by journal – Page 3 – Retraction Watch

Stanford president retracts two Science papers following investigation

Marc Tessier-Lavigne, whose resignation as president of Stanford University becomes effective today, is retracting two papers from Science following an institutional investigation that found data manipulation in multiple figures.

Both articles, “Hierarchical Organization of Guidance Receptors: Silencing of Netrin Attraction by Slit Through a Robo/DCC Receptor Complex,” and “Binding of DCC by Netrin-1 to Mediate Axon Guidance Independent of Adenosine A2B Receptor Activation,” were published in 2001, when Tessier-Lavigne, the corresponding author, was at the University of California, San Francisco. They have been cited well over 600 times in total, according to Clarivate’s Web of Science.

Anonymous users on PubPeer posted concerns about potentially manipulated images in the papers as early as 2015. Reporting by The Stanford Daily in November 2022 spurred the university to launch an investigation into several of Tessier-Lavigne’s papers, how he responded when others identified issues in his articles, and the culture of his lab.

The university published the final report last month, finding that four of the five papers it reviewed on which Tessier-Lavigne was a principal author contained “apparent manipulation of research data by others.” Tessier-Lavigne, the investigation committee concluded:

Nature editors retract influential cancer paper with “unreliable” data

Editors at Nature have retracted a 2015 paper on breast cancer metastases citing trouble with the data in the supplementary materials.

The paper, “The hypoxic cancer secretome induces pre-metastatic bone lesions through lysyl oxidase,” was first published in May 2015 and has been cited 352 times, according to Clarivate’s Web of Science.

This marks the second retraction for corresponding author Janine Erler, a professor in cancer biology at the University of Copenhagen. As previously reported by Retraction Watch, Nature in 2020 pulled a 2006 paper on which she was first author because of “image anomalies” and the absence of original data. Two other papers co-authored by Erler have been corrected and one additional paper has an expression of concern.

Journal investigating Sodom comet paper for data problems

Fig. 53 from the paper: A simulation of an airburst by physicist Mark Boslough, to which he says incorrect labels were added

A paper that caught flak for its claims that an ancient city in the Middle East was destroyed by an exploding celestial body – and the authors’ suggestion that the event could have inspired the Biblical account of Sodom and Gomorrah – now has an editor’s note acknowledging the journal is looking into concerns about its data and conclusions.

The note follows a litany of criticism on Twitter, PubPeer, and in a “Matters Arising” response, as well as an extensive correction published last year. It appeared just days after Retraction Watch asked the publisher for an update on the case.

The article, “A Tunguska sized airburst destroyed Tall el-Hammam a Middle Bronze Age city in the Jordan Valley near the Dead Sea,” was published in Scientific Reports, a Springer Nature title, in September 2021. It has been cited six times in the scientific literature, according to Clarivate’s Web of Science, and Altmetric shows it has gotten more online attention than most other papers of a similar age.

Soon after the article’s publication, its claims attracted scrutiny on Twitter, as we reported at the time. Mark Boslough, a ~~retired~~ physicist at the University of New Mexico and expert in planetary impacts and airbursts (when celestial bodies explode above the earth’s surface) kicked off the criticism, and other scientists quickly joined in.

Reddit post prompts retraction of article that called Trump ‘the main driver of vaccine misinformation on Twitter’

In October 2021, a Reddit user on the r/badscience subforum posted a long critique of an article published in PLOS ONE earlier that year that had analyzed the “anti-vaccination infodemic” on Twitter and concluded that former U.S. president Donald Trump was “the main driver of vaccine misinformation” on the platform before his account was suspended.

The critique, titled “Terrible PlosOne Paper Dissected,” listed concerns about the sample size (50 pro-vaccine and 50 anti-vaccine accounts), method of selecting the sample and control groups, and data analysis. The Redditor also looked at the reviews of the article which PLOS ONE made available, and concluded that “clearly neither reviewer actually read it in any detail.”

The day after the comment was posted, an account for PLOS Communications responded, thanking the user “for your post publication peer review” and saying that PLOS ONE was looking into the article.

Contamination leads to swift retraction for Science paper on the origins of Omicron in Africa

The authors of a paper that proposed the Omicron variant of SARS-Cov-2 had evolved in Western Africa months before it was first detected in South Africa have retracted their study after discovering contamination in their samples, as several scientists had suggested on Twitter was the case.

The article, “Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa,” was published in Science on December 1 by a team led by Jan Felix Drexler of Charité – Universitätsmedizin Berlin.

Soon after publication, many geneticists expressed skepticism on social media about the study, including questioning whether the results came from contamination during the sequencing process.

Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation and the KwaZulu-Natal Research Innovation and Sequencing Platform at the University of KwaZulu-Natal in South Africa, tweeted on December 4 about “weaknesses” in the study, including that “the quality of the sequences seems problematic”:

PLOS flags nearly 50 papers by controversial French COVID researcher for ethics concerns

The publisher PLOS is marking nearly 50 articles by Didier Raoult, the French scientist who became controversial for promoting hydroxychloroquine for treating COVID-19, with expressions of concern while it investigates potential research ethics violations in the work.

PLOS has been looking into more than 100 articles by Raoult, but determined that the issues in 49 of the papers, including reuse of ethics approval reference numbers, warrant expressions of concern while the publisher continues its inquiry.

In August of 2021, scientific sleuth Elisabeth Bik wrote on her blog about a series of 17 articles from IHU-Méditerranée Infection that described different studies involving homeless people in Marseille over a decade, but all listed the same institutional ethics approval number. One of those papers, “Distinguishing Body Lice from Head Lice by Multiplex Real-Time PCR Analysis of the Phum_PHUM540560 Gene,” about which Bik also posted on PubPeer, was published in PLOS ONE in 2013, and is receiving an expression of concern today.

Board members decry their own journal’s retraction of paper on predatory publishers

Academics affiliated with a journal that retracted a paper on predatory publishing last year — after one of the publishers mentioned in the analysis complained — have put out a letter critiquing the decision, saying the retraction “lacks justification.”

The authors of the retracted article appealed the decision to the Committee on Publication Ethics (COPE), but lost. They republished their work in another journal last month.

As we reported last September, the Springer Nature journal Scientometrics retracted “Predatory publishing in Scopus: evidence on cross-country differences,” after receiving a letter from Fred Fenter, chief executive editor of Frontiers, one of the publishers included in the analysis, demanding the paper’s “swift retraction.” His key complaint: the article’s reliance on librarian Jeffrey Beall’s now-defunct list of allegedly predatory publishers.

Buzzy Lancet long COVID paper under investigation for ‘data errors’

An early and influential paper on long COVID that appeared in The Lancet has been flagged with an expression of concern while the journal investigates “data errors” brought to light by a reader.

An editorial that accompanied the paper when it was published in January of last year described it as “the first large cohort study with 6-months’ follow-up” of people hospitalized with COVID-19. The article has received plenty of attention since then.

Titled “6-month consequences of COVID-19 in patients discharged from hospital: a cohort study,” the paper has been cited nearly 1,600 times, according to Clarivate’s Web of Science. Altmetric finds references to it in multiple documents from the World Health Organization.

‘Liberals lecture, conservatives communicate’ paper gets lengthy expression of concern

An article from 2019 that caught some media buzz – including from the New York Times – for its analysis of political speeches now bears an expression of concern that’s almost as long as the original paper.

In “Liberals lecture, conservatives communicate: Analyzing complexity and ideology in 381,609 political speeches,” published in PLOS ONE, the authors concluded that “speakers from culturally liberal parties use more complex language than speakers from culturally conservative parties,” as they stated in their abstract.

But after reading the article, linguist Joe McVeigh, a university teacher at the University of Jyväskylä in Finland, wrote an online comment on the article detailing “several fundamental and critical flaws in its methodology.” A key issue: applying the Flesh-Kincaid test, which was developed for assessing the readability of a written text, to political speeches. As McVeigh told us:

Science paper on sense of taste gets expression of concern as university investigates

Science has published an expression of concern for a recent article on a receptor for bitter taste while the authors’ institution investigates “potential discrepancies” with a figure.

The article, “Structural basis for strychnine activation of human bitter taste receptor TAS2R46,” was published in September of this year.

According to the abstract:

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