Caught Our Notice: Former rising star loses fourth paper

Title: Haemophilus influenzae responds to glucocorticoids used in asthma therapy by modulation of biofilm formation and antibiotic resistance

What Caught Our Attention: This is the fourth retraction for Robert Ryan, formerly a high-profile researcher studying infections that can be deadly in people with lung diseases such as cystic fibrosis. In 2016, the University of Dundee in Scotland determined that Ryan had committed research misconduct, including misrepresenting clinical data and duplicating images in a dozen different publications. (Ryan tried to appeal the decision, then resigned.) The latest retraction cites a few problems with the paper, including uncertainty about the provenance of some data.

According to the notice, the second-to-last author, George A. O’Toole at Dartmouth, disagrees with the text of the notice, not the decision to retract. We contacted O’Toole, who declined to comment.

We received a statement from Ryan about the retraction:

Continue reading Caught Our Notice: Former rising star loses fourth paper

Overlooked virus “generated a mess,” infected highly cited Cell, PNAS papers

When Alexander Harms arrived at the University of Copenhagen in August 2016, as a postdoc planning to study a type of antibiotic resistance in bacteria, he carried with him a warning from another lab who had recruited him:

People said, “If you go there, you have to deal with these weird articles that nobody believes.”

The papers in question had been published in the Proceedings of the National Academy of Sciences in 2011 and Cell in 2013. Led by Kenn Gerdes, Harms’s new lab director, the work laid out a complex chain of events that mapped out how an E. coli bacterium can go into a dormant state, called persistence, that allows it to survive while the rest of its colony is wiped out.

Despite some experts’ skepticism, each paper had been cited hundreds of times. And Harms told us:

I personally did believe in the published work. There had been papers from others that kind of attacked [the Gerdes lab’s theory], but that was not high-quality work.

But by November 2016, Harms figured out that the skeptics had been right.  Continue reading Overlooked virus “generated a mess,” infected highly cited Cell, PNAS papers

Florida investigation can’t ID culprit who falsified data in retracted PNAS paper

When the Proceedings of the National Academy of Sciences retracted a gene therapy paper in December, it declared that some of the data had been falsified and mentioned a research misconduct investigation. But the notice said nothing about who was responsible.

Via a public records request, Retraction Watch has obtained investigation documents from the University of Florida, which show the focus had been narrowed down to two of the paper’s three co-first authors. But the investigation committee didn’t assign blame to either one. According to their final report, dated Oct. 24, 2016:

there was not enough direct evidence to either implicate or exonerate either of these individuals.

Over the course of the formal investigation, which lasted from early August to late October 2016,  the committee was able to determine that data in the PNAS paper had been falsified. However, it said: Continue reading Florida investigation can’t ID culprit who falsified data in retracted PNAS paper

BMJ journal pulls case report after UK tabloids publish graphic photos

A BMJ journal has retracted a medical case report about a couple in the United Kingdom who were infected by parasitic worms while on a Caribbean cruise.

The paper in BMJ Case Reports included graphic photos of the patients’ buttocks, the site of the infection, which were republished within a week by UK tabloids.

Specifics about when and why the journal retracted the paper remains unclear. BMJ Publishing Group, the journal, and the corresponding author have not responded to multiple requests for comment.

A UK-based lawyer, who has represented doctors in cases that touch on publishing and media law, told us there could be legal trouble. Martin Soames, of London firm Simons Muirhead & Burton, told Retraction Watch that UK laws governing patient confidentiality or protection of personal information could apply, raising problems for both the publisher and the doctors who wrote the paper. [See update at the end of the post, in which the editor says the paper was removed, and “does not consider that there are any issues of liability.”]  Continue reading BMJ journal pulls case report after UK tabloids publish graphic photos

For the second time, researchers retract — then republish — a vaccine paper

Photo credit: Blake Patterson

Two researchers with a troubled publication history about vaccine safety have withdrawn their third paper.

Along with several other co-authors, Christopher Shaw, of the University of British Columbia, and Lucija Tomljenovic, of the Neural Dynamics Research Group, recently withdrew a 2017 paper about a controversy over a tetanus vaccination program in Kenya.  

The paper has been republished in the same journal, adding another chapter to Shaw and Tomljenovic’s confusing record of publishing and withdrawing papers. The journal did not respond to our request for comment, but Shaw told Retraction Watch:

Continue reading For the second time, researchers retract — then republish — a vaccine paper

US court denies virus researcher’s latest appeal challenging 7-year funding ban

Scott Brodie has almost run out of options.

A former professor at the University of Washington, Brodie is currently involved in his third lawsuit challenging a finding of scientific misconduct and a seven-year funding ban handed down in 2010 by the U.S. Department of Health and Human Services’ Office of Research Integrity. He says that in the time since his case was heard by an administrative law judge at the ORI level, new evidence has come to light that shows he “did not have a ‘full and fair opportunity to litigate’ the issues.” His lawsuit sought a court order to have the ORI revisit its decision.

Last year, a U.S. District Court judge dismissed the case, saying it revisited old issues that had already been litigated, but Brodie appealed that decision. Now, his quest may have come to an end: On Nov. 27, the U.S. Court of Appeals for the D.C. Circuit dismissed the appeal. If he wants to continue the case, Brodie’s only remaining option is to appeal the decision to the U.S. Supreme Court.

In the court order, the panel of three judges wrote:

Continue reading US court denies virus researcher’s latest appeal challenging 7-year funding ban

Publisher issues first retractions for fake peer review, starts new checking policy

The publisher Frontiers has retracted four papers in three of its journals after discovering they had been accepted with fake peer reviews.

The problem of fake reviews has been on the research community’s radar since at least 2014, and several major publishers—including Springer, SAGE and BioMed Central—have retracted hundreds of papers accepted via fake peer reviews. But Gearóid Ó Faoleán, the ethics and integrity manager at Frontiers, told us this is the first time Frontiers had had to issue retractions for this reason.

The papers, published between 2015 and 2017, are from researchers based at the Council of Scientific & Industrial Research (CSIR)–National Institute for Interdisciplinary Science and Technology (NIIST) in Thiruvananthapuram, India. S. Nishanth Kumar is the only author in common to all four paper and a corresponding on two of them; Dileep Kumar, a scientist at CSIR, is a corresponding author on three of the papers.

Ó Faoleán told us: Continue reading Publisher issues first retractions for fake peer review, starts new checking policy

Journal replaces anti-vaccine paper it retracted for missing conflicts, “number of errors”

A journal retracted a paper about how conflicts of interest might be influencing research into the link between vaccines and autism because — wait for it — the authors failed to disclose conflicts of interest.

According to the retraction notice, the editors retracted the paper without the authors’ agreement, because the authors had a host of personal and professional interests in the field they didn’t declare, such as being associated with organizations involved in autism and vaccine safety. What’s more, the article also contained “a number of errors, and mistakes of various types that raise concerns about the validity of the conclusion.”

But now, Science and Engineering Ethics has published a new version of the article that draws similar conclusions to the retracted one, albeit with an updated conflict of interest statement, among other changes. From the abstract of the revised version: Continue reading Journal replaces anti-vaccine paper it retracted for missing conflicts, “number of errors”

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

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  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”