Category: wrong reagents

Drug researchers retract two papers, one because “human stem cells were actually mouse stem cells”

via Flickr

A group of drug researchers has lost a pair of 2020 papers for a lack of reproducibility and other problems, including the unfortunate mislabeling of murine stem cells as having come from humans. (In case you’re wondering, mouse and human stem cells are at once quite similar and highly divergent.)  

One article, “Divergent synthesis of 5-substituted pyrimidine 2′-deoxynucleosides and their incorporation into oligodeoxynucleotides for the survey of uracil DNA glycosylases,” appeared in Chemical Science. The second, “Convenient synthesis of pyrimidine 2′-deoxyribonucleoside monophosphates with important epigenetic marks at the 5-position,” was published in Organic & Biomolecular Chemistry. Both journals belong to the Royal Society of Chemistry. 

The senior author on the papers was Yana Cen,  a medicinal chemist now at Virginia Commonwealth University in Richmond. Cen has not responded to a request for comment.

According to the abstract of the Chemical Science paper: 

Continue reading Drug researchers retract two papers, one because “human stem cells were actually mouse stem cells”

Researchers retract a paper because it turns out not to be about bullshit

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Sometimes what science really needs is more bullshit.

Just ask a group of environmental scientists in China, who lost their 2019 article on soil contamination because what they thought was manure was in fact something else.

The article, titled “Immobilization of heavy metals in e-waste contaminated soils by combined application of biochar and phosphate fertilizer,” appeared in February in Water, Air, & Soil Pollution, and was written a team from the South China Institute of Environmental Science and Sun Yat-sen University, both in Guangzhou.

According to the researchers:

Continue reading Researchers retract a paper because it turns out not to be about bullshit

Semi-automated fact-checking for scientific papers? Here’s one method.

Jennifer Byrne

Wouldn’t it be terrific if manuscripts and published papers could be checked automatically for errors? That was the premise behind an algorithmic approach we wrote about last week, and today we bring you a Q&A with Jennifer Byrne, the last author of a new paper in PLOS ONE that describes another approach, this one designed to find incorrect nucleotide sequence reagents. Byrne, a scientist at the University of Sydney, has worked with the first author of the paper, Cyril Labbé, and has become a literature watchdog. Their efforts have already led to retractions. She answered several questions about the new paper.

Retraction Watch (RW): Seek & Blastn allows for “semi-automated fact-checking of nucleotide sequence reagents.” Can you explain what these reagents are used for, and what Seek & Blastn does? Continue reading Semi-automated fact-checking for scientific papers? Here’s one method.

How a typo in a catalog number led to the correction of a scientific paper — and what we can learn from that

Anita Bandrowski

Papers are corrected for lots of different reasons. In this guest post, Anita Bandrowski, who leads an initiative designed to help researchers identify their reagents correctly, describes one unusual reason for a correction — and explains what researchers can learn from the episode.

Last December, Tianyi Wang and her colleagues published a very interesting paper in Cell Metabolism on the potential link between a gene called JAK/STAT3 and breast cancer. It turns out that breast cancers become resistant to chemotherapy via a pathway that involves JAK/STAT3, and blocking this pathway can re-sensitize the tumor to chemotherapy.

But six months later, they corrected the paper — because of typos in the catalog numbers they’d used. Continue reading How a typo in a catalog number led to the correction of a scientific paper — and what we can learn from that

Child took wrong compound for over a year after “communication error”

Credit: Steven Depolo, Flickr

A journal is retracting a paper after it discovered researchers gave a child the wrong supplement for more than a year.

Rhiannon Bugno, managing editor for Biological Psychiatry, told Retraction Watch the mix-up did not put the patient at risk. However, the mistake was enough for the journal’s editor, John Krystal, of Yale University, to request the retraction of a 2016 paper describing the young girl’s experience taking the compound,“Rett-like Severe Encephalopathy Caused by a De Novo GRIN2B Mutation Is Attenuated by D-serine Dietary Supplement.”

Originally published June 17, 2016, the paper was retracted Jan. 15. Led by corresponding author Xavier Altafaj, of the University of Barcelona (UB) and Bellvitge Biomedical Research Institute (IDIBELL), researchers described using an amino acid, D-serine, to treat a child with a rare genetic disorder that affects neurons.

According to the notice, the researchers did use D-serine in lab work used as proof-of-concept; however, when it came time to try it in the patient, as a result of a “communication error:”

Continue reading Child took wrong compound for over a year after “communication error”

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

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?

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

Authors retract plant biology paper after they realized sample was contaminated

Plant biologists from China have retracted a 2013 paper in The Plant Cell after discovering that some of the plant material used was “inadvertently contaminated.”

According to the retraction notice, the authors believe the contamination affects the main conclusion of their paper. Continue reading Authors retract plant biology paper after they realized sample was contaminated

Project to “fact check” genetic studies leads to three more retractions. And it’s just getting started.

Jennifer Byrne

A project to identify studies doomed by problematic reagents has triggered three more retractions, bringing the total to five.

Jennifer Byrne, a scientist at the University of Sydney, who developed the the idea of double-checking the nucleic acid sequences of research materials — thereby ensuring studies were testing the gene in question — told Retraction Watch that all three retractions came after she started emailing journals in January  to alert them to the problems: Continue reading Project to “fact check” genetic studies leads to three more retractions. And it’s just getting started.

“We were devastated:” Authors retract paper after realizing they had used the wrong mice

Raymond Pasek and Maureen Gannon

Longtime readers of Retraction Watch may recall a 2011 post about a research team that retracted a paper after realizing that they had ordered the wrong mice. Maureen Gannon and Raymond Pasek of Vanderbilt University contacted us earlier this week to alert us to a similar case: Their retraction, earlier this month, of a 2016 paper from American Journal of Physiology – Endocrinology and Metabolism after discovering that “a colleague from another lab had mistakenly supplied us with the wrong transgenic mouse line.”

“We strongly believe that sharing this example will encourage other researchers to do the right thing when a mistake is discovered and promote academic integrity,” they wrote. So we asked them to answer a few questions about their experience with “Connective tissue growth factor is critical for proper β-cell function and pregnancy-induced β-cell hyperplasia in adult mice,” a paper that has been cited twice, according to Clarivate Analytics’ Web of Science. 

Retraction Watch: How, and when, did you become aware of the error? Continue reading “We were devastated:” Authors retract paper after realizing they had used the wrong mice

Nuclear fuel container material isn’t as novel as it appeared in now-retracted paper

A layer of copper sprayed onto steel. (Figure 6 from “Structure and Mechanical Properties of Thick Copper Coating Made by Cold Spray“)

A paper describing the construction of a material that could be used in nuclear fuel containers has been retracted after the authors left out key details.

According to the editor, the omission made the authors’ method seem more novel than it was.

The material is described in “Structure and Mechanical Properties of Thick Copper Coating Made by Cold Spray.” It was published in the January 2016 issue of the Journal of Thermal Spray Technology.

According to the retraction notice, the authors did not specify in the paper how the first layer of copper was sprayed onto the steel:

Continue reading Nuclear fuel container material isn’t as novel as it appeared in now-retracted paper