Refining & revising research on the public record

179024690The life of a research project often doesn’t end when a publication appears in a journal. Experiments continue. Errors are found. Supporting or refuting data is published. Alternative explanations emerge… So PubMed Commons members are posting updated and complementary information to keep work current.

Honing interpretations

Consider, for example, Daniel Haft’s reflection on his publication from 2009. He identified some peptides in two Bacillus strains that he referred to as putative “bacteriocins”. The term describes bacterial peptides that are toxic to related strains. Use of the term was “overconfident”, he notes, “…given the lack of evidence then that these heterocycle-containing natural products were toxins rather than, say, peptide pheromones.” But now results from another group suggest he was on the right track after all.

Andrew Sharp’s group studies how genome structure relates to human disease including X-chromosome inactivation. He considers how a new publication describing DNA methylation in development might be relevant to their own work.

Meta-analysis can show patterns and discrepancies between results from different studies. The data can be calculated in different ways. Valeria Fadda provides alternative data visualizations by posting forest plots for risk differences from published meta-analyses.

Dopamine is a central player in addiction in rodents. Many factors, including where it acts, influence the effects of this neurotransmitter. Roy Wise notes how his group’s work supports recent findings on the consequences of location and what this might mean for the field.

“The mechanisms for establishing, maintaining, and reinstatement of cocaine self-administration have been studied extensively, but have not yet led to a proven medication for cocaine addiction,” Wise remarks. “Perhaps it is time to turn attention to the endogenous mechanisms for what appears to be a state of drug satiety.”

Amending prior work

Some authors highlight work that might strengthen or refine interpretations. Others note how new or existing data might change conclusions.

With co-author Raphael Silberzahn, Eric Uhlmann documents their new work on names and career outcomes. They had previously reported, “Germans with noble-sounding surnames, such as Kaiser (“emperor”), König (“king”), and Fürst (“prince”), more frequently hold managerial positions…” Their new analysis seems to overturn their previous conclusions.

Like many researchers trying to identify new antitumor agents, Miguel Lopez-Lazaro and his colleagues began by testing compounds in a cancer cell line. Since publishing their work, they followed up in other cell lines. Now he considers whether these in vitro effects will really translate to therapeutic potential.

Teasing apart the functions of specific proteins in cells or animals can get complicated. Using inhibitors or genetic manipulation doesn’t always provide a clear picture.

For example, Jens Staal explored the interplay of the protease MALT1 and the deubiquitnase CYLD in immune cells. After further experiments, he updates his interpretation.

Meanwhile, Jim Woodgett notes that care should be taken with assigning specific functions to a single protein isoform. He highlights the trouble with glycogen synthase kinase-3 inhibitors. After a few comments on the subject, he remarks, “…no small molecule inhibitors are isoform selective – I am a scratched record.”

Bridging published updates

When substantive errors are found, updates are not always clearly connected to original publications. PubMed Commons gives authors a chance to link pieces together in PubMed.

Sometimes errors are reported in follow-up studies. Consider a mutation in an HIV protein that was correlated with survival. Stuart Ray notes that a subsequent report of an alignment error invalidates the findings.

Other times, flaws in methods or results lead to correction or retraction of a report.

Randy Blakely finds that a paper about the human dopamine transporter continues to be improperly cited, despite a correction to the results. He says, “I am hoping the PubMed Commons forum will provide a suitable opportunity to redirect readers attention to the, as yet, unknown properties of the E602G mutation…”

Ivan Oransky uses PubMed Commons to annotate recent retractions. He includes links with more about the history of the publication and why it was withdrawn. For instance, here he points to where co-blogger Adam Marcus notes, “Failure to cite leads to ignoble end for xenon paper, and a correction.”

If you’re an author of a PubMed-indexed publication and ready to get involved, check out this page to learn how you can get started.

The PubMed Commons Team

 

This entry was posted in On the Commons and tagged , by NCBI Staff. Bookmark the permalink.

About NCBI Staff

The National Center for Biotechnology Information (NCBI), a division of the U.S. National Library of Medicine, provides access to scientific and biomedical databases, software tools for analyzing molecular data, and performs research in computational biology.

3 thoughts on “Refining & revising research on the public record

  1. How come most of the retractions Oransky has annotated are not yet noted in PubMed?

    does PubMed only accept such notices from publishers, and if so, can publishers delay the posting of retraction notices indefinitely just by not submitting them?

  2. Pingback: Commenting on PubMed: A Successful Pilot | PubMed Commons Blog

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