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in For Better Science on 2024-09-18 05:00:00 UTC.

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First paper retracted in string of studies using the wrong medication name

A scientific sleuth and a mother who nearly lost her daughter to a hormonal condition teamed up in January to flag a series of papers that misnamed a medication for pregnant women. They have recently started to see the fruits of their labors: one retraction and three corrections. 

In 2014, Tara Skopelitis, a lab manager at Cold Spring Harbor Laboratory, was given weekly progesterone injections to prevent preterm birth for her daughter, as reported by STAT. Six years later, after her daughter showed symptoms of an unknown hormonal condition which still hasn’t been formally diagnosed, Skopelitis discovered she should have received synthetic progesterone variant 17α-hydroxyprogesterone caproate, often referred to as 17-OHPC, 17P, sold as Makena. When the drug wasn’t available, her doctor had ordered the wrong replacement from a compounding pharmacy. Skopelitis suspects her daughter’s condition could be a result of the mixup.

The confusion lies within the literature, Skopelitis says: Many clinical trials and papers refer to 17P as intramuscular progesterone, as if they are interchangeable or even the same compound. 

While 17P was FDA-approved for a time and had been tested in several clinical trials, “intramuscular progesterone has never been tested for safety or recommended for use in preventing preterm labor,” Skopelitis told us. 

Skopelitis identified 69 papers that misname 17P as intramuscular progesterone. She enlisted the help of Sholto David, a sleuth and scientist who has helped manage their correspondence with the journals that published the papers. “It’s a story that forces you to sound like a conspiracy theorist. I had a hard time listening to Tara at first,” David told us in an email. 

A recent retraction takes the duo a step closer to correcting the body of literature surrounding intramuscular progesterone. The Journal of Maternal-Fetal & Neonatal Medicine in June retracted the 2012 paper, “Matched sample comparison of intramuscular versus vaginal micronized progesterone for prevention of preterm birth.” This trial was a special case, however, since “the authors seem to have actually used intramuscular progesterone, under the impression that there simply is no difference to 17P,” David wrote in an email to a member of the editorial board in February.

Intramuscular progesterone at that dose “has never been tested for safety or even believed by anyone to be effective,” David wrote. “The entire premise of the study seems to have been based on a nomenclature misunderstanding.” 

He also noted the authors compared their results to trials of intramuscular 17P, further evidence they believed the two compounds to be interchangeable, he said.

David forwarded the unanswered correspondence to the ethics department of the journal’s publisher, Taylor and Francis, in April. Julia Gunn, a research integrity manager at the company, responded in June that the paper had been retracted.

According to the retraction notice, when the journal reached out to the authors, they were informed that Mohamed Nabih EL-Gharib, the lead and corresponding author of the study listed as a researcher at Tanta University in Egypt, had died. The second author, T. M. EL-Hawary, also a researcher at Tanta University, “did not provide responses to our queries about the study, the raw data for review, or evidence to confirm that the study complied with the journal’s policies,” the notice stated. 

EL-Hawary did not respond to our request for comment. He also publishes research under the name “Tarek Elhawary.” 

“As for whether the trial actually happened, it’s certainly quite probable that it was just made up,” David told Retraction Watch in an email. Indeed, sleuths have identified many fabricated clinical trials in the obstetrics literature. If the drug was used as described in the study, “the consequences would be great,” David told us. 

A slew of other articles that made the same nomenclature mistake have received corrections. 

The paper that seemed to be the origin of the confusion, “Prevention of Recurrent Preterm Delivery by 17 Alpha-Hydroxyprogesterone Caproate,” was published in the New England Journal of Medicine in 2003. The journal issued a correction in June 2024, after David and Skopelitis’ prompting. 

The American Journal of Obstetrics and Gynecology MFM issued a correction for a 2020 paper in September, stating that “intramuscular progesterone should be replaced with 17α-hydroxyprogesterone caproate (17-OHPC) in the title and throughout the body of the paper.” 

Also in September, a multi-article correction was issued by the American Journal of Obstetrics and Gynecology (AJOG). It applies to seven studies and controlled trials. The authors “regret that there have been instances where the terms progesterone and 17α-hydroxyprogesterone caproate (17-OHPC) have been used interchangeably,” according to the notice. 

Roberto Romero, an editor-in-chief of AJOG, told Skopelitis in an email seen by Retraction Watch he contacted Elsevier, and “The Publisher agrees there is a need for corrections of all instances for which there are inaccuracies.” Elsevier did not respond to our request for comment. 

“Hundreds of doctors lazily misnamed a drug and it was allowed to cascade through the peer reviewed literature with serious implications for patient care,” David told us. “That can’t just be an ‘oops’ moment.”

Like Retraction Watch? You can make a tax-deductible contribution to support our work, follow us on Twitter, like us on Facebook, add us to your RSS reader, or subscribe to our daily digest. If you find a retraction that’s not in our database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.

in Retraction watch on 2024-09-17 21:02:54 UTC.

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How to spot tiny black holes that might pass through the solar system 

in Science News on 2024-09-17 15:00:29 UTC.

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Projectile pollen helps this flower edge out reproductive competition

in Science News on 2024-09-17 13:00:00 UTC.

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Exclusive: One university’s three-year battle to retract papers with fake data

In 2021, the provost of the University of Maryland, Baltimore sounded the alarm about a troubling batch of papers from the lab of Richard Eckert, the former chair of the Department of Biochemistry and Molecular Biology at the institution. 

The provost sent letters to the editors of seven journals calling out a string of serious issues.  Based on the university’s investigation, the papers contained duplicated, fabricated and falsified data, according to emails obtained by Retraction Watch. 

But more than three years later, the results of those alerts are mixed: Of the 11 papers the university flagged in 2021, editors corrected three and retracted two. Six still await resolution, with no apparent action taken by the journals. 

Maryland’s internal investigation into Eckert wrapped up in January 2020. Based on that investigation, the Office of Research Integrity (ORI) last month found Eckert committed research misconduct by faking data in 13 published papers and two grant applications. 

Through a public records request, we obtained a redacted copy of the investigation report, as well as the university’s correspondence with the journal editors. The records show that two years after the university initially alerted the journals, they followed up with some journals that had yet to act. The university also sent emails recommending retraction or correction of five more problematic papers.

But the second attempt didn’t change much: Collectively, 10 of 17 suspect papers await action. 

After receiving an anonymous allegation through a reporting hotline, Maryland began the process of investigating Eckert’s work in January 2019. According to a redacted version of the report, dated Jan. 7, 2020, and forensic evidence, the university found Eckert had engaged in several deceptive practices, among them: fabricating data to purportedly show gene expression, splicing and duplicating Western blots while using a paint brush tool to mask the alterations, and using empty areas of film to fake control conditions. 

A year after the investigation concluded, Roger Ward, the provost and executive vice president of the university, wrote letters to seven journals about the compromised papers. In response, two were retracted and three corrected: 

• Retracted: Inhibition of YAP function overcomes BRAF inhibitor resistance in melanoma cancer stem cells, Oncotarget 
• Retracted: Suppression of AP1 transcription factor function in keratinocyte suppresses differentiation, PLOS One
• Corrected: Bmi-1 helix–turn and ring finger domains are required for Bmi-1 antagonism of (−) epigallocatechin-3-gallate suppression of skin cancer cell survival, Cellular Signalling
• Corrected: Suppressing AP1 factor signaling in suprabasal epidermis produces a keratoderma phenotype, Journal of Investigative Dermatology
• Corrected: Transamidase site-targeted agents alter the conformation of the transglutaminase cancer stem cell survival protein to reduce GTP binding activity and cancer stem cell survival, Oncogene

The documents we obtained reveal a series of delays and inaction. 

The university reported deleted data in a paper published in Molecular Carcinogenesis, ‘Combination cisplatin and sulforaphane treatment reduces proliferation, invasion, and tumor formation in epidermal squamous cell carcinoma’, and recommended the journal retract the article. Independent experts recruited by Wiley, the journal’s publisher, couldn’t determine whether the error was honest. They requested additional evidence that the university was unable to provide, citing confidentiality. The article does not yet have any published notice. When asked about the matter, the journal editor deferred to a representative from Wiley, who did not respond to our queries. 

The university called out three papers published in the Journal of Biological Chemistry for containing falsified Western blots.  One of these was doctored using a paintbrush tool “in order to support the data presented in the article.”

For one article, the university’s investigators concluded “either the actual experiments have never been performed or the western blots never showed the results described in the article.” 

According to a log of email exchanges, the then-editor of the journal responded the same day, promising to “follow up in terms of action” regarding the three problematic articles. None have yet been retracted or corrected. 

In February 2023, Stephan Vigues, the university’s research integrity officer, followed up with the current editor-in-chief of JBC, Alex Toker. Toker wrote back, “Rest assured we take these cases with the utmost seriousness.” 

When Vigues followed up again in April 2023, a data integrity manager at the American Society for Biochemistry and Molecular Biology, which publishes the journal, said the investigation was still ongoing. 

Vigues inquired again in January of this year, stressing his institution had “investigated the entire lab” and had “gathered enough information to ask for retraction because the published data was manipulated and does not represent accurately the raw data.” 

A response from the director of publications, Isabel Casas, revealed the data manager handling the case had left, and the investigation was still unresolved. Neither Toker nor Casas has responded to requests for comment. 

In another instance, the Journal of Investigative Dermatology had corrected a paper, ‘Suppressing AP1 factor signaling in suprabasal epidermis produces a keratoderma phenotype’, following a letter from the university in 2021. In February 2023, Vigues notified editor-in-chief Erwin Tschachler about another two problematic articles. One figure contained a Western blot that had been replicated three times, using a paint brush tool to conceal the splices, and copy-and-pasted data modified to make the bands look slightly different. 

Tschachler responded a few days later, saying the editorial team “will publish the respective retractions/corrections in one of the up-coming issues of our Journal.” While neither article appears to have any published notice, Tschachler told Retraction Watch he had also been contacted by the US National Institutes of Health Office of Research Integrity, and said the journal would pursue retractions for the articles “given the pattern of misconduct.” 

These 10 articles are still awaiting action: 

• Methylosome protein 50 and PKCδ/p38δ protein signaling control keratinocyte proliferation via opposing effects on p21Cip1 Gene Expression, Journal of Biological Chemistry
• p38δ regulates p53 to control p21Cip1 expression in human epidermal keratinocytes, Journal of Biological Chemistry
• Protein Kinase C (PKC) Suppresses Keratinocyte Proliferation by Increasing p21Cip1 Level by a KLF4 Transcription Factor-dependent Mechanism, Journal of Biological Chemistry
• Localization of the TIG3 transglutaminase interaction domain and demonstration that the amino-terminal region is required for TIG3 function as a keratinocyte differentiation regulator, Journal of Investigative Dermatology
• PKC-delta and –eta, MEKK-1, MEK-6, MEK-3, and p38-delta are essential mediators of the response of normal human epidermal keratinocytes to differentiating agents, Journal of Investigative Dermatology
• Combination cisplatin and sulforaphane treatment reduces proliferation, invasion, and tumor formation in epidermal squamous cell carcinoma, Molecular Carcinogenesis
• The Bmi-1 polycomb protein antagonizes the (2)-epigallocatechin-3-gallate-dependent suppression of skin cancer cell survival, Carcinogenesis
• NRP-1 interacts with GIPC1 and α6/β4-integrins to increase YAP1/Δ Np63α-dependent epidermal cancer stem cell survival, Oncogene

• Transglutaminase is a mesothelioma cancer stem cell survival protein that is required for tumor formation, Oncotarget
• Transglutaminase interaction with α6/β4-integrin stimulates YAP1-Dependent ∆Np63α stabilization and leads to enhanced cancer stem cell survival and tumor formation, Cancer Research

Editors for Carcinogenesis, Oncogene and Oncotarget do not appear to have responded to alerts from the University of Maryland, Baltimore. The editor in chief at Carcinogenesis said the editorial team is still investigating the university’s claims.

The Office of Scientific Integrity at Oncotarget said they “do not have records that anyone from the University contacted us about the papers in 2021,” though we obtained a letter addressed to the journal’s EIC, Andrei Gudkov, dated January of that year. Oncotarget’s scientific integrity office wrote that an image forensic team is checking the paper, and would contact the authors if they found anything. After we shared that letter with the office, they said they would take “immediate action.” 

The EIC at Oncogene referred us to the publisher, Springer Nature, who hasn’t yet responded. The Cancer Research article was included in ORI’s findings, but not in the documents we obtained. The editor there has not responded to our queries. 

According to the ORI, Eckert is also required to request retractions himself. Eckert has not responded to requests for comment.

Like Retraction Watch? You can make a tax-deductible contribution to support our work, follow us on Twitter, like us on Facebook, add us to your RSS reader, or subscribe to our daily digest. If you find a retraction that’s not in our database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.

in Retraction watch on 2024-09-17 09:54:06 UTC.

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‘I Told Him I’m Not Getting in It’: Former Titan Submersible Engineer Testifies

in WIRED Science on 2024-09-17 00:48:46 UTC.

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The Polaris Dawn Spaceflight Was More Than Just a Billionaire Joyride

in WIRED Science on 2024-09-16 17:20:55 UTC.

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Pregnancy overhauls the brain. Here’s what that looks like

in Science News on 2024-09-16 15:00:00 UTC.

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Scientists Crack a 50-Year Mystery to Discover a New Set of Blood Groups

in WIRED Science on 2024-09-16 14:13:35 UTC.

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How a dying star is similar to a lava lamp

in Science News on 2024-09-16 13:00:00 UTC.

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This Brain Implant Lets People Control Amazon Alexa With Their Minds

in WIRED Science on 2024-09-16 11:00:00 UTC.

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Bushell on the Hill, or legitimate errors which do crop into papers

in For Better Science on 2024-09-16 05:00:00 UTC.

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Stephen Hawking Was Wrong—Extremal Black Holes Are Possible

in WIRED Science on 2024-09-15 11:00:00 UTC.

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South Sudan May See the First Permanent Mass Displacement Due to Climate Change

in WIRED Science on 2024-09-14 12:00:00 UTC.

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Weekend reads: Lawsuits filed and dismissed; ‘the rise of the science sleuths;’ research assessment culture

Would you consider a donation to support Weekend Reads, and our daily work?

The week at Retraction Watch featured:

• Pakistan university’s pharmacy department chair notches two retractions
• Former Harvard cancer researcher plagiarized data, federal watchdog says
• Penn State prof earns second retraction, faces third following university probe
• ‘Stealth corrections’: when journals quietly fix papers
• Nobel prize-winner tallies two more retractions, bringing total to 13

Our list of retracted or withdrawn COVID-19 papers is up past 400. There are more than 50,000 retractions in The Retraction Watch Database — which is now part of Crossref. The Retraction Watch Hijacked Journal Checker now contains more than 250 titles. And have you seen our leaderboard of authors with the most retractions lately — or our list of top 10 most highly cited retracted papers? What about The Retraction Watch Mass Resignations List — or our list of nearly 100 papers with evidence they were written by ChatGPT?

Here’s what was happening elsewhere (some of these items may be paywalled, metered access, or require free registration to read):

• A biotech company in India has sued researchers over a study they published about their COVID-19 vaccine.
• “Academic publishers face class action over ‘peer review’ pay, other restrictions.”
• “Francesca Gino’s Libel Claims Against Harvard Business School and Data Colada Dismissed.”
• “The Rise of the Science Sleuths” and an Alzheimer’s paper that “came under scrutiny.”
• “Springer Nature plans Frankfurt IPO in latest test of market.”
• “Opium in science and society: numbers and other quantifications.
• “The human costs of the research-assessment culture.”
• The parent agency of the U.S. Office of Research Integrity finalizes research misconduct regulations.
• “Suspicious phrases” in peer reviews point to template use.
• “New academic AI guidelines aim to curb research misconduct” from the Chinese Academy of Sciences.
• Author-led initiatives “to reform the publishing system are being undermined by indirect government subsidies which uphold the status quo,” authors say. 
• Researchers address “survey farming” and its “significant threats to data integrity” in marginalized community research.
• “Sleuths unearthing malpractice should receive gratitude, not hostility.”
• A pro-life researcher cited in court cases earns an expression of concern. Her earlier retraction.
• A researcher says a journal published an “apparently AI-generated, research article purporting to have been written by me.” Three similar cases we’ve reported on. 
• “Our findings suggest that journalists’ perceptions of debates in scholarly communication vary widely, with some displaying a highly critical and nuanced understanding and others presenting a more limited awareness.”
• “What we should learn from pandemic publishing.”
• “Citation indexes make research more unequal,” researchers say.
• A book on the philosophy of retraction.
• “The ‘Gollum effect’ is having a horrid, nasty, filthy impact on academia”: When scientists get “too possessive over their research.”
• Creator of CRISPR babies, whose research was deemed “unpublishable,” tweets that he will only publish in Nature or Science.
• “Shining a light on conflict of interest statements.”
• “Prominent” Harvard professor “Accused of Plagiarism by Former Co-Author.”
• A “researcher’s quest to keep his own work from being plagiarized.” A link to our coverage.
• “Trends in research integrity concerns and the evolving role of the publisher.”
• Former professor & whistleblower “alleges theft of research. His efforts for redressal remain unaddressed.”
• “[R]emedies to the problem of irreproducible research, and how we might move towards more sustainable and trustworthy research in biomedical science.”
• “‘End UKRI funds for open access publishing,’ urges report.”
• Watchdogs flag India as a “top producer of ‘low-quality and fraudulent’ research.”
• Researcher who won lawsuit against her university for racial discrimination also claimed she reported “evidence of data falsification and manipulation” at a university lab.
• Author-led initiatives “to reform the publishing system are being undermined by indirect government subsidies which uphold the status quo,” authors say. 
• “Do citation metrics function as an accountability sink?”
• “Haitian American Group Demands Retraction of Trump’s Statements.”

Like Retraction Watch? You can make a tax-deductible contribution to support our work, follow us on Twitter, like us on Facebook, add us to your RSS reader, or subscribe to our daily digest. If you find a retraction that’s not in our database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.

in Retraction watch on 2024-09-14 10:00:00 UTC.

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An ER Doctor’s Cure for America’s Gun Epidemic

in WIRED Science on 2024-09-14 10:00:00 UTC.

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AI Has Helped Shein Become Fast Fashion’s Biggest Polluter

in WIRED Science on 2024-09-14 06:00:00 UTC.

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Can solar farms and crop farms coexist?

in Science News on 2024-09-13 17:00:00 UTC.

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The Bird Flu Outbreak Takes a Mysterious Turn

in WIRED Science on 2024-09-13 16:58:53 UTC.

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Can taking ashwagandha supplements improve health?

in Science News on 2024-09-13 15:00:00 UTC.

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Attention arXiv users: arXiv mirrors to shut down September 15th, 2024

It is time to say goodbye . . . to the arXiv mirrors. After many years of service, all remaining arXiv mirrors will be officially shut down after Sunday, September 15, 2024.

The arXiv mirrors were originally created in an attempt to provide better local access to the arXiv corpus. In the early days of both arXiv and the internet, local mirrors were the best way to facilitate speed for arXiv users across the globe. arXiv’s mirror network expanded in the late 1990’s as arXiv grew, and for decades they were heavily used and provided faithful backups and replicas of arXiv’s scientific corpus.

As the modern internet has improved and arXiv has updated to a fully cloud-centric architecture for our services, geographic locality is no longer the determining factor it once was for speed of use for international arXiv users. Now, most users close to arXiv mirrors have better access to the main arxiv.org site than to the “nearby” mirror. Because of this, over time the utility and utilization of the arXiv mirrors has dwindled significantly (many down to near zero). While, until now, arXiv has continued to provide replication services to all mirrors, in the last few years, most of these read-only mirrors have shut down on their own or stopped accepting updates.

The arXiv mirror network served a role – acting as a backup for the corpus, allowing some degree of load distribution, and providing improved access for users who were geographically closer to a mirror – that is no longer necessary. arXiv now has multiple backups for the arXiv corpus in place, and the Fastly CDN (Content Delivery Network) that we use to deliver content provides excellent service throughout the world.

The arXiv mirrors took significant effort of both arXiv staff and hosting volunteer institutions to maintain, implement and update, and we are thankful for the volunteers across the world who gave their time, expertise, and effort over the years to maintain them and help arXiv reach users globally.

arXiv shutting down replication services for all mirror sites will not affect arXiv users. If you have questions about this, or other arXiv updates, we welcome your comments below.

in arXiv.org blog on 2024-09-13 14:26:32 UTC.

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Scientists find a long-sought electric field in Earth’s atmosphere

in Science News on 2024-09-13 13:00:00 UTC.

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How to View the ‘Comet of the Century’ C/2023 A3

in WIRED Science on 2024-09-13 13:00:00 UTC.

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Nobel prize-winner tallies two more retractions, bringing total to 13

A Nobel prize-winning genetics researcher has retracted two more papers, bringing his total to 13. 

Gregg Semenza, a professor of genetic medicine and director of the vascular program at Johns Hopkins’ Institute for Cell Engineering in Baltimore, shared the 2019 Nobel prize in physiology or medicine for “discoveries of how cells sense and adapt to oxygen availability.” 

Since pseudonymous sleuth Claire Francis and others began using PubPeer to point out potential duplicated or manipulated images in Semenza’s work in 2019, the researcher has retracted 12 papers. A previous retraction from 2011 for a paper co-authored with Naoki Mori – who with 31 retractions sits at No. 25 on our leaderboard – brings the total to 13. 

The authors requested the latest pair of retractions, published September 4 in Cancer Research, according to the notices, which also mention “an institutional review by Johns Hopkins University.” 

One of the papers, “PHGDH Expression Is Required for Mitochondrial Redox Homeostasis, Breast Cancer Stem Cell Maintenance, and Lung Metastasis,” was originally published in 2016 and has been cited 190 times, according to Clarivate’s Web of Science.

In October 2020, a PubPeer user commented that images labeled as representing tissue from two different mice looked “much more similar than expected.” The authors corrected the figure in 2022. 

The retraction notice stated Johns Hopkins’ review determined the two images “had contiguous features, suggesting the images may be from the same mouse,” and “certain raw data” labeled to be from two different mice might also be from the same mouse. “The authors do not have confidence in the integrity of the data,” according to the notice. 

The other recently retracted paper, “Collagen Prolyl Hydroxylases Are Essential for Breast Cancer Metastasis,” originally published in 2013, has been cited nearly 240 times. . PubPeer comments pointing out potential image duplications, including from Elisabeth Bik, began appearing in October 2020. The Hopkins review found some of the Western blot lanes were duplicated, as flagged on PubPeer.

“The authors apologize to the scientific community and deeply regret any inconveniences or challenges resulting from the publication and subsequent retraction of this article,” the notice stated.

Semenza has not responded to our request for comment, nor has Johns Hopkins. [See update at end.] Christine A. Iacobuzio-Donahue, editor in chief of Cancer Research, has not responded either.   

Other Nobel prize-winners have retracted papers – Frances Arnold did so quite publicly in 2020 – but Semenza’s 13 retractions are the most among scientists who have garnered that recognition, as far as we’re aware.

Update, 1800 UTC: Johns Hopkins sent us this statement:

Johns Hopkins maintains the highest standards for accuracy and integrity in research. We have strict protocols and processes in place to evaluate any allegations of research impropriety and to determine an appropriate path forward, if necessary. Due to federal confidentiality laws and our policies, we cannot disclose further details.

Like Retraction Watch? You can make a tax-deductible contribution to support our work, follow us on Twitter, like us on Facebook, add us to your RSS reader, or subscribe to our daily digest. If you find a retraction that’s not in our database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.

in Retraction watch on 2024-09-13 12:00:00 UTC.

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The Coast Guard’s OceanGate Hearings Start Next Week—but Key Witnesses Won’t Appear

in WIRED Science on 2024-09-13 11:00:00 UTC.

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Schneider Shorts 13.09.2024 – The press’ need to scandalize

in For Better Science on 2024-09-13 05:00:00 UTC.

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Episode 291 - Brian Lundstrom, MD, PhD

On September 12, 2024 we got to talk with Brian Lundstrom about the origin of epilepsy, the use of electrical recordings in its diagnosis, and brain stimulation as a treatment. Brian explained the difficulties of inferring cortical network function from EEG signals, and the problem of studying a disease whose symptoms manifest rarely and intermittently.

Guest:

Brian Lundstrom, Associate Professor in Neurology and Biophysics in the division of Epilepsy, Department of Neurology, in Mayo Clinic

Participating:

Fidel Santamaria, Department of Neuroscience, Developmental and Regenerative Biology, UTSA

Host:

Charles Wilson, Department of Neuroscience, Developmental and Regenerative Biology, UTSA

Thanks to Jim Tepper for original music

in Neuroscientists talk shop on 2024-09-12 22:00:00 UTC.

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Talking to a chatbot may weaken someone’s belief in conspiracy theories

in Science News on 2024-09-12 18:00:00 UTC.

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Mega El Niños kicked off the world’s worst mass extinction

in Science News on 2024-09-12 18:00:00 UTC.

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Amazon’s Shipping and Delivery Emissions Just Keep Going Up

in WIRED Science on 2024-09-12 14:56:50 UTC.

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How much is climate change to blame for extreme weather?

in Science News on 2024-09-12 14:00:00 UTC.

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‘Stealth corrections’: when journals quietly fix papers

Last March, René Aquarius noticed some overlapping patterns in a figure about a 2016 study on the blood-brain barrier. So he took to PubPeer, an online site where scientists often discuss papers, to raise his concerns. 

An author of the  study published in Neuroscience Letters responded saying they are checking the original data to figure out the problem. A month later, when Aquarius, a postdoctoral researcher at Radboud University Medical Center in Nijmegen, Netherlands, revisited the paper, the figure had been replaced without any note that the publisher had fixed the issue. 

Aquarius once again took to PubPeer to express his concerns. “I don’t see any notification when looking at the landing site for the paper: no erratum, corrigendum or a simple log-entry that something has been changed,” he wrote, noting that he had informed Elsevier, the journal’s publisher about the issue. In July, the journal issued a corrigendum for the paper. 

“I was quite a bit upset about it,” Aquarius told Retraction Watch. “It takes away one of the key elements for any reader to be critical, namely that you know what has happened.”

What Aquarius uncovered wasn’t an isolated case. He and his fellow research-integrity sleuths, who police various issues in scholarly literature alongside their day jobs, found 130 more cases of what they dub stealth corrections, where journals fix papers without acknowledging that they have done so. They outline their findings in a paper published as a preprint on arXiv on September 10. 

“The fact that they are interested in correcting the record is commendable but the way in which it’s being done is clearly suboptimal and suggests in some cases it’s self serving rather than serving science as a whole,” said Tom Heyman, a statistics and methodology researcher at Leiden University in the Netherlands, who wasn’t involved with the new study. 

Aquarius and colleagues found the cases of stealth corrections by revisiting papers flagged on PubPeer and via social media accounts of sleuths. Aquarius said  the scale of the problem is unclear.  One would need to have access to different versions of papers before and after changes are made to spot any tweaks. 

Of the 131 papers in the study sample, 76 were published by the Journal of the Balkan Union of Oncology. None has an associated digital object identifier but all have PubMed IDs. We reached out to the journal and its publisher, Bakis Productions, for comment but have not heard back. 

“At MDPI, we broadly agree with the overall sentiment of the article,” a spokesperson for the publisher said. “To this end, we have fully updated our correction process to increase the overall transparency of our post-publication updates, using ‘minor correction’ as a way of publicly announcing non-scientific changes to a manuscript.”

But removing articles published in a special issue from the digital special issue website shouldn’t be considered a stealth correction as the paper suggests, the MDPI spokesperson added in a statement provided to Retraction Watch. “[W]e are very transparent [about] our process, and as this change does not impact the scientific record, we do not accept that a public correction notice is required.”

“Articles that have been published shall remain extant, exact and unaltered as far as is possible. However, circumstances may arise where an article needs to be corrected, retracted or even removed,” a spokesperson for Elsevier added. “We do not correct articles without a formal notice and our policy outlines this. We will investigate the journal papers that have been brought to our attention.”

Although Aquarius and his team are pleased journals are fixing problems, they argue doing so silently is not the right solution. “You’re never sure who might have read the paper in the meantime and is not aware of the problem that was there and has been addressed,” Aquarius said. 

Another issue journals have been silently fixing are fingerprints left by generative AI tools like ChatGPT when they are used to write manuscripts, said study co-author Guillaume Cabanac, a computer scientist at the University of Toulouse in France. Cabanac has developed a tool that finds mentions of odd turns of phrases that are indicative of fabricated research papers. 

“We would like the authors to be accountable,” Cabanac said. “If they use any technology and don’t disclose it, that’s a problem,” he added. Journals should be asking authors to what extent they used ChatGPT and if they checked the tools’ outputs, Cabanac says. 

Other corrections being fixed quietly include paper titles, authors names, ethical disclosures, images, abstracts, affiliations, among others, Cabanac said. For him, one way to implement what he calls “enforced transparency” might be in the form of blockchain technology. “You cannot cook the books with the blockchain technology,” he said. “Once the information is stored, you cannot alter it without the public knowing about it.” 

Julia Rohrer, a psychologist at Leipzig University in Germany who wasn’t involved with the study, called stealth corrections “very troubling.” Rohrer, who previously ran the Loss of Confidence project — which provided a platform for scientists to document instances when they lose faith in their previous findings — said removing figures, authors, and markers of ChatGPT use is particularly concerning. 

“It feels like we’re not at the level of transparency that we should be as a science as a whole,” Heyman, who co-authored a 2020 study on correction notices issued by psychology journals, added. 

Heyman notes that different types of issues are being corrected publicly and stealthily. For instance, the new study found that many stealth corrections are of the content of papers while Heyman’s 2020 study on publicly issued corrections identified changes in metadata such as information about funders. 

“If you look at the content changes that were stealthily corrected, they seem often to involve really impactful changes,” Heyman said. “Whereas, if you look at the public correction notices, they regularly mention that there were changes but they were minor [and] they didn’t affect the conclusions.”

In some cases, corrections may be framed as making minor changes, Heyman said, but they may affect the conclusions. “So you also have a lack of transparency at that level,” he said. “Yes, there the correction is public but then the way the correction is being described is maybe not as transparent as it could have been.”

Journals don’t typically ask peer reviewers to assess corrections, corrigenda and errata, but doing so might make it harder for authors to falsely claim tweaks don’t affect the study’s conclusions, Heyman said. In addition to software companies sending researchers notifications when they cite retracted papers, Rohrer said similar alerts should also exist for lengthy corrections. 

As for corrections that are more benign, Rohrer said she is fine with those being corrected stealthily. Recently, Rohrer herself was involved with a stealth correction in one of her papers where she forgot to include her middle initial, which, she noted, raises particular problems in citation management software. 

“I think it’s perfectly fine for these instances,” Rohrer said. “Given that people’s attention is a limited resource, I think what we additionally need besides transparently tracking all changes and a complete version history, is some clear guidelines for what needs to be flagged and what does not.”

Like Retraction Watch? You can make a tax-deductible contribution to support our work, follow us on Twitter, like us on Facebook, add us to your RSS reader, or subscribe to our daily digest. If you find a retraction that’s not in our database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.

in Retraction watch on 2024-09-12 11:48:14 UTC.

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Penn State prof earns second retraction, faces third following university probe

A professor of biomedical engineering at the Pennsylvania State University today lost a government-funded study in Science Advances, marking her second retraction. 

The researcher, Deborah Kelly, is also facing retraction of a paper in Current Opinion in Structural Biology after a review undertaken by her institution found “serious data integrity concerns” in the work, according to emails obtained by Retraction Watch. Kelly has hired a lawyer to fight the retraction, apparently without success. (Update on Sept. 12: The paper has now been retracted.)

Today’s retraction of “Structural analysis of BRCA1 reveals modification hotspot” cites “unresolved concerns in the integrity of the data presented,” including what appears to be alterations of cryogenic electron microscopy (cryo-EM) maps using an “eraser tool.” The study was funded in part through a National Institutes of Health (NIH) grant for US$353,386 to Kelly.

In a statement to Retraction Watch sent via her legal counsel, Kelly stood by her work. 

Due to “ongoing confidential proceedings” regarding the proposed retractions, “I consider substantive discussion about them to be premature at this juncture,” Kelly said. “At least one external review has very recently contradicted the conclusions of the journals as presented in the respective retraction notices.” 

“I remain confident that the ultimate results of these ongoing proceedings will confirm that the findings and data presented in these papers remain accurate, reliable, and scientifically sound.”

Concerns have been swirling around Kelly, a former president of the Microscopy Society of America, at least since early last year when a scientist at Newcastle University in the United Kingdom began flagging problems in her work on PubPeer. So far, Thomas McCorvie has pointed out issues with 21 of Kelly’s publications.

McCorvie said he first noticed problems with Kelly’s work when the now-retracted paper in Science Advances appeared in 2017. 

“At the time a colleague emailed Deb Kelly due to our concerns, but the conversation was not productive, and Kelly stopped replying,” McCorvie told us. “As far as I am aware Kelly did not acknowledge the erased regions in their two maps. This was all very suspicious, but we didn’t follow up on it at the time.”

Then a paper from 2022 in ChemBioChem rekindled McCorvie’s apprehensions. He also noticed further problems with the 2017 paper in Science Advances that made him suspect the cryo-EM maps had been “fabricated,” he said in an email. 

“Due to all these issues, I looked further into the Kelly lab’s work last year,” McCorvie explained. He said the 21 papers he has flagged on PubPeer:

are from the Kelly lab’s time at Penn State and Virginia Tech. There are also three papers with issues from Kelly’s time as a postdoc at Harvard medical school. The general concerns cover:

1. Reuses of figures and images (micrographs, orientation distribution plots) for different conditions and samples, 
2. Electron microscopy maps not having the expected pixel sizes,
3. Atomic models not correlating with the electron microscopy maps,
4. The electron microscopy maps not having the expected features at their stated resolutions.

There are many problems, and I believe it to be a deep-rooted issue. None of the authors have contacted me to explain why there are these problems.  

Kelly’s LinkedIn page says she is also the executive director of the new non-profit think tank Structural Oncology LLC.

The retraction notice in Science Advances, which follows an editorial expression of concern from March, stated:

After publication, readers raised concerns that the cryo-EM maps had been altered. As a particular example, the map for EMDB-8834 appeared to be altered using a volume eraser tool to create a spherical hole in the map. These concerns were presented to the authors and an editorial expression of concern was issued on the paper on March 13, 2024. The authors’ response was reviewed by multiple experts in Cryo-EM, and this review concluded that unresolved concerns in the integrity of the data presented in this paper remained. As a consequence, the editors of Science Advances have decided to retract this paper. Some but not all of the authors agree with this retraction, and others have not responded. Dr. Kelly does not agree with the retraction.

McCorvie’s PubPeer comments give a detailed account of the issues with the paper, including the apparent use of an eraser tool in two density maps. 

“Overall, I am incredibly concerned with the state of these maps. They have been clearly edited and their origin appears questionable,” McCorvie wrote in one comment, noting in another that he kept “finding inconsistencies” in the paper.

McCorvie added a caveat:

Any students involved in this paper should not be judged for the veracity of the findings, and maps. I am sure they are all very capable scientists. Responsibility of the edited maps however lies solely on the PI. This is clear as they are the common denominator across all flagged manuscripts and are the head of the lab. This also applies to other students in the Kelly Lab.

The new retraction comes just a month after the journal Nanoscale pulled a 2021 article titled “Microchip-based structure determination of low-molecular weight proteins using cryo-electron microscopy,” for “concerns about the reliability of the electron microscopy data.” (McCorvie described the problems here.)

Kelly was the senior and corresponding author, and opposed the retraction, according to the notice. 

“Independent experts were consulted who were not satisfied with the explanation provided by the authors, therefore this article is being retracted to protect the integrity and accuracy of the scientific record,” the notice stated.

Edward H. Egelman, a professor of biochemistry and molecular genetics at the University of Virginia in Charlottesville, was one of those independent experts. An editor for the Royal Society of Chemistry, which publishes Nanoscale, contacted him in July 2023 to ask for his assistance in evaluating the article, critiques of the data, and the authors’ response, according to emails seen by Retraction Watch. 

In Egelman’s assessment, “there are fundamental concerns about the paper.” 

Based on input from Egelman and another expert, the journal decided to retract the article, the editor informed Egelman in October. 

However, once the journal sent Kelly the proposed retraction, she responded with a rebuttal, which the journal asked Egelman to review in December. Kelly’s response did not change his mind. 

After some back and forth regarding raw data Egelman suggested the journal request from Kelly, the journal published an expression of concern in February “in order to alert readers that concerns have been raised regarding the accuracy” of some of the data in the article. “An investigation is underway,” the notice stated.

Frustrated that Nanoscale still had not retracted the paper, Egelman submitted a concern to the Committee on Publication Ethics (COPE) in March. In August, after the retraction was published, COPE informed Egelman it could no longer consider the concern due to “ongoing legal procedures.” 

The two retracted works have been cited 27 times in total, according to Clarivate’s Web of Science. 

Separately, in July Egelman published a detailed critique of another of Kelly’s papers that appeared in Advanced Materials. “Basic principles in mathematics and physics would need to be violated” to achieve the reported results, he wrote. 

McCorvie said Current Opinion in Structural Biology would soon be pulling another paper by Kelly and her colleagues – “Liquid-EM goes viral – visualizing structure and dynamics” – that he did not flag, and that all of the authors had been informed of the move. 

That article, which has been cited six times, was the subject of “a lengthy and comprehensive peer review process” undertaken by Penn State and “conducted by three independent experts from outside of Penn State,” according to a July 26, 2024, email from the school’s Office for Research Protections obtained by Retraction Watch.

The “review process concluded that there are serious data integrity concerns relating to volume and model” in the article, wrote Chief of Staff Courtney Karmelita. She added:

In addition, the corresponding author, when asked to produce original research data to justify the data, maps and models in question, did not do so. For these reasons, Penn State recommends that this paper be retracted. The corresponding author who is copied here (along with the other co-authors whose contact information I could find) declined to seek retraction despite having been urged to do so by the peer review panel, thus requiring that I, as Research Integrity Officer, reach out to you directly with this institutional recommendation for retraction.

A spokesperson for Elsevier, the publisher of Current Opinion in Structural Biology, confirmed they were investigating the article.

Egelman told us:

The investigation at Penn State concluded in May, and they refused to make any of their report public but passed the matter to ORI [the federal Office of Research Integrity] that they said would ultimately issue a report. Kelly was the Chair of an NIH study section as well as the recipient of funds for many years from [the National Cancer Institute], so there is potential embarrassment for many parties.

In a statement, Penn State said it had “conducted a peer review with external subject matter experts” which “confirmed the presence of unreliable data in several papers.” The university contacted journals to request retraction of the papers and reported its findings to ORI, the statement confirmed.  

A spokesperson for ORI said the office was “not able to confirm or deny the existence of any potential pending cases.” 

In a letter to Current Opinion in Structural Biology on Kelly’s behalf, Paul Thaler, a partner at the Washington, D.C. firm Cohen Seglias Pallas Greenhall & Furman, disputed the retraction. Thaler argued the editors and university investigation had not provided Kelly with sufficient evidence the data in the paper were unreliable.
Thaler copied another lawyer, Pittsburgh, Penn.-based Heather S. Heidelbaugh of Leech Tishman. (In 2020, Heidelbaugh ran for attorney general of Pennsylvania against incumbent Josh Shapiro (now governor of the state) and lost.)

Like Retraction Watch? You can make a tax-deductible contribution to support our work, follow us on Twitter, like us on Facebook, add us to your RSS reader, or subscribe to our daily digest. If you find a retraction that’s not in our database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.

in Retraction watch on 2024-09-11 18:00:00 UTC.

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Ancient DNA unveils a previously unknown line of Neandertals

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California droughts may help valley fever spread

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Former Harvard cancer researcher plagiarized data, federal watchdog says

A former research fellow at Harvard Medical School faked data and used images from another scientist without attribution in a published paper and two grant applications, according to findings from the U.S. Office of Research Integrity. 

The researcher, Arunoday K. Bhan, was also a former staff scientist at City of Hope Medical Center in Duarte, Calif., and first author on “Human induced pluripotent stem cell-derived platelets loaded with lapatinib effectively target HER2+ breast cancer metastasis to the brain,” which appeared in Scientific Reports in October 2021. The article has been cited eight times. 

The paper was retracted in March. The retraction note cited an investigation by City of Hope and detailed “discrepancies in the data” that match ORI’s findings. 

ORI said it found Bhan relabeled multiple images in the paper as representing different cells than they portrayed, “without appropriate citation to the researcher who generated the image[s].” 

According to the agency, Bhan received funding from a grant to Boston Children’s Hospital meant to support postdoctoral fellows in transfusion medicine and cellular therapies “enabling them to move on to leading positions in academia or industry.”

Bhan agreed to have his research supervised for four years, and not to serve in any advisory role for the U.S. Public Health Service, which includes peer review committees at the National Institutes of Health. 

Bhan did not immediately respond to a request for comment sent to his City of Hope address, which did not bounce. We were not able to find information on his current position.

Like Retraction Watch? You can make a tax-deductible contribution to support our work, follow us on Twitter, like us on Facebook, add us to your RSS reader, or subscribe to our daily digest. If you find a retraction that’s not in our database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.

in Retraction watch on 2024-09-10 17:32:19 UTC.

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AI generates harsher punishments for people who use Black dialect

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A quantum computer corrected its own errors, improving its calculations 

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Billionaire Finally Launches on First Private Space-Walk Mission

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Crispr-Enhanced Viruses Are Being Deployed Against UTIs

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Episode 290 - Marina Silveira, PhD

On September 9, 2024 we got to talk to Marina Silveira about the inferior colliculus, its place in the auditory pathway, and the effort to understand its cellular makeup, internal structure, and auditory functions.

Guest:

Marina Silveira, Assistant Professor, Department of Neuroscience, Developmental and Regenerative Biology, UTSA

Host:

Charles Wilson, Department of Neuroscience, Developmental and Regenerative Biology, UTSA

Thanks to Jim Tepper for original music

in Neuroscientists talk shop on 2024-09-09 22:00:00 UTC.

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The first face transplant to include an eye shows no rejection a year later

in Science News on 2024-09-09 15:00:00 UTC.

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How earthquakes build beefy gold nuggets

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Pakistan university’s pharmacy department chair notches two retractions

Kashif Barkat, who heads the Department of Pharmacy at the University of Lahore in Punjab, Pakistan, has had two of his studies retracted and two more corrected, all for issues related to images in the papers. Several more of his studies are flagged on PubPeer for similar reasons. 

According to the retraction notice for one of the retracted articles, which appeared in  Polymer Bulletin in 2020, Barkat does not agree with the journal’s decision to pull the paper. 

The paper, “Understanding mechanical characteristics of pH-responsive PEG 4000-based polymeric network for colorectal carcinoma: its acute oral toxicity study,” has been cited three times so far, according to Clarivate’s Web of Science. 

The retraction note, issued in June, reads: 

The Editors-in-Chief have retracted this article. After publication, concerns were raised regarding highly similar areas between the group I and II images in Fig. 11 representing stomach, lung and intestine tissues. In addition, the heart group II and intestine both group images appear highly similar to Fig. 10 heart I and intestine II images, respectively, in [1].

The Editors-in-Chief therefore no longer have confidence in the presented data.

Kashif Barkat does not agree to this retraction. The other authors have not responded to any correspondence from the editor or publisher about this retraction.

Barkat has not responded to our request for comment. 

The other retraction for Barkat is of a 2022 paper published in BioMed Research International. The study, “Polyvinylpyrrolidone K-30-Based Crosslinked Fast Swelling Nanogels: An Impeccable Approach for Drug’s Solubility Improvement,” has been cited nine times, according to Clarivate’s Web of Science. 

Here’s the retraction notice, dated January 9: 

This article has been retracted by Hindawi, as publisher, following an investigation undertaken by the publisher [1]. This investigation has uncovered evidence of systematic manipulation of the publication and peer-review process. We cannot, therefore, vouch for the reliability or integrity of this article.

Please note that this notice is intended solely to alert readers that the peer-review process of this article has been compromised.

Wiley and Hindawi regret that the usual quality checks did not identify these issues before publication and have since put additional measures in place to safeguard research integrity.

We wish to credit our Research Integrity and Research Publishing teams and anonymous and named external researchers and research integrity experts for contributing to this investigation.

The corresponding author, as the representative of all authors, has been given the opportunity to register their agreement or disagreement to this retraction. We have kept a record of any response received.

For the two corrected articles, Barkat and his colleagues acknowledge errors in the published images but that those mistakes did not affect the main conclusions of the work. 

One correction, issued by the Journal of Applied Polymer Science in June, was for a 2017 study published by Barkat and colleagues, titled “Oxaliplatin-loaded crosslinked polymeric network of chondroitin sulfate-co-poly(methacrylic acid) for colorectal cancer: Its toxicological evaluation.” That paper has been cited 48 times.

The other corrigendum, issued in January 2023 by Frontiers in Chemistry, was for a 2022 paper titled, “Chitosan/Xanthan Gum based hydrogels as potential carrier for an antiviral drug: Fabrication, characterization, and safety evaluation,” cited 88 times.

At the end of the corrigendum, Frontiers in Chemistry published a separate note, which reads: 

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.

In addition to these four, 10 other studies coauthored by Barkat are being discussed on PubPeer.

Like Retraction Watch? You can make a tax-deductible contribution to support our work, follow us on Twitter, like us on Facebook, add us to your RSS reader, or subscribe to our daily digest. If you find a retraction that’s not in our database, you can let us know here. For comments or feedback, email us at team@retractionwatch.com.

in Retraction watch on 2024-09-09 12:00:00 UTC.

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Nobelists advertise for russian papermill?

in For Better Science on 2024-09-09 05:00:00 UTC.

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Alien Spaceships Could Be Detected Using Gravitational Waves

in WIRED Science on 2024-09-08 12:00:00 UTC.

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The Biggest Controversy in Cosmology Just Got Bigger

in WIRED Science on 2024-09-08 11:00:00 UTC.