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How to Write and Publish a Research Paper for a Peer-Reviewed Journal

  • Open access
  • Published: 30 April 2020
  • Volume 36 , pages 909–913, ( 2021 )

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  • Clara Busse   ORCID: orcid.org/0000-0002-0178-1000 1 &
  • Ella August   ORCID: orcid.org/0000-0001-5151-1036 1 , 2  

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Communicating research findings is an essential step in the research process. Often, peer-reviewed journals are the forum for such communication, yet many researchers are never taught how to write a publishable scientific paper. In this article, we explain the basic structure of a scientific paper and describe the information that should be included in each section. We also identify common pitfalls for each section and recommend strategies to avoid them. Further, we give advice about target journal selection and authorship. In the online resource 1 , we provide an example of a high-quality scientific paper, with annotations identifying the elements we describe in this article.

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Avoid common mistakes on your manuscript.

Introduction

Writing a scientific paper is an important component of the research process, yet researchers often receive little formal training in scientific writing. This is especially true in low-resource settings. In this article, we explain why choosing a target journal is important, give advice about authorship, provide a basic structure for writing each section of a scientific paper, and describe common pitfalls and recommendations for each section. In the online resource 1 , we also include an annotated journal article that identifies the key elements and writing approaches that we detail here. Before you begin your research, make sure you have ethical clearance from all relevant ethical review boards.

Select a Target Journal Early in the Writing Process

We recommend that you select a “target journal” early in the writing process; a “target journal” is the journal to which you plan to submit your paper. Each journal has a set of core readers and you should tailor your writing to this readership. For example, if you plan to submit a manuscript about vaping during pregnancy to a pregnancy-focused journal, you will need to explain what vaping is because readers of this journal may not have a background in this topic. However, if you were to submit that same article to a tobacco journal, you would not need to provide as much background information about vaping.

Information about a journal’s core readership can be found on its website, usually in a section called “About this journal” or something similar. For example, the Journal of Cancer Education presents such information on the “Aims and Scope” page of its website, which can be found here: https://www.springer.com/journal/13187/aims-and-scope .

Peer reviewer guidelines from your target journal are an additional resource that can help you tailor your writing to the journal and provide additional advice about crafting an effective article [ 1 ]. These are not always available, but it is worth a quick web search to find out.

Identify Author Roles Early in the Process

Early in the writing process, identify authors, determine the order of authors, and discuss the responsibilities of each author. Standard author responsibilities have been identified by The International Committee of Medical Journal Editors (ICMJE) [ 2 ]. To set clear expectations about each team member’s responsibilities and prevent errors in communication, we also suggest outlining more detailed roles, such as who will draft each section of the manuscript, write the abstract, submit the paper electronically, serve as corresponding author, and write the cover letter. It is best to formalize this agreement in writing after discussing it, circulating the document to the author team for approval. We suggest creating a title page on which all authors are listed in the agreed-upon order. It may be necessary to adjust authorship roles and order during the development of the paper. If a new author order is agreed upon, be sure to update the title page in the manuscript draft.

In the case where multiple papers will result from a single study, authors should discuss who will author each paper. Additionally, authors should agree on a deadline for each paper and the lead author should take responsibility for producing an initial draft by this deadline.

Structure of the Introduction Section

The introduction section should be approximately three to five paragraphs in length. Look at examples from your target journal to decide the appropriate length. This section should include the elements shown in Fig.  1 . Begin with a general context, narrowing to the specific focus of the paper. Include five main elements: why your research is important, what is already known about the topic, the “gap” or what is not yet known about the topic, why it is important to learn the new information that your research adds, and the specific research aim(s) that your paper addresses. Your research aim should address the gap you identified. Be sure to add enough background information to enable readers to understand your study. Table 1 provides common introduction section pitfalls and recommendations for addressing them.

figure 1

The main elements of the introduction section of an original research article. Often, the elements overlap

Methods Section

The purpose of the methods section is twofold: to explain how the study was done in enough detail to enable its replication and to provide enough contextual detail to enable readers to understand and interpret the results. In general, the essential elements of a methods section are the following: a description of the setting and participants, the study design and timing, the recruitment and sampling, the data collection process, the dataset, the dependent and independent variables, the covariates, the analytic approach for each research objective, and the ethical approval. The hallmark of an exemplary methods section is the justification of why each method was used. Table 2 provides common methods section pitfalls and recommendations for addressing them.

Results Section

The focus of the results section should be associations, or lack thereof, rather than statistical tests. Two considerations should guide your writing here. First, the results should present answers to each part of the research aim. Second, return to the methods section to ensure that the analysis and variables for each result have been explained.

Begin the results section by describing the number of participants in the final sample and details such as the number who were approached to participate, the proportion who were eligible and who enrolled, and the number of participants who dropped out. The next part of the results should describe the participant characteristics. After that, you may organize your results by the aim or by putting the most exciting results first. Do not forget to report your non-significant associations. These are still findings.

Tables and figures capture the reader’s attention and efficiently communicate your main findings [ 3 ]. Each table and figure should have a clear message and should complement, rather than repeat, the text. Tables and figures should communicate all salient details necessary for a reader to understand the findings without consulting the text. Include information on comparisons and tests, as well as information about the sample and timing of the study in the title, legend, or in a footnote. Note that figures are often more visually interesting than tables, so if it is feasible to make a figure, make a figure. To avoid confusing the reader, either avoid abbreviations in tables and figures, or define them in a footnote. Note that there should not be citations in the results section and you should not interpret results here. Table 3 provides common results section pitfalls and recommendations for addressing them.

Discussion Section

Opposite the introduction section, the discussion should take the form of a right-side-up triangle beginning with interpretation of your results and moving to general implications (Fig.  2 ). This section typically begins with a restatement of the main findings, which can usually be accomplished with a few carefully-crafted sentences.

figure 2

Major elements of the discussion section of an original research article. Often, the elements overlap

Next, interpret the meaning or explain the significance of your results, lifting the reader’s gaze from the study’s specific findings to more general applications. Then, compare these study findings with other research. Are these findings in agreement or disagreement with those from other studies? Does this study impart additional nuance to well-accepted theories? Situate your findings within the broader context of scientific literature, then explain the pathways or mechanisms that might give rise to, or explain, the results.

Journals vary in their approach to strengths and limitations sections: some are embedded paragraphs within the discussion section, while some mandate separate section headings. Keep in mind that every study has strengths and limitations. Candidly reporting yours helps readers to correctly interpret your research findings.

The next element of the discussion is a summary of the potential impacts and applications of the research. Should these results be used to optimally design an intervention? Does the work have implications for clinical protocols or public policy? These considerations will help the reader to further grasp the possible impacts of the presented work.

Finally, the discussion should conclude with specific suggestions for future work. Here, you have an opportunity to illuminate specific gaps in the literature that compel further study. Avoid the phrase “future research is necessary” because the recommendation is too general to be helpful to readers. Instead, provide substantive and specific recommendations for future studies. Table 4 provides common discussion section pitfalls and recommendations for addressing them.

Follow the Journal’s Author Guidelines

After you select a target journal, identify the journal’s author guidelines to guide the formatting of your manuscript and references. Author guidelines will often (but not always) include instructions for titles, cover letters, and other components of a manuscript submission. Read the guidelines carefully. If you do not follow the guidelines, your article will be sent back to you.

Finally, do not submit your paper to more than one journal at a time. Even if this is not explicitly stated in the author guidelines of your target journal, it is considered inappropriate and unprofessional.

Your title should invite readers to continue reading beyond the first page [ 4 , 5 ]. It should be informative and interesting. Consider describing the independent and dependent variables, the population and setting, the study design, the timing, and even the main result in your title. Because the focus of the paper can change as you write and revise, we recommend you wait until you have finished writing your paper before composing the title.

Be sure that the title is useful for potential readers searching for your topic. The keywords you select should complement those in your title to maximize the likelihood that a researcher will find your paper through a database search. Avoid using abbreviations in your title unless they are very well known, such as SNP, because it is more likely that someone will use a complete word rather than an abbreviation as a search term to help readers find your paper.

After you have written a complete draft, use the checklist (Fig. 3 ) below to guide your revisions and editing. Additional resources are available on writing the abstract and citing references [ 5 ]. When you feel that your work is ready, ask a trusted colleague or two to read the work and provide informal feedback. The box below provides a checklist that summarizes the key points offered in this article.

figure 3

Checklist for manuscript quality

Data Availability

Michalek AM (2014) Down the rabbit hole…advice to reviewers. J Cancer Educ 29:4–5

Article   Google Scholar  

International Committee of Medical Journal Editors. Defining the role of authors and contributors: who is an author? http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authosrs-and-contributors.html . Accessed 15 January, 2020

Vetto JT (2014) Short and sweet: a short course on concise medical writing. J Cancer Educ 29(1):194–195

Brett M, Kording K (2017) Ten simple rules for structuring papers. PLoS ComputBiol. https://doi.org/10.1371/journal.pcbi.1005619

Lang TA (2017) Writing a better research article. J Public Health Emerg. https://doi.org/10.21037/jphe.2017.11.06

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Acknowledgments

Ella August is grateful to the Sustainable Sciences Institute for mentoring her in training researchers on writing and publishing their research.

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Clara Busse & Ella August

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Busse, C., August, E. How to Write and Publish a Research Paper for a Peer-Reviewed Journal. J Canc Educ 36 , 909–913 (2021). https://doi.org/10.1007/s13187-020-01751-z

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Peer Review in Scientific Publications: Benefits, Critiques, & A Survival Guide

Jacalyn kelly.

1 Clinical Biochemistry, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada

Tara Sadeghieh

Khosrow adeli.

2 Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada

3 Chair, Communications and Publications Division (CPD), International Federation for Sick Clinical Chemistry (IFCC), Milan, Italy

The authors declare no conflicts of interest regarding publication of this article.

Peer review has been defined as a process of subjecting an author’s scholarly work, research or ideas to the scrutiny of others who are experts in the same field. It functions to encourage authors to meet the accepted high standards of their discipline and to control the dissemination of research data to ensure that unwarranted claims, unacceptable interpretations or personal views are not published without prior expert review. Despite its wide-spread use by most journals, the peer review process has also been widely criticised due to the slowness of the process to publish new findings and due to perceived bias by the editors and/or reviewers. Within the scientific community, peer review has become an essential component of the academic writing process. It helps ensure that papers published in scientific journals answer meaningful research questions and draw accurate conclusions based on professionally executed experimentation. Submission of low quality manuscripts has become increasingly prevalent, and peer review acts as a filter to prevent this work from reaching the scientific community. The major advantage of a peer review process is that peer-reviewed articles provide a trusted form of scientific communication. Since scientific knowledge is cumulative and builds on itself, this trust is particularly important. Despite the positive impacts of peer review, critics argue that the peer review process stifles innovation in experimentation, and acts as a poor screen against plagiarism. Despite its downfalls, there has not yet been a foolproof system developed to take the place of peer review, however, researchers have been looking into electronic means of improving the peer review process. Unfortunately, the recent explosion in online only/electronic journals has led to mass publication of a large number of scientific articles with little or no peer review. This poses significant risk to advances in scientific knowledge and its future potential. The current article summarizes the peer review process, highlights the pros and cons associated with different types of peer review, and describes new methods for improving peer review.

WHAT IS PEER REVIEW AND WHAT IS ITS PURPOSE?

Peer Review is defined as “a process of subjecting an author’s scholarly work, research or ideas to the scrutiny of others who are experts in the same field” ( 1 ). Peer review is intended to serve two primary purposes. Firstly, it acts as a filter to ensure that only high quality research is published, especially in reputable journals, by determining the validity, significance and originality of the study. Secondly, peer review is intended to improve the quality of manuscripts that are deemed suitable for publication. Peer reviewers provide suggestions to authors on how to improve the quality of their manuscripts, and also identify any errors that need correcting before publication.

HISTORY OF PEER REVIEW

The concept of peer review was developed long before the scholarly journal. In fact, the peer review process is thought to have been used as a method of evaluating written work since ancient Greece ( 2 ). The peer review process was first described by a physician named Ishaq bin Ali al-Rahwi of Syria, who lived from 854-931 CE, in his book Ethics of the Physician ( 2 ). There, he stated that physicians must take notes describing the state of their patients’ medical conditions upon each visit. Following treatment, the notes were scrutinized by a local medical council to determine whether the physician had met the required standards of medical care. If the medical council deemed that the appropriate standards were not met, the physician in question could receive a lawsuit from the maltreated patient ( 2 ).

The invention of the printing press in 1453 allowed written documents to be distributed to the general public ( 3 ). At this time, it became more important to regulate the quality of the written material that became publicly available, and editing by peers increased in prevalence. In 1620, Francis Bacon wrote the work Novum Organum, where he described what eventually became known as the first universal method for generating and assessing new science ( 3 ). His work was instrumental in shaping the Scientific Method ( 3 ). In 1665, the French Journal des sçavans and the English Philosophical Transactions of the Royal Society were the first scientific journals to systematically publish research results ( 4 ). Philosophical Transactions of the Royal Society is thought to be the first journal to formalize the peer review process in 1665 ( 5 ), however, it is important to note that peer review was initially introduced to help editors decide which manuscripts to publish in their journals, and at that time it did not serve to ensure the validity of the research ( 6 ). It did not take long for the peer review process to evolve, and shortly thereafter papers were distributed to reviewers with the intent of authenticating the integrity of the research study before publication. The Royal Society of Edinburgh adhered to the following peer review process, published in their Medical Essays and Observations in 1731: “Memoirs sent by correspondence are distributed according to the subject matter to those members who are most versed in these matters. The report of their identity is not known to the author.” ( 7 ). The Royal Society of London adopted this review procedure in 1752 and developed the “Committee on Papers” to review manuscripts before they were published in Philosophical Transactions ( 6 ).

Peer review in the systematized and institutionalized form has developed immensely since the Second World War, at least partly due to the large increase in scientific research during this period ( 7 ). It is now used not only to ensure that a scientific manuscript is experimentally and ethically sound, but also to determine which papers sufficiently meet the journal’s standards of quality and originality before publication. Peer review is now standard practice by most credible scientific journals, and is an essential part of determining the credibility and quality of work submitted.

IMPACT OF THE PEER REVIEW PROCESS

Peer review has become the foundation of the scholarly publication system because it effectively subjects an author’s work to the scrutiny of other experts in the field. Thus, it encourages authors to strive to produce high quality research that will advance the field. Peer review also supports and maintains integrity and authenticity in the advancement of science. A scientific hypothesis or statement is generally not accepted by the academic community unless it has been published in a peer-reviewed journal ( 8 ). The Institute for Scientific Information ( ISI ) only considers journals that are peer-reviewed as candidates to receive Impact Factors. Peer review is a well-established process which has been a formal part of scientific communication for over 300 years.

OVERVIEW OF THE PEER REVIEW PROCESS

The peer review process begins when a scientist completes a research study and writes a manuscript that describes the purpose, experimental design, results, and conclusions of the study. The scientist then submits this paper to a suitable journal that specializes in a relevant research field, a step referred to as pre-submission. The editors of the journal will review the paper to ensure that the subject matter is in line with that of the journal, and that it fits with the editorial platform. Very few papers pass this initial evaluation. If the journal editors feel the paper sufficiently meets these requirements and is written by a credible source, they will send the paper to accomplished researchers in the field for a formal peer review. Peer reviewers are also known as referees (this process is summarized in Figure 1 ). The role of the editor is to select the most appropriate manuscripts for the journal, and to implement and monitor the peer review process. Editors must ensure that peer reviews are conducted fairly, and in an effective and timely manner. They must also ensure that there are no conflicts of interest involved in the peer review process.

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Overview of the review process

When a reviewer is provided with a paper, he or she reads it carefully and scrutinizes it to evaluate the validity of the science, the quality of the experimental design, and the appropriateness of the methods used. The reviewer also assesses the significance of the research, and judges whether the work will contribute to advancement in the field by evaluating the importance of the findings, and determining the originality of the research. Additionally, reviewers identify any scientific errors and references that are missing or incorrect. Peer reviewers give recommendations to the editor regarding whether the paper should be accepted, rejected, or improved before publication in the journal. The editor will mediate author-referee discussion in order to clarify the priority of certain referee requests, suggest areas that can be strengthened, and overrule reviewer recommendations that are beyond the study’s scope ( 9 ). If the paper is accepted, as per suggestion by the peer reviewer, the paper goes into the production stage, where it is tweaked and formatted by the editors, and finally published in the scientific journal. An overview of the review process is presented in Figure 1 .

WHO CONDUCTS REVIEWS?

Peer reviews are conducted by scientific experts with specialized knowledge on the content of the manuscript, as well as by scientists with a more general knowledge base. Peer reviewers can be anyone who has competence and expertise in the subject areas that the journal covers. Reviewers can range from young and up-and-coming researchers to old masters in the field. Often, the young reviewers are the most responsive and deliver the best quality reviews, though this is not always the case. On average, a reviewer will conduct approximately eight reviews per year, according to a study on peer review by the Publishing Research Consortium (PRC) ( 7 ). Journals will often have a pool of reviewers with diverse backgrounds to allow for many different perspectives. They will also keep a rather large reviewer bank, so that reviewers do not get burnt out, overwhelmed or time constrained from reviewing multiple articles simultaneously.

WHY DO REVIEWERS REVIEW?

Referees are typically not paid to conduct peer reviews and the process takes considerable effort, so the question is raised as to what incentive referees have to review at all. Some feel an academic duty to perform reviews, and are of the mentality that if their peers are expected to review their papers, then they should review the work of their peers as well. Reviewers may also have personal contacts with editors, and may want to assist as much as possible. Others review to keep up-to-date with the latest developments in their field, and reading new scientific papers is an effective way to do so. Some scientists use peer review as an opportunity to advance their own research as it stimulates new ideas and allows them to read about new experimental techniques. Other reviewers are keen on building associations with prestigious journals and editors and becoming part of their community, as sometimes reviewers who show dedication to the journal are later hired as editors. Some scientists see peer review as a chance to become aware of the latest research before their peers, and thus be first to develop new insights from the material. Finally, in terms of career development, peer reviewing can be desirable as it is often noted on one’s resume or CV. Many institutions consider a researcher’s involvement in peer review when assessing their performance for promotions ( 11 ). Peer reviewing can also be an effective way for a scientist to show their superiors that they are committed to their scientific field ( 5 ).

ARE REVIEWERS KEEN TO REVIEW?

A 2009 international survey of 4000 peer reviewers conducted by the charity Sense About Science at the British Science Festival at the University of Surrey, found that 90% of reviewers were keen to peer review ( 12 ). One third of respondents to the survey said they were happy to review up to five papers per year, and an additional one third of respondents were happy to review up to ten.

HOW LONG DOES IT TAKE TO REVIEW ONE PAPER?

On average, it takes approximately six hours to review one paper ( 12 ), however, this number may vary greatly depending on the content of the paper and the nature of the peer reviewer. One in every 100 participants in the “Sense About Science” survey claims to have taken more than 100 hours to review their last paper ( 12 ).

HOW TO DETERMINE IF A JOURNAL IS PEER REVIEWED

Ulrichsweb is a directory that provides information on over 300,000 periodicals, including information regarding which journals are peer reviewed ( 13 ). After logging into the system using an institutional login (eg. from the University of Toronto), search terms, journal titles or ISSN numbers can be entered into the search bar. The database provides the title, publisher, and country of origin of the journal, and indicates whether the journal is still actively publishing. The black book symbol (labelled ‘refereed’) reveals that the journal is peer reviewed.

THE EVALUATION CRITERIA FOR PEER REVIEW OF SCIENTIFIC PAPERS

As previously mentioned, when a reviewer receives a scientific manuscript, he/she will first determine if the subject matter is well suited for the content of the journal. The reviewer will then consider whether the research question is important and original, a process which may be aided by a literature scan of review articles.

Scientific papers submitted for peer review usually follow a specific structure that begins with the title, followed by the abstract, introduction, methodology, results, discussion, conclusions, and references. The title must be descriptive and include the concept and organism investigated, and potentially the variable manipulated and the systems used in the study. The peer reviewer evaluates if the title is descriptive enough, and ensures that it is clear and concise. A study by the National Association of Realtors (NAR) published by the Oxford University Press in 2006 indicated that the title of a manuscript plays a significant role in determining reader interest, as 72% of respondents said they could usually judge whether an article will be of interest to them based on the title and the author, while 13% of respondents claimed to always be able to do so ( 14 ).

The abstract is a summary of the paper, which briefly mentions the background or purpose, methods, key results, and major conclusions of the study. The peer reviewer assesses whether the abstract is sufficiently informative and if the content of the abstract is consistent with the rest of the paper. The NAR study indicated that 40% of respondents could determine whether an article would be of interest to them based on the abstract alone 60-80% of the time, while 32% could judge an article based on the abstract 80-100% of the time ( 14 ). This demonstrates that the abstract alone is often used to assess the value of an article.

The introduction of a scientific paper presents the research question in the context of what is already known about the topic, in order to identify why the question being studied is of interest to the scientific community, and what gap in knowledge the study aims to fill ( 15 ). The introduction identifies the study’s purpose and scope, briefly describes the general methods of investigation, and outlines the hypothesis and predictions ( 15 ). The peer reviewer determines whether the introduction provides sufficient background information on the research topic, and ensures that the research question and hypothesis are clearly identifiable.

The methods section describes the experimental procedures, and explains why each experiment was conducted. The methods section also includes the equipment and reagents used in the investigation. The methods section should be detailed enough that it can be used it to repeat the experiment ( 15 ). Methods are written in the past tense and in the active voice. The peer reviewer assesses whether the appropriate methods were used to answer the research question, and if they were written with sufficient detail. If information is missing from the methods section, it is the peer reviewer’s job to identify what details need to be added.

The results section is where the outcomes of the experiment and trends in the data are explained without judgement, bias or interpretation ( 15 ). This section can include statistical tests performed on the data, as well as figures and tables in addition to the text. The peer reviewer ensures that the results are described with sufficient detail, and determines their credibility. Reviewers also confirm that the text is consistent with the information presented in tables and figures, and that all figures and tables included are important and relevant ( 15 ). The peer reviewer will also make sure that table and figure captions are appropriate both contextually and in length, and that tables and figures present the data accurately.

The discussion section is where the data is analyzed. Here, the results are interpreted and related to past studies ( 15 ). The discussion describes the meaning and significance of the results in terms of the research question and hypothesis, and states whether the hypothesis was supported or rejected. This section may also provide possible explanations for unusual results and suggestions for future research ( 15 ). The discussion should end with a conclusions section that summarizes the major findings of the investigation. The peer reviewer determines whether the discussion is clear and focused, and whether the conclusions are an appropriate interpretation of the results. Reviewers also ensure that the discussion addresses the limitations of the study, any anomalies in the results, the relationship of the study to previous research, and the theoretical implications and practical applications of the study.

The references are found at the end of the paper, and list all of the information sources cited in the text to describe the background, methods, and/or interpret results. Depending on the citation method used, the references are listed in alphabetical order according to author last name, or numbered according to the order in which they appear in the paper. The peer reviewer ensures that references are used appropriately, cited accurately, formatted correctly, and that none are missing.

Finally, the peer reviewer determines whether the paper is clearly written and if the content seems logical. After thoroughly reading through the entire manuscript, they determine whether it meets the journal’s standards for publication,

and whether it falls within the top 25% of papers in its field ( 16 ) to determine priority for publication. An overview of what a peer reviewer looks for when evaluating a manuscript, in order of importance, is presented in Figure 2 .

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How a peer review evaluates a manuscript

To increase the chance of success in the peer review process, the author must ensure that the paper fully complies with the journal guidelines before submission. The author must also be open to criticism and suggested revisions, and learn from mistakes made in previous submissions.

ADVANTAGES AND DISADVANTAGES OF THE DIFFERENT TYPES OF PEER REVIEW

The peer review process is generally conducted in one of three ways: open review, single-blind review, or double-blind review. In an open review, both the author of the paper and the peer reviewer know one another’s identity. Alternatively, in single-blind review, the reviewer’s identity is kept private, but the author’s identity is revealed to the reviewer. In double-blind review, the identities of both the reviewer and author are kept anonymous. Open peer review is advantageous in that it prevents the reviewer from leaving malicious comments, being careless, or procrastinating completion of the review ( 2 ). It encourages reviewers to be open and honest without being disrespectful. Open reviewing also discourages plagiarism amongst authors ( 2 ). On the other hand, open peer review can also prevent reviewers from being honest for fear of developing bad rapport with the author. The reviewer may withhold or tone down their criticisms in order to be polite ( 2 ). This is especially true when younger reviewers are given a more esteemed author’s work, in which case the reviewer may be hesitant to provide criticism for fear that it will damper their relationship with a superior ( 2 ). According to the Sense About Science survey, editors find that completely open reviewing decreases the number of people willing to participate, and leads to reviews of little value ( 12 ). In the aforementioned study by the PRC, only 23% of authors surveyed had experience with open peer review ( 7 ).

Single-blind peer review is by far the most common. In the PRC study, 85% of authors surveyed had experience with single-blind peer review ( 7 ). This method is advantageous as the reviewer is more likely to provide honest feedback when their identity is concealed ( 2 ). This allows the reviewer to make independent decisions without the influence of the author ( 2 ). The main disadvantage of reviewer anonymity, however, is that reviewers who receive manuscripts on subjects similar to their own research may be tempted to delay completing the review in order to publish their own data first ( 2 ).

Double-blind peer review is advantageous as it prevents the reviewer from being biased against the author based on their country of origin or previous work ( 2 ). This allows the paper to be judged based on the quality of the content, rather than the reputation of the author. The Sense About Science survey indicates that 76% of researchers think double-blind peer review is a good idea ( 12 ), and the PRC survey indicates that 45% of authors have had experience with double-blind peer review ( 7 ). The disadvantage of double-blind peer review is that, especially in niche areas of research, it can sometimes be easy for the reviewer to determine the identity of the author based on writing style, subject matter or self-citation, and thus, impart bias ( 2 ).

Masking the author’s identity from peer reviewers, as is the case in double-blind review, is generally thought to minimize bias and maintain review quality. A study by Justice et al. in 1998 investigated whether masking author identity affected the quality of the review ( 17 ). One hundred and eighteen manuscripts were randomized; 26 were peer reviewed as normal, and 92 were moved into the ‘intervention’ arm, where editor quality assessments were completed for 77 manuscripts and author quality assessments were completed for 40 manuscripts ( 17 ). There was no perceived difference in quality between the masked and unmasked reviews. Additionally, the masking itself was often unsuccessful, especially with well-known authors ( 17 ). However, a previous study conducted by McNutt et al. had different results ( 18 ). In this case, blinding was successful 73% of the time, and they found that when author identity was masked, the quality of review was slightly higher ( 18 ). Although Justice et al. argued that this difference was too small to be consequential, their study targeted only biomedical journals, and the results cannot be generalized to journals of a different subject matter ( 17 ). Additionally, there were problems masking the identities of well-known authors, introducing a flaw in the methods. Regardless, Justice et al. concluded that masking author identity from reviewers may not improve review quality ( 17 ).

In addition to open, single-blind and double-blind peer review, there are two experimental forms of peer review. In some cases, following publication, papers may be subjected to post-publication peer review. As many papers are now published online, the scientific community has the opportunity to comment on these papers, engage in online discussions and post a formal review. For example, online publishers PLOS and BioMed Central have enabled scientists to post comments on published papers if they are registered users of the site ( 10 ). Philica is another journal launched with this experimental form of peer review. Only 8% of authors surveyed in the PRC study had experience with post-publication review ( 7 ). Another experimental form of peer review called Dynamic Peer Review has also emerged. Dynamic peer review is conducted on websites such as Naboj, which allow scientists to conduct peer reviews on articles in the preprint media ( 19 ). The peer review is conducted on repositories and is a continuous process, which allows the public to see both the article and the reviews as the article is being developed ( 19 ). Dynamic peer review helps prevent plagiarism as the scientific community will already be familiar with the work before the peer reviewed version appears in print ( 19 ). Dynamic review also reduces the time lag between manuscript submission and publishing. An example of a preprint server is the ‘arXiv’ developed by Paul Ginsparg in 1991, which is used primarily by physicists ( 19 ). These alternative forms of peer review are still un-established and experimental. Traditional peer review is time-tested and still highly utilized. All methods of peer review have their advantages and deficiencies, and all are prone to error.

PEER REVIEW OF OPEN ACCESS JOURNALS

Open access (OA) journals are becoming increasingly popular as they allow the potential for widespread distribution of publications in a timely manner ( 20 ). Nevertheless, there can be issues regarding the peer review process of open access journals. In a study published in Science in 2013, John Bohannon submitted 304 slightly different versions of a fictional scientific paper (written by a fake author, working out of a non-existent institution) to a selected group of OA journals. This study was performed in order to determine whether papers submitted to OA journals are properly reviewed before publication in comparison to subscription-based journals. The journals in this study were selected from the Directory of Open Access Journals (DOAJ) and Biall’s List, a list of journals which are potentially predatory, and all required a fee for publishing ( 21 ). Of the 304 journals, 157 accepted a fake paper, suggesting that acceptance was based on financial interest rather than the quality of article itself, while 98 journals promptly rejected the fakes ( 21 ). Although this study highlights useful information on the problems associated with lower quality publishers that do not have an effective peer review system in place, the article also generalizes the study results to all OA journals, which can be detrimental to the general perception of OA journals. There were two limitations of the study that made it impossible to accurately determine the relationship between peer review and OA journals: 1) there was no control group (subscription-based journals), and 2) the fake papers were sent to a non-randomized selection of journals, resulting in bias.

JOURNAL ACCEPTANCE RATES

Based on a recent survey, the average acceptance rate for papers submitted to scientific journals is about 50% ( 7 ). Twenty percent of the submitted manuscripts that are not accepted are rejected prior to review, and 30% are rejected following review ( 7 ). Of the 50% accepted, 41% are accepted with the condition of revision, while only 9% are accepted without the request for revision ( 7 ).

SATISFACTION WITH THE PEER REVIEW SYSTEM

Based on a recent survey by the PRC, 64% of academics are satisfied with the current system of peer review, and only 12% claimed to be ‘dissatisfied’ ( 7 ). The large majority, 85%, agreed with the statement that ‘scientific communication is greatly helped by peer review’ ( 7 ). There was a similarly high level of support (83%) for the idea that peer review ‘provides control in scientific communication’ ( 7 ).

HOW TO PEER REVIEW EFFECTIVELY

The following are ten tips on how to be an effective peer reviewer as indicated by Brian Lucey, an expert on the subject ( 22 ):

1) Be professional

Peer review is a mutual responsibility among fellow scientists, and scientists are expected, as part of the academic community, to take part in peer review. If one is to expect others to review their work, they should commit to reviewing the work of others as well, and put effort into it.

2) Be pleasant

If the paper is of low quality, suggest that it be rejected, but do not leave ad hominem comments. There is no benefit to being ruthless.

3) Read the invite

When emailing a scientist to ask them to conduct a peer review, the majority of journals will provide a link to either accept or reject. Do not respond to the email, respond to the link.

4) Be helpful

Suggest how the authors can overcome the shortcomings in their paper. A review should guide the author on what is good and what needs work from the reviewer’s perspective.

5) Be scientific

The peer reviewer plays the role of a scientific peer, not an editor for proofreading or decision-making. Don’t fill a review with comments on editorial and typographic issues. Instead, focus on adding value with scientific knowledge and commenting on the credibility of the research conducted and conclusions drawn. If the paper has a lot of typographical errors, suggest that it be professionally proof edited as part of the review.

6) Be timely

Stick to the timeline given when conducting a peer review. Editors track who is reviewing what and when and will know if someone is late on completing a review. It is important to be timely both out of respect for the journal and the author, as well as to not develop a reputation of being late for review deadlines.

7) Be realistic

The peer reviewer must be realistic about the work presented, the changes they suggest and their role. Peer reviewers may set the bar too high for the paper they are editing by proposing changes that are too ambitious and editors must override them.

8) Be empathetic

Ensure that the review is scientific, helpful and courteous. Be sensitive and respectful with word choice and tone in a review.

Remember that both specialists and generalists can provide valuable insight when peer reviewing. Editors will try to get both specialised and general reviewers for any particular paper to allow for different perspectives. If someone is asked to review, the editor has determined they have a valid and useful role to play, even if the paper is not in their area of expertise.

10) Be organised

A review requires structure and logical flow. A reviewer should proofread their review before submitting it for structural, grammatical and spelling errors as well as for clarity. Most publishers provide short guides on structuring a peer review on their website. Begin with an overview of the proposed improvements; then provide feedback on the paper structure, the quality of data sources and methods of investigation used, the logical flow of argument, and the validity of conclusions drawn. Then provide feedback on style, voice and lexical concerns, with suggestions on how to improve.

In addition, the American Physiology Society (APS) recommends in its Peer Review 101 Handout that peer reviewers should put themselves in both the editor’s and author’s shoes to ensure that they provide what both the editor and the author need and expect ( 11 ). To please the editor, the reviewer should ensure that the peer review is completed on time, and that it provides clear explanations to back up recommendations. To be helpful to the author, the reviewer must ensure that their feedback is constructive. It is suggested that the reviewer take time to think about the paper; they should read it once, wait at least a day, and then re-read it before writing the review ( 11 ). The APS also suggests that Graduate students and researchers pay attention to how peer reviewers edit their work, as well as to what edits they find helpful, in order to learn how to peer review effectively ( 11 ). Additionally, it is suggested that Graduate students practice reviewing by editing their peers’ papers and asking a faculty member for feedback on their efforts. It is recommended that young scientists offer to peer review as often as possible in order to become skilled at the process ( 11 ). The majority of students, fellows and trainees do not get formal training in peer review, but rather learn by observing their mentors. According to the APS, one acquires experience through networking and referrals, and should therefore try to strengthen relationships with journal editors by offering to review manuscripts ( 11 ). The APS also suggests that experienced reviewers provide constructive feedback to students and junior colleagues on their peer review efforts, and encourages them to peer review to demonstrate the importance of this process in improving science ( 11 ).

The peer reviewer should only comment on areas of the manuscript that they are knowledgeable about ( 23 ). If there is any section of the manuscript they feel they are not qualified to review, they should mention this in their comments and not provide further feedback on that section. The peer reviewer is not permitted to share any part of the manuscript with a colleague (even if they may be more knowledgeable in the subject matter) without first obtaining permission from the editor ( 23 ). If a peer reviewer comes across something they are unsure of in the paper, they can consult the literature to try and gain insight. It is important for scientists to remember that if a paper can be improved by the expertise of one of their colleagues, the journal must be informed of the colleague’s help, and approval must be obtained for their colleague to read the protected document. Additionally, the colleague must be identified in the confidential comments to the editor, in order to ensure that he/she is appropriately credited for any contributions ( 23 ). It is the job of the reviewer to make sure that the colleague assisting is aware of the confidentiality of the peer review process ( 23 ). Once the review is complete, the manuscript must be destroyed and cannot be saved electronically by the reviewers ( 23 ).

COMMON ERRORS IN SCIENTIFIC PAPERS

When performing a peer review, there are some common scientific errors to look out for. Most of these errors are violations of logic and common sense: these may include contradicting statements, unwarranted conclusions, suggestion of causation when there is only support for correlation, inappropriate extrapolation, circular reasoning, or pursuit of a trivial question ( 24 ). It is also common for authors to suggest that two variables are different because the effects of one variable are statistically significant while the effects of the other variable are not, rather than directly comparing the two variables ( 24 ). Authors sometimes oversee a confounding variable and do not control for it, or forget to include important details on how their experiments were controlled or the physical state of the organisms studied ( 24 ). Another common fault is the author’s failure to define terms or use words with precision, as these practices can mislead readers ( 24 ). Jargon and/or misused terms can be a serious problem in papers. Inaccurate statements about specific citations are also a common occurrence ( 24 ). Additionally, many studies produce knowledge that can be applied to areas of science outside the scope of the original study, therefore it is better for reviewers to look at the novelty of the idea, conclusions, data, and methodology, rather than scrutinize whether or not the paper answered the specific question at hand ( 24 ). Although it is important to recognize these points, when performing a review it is generally better practice for the peer reviewer to not focus on a checklist of things that could be wrong, but rather carefully identify the problems specific to each paper and continuously ask themselves if anything is missing ( 24 ). An extremely detailed description of how to conduct peer review effectively is presented in the paper How I Review an Original Scientific Article written by Frederic G. Hoppin, Jr. It can be accessed through the American Physiological Society website under the Peer Review Resources section.

CRITICISM OF PEER REVIEW

A major criticism of peer review is that there is little evidence that the process actually works, that it is actually an effective screen for good quality scientific work, and that it actually improves the quality of scientific literature. As a 2002 study published in the Journal of the American Medical Association concluded, ‘Editorial peer review, although widely used, is largely untested and its effects are uncertain’ ( 25 ). Critics also argue that peer review is not effective at detecting errors. Highlighting this point, an experiment by Godlee et al. published in the British Medical Journal (BMJ) inserted eight deliberate errors into a paper that was nearly ready for publication, and then sent the paper to 420 potential reviewers ( 7 ). Of the 420 reviewers that received the paper, 221 (53%) responded, the average number of errors spotted by reviewers was two, no reviewer spotted more than five errors, and 35 reviewers (16%) did not spot any.

Another criticism of peer review is that the process is not conducted thoroughly by scientific conferences with the goal of obtaining large numbers of submitted papers. Such conferences often accept any paper sent in, regardless of its credibility or the prevalence of errors, because the more papers they accept, the more money they can make from author registration fees ( 26 ). This misconduct was exposed in 2014 by three MIT graduate students by the names of Jeremy Stribling, Dan Aguayo and Maxwell Krohn, who developed a simple computer program called SCIgen that generates nonsense papers and presents them as scientific papers ( 26 ). Subsequently, a nonsense SCIgen paper submitted to a conference was promptly accepted. Nature recently reported that French researcher Cyril Labbé discovered that sixteen SCIgen nonsense papers had been used by the German academic publisher Springer ( 26 ). Over 100 nonsense papers generated by SCIgen were published by the US Institute of Electrical and Electronic Engineers (IEEE) ( 26 ). Both organisations have been working to remove the papers. Labbé developed a program to detect SCIgen papers and has made it freely available to ensure publishers and conference organizers do not accept nonsense work in the future. It is available at this link: http://scigendetect.on.imag.fr/main.php ( 26 ).

Additionally, peer review is often criticized for being unable to accurately detect plagiarism. However, many believe that detecting plagiarism cannot practically be included as a component of peer review. As explained by Alice Tuff, development manager at Sense About Science, ‘The vast majority of authors and reviewers think peer review should detect plagiarism (81%) but only a minority (38%) think it is capable. The academic time involved in detecting plagiarism through peer review would cause the system to grind to a halt’ ( 27 ). Publishing house Elsevier began developing electronic plagiarism tools with the help of journal editors in 2009 to help improve this issue ( 27 ).

It has also been argued that peer review has lowered research quality by limiting creativity amongst researchers. Proponents of this view claim that peer review has repressed scientists from pursuing innovative research ideas and bold research questions that have the potential to make major advances and paradigm shifts in the field, as they believe that this work will likely be rejected by their peers upon review ( 28 ). Indeed, in some cases peer review may result in rejection of innovative research, as some studies may not seem particularly strong initially, yet may be capable of yielding very interesting and useful developments when examined under different circumstances, or in the light of new information ( 28 ). Scientists that do not believe in peer review argue that the process stifles the development of ingenious ideas, and thus the release of fresh knowledge and new developments into the scientific community.

Another issue that peer review is criticized for, is that there are a limited number of people that are competent to conduct peer review compared to the vast number of papers that need reviewing. An enormous number of papers published (1.3 million papers in 23,750 journals in 2006), but the number of competent peer reviewers available could not have reviewed them all ( 29 ). Thus, people who lack the required expertise to analyze the quality of a research paper are conducting reviews, and weak papers are being accepted as a result. It is now possible to publish any paper in an obscure journal that claims to be peer-reviewed, though the paper or journal itself could be substandard ( 29 ). On a similar note, the US National Library of Medicine indexes 39 journals that specialize in alternative medicine, and though they all identify themselves as “peer-reviewed”, they rarely publish any high quality research ( 29 ). This highlights the fact that peer review of more controversial or specialized work is typically performed by people who are interested and hold similar views or opinions as the author, which can cause bias in their review. For instance, a paper on homeopathy is likely to be reviewed by fellow practicing homeopaths, and thus is likely to be accepted as credible, though other scientists may find the paper to be nonsense ( 29 ). In some cases, papers are initially published, but their credibility is challenged at a later date and they are subsequently retracted. Retraction Watch is a website dedicated to revealing papers that have been retracted after publishing, potentially due to improper peer review ( 30 ).

Additionally, despite its many positive outcomes, peer review is also criticized for being a delay to the dissemination of new knowledge into the scientific community, and as an unpaid-activity that takes scientists’ time away from activities that they would otherwise prioritize, such as research and teaching, for which they are paid ( 31 ). As described by Eva Amsen, Outreach Director for F1000Research, peer review was originally developed as a means of helping editors choose which papers to publish when journals had to limit the number of papers they could print in one issue ( 32 ). However, nowadays most journals are available online, either exclusively or in addition to print, and many journals have very limited printing runs ( 32 ). Since there are no longer page limits to journals, any good work can and should be published. Consequently, being selective for the purpose of saving space in a journal is no longer a valid excuse that peer reviewers can use to reject a paper ( 32 ). However, some reviewers have used this excuse when they have personal ulterior motives, such as getting their own research published first.

RECENT INITIATIVES TOWARDS IMPROVING PEER REVIEW

F1000Research was launched in January 2013 by Faculty of 1000 as an open access journal that immediately publishes papers (after an initial check to ensure that the paper is in fact produced by a scientist and has not been plagiarised), and then conducts transparent post-publication peer review ( 32 ). F1000Research aims to prevent delays in new science reaching the academic community that are caused by prolonged publication times ( 32 ). It also aims to make peer reviewing more fair by eliminating any anonymity, which prevents reviewers from delaying the completion of a review so they can publish their own similar work first ( 32 ). F1000Research offers completely open peer review, where everything is published, including the name of the reviewers, their review reports, and the editorial decision letters ( 32 ).

PeerJ was founded by Jason Hoyt and Peter Binfield in June 2012 as an open access, peer reviewed scholarly journal for the Biological and Medical Sciences ( 33 ). PeerJ selects articles to publish based only on scientific and methodological soundness, not on subjective determinants of ‘impact ’, ‘novelty’ or ‘interest’ ( 34 ). It works on a “lifetime publishing plan” model which charges scientists for publishing plans that give them lifetime rights to publish with PeerJ, rather than charging them per publication ( 34 ). PeerJ also encourages open peer review, and authors are given the option to post the full peer review history of their submission with their published article ( 34 ). PeerJ also offers a pre-print review service called PeerJ Pre-prints, in which paper drafts are reviewed before being sent to PeerJ to publish ( 34 ).

Rubriq is an independent peer review service designed by Shashi Mudunuri and Keith Collier to improve the peer review system ( 35 ). Rubriq is intended to decrease redundancy in the peer review process so that the time lost in redundant reviewing can be put back into research ( 35 ). According to Keith Collier, over 15 million hours are lost each year to redundant peer review, as papers get rejected from one journal and are subsequently submitted to a less prestigious journal where they are reviewed again ( 35 ). Authors often have to submit their manuscript to multiple journals, and are often rejected multiple times before they find the right match. This process could take months or even years ( 35 ). Rubriq makes peer review portable in order to help authors choose the journal that is best suited for their manuscript from the beginning, thus reducing the time before their paper is published ( 35 ). Rubriq operates under an author-pay model, in which the author pays a fee and their manuscript undergoes double-blind peer review by three expert academic reviewers using a standardized scorecard ( 35 ). The majority of the author’s fee goes towards a reviewer honorarium ( 35 ). The papers are also screened for plagiarism using iThenticate ( 35 ). Once the manuscript has been reviewed by the three experts, the most appropriate journal for submission is determined based on the topic and quality of the paper ( 35 ). The paper is returned to the author in 1-2 weeks with the Rubriq Report ( 35 ). The author can then submit their paper to the suggested journal with the Rubriq Report attached. The Rubriq Report will give the journal editors a much stronger incentive to consider the paper as it shows that three experts have recommended the paper to them ( 35 ). Rubriq also has its benefits for reviewers; the Rubriq scorecard gives structure to the peer review process, and thus makes it consistent and efficient, which decreases time and stress for the reviewer. Reviewers also receive feedback on their reviews and most significantly, they are compensated for their time ( 35 ). Journals also benefit, as they receive pre-screened papers, reducing the number of papers sent to their own reviewers, which often end up rejected ( 35 ). This can reduce reviewer fatigue, and allow only higher-quality articles to be sent to their peer reviewers ( 35 ).

According to Eva Amsen, peer review and scientific publishing are moving in a new direction, in which all papers will be posted online, and a post-publication peer review will take place that is independent of specific journal criteria and solely focused on improving paper quality ( 32 ). Journals will then choose papers that they find relevant based on the peer reviews and publish those papers as a collection ( 32 ). In this process, peer review and individual journals are uncoupled ( 32 ). In Keith Collier’s opinion, post-publication peer review is likely to become more prevalent as a complement to pre-publication peer review, but not as a replacement ( 35 ). Post-publication peer review will not serve to identify errors and fraud but will provide an additional measurement of impact ( 35 ). Collier also believes that as journals and publishers consolidate into larger systems, there will be stronger potential for “cascading” and shared peer review ( 35 ).

CONCLUDING REMARKS

Peer review has become fundamental in assisting editors in selecting credible, high quality, novel and interesting research papers to publish in scientific journals and to ensure the correction of any errors or issues present in submitted papers. Though the peer review process still has some flaws and deficiencies, a more suitable screening method for scientific papers has not yet been proposed or developed. Researchers have begun and must continue to look for means of addressing the current issues with peer review to ensure that it is a full-proof system that ensures only quality research papers are released into the scientific community.

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Stanford Medicine study identifies distinct brain organization patterns in women and men

Stanford Medicine researchers have developed a powerful new artificial intelligence model that can distinguish between male and female brains.

February 20, 2024

sex differences in brain

'A key motivation for this study is that sex plays a crucial role in human brain development, in aging, and in the manifestation of psychiatric and neurological disorders,' said Vinod Menon. clelia-clelia

A new study by Stanford Medicine investigators unveils a new artificial intelligence model that was more than 90% successful at determining whether scans of brain activity came from a woman or a man.

The findings, published Feb. 20 in the Proceedings of the National Academy of Sciences, help resolve a long-term controversy about whether reliable sex differences exist in the human brain and suggest that understanding these differences may be critical to addressing neuropsychiatric conditions that affect women and men differently.

“A key motivation for this study is that sex plays a crucial role in human brain development, in aging, and in the manifestation of psychiatric and neurological disorders,” said Vinod Menon , PhD, professor of psychiatry and behavioral sciences and director of the Stanford Cognitive and Systems Neuroscience Laboratory . “Identifying consistent and replicable sex differences in the healthy adult brain is a critical step toward a deeper understanding of sex-specific vulnerabilities in psychiatric and neurological disorders.”

Menon is the study’s senior author. The lead authors are senior research scientist Srikanth Ryali , PhD, and academic staff researcher Yuan Zhang , PhD.

“Hotspots” that most helped the model distinguish male brains from female ones include the default mode network, a brain system that helps us process self-referential information, and the striatum and limbic network, which are involved in learning and how we respond to rewards.

The investigators noted that this work does not weigh in on whether sex-related differences arise early in life or may be driven by hormonal differences or the different societal circumstances that men and women may be more likely to encounter.

Uncovering brain differences

The extent to which a person’s sex affects how their brain is organized and operates has long been a point of dispute among scientists. While we know the sex chromosomes we are born with help determine the cocktail of hormones our brains are exposed to — particularly during early development, puberty and aging — researchers have long struggled to connect sex to concrete differences in the human brain. Brain structures tend to look much the same in men and women, and previous research examining how brain regions work together has also largely failed to turn up consistent brain indicators of sex.

test

Vinod Menon

In their current study, Menon and his team took advantage of recent advances in artificial intelligence, as well as access to multiple large datasets, to pursue a more powerful analysis than has previously been employed. First, they created a deep neural network model, which learns to classify brain imaging data: As the researchers showed brain scans to the model and told it that it was looking at a male or female brain, the model started to “notice” what subtle patterns could help it tell the difference.

This model demonstrated superior performance compared with those in previous studies, in part because it used a deep neural network that analyzes dynamic MRI scans. This approach captures the intricate interplay among different brain regions. When the researchers tested the model on around 1,500 brain scans, it could almost always tell if the scan came from a woman or a man.

The model’s success suggests that detectable sex differences do exist in the brain but just haven’t been picked up reliably before. The fact that it worked so well in different datasets, including brain scans from multiple sites in the U.S. and Europe, make the findings especially convincing as it controls for many confounds that can plague studies of this kind.

“This is a very strong piece of evidence that sex is a robust determinant of human brain organization,” Menon said.

Making predictions

Until recently, a model like the one Menon’s team employed would help researchers sort brains into different groups but wouldn’t provide information about how the sorting happened. Today, however, researchers have access to a tool called “explainable AI,” which can sift through vast amounts of data to explain how a model’s decisions are made.

Using explainable AI, Menon and his team identified the brain networks that were most important to the model’s judgment of whether a brain scan came from a man or a woman. They found the model was most often looking to the default mode network, striatum, and the limbic network to make the call.

The team then wondered if they could create another model that could predict how well participants would do on certain cognitive tasks based on functional brain features that differ between women and men. They developed sex-specific models of cognitive abilities: One model effectively predicted cognitive performance in men but not women, and another in women but not men. The findings indicate that functional brain characteristics varying between sexes have significant behavioral implications.

“These models worked really well because we successfully separated brain patterns between sexes,” Menon said. “That tells me that overlooking sex differences in brain organization could lead us to miss key factors underlying neuropsychiatric disorders.”

While the team applied their deep neural network model to questions about sex differences, Menon says the model can be applied to answer questions regarding how just about any aspect of brain connectivity might relate to any kind of cognitive ability or behavior. He and his team plan to make their model publicly available for any researcher to use.

“Our AI models have very broad applicability,” Menon said. “A researcher could use our models to look for brain differences linked to learning impairments or social functioning differences, for instance — aspects we are keen to understand better to aid individuals in adapting to and surmounting these challenges.”

The research was sponsored by the National Institutes of Health (grants MH084164, EB022907, MH121069, K25HD074652 and AG072114), the Transdisciplinary Initiative, the Uytengsu-Hamilton 22q11 Programs, the Stanford Maternal and Child Health Research Institute, and the NARSAD Young Investigator Award.

About Stanford Medicine

Stanford Medicine is an integrated academic health system comprising the Stanford School of Medicine and adult and pediatric health care delivery systems. Together, they harness the full potential of biomedicine through collaborative research, education and clinical care for patients. For more information, please visit med.stanford.edu .

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A Columbia Surgeon’s Study Was Pulled. He Kept Publishing Flawed Data.

The quiet withdrawal of a 2021 cancer study by Dr. Sam Yoon highlights scientific publishers’ lack of transparency around data problems.

Supported by

Benjamin Mueller

By Benjamin Mueller

Benjamin Mueller covers medical science and has reported on several research scandals.

  • Feb. 15, 2024

The stomach cancer study was shot through with suspicious data. Identical constellations of cells were said to depict separate experiments on wholly different biological lineages. Photos of tumor-stricken mice, used to show that a drug reduced cancer growth, had been featured in two previous papers describing other treatments.

Problems with the study were severe enough that its publisher, after finding that the paper violated ethics guidelines, formally withdrew it within a few months of its publication in 2021. The study was then wiped from the internet, leaving behind a barren web page that said nothing about the reasons for its removal.

As it turned out, the flawed study was part of a pattern. Since 2008, two of its authors — Dr. Sam S. Yoon, chief of a cancer surgery division at Columbia University’s medical center, and a more junior cancer biologist — have collaborated with a rotating cast of researchers on a combined 26 articles that a British scientific sleuth has publicly flagged for containing suspect data. A medical journal retracted one of them this month after inquiries from The New York Times.

A person walks across a covered walkway connecting two buildings over a road with parked cars. A large, blue sign on the walkway says "Columbia University Irving Medical Center."

Memorial Sloan Kettering Cancer Center, where Dr. Yoon worked when much of the research was done, is now investigating the studies. Columbia’s medical center declined to comment on specific allegations, saying only that it reviews “any concerns about scientific integrity brought to our attention.”

Dr. Yoon, who has said his research could lead to better cancer treatments , did not answer repeated questions. Attempts to speak to the other researcher, Changhwan Yoon, an associate research scientist at Columbia, were also unsuccessful.

The allegations were aired in recent months in online comments on a science forum and in a blog post by Sholto David, an independent molecular biologist. He has ferreted out problems in a raft of high-profile cancer research , including dozens of papers at a Harvard cancer center that were subsequently referred for retractions or corrections.

From his flat in Wales , Dr. David pores over published images of cells, tumors and mice in his spare time and then reports slip-ups, trying to close the gap between people’s regard for academic research and the sometimes shoddier realities of the profession.

When evaluating scientific images, it is difficult to distinguish sloppy copy-and-paste errors from deliberate doctoring of data. Two other imaging experts who reviewed the allegations at the request of The Times said some of the discrepancies identified by Dr. David bore signs of manipulation, like flipped, rotated or seemingly digitally altered images.

Armed with A.I.-powered detection tools, scientists and bloggers have recently exposed a growing body of such questionable research, like the faulty papers at Harvard’s Dana-Farber Cancer Institute and studies by Stanford’s president that led to his resignation last year.

But those high-profile cases were merely the tip of the iceberg, experts said. A deeper pool of unreliable research has gone unaddressed for years, shielded in part by powerful scientific publishers driven to put out huge volumes of studies while avoiding the reputational damage of retracting them publicly.

The quiet removal of the 2021 stomach cancer study from Dr. Yoon’s lab, a copy of which was reviewed by The Times, illustrates how that system of scientific publishing has helped enable faulty research, experts said. In some cases, critical medical fields have remained seeded with erroneous studies.

“The journals do the bare minimum,” said Elisabeth Bik, a microbiologist and image expert who described Dr. Yoon’s papers as showing a worrisome pattern of copied or doctored data. “There’s no oversight.”

Memorial Sloan Kettering, where portions of the stomach cancer research were done, said no one — not the journal nor the researchers — had ever told administrators that the paper was withdrawn or why it had been. The study said it was supported in part by federal funding given to the cancer center.

Dr. Yoon, a stomach cancer specialist and a proponent of robotic surgery, kept climbing the academic ranks, bringing his junior researcher along with him. In September 2021, around the time the study was published, he joined Columbia, which celebrated his prolific research output in a news release . His work was financed in part by half a million dollars in federal research money that year, adding to a career haul of nearly $5 million in federal funds.

The decision by the stomach cancer study’s publisher, Elsevier, not to post an explanation for the paper’s removal made it less likely that the episode would draw public attention or affect the duo’s work. That very study continued to be cited in papers by other scientists .

And as recently as last year, Dr. Yoon’s lab published more studies containing identical images that were said to depict separate experiments, according to Dr. David’s analyses.

The researchers’ suspicious publications stretch back 16 years. Over time, relatively minor image copies in papers by Dr. Yoon gave way to more serious discrepancies in studies he collaborated on with Changhwan Yoon, Dr. David said. The pair, who are not related, began publishing articles together around 2013.

But neither their employers nor their publishers seemed to start investigating their work until this past fall, when Dr. David published his initial findings on For Better Science, a blog, and notified Memorial Sloan Kettering, Columbia and the journals. Memorial Sloan Kettering said it began its investigation then.

None of those flagged studies was retracted until last week. Three days after The Times asked publishers about the allegations, the journal Oncotarget retracted a 2016 study on combating certain pernicious cancers. In a retraction notice , the journal said the authors’ explanations for copied images “were deemed unacceptable.”

The belated action was symptomatic of what experts described as a broken system for policing scientific research.

A proliferation of medical journals, they said, has helped fuel demand for ever more research articles. But those same journals, many of them operated by multibillion-dollar publishing companies, often respond slowly or do nothing at all once one of those articles is shown to contain copied data. Journals retract papers at a fraction of the rate at which they publish ones with problems.

Springer Nature, which published nine of the articles that Dr. David said contained discrepancies across five journals, said it was investigating concerns. So did the American Association for Cancer Research, which published 10 articles under question from Dr. Yoon’s lab across four journals.

It is difficult to know who is responsible for errors in articles. Eleven of the scientists’ co-authors, including researchers at Harvard, Duke and Georgetown, did not answer emailed inquiries.

The articles under question examined why certain stomach and soft-tissue cancers withstood treatment, and how that resistance could be overcome.

The two independent image specialists said the volume of copied data, along with signs that some images had been rotated or similarly manipulated, suggested considerable sloppiness or worse.

“There are examples in this set that raise pretty serious red flags for the possibility of misconduct,” said Dr. Matthew Schrag, a Vanderbilt University neurologist who commented as part of his outside work on research integrity.

One set of 10 articles identified by Dr. David showed repeated reuse of identical or overlapping black-and-white images of cancer cells supposedly under different experimental conditions, he said.

“There’s no reason to have done that unless you weren’t doing the work,” Dr. David said.

One of those papers , published in 2012, was formally tagged with corrections. Unlike later studies, which were largely overseen by Dr. Yoon in New York, this paper was written by South Korea-based scientists, including Changhwan Yoon, who then worked in Seoul.

An immunologist in Norway randomly selected the paper as part of a screening of copied data in cancer journals. That led the paper’s publisher, the medical journal Oncogene, to add corrections in 2016.

But the journal did not catch all of the duplicated data , Dr. David said. And, he said, images from the study later turned up in identical form in another paper that remains uncorrected.

Copied cancer data kept recurring, Dr. David said. A picture of a small red tumor from a 2017 study reappeared in papers in 2020 and 2021 under different descriptions, he said. A ruler included in the pictures for scale wound up in two different positions.

The 2020 study included another tumor image that Dr. David said appeared to be a mirror image of one previously published by Dr. Yoon’s lab. And the 2021 study featured a color version of a tumor that had appeared in an earlier paper atop a different section of ruler, Dr. David said.

“This is another example where this looks intentionally done,” Dr. Bik said.

The researchers were faced with more serious action when the publisher Elsevier withdrew the stomach cancer study that had been published online in 2021. “The editors determined that the article violated journal publishing ethics guidelines,” Elsevier said.

Roland Herzog, the editor of Molecular Therapy, the journal where the article appeared, said that “image duplications were noticed” as part of a process of screening for discrepancies that the journal has since continued to beef up.

Because the problems were detected before the study was ever published in the print journal, Elsevier’s policy dictated that the article be taken down and no explanation posted online.

But that decision appeared to conflict with industry guidelines from the Committee on Publication Ethics . Posting articles online “usually constitutes publication,” those guidelines state. And when publishers pull such articles, the guidelines say, they should keep the work online for the sake of transparency and post “a clear notice of retraction.”

Dr. Herzog said he personally hoped that such an explanation could still be posted for the stomach cancer study. The journal editors and Elsevier, he said, are examining possible options.

The editors notified Dr. Yoon and Changhwan Yoon of the article’s removal, but neither scientist alerted Memorial Sloan Kettering, the hospital said. Columbia did not say whether it had been told.

Experts said the handling of the article was symptomatic of a tendency on the part of scientific publishers to obscure reports of lapses .

“This is typical, sweeping-things-under-the-rug kind of nonsense,” said Dr. Ivan Oransky, co-founder of Retraction Watch, which keeps a database of 47,000-plus retracted papers. “This is not good for the scientific record, to put it mildly.”

Susan C. Beachy contributed research.

Benjamin Mueller reports on health and medicine. He was previously a U.K. correspondent in London and a police reporter in New York. More about Benjamin Mueller

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February 19, 2024 report

This article has been reviewed according to Science X's editorial process and policies . Editors have highlighted the following attributes while ensuring the content's credibility:

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AI-generated disproportioned rat genitalia makes its way into peer-reviewed journal

by Bob Yirka , Phys.org

rat anatomy

The editors at the journal Frontiers in Cell and Developmental Biology have retracted a paper after it was pointed out to them by readers that supporting images had been generated improperly by an AI image generator. In their retraction, the editors report that the reason for the retraction was that "concerns were raised regarding the nature of its AI-generated figures."

In the article, which involved research surrounding stem cells in small mammals , the authors included images depicting rat anatomy that an AI system had clearly created. In one picture, a single rat appeared to have a penis and testicles that were larger than the rest of its body—not something that occurs in nature. Some of the accompanying text was also incomprehensible. Another image showed a rat cell that did not resemble the true structure of a rat cell.

The disproportioned images in the paper are likely to add to ongoing discussions in the science community surrounding the use of AI in generating text or imagery for use in technical papers—particularly those published in established journals.

In this case, it is not clear how such problematic images wound up in a peer-reviewed journal. The authors, a combined team from Hong Hui Hospital and Jiaotong University in China, did not try to hide the fact that they had used AI to create the images ; they even credited Midjourney.

Some in the press have noted that Frontiers has a policy that allows for the use of AI-generated materials as long as their use is disclosed, which was the case in this instance. But the policy also notes that attempts must be made to fact-check anything produced by such systems, which clearly was not the case in this mix-up.

The editors at Frontiers initially posted a note on the paper claiming that the article had been corrected and that a new version would be published in short order. Not much later, the paper was retracted.

The mistakes made by the authors of the paper and the team at the journal that approved its publication are likely to be the first of many to come, though it is still not clear what changes will be required to prevent such mistakes from happening in the future.

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Collection  10 March 2022

Journal Top 100

This collection highlights our most downloaded* research papers published in 2021. Featuring authors from around the world, these papers highlight valuable research from an international community.

*Data obtained from SN Insights which is based on Digital Science’s Dimensions.

image of abstract blue network

A well-trained artificial neural network for predicting the rheological behavior of MWCNT–Al 2 O 3 (30–70%)/oil SAE40 hybrid nanofluid

  • Mohammad Hemmat Esfe
  • S. Ali Eftekhari
  • Davood Toghraie

research paper for scientific journal

More than 50 long-term effects of COVID-19: a systematic review and meta-analysis

  • Sandra Lopez-Leon
  • Talia Wegman-Ostrosky
  • Sonia Villapol

research paper for scientific journal

Adults who microdose psychedelics report health related motivations and lower levels of anxiety and depression compared to non-microdosers

  • Joseph M. Rootman
  • Pamela Kryskow

research paper for scientific journal

Detection of persistent SARS-CoV-2 IgG antibodies in oral mucosal fluid and upper respiratory tract specimens following COVID-19 mRNA vaccination

  • Aubree Mades
  • Prithivi Chellamathu
  • Albina Ibrayeva

Causes of death and comorbidities in hospitalized patients with COVID-19

  • Sefer Elezkurtaj
  • Selina Greuel
  • David Horst

research paper for scientific journal

5G as a wireless power grid

  • Jimmy G. D. Hester
  • Manos M. Tentzeris

research paper for scientific journal

Saliva is more sensitive than nasopharyngeal or nasal swabs for diagnosis of asymptomatic and mild COVID-19 infection

  • Alvin Kuo Jing Teo
  • Yukti Choudhury
  • Li Yang Hsu

research paper for scientific journal

Mathematical modelling of SARS-CoV-2 variant outbreaks reveals their probability of extinction

  • Henrik Schiøler
  • Torben Knudsen
  • Martin Bøgsted

research paper for scientific journal

Mapping the NFT revolution: market trends, trade networks, and visual features

  • Matthieu Nadini
  • Laura Alessandretti
  • Andrea Baronchelli

research paper for scientific journal

Overcooling of offices reveals gender inequity in thermal comfort

  • Thomas Parkinson
  • Stefano Schiavon
  • Gail Brager

research paper for scientific journal

Clinical course of COVID-19 patients needing supplemental oxygen outside the intensive care unit

  • Ayham Daher
  • Paul Balfanz
  • Christian G. Cornelissen

research paper for scientific journal

Positive effects of COVID-19 lockdown on air quality of industrial cities (Ankleshwar and Vapi) of Western India

  • Ritwik Nigam
  • Kanvi Pandya
  • Mahender Kotha

Proportion of people identified as transgender and non-binary gender in Brazil

  • Giancarlo Spizzirri
  • Raí Eufrásio
  • Carmita Helena Najjar Abdo

research paper for scientific journal

Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals

  • Swapnil Mahajan
  • Vasumathi Kode
  • Amitabha Chaudhuri

research paper for scientific journal

Positive expectations predict improved mental-health outcomes linked to psychedelic microdosing

  • L. S. Kaertner
  • M. B. Steinborn
  • R. L. Carhart-Harris

research paper for scientific journal

Effect of vitamin D on cognitive decline: results from two ancillary studies of the VITAL randomized trial

  • Jae H. Kang
  • Chirag M. Vyas
  • JoAnn E. Manson

research paper for scientific journal

Low HDL and high triglycerides predict COVID-19 severity

  • Lluís Masana
  • Eudald Correig
  • the STACOV-XULA research group

research paper for scientific journal

Shorter headed dogs, visually cooperative breeds, younger and playful dogs form eye contact faster with an unfamiliar human

  • Zsófia Bognár
  • Enikő Kubinyi

research paper for scientific journal

Cannabis compounds exhibit anti-inflammatory activity in vitro in COVID-19-related inflammation in lung epithelial cells and pro-inflammatory activity in macrophages

  • Seegehalli M. Anil
  • Nurit Shalev
  • Hinanit Koltai

research paper for scientific journal

The first true millipede—1306 legs long

  • Paul E. Marek
  • Bruno A. Buzatto
  • Juanita Rodriguez

research paper for scientific journal

The poor prognosis and influencing factors of high D-dimer levels for COVID-19 patients

  • Xiaokang He
  • Qingming Wu

research paper for scientific journal

Pruritus is common in patients with chronic liver disease and is improved by nalfurafine hydrochloride

  • Shuhei Yoshikawa
  • Takeharu Asano
  • Hirosato Mashima

research paper for scientific journal

Lethal coalitionary attacks of chimpanzees ( Pan troglodytes troglodytes ) on gorillas ( Gorilla gorilla gorilla ) in the wild

  • Lara M. Southern
  • Tobias Deschner
  • Simone Pika

research paper for scientific journal

Secondary bacterial infection in COVID-19 patients is a stronger predictor for death compared to influenza patients

  • Noa Shafran
  • Inbal Shafran
  • Ella H. Sklan

research paper for scientific journal

SARS-CoV-2 virus transfers to skin through contact with contaminated solids

  • Saeed Behzadinasab
  • Alex W. H. Chin
  • William A. Ducker

research paper for scientific journal

The in-vitro effect of famotidine on SARS-CoV-2 proteases and virus replication

  • Madeline Loffredo
  • Hector Lucero
  • Ali H. Munawar

Ferritin is associated with the severity of lung involvement but not with worse prognosis in patients with COVID-19: data from two Italian COVID-19 units

  • Francesco Carubbi
  • Lia Salvati
  • Davide Grassi

research paper for scientific journal

Outcomes of COVID-19 patients intubated after failure of non-invasive ventilation: a multicenter observational study

  • Annalisa Boscolo
  • Laura Pasin
  • FERS, for the COVID-19 VENETO ICU Network

research paper for scientific journal

The consequences of COVID-19 on social interactions: an online study on face covering

  • Marta Calbi
  • Nunzio Langiulli
  • Maria Alessandra Umiltà

research paper for scientific journal

Dogs distinguish human intentional and unintentional action

  • Britta Schünemann
  • Judith Keller
  • Juliane Bräuer

research paper for scientific journal

Positive Epstein–Barr virus detection in coronavirus disease 2019 (COVID-19) patients

  • Changzheng Chen

research paper for scientific journal

Alarming coastal vulnerability of the deltaic and sandy beaches of North Africa

  • Abderraouf Hzami
  • Essam Heggy
  • Saâdi Abdeljaouad

research paper for scientific journal

Defining priority areas for blue whale conservation and investigating overlap with vessel traffic in Chilean Patagonia, using a fast-fitting movement model

  • Luis Bedriñana-Romano
  • Rodrigo Hucke-Gaete
  • Daniel M. Palacios

research paper for scientific journal

Observation of rescue behaviour in wild boar ( Sus scrofa )

  • Michaela Masilkova
  • Miloš Ježek
  • Hynek Burda

research paper for scientific journal

Time course of the sensitivity and specificity of anti-SARS-CoV-2 IgM and IgG antibodies for symptomatic COVID-19 in Japan

  • Yuki Nakano
  • Makoto Kurano
  • Yutaka Yatomi

research paper for scientific journal

Multidisciplinary assessment of the Abbott BinaxNOW SARS-CoV-2 point-of-care antigen test in the context of emerging viral variants and self-administration

  • Jennifer K. Frediani
  • Joshua M. Levy
  • Wilbur A. Lam

research paper for scientific journal

Regular intake of energy drinks and multivitamin supplements is associated with elevated plasma vitamin B6 levels in post-bariatric patients

  • Martina Tynes
  • Matthias Hepprich
  • Katharina Timper

research paper for scientific journal

Aggressive behaviour is affected by demographic, environmental and behavioural factors in purebred dogs

  • Salla Mikkola
  • Milla Salonen
  • Hannes Lohi

research paper for scientific journal

In vitro efficacy of artemisinin-based treatments against SARS-CoV-2

  • Yuyong Zhou
  • Kerry Gilmore
  • Peter H. Seeberger

research paper for scientific journal

Anthropogenic drought dominates groundwater depletion in Iran

  • Samaneh Ashraf
  • Amir AghaKouchak

research paper for scientific journal

COVID-19 vaccines that reduce symptoms but do not block infection need higher coverage and faster rollout to achieve population impact

  • David A. Swan
  • Chloe Bracis
  • Dobromir Dimitrov

research paper for scientific journal

A metabolomics comparison of plant-based meat and grass-fed meat indicates large nutritional differences despite comparable Nutrition Facts panels

  • Stephan van Vliet
  • James R. Bain
  • Kim M. Huffman

research paper for scientific journal

Detection of volcanic unrest onset in La Palma, Canary Islands, evolution and implications

  • José Fernández
  • Joaquín Escayo
  • Eumenio Ancochea

research paper for scientific journal

Internet memes related to the COVID-19 pandemic as a potential coping mechanism for anxiety

  • Umair Akram
  • Kamila Irvine
  • Jennifer Drabble

research paper for scientific journal

A molecular test based on RT-LAMP for rapid, sensitive and inexpensive colorimetric detection of SARS-CoV-2 in clinical samples

  • Catarina Amaral
  • Wilson Antunes
  • Catarina Pimentel

research paper for scientific journal

Country-level factors dynamics and ABO/Rh blood groups contribution to COVID-19 mortality

  • Alfonso Monaco
  • Ester Pantaleo
  • Roberto Bellotti

research paper for scientific journal

Musical components important for the Mozart K448 effect in epilepsy

  • Robert J. Quon
  • Michael A. Casey
  • Barbara C. Jobst

research paper for scientific journal

Investigation of diets associated with dilated cardiomyopathy in dogs using foodomics analysis

  • Caren E. Smith
  • Laurence D. Parnell
  • Lisa M. Freeman

research paper for scientific journal

Earliest evidence of herd-living and age segregation amongst dinosaurs

  • Adriana C. Mancuso
  • Vincent Fernandez

research paper for scientific journal

Canadian undergraduate men’s visual attention to cisgender women, cisgender men, and feminine trans individuals

  • Lanna J. Petterson
  • Paul L. Vasey

research paper for scientific journal

Brain structure changes associated with sexual orientation

  • Mikhail Votinov
  • Katharina S. Goerlich

research paper for scientific journal

Extreme miniaturization of a new amniote vertebrate and insights into the evolution of genital size in chameleons

  • Jörn Köhler
  • Miguel Vences

COVID-19 vaccine acceptance among adults in four major US metropolitan areas and nationwide

  • Ayman El-Mohandes
  • Trenton M. White
  • Jeffrey V. Lazarus

research paper for scientific journal

Weeklong improved colour contrasts sensitivity after single 670 nm exposures associated with enhanced mitochondrial function

  • Harpreet Shinhmar
  • Glen Jeffery

research paper for scientific journal

Modeling the effect of lockdown timing as a COVID-19 control measure in countries with differing social contacts

  • Tamer Oraby
  • Michael G. Tyshenko
  • Mustafa Al-Zoughool

research paper for scientific journal

Identification of CRF89_BF, a new member of an HIV-1 circulating BF intersubtype recombinant form family widely spread in South America

  • Elena Delgado
  • Aurora Fernández-García
  • Michael M. Thomson

research paper for scientific journal

Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain

  • Fabien Dachet
  • James B. Brown
  • Jeffrey A. Loeb

research paper for scientific journal

Effects of cannabis on visual function and self-perceived visual quality

  • Sonia Ortiz-Peregrina
  • Carolina Ortiz
  • Rosario G. Anera

research paper for scientific journal

Particulate matter (PM 2.5 ) as a potential SARS-CoV-2 carrier

  • Norefrina Shafinaz Md Nor
  • Chee Wai Yip
  • Mohd Shahrul Mohd Nadzir

research paper for scientific journal

The effect of ABO blood group and antibody class on the risk of COVID-19 infection and severity of clinical outcomes

  • Marwa Ali Almadhi
  • Abdulkarim Abdulrahman
  • Manaf AlQahtani

research paper for scientific journal

A retrospective cohort study of 12,306 pediatric COVID-19 patients in the United States

  • Vibhu Parcha
  • Katherine S. Booker
  • Pankaj Arora

research paper for scientific journal

Climate and the spread of COVID-19

  • Simiao Chen
  • Klaus Prettner
  • David E. Bloom

research paper for scientific journal

Examining the interplay between face mask usage, asymptomatic transmission, and social distancing on the spread of COVID-19

  • Adam Catching
  • Sara Capponi
  • Raul Andino

research paper for scientific journal

Association between coffee and green tea intake and pneumonia among the Japanese elderly: a case-control study

  • Kyoko Kondo
  • Kanzo Suzuki
  • The Pneumonia in Elderly People Study Group

research paper for scientific journal

Discovery of a new mammal species (Soricidae: Eulipotyphla) from Narcondam volcanic island, India

  • Manokaran Kamalakannan
  • Chandrakasan Sivaperuman
  • Kailash Chandra

research paper for scientific journal

Role of IgG against N-protein of SARS-CoV2 in COVID19 clinical outcomes

  • Mayank Batra
  • Runxia Tian
  • Mehdi Mirsaeidi

research paper for scientific journal

Menopause impacts human brain structure, connectivity, energy metabolism, and amyloid-beta deposition

  • Lisa Mosconi
  • Valentina Berti
  • Roberta Diaz Brinton

research paper for scientific journal

Ivermectin reduces in vivo coronavirus infection in a mouse experimental model

  • A. P. Arévalo

research paper for scientific journal

Excess protein enabled dog domestication during severe Ice Age winters

  • Maria Lahtinen
  • David Clinnick
  • Suvi Viranta

research paper for scientific journal

Psychedelics alter metaphysical beliefs

  • Christopher Timmermann
  • Hannes Kettner
  • Robin L. Carhart-Harris

research paper for scientific journal

Real world evidence of calcifediol or vitamin D prescription and mortality rate of COVID-19 in a retrospective cohort of hospitalized Andalusian patients

  • Carlos Loucera
  • María Peña-Chilet
  • Jose Manuel Quesada Gomez

research paper for scientific journal

Exercise improves the quality of slow-wave sleep by increasing slow-wave stability

  • Insung Park
  • Javier Díaz
  • Kaspar E. Vogt

research paper for scientific journal

Gradual onset of the Maunder Minimum revealed by high-precision carbon-14 analyses

  • Hiroko Miyahara
  • Fuyuki Tokanai
  • Hideyuki Hotta

research paper for scientific journal

Results of an early second PCR test performed on SARS-CoV-2 positive patients may support risk assessment for severe COVID-19

  • Barak Mizrahi
  • Maytal Bivas-Benita
  • Gabriel Chodick

research paper for scientific journal

Satellite mega-constellations create risks in Low Earth Orbit, the atmosphere and on Earth

  • Aaron C. Boley
  • Michael Byers

research paper for scientific journal

Influenza vaccination and the risk of COVID-19 infection and severe illness in older adults in the United States

  • Kelly Huang
  • Shu-Wen Lin
  • Chi-Chuan Wang

research paper for scientific journal

New spinosaurids from the Wessex Formation (Early Cretaceous, UK) and the European origins of Spinosauridae

  • Chris T. Barker
  • David W. E. Hone
  • Neil J. Gostling

research paper for scientific journal

Expansion and characterization of epithelial stem cells with potential for cyclical hair regeneration

  • Makoto Takeo
  • Kyosuke Asakawa
  • Takashi Tsuji

research paper for scientific journal

Durability of antibody response to vaccination and surrogate neutralization of emerging variants based on SARS-CoV-2 exposure history

  • Thomas W. McDade
  • Alexis R. Demonbreun
  • Elizabeth M. McNally

research paper for scientific journal

Multiwave pandemic dynamics explained: how to tame the next wave of infectious diseases

  • Giacomo Cacciapaglia
  • Corentin Cot
  • Francesco Sannino

research paper for scientific journal

An international comparison of age and sex dependency of COVID-19 deaths in 2020: a descriptive analysis

  • Peter Bauer
  • Jonas Brugger
  • Martin Posch

research paper for scientific journal

Organic matter and water from asteroid Itokawa

  • Q. H. S. Chan
  • A. Stephant
  • M. M. Grady

research paper for scientific journal

Origin and evolutionary history of domestic chickens inferred from a large population study of Thai red junglefowl and indigenous chickens

  • Mitsuo Nunome
  • Kornsorn Srikulnath

research paper for scientific journal

COVID-19 diagnosis by routine blood tests using machine learning

  • Matjaž Kukar
  • Gregor Gunčar
  • Marko Notar

research paper for scientific journal

The serotonin reuptake inhibitor Fluoxetine inhibits SARS-CoV-2 in human lung tissue

  • Melissa Zimniak
  • Luisa Kirschner
  • Jochen Bodem

research paper for scientific journal

Long-term stress in dogs is related to the human–dog relationship and personality traits

  • Amanda Höglin
  • Enya Van Poucke
  • Lina S. V. Roth

research paper for scientific journal

Correlation between CT findings and outcomes in 46 patients with coronavirus disease 2019

  • Guangming Li
  • Guihua Jiang

research paper for scientific journal

Inhibition of mitochondrial function by metformin increases glucose uptake, glycolysis and GDF-15 release from intestinal cells

  • Tamana Darwish
  • Fiona M. Gribble

research paper for scientific journal

Global prevalence of mental health issues among the general population during the coronavirus disease-2019 pandemic: a systematic review and meta-analysis

  • Surapon Nochaiwong
  • Chidchanok Ruengorn
  • Tinakon Wongpakaran

research paper for scientific journal

Probenecid inhibits SARS-CoV-2 replication in vivo and in vitro

  • Jackelyn Murray
  • Robert J. Hogan
  • Ralph A. Tripp

research paper for scientific journal

UV-C irradiation is highly effective in inactivating SARS-CoV-2 replication

  • Mara Biasin
  • Andrea Bianco
  • Mario Clerici

research paper for scientific journal

The 20-million-year old lair of an ambush-predatory worm preserved in northeast Taiwan

  • Masakazu Nara
  • Shahin E. Dashtgard

research paper for scientific journal

Age constraints for the Trachilos footprints from Crete

  • Uwe Kirscher
  • Haytham El Atfy
  • Madelaine Böhme

research paper for scientific journal

Divergent reflections around the photon sphere of a black hole

  • Albert Sneppen

research paper for scientific journal

The impact of the COVID-19 pandemic on wellbeing and cognitive functioning of older adults

  • Sarah De Pue
  • Céline Gillebert
  • Eva Van den Bussche

research paper for scientific journal

Origin and diffusion of human Y chromosome haplogroup J1-M267

  • Hovhannes Sahakyan
  • Ashot Margaryan
  • Richard Villems

The association of dietary patterns with dietary inflammatory index, systemic inflammation, and insulin resistance, in apparently healthy individuals with obesity

  • Maryam Saghafi-Asl
  • Susan Mirmajidi
  • Vahideh Ebrahimzadeh Attari

research paper for scientific journal

Developing and validating COVID-19 adverse outcome risk prediction models from a bi-national European cohort of 5594 patients

  • Espen Jimenez-Solem
  • Tonny S. Petersen
  • Martin Sillesen

research paper for scientific journal

COVID-19 in South Africa: outbreak despite interventions

  • Malte Schröder
  • Andreas Bossert
  • Jan Schlüter

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Reproductive rights in America

Research at the heart of a federal case against the abortion pill has been retracted.

Selena Simmons-Duffin

Selena Simmons-Duffin

research paper for scientific journal

The Supreme Court will hear the case against the abortion pill mifepristone on March 26. It's part of a two-drug regimen with misoprostol for abortions in the first 10 weeks of pregnancy. Anna Moneymaker/Getty Images hide caption

The Supreme Court will hear the case against the abortion pill mifepristone on March 26. It's part of a two-drug regimen with misoprostol for abortions in the first 10 weeks of pregnancy.

A scientific paper that raised concerns about the safety of the abortion pill mifepristone was retracted by its publisher this week. The study was cited three times by a federal judge who ruled against mifepristone last spring. That case, which could limit access to mifepristone throughout the country, will soon be heard in the Supreme Court.

The now retracted study used Medicaid claims data to track E.R. visits by patients in the month after having an abortion. The study found a much higher rate of complications than similar studies that have examined abortion safety.

Sage, the publisher of the journal, retracted the study on Monday along with two other papers, explaining in a statement that "expert reviewers found that the studies demonstrate a lack of scientific rigor that invalidates or renders unreliable the authors' conclusions."

It also noted that most of the authors on the paper worked for the Charlotte Lozier Institute, the research arm of anti-abortion lobbying group Susan B. Anthony Pro-Life America, and that one of the original peer reviewers had also worked for the Lozier Institute.

The Sage journal, Health Services Research and Managerial Epidemiology , published all three research articles, which are still available online along with the retraction notice. In an email to NPR, a spokesperson for Sage wrote that the process leading to the retractions "was thorough, fair, and careful."

The lead author on the paper, James Studnicki, fiercely defends his work. "Sage is targeting us because we have been successful for a long period of time," he says on a video posted online this week . He asserts that the retraction has "nothing to do with real science and has everything to do with a political assassination of science."

He says that because the study's findings have been cited in legal cases like the one challenging the abortion pill, "we have become visible – people are quoting us. And for that reason, we are dangerous, and for that reason, they want to cancel our work," Studnicki says in the video.

In an email to NPR, a spokesperson for the Charlotte Lozier Institute said that they "will be taking appropriate legal action."

Role in abortion pill legal case

Anti-abortion rights groups, including a group of doctors, sued the federal Food and Drug Administration in 2022 over the approval of mifepristone, which is part of a two-drug regimen used in most medication abortions. The pill has been on the market for over 20 years, and is used in more than half abortions nationally. The FDA stands by its research that finds adverse events from mifepristone are extremely rare.

Judge Matthew Kacsmaryk, the district court judge who initially ruled on the case, pointed to the now-retracted study to support the idea that the anti-abortion rights physicians suing the FDA had the right to do so. "The associations' members have standing because they allege adverse events from chemical abortion drugs can overwhelm the medical system and place 'enormous pressure and stress' on doctors during emergencies and complications," he wrote in his decision, citing Studnicki. He ruled that mifepristone should be pulled from the market nationwide, although his decision never took effect.

research paper for scientific journal

Matthew Kacsmaryk at his confirmation hearing for the federal bench in 2017. AP hide caption

Matthew Kacsmaryk at his confirmation hearing for the federal bench in 2017.

Kacsmaryk is a Trump appointee who was a vocal abortion opponent before becoming a federal judge.

"I don't think he would view the retraction as delegitimizing the research," says Mary Ziegler , a law professor and expert on the legal history of abortion at U.C. Davis. "There's been so much polarization about what the reality of abortion is on the right that I'm not sure how much a retraction would affect his reasoning."

Ziegler also doubts the retractions will alter much in the Supreme Court case, given its conservative majority. "We've already seen, when it comes to abortion, that the court has a propensity to look at the views of experts that support the results it wants," she says. The decision that overturned Roe v. Wade is an example, she says. "The majority [opinion] relied pretty much exclusively on scholars with some ties to pro-life activism and didn't really cite anybody else even or really even acknowledge that there was a majority scholarly position or even that there was meaningful disagreement on the subject."

In the mifepristone case, "there's a lot of supposition and speculation" in the argument about who has standing to sue, she explains. "There's a probability that people will take mifepristone and then there's a probability that they'll get complications and then there's a probability that they'll get treatment in the E.R. and then there's a probability that they'll encounter physicians with certain objections to mifepristone. So the question is, if this [retraction] knocks out one leg of the stool, does that somehow affect how the court is going to view standing? I imagine not."

It's impossible to know who will win the Supreme Court case, but Ziegler thinks that this retraction probably won't sway the outcome either way. "If the court is skeptical of standing because of all these aforementioned weaknesses, this is just more fuel to that fire," she says. "It's not as if this were an airtight case for standing and this was a potentially game-changing development."

Oral arguments for the case, Alliance for Hippocratic Medicine v. FDA , are scheduled for March 26 at the Supreme Court. A decision is expected by summer. Mifepristone remains available while the legal process continues.

  • Abortion policy
  • abortion pill
  • judge matthew kacsmaryk
  • mifepristone
  • retractions
  • Abortion rights
  • Supreme Court

A once-ignored community of science sleuths now has the research community on its heels

research paper for scientific journal

A community of sleuths hunting for errors in scientific research have sent shockwaves through some of the most prestigious research institutions in the world — and the science community at large.

High-profile cases of alleged image manipulations in papers authored by the former president at Stanford University and leaders at the Dana-Farber Cancer Institute have made national media headlines, and some top science leaders think this could be just the start.

“At the rate things are going, we expect another one of these to come up every few weeks,” said Holden Thorp, the editor-in-chief of the Science family of scientific journals, whose namesake publication is one of the two most influential in the field. 

The sleuths argue their work is necessary to correct the scientific record and prevent generations of researchers from pursuing dead-end topics because of flawed papers. And some scientists say it’s time for universities and academic publishers to reform how they address flawed research. 

“I understand why the sleuths finding these things are so pissed off,” said Michael Eisen, a biologist, the former editor of the journal eLife and a prominent voice of reform in scientific publishing. “Everybody — the author, the journal, the institution, everybody — is incentivized to minimize the importance of these things.” 

For about a decade, science sleuths unearthed widespread problems in scientific images in published papers, publishing concerns online but receiving little attention. 

That began to change last summer after then-Stanford President Marc Tessier-Lavigne, who is a neuroscientist, stepped down from his post after scrutiny of alleged image manipulations in studies he helped author and a report criticizing his laboratory culture. Tessier-Lavigne was not found to have engaged in misconduct himself, but members of his lab appeared to manipulate images in dubious ways, a report from a scientific panel hired to examine the allegations said. 

In January, a scathing post from a blogger exposed questionable work from top leaders at the Dana-Farber Cancer Institute , which subsequently asked journals to retract six articles and issue corrections for dozens more. 

In a resignation statement , Tessier-Lavigne noted that the panel did not find that he knew of misconduct and that he never submitted papers he didn’t think were accurate. In a statement from its research integrity officer, Dana-Farber said it took decisive action to correct the scientific record and that image discrepancies were not necessarily evidence an author sought to deceive. 

“We’re certainly living through a moment — a public awareness — that really hit an inflection when the Marc Tessier-Lavigne matter happened and has continued steadily since then, with Dana-Farber being the latest,” Thorp said. 

Now, the long-standing problem is in the national spotlight, and new artificial intelligence tools are only making it easier to spot problems that range from decades-old errors and sloppy science to images enhanced unethically in photo-editing software.  

This heightened scrutiny is reshaping how some publishers are operating. And it’s pushing universities, journals and researchers to reckon with new technology, a potential backlog of undiscovered errors and how to be more transparent when problems are identified. 

This comes at a fraught time in academic halls. Bill Ackman, a venture capitalist, in a post on X last month discussed weaponizing artificial intelligence to identify plagiarism of leaders at top-flight universities where he has had ideological differences, raising questions about political motivations in plagiarism investigations. More broadly, public trust in scientists and science has declined steadily in recent years, according to the Pew Research Center .

Eisen said he didn’t think sleuths’ concerns over scientific images had veered into “McCarthyist” territory.

“I think they’ve been targeting a very specific type of problem in the literature, and they’re right — it’s bad,” Eisen said. 

Scientific publishing builds the base of what scientists understand about their disciplines, and it’s the primary way that researchers with new findings outline their work for colleagues. Before publication, scientific journals consider submissions and send them to outside researchers in the field for vetting and to spot errors or faulty reasoning, which is called peer review. Journal editors will review studies for plagiarism and for copy edits before they’re published. 

That system is not perfect and still relies on good-faith efforts by researchers to not manipulate their findings.

Over the past 15 years, scientists have grown increasingly concerned about problems that some researchers were digitally altering images in their papers to skew or emphasize results. Discovering irregularities in images — typically of experiments involving mice, gels or blots — has become a larger priority of scientific journals’ work.   

Jana Christopher, an expert on scientific images who works for the Federation of European Biochemical Societies and its journals, said the field of image integrity screening has grown rapidly since she began working in it about 15 years ago. 

At the time, “nobody was doing this and people were kind of in denial about research fraud,” Christopher said. “The common view was that it was very rare and every now and then you would find someone who fudged their results.” 

Today, scientific journals have entire teams dedicated to dealing with images and trying to ensure their accuracy. More papers are being retracted than ever — with a record 10,000-plus pulled last year, according to a Nature analysis . 

A loose group of scientific sleuths have added outside pressure. Sleuths often discover and flag errors or potential manipulations on the online forum PubPeer. Some sleuths receive little or no payment or public recognition for their work.

“To some extent, there is a vigilantism around it,” Eisen said. 

An analysis of comments on more than 24,000 articles posted on PubPeer found that more than 62% of comments on PubPeer were related to image manipulation. 

For years, sleuths relied on sharp eyes, keen pattern recognition and an understanding of photo manipulation tools. In the past few years, rapidly developing artificial intelligence tools, which can scan papers for irregularities, are supercharging their work. 

Now, scientific journals are adopting similar technology to try to prevent errors from reaching publication. In January, Science announced that it was using an artificial intelligence tool called Proofig to scan papers that were being edited and peer-reviewed for publication. 

Thorp, the Science editor-in-chief, said the family of six journals added the tool “quietly” into its workflow about six months before that January announcement. Before, the journal was reliant on eye-checks to catch these types of problems. 

Thorp said Proofig identified several papers late in the editorial process that were not published because of problematic images that were difficult to explain and other instances in which authors had “logical explanations” for issues they corrected before publication.

“The serious errors that cause us not to publish a paper are less than 1%,” Thorp said.

In a statement, Chris Graf, the research integrity director at the publishing company Springer Nature, said his company is developing and testing “in-house AI image integrity software” to check for image duplications. Graf’s research integrity unit currently uses Proofig to help assess articles if concerns are raised after publication. 

Graf said processes varied across its journals, but that some Springer Nature publications manually check images for manipulations with Adobe Photoshop tools and look for inconsistencies in raw data for experiments that visualize cell components or common scientific experiments.

“While the AI-based tools are helpful in speeding up and scaling up the investigations, we still consider the human element of all our investigations to be crucial,” Graf said, adding that image recognition software is not perfect and that human expertise is required to protect against false positives and negatives. 

No tool will catch every mistake or cheat. 

“There’s a lot of human beings in that process. We’re never going to catch everything,” Thorp said. “We need to get much better at managing this when it happens, as journals, institutions and authors.”

Many science sleuths had grown frustrated after their concerns seemed to be ignored or as investigations trickled along slowly and without a public resolution.  

Sholto David, who publicly exposed concerns about Dana-Farber research in a blog post, said he largely “gave up” on writing letters to journal editors about errors he discovered because their responses were so insufficient. 

Elisabeth Bik, a microbiologist and longtime image sleuth, said she has frequently flagged image problems and “nothing happens.” 

Leaving public comments questioning research figures on PubPeer can start a public conversation over questionable research, but authors and research institutions often don’t respond directly to the online critiques. 

While journals can issue corrections or retractions, it’s typically a research institution’s or a university’s responsibility to investigate cases. When cases involve biomedical research supported by federal funding, the federal Office of Research Integrity can investigate. 

Thorp said the institutions need to move more swiftly to take responsibility when errors are discovered and speak plainly and publicly about what happened to earn the public’s trust.  

“Universities are so slow at responding and so slow at running through their processes, and the longer that goes on, the more damage that goes on,” Thorp said. “We don’t know what happened if instead of launching this investigation Stanford said, ‘These papers are wrong. We’re going to retract them. It’s our responsibility. But for now, we’re taking the blame and owning up to this.’” 

Some scientists worry that image concerns are only scratching the surface of science’s integrity issues — problems in images are simply much easier to spot than data errors in spreadsheets. 

And while policing bad papers and seeking accountability is important, some scientists think those measures will be treating symptoms of the larger problem: a culture that rewards the careers of those who publish the most exciting results, rather than the ones that hold up over time. 

“The scientific culture itself does not say we care about being right; it says we care about getting splashy papers,” Eisen said. 

Evan Bush is a science reporter for NBC News. He can be reached at [email protected].

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