Caught Our Notice: “The first author cut the thermoprinter paper printout into pieces and reassembled them”

Title: A mitochondrial ferredoxin is essential for biogenesis of cellular iron-sulfur proteins

What Caught Our Attention: Here’s a cut-and-paste issue that gave us pause. The authors of an 18-year-old paper in PNAS corrected it after realizing some bands in a figure were duplicated (an issue raised on PubPeer one year ago). It turns out, the first author had cut the paper into pieces and reassembled them to present the blots in the “desired order,” and some had become duplicated by mistake. The overall results were unaffected, so the journal swapped the image with a corrected version. Continue reading Caught Our Notice: “The first author cut the thermoprinter paper printout into pieces and reassembled them”

Caught Our Notice: Voinnet co-author issues another correction

Title: AtsPLA2-α nuclear relocalization by the Arabidopsis transcription factor AtMYB30 leads to repression of the plant defense response

What Caught Our Attention:  A previous collaborator with high-profile plant biologist Olivier Voinnet (who now has eight retractions) has issued an interesting correction to a 2010 PNAS paper. Susana Rivas is last author on the paper, the correction for which notes some images were duplicated, and others were “cropped and/or stretched to match the other blots.” Rivas is currently a group leader at The Laboratory of Plant-Microbe Interactions (LIPM), “a combined INRA-CNRS Research Unit.” Continue reading Caught Our Notice: Voinnet co-author issues another correction

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

They thought they might solve the world’s energy problems. Then they realized they were wrong.

Frederick MacDonnell

Researchers are retracting a 2016 PNAS paper that described a way to create gasoline-like fuels directly from carbon dioxide in the atmosphere.

Senior author Frederick MacDonnell, a professor at the University of Texas at Arlington (UTA), told us he originally thought his team had made a preliminary breakthrough that might “solve the world’s energy problems.” Instead, he said:

It was an elaborate trap we fell into.

In a retraction notice that contains more information than we usually see, MacDonnell and his co-authors wrote: Continue reading They thought they might solve the world’s energy problems. Then they realized they were wrong.

University finds falsified data in PNAS gene therapy paper, authors retract

A university investigation has found falsified data in a 2011 paper about the side effects of a virus commonly used in gene therapy.

The authors are retracting the paper, but one co-author told Retraction Watch they stand by their main conclusions. According to Roland Herzog, a professor at the University of Florida (UF) College of Medicine and a co-author of the paper, the falsified data were related to a minor part of the paper.

The paper, “Activation of the NF-κB pathway by adeno-associated virus (AAV) vectors and its implications in immune response and gene therapy,” was published in the Proceedings of the National Academy of Sciences (PNAS) in March 2011. All authors were affiliated with UF at the time; the handling editor, Kenneth Berns, is an emeritus professor at UF. The paper has been cited 50 times, according to Clarivate Analytics’ Web of Science. Continue reading University finds falsified data in PNAS gene therapy paper, authors retract

PNAS retraction weakens theory that fish travel with siblings

In 2016, researchers at Oregon State University published a paper in PNAS that surprised the research community. They showed that certain fish species travel with their siblings — even fighting against the currents of the Pacific Ocean to stay together.

Needless to say, the research community was skeptical, given how difficult a feat this would be. And their skepticism appears to have been warranted.

Recently, the authors — led by Su Sponaugle — retracted the paper, saying a re-analysis of their data using newly developed research tools has erased their confidence in the results. According to Sponaugle, the quick reversal was thanks to the new technology and open data sharing, which led their findings to be successfully challenged within months of publication. She said her team conducted the study with the “best available knowledge we had at the time,” including what they thought were the most advanced tools available to them: 

Continue reading PNAS retraction weakens theory that fish travel with siblings

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

“Clumsy but genuine errors” prompt PNAS correction

Some accidental mistakes have led researchers to issue a long correction to a 2016 PNAS paper.

According to the notice, when the cell biology paper’s corresponding authors became aware of duplications in two images, they immediately notified the journal and the University of Nottingham. After examining the original data archives, the university found that the authors generated the correct images, but the person who prepared the figures selected the wrong images from the data archive.

According to John Atherton, faculty pro-vice-chancellor for the Faculty of Medicine and Health Sciences at the University of Nottingham in the UK, who oversaw the investigation: Continue reading “Clumsy but genuine errors” prompt PNAS correction

Cancer researcher has dodged accusations for decades (and has a new correction)

Today isn’t a great day for Carlo Croce, chair of the department of cancer biology and genetics at The Ohio State University (OSU).

The New York Times has a lengthy article detailing the misconduct accusations that have swirled around Croce for years. We’ve covered many, but The Gray Lady obtained documents that show there have been many more.

The story mentions a 2013 letter from Ohio State University to pseudonymous whistleblower Clare Francis (which we reported on in 2014), acknowledging Francis’s allegations against Croce. However, in the letter, an administrator said OSU saw no reason to investigate Croce.

The story didn’t stop there, as the Times reports:

Continue reading Cancer researcher has dodged accusations for decades (and has a new correction)