Retraction Watch

Tracking retractions as a window into the scientific process

Archive for the ‘methodological problems’ Category

“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 »

Instead of retracting a flawed study, a journal let authors re-do it. It got retracted anyway.

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When a journal discovers elementary design flaws in a paper, what should it do? Should it retract immediately, or are there times when it makes sense to give the researchers time to perform a “do-over?”

These are questions the editors at Scientific Reports recently faced with a somewhat controversial 2016 paper, which reported that microRNAs from broccoli could make their way into the nuclei of human cells — suggesting that the food we eat could affect our gene expression.

After the paper appeared, researcher Kenneth Witwer at Johns Hopkins — who was not a co-author — posted comments on PubMed Commons and the paper itself, noting that the authors hadn’t properly designed the experiment, making it impossible for them to detect broccoli microRNAs. 

But instead of retracting the paper, the journal decided to give the authors time to do the experiments again, this time with correctly designed molecular biology tools. When that failed, they retracted it — and as part of the notice, reported the exact opposite conclusion of the original.

Witwer said the authors did a “tremendous job” with the follow-up study, but he still thinks the journal should have retracted the paper immediately. Letting the authors redo it is “a dangerous precedent to set,” he told us:   

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Journal alerts readers to “technical criticism” of CRISPR study

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A Nature journal has posted a editor’s note to a recent letter on potential unintended consequences of CRISPR gene editing, after an executive at a company trying to commercialize the technology said the paper should be retracted.

The original article, published on May 30 as a correspondence in Nature Methods, suggested that using CRISPR in mice can lead to unexpected mutations. But last week, the journal added an “Editorial note” online. Nature Methods says the notice is not an expression of concern, which would be a stronger suggestion that the paper is problematic; it simply wants to alert readers to the fact that, as the note states:

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Rutgers prof announces retraction on his blog

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A Rutgers computer scientist is retracting conference proceedings via an unusual channel: his personal blog.

On April 7, Anand Sarwate wrote that he was retracting a mathematical proof from the proceedings from the 2016 IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), after discovering errors that invalidated the result.

He explains in the blog post why the mistake occurred:

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Authors retract much-debated blockchain paper from F1000

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The authors of a popular — and heavily debated — F1000Research paper proposing a method to prevent scientific misconduct have decided to retract it.

The paper was initially criticized for allegedly plagiarizing from a graduate student’s blog — and revised to try to “rectify the overlap.” But according to F1000, it is now being retracted after an additional expert identified problems with the methodology.

Today, F1000 added this editorial note to the paper:

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Written by Alison McCook

May 24th, 2017 at 12:35 pm

Author retracts nanotechnology paper over doubts about key results

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The corresponding author of a 2015 nanotechnology paper has penned a lengthy — and revealing — retraction notice, explaining why he is not certain about the findings.

In the notice, Chang Ming Li from the Institute for Clean Energy & Advanced Materials (ICEAM) at Southwest University in China, states that there is “insufficient evidence to conclusively” identify the composition of the nanowire array described in the article, which “severely undermines the validity of the reported conclusions.”

The 2015 paper has been considered “highly cited” by Clarivate Analytics’ Web of Science, formerly part of Thomson Reuters, meaning it has received a disproportionate amount of cites given its field and publication year.

Li also said that the paper — which appeared in Physical Chemistry, Chemical Physics — was “submitted and published without my knowledge or permission.” He has not responded to our request to explain how that could have happened, given that he was the corresponding author. Read the rest of this entry »