To wit: The Journal of Clinical Pathology (JCP) has withdrawn/retracted a 2008 paper by a group of Indian authors (from the National Institute of Mental Health and Neuro Sciences, at Deemed University) whose cliff-hanging title asks the question “Tracking the footprints of the rabies virus: are we any closer to decoding this elusive virus?”

The authors have withdrawn the paper following an allegation of plagiarism

Would that be a no, then?

The JCP has another recent withdrawal of a paper, but this one provides nothing in the way of information for its readers:

Yamaguchi R, Mitsuyama S, Tanaka M, et al. Practical considerations in the detection of HER2 status: the pathological perspective. J Clin Path 2011. Published Online First 21 September 2011. doi:10.1136/jclinpath-2011-200046. This article has been withdrawn.

We asked C. Soon Lee, editor-in-chief of JCP, for elaboration and he told us that

Both were withdrawn because of plagiarism of other authors’ work.

Meanwhile, we understand that the JCP will be retracting yet another paper soon, this time for duplication. The article, “Immunohistochemical prognostic markers in diffuse large B-cell lymphoma: validation of tissue microarray as a prerequisite for broad clinical applications (a study from the Lunenburg Lymphoma Biomarker Consortium,” by a group of Dutch scientists led by Daphne de Jong, appeared online in September 2008.

But it was strikingly similar to a 2007 article in the  Journal of Clinical Oncology by the same group, titled “Immunohistochemical prognostic markers in diffuse large B-cell lymphoma: validation of tissue microarray as a prerequisite for broad clinical applications (a study from the Lunenburg Lymphoma Biomarker Consortium).” The JCP article has been cited 30 times, according to Thomson Scientific’s Web of Knowledge.

The similarity was first brought to the attention of Lee last July by the JCO and its publisher, the American Cancer Society. Email traffic we have seen shows that Lee contacted de Jong in October asking for her explanation for the apparent overlap. Here’s her response:

At the time of publication of our paper in the Journal of Clinical Pathology , this issue was also brought up by your predecessor. Much to my embarrassment, I must admit. We have had correspondence at that time in which I have clarified the essential differences between our two papers and indeed the discussion was concluded to our mutual satisfaction.

In brief, the Journal Clinical Oncology paper addresses the ability of pathologists to reliably score optimized immunohistochemical stains and elaborates on the consequences for the interpretation of clinico-pathological correlations and the weight that clinicians should put to these publications. The Journal of Clinical Pathology paper, however, addresses technical reproducibility by pathology labs, the causes of lack of reproducibility and their various solutions. Therefore, of the large validation project performed by LLBC, two largely independent validation studies are reported in the two publications and there is little overlap in the actual information content albeit that the overall conclusions are largely similar: immunohistochemistry is not a sufficiently reproducible method for patient stratification in daily practice.

I hope that this further clarifies this matter and that you can also convince the editor-in-chief of the Journal Clinical Oncology that indeed this matter was taken seriously both by your predecessor at JCP and by myself at the time of publication and in depth discussed and concluded at that time.

That reply evidently neither clarified the matter nor did much convincing — not, at least, quite how de Jong might have hoped.

In late December, Lee sent this reply:

The Editors of the Journal of Clinical Pathology (JCP) and our publisher, BMJ Publishing Group, have met on 6 Dec, 2011, to discussed your publication in JCP in 2009. As alerted by the Editor-in-Chief, Dr Stephen Cannistra, of the Journal of Clinical Oncology (JCO), we agreed with him that most of the content of the JCO publication was reproduced word for word in the JCP paper. In view of the later publication of JCP, we regret to inform you that a unanimous decision was made to retract your publication in the Journal of Clinical Pathology, entitled: “Immunohistochemical prognostic markers in diffuse large B-cell lymphoma: validation of tissue microarray as a prerequisite for broad clinical applications (a study from the Lunenburg Lymphoma Biomarker Consortium D de Jong, W Xie, A Rosenwald, M Chhanabhai, P Gaulard, W Klapper, A Lee, B Sander, C Thorns, E Campo, T Molina, A Hagenbeek, S Horning, A Lister, J Raemaekers, G Salles, R D Gascoyne, E Weller Journal of Clinical Pathology February 2009:128-38
DOI:10.1136/jcp.2008.057257

A notice on this matter will be made in the next available issue of JCP, and also to PubMed.

We’re curious whether that notice, when it arrives, will state the reason for the retraction.

Hat tip: Clare Francis

The American Chemical Society (ACS) Nano journal retracted a study, “Retraction of Nanoembossing Induced Ferroelectric Lithography on PZT Films for Silver Particle Patterning,”  late last month because of such duplication:

This article was withdrawn at the request of the Editor-in-Chief, with agreement by the authors, due to unacceptable redundant text and figures with a previously published article by the same authors (Langmuir 2011, 27, 5167-5170. DOI: 10.1021/la200377b).

This wasn’t the first such retraction for the journal. In May, they retracted ”Conductance Preservation of Carbene-Functionalized Metallic Single-Walled Carbon Nanotubes for the same reason:”

This article was withdrawn at the request of the Editor-in-Chief, with agreement by the authors, due to unacceptable overlapwith a previously published paper by the same authors (Small 2011, 7, 1257-1263; DOI:10.1002/smll.201002307) prior to the publication of the article in ACS Nano. 

Perhaps it’s not surprising, then, that the editors recently published an editorial titled “Recycling Is Not Always Good: The Dangers of Self-Plagiarism.” In it, they walk through what’s wrong with duplicating your own work and passing it off as new. They don’t say how often they’ve seen the practice, but they describe a number of anonymized cases:

The motivation for self-plagiarism is simple and relates back to the overused saying “publish or perish”.7,8 The conflict of interest inherent in a highly competitive system that “counts” papers when promotions and grant proposals are being evaluated can lead to dangerous temptation. 

Some researchers — including a number of commenters on this blog — have said that it’s silly that authors can’t re-use sentences in their methodology sections, for example. But intent is important, write the editors:

It all comes down to the central issue of deception; were the authors trying to deceive the editors, the referees, and the readers into presenting recycled data, text, and figures as entirely new material? We understand that experimental sections may run into difficulties of similar textual descriptions, and while care should be taken with the experimental method descriptions, these have not been the source of problems.

The authors also mention a blog we may have to check out. Duplication is a problem, write the editors, because it

may and likely will conclude with getting caught, and, in the most serious cases, manuscripts will be retracted and featured on the Retraction Watch Web site.9 Retraction Watch is a Web site set up by two science journalists, Adam Marcus and Ivan Oransky, who have received international attention for tracking high-profile retractions of papers, many of which were for self-plagiarism. In their invited year-end contribution to Nature entitled “Science Publishing: The Paper is Not Sacred” (December 22, 2011), Marcus and Oransky remind all authors that “peer review continues long after a paper is published”,10 as the scientific community continues to read, to reference, and to scrutinize the literature. With over 150,000 views per month, Retraction Watch has a large following of scientists, editors, and journalists who want to keep the record straight.

Sounds bad! But it’s actually quite simple to avoid ending up on Retraction Watch. Just cite yourself, for goodness’ sake, the editors urge, quoting the ACS’ guidelines, revised last month:

“Authors should not engage in self-plagiarism (also known as duplicate publication); unacceptably close replication of the author’s own previously published text or results without acknowledgement of the source. ACS applies a “reasonable person” standard when deciding whether a submission constitutes self-plagiarism/duplicate publication. If one or two identical sentences previously published by an author appear in a subsequent work by the same author, this is unlikely to be regarded as duplicate publication. Material quoted verbatim from the author’s previously published work must be placed in quotation marks. In contrast, it is unacceptable for an author to include significant verbatim or near-verbatim portions of his/her own work, or to depict his/her previously published results or methodology as new, without acknowledging the source. (Modeled with permission from Society for Industrial and Applied Mathematics: Authorial Integrity in Scientific Publication)”11 

Hat tip: desantoos

has been looking into it and I think that they will tell everybody what it is all about. I think that somebody out there is putting this whole thing together and their mind is made up.

However, Aggarwal, chief of the center’s cytokine research section, denied that any retractions of his papers were forthcoming. He refused to comment on whether officials had confiscated his computer, as a commenter to this blog has claimed.

Allegations of misconduct by Aggarwal have surfaced recently on at least two blogs. One, devoted to the subject, lists 14 papers. Abnormal Science also been on the trail and has posted images for evaluation.

Aggarwal’s papers are highly cited. One, published in Science when he was still at Genentech in 1985, has been cited more than 1,700 times. according to Thomson Scientific’s Web of Knowledge. Another, about the potential anti-cancer effects of curcumin, has been cited 700 times.

He has also published on resveratrol, the component in red wine that some researchers claim has anti-aging and other healthy properties. One of his papers on the subject has been cited 370 times. He also edited a book on the topic that included a contribution from Dipak Das, the UConn researcher found to have committed 145 counts of scientific misconduct.

Aggarwal’s bio is worth a look:

Dr. Aggarwal has published more than 600 papers in peer-reviewed international journals (including Science, Nature, Cancer Cell, PNAS, Journal of Exp. Medicine, JBC, Cancer Research, Journal of Immunology), invited reviews and book chapters. He has been listed as one of the most highly cited scientist by ISI since 2001; and has been included in ISI Highly Cited among most highly cited authors in Immunology category. He has also been listed as top 25 researchers in apoptosis area in the World. His papers exhibit high-citation index (over 1000 for some).

Dr. Aggarwal is inventor/coinventor on over 33 patents.

Dr. Aggarwal has received numerous awards including World Congress Science Prize from Oxygen Club of California 2010, Excellance in Research Award of McCormick Research Institute from the American Association of Nutrition, 2008, Outstanding Scientist Award from the American Association of Indian Scientists in Cancer Research, 2006, Ranbaxy Award for Outstanding Scientist of the year, 2004.

Needless to say, we’ll be following this case closely.

We figured more retractions might be on the way, so we weren’t surprised when a commenter informed us earlier today of “very interesting and odd retraction letter.” Miller has had at least one other retraction, it turns out, this one in Developmental Neuroscience for 2009′s “Lability of Neuronal Lineage Decisions Is Revealed by Acute Exposures to Ethanol.” Here’s the notice, published online on January 19:

On August 6, 2010, the Editor-in-Chief of Developmental Neuroscience , Steven W. Levison, was contacted by the legal counsel for SUNY Upstate Medical University and informed that an investigative committee at SUNY Upstate had determined that Dr. Michael Miller was guilty of multiple counts of research misconduct, and they requested that Developmental Neuroscience retract the 2009 article authored by Drs. Miller and Huaiyu Hu. The committee did not find Dr. Hu at fault for any scientific misconduct. After independently reviewing the reports of the investigative committee and the rebuttals provided by Dr. Miller, the Editor-in-Chief and the publisher concurred that there were errors in reporting sample sizes and in mathematical calculations that affected the statistical analyses. However, at that time it was our view that an erratum was more appropriate than a retraction of the article. Despite the flaws in the analyses of the data, it was our determination that those flaws could be corrected in a published erratum to produce a final product that would be more useful to the scientific community than a complete retraction of the work. On December 10, 2010, we requested that Dr. Miller provide a corrected figure with an explanation of the mistakes that had been previously published.

However, that erratum was never published as we were provided with additional information and testimonies that convinced us that the collected data may also be unreliable.

Accordingly, on October 18, 2011, we requested that a letter of retraction be provided that was co-authored and co-signed by both authors. It was our view that for an action as severe as an article retraction, both authors needed to sign the retraction letter. However, Drs. Miller and Hu were unable to agree upon a letter that could be jointly signed.

Therefore, at the request of the President of SUNY Upstate, with this statement we formally retract the article by Drs. Miller and Hu, Developmental Neuroscience 2009;31:50–57.

We have sent correspondence to both authors, to the President of SUNY Upstate and to Dr. Steven Goodman, Vice President for Research at SUNY Upstate, to inform them in advance that this action is being taken by the journal.

The paper has been cited just once, according to Thomson Scientific’s Web of Knowledge.

The level of detail in the notice is commendable, and as in the last retraction by Miller we covered, the journal takes pains to make it clear that his co-author is not responsible for the misconduct.

But what’s particularly interesting is that the journal chose to give Miller the benefit of the doubt — which we agree should be the default in most cases — even after being presented with what sounds like clear evidence of misconduct.  That’s noteworthy because journals often blame institutions for their delays in taking action, usually when those institutions drag their heels on investigations and won’t release the results when they’re complete. Here’s a case in which Upstate seemed to be transparent — to the journal, anyway; they haven’t made any public statements about Miller, as far as we know — and the journal needed to be prodded.

This article has been withdrawn by the authors.

Late last week, we heard back from corresponding author Takashi Tsuji by email. It turns out one of our commenters had basically figured out what was wrong. It was, as seems to often be the case lately in retractions we cover, troubles with Western blots:

In September of 2011, an editor have informed me that the JBC office have received complaints concerning our published paper in JBC from a reader.  We have checked the indicated figures in compared to those source files according to the complaints carefully and found our mistakes.

We have displayed the data of Western blot analysis for beta-actin and we had used the same data in several figures by our mistake.  After the Western blot analysis for many samples, only the image for target protein was transferred to figure file by the trimming of the source file.  In these processes, those mistakes would be occurred.  We checked original source files and experimental notebook carefully, and confirmed the existence of those original data with reproducibility.  Furthermore, the meanings and explanations about our results in our paper are correct and need not to change the explanation in response to the replacements of those figures, even if the incorrect WB is replaced with correct one in those figures.

However, we should sincerely apologize to being our careless to prepare those figures and troubling on readers of JBC.  Thus, we have withdrawn our paper by ourselves.  We do not  plan to withdraw another our published paper in near future.

So it’s not surprising that F1000 is announcing today that they’re launching a new journal, F1000 Research,

intended to address three major issues afflicting scientific publishing today: timely dissemination of research, peer review and sharing of data.

 The journal will publish all submissions immediately, “beyond an initial sanity check:”

It no longer makes sense to wait months or years to read, comment, or build upon another lab’s work, and similarly to hold back your own data and insights until the archival version is released, without the benefit of wider peer feedback. All work at pre-review stage will be very clearly indicated as such.

I asked F1000′s Rebecca Lawrence what comprised a “sanity check:”

Sanity check is really just a check that it isn’t complete rubbish – it is a basic in-house editorial check, similar to what is done by most publishers (e.g. like PLoS One) before anything would be sent for referee.

Lawrence said that the new journal’s approach meshed with the ideas we — and others — have proposed for post-publication peer review:

What we are planning to do fits well with that general idea – i.e. inclusion of all comments, referee reports, author responses, corrections, updates etc, as well as trying to pull together metrics and relevant discussion around the paper that is hosted elsewhere e.g. blogs, tweets etc. The idea is that the paper never finishes refereeing – at the moment we have a largely arbitrary cut-off point when the paper is published but by making all the refereeing post-publication means that anyone can comment on it at any point in the future – and in fact the authors can correct/update it at any point in the future.  What we will need to work out is what constitutes a minor update versus a linked but new manuscript.

The journal will work much as arXiv does for physics, in which papers are published as pre-publication drafts and usually published elsewhere after peer review. One question, however, is whether publishing a dataset and protocol on F1000 Research would count as a violation of the Ingelfinger Rule, in which journals say they won’t publish anything after it’s already run in the media or other journals. Lawrence has been looking into that, as she did with another project, F1000 Posters:

Everyone confirmed to me that it would not be considered prior publication (including the likes of NEJM, Science, J Clin Invest, Lancet, BMJ, PNAS, Nature-titled journals, Elsevier journals, BMC, PLoS etc and even the RSC journals) except for Cell Press and Ann Oncol, and possibly a couple more who are veering in that direction at the moment.  A full list of responses will be on the f1000research.com site later today.

Naturally, at Retraction Watch we were interested in what the journal’s approach might mean for retractions:

In terms of retractions, it is an interesting question. The ability to continue to update your article following publication will help with some of the issues but if articles are plagiarised or turn out to be a fabrication then we still need to be able to retract in such circumstances.  Of course the advantage we have is that all such retractions etc will be very obvious at source rather than needing a later publication that is unlinked to the original article.

We’ll certainly keep an eye on F1000 Research and see what develops.

Update, 3 p.m. Eastern, 1/30/12: See comments for a number of questions for F1000, particularly about how the journal will differ from Nature Precedings, along with responses from Rebecca Lawrence. Also, Nature‘s Richard van Noorden explains how arXiv deals with retractions.

Stefano Fiorucci, a gastroenterology researcher at the University of Perugia in Italy, has been indicted for fraud and embezzlement, after a university investigation found that he had manipulated images in papers that he used to win about 2 million Euros in grant funding.

The case, which has so far resulted in four retractions and nine Expressions of Concern, has dragged on for several years. The trial is scheduled for July. It’s the first time that embezzlement charges have been brought against a scientist found to have committed fraud, according to reports in Umbria 24 and the Umbria Journal.

Fiorucci’s attorney, Stefano Bagianti, told Umbria 24 that there was

No photomontage, no manipulation and  no misappropriation of public funds.

Umbria 24 notes (translation):

Fiorucci said he had scanned the images to ensure they were well presented, but had not manipulated them in any way. As for money, he denied that he made use of money  that was allocated to the university department where he worked.

Fiorucci was first arrested in June of 2008 for fraud and embezzlement, but has remained in his post since then, and has published some 19 papers. The police are quoted in an APM story published at the time of his arrest:

“During the course of the investigation it was ascertained that some scientific works were inaccurate because they were based on laboratory results which had been manipulated.”

They added that there was evidence that images had been photocopied or electronically altered.

The police said they believe charges of embezzlement could be brought against Fiorucci because of allegations that he used public funds for uses that had not been authorised and for research which proved to be false.

He may also be charged with fraud because worked as a consultant and scientific director for pharmaceutical companies with authorisation, they said.

For example, Fiorucci is quoted in a 2003 press release by NicOx about work of his they funded which was later published in the Journal of the American College of Cardiology. That paper does not appear to have been subject to an Expression of Concern or retraction. (The company’s stock price took a dive in 2010.)

Antonio Morelli, head of the University of Perugia research team that included Fiorucci, brought the matter to the university’s attention. He is “demanding compensation for damage  to his  personal moral standing  and image  as well as  for  those of the Gastroenterology Section,” according to Umbria 24.

We’ve tried to reach Fiorucci, and will update with anything we hear back.

Here are the four retractions:

• “NO-mesalamine protects colonic epithelial cells against apoptotic damage induced by proinflammatory cytokines,” originally published in 2001 in the American Journal of Physiology: Gastrointestinal and Liver Physiology and cited 16 times, according to Thomson Scientific’s Web of Knowledge:

The University of Perugia appointed an internal Investigatory Commission to investigate the validity of claims of alleged academic misconduct with respect to several publications including Am J Physiol Gastrointest Liver Physiol 281: G654-G665, 2001. The Commission determined that Professor Stefano Fiorucci, the first and corresponding author of the above mentioned paper, while not necessarily involved in manipulating data himself, should have provided greater oversight of this and other papers submitted from his laboratory and thus is ultimately responsible for any violation of appropriate standards. Review of this article by the American Physiological Society (APS) has led to the conclusion that Figure 1B is fraudulent and that Figure 3F is an inappropriate composite of different images, which may invalidate its conclusions. In accordance with APS publication policies, the above-referenced paper is being retracted due to ethical concerns.

• “A NO-releasing derivative of acetaminophen spares the liver by acting at several checkpoints in the Fas pathway,” first published in the British Journal of Pharmacology in 2001, cited 33 times:

A NO-releasing derivative of acetaminophen spares the liver by acting at several checkpoints in the Fas pathway by Stefano Fiorucci, Elisabetta Antonelli, Andrea Mencarelli, Barbara Palazzetti, Lorena Alvarez-Miller, Marcelo Muscara, Piero Del Soldato, Laura Sanpaolo, John L Wallace and Antonio Morelli (Br J Pharmacol 135; 589–599; 2002) has been retracted by agreement between Professor A Morelli (Head of Gastroenterology, University of Perugia); other co-authors of the paper E Antonelli, B Palazzetti, MN Muscara, P Del Soldato, JLWallace; the Editor-in-Chief of the British Journal of Pharmacology andWiley-Blackwell.

Concerns were raised about the authenticity of PCR gel band images in several papers of Fiorucci et al; and were investigated by an official Committee of Inquiry set up by the University of Perugia. Although the inquiry was unable to draw conclusions regarding this paper because the original records were not available, it is clear to the Editors that part of a gel band in Figure 4 has been blacked out, without any comment in the text or legend, so this paper is being retracted based upon the Journal’s own expert opinion.

• “Liver delivery of NO by NCX-1000 protects against acute liver failure and mitochondrial dysfunction induced by APAP in mice,” first published in the British Journal of Pharmacology in 2001, cited 18 times:

Liver delivery of NO by NCX-1000 protects against acute liver failure and mitochondrial dysfunction induced by APAP in mice by Stefano Fiorucci, Elisabetta Antonelli, Eleonora Distrutti, Andrea Mencarelli, Silvana Farneti, Piero Del Soldato and Antonio Morelli (Br J Pharmacol 143; 33–42; 2004) has been retracted by agreement between Professor A Morelli (Head of Gastroenterology, University of Perugia); other co-authors of the paper, E Antonelli, P Del Soldato; the Editor-in-Chief of the British Journal of Pharmacology and Wiley-Blackwell.

Concerns were raised about the authenticity of PCR gel band images in Figure 2 of Fiorucci et al; and were investigated by an official Committee of Inquiry set up by the University of Perugia. This retraction was subsequently agreed based on the conclusions of this inquiry together with the Journal’s own expert opinion.

“A role for proteinase-activated receptor-1 in inflammatory bowel diseases,” first published in the Journal of Clinical Investigation in 2004 and cited 62 times:

RT-PCR blots published in panel C of Figure 8 of this paper were mistakenly reproduced from a previous publication. The senior author sincerely regrets this error and would like to emphasize that this in no way diminishes the validity of the data contributed by the coauthors of the paper. However, the paper is being retracted in accordance with JCI policy.

The authors apologize for any inconvenience this error has caused.

Here are the nine Expressions of Concern:

• Three in the Proceedings of the National Academy of Sciences (PNAS), for “NCX-1000, a NO-releasing derivative of ursodeoxycholic acid, selectively delivers NO to the liver and protects against development of portal hypertension” (cited 85 times), “NCX-1015, a nitric-oxide derivative of prednisolone, enhances regulatory T cells in the lamina propria and protects against 2,4,6-trinitrobenzene sulfonic acid-induced colitis in mice” (cited 57 times), and “A β-oxidation-resistant lipoxin A₄ analog treats hapten-induced colitis by attenuating inflammation and immune dysfunction” (cited 94 times):

The editors wish to note that a reader has raised questions about the apparent duplication in the use of certain figures in the foregoing articles. We have been informed by the University of Perugia, Italy, of an ongoing review conducted by an inquiry committee at the university. We are awaiting the findings of the committee to determine the appropriate next steps.

• “A FXR-SHP Regulatory Cascade Modulates TIMP-1 and MMPs Expression in HSCs and Promotes Resolution of Liver Fibrosis,” originally published in 2005 in The Journal of Pharmacology and Experimental Therapeutics and cited 60 times:

The Journal of Pharmacology and Experimental Therapeutics is publishing an Editorial Expression of Concern regarding allegations of figure manipulation or figure duplication in several figures published in JPET. An investigation by an inquiry committee at the University of Perugia, Italy has confirmed or validated findings compatible with alleged hypotheses of electronic duplication and/or figure manipulation. The figure in question in this article is Fig. 6.

• “Cooperation between Aspirin-triggered lipoxin and nitric oxide (NO) mediates anti-adhesive properties of NCX-4016 (NO-aspirin) on neutrophil-endothelial cell adherence,” originally published in 2004 in The Journal of Pharmacology and Experimental Therapeutics and cited 25 times:

The Journal of Pharmacology and Experimental Therapeutics is publishing an Editorial Expression of Concern regarding allegations of figure manipulation or figure duplication in several figures published in JPET. An investigation by an inquiry committee at the University of Perugia, Italy has confirmed or validated findings compatible with alleged hypotheses of electronic duplication and/or figure manipulation. The figures in question in this article are Figs. 2 and 6.

• “Crosstalk Between Farnesoid X-receptor (FXR) and Peroxisome Proliferator-Activated Receptor (PPAR)γ Contributes To the Anti-Fibrotic Activity of FXR Ligands In Rodent Models of Liver Cirrhosis,” originally published in 2005 in The Journal of Pharmacology and Experimental Therapeutics and cited 55 times:

The Journal of Pharmacology and Experimental Therapeutics is publishing an Editorial Expression of Concern regarding allegations of figure manipulation or figure duplication in several figures published in JPET. An investigation by an inquiry committee at the University of Perugia, Italy has confirmed or validated findings compatible with alleged hypotheses of electronic duplication and/or figure manipulation. The figure in question in this article is Fig. 2.

• “Evidence that hydrogen sulfide exerts antinociceptive effects in the gastrointestinal tract by activating KATP channels,”  originally published in 2005 in The Journal of Pharmacology and Experimental Therapeutics and cited 99 times:

The Journal of Pharmacology and Experimental Therapeutics is publishing an Editorial Expression of Concern regarding allegations of figure manipulation or figure duplication in several figures published in JPET. An investigation by an inquiry committee at the University of Perugia, Italy has confirmed or validated findings compatible with alleged hypotheses of electronic duplication and/or figure manipulation. The figure in question in this article is Fig. 1.

• “Nitric oxide (NO)-releasing naproxen (HCT-3012) interactions with aspirin in gastric mucosa of arthritic rats reveals a role for aspirin-triggered lipoxin, prostaglandins and NO in gastric protection,” first published in The Journal of Pharmacology and Experimental Therapeutics in 2004 and cited 19 times:

The Journal of Pharmacology and Experimental Therapeutics is publishing an Editorial Expression of Concern regarding allegations of figure manipulation or figure duplication in several figures published in JPET. An investigation by an inquiry committee at the University of Perugia, Italy has confirmed or validated findings compatible with alleged hypotheses of electronic duplication and/or figure manipulation. The figure in question in this article is Fig. 5.

• “NCX-4016 (NO-Aspirin) Inhibits Lipopolysaccharide-Induced Tissue Factor Expression In Vivo: Role of Nitric Oxide,” first published in Circulation in 2002 and cited 41 times. (The original paper makes no mention of the Expression of Concern.)

Other scientists have also raised concerns about a 2002 paper in Immunity, “Importance of Innate Immunity
and Collagen Binding Integrin alpha-1-beta-1 in TNBS-Induced Colitis.”

Yesterday, Ivan wrote on his Tumblr about Case Western’s Erik D. Andrulis‘ paper, “Theory of the Origin, Evolution, and Nature of Life:”

The paper is 105 pages, which includes a whopping 800 references. It depends heavily on the gyre:

In the theory proposed herein, I use the heterodox yet simple gyre—a spiral, vortex, whorl, or similar circular pattern—as a core model for understanding life. Because many elements of the gyre model (gyromodel) are alien, I introduce neologisms and important terms in bold italics to identify them; a theoretical lexicon is presented in Table 1. The central idea of this theory is that all physical reality, stretching from the so-called inanimate into the animate realm and from micro- to meso- to macrocosmic scales, can be interpreted and modeled as manifestations of a single geometric entity, the gyre.

Andrulis concludes:

…this catholic theory provides an innovative and elegant solution to the origin, evolution, and nature of life in the cosmos. I humbly proffer my theory as a viable system for knowing life.

Our humble author also includes paragraphs like this, which led some on Twitter to wonder if the paper was for real:

The philosopher Bachelard claimed that scientific history is replete with unconsciously constructed or immanent “epistemological obstacles,” that are eventually broken through and shed during “epistemological rupture [796].” I conclude that my theoretical work elicits a Bachelardian rupture of intradisciplinary noöspheres and interdisciplinary boundaries. Kuhn proposed a related concept of “paradigm shift” to explain the process surrounding worldview conversion during a scientific revolution [797]. Whether the advent of this theory elicits a Kuhnian gestalt switch is debatable, though such an iconoclastic event has been foretold [798-800].

On Thursday, Case Western had put out a press release about the study. That release is still available on ScienceDaily and other sites, but the medical school removed it from their own site. Today, Liz Lear, senior director, School of Medicine Marketing and Communications, tells us:

The School of Medicine’s public affairs office promotes all faculty research as possible. We have been evaluating our processes regarding media outreach and elected to remove the release from our website while we assess our policies surrounding promotional communications.

We’ll continue to update this story as we find out more. In the meantime, you can read PZ Myers’ take, in which he suggests that “the comparison to jabberwocky” is inevitable, and John Timmer’s, in which he wonders “How the craziest f#@!ing “theory of everything” got published and promoted.”

Update, 5:45 p.m. Eastern, 1/31/12: Carl Zimmer reports that a number of the journal’s editors have resigned.

The retraction notice for “Multiple HLA class I and II associations in classical Hodgkin lymphoma and EBV status defined subgroups,” dated January 20 and signed by all of the authors, clearly explains what went wrong, taking pains to note that there was no misconduct involved:

The authors wish to retract the 10 November 2011 article cited above, prepublished on 14 September 2011, because they miscalculated some of the HLA allele frequencies due to missing information on split alleles (mainly in controls). Individuals with missing split allele information were erroneously left out of the analyses, which caused some (3/11) of the reported significant associations to be incorrect. The authors noticed the errors themselves and directly contacted the editors of Blood. It was an honest mistake, not fraud or scientific misconduct. The authors sincerely apologize to the readers, reviewers and editors of Blood for making this unfortunate mistake.

Corresponding author Anke van den Berg told us she had nothing to add:

I think that all relevant information is already mentioned in the retraction and I have no further comments. Our and the journal’s goal was to correct the scientific record.

We asked Blood editor Cynthia Dunbar how the errors came the group’s attention:

Dr. van den Berg contacted us, I believe her group internally discovered the issue. Another investigator also brought the issue to our attention in a letter to the editor submitted a few days later, having read the paper and working the data in comparison with some of his own, realized the control allele frequencies had to be incorrect, but he told me he had not contacted Dr. van den Berg himself.

Hat tip: Clare Francis

Here’s the notice for the paper, which has been cited 23 times, according to Thomson Scientific’s Web of Knowledge:

Retraction for “Structural basis for nucleotide exchange on Gαi subunits and receptor coupling specificity,” by Christopher A. Johnston and David P. Siderovski, which appeared in issue 6, February 6, 2007, of Proc Natl Acad Sci USA (104:2001–2006; first published January 30, 2007; 10.1073/pnas.0608599104).

The authors wish to note the following: “In our paper, a cocrystal structure at 2.2 Å resolution was described of the heterotrimeric G-protein alpha subunit Gαi1 bound to two peptides: one from an artificial sequence that promotes nucleotide exchange (KB-752) and a second peptide (D2N) from the third intracellular loop of the D2 dopamine receptor (PDB ID code 2HLB). Further examination of the unbiased electron density map has revealed that, while electron density exists for the KB-752 peptide, there is a lack of clear and continuous electron density for the D2N receptor peptide in the complex. Because the structural model represents a major conclusion of the paper but is unsupported by the experimental electron density map, we wish to retract the paper. Both authors deeply regret this mistake and sincerely apologize.”

The reason for the retraction is essentially the same as the one for the Structure paper. We’ve contacted Siderovski for comment, and will update with anything we hear back.

Siderovski has collaborated with the late Maria Diverse-Pierluissi, four of whose papers were retracted after her death. Siderovski and Diverse-Pierluissi published two papers together, neither of which has been retracted — although a former postdoc in Diverse-Pierluissi’s lab suggests there may be issues with one of them. And Mount Sinai, where Diverse-Pierluissi worked, told us several months ago that they considered their investigation closed.

In other words, we have no reason to think the retractions are related. But this seems to be the first case of two groups linked by disparate retractions.

Update, 2 p.m. Eastern, 1/26/12: It turns out we missed a correction by the same group that was released the same day in PNAS — and for basically the same reason as the retraction:

Correction for “Regulators of G-protein Signaling accelerate GPCR signaling kinetics and govern sensitivity solely by accelerating GTPase activity,” by Nevin A. Lambert, Christopher A. Johnston, Steven D. Cappell, Sudhakiranmayi Kuravi, Adam J. Kimple, Francis S. Willard, andDavid P. Siderovski, which appeared in issue 15, April 13, 2010, of Proc Natl Acad Sci USA (107:7066–7071; first published March 29, 2010; 10.1073/pnas.0912934107).

The authors note that Fig. 1 appeared incorrectly. They also wish to note the following: “Upon further evaluation of the unbiased electron density maps for the structural models of Gαi1(G202A)·GDP (PDB id 2PZ2) and Gαi1(G202A)·GDP·AlF4–(PDB id 2PZ3), there is a lack of clear and continuous density to support an entirely ordered switch II region or to support the presence of aluminum tetrafluoride in the latter structure. We have therefore obsoleted the x-ray structure model PDB 2PZ3 from the Protein Data Bank. We have replaced PDB 2PZ2 with PDB 3UMS in the Protein Data Bank to reflect the more accurate refinement of the Gαi1(G202A)·GDP structural model.”

The corrected figure and its corresponding legend appear below. This error does not affect the conclusions of the article.

Hat tips: Clare Francis, Vladimir Svetlov