Category: infectious disease

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

Via Wikimedia

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

Journal to retract paper called “anti-vaccine pseudoscience”

A journal is planning to retract a paper that purported to link a component of vaccines to autism in mice.

The paper, about the effects of aluminum adjuvants in vaccines on the immune response in the brains of mice, is the second retraction for co-authors Christopher Shaw and Lucija Tomljenovic, of the University of British Columbia. The journal’s editor told us he and the authors are jointly retracting the paper. 

Just over a month old, the paper has already received plenty of criticism. Numerous commenters on PubPeer have allegedly identified image duplications and other problems with the paper. One commenter described “clear and deliberate” removal of control results in the paper, while others suggested gel bands were duplicated within the paper, and appear similar to those from another paper published in 2014 by Shaw and Tomljenovic. In a blog post, David Gorski, a professor and surgeon at Wayne State University, called the paper “antivaccine pseudoscience.”

Shaw, the paper’s last author, told us that his lab became aware of the PubPeer discussion a few weeks after publication:  Continue reading Journal to retract paper called “anti-vaccine pseudoscience”

Third retraction for former rising star found guilty of misconduct

A once-prominent researcher in the field of infectious disease — who was found guilty of misconduct last year— has had a third paper retracted, a 2006 article in PNAS.

Last year, the University of Dundee in Scotland found that Robert Ryan had committed research misconduct, which included misrepresenting clinical data and duplicating images in a dozen different publications. After a failed attempt to appeal the decision, Ryan resigned.

In April, we covered Ryan’s first two retractions – a 2012 paper in Molecular Microbiology, which cited image errors, and a 2011 paper in Journal of Bacteriology, which cited image duplication.

Now, PNAS has retracted a 2006 paper, which cites potential image duplication as well as “irregularities” in the data.

Here’s the retraction notice for “Cell–cell signaling in Xanthomonas campestris involves an HD-GYP domain protein that functions in cyclic di-GMP turnover:”

Continue reading Third retraction for former rising star found guilty of misconduct

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

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

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

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

Updated: Vaccine-autism study retracted — again

For the second time, a journal has quickly retracted a study that suggested vaccines raise the risk of autism and other neurodevelopmental disorders.

The study first raised a furor last year, prompting a Frontiers journal to quickly retract it. After it was republished in the Journal of Translational Science this month, that journal has also retracted it.

Although the titles of the two papers changed, the abstracts were nearly identical. Both studies surveyed the parents of 666 home-schooled children, 39% of whom where not vaccinated, and concluded that vaccination increased the risk of neurodevelopmental problems, particularly if children were born prematurely.

A representative of the Journal of Translational Science told us “Pilot comparative study on the health of vaccinated and unvaccinated 6- to 12-year-old U.S. children” has been retracted, and it will update us with an explanation.

Here’s more from the (now-retracted) abstract:

Continue reading Updated: Vaccine-autism study retracted — again

Former rising star found guilty of misconduct issues 2nd retraction

A once-lauded researcher in the field of infectious disease — who has since been found guilty of misconduct — has retracted a second paper.

Last year, the University of Dundee in Scotland investigated and ultimately concluded that Robert Ryan — whose work focused on infections that can be deadly in people with lung diseases such as cystic fibrosis — had committed “serious research misconduct,” affecting multiple publications. After appealing the decision, Ryan resigned.

We covered his first retraction earlier this month, which cited multiple instances of image duplication. Now Ryan has retracted his second paper, published in 2011 in Journal of Bacteriology, also due to image problems.

Here’s the retraction notice: Continue reading Former rising star found guilty of misconduct issues 2nd retraction

“Think of the unthinkable:” JAMA retraction prompts author to urge others to share data

A few months ago, a researcher told Evelien Oostdijk there might be a problem with a 2014 JAMA study she had co-authored.

The study had compared two methods of preventing infection in the intensive care unit (ICU). But a separate analysis had produced different results.

Oostdijk, from the University Medical Center Utrecht in The Netherlands, immediately got to work to try to figure out what was going on. And she soon discovered the problem: The coding for the two interventions had been reversed at one of the 16 ICUs. This switch had “a major impact on the study outcome,” last author Marc Bonten, also from the University Medical Center Utrecht, wrote in a blog post about the experience yesterday, because it occurred at “one of the largest participating ICUs.”

When Oostdijk and a researcher not involved in the study analyzed the data again, they discovered a notable difference between the revised and original findings: The new analysis revealed that one of the interventions had a small but significant survival benefit over the other.

Oostdijk and Bonten, who supervised the re-analysis, notified their colleagues of the revised study outcomes and contacted the journal requesting a retraction and replacement, which was published yesterday in JAMA.

According to the notice of retraction and replacement:

Continue reading “Think of the unthinkable:” JAMA retraction prompts author to urge others to share data

Once-prominent researcher logs retraction following misconduct finding

A researcher who resigned from the University of Dundee in Scotland after it concluded he was guilty of misconduct has issued his first retraction.

According to an internal email to staff forwarded to us last year, the university concluded that Robert Ryan had misrepresented clinical data and images in 12 different publications. The first retraction, published by Molecular Microbiology, cites image duplications in multiple figures.

Here’s the full notice:

Continue reading Once-prominent researcher logs retraction following misconduct finding

Nature paper adds non-reproducibility to its list of woes

Despite taking some serious hits, a 2006 letter in Nature isn’t going anywhere.

Years ago, a university committee determined that two figures in the letter had been falsified. The journal chose to correct the paper, rather than retract it — and then, the next year, published a correction of that correction due to “an error in the production process.” To round it out, in June of last year, Nature published a rebuttal from a separate research group, who had failed to replicate the letter’s results.

Still, the first author told us there are no plans to retract the paper, since the follow up experiments published in the corrections confirmed the paper’s conclusions.

Continue reading Nature paper adds non-reproducibility to its list of woes