Retraction Watch

Tracking retractions as a window into the scientific process

“An example for all authors to uphold:” Researcher logs 5 corrections

with 6 comments

A scientist in Ireland has corrected five of his papers in a single journal dating back more than a decade, after image-related problems were brought to his attention.

Four of the newly corrected papers have a common last and corresponding author: Luke O’Neill of Trinity College Dublin in the Republic of Ireland. O’Neill is also a co-author of the remaining paper that was fixed. O’Neill told us the mistakes were a “bit sloppy,” noting that he takes responsibility for the errors in the four papers on which he is last author.

O’Neill forwarded Retraction Watch a comment he received from Kaoru Sakabe — data integrity manager at the American Society for Biochemistry and Molecular Biology (which publishes The Journal of Biological Chemistry (JBC)) — that reads:

The efforts you went through for these corrections are commendable and an example for all authors to uphold.

Sakabe confirmed that she had send the comment, telling Retraction Watch:

Throughout the process, Dr. O’Neill was cooperative and prompt.

O’Neill told us:

Back in September the journal in question -J Biol Chem – contacted me about errors in the top 4 papers listed. I was able to correct the errors and the journal was happy with the corrections…

Sakabe added:

The JBC investigates all credible concerns. If a corresponding author requests a correction, that spurs an investigation. If a reader raises a concern, that spurs an investigation. Every correction, retraction, or withdrawal starts with an investigation. During an investigation, the corresponding author is required to provide original data and an explanation.  If the corresponding author provides the original data and a satisfactory explanation, and if the results of the study still stand, then a correction may be in order.

Let’s take a look at the corrections.

Here’s the correction notice for “IRAK1 and IRAK4 promote phosphorylation, ubiquitination, and degradation of MyD88 adaptor-like (Mal):”

Fig. 1E did not conform with the JBC policy that the groupings of images from different parts of the same immunoblot must be made explicit. This error has now been corrected. This error does not affect the results or conclusions of the work.

For this 2010 paper — which has been cited 22 times, according to according to Clarivate Analytics’ Web of Science, formerly part of Thomson Reuters — O’Neill sent JBC the original blot, he said.

Here’s the second correction notice:

Fig. 1B did not conform with the JBC policy that groupings of images from different parts of the same immunoblot must be made explicit. This error has now been corrected. Additionally, ASC was included in the panel on the right as a positive control. Fig. 3, F and G, also did not conform to JBC‘s policy on grouping. This error has now been corrected. These errors do not affect the results or conclusions of this work.

The 2009 paper, “Rab39a Binds Caspase-1 and Is Required for Caspase-1-dependent Interleukin-1β Secretion,” has been cited 30 times. Original data in question in this paper could not be located, O’Neill said.

To his knowledge, the two papers above were published after guidelines on how figures should be spliced (by adding black lines in to make splicing evident) were released by the JBC, O’Neill noted.

From the JBC’s instruction for authors:

Avoid assembling immunoblot figures by splicing lanes from different sections of a gel. If blots must be spliced, borders between separate sections must be clearly marked and explained in the figure legend.

Here’s the next correction notice:

Several blots were inadvertently duplicated in Figs. 1D, 2A, 4E, and 6, A and G. These errors have now been corrected and do not affect the results or conclusions of this work.

The 2005 paper, “Schlafen-1 causes a cell cycle arrest by inhibiting induction of cyclin D1,” has accumulated 40 citations.

Duplicate loadings in this paper were the result of a “sloppy mistake,” said O’Neill, noting that the original blots were available, and sent to the journal.

Here’s the next correction notice:

There was an error in Fig. 2B. In the original data provided by the authors to the journal, lanes 1–6 of Fig. 2B were electrophoresed on a different gel from lanes 7 and 8. During figure assembly, the authors erroneously reused lane 4 to represent lane 7. The authors have repeated the experiment, and the results are shown. This error does not affect the results or conclusions of the work.

This 2006 paper, “MyD88 adapter-like (Mal) is phosphorylated by Bruton’s tyrosine kinase during TLR2 and TLR4 signal transduction” has garnered 131 citations.

According to O’Neill, the authors have redone the experiment for this correction to produce a new figure, as there were “too many intervening lanes” in the published version. 

A side note: Caroline Jefferies, one of the middle authors of this corrected 2006 paper, was also a middle author of a paper retracted in 2014. That Immunity paper was pulled for inappropriate presentation but “no evidence of intentional misconduct.”

Finally, here’s the correction notice for a 2010 paper on which O’Neill is third-to-last author:

Because of clerical errors in preparing the figures, in Fig. 1A, the last portions of the mouse and human TILRR sequences are not aligned with the consensus sequence, and the human form is mislabeled as 716 amino acids (aa). In Fig. 2C (and on page 7227, right column, line 4), the most potent form of the human protein is mislabeled as 710 aa. Supplemental Fig. S1 correctly shows the alignment and the length of the human TILRR protein as 715 aa, with the most potent form, lacking the N-terminal 6 aa, as 709 aa. The amino acid sequence is correct as shown in all figures, and the clerical errors have no impact on any of the results, including the function of the protein, the probes used, or the numbering of the mutants.

This 2010 paper, “TILRR, a novel IL-1RI co-receptor, potentiates MyD88 recruitment to control Ras-dependent amplification of NF-κB,” has been cited 14 times.

O’Neill told us he doesn’t know about the problems with the final paper, so we’ve reached out to its last and corresponding author, Eva Qwarnstrom, based at The University of Sheffield in the UK. We’ll update the post if we hear back. 

In 2013, O’Neill, Jeffries, and Aisling Dunne (lead author of first of the now-corrected JBC papers listed above) logged another correction due to problems with a figure in a 2007 PNAS paper, on which O’Neill is last author.

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Comments
  • Morty January 9, 2017 at 4:53 pm

    “An example for all authors to uphold”.

    To be so sloppy?

    Problematic issues with 16 articles from the same senior author are listed at PubPeer:

    https://pubpeer.com/search?q=Luke+O%E2%80%99Neill+&sessionid=BCAA0C8789C3D99EFC46

    • Anonymous January 10, 2017 at 2:51 am

      The data integrity manager’s comments were regarding cooperative conduct during an investigation, not his original work. While it looks like Dr. O’Neill’s lab might produce sloppy science, at least he owns up to it and appears to be committed to correcting the literature. I think that’s a lot better than what some others do in these situations. Not ideal, but could be a lot worse.

      • fernandopessoa January 10, 2017 at 7:47 am

        “at least he owns up to it” Where is the evidence of that?

        • TL January 10, 2017 at 8:42 am

          How can all these figures be incorrect yet nothing affects the conclusions of anything?

        • Anonymous January 11, 2017 at 12:05 pm

          “O’Neill told us the mistakes were a “bit sloppy,” noting that he takes responsibility for the errors in the four papers on which he is last author.”

  • Neuroskeptic January 10, 2017 at 5:24 am

    I’m not sure that this is a case of “doing the right thing”.

    It sounds like O’Neill did not alert the journal to the problems himself, rather someone else alerted the journal and they asked O’Neill for his response. If so, O’Neill’s corrections are no more “the right thing” than any other correction.

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