A pair of expressions of concern in PLOS ONE over vet science papers

PLoS ONE has issued two Expressions of Concern on unrelated studies, each of which offers plenty to be concerned about — and not just about the research itself.

One is a casualty of our old friend,  Jesús Lemus, the Spanish veterinary scientist accused of fabricating his data.

The article, titled “The PHA-Skin Test Reflects Acquired T-Cell Mediated Immunocompetence in Birds,” was published in September 2008 and cited 61 times, according to Google Scholar.

Back in April, the publisher posted this comment to the paper:

The PLoS ONE editorial team has become aware that the Consejo Superior de Investigaciones Científicas (CSIC) is carrying out an investigation into the research by Dr Jesús Ángel Lemus. The PLoS ONE editors have contacted the CSIC and requested to be informed of the outcome of the ongoing investigation. The PLoS ONE editors will consider whether any specific action is required in relation to Dr Lemus’ publications at PLoS ONE as soon as we are notified of the outcome of the institutional investigation.

Now comes the following:

The authors and the editors are issuing this Expression of Concern on the PLOS ONE article entitled “The PHA-skin test reflects acquired T-cell mediated immunocompetence in birds”, to make readers aware of concerns over part of the results and conclusions of the study.

The study consisted of two experiments. Experiment #1 was entirely conducted by José L. Tella (JLT) and Martina Carrete (MC), who performed the experimental assays, recorded data and conducted all statistical analyses. Results showed that the PHA test produces a larger secondary than primary immune response, suggesting an acquired immunocompetence in such a response. Experiment # 2 was aimed to assess to what extent the tissue swelling elicited by the PHA test was related to changes in cell profiles circulating in the bloodstream. Experimental assays were again conducted by JLT and MC, who also bled the birds and sent plasma samples to Dr. Lemus for laboratory analyses. Dr. Lemus did not have any contact with the birds used in this experiment and conducted the laboratory analyses blindly (the plasma samples were labeled with a code). MC crossed the laboratory results provided by Dr. Lemus with the tissue swelling measurements, body masses and identity of birds obtained by JLT and MC, which were unknown to Dr. Lemus, and performed the statistical analyses. These analyses showed highly significant correlations between individual tissue swelling and circulating CD5+ and CD8+ lymphocyte subsets (Figure 3), thus supporting the conclusions of experiment #1 on the use of the PHA test as an indicator of acquired T-cell mediated immunocompetence in birds.

In January 2012, the Ethics Committee of the Spanish Superior Council of Scientific Research (CSIC) initiated a formal investigation in relation to concerns about potential scientific misconduct by Dr. Lemus. The investigation was recently completed and in relation to this article, the Ethics Committee of CSIC was not able to clarify in which external laboratory Dr. Lemus conducted the flow cytometry analyses. The fact that the analyses were carried out blindly makes it unlikely for the significant correlations between tissue swelling and circulating CD5+ and CD8+ lymphocyte subsets shown in Figure 3 to be the result of data fabrication. The published correlation coefficients significantly differ from those obtained by chance, being near twice the upper confidence intervals for coefficients of correlations obtained from 100 randomizations of tissue swelling data. However, the uncertainty about the laboratory where the cytometry analyses were performed does raise concerns about the reliability of the results.

The validity of the results and conclusions derived from Experiment # 1 has not been questioned. However, in light of the outcome of the institutional investigation, we want to make readers aware that concerns remain in relation to the cytometry analyses included in Experiment # 2.

The authors sincerely apologize for all inconvenience to the PLOS ONE readership.

Is concern the right move here rather than retraction? Hard to say. But, given that other journals — including PLoS ONE — retracted other papers by Lemus, we’re thinking: If it looks like a pearly parakeet (one of the birds in the study) and squawks like a pearly parakeet, it’s probably a pearly parakeet.

The second notice affects “Novel Allelic Variants in the Canine Cyclooxgenase-2 (Cox-2) Promoter Are Associated with Renal Dysplasia in Dogs,” a 2011 article whose authors include researchers in industry, Tufts and (we never thought we’d write this) the American Lhasa Apso Club.

But, as they say, evidently that dog wouldn’t hunt. According to the notice:

After the publication of this article, a number of concerns were raised in relation to different aspects of the research reported. The PLOS ONE editors carried out an evaluation of the history of the manuscript, which revealed that due to a failure in the peer review process, several aspects of the research were not adequately evaluated before publication.

As a result, the PLOS ONE editors have undertaken a thorough re-examination of this study, involving both external and internal advisers. This assessment has revealed the following concerns regarding the study:

  1. The description of the alleles in the article is inadequate.
  2. There are concerns over the study design employed to study the association; a single-gene association study based on Cox-2 or a genome-wide association study have been recommended as more appropriate approaches to study this association.
  3. The validity of the control population employed in the study is compromised as it involved a different breed.
  4. There are concerns about the strength of the evidence shown to support an association between the Cox-2 variant and the dogs’ phenotypes, as the evidence from other breeds suggests that this may be a neutral DNA variant.

In the light of the concerns outlined above, the PLOS ONE editors are issuing this Expression of Concern in order to make readers aware of the concerns about the reliability of the results and conclusions reported in the article.

This strikes us a strong entry in the best-of-breed for mega-corrections. After all, what, exactly, remains after pretty significant caveats?

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