In unusual move, gov’t database delists 14 journals from one publisher

Since the U.S. government launched a database of freely available journal articles in 2000, it has deselected roughly only 30 titles over concerns about journal quality. Fourteen of those titles were removed last August, all associated with one publisher — Kowsar.

According to a spokesperson for the National Library of Medicine (NLM), which manages the database — PubMed Central (PMC) — the decision stemmed from its review of the journals’ adherence to its policy on scientific and editorial standards:

Continue reading In unusual move, gov’t database delists 14 journals from one publisher

Clue fans, here’s scientific proof that it was Colonel Mustard with a candlestick

Leo Reynolds, via Flickr

When we last heard from Eve Armstrong one year ago today, she was a postdoc at the BioCircuits Institute at the University of California, San Diego, musing mathematically about what would have happened if she had asked one Barry Cottonfield to her high school prom in 1997. Today, she is a postdoc at the Computational Neuroscience Initiative at the University of Pennsylvania — where, it would appear from a new preprint, titled “Colonel Mustard in the Aviary with the Candlestick: a limit cycle attractor transitions to a stable focus via supercritical Andronov-Hopf bifurcation,” she has solved a brutal murder.

To be more precise:

We establish the means by which Mr. Boddy came to transition from a stable trajectory within the global phase space of Philadelphia, Pennsylvania to a stable point on the cement floor of an aviary near the west bank of the Schuylkill River.

The preprint will be posted at arXiv tomorrow, but Armstrong did not want to keep the world in suspense any longer, so we are hosting the manuscript here at Retraction Watch on a more appropriate day, April 1. She was also kind enough to answer a few questions about the work: Continue reading Clue fans, here’s scientific proof that it was Colonel Mustard with a candlestick

Weekend reads: “Weaponized transparency;” fighting academic spam with humor; NIH cracks down

Before we present this week’s Weekend Reads, a question: Do you enjoy our weekly roundup? If so, would you consider a tax-deductible donation of $25, or a recurring donation of an amount of your choosing, to support it? Thanks in advance.

The week at Retraction Watch featured a major case of misconduct at The Ohio State University, the retraction of a much-criticized paper claiming to show “off-target” mutations when using CRISPR, and how fallout from a stem cell scandal ensnared a Nobel Prize winner. Here’s what was happening elsewhere: Continue reading Weekend reads: “Weaponized transparency;” fighting academic spam with humor; NIH cracks down

Ohio State just released a 75-page report finding misconduct by a cancer researcher. What can we learn?

C. K. Gunsalus

Today, the Ohio State University (OSU) announced that Ching-Shih Chen, who resigned from a professorship there in September, was guilty of “deviating from the accepted practices of image handling and figure generation and intentionally falsifying data” in 14 images from eight papers. Chen had earned more than $8 million in Federal grants, and his work had led to a compound now being testing in clinical trials for cancer. (For details of the case, see our story in Science.)

Ching-Shih Chen

OSU — which has been involved in several high-profile cases of misconduct recently — released a lightly-redacted version of their investigation report, and we asked C.K. Gunsalus, who has decades of experience reviewing similar cases, to examine it for us. A Q&A follows.

 

Retraction Watch (RW): What’s your impression of the case? How does it compare in significance with others you’ve looked at? Continue reading Ohio State just released a 75-page report finding misconduct by a cancer researcher. What can we learn?

Nature journal retracts controversial CRISPR paper after authors admit results may be wrong

Nature Methods has retracted a 2017 paper suggesting a common gene editing technique may cause widespread collateral damage to the genome.

The notice has a long backstory: After the paper was published, it immediately drew an outcry from critics (including representatives from companies who sell the tool, whose stock fell after publication). Some critics argued that the authors, led by Vinit B. Mahajan at Stanford University, hadn’t employed sufficient controls, so they couldn’t be sure that the observed mutations stemmed from the tool, rather than normal background variation between mice. Only months after the paper appeared, the journal issued an expression of concern about the article. In a new preprint posted on BioRxiv on Monday, the authors concede that their critics may be right.

In the new preprint, Mahanjan and his colleagues acknowledge that the gene editing technique — known as CRISPR-Cas9 — “may not introduce numerous, unintended, off-target mutations.”

However, according to the retraction notice, Mahajan and several of his co-authors object to the retraction: Continue reading Nature journal retracts controversial CRISPR paper after authors admit results may be wrong

A new publishing approach — retract and replace — is having growing pains

Ana Marušić

Many journals are adopting a recently developed mechanism for correcting the scientific record known as “retract and replace” — usually employed when the original paper has been affected by honest errors. But if an article is retracted and replaced, can readers always tell? To find out, Ana Marušić at the University of Split School of Medicine in Croatia and her colleagues reviewed 29 “Corrected and Republished Articles” issued between January, 2015 and December, 2016, noting how they were marked by Web of Science, Scopus, and the journals themselves. They report their findings today in The Lancet.

Retraction Watch: You found some inconsistencies in how articles are handled by journals and other databases. What were the most surprising and/or troubling to you?

Continue reading A new publishing approach — retract and replace — is having growing pains

Stem cell paper falsification leads to firing; Nobelist also penalized

Shinya Yamanaka

Kyoto University has “punitively dismissed” a researcher found guilty of falsifying nearly all of the figures in a 2017 stem cell paper.  

According to an announcement Wednesday, the university fired the paper’s corresponding author, Kohei Yamamizu, after determining he had fabricated and falsified data in all but one figure in the 2017 Stem Cell Reports paper. The findings of the investigation, which were announced in January, found that Yamamizu, who worked at the Center for iPS Cell Research and Application (CiRA), was the only person responsible for the manipulation.

But CiRA’s director, Shinya Yamanaka—who shared a Nobel Prize for his work in stem cell biology—has taken responsibility for the incident as well. In an official statement, Yamanaka said he felt “a strong responsibility for not having prevented research misconduct at our institute:”
Continue reading Stem cell paper falsification leads to firing; Nobelist also penalized

Caught Our Notice: Duplicates, errors prompt two retractions for same author

Titles: 1) Angiopoietin-Like 4 Confers Resistance to Hypoxia/Serum Deprivation-Induced Apoptosis through PI3K/Akt and ERK1/2 Signaling Pathways in Mesenchymal Stem Cells

2) Novel Mechanism of Inhibition of Dendritic Cells Maturation by Mesenchymal Stem Cells via Interleukin-10 and the JAK1/STAT3 Signaling Pathway

What Caught Our Attention: In the span of 48 hours, PLOS ONE retracted two papers this month that were co-authored by Bo Yu, based at Key Laboratories of Education Ministry for Myocardial Ischemia Mechanism and Treatment and The Second Affiliated Hospital of Harbin Medical University in China. Both notices cite multiple duplications and errors, and conclude:

Continue reading Caught Our Notice: Duplicates, errors prompt two retractions for same author

Why detailed retraction notices are important (according to economists)

Adam Cox

When journals retract a paper but don’t explain why, what should readers think? Was the problem as simple as an administrative error by the publisher, or more concerning, like fraud? In a recent paper in Research Policy, economists led by Adam Cox at the University of Portsmouth, UK, analyzed 55 retractions from hundreds of economics journals, mostly issued between 2001 and 2016. (Does that number sound low? It should — a 2012 analysis of retractions in business and economics found they are a relatively rare occurrence.) In the new paper, Cox and his colleagues analyzed how many notices failed to provide detailed information, the potential costs of these information gaps, and what journals should do about it.

Retraction Watch: You used “rational crime theory” to analyze retraction notices and their consequence to offenders in economics. Could you explain briefly how rational crime theory works in this context?

Continue reading Why detailed retraction notices are important (according to economists)

PNAS wouldn’t let authors cite unpublished manuscript. Now, it admits it was wrong.

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When researchers submitted a paper about a type of microparticle to PNAS, they wanted to give credit where it was due, and cite an unpublished manuscript that helped guide their work. But the journal’s policy forbid citing unpublished work, and the reference was removed before publication. Now, concerns from the authors of that unpublished work have prompted the journal to have a change of heart.  

Continue reading PNAS wouldn’t let authors cite unpublished manuscript. Now, it admits it was wrong.