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.

How can meta-research be used to evaluate and improve the quality of research in the field of traditional, complementary, and integrative medicine?

The field of traditional, complementary, and integrative medicine (TCIM) has garnered increasing attention due to its holistic approach to health and well-being. While the quantity of published research about TCIM has increased exponentially, critics have argued that the field faces challenges related to methodological rigour, reproducibility, and overall quality. This article proposes meta-research as one approach to evaluating and improving the quality of TCIM research. Meta-research, also known as research about research, can be defined as "the study of research itself: its methods, reporting, reproducibility, evaluation, and incentives". By systematically evaluating methodological rigour, identifying biases, and promoting transparency, meta-research can enhance the reliability and credibility of TCIM research. Specific topics of interest that are discussed in this article include the following: 1) study design and research methodology, 2) reporting of research, 3) research ethics, integrity, and misconduct, 4) replicability and reproducibility, 5) peer review and journal editorial practices, 6) research funding: grants and awards, and 7) hiring, promotion, and tenure. For each topic, we provide case examples to illustrate meta-research applications in TCIM. We argue that meta-research initiatives can contribute to maintaining public trust, safeguarding research integrity, and advancing evidence based TCIM practice, while challenges include navigating methodological complexities, biases, and disparities in funding and academic recognition. Future directions involve tailored research methodologies, interdisciplinary collaboration, policy implications, and capacity building in meta-research.

Nonparametric worst-case bounds for publication bias on the summary receiver operating characteristic curve.

The summary receiver operating characteristic (SROC) curve has been recommended as one important meta-analytical summary to represent the accuracy of a diagnostic test in the presence of heterogeneous cutoff values. However, selective publication of diagnostic studies for meta-analysis can induce publication bias (PB) on the estimate of the SROC curve. Several sensitivity analysis methods have been developed to quantify PB on the SROC curve, and all these methods utilize parametric selection functions to model the selective publication mechanism. The main contribution of this article is to propose a new sensitivity analysis approach that derives the worst-case bounds for the SROC curve by adopting nonparametric selection functions under minimal assumptions. The estimation procedures of the worst-case bounds use the Monte Carlo method to approximate the bias on the SROC curves along with the corresponding area under the curves, and then the maximum and minimum values of PB under a range of marginal selection probabilities are optimized by nonlinear programming. We apply the proposed method to real-world meta-analyses to show that the worst-case bounds of the SROC curves can provide useful insights for discussing the robustness of meta-analytical findings on diagnostic test accuracy.

Tools, techniques, methods, and processes for the detection and mitigation of fraudulent or erroneous data in evidence synthesis: a scoping review protocol.

OBJECTIVE: This scoping review aims to identify, catalogue, and characterize previously reported tools, techniques, methods, and processes that have been recommended or used by evidence synthesizers to detect fraudulent or erroneous data and mitigate its impact. INTRODUCTION: Decision-making for policy and practice should always be underpinned by the best available evidence-typically peer-reviewed scientific literature. Evidence synthesis literature should be collated and organized using the appropriate evidence synthesis methodology, best exemplified by the role systematic reviews play in evidence-based health care. However, with the rise of "predatory journals," fraudulent or erroneous data may be invading this literature, which may negatively affect evidence syntheses that use this data. This, in turn, may compromise decision-making processes. INCLUSION CRITERIA: This review will include peer-reviewed articles, commentaries, books, and editorials that describe at least 1 tool, technique, method, or process with the explicit purpose of identifying or mitigating the impact of fraudulent or erroneous data for any evidence synthesis, in any topic area. Manuals, handbooks, and guidance from major organizations, universities, and libraries will also be considered. METHODS: This review will be conducted using the JBI methodology for scoping reviews and reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). Databases and relevant organizational websites will be searched for eligible studies. Title and abstract, and subsequently full-text screening will be conducted in duplicate using Covidence. Data from identified full texts will be extracted using a pre-determined checklist, while the findings will be summarized descriptively and presented in tables. THIS SCOPING REVIEW PROTOCOL WAS REGISTERED IN OPEN SCIENCE FRAMEWORK: https://osf.io/u8yrn.

Sensitivity analysis for publication bias in meta-analysis of sparse data based on exact likelihood.

Meta-analysis is a powerful tool to synthesize findings from multiple studies. The normal-normal random-effects model is widely used to account for between-study heterogeneity. However, meta-analyses of sparse data, which may arise when the event rate is low for binary or count outcomes, pose a challenge to the normal-normal random-effects model in the accuracy and stability in inference since the normal approximation in the within-study model may not be good. To reduce bias arising from data sparsity, the generalized linear mixed model can be used by replacing the approximate normal within-study model with an exact model. Publication bias is one of the most serious threats in meta-analysis. Several quantitative sensitivity analysis methods for evaluating the potential impacts of selective publication are available for the normal-normal random-effects model. We propose a sensitivity analysis method by extending the likelihood-based sensitivity analysis with the $t$-statistic selection function of Copas to several generalized linear mixed-effects models. Through applications of our proposed method to several real-world meta-analyses and simulation studies, the proposed method was proven to outperform the likelihood-based sensitivity analysis based on the normal-normal model. The proposed method would give useful guidance to address publication bias in the meta-analysis of sparse data.

Fostering Responsible Conduct of Research for Early-Stage Investigators: Challenges and Opportunities.

The rise of academic misconduct poses significant challenges to the integrity and credibility of scholarly research. Early-stage investigators (ESIs), particularly those representing marginalized groups, face unique pressures in navigating the "publish or perish" paradigm while establishing their careers. This commentary articulates strategies for cultivating research environments conducive to the responsible conduct of research (RCR) for ESIs. By establishing shared values, planning research meticulously, conducting research collaboratively, and reporting findings transparently, ESIs can foster a culture of prevention and accountability in research. Ultimately, navigating beyond traditional methodologies to support RCR necessitates a fundamental reimagining of academic culture, reconceptualizing productivity to prioritize quality over quantity, and to encompass "invisible" work often shouldered by investigators with marginalized identities. Addressing scientific misconduct challenges requires a whole-system approach, encompassing individual leadership, policy changes, and institutional accountability. By implementing concrete strategies and systemic reforms, academia can reaffirm its commitment to responsible research conduct and safeguard the integrity of scholarly endeavors.

RETRACTION: Impact of Histone Deacetylase Inhibitors SAHA and MS-275 on DNA Repair Pathways in Human Mesenchymal Stem Cells.

RETRACTION: G. Di Bernardo, N. Alessio, C. Dell'Aversana, F. Casale, D. Teti, M. Cipollaro, L. Altucci, and U. Galderisi, "Impact of Histone Deacetylase Inhibitors SAHA and MS-275 on DNA Repair Pathways in Human Mesenchymal Stem Cells," Journal of Cellular Physiology 225, no. 2 (2010): 537-544, https://doi.org/10.1002/jcp.22236. The above article, published online on 17 March 2024 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor-in-Chief, Robert Heath; and Wiley Periodicals LLC. The retraction has been agreed upon following an investigation into concerns raised by a third party, which revealed unambiguous image manipulation in Figure 3, SAHA - H2O2 Treatment and SAHA - Untreated panels. The authors admitted to these image alterations, cooperated with the investigation, and were able to provide partial raw data of the article including some of the original, unmodified images. Nonetheless, the modification of the images to change the appearance is clearly against the ethical policy of the journal and Wiley's Best Practice Guidelines on Research Integrity and Publishing Ethics. In addition, based on the received partial raw data, regarding the positive cell counts for the 8oxodG assay, the journal team could not exclude that the visual modification of these images affects the number of counted 8oxodG-positive cells, and consequently the related conclusions of the article. Therefore, the editors have lost confidence in the data presented and have decided to retract the article. The authors were informed of the decision to retract but did not agree to the retraction.

Academic Citation Partnership: A Predatory Practice that Undermines Scholarly Integrity.

Recently, academic circles have raised concerns about academic citation partnerships. Many researchers receive emails offering these partnerships, often landing in their spam folders. In this paper, I refer to academic citation partnerships as unethical collaborative arrangements where researchers or authors agree to cite each other's work in their academic publications to enhance their academic profiles, often measured by metrics like the h-index. I discuss the characteristics of such partnerships, individuals, and groups who are commonly involved in academic citation partnerships, and clarify what is not considered an academic citation partnership. I argue that these partnerships are predatory and pose a serious threat to scholarly integrity. Such solicitations blur ethical boundaries by treating citations as commodities, similar to predatory journals and conferences. These partnerships compromise the authenticity of scholarly discourse, artificially inflate perceived impacts, and distort academic evaluations. They undermine the pursuit of knowledge for its intrinsic value and exacerbate inequalities in academia by favoring those who can manipulate citation metrics through resources or networks. Addressing this issue requires a commitment to vigilance and adherence to ethical citation standards, ensuring academic discourse that is intellectually honest and genuinely beneficial to academia.

[Predatory journals: What are they and how to avoid them?] / Las revistas depredadoras: ¿qué son y cómo evitarlas?

Currently, a large number of predatory journals have proliferated. Their purpose is to obtain fraudulent profits by promising the rapid publication of scientific works, without fulfilling the services of quality review. These publishers have managed to copy the models of open access journals, which is why they are increasingly difficult to identify, coupled with the fact that many of them have opened spaces in the most important indexes of scientific journals, such as Medline, Web of Science (WoS), Scopus, Embase, among others. These publishers cheat not only the authors of the research they intend to publish but also the readers and general public with publications that have not been reviewed and evaluated properly by a system of peers or academic experts. Therefore, the aim of this work is to make known some of the most common practices of predatory journals, so that anyone interested in the editorial process, whether as an author, editor or reader, has the elements to identify these fraudulent journals, and this bad practice in the editorial process.

Actualmente han proliferado una gran cantidad de revistas depredadoras, cuyo fin es obtener ganancias fraudulentas mediante la promesa de la publicación rápida de trabajos científicos, sin cumplir con los servicios de una revisión de calidad. Estas editoriales han logrado copiar los modelos de las revistas con acceso abierto, por lo que cada vez son más difíciles de identificar, aunado a que muchas de ellas se han abierto espacios en los índices más importantes de las revistas científicas, como Medline, Web of Science (WoS), Scopus, Embase, entre otros. Estas editoriales defraudan no solo a los autores de las investigaciones que intentan publicar sino también a los lectores y al público en general con publicaciones que no han sido debidamente revisadas y evaluadas por un sistema de pares o expertos académicos. Por lo tanto, el objetivo de este trabajo es dar a conocer algunas de las prácticas más comunes de las revistas depredadoras para que toda persona interesada en el proceso editorial, ya sea como autor, editor o lector, tenga los elementos para identificar estas revistas fraudulentas y esta mala práctica en el proceso editorial.

RETRACTION: Multi-Stimuli Nanocomposite Therapeutic: Docetaxel Targeted Delivery and Synergies in Treatment of Human Breast Cancer Tumor.

Small 2020, 16, 2002733 DOI: 10.1002/smll.202002733 The above article, published online on 18 September 2020 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor-in-Chief, Neville Compton; and Wiley-VCH GmbH. Following publication, concerns were raised by a third-party regarding the appearance of Figures 7d, 11a and 12a. The subsequent investigation uncovered inappropriate duplication of images (panels of Figures 7d and 12a) between this and other articles that were previously published in a different scientific context elsewhere and the manipulation of images in Figure 11a. The investigation also revealed that the animal experiments were neither conducted at, nor received ethical approval from the Department of Nuclear Medicine, West China Hospital, Sichuan University. Given the extent of the identified issues, the editors have decided to retract the article.

RETRACTION: Evaluation of proteome dynamics: Implications for statistical confidence in mass spectrometric determination.

Retraction: I. Popova, E. Savelyeva, T. Degtyarevskaya, D. Babaskin, & A. Vokhmintsev (2024). Evaluation of proteome dynamics: Implications for statistical confidence in mass spectrometric determination. Proteomics, 24(14), 2300351. https://doi.org/10.1002/pmic.202300351 The above article, published online on May 3, 2024 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor-in-Chief, Lucie Kalvodova; and Wiley-VCH GmbH. The retraction has been agreed due to a major unattributed overlap between the figures and figure legends of this article (Figures 2-7) and another article previously published elsewhere by a different group of authors [1]. Such publishing practice is against the journal's policy and Wiley's Best Practice Guidelines on Research Integrity and Publishing Ethics. The co-authors, I. Popova, T. Degtyarevskaya, D. Babaskin, and A. Vokhmintsev, stated that they did not participate in the writing and submission of the article and gave no consent for publication. E. Savelyeva remained unresponsive. REFERENCE Boekweg, H., Guise, A. J., Plowey, E. D., Kelly, R. T., & Payne, S. (2021). Calculating sample size requirements for temporal dynamics in single-cell proteomics. Molecular & Cellular Proteomics, 20, 100085. https://doi.org/10.1016/j.mcpro.2021.100085.

Retraction: Comparative study of the ciliary body and iris morphology in the anterior eye chamber of five different vertebrate classes.

RETRACTION: A.A. Seleem, and A.H. Badr, 'Comparative Study of The Ciliary Body and Iris Morphology In The Anterior Eye Chamber of Five Different Vertebrate Classes', Anatomia Histologia Embryologia 53, no. 3 (2024): e13052, https://doi.org/10.1111/ahe.13052. The above article, published online on 12 May 2024 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor-in-Chief, Fred Sinowatz; and Wiley-VCH GmbH, Published by John Wiley & Sons Ltd. The retraction has been agreed after an investigation found that this article was the resubmitted version of a manuscript which had been rejected a month previously, primarily due to concerns about compliance with animal ethical best practices concerning killing. Upon submission of the second manuscript, there was no clearly identifiable indication that it was a resubmission, as required by the journal during the submission process. Without knowledge that the new manuscript was the resubmission of a rejected manuscript, the new handling editors could not benefit from the peer review history. Because of this, they did not appreciate the necessity to confirm whether the ethical concerns raised in the rejected version had been addressed in the resubmitted version. Had the handling editors seen the peer review history, they would have rejected the second manuscript prior to peer review. Additionally, the second manuscript had been edited to omit mention of the unethical practice and investigators were therefore unable to verify which methods were used in the published study, nor could they evaluate them against the accepted ethical practices for handling animals. The authors responded to our inquiry but could not provide either adequate raw data or explanations for our concerns. Therefore, the article must be retracted. The authors have been informed of the retraction and Dr. Seleem, on behalf of both authors, disagrees with this decision.

Integrity at stake: confronting "publish or perish" in the developing world and emerging economies.

The scientific community faces significant ethical challenges due to the "publish or perish" culture, particularly in developing and emerging economies. This paper explores the widespread unethical practices in scientific publishing, including the sale of authorships, the proliferation of "paper mills," and the misuse of artificial intelligence to produce fraudulent research. These practices undermine the integrity of scientific research, skew publication metrics, and distort academic rankings. This study examines various instances of academic fraud, emphasizing the impact on low-income countries, with specific cases from Latin America. Recommendations include stricter verification of authorship, disciplinary measures for scientific fraud, and policies promoting transparency and accountability in research. Addressing these challenges is crucial for maintaining the integrity and credibility of scientific endeavors globally.

Scientists and scientific journals should adhere to ethical standards for the use and reporting of data from Indigenous people.

Internationally, governments and scientists are bound by legal and treaty rights when working with Indigenous nations. These rights include the right of Indigenous people to control the conduct of science with Indigenous nations. Unfortunately, in some cases, individual scientists and scientific teams working with biological and genetic data collected from Indigenous people have not respected these international rights. Here, we argue that the scientific community should understand and acknowledge the historical harms experienced by Indigenous people under the veil of scientific progress (truth) and implement existing standards for ethical conduct of research and sovereign control of data collected within Indigenous communities (reconciliation). Specifically, we outline the rationale for why scientists, scientific journals and research integrity and institutional review boards/ethics committees should adopt, and be held accountable for upholding, current international standards of Indigenous data sovereignty and ethical use of Indigenous biological samples.

Investigating Country-Specific Perceptions of Predatory Journals and Their Impact on Scholarly Integrity: A Systematic Review.

This systematic review aims to identify the countries most active in combatting predatory journals and their definitions of such practices. It also seeks to assess awareness within academic communities, examine the impact of predatory journals on research quality and integrity, and compile existing policies to mitigate their negative effects and strengthen global scholarly integrity. A systematic search was performed in the PubMed, Scopus, and Embase databases on February 7, 2024, in line with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The focus was solely on identifying studies that examined the unique experiences and interventions associated with predatory journals in distinct national contexts. The analysis included a presentation of quantitative results and a thematic examination of qualitative data. A total of 40 articles covering 19 countries were included. Twenty-four countries (60%) were in Asia, 11 (27.5%) in Africa, two (5%) in Europe, and one (2.5%) each in Australia, North America, and South America. Although not all articles cited Beall's list to identify predatory journals, the thematic analysis showed consistent topics across various definitions and Beall's themes. Our analysis identified factors affecting academic publishing perceptions globally, highlighting publication pressure, predatory practices, and policy impacts on ethics and standards. This systematic review examined the literature on predatory publishing and identified the leading countries in the fight against these predatory publications. This analysis underscores a complex interplay of factors affecting academic publishing globally, from the push towards predatory journals as a response to publishing pressures, to the critical role of government and institutional frameworks.

Unveiling the Hidden Menace: A Topic Modeling Analysis of Hijacked Medical Journals.

Purpose: Nowadays, many studies discuss scholarly publishing and associated challenges, but the problem of hijacked journals has been neglected. Hijacked journals are cloned websites that mimic original journals but are managed by cybercriminals. The present study uses a topic modeling approach to analyze published papers in hijacked versions of medical journals. Methods: A total of 3384 papers were downloaded from 21 hijacked journals in the medical domain and analyzed by topic modeling algorithm. Results: Results indicate that hijacked versions of medical journals are published in most fields of the medical domain and typically respect the primary domain of the original journal. Conclusion: The academic world is faced with the third-generation of hijacked journals, and their detection may be more complex than common ones. The usage of artificial intelligence (AI) can be a powerful tool to deal with the phenomenon.