Years after papers were withdrawn, JBC issues notices

Journal of Biological Chemistry.coverThe Journal of Biological Chemistry has posted withdrawal notices for six papers that had already been withdrawn, some more than a decade ago, in an effort to resolve “PubMed indexing problems.”

Each paper had been pulled by the author before it appeared in print, but still appeared online on the the journal’s website and in PubMed. 

By our count, the journal has posted six notices so far, and said we should expect to see more in the future.

Kaoru Sakabe the Manager of Publication Issues at the American Society for Biochemistry and Molecular Biology, which publishes JBC, provided a statement on the new withdrawal notices:

It recently came to our attention that a number of our articles that were published online as Papers in Press and were withdrawn by the authors before final publication were still indexed in PubMed as Papers in Press.  Publishing these withdrawal notices now should mark these citations correctly in PubMed.

Sakabe also said that the journal was looking into providing the scientific community more information:

Also, we are conducting an internal investigation to see what additional information we can provide to the scientific community about the reasons for these in-press withdrawals. Some of these manuscripts were withdrawn quite a while ago, and we don’t have a lot of information. But we should be able to provide some information about the more recent ones.

Sakabe affirmed that:

these articles were published online as Papers in Press, but never appeared in their final form.  We plan on issuing more withdrawal notices in the near future to correct the PubMed indexing problems.

It’s an unusual insight at a journal which, as we’ve come to expect, doesn’t usually discuss retractions or withdrawals with anybody outside of the process.

“Silencing of Human Methionine Adenosyltransferase 1A Expression by Methylation of the Coding Region” was posted more than 10 years ago — in 2004 — and looked at the role of epigenetics in the spontaneous development of hepatocellular carcinoma in mice. The paper has only been cited once, by the withdrawal notice.

It was authored by scientists at the Keck School of Medicine at the University of Southern California and the Center for Cooperative Research in Biosciences in Bizkaia, Spain.

The withdrawal notice, however, didn’t appear until August, 2015:

This article was withdrawn by the authors before final publication on December 10, 2004. 

Shelly Lu, a professor at USC and the paper’s corresponding author, confirmed the paper should have been withdrawn more than a decade ago:

This was withdrawn the day after acceptance in 2004 when my postdoc admitted to me that some of the data was made up.

Another paper with a newly issued withdrawal notice, “RhoB-dependent modulation of early endocytic traffic in Madin-Darby canine kidney cells,” was originally posted in September, 2004. Authors at the University of Pittsburgh and Indiana University Medical Center studied the localization and function of RhoB GTPase. 

When reached for a statement, final author Gerard L. Apodaca, a professor at UPitt and head of the Apodaca Laboratory, said:

Soon after having this manuscript accepted for publication in June of 2004, we realized that the RhoB construct we were using had a point mutation. Because we did not know how this affected our results, we withdrew the manuscript.

The withdrawal notice, published last month, said as much:

This article was withdrawn by the authors before final publication on September 16, 2004.

Apodaca said that they repeated the experiment and re-published with additional data in 2007 in Traffic.

We subsequently repeated all of the experiments using a RhoB construct that lacked the offending mutation and after adding some additional data published the results in this article:

RhoB-dependent modulation of postendocytic traffic in polarized Madin-Darby canine kidney cells.

Rondanino C, Rojas R, Ruiz WG, Wang E, Hughey RP, Dunn KW, Apodaca G.

Traffic. 2007 Jul;8(7):932-49. Epub 2007 Jun 4.

PMID: 17547697

The paper has only been cited by the withdrawal notice.

The withdrawal notice for “Heat shock protein 70 interacts with nucleolin and inhibits its cleavage, downregulation and apoptosis induced by hydrogen peroxide in myocytes,” was published on August 14th:

This article was withdrawn by the authors before final publication on April 12, 2010.

The JBC also posted a notice for “The troponin T isoform shift may constitute a protective compensatory mechanism in hypertrophic cardiomyopathy,” after the paper was posted online:

This article was withdrawn by the authors before final publication on April 22, 2008. 

“TcJAMYC: a bHLH transcription factor that activates paclitaxel biosynthetic pathway genes in yew” was published and withdrawn in 2009. The notice was also published on August 14th:

This article was withdrawn by the authors before final publication on October 1, 2009.

The most recent paper, “Hypoxic induction of vascular endothelial growth factor (VEGF) and angiogenesis in muscle by N-Terminus Peroxisome Proliferator-Activated Receptor Gamma Coactivator (NT-PGC)-1alpha,” was published online last January.

The study, authored by a group of researchers at the Harvard Medical School, was withdrawn last January. The notice was posted in the beginning of August:

This article was withdrawn by the authors before final publication on January 15, 2014.

Corresponding author Zoltan Arany, who is now an associate professor at the University of Pennsylvania’s Perelman School of Medicine, said that the article was withdrawn “due to nomenclature errors” and “resubmitted a week later.” The article was published by the JBC two months later under a slightly different name.

The 2014 paper has been only been cited by the withdrawal notice.

We’ve contacted all other corresponding authors for statements and we’ll update with any reply.

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