Analysis and Correction of Inappropriate Image Duplication: the Molecular and Cellular Biology Experience

The changing roles of scientific journals

After centuries of relative stability, the scientific publishing world has undergone tremendous disruption and change during the first decades of the 21st century. The causes for disruption can be traced to the information revolution, which brought such benefits as rapid publication, greater connectivity, and ready access to large databases, along with less desirable practices including image manipulation, plagiarism, and other ethical transgressions. The information revolution has driven the proliferation of journals, expansion of for-profit academic publishing, and empowerment of the open-access movement, each of which has exerted new financial pressures on traditional publishing models. As journals became the focal point for ethical concerns in science, they have adapted by increasing the scope of their duties, which now include archiving of data, enforcement of good practices, establishment of standards for rigor, and training the next generation of reviewers and editors. Here, we consider the seismic changes occurring in scientific publishing and place them into the context of a rapidly changing landscape of scientific and publishing norms.

Five problems plaguing publishing in the life sciences-and one common cause

Although publication in scholarly peer-reviewed journals remains the gold standard for communication of findings in the life sciences, the gold has been debased in the digital age by various impurities, including (a) reviewer fatigue, (b) fraud, paper mills, and the perils of artificial intelligence, (c) predatory journals, (d) the ongoing use of journal impact factor as a proxy for individual article quality, and (e) salami-slicing and other unethical practices. In this article, I present a detailed overview of these problems, as well as solutions proposed and implemented to counter them. Finally, I suggest that these are all symptomatic of a wider problem, namely the culture of 'publish or perish' and ongoing issues with how researcher performance is evaluated for grant, hiring, and promotion decisions. Only by working towards a global shift in the way scientists view the purpose of publication can we finally remove the impurities and refine the gold.

The Importance, Challenges, and Possible Solutions for Sharing Proteomics Data While Safeguarding Individuals' Privacy

Proteomics data sharing has profound benefits at the individual level as well as at the community level. While data sharing has increased over the years, mostly due to journal and funding agency requirements, the reluctance of researchers with regard to data sharing is evident as many shares only the bare minimum dataset required to publish an article. In many cases, proper metadata is missing, essentially making the dataset useless. This behavior can be explained by a lack of incentives, insufficient awareness, or a lack of clarity surrounding ethical issues. Through adequate training at research institutes, researchers can realize the benefits associated with data sharing and can accelerate the norm of data sharing for the field of proteomics, as has been the standard in genomics for decades. In this article, we have put together various repository options available for proteomics data. We have also added pros and cons of those repositories to facilitate researchers in selecting the repository most suitable for their data submission. It is also important to note that a few types of proteomics data have the potential to re-identify an individual in certain scenarios. In such cases, extra caution should be taken to remove any personal identifiers before sharing on public repositories. Data sets that will be useless without personal identifiers need to be shared in a controlled access repository so that only authorized researchers can access the data and personal identifiers are kept safe.

Community-developed checklists for publishing images and image analyses

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However, for scientists wishing to publish obtained images and image-analysis results, there are currently no unified guidelines for best practices. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here, we present community-developed checklists for preparing light microscopy images and describing image analyses for publications. These checklists offer authors, readers and publishers key recommendations for image formatting and annotation, color selection, data availability and reporting image-analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby to heighten the quality and explanatory power of microscopy data.

Inappropriate image duplications in rhinology research publications

KEY POINTS

Duplicated images in research articles erode integrity and credibility of biomedical science. Forensic software is necessary to detect figures with inappropriately duplicated images. This analysis reveals a significant issue of inappropriate image duplication in our field.

A community-driven approach to enhancing the quality and interpretability of microscopy images

Scientific publications in the life sciences regularly include image data to display and communicate revelations about cellular structure and function. In 2016, a set of guiding principles known as the 'FAIR Data Principles' were put forward to ensure that research data are findable, accessible, interoperable and reproducible. However, challenges still persist regarding the quality, accessibility and interpretability of image data, and how to effectively communicate microscopy data in figures. This Perspective article details a community-driven initiative that aims to promote the accurate and understandable depiction of light microscopy data in publications. The initiative underscores the crucial role of global and diverse scientific communities in advancing the standards in the field of biological images. Additionally, the perspective delves into the historical context of scientific images, in the hope that this look into our past can help ongoing community efforts move forward.

Community-developed checklists for publishing images and image analyses

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However for scientists wishing to publish the obtained images and image analyses results, there are to date no unified guidelines. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here we present community-developed checklists for preparing light microscopy images and image analysis for publications. These checklists offer authors, readers, and publishers key recommendations for image formatting and annotation, color selection, data availability, and for reporting image analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby heighten the quality and explanatory power of microscopy data is in publications.

A Synthesis of the Formats for Correcting Erroneous and Fraudulent Academic Literature, and Associated Challenges

Academic publishing is undergoing a highly transformative process, and many established rules and value systems that are in place, such as traditional peer review (TPR) and preprints, are facing unprecedented challenges, including as a result of post-publication peer review. The integrity and validity of the academic literature continue to rely naively on blind trust, while TPR and preprints continue to fail to effectively screen out errors, fraud, and misconduct. Imperfect TPR invariably results in imperfect papers that have passed through varying levels of rigor of screening and validation. If errors or misconduct were not detected during TPR's editorial screening, but are detected at the post-publication stage, an opportunity is created to correct the academic record. Currently, the most common forms of correcting the academic literature are errata, corrigenda, expressions of concern, and retractions or withdrawals. Some additional measures to correct the literature have emerged, including manuscript versioning, amendments, partial retractions and retract and replace. Preprints can also be corrected if their version is updated. This paper discusses the risks, benefits and limitations of these forms of correcting the academic literature.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10838-022-09607-4.

Correction of the Scientific Production: Publisher Performance Evaluation Using a Dataset of 4844 PubMed Retractions

Background. Retraction of problematic scientific articles after publication is one of the mechanisms for correcting the literature available to publishers. The market volume and the business model justify publishers’ ethical involvement in the post-publication quality control (PPQC) of human-health-related articles. The limited information about this subject led us to analyze PubMed-retracted articles and the main retraction reasons grouped by publisher. We propose a score to appraise publisher’s PPQC results. The dataset used for this article consists of 4844 PubMed-retracted papers published between 1.01.2009 and 31.12.2020. Methods. An SDTP score was constructed from the dataset. The calculation formula includes several parameters: speed (article exposure time (ET)), detection rate (percentage of articles whose retraction is initiated by the editor/publisher/institution without the authors’ participation), transparency (percentage of retracted articles available online and the clarity of the retraction notes), and precision (mention of authors’ responsibility and percentage of retractions for reasons other than editorial errors). Results. The 4844 retracted articles were published in 1767 journals by 366 publishers, the average number of retracted articles/journal being 2.74. Forty-five publishers have more than 10 retracted articles, holding 88% of all papers and 79% of journals. Combining our data with data from another study shows that less than 7% of PubMed dataset journals retracted at least one article. Only 10.5% of the retraction notes included the individual responsibility of the authors. Nine of the top 11 publishers had the largest number of retracted articles in 2020. Retraction-reason analysis shows considerable differences between publishers concerning the articles’ ET: median values between 9 and 43 months (mistakes), 9 and 73 months (images), and 10 and 42 months (plagiarism and overlap). The SDTP score shows, from 2018 to 2020, an improvement in PPQC of four publishers in the top 11 and a decrease in the gap between 1st and 11th place. The group of the other 355 publishers also has a positive evolution of the SDTP score. Conclusions. Publishers have to get involved actively and measurably in the post-publication evaluation of scientific products. The introduction of reporting standards for retraction notes and replicable indicators for quantifying publishing QC can help increase the overall quality of scientific literature.

Retracted articles in the biomedical literature from Indian authors

The aim of the present study is to identify retracted articles in the biomedical literature (co) authored by Indian authors and to examine the features of retracted articles. The PubMed database was searched to find the retracted articles in order to reach the goal. The search yielded 508 records and retrieved for the detailed analysis of: authorships and collaboration type, funding information, who retracts? journals and impact factors, and reasons for retraction. The results show that most of the biomedical articles retracted were published after 2010 and common reasons are plagiarism and fake data for retraction. More than half of the retracted articles were co-authored within the institutions and there is no repeat offender. 25% of retracted articles were published in the top 15 journals and 33% were published in the non-impact factor journals. Average time from publication to retraction is calculated to 2.86 years and retractions due to fake data takes longest period among the reasons. Majority of the funded research was retracted due to fake data whereas it is plagiarism for non-funded.

The thin ret(raction) line: biomedical journal responses to incorrect non-targeting nucleotide sequence reagents in human gene knockdown publications

The capacity of the scientific literature to self-correct is of vital importance, but few studies have compared post-publication journal responses to specific error types. We have compared journal responses to a specific reagent error in 31 human gene knockdown publications, namely a non-targeting or negative control nucleotide sequence that is instead predicted to target a human gene. The 31 papers published by 13 biomedical journals generated 26 published responses (14 retractions, 5 expressions of concern, 7 author corrections which included one resolved expression of concern) as well as 6 stated decisions to take no action. Variations in published responses were noted both between journals and by 4 journals that published different responses to at least 2 papers. A subset of published responses revealed conflicting explanations for the wrongly identified control reagent, despite 30/31 papers obtaining their gene knockdown reagents from the same external supplier. Viewed collectively, different journal responses to human gene knockdown publications with a common reagent error type suggest that editorial staff require more support to interpret post-publication notifications of incorrect nucleotide sequence reagents. We propose a draft template to facilitate the communication, interpretation and investigation of published errors, including errors affecting research reagents.

Should research misconduct be criminalized?

For more than 25 years, research misconduct (research fraud) is defined as fabrication, falsification, or plagiarism (FFP)—although other research misbehaviors have been also added in codes of conduct and legislations. A critical issue in deciding whether research misconduct should be subject to criminal law is its definition, because not all behaviors labeled as research misconduct qualifies as serious crime. But assuming that all FFP is fraud and all non-FFP not is far from obvious. In addition, new research misbehaviors have recently been described, such as prolific authorship, and fake peer review, or boosted such as duplication of images. The scientific community has been largely successful in keeping criminal law away from the cases of research misconduct. Alleged cases of research misconduct are usually looked into by committees of scientists usually from the same institution or university of the suspected offender in a process that often lacks transparency. Few countries have or plan to introduce independent bodies to address research misconduct; so for the coming years, most universities and research institutions will continue handling alleged research misconduct cases with their own procedures. A global operationalization of research misconduct with clear boundaries and clear criteria would be helpful. There is room for improvement in reaching global clarity on what research misconduct is, how allegations should be handled, and which sanctions are appropriate.

Reasons for and time to retraction of genetics articles published between 1970 and 2018

Introduction

Between 0.02% and 0.04% of articles are retracted. We aim to: (a) describe the reasons for retraction of genetics articles and the time elapsed between the publication of an article and that of the retraction notice because of research misconduct (ie, fabrication, falsification, plagiarism); and (b) compare all these variables between retracted medical genetics (MG) and non-medical genetics (NMG) articles.

Methods

All retracted genetics articles published between 1970 and 2018 were retrieved from the Retraction Watch database. The reasons for retraction were fabrication/falsification, plagiarism, duplication, unreliability, and authorship issues. Articles subject to investigation by company/institution, journal, US Office for Research Integrity or third party were also retrieved.

Results

1582 retracted genetics articles (MG, n=690; NMG, n=892) were identified . Research misconduct and duplication were involved in 33% and 24% of retracted papers, respectively; 37% were subject to investigation. Only 0.8% of articles involved both fabrication/falsification and plagiarism. In this century the incidence of both plagiarism and duplication increased statistically significantly in genetics retracted articles; conversely, fabrication/falsification was significantly reduced. Time to retraction due to scientific misconduct was statistically significantly shorter in the period 2006–2018 compared with 1970–2000. Fabrication/falsification was statistically significantly more common in NMG (28%) than in MG (19%) articles. MG articles were significantly more frequently investigated (45%) than NMG articles (31%). Time to retraction of articles due to fabrication/falsification was significantly shorter for MG (mean 4.7 years) than for NMG (mean 6.4 years) articles; no differences for plagiarism (mean 2.3 years) were found. The USA (mainly NMG articles) and China (mainly MG articles) accounted for the largest number of retracted articles.

Conclusion

Genetics is a discipline with a high article retraction rate (estimated retraction rate 0.15%). Fabrication/falsification and plagiarism were almost mutually exclusive reasons for article retraction. Retracted MG articles were more frequently subject to investigation than NMG articles. Retracted articles due to fabrication/falsification required 2.0–2.8 times longer to retract than when plagiarism was involved.

Editors Should Declare Conflicts of Interest

Editors have increasing pressure as scholarly publishing tries to shore up trust and reassure academics and the public that traditional peer review is robust, fail-safe, and corrective. Hidden conflicts of interest (COIs) may skew the fairness of the publishing process because they could allow the status of personal or professional relationships to positively influence the outcome of peer review or reduce the processing period of this process. Not all authors have such privileged relationships. In academic journals, editors usually have very specialized skills and are selected as agents of trust, entrusted with the responsibility of serving as quality control gate-keepers during peer review. In many cases, editors form extensive networks, either with other professionals, industry, academic bodies, journals, or publishers. Such networks and relationships may influence their decisions or even their subjectivity towards a set of submitting authors, paper, or institute, ultimately influencing the peer review process. These positions and relationships are not simply aspects of a curriculum, they are potential COIs. Thus, on the editorial board of all academic journals, editors should carry a COI statement that reflects their past history, as well as actual relationships and positions that they have, as these may influence their editorial functions.

Figure errors, sloppy science, and fraud: keeping eyes on your data

Recent reports suggest that there has been an increase in the number of retractions and corrections of published articles due to post-publication detection of problematic data. Moreover, fraudulent data and sloppy science have long-term effects on the scientific literature and subsequent projects based on false and unreproducible claims. At the JCI, we have introduced several data screening checks for manuscripts prior to acceptance in an attempt to reduce the number of post-publication corrections and retractions, with the ultimate goal of increasing confidence in the papers we publish.