Mary Beth O’Leary, a spokeswoman for Cell Press — an Elsevier title — tells us that:

Based on our own initial in-house assessment of the issues raised in PubPeer and in initial discussions with the authors, it seems that there were some minor errors made by the authors when preparing the figures for initial submission.  While we are continuing discussions with the authors, we do not believe these errors impact the scientific findings of the paper in any way. 

O’Leary also dismissed the notion that rushing the article into print compromised the review and editorial processes:

A number of comments about these errors in articles and blogs have drawn connections to the speed of the peer review process for this paper.  Given the broad interest, importance, anticipated scrutiny of the claims of the paper and the preeminence of the reviewers, we have no reason to doubt the thoroughness or rigor of the review process. The comparatively rapid turnaround for this paper can be attributed to the fact that the reviewers graciously agreed to prioritize attention to reviewing this paper in a timely way. It is a misrepresentation to equate slow peer review with thoroughness or rigor or to use timely peer review as a justification for sloppiness in manuscript preparation.

The article, “The effect of alendronate on the expression of osteopontin and osteoprotegerin in calcified aortic tissue of the rat,”  came from the Institute of Cardiovascular Disease at Tongji Hospital, part of of Huazhong University of Science and Technology.

As the retraction notice states:

This article has been retracted at the request of the Authors due to a disagreement regarding authorship.

Jaap van Harten, executive publisher of the EJP, tells us that:

This dispute was brought to my attention by the authors themselves. They were unanimous in their request, and no matter what further clarifications I asked them, I did not get any further than that the authorship dispute was so serious that each of the authors explicitly informed me that the wanted to have the article retracted for that reason. Not very satisfactory, but the max I could do.

Indeed. We think van Harten did the right thing, given that all of the authors had a problem with the paper. But it would be nice to know what, in particular, the problem was, yes?

The article, “Exvivo experiments of human ovarian cancer ascites-derived exosomes presented by dendritic cells derived from umbilical cord blood for immunotherapy treatment,” purported to show that:

tumor-specific antigens present on exosomes can be presented by DCs [dendritic cells] derived from unrelated umbilical cord blood to induce tumor specific cytotoxicity and this may represent as a novel immunotherapy for ovarian cancer.

But according to William C. S. Cho, editor of the journal, there’s reason to doubt the conclusions. As the notice explains:

In 2012 the journal was informed of apparent flaws in Figure 2 of Qi-Ling Li, Ning Bu, Yue-Cheng Yu, Wei Hua and Xiao-Yan Xin. Exvivo experiments of human ovarian cancer ascites-derived exosomes presented by dendritic cells derived from umbilical cord blood for immunotherapy treatment. Clinical Medicine: Oncology. 2008;2;461–7. doi: 10.4137/CMO.S776. The journal commenced an investigation in accordance with the Committee on Publication Ethics (COPE) guidelines.

The journal was unable to complete a full investigation in accordance with the guidelines. In view of this, the journal must emphasise that no conclusions have been drawn on responsibility for the apparent flaws. In accordance with COPE guidelines the journal has published this expression of concern and recommends that readers interpret Figure 2 with caution.

The paper has yet to be cited, according to Thomson Scientific’s Web of Knowledge.

Although we don’t have enough data at this point, we seem to be covering more expressions of concern lately. Is it just our imagination, or are they become more common?

This one appears in PLOS ONE, for “Infectious Offspring: How Birds Acquire and Transmit an Avian Polyomavirus in the Wild:”

The authors Drs Potti, Blanco and Canal retract this publication.

The Ethics Committee of the Spanish Superior Council of Scientific Research (CSIC) has carried out a formal investigation in relation to concerns about potential scientific misconduct by Jesús A. Lemus, the third author of this article. The investigation has questioned the validity of the laboratory analyses conducted by Dr. Lemus. Although the published field and statistical procedures reported in our article are correct, we have been unable to clarify in which external laboratories Dr Lemus conducted the molecular analyses and which primers he used.

We have now partially replicated the work by submitting blood aliquots of the same samples employed in the original study to two different independent laboratories to assess the validity of the published results on avian polyomavirus (APV) in pied flycatchers. In both cases, replicate samples with different IDs were also submitted as controls.

The first re-analysis (Technoscience, Seville, Spain) used the protocol followed by Tomasek et al. [1] on 40 samples previously scored by Dr Lemus as 27 positive and 13 negative for APV. Only 37% (10 out of 27) of the samples originally scored as positive for APV were also positive in the re-analysis carried out by Technoscience, while the consistency was greater for negative scores (86.5%, 11 out of 13 samples scored negative for APV in the re-analysis).

A second, more extended re-analysis (NBT, Seville, Spain) used the protocol by Johne et al. [2] on 276 of the original samples. In addition, the NBT laboratory ran additional PCRs using their own designed primers for a conserved region of APV. All of these analyses have returned negative scores for APV presence in all samples.

In the light of the lack of consistency in relation to the prevalence of APV between the published results and the re-analyses undertaken, the authors Drs Potti, Blanco and Canal wish to retract this article. We sincerely apologize for any inconvenience to the readership of PLOS ONE.

References

1. Tomasek O, Kubicek O, Tukac V (2008) Comparison of three template preparation methods for routine detection of beak and feather disease virus and avian polyomavirus with single and nested polymerase chain reaction in clinical specimens. Avian Pathol. 37: 145-149. doi:10.1080/03079450801902047
2. Johne R, Enderlein D, Nieper H, Müller H (2005) Novel polyomavirus detected in the feces of a chimpanzee by nested broad-spectrum PCR. J. Virol. 79:3883-3887. doi:10.1128/JVI.79.6.3883-3887.

Lemus already has two retractions in PLOS ONE, along with an Expression of Concern. The newly retracted paper has been cited nine times, according to Thomson Scientific’s Web of Knowledge.

When writing updates on some of the scientists whose names appear frequently on Retraction Watch, we can’t help being reminded that tearing off a Band-Aid quickly causes less pain than doing it slowly.

The potential image problems came to light on PubPeer, a site designed to allow for post-publication peer review. A commenter, identified as Peer1, identified “several examples of image reuse which might be of interest to PubPeer members and readers:”

- Fig. 2F is a slightly cropped version of the cell microscopy image in Fig. 6D top left.

- Fig. 6D top right, the cell microscopy image is a slightly cropped version of supplementary Fig. s5, top right. The cells in 6D are labelled as “h-ESO-NT1 Ph” yet in figure s5 they are labelled to be “hESO-7″. We understand the former to inherit caffeine-treated somatic nuclei whereas the latter are original stem cells.

Under pressure to assemble the figures for rapid publication, one can understand making a cut and paste figure assembly mistake. Nevertheless it should be noted that image cropping does take extra work.

- Figure S6 top centre and top right are the same image.

- Figure S6 middle left and lower right are reported to be biological replicates of microarray expression quantitation. In those cases however the narrow spread indicates that the data are extremely similar and are only understandable as technical replicates (where the same RNA sample is hybridised to two different arrays). It is useful to do technical replicates to control experimental reproducibility, but biological replicates are more valuable when reporting results. They are not the same thing and should not be conflated. (For the record, we did check the microarray data deposited at Gene Expression Omnibus (GSE46397)).

Cell tells us that

Our editorial team is currently assessing the allegations brought up in the PubPeer piece.

It’s not clear whether these alleged manipulations are central to the claims of the paper. We’ll keep an eye on this and update as we learn more from Cell.

Please see an update on this post, with more details from Cell.

Hat tip: Ed Yong

Here’s the notice for “The Emergence of Orthographic Word Representations in the Brain: Evaluating a Neural Shape-Based Framework Using fMRI and the HMAX Model,” by Wouter Braet, Jonas Kubilius, Johan Wagemans, and Hans P. Op de Beeck:

The authors retract this publication. Because of human errors by the first/corresponding author, the fMRI data reported in this retracted paper were not analyzed properly. The errors were detected when other lab members reanalyzed the data for another purpose. At that point, it turned out that the original data analyses by the first author included several operations which are hard to replicate and which do not fit fully with the methods as agreed upon with the co-authors and as described in the paper. Because of this we no longer consider these results trustworthy.

The computational work in the manuscript, which was the sole contribution of co-author, J. Kubilius, is not compromised per se, but we decided for a full retraction given the weight of the fMRI data in this publication.

The first author regrets the errors and takes responsibility for them, and he cooperated fully with the investigation once the initial doubts had surfaced. All authors of the original publication agree with this retraction.

The first author, Wouter Braet, left KU Leuven in October 2012 for the University of Kaiserslautern in Germany. He tells us he is there “on a fixed-term contract that is due to end in a few months.”

Except for the fact that the notice is behind a paywall — which is the publisher’s fault, not the authors’ — this would seem to be a model retraction. It’s specific, detailed, and is a clear attempt to correct the literature, even at a personal cost.

As the senior author, Hans Op de Beeck, tells us:

As PI I have made the decision to retract once an internal lab investigation provided me with a full understanding of what had gone wrong and why. All authors support this decision, the author who made the errors fully collaborated with the investigation, and thus there was no reason to wait for lawyers or administrative reports (which can give very long delays and related frustration, as you know very well). The decision to retract is also a conservative decision, in the sense that one could wonder whether it would have been possible to save parts of the paper through a correction, but we preferred to follow a high standard in this matter.

Op de Beeck also reported the issue to a board for scientific integrity at KU Leuven, which prompted an institutional investigation. It’s not clear when that will be completed, and Op de Beeck decided to retract in the meantime, which seems like the right thing to do. We hope the university will release the report when their investigation is complete, and clear up any remaining questions — which will also be the right thing to do.

It’s a clear and comprehensive notice, from the Journal of Applied Ecology, despite the bizarre nature of the case:

The retraction has been agreed following doubts raised by an investigation carried out by the Ethics Committee of the Spanish Superior Council of Scientific Research (CSIC) relating to the validity of the laboratory analyses conducted by Dr Lemus, as well as the existence of Dr Lemus’s collaborator, Javier Grande.

The Journal of Applied Ecology article did not form part of the CSIC investigation. However, following this investigation, the lead author of the article was unable to confirm the identity of the laboratories where Dr Lemus carried out the analyses or to identify the co-author.

Although the field and statistical procedures and the diet data reported in the paper are not subject to any concerns, there are doubts about the validity of the results on the bacterial flora composition, which were combined with the other data for overall analysis. Therefore, the overall findings of the study are cast into doubt.

The Aging Male

The article, “Testosterone therapy improves psychological distress and health-related quality of life in Chinese men with symptomatic late-onset hypogonadism patients,” came from a group at Peking University People’s Hospital, in Beijing.

But as the retraction notice explains:

The Editor and Publisher would like to inform the readers the following article published Early Online has been retracted from publication in The Aging Male: Xiaowei Z, Zhenhua L, Yeqing Y, Wenjun B, Xiaofeng W, Huan S, Yongping Z. Testosterone therapy improves psychological distress and health-related quality of life in Chinese men with symptomatic late-onset hypogonadism patients. Aging Male. 2013 Jan 10. [Epub ahead of print]. (doi:10.3109/13685538.2012.754007).

This article has been found to reproduce content to a high degree of similarity, without appropriate attribution or acknowledgement by the authors, from the following original article: Zhang XW, Liu ZH, Hu XW, Yuan YQ, Bai WJ, Wang XF, Shen H, Zhao YP. Androgen replacement therapy improves psychological distress and health-related quality of life in late onset hypogonadism patients in Chinese population. Chin Med J (Engl). 2012 Nov;125(21):3806–10. (doi:10.3760/cma.j.issn.0366-6999.2012.21.011).

The majority of the text in the manuscript published in The Aging Male is almost word-for-word identical to the text published in the Chinese Medical Journal and the data presented in all four tables is also essentially the same. The authors have been fully co-operative with our investigations and agree with the Editor and Publisher on this course of action to correct the redundancy in the literature record.

The journal’s policy in this respect is clear: The Aging Male considers all manuscripts on the strict condition that they have been submitted only to The Aging Male, that they have not been published already, nor are they under consideration for publication or in press elsewhere.

The Aging Male published this article in good faith, and on the basis of signed statements made by the corresponding author regarding the originality of their work. The article is withdrawn from all print and electronic editions.

To which we say to The Aging Male: Don’t feel so bad, it happens to lots of journals.

Update, 3 p.m. Eastern, 5/21/13: Corrected first sentence, using strikethroughs, as this was plagiarism, not duplication (see Rob Siebers comment below).

Update, 11:45 a.m. Eastern, 5/22/13: Turns out the post was correct to begin with, and this was duplication, so we’ve reverted the original first sentence. Have a look at the comments below for an explanation, which is actually pretty interesting.

Here’s the notice for the paper, “Optimal quantum communication using multiparticle partially entangled states,” by Atul Kumar, Satyabrata Adhikari, Subhashish Banerjee, and Sovik Roy:

This article should be considered withdrawn from publication. Although the paper shows that maximal slice (MS) states are not locally equivalent to the χ states, it fails to reference and discuss the closely related material presented in the following article: T. Gao, F. L. Yan, and Y. C. Li, Europhys. Lett. 84, 5001 (2008).

The article also makes extensive use of a preprint by Dr. A. Kumar, Dr. A. Kalchenko, and Dr. S. Ghose. Although the article acknowledges S. Ghose, Dr. Ghose and Dr. A. Kaltchenko are not included as authors.

Although Drs. Adhikari, Banerjee, and Roy did not know about the preprint, Drs. Kumar, Adhikari, Banerjee, and Roy, together with Physical Review A, apologize to both Drs. Ghose and Kaltchenko, and also to Dr. Gao and his coauthors for these omissions.

Taking the reasons for the retraction in order: Failing to reference a prior study is clearly bad practice, but if journals consistently used that as a reason to retract, the retraction figures would be staggering.

Making “extensive use” of a preprint without including its authors on the subsequent paper, however, seems like typical grounds for a retraction. And this notice places the blame pretty squarely on the shoulders of Atul Kumar, of the Indian Institute of Technology Rajasthan, in Jodhpur, India — the only one of the study’s authors who seems to have known about the preprint.

That’s kind of puzzling, though, given that Adhikari, Banerjee, and Roy are all co-authors on the preprint.

Partially entangled states, indeed.

Hat tip: Chris Lee

Update, 10:30 a.m. Eastern, 5/21/13: Struck through line about authors of the preprint, and removed link in the previous sentence. As commenter Schlupp points out, the notice appears to be referring to a different preprint (which doesn’t seem to be on arXiv).

The article, “Isolation and Functional Characterization of an Antifreeze Protein Gene, TaAFPIII, from Wheat (Triticum aestivum),” came from the same group we wrote about in April 2012 when they retracted a paper from Acta Biochimica et Biophysica Sinica, also about genetically altered wheat.

At the time, the authors said they were pulling the other paper because they were having trouble replicating their findings. That now seems accurate, but not entirely complete.

As the new retraction notice states:

This article has been retracted due to fraudulent content with serious consequences to wheat production and its economic impact.

We haven’t been able to reach anyone involved in the case to know whether this retraction and the misconduct that precipitated it are indeed dire for wheat production. We note that the leader of the group, Guangyuan He, directs a joint lab between China and the United Kingdom.