by journal – Page 4 – Retraction Watch

Former Stanford president retracts Nature paper as another gets expression of concern

Marc Tessier-Lavigne, the former president of Stanford University who resigned earlier this year after an institutional research misconduct investigation, has retracted a paper from Nature. The journal’s editorial office marked another of Tessier-Lavigne’s articles with an expression of concern.

The two Nature papers – which have together been cited more than 1,000 times, according to Clarivate’s Web of Science – were among five the university investigation examined on which Tessier-Lavigne was the principal author. The other three have been retracted – two from Science and one from Cell. In a statement posted to his lab website July 19, Tessier-Lavigne wrote that he planned to correct the two papers in Nature.

The retracted article, “APP binds DR6 to trigger axon pruning and neuron death via distinct caspases,” appeared in 2009. It has been cited 816 times, according to Clarivate’s Web of Science. The retraction notice stated:

PLOS backs down from expression of concern after author’s lawsuit

A researcher who sued the publisher PLOS to prevent it from posting an expression of concern for one of her papers has dropped her suit, and the publisher tells us it will add a correction to the article instead – but may “revisit this case” to deal with “unresolved issues.”

We’ve previously reported on the lawsuit Soudamani Singh, an assistant professor in the Department of Clinical and Translational Sciences at Marshall University’s Joan C. Edwards School of Medicine in Huntington, W. Va., filed against PLOS in April, as well as signs of a pending settlement.

According to an order filed November 2, Singh informed the court that she “voluntarily dismisses” the claims in her complaint, without the possibility of re-filing them, and the judge dismissed the case.

In her complaint, Singh alleged that PLOS planned to place an expression of concern on one of her papers, “Cyclooxygenase pathway mediates the inhibition of Na-glutamine co-transporter B0AT1 in rabbit villus cells during chronic intestinal inflammation,” published in PLOS ONE in September 2018, after she and her co-authors had requested a correction of a duplicated image. The paper has been cited nine times, according to Clarivate’s Web of Science, but not since April 2021.

Nature pulls study that found climate fears were overblown

It was that rarest of things: a sliver of good news about climate change.

According to calculations published last year in Nature, our planet was keeping pace, and then some, with rising emissions from tropical forest clearance by gobbling up more and more atmospheric carbon.

“What we can mainly prove is that the worst nightmare scenarios of an impaired carbon sink have not yet materialised and that the news is not quite as bad,” Guido van der Werf, a professor at Vrije Universiteit Amsterdam, said in a press release at the time.

His coauthor Dave van Wees added:

Frontiers retracts nearly 40 papers linked to ‘authorship-for-sale’

The publisher Frontiers has retracted nearly 40 papers across multiple journals linked to “the unethical practice of buying or selling authorship on research papers,” according to a press release posted to a company website Monday.

The release also states Frontiers is adopting new policies to prevent the sale of authorships on papers it publishes.

The publisher’s old policy simply stated that “Requests to modify the author list after submission should be made to the editorial office using the authorship change form.”

Now, such requests “will only be granted under exceptional circumstances and after in-depth assessment by the Frontiers’ research integrity unit,” according to the release. The publisher will also keep track of the requests “to identify suspicious patterns and trends.”

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.

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