‘Aggressive’ COVID-19 strains: What it takes to correct a flawed paper

A group of researchers in Scotland have taken aim at a study published in early March which reported surprising findings on the genetics of the SARS-CoV-2 virus responsible for the Covid-19 pandemic. 

But the story of what it took to correct the record about the paper is likely to be all too familiar to those who attempt such feats. It involved a blog post and a new paper — neither of which appeared on the site of the original journal that published the work, and neither of which is seeing the kind of attention paid to the original article.

The paper, “On the origin and continuing evolution of SARS-CoV-2,” appeared in National Science Review, published by Oxford Academic. According to the abstract

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Authors to correct influential Imperial College COVID-19 report after learning it cited a withdrawn preprint

A March paper by researchers at Imperial College London that, in the words of the Washington Post, “helped upend U.S. and U.K. coronavirus strategies,” cited a preprint that had been withdrawn.

Retraction Watch became aware of the issue after being contacted by a PubPeer commenter who had noted the withdrawal earlier this month. Following questions from Retraction Watch this weekend, the authors said they plan to submit a correction.

In March, the New York Times wrote:

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Elsevier investigating hydroxychloroquine-COVID-19 paper

Elsevier has weighed in on the handling of a controversial paper about the utility of hydroxychloroquine to treat Covid-19 infection, defending the rigor of the peer review process for the article in the face of concerns that the authors included the top editor of the journal that published the work. 

On April 3, as we reported, the International Society of Antimicrobial Chemotherapy issued an expression of concern (without quite calling it that) about the paper, which had appeared in March in the International Journal of Antimicrobial Agents, which the ISAC publishes, along with Elsevier. According to the society, the article, by the controversial French scientist  Didier Raoult, of the University of Marseille, and colleagues:

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Hydroxychloroquine-COVID-19 study did not meet publishing society’s “expected standard”

The paper that appears to have triggered the Trump administration’s obsession with hydroxychloroquine as a treatment for infection with the novel coronavirus has received a statement of concern from the society that publishes the journal in which the work appeared. 

The April 3, 2020, notice, from the International Journal of Antimicrobial Agents, states that the March 20 article, “Hydroxychloroquine and azithromycin as a treatment of Covid-19: results of an open-label non-randomized clinical trial” 

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‘Harming‌ ‌the‌ ‌scientific‌ ‌process‌:’ An attempt to correct the sports science literature, part 3

Matthew Tenan

Why is it so difficult to correct the scientific record in sports science? In the first installment in this series of guest posts, Matthew Tenan, a data scientist with a PhD in neuroscience, began the story of how he and some colleagues came to scrutinize a paper. In the second, he explained what happened next. In today’s final installment, he reflects on the editors’ response and what he thinks it means for his field.

In‌ ‌refusing‌ ‌to‌ ‌retract‌ ‌the‌ ‌Dankel‌ ‌and‌ ‌Loenneke‌ ‌manuscript‌ ‌we‌ ‌showed‌ ‌to‌ ‌be‌ ‌mathematically‌ ‌flawed,‌ ‌the‌ ‌editors‌ referred to “feedback‌ ‌from‌ ‌someone‌ ‌with‌ ‌greater‌ ‌expertise”‌ and ‌included‌ ‌the‌ ‌following:‌ ‌

Continue reading ‘Harming‌ ‌the‌ ‌scientific‌ ‌process‌:’ An attempt to correct the sports science literature, part 3

‘A flawed decision:’ What happened when sports scientists tried to correct the scientific record, part 2

Matthew Tenan

Why is it so difficult to correct the scientific record in sports science? In the first installment in this series of guest posts, Matthew Tenan, a data scientist with a PhD in neuroscience, began the story of how he and some colleagues came to scrutinize a paper. In this post, he explains what happened next.

The‌ ‌journal‌ ‌Sports‌ ‌Medicine‌ ‌is‌ ‌widely‌ ‌considered‌ ‌one‌ ‌of‌ ‌the‌ ‌top‌ ‌journals‌ ‌–‌ ‌if‌ ‌not‌ ‌the‌ ‌top‌ ‌journal‌ ‌–‌ ‌in‌ ‌the‌ ‌fields‌ ‌of‌ ‌sport‌ ‌science,‌ ‌exercise‌ ‌science‌ ‌and‌ ‌physical‌ ‌education.‌  ‌This‌ ‌journal‌ ‌is‌ ‌managed‌ ‌by‌ ‌two‌ ‌professional‌ ‌editors‌ ‌who‌ ‌do‌ ‌not‌ ‌hold‌ ‌PhDs‌ ‌in‌ ‌the‌ ‌journal’s‌ ‌subject‌ ‌area‌ ‌but‌ ‌are‌ ‌generally‌ ‌versed‌ ‌in‌ ‌the‌ ‌topic‌ ‌and‌ ‌have‌ ‌the‌ ‌goal‌ ‌of‌ ‌managing‌ ‌a‌ ‌successful‌ ‌journal‌ ‌for‌ ‌SpringerNature.‌ ‌

The‌ ‌manuscript‌ ‌by‌ ‌Dankel‌ ‌and‌ ‌Loenneke‌ ‌was‌ ‌reviewed‌ ‌by‌ ‌three‌ ‌reviewers.‌  ‌I‌ ‌know‌ ‌this‌ ‌because‌ ‌I‌ ‌was‌ ‌one‌ ‌of‌ ‌the‌ ‌reviewers‌ ‌and,‌ ‌as‌ ‌noted‌ ‌in‌ ‌the‌ ‌first‌ ‌post‌ ‌in‌ ‌this‌ ‌series,‌ ‌I‌ ‌strongly‌ ‌advised‌ ‌against‌ ‌its‌ ‌publication.‌ ‌Greg‌ ‌Atkinson,‌ ‌a‌ ‌practicing‌ ‌scientist‌ ‌in‌ ‌the‌ ‌area‌ ‌of‌ ‌health‌ sciences,‌ ‌has‌ ‌publicly‌ ‌stated‌, in a private Facebook group, that he‌ ‌was‌ ‌one‌ ‌of‌ ‌the‌ ‌reviewers‌ ‌who‌ ‌recommended‌ ‌the‌ ‌paper‌ be‌ ‌published.‌ ‌Both‌ ‌myself,‌ ‌Atkinson,‌ ‌and‌ ‌the‌ ‌senior‌ ‌author‌ ‌on‌ ‌the‌ ‌manuscript,‌ ‌Loenneke,‌ ‌sit‌ ‌on‌ the‌ ‌editorial‌ ‌board‌ ‌of‌ ‌the‌ ‌journal‌ ‌Sports‌ ‌Medicine.‌ ‌And‌ ‌while‌ ‌the‌ ‌paper‌ ‌published‌ ‌in‌ ‌the‌ ‌journal‌ ‌by‌ ‌Dankel‌ ‌and‌ ‌Loenneke‌ ‌proposes‌ ‌a‌ ‌novel‌ ‌statistical‌ ‌method,‌ ‌neither‌ ‌of‌ ‌the‌ ‌two‌ ‌authors‌ ‌on‌ ‌the‌ ‌manuscript,‌ ‌myself,‌ ‌nor‌ ‌Atkinson,‌ ‌have‌ ‌PhDs‌ ‌in‌ ‌statistics.‌ ‌The‌ ‌published‌ ‌paper‌ ‌does‌ ‌not‌ ‌cite‌ ‌a‌ ‌single‌ ‌statistics‌ ‌journal‌ ‌in‌ ‌the‌ ‌course‌ ‌of‌ ‌reporting‌ ‌their‌ ‌“novel‌ ‌method.”‌

‌What‌ ‌could‌ ‌go‌ ‌wrong,‌ ‌right?‌ ‌

Continue reading ‘A flawed decision:’ What happened when sports scientists tried to correct the scientific record, part 2

Why — even after reforms for an episode involving bad statistics — is it so difficult to correct the sports medicine literature? Part 1

Matthew Tenan

Two years ago, following heated debate, a sports science journal banned a statistical method from its pages, and a different journal — which had published a defense of that method earlier — decided to boost its statistical chops. But as Matthew Tenan, a data scientist with a PhD in neuroscience relates in this three-part series, that doesn’t seem to have made it any easier to correct the scientific record. Here’s part one.

In‌ ‌July‌ ‌2019,‌ ‌my‌ ‌colleague‌ ‌‌Andrew‌ ‌Vigotsky‌‌ ‌contacted‌ ‌me.‌ ‌He‌ ‌was‌ ‌curious,‌ ‌he‌ ‌said,‌ ‌whether‌ ‌a‌ paper‌ ‌published‌ ‌in‌ ‌Sports‌ ‌Medicine‌ ‌had‌ ‌undergone‌ ‌statistical‌ ‌review ‌ ‌because‌ ‌he‌ ‌was‌ concerned‌ ‌about‌ ‌some‌ ‌of‌ ‌its‌ ‌claims.‌ ‌The‌ ‌link‌ ‌he‌ ‌sent‌ ‌me‌ ‌was‌ ‌to‌ ‌“‌A‌ ‌Method‌ ‌to‌ ‌Stop‌ ‌Analyzing‌ Random‌ ‌Error‌ ‌and‌ ‌Start‌ ‌Analyzing‌ ‌Differential‌ ‌Responders‌ ‌to‌ ‌Exercise‌,”‌ ‌a‌ ‌paper‌ ‌published‌ ‌on‌ June‌ ‌28,‌ ‌2019‌ ‌by‌ ‌‌Scott‌ ‌Dankel‌‌ ‌and‌ ‌‌Jeremy‌ ‌Loenneke‌.‌

As‌ ‌it‌ ‌happened,‌ ‌I‌ ‌knew‌ ‌that‌ ‌paper,‌ ‌and‌ ‌I‌ ‌had‌ ‌also‌ ‌expressed‌ ‌concerns‌ ‌about‌ ‌it‌ ‌–‌ ‌when‌ ‌I reviewed‌ ‌it‌ ‌before‌ ‌publication‌ ‌as‌ ‌one‌ ‌of‌ ‌the‌ ‌members‌ ‌of‌ ‌the‌ ‌journal’s‌ ‌editorial‌ ‌board.‌ ‌Indeed,‌ ‌I was‌ ‌brought‌ ‌on‌ ‌to‌ ‌the‌ ‌editorial‌ ‌board‌ ‌of‌ ‌‌Sports‌ ‌Medicine‌‌ ‌because‌ ‌the‌ ‌journal‌ ‌had‌ ‌recently‌ received‌ ‌a‌ ‌lot‌ ‌of‌ ‌bad‌ ‌press‌ ‌for‌ ‌publishing‌ ‌a‌ ‌paper‌ ‌about‌ ‌another‌ ‌“novel‌ ‌statistical‌ ‌method”‌ ‌with‌ significant‌ ‌issues and I had been a vocal critic of the sports medicine and sport science‌ field developing their own statistical methods that are not used outside of the field and validated by the wider statistics community.‌ ‌

Continue reading Why — even after reforms for an episode involving bad statistics — is it so difficult to correct the sports medicine literature? Part 1

Journal retracts hotly contested paper on vaping and heart attacks

ecigarettereviewed.com via Wikimedia

The Journal of the American Heart Association (JAHA) today retracted a paper it published last year claiming that vaping was linked to heart attacks.

The paper, by Dharma Bhatta and Stanton Glantz of the University of California, San Francisco, has faced a barrage of criticism since its publication last June — and Glantz’s claims, in a blog post, that the study was “More evidence that e-cigs cause heart attacks.”

Brad Rodu, a professor at the University of Louisville who comments frequently on vaping, asked the journal to retract the study shortly after it was published. The study, he said, had failed to account for which happened first — heart attacks or vaping. The contretemps was the subject of a July 2019 story by USA Today:

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WHO formally retracts opioid guidelines that came under fire

via Flickr

The World Health Organization has officially retracted its controversial guidelines on the use of opioid analgesics. 

The agency’s move applies to two statements, issued in 2011 and 2012. Last June, WHO announced that it was “discontinuing” the guidelines in the wake of a critical report which said the documents were heavily tainted by commercial bias. According to a BMJ story published at the time

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Prominent cancer researcher loses nine papers, making 10

Andrew Dannenberg (credit Patricia Kuharic)

The Journal of Biological Chemistry (JBC) has retracted nine papers in bulk by a group of cancer researchers in New York led by the prominent scientist Andrew Dannenberg

The work of Dannenberg’s group at Weill Cornell — and the figures in particular — has been the subject of scrutiny on PubPeer for more than two years. 

The group also lost an article more than a decade ago in The Lancet, bringing their total so far to 10. Cancer Discovery subjected a paper to an expression of concern in August. Much of the tainted work was funded by grants from the U.S. government, as well as from funding authorities in other countries.  

According to the notice for 2014’s “p53 protein regulates Hsp90 ATPase activity and thereby Wnt signaling by modulating Aha1 expression“:

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