whether some of these characteristics could be used to detect fake papers. For that purpose, we examined metadata of 12 fake papers that were retracted by Naunyn-Schmiedeberg's Archives of Pharmacology (NSAP) in recent years. We also compared many of these metadata with those of a reference group of 733 articles published by NSAP. It turned out that in many characteristics the fake papers we examined did not differ substantially from the other articles. It was only noticeable that the fake papers came almost exclusively from a certain country, used non-institutional email addresses more often than average, and referenced dubious literature significantly more often. However, these three features are only of limited use in identifying fake papers. We were also able to show that fake papers not only contaminate the scientific record while they are unidentified but also continue to do so even after retraction. Our results indicate that fake papers are well made and resemble honest papers even at the metadata level. Because they contaminate the scientific record in the long term and this cannot be fully contained even by their retraction, it is particularly important to identify them before publication. Further research on the topic of fake papers is therefore urgently needed.

Metadata integrity in bioinformatics: Bridging the gap between data and knowledge

In the fast-evolving landscape of biomedical research, the emergence of big data has presented researchers with extraordinary opportunities to explore biological complexities. In biomedical research, big data imply also a big responsibility. This is not only due to genomics data being sensitive information but also due to genomics data being shared and re-analysed among the scientific community. This saves valuable resources and can even help to find new insights in silico. To fully use these opportunities, detailed and correct metadata are imperative. This includes not only the availability of metadata but also their correctness. Metadata integrity serves as a fundamental determinant of research credibility, supporting the reliability and reproducibility of data-driven findings. Ensuring metadata availability, curation, and accuracy are therefore essential for bioinformatic research. Not only must metadata be readily available, but they must also be meticulously curated and ideally error-free. Motivated by an accidental discovery of a critical metadata error in patient data published in two high-impact journals, we aim to raise awareness for the need of correct, complete, and curated metadata. We describe how the metadata error was found, addressed, and present examples for metadata-related challenges in omics research, along with supporting measures, including tools for checking metadata and software to facilitate various steps from data analysis to published research.

Exploring the clinical translation intensity of papers published by the world's top scientists in basic medicine

The extent to which basic medical research is translated into clinical practice is a topic of interest to all stakeholders. In this study, we assessed the clinical translation intensity of papers published by scientists who have made outstanding contributions to the field of basic medicine (Lasker Prize winners for Basic Medical Research). Approximate Potential for Translation (APT), Translational science scores (TS), and Citations by clinical research (Cited by Clin.) were analyzed as dependent variables. A traditional citation indicator was used as a reference (relative citation ratio, RCR). In order to examine the correlation between these different indicators and the characteristics of the paper, the author, and the institution. we used nonparametric tests, Spearman correlations, ordinal least squares regressions (OLS), quantile regressions, and zero-inflated negative binomial regression methods. We found that among the basic medical research papers published by Lasker Basic Medicine Award winners, (1) 20% are cited by clinical research; 11.6% of the papers were more valuable for clinical research than basic research; 12.8% have a probability of more than 50% to be cited in future clinical studies; (2) Spearman correlations were conducted among APT, TS, Cited by Clin., RCR, and all of the other continuous variables. There is a significant, positive, low to moderate correlation between APT, TS, and Cited by Clin (APT and TS: r = 0.549, p < 0.01; APT and Cited by Clin: r = 0.530, p < 0.01; TS and Cited by Clin: r = 0.383, p < 0.01). However, the relationship between RCR and the three indicators of clinical translation intensity was not consistent. APT was positively correlated with RCR (r = 0.553, p < 0.01). Cited by Clin. is weakly positively correlated with RCR (r = 0.381, p < 0.01). There is almost no correlation between TS and RCR (r = 0.184, p < 0.01). (3) Publication age, primary research paper, multidisciplinary science, number of disciplines, authors, institutions, funded projects, references, length of the title, length of paper, physical age, gender, nationality, institutional type, Nobel Prize have a significant relationship with 1 to 3 types of clinical translation intensity measures. In a sample of basic medical research papers published by the world's top scientists in basic medicine, we came to the following conclusions: the three indicators, APT, TS and Cited by Clin., measured the clinical translation intensity of the papers from different perspectives. They are both related to each other and have their own characteristics. In a sample of basic medical research papers published by the world's top scientists in basic medicine, characteristics at the paper, winner, and institution level significantly correlated with the measures of clinical translation intensity. Gender effect on the clinical translation intensity of papers was confirmed. Traditional citation-based indicators and translational-focused indicators measure academic impact and clinical impact respectively. There is a certain degree of disconnect between them. Two types of indicators should be used in combination in future assessments of basic medical research.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11192-023-04634-4.

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

Human gene research generates new biology insights with translational potential, yet few studies have considered the health of the human gene literature. The accessibility of human genes for targeted research, combined with unreasonable publication pressures and recent developments in scholarly publishing, may have created a market for low-quality or fraudulent human gene research articles, including articles produced by contract cheating organizations known as paper mills. This review summarises the evidence that paper mills contribute to the human gene research literature at scale and outlines why targeted gene research may be particularly vulnerable to systematic research fraud. To raise awareness of targeted gene research from paper mills, we highlight features of problematic manuscripts and publications that can be detected by gene researchers and/or journal staff. As improved awareness and detection could drive the further evolution of paper mill-supported publications, we also propose changes to academic publishing to more effectively deter and correct problematic publications at scale. In summary, the threat of paper mill-supported gene research highlights the need for all researchers to approach the literature with a more critical mindset, and demand publications that are underpinned by plausible research justifications, rigorous experiments and fully transparent reporting.