Retraction Watch

Tracking retractions as a window into the scientific process

Archive for the ‘methodological problems’ Category

Caught Our Notice: Don’t count your chicken (genes) before they’re hatched

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Via Wikimedia

Title: Molecular Characterization and Biological Activity of Interferon-α in Indian Peafowl (Pavo cristatus)

What Caught Our Attention: Soon after the paper appeared, the journal was alerted to the fact its findings were at odds with others in the field. When the editor approached the authors, everything fell apart: The authors couldn’t repeat the experiments, and “were also unsure of the molecular probes that were used in the study.” While it isn’t unusual to have doubts about data — since since research is a process of experimentation — it is odd not to know how your experiment was conducted. The paper was retracted less than two months after it was published. The manuscript was accepted two months after it was submitted in early May, theoretically giving reviewers enough time to catch these issues (along with the authors’ failure to cite relevant papers).  

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Caught Our Notice: Dear peer reviewer, please read the methods section. Sincerely, everyone

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Via Wikimedia

TitlePlasma contributes to the antimicrobial activity of whole blood against Mycobacterium tuberculosis

What Caught Our Attention: A big peer review (and perhaps academic mentorship) fail.  These researchers used the wrong anticoagulant for their blood samples, leading them to believe that certain blood components were fighting microbes. The authors counted the number of colonies to show how well or poorly Tuberculin mycobacteria were growing in cultures — but blood samples need anticoagulants to prevent clots before analysis, and they used an anticoagulant that actually prevented the microbes from colonizing. The authors (and reviewers) should have known this from  Read the rest of this entry »

Written by Alison Abritis

November 13th, 2017 at 8:00 am

Retract, replace, retract: Beleaguered food researcher pulls article from JAMA journal (again)

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Brian Wansink

A high-profile food researcher who’s faced heavy criticism about his work has retracted the revised version of an article he’d already retracted last month.

Yes, you read that right: Brian Wansink at Cornell University retracted the original article from JAMA Pediatrics in September, replacing it with a revised version. Now he’s retracting the revised version, citing a major error: The study, which reported children were more likely to choose an apple over a cookie if the apple included an Elmo sticker, was conducted in children 3-5 years old, not 8-11, as the study reported.

Although Wansink told BuzzFeed he asked the journal to retract the paper, Annette Flanagin, Executive Managing Editor for The JAMA Network, told us the editors requested the retraction:

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Estimate: Nearly 33,000 papers include misidentified cell lines. Experts talk ways to combat growing problem

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Willem Halffman

Serge Horbach

Although most researchers realize too many are using misidentified cell lines in their work, they may be shocked to see the scope of the problem: Approximately 32,755 articles report on research that relied on misidentified cells, according to a new report in PLoS ONE. And even though more people may be aware of the problem, it hasn’t slowed it down: Most of the papers the authors flagged were written after 2000, and the number of new publications relying on misidentified cells continues to grow. We’ve tackled the issue — a 2015 poll of RW readers showed most believed the papers that report data from misidentified cell line should be either retracted or corrected, and our co-founders have recommended journals at least post “expressions of concern.” We spoke with the authors of the latest paper (also covered by The Scientist), Serge Horbach and Willem Halffman at Radboud University Nijmegen in the Netherlands.

Retraction Watch: You estimate more than 32,000 articles that used misidentified cells. That’s a very large number, to say the least — were you surprised at the scope of the problem?

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Written by Alison McCook

October 20th, 2017 at 8:00 am

Prominent food researcher retracts paper from JAMA journal, replaces it with multiple fixes

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Brian Wansink

Earlier this week, we reported that high-profile food researcher Brian Wansink — who’s faced months of criticisms about his research — had issued his second retraction. On Thursday, he issued his third.

The retracted paper — a 2012 research letter in the Archives of Pediatrics and Adolescent Medicine, now JAMA Pediatrics — reported that children were more likely to choose an apple over a cookie if the apple included an Elmo sticker. The same day the paper was retracted, Wansink and his co-authors published a replacement version that includes multiple changes, including to the methodology and the results.

The retraction notice lists the mistakes, which the authors say they made “inadvertently:”

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“The paper is extremely flawed:” Journal retracts article linked to vaccines

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A journal has retracted a 2016 paper after receiving criticism from outside researchers who raised concerns about its methodology and data.

The paper shares multiple authors with another paper that linked the vaccine for human papillomavirus (HPV) to behavioral problems in mice. Last year, a journal removed the study; later that year, the authors published a revised version in another journal. The latest retracted paper focuses on the antibodies present in a form of lupus.

Yehuda Shoenfeld at Tel-Aviv University in Israel, the corresponding author on both this latest retraction and the HPV vaccine paper, recently edited a textbook that explored how vaccines can induce autoimmunity in some people.  He told us the 2016 lupus paper does have a link to vaccines [his emphasis]:

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Researchers retract a paper when they realize they had sequenced the wrong snail’s genome

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Researchers in China thought they had sequenced the genomes of two snails that help transmit diseases to other species — an important first step to stopping the spread. But their hopes were soon dashed after they realized they had misidentified one of the snails.

The researchers published their findings earlier this year in the journal Parasites & Vectors. In the paper, the authors stressed that understanding the genetic makeup of these molluscs is important because many “freshwater snails are intermediate hosts for flatworm parasites and transmit infectious diseases” to humans and other animals. They also acknowledged that identifying snail species from their appearance alone can be tricky. Read the rest of this entry »

Newspaper series prompts CDC to correct paper on Legionnaire’s disease

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Post-publication peer review isn’t just for scientists. Newspaper reporters can help correct the scientific record, too.

The U.S. Centers for Disease Control and Prevention (CDC) has corrected a journal article on Legionnaire’s disease after the Pittsburgh Post-Gazette revealed what seems to be efforts by the researchers to misrepresent their data.

In a series of articles last December, the newspaper raised questions about the CDC’s actions in the aftermath of outbreaks in 2011 and 2012 of Legionnaire’s that sickened 22 veterans, killing six. The Post-Gazette obtained emails from CDC scientists that appeared to reveal their disdain for the sterilization method the hospital had been using to suppress the growth of Legionella bacteria. That method, a copper-silver system, is widely considered to be effective. But according to the newspaper, the CDC investigators were so critical of the copper-silver disinfectant technology that the VA ultimately switched to a system based on chlorine.   Read the rest of this entry »

Are there foxes in Tasmania? Follow the poop

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Stephen Sarre, based at the University of Canberra in Australia, has made a career out of collecting and analyzing poop.

It’s a tough job, but someone’s got to do it. Part of his work is designed to answer a multi-million dollar question: Is Tasmania home to foxes, a pest that carries rabies and other diseases and can ravage local wildlife? According to the Australian news outlet ABCthe Tasmanian and Australian governments have spent $50 million (AUD) on hunting foxes on the island since 2001 — even though many have debated whether they are even there.

In 2012, after analyzing thousands of fecal samples, Sarre published a paper in the Journal of Applied Ecology which boldly claimed that “Foxes are now widespread in Tasmania.” But many outside researchers didn’t buy it, and quickly voiced their criticisms of the paper, namely that there may be problems with false positives and the methodology used to analyze the samples. Recently, the journal issued an expression of concern for the paper, citing an ongoing investigation into the allegations.

Here’s the expression of concern (paywalled, tsk tsk):

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“Some experiments were not performed appropriately:” Florida researchers lose two papers

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Two molecular biologists have withdrawn two 2015 papers published in the same journal, citing image duplication and manipulation, among other issues.

One notice — published in June — explains that, after further investigation, the Journal of Biological Chemistry (JBC) found certain experiments “were not performed appropriately.” The other notice cites “missing data” and notes that certain data “did not accurately represent experimental conditions.”

The authors of the papers—Daniel L. Kaplan, associate professor at Florida State University who heads a genomics lab, and Irina Bruck, assistant scholar scientist in Kaplan’s lab—also received a correction in JBC this month, which cites image duplication.

The three notices, all published this month in JBC, may reveal a pattern, but there’s still a lot we don’t know. One of the two papers was questioned on PubPeer. Several commenters flagged duplicated images and had questions about the antibody used.

Here’s one retraction notice, published this month: Read the rest of this entry »