Archive for the ‘pnas’ Category
By now, most of our readers are aware that some fields of science have a reproducibility problem. Part of the problem, some argue, is the publishing community’s bias toward dramatic findings — namely, studies that show something has an effect on something else are more likely to be published than studies that don’t.
Many have argued that scientists publish such data because that’s what is rewarded — by journals and, indirectly, by funders and employers, who judge a scientist based on his or her publication record. But a new meta-analysis in PNAS is saying it’s a bit more complicated than that.
In a paper released today, researchers led by Daniele Fanelli and John Ioannidis — both at Stanford University — suggest that the so-called “pressure-to-publish” does not appear to bias studies toward larger so-called “effect sizes.” Instead, the researchers argue that other factors were a bigger source of bias than the pressure-to-publish, namely the use of small sample sizes (which could contain a skewed sample that shows stronger effects), and relegating studies with smaller effects to the “gray literature,” such as conference proceedings, PhD theses, and other less publicized formats.
However, Ferric Fang of the University of Washington — who did not participate in the study — approached the findings with some caution:
The chair of a biology department who has faced years of misconduct accusations has taken another hit—a lengthy correction due to text “overlap” between one of his PNAS papers and six other articles.
According to the correction, a reader contacted the journal to notify the editors that text and sentences in multiple sections of the 2015 paper — on which Carlo Croce is last author — were lifted from other sources without quotation marks.
This is the second correction for Croce in PNAS regarding overlap issues in just the last few weeks—the first was published on March 7 (see here). In both instances, PNAS did not call the textual similarities plagiarism, but the notice details multiple instances of overlap.
Croce, the chair of the department of cancer biology and genetics at The Ohio State University (OSU), is no stranger to controversy.
Last week, a study brought into question years of research conducted using the neuroimaging technique functional magnetic resonance imaging (fMRI). The new paper, published in PNAS, particularly raised eyebrows for suggesting that the rates of false positives in studies using fMRI could be up to 70%, which may affect many of the approximately 40,000 studies in academic literature that have so far used the technique. We spoke to the Anders Eklund, from Linköping University in Sweden, who was the first author of the study. Read the rest of this entry »
Researchers are retracting two papers about molecular signalling in plants — including one from the Proceedings of the National Academy of Sciences (PNAS) — after discovering some inadvertent genotyping errors. But that was only after they used the problematic plants for an entire year without realizing they’d made a mistake.
In a pair of refreshingly transparent and detailed notices, the authors explain that the transgenic plants used in the papers included genotyping errors, which invalidated their findings. According to the notices, first author Man-Ho Oh generated the problematic transgenic plants, while corresponding author Steven C. Huber, based at University of Illinois, Urbana-Champaign (UIUC), took responsibility for omitting some critical oversight.
Huber told us that there were only two papers that used the transgenic plants in question, so no other retractions will be forthcoming.
A PNAS paper that caught the media’s attention for suggesting that adding silk could stabilize vaccines and antibiotics has been pulled after the authors realized there were significant errors in the data analysis.
According to the notice, the authors agreed to retract the 2012 paper; however, the corresponding author told us the authors did not think a retraction was required as, according to him, the conclusions remained valid.
The paper presented a solution to the long-standing problem that sensitive biological compounds such as vaccines and antibiotics begin to lose their effectiveness outside the recommended temperature range, and naturally biodegrade over time. The degradation process cannot be reversed, and may even speed up during transport or storage under less ideal temperatures.
The study, published today in the Proceedings of the National Academy of Sciences, used data from the psychology replication project, which found only 39 out of 100 experiments live up to their original claims. The authors conclude that more “contextually sensitive” papers — those whose background factors are more likely to affect their replicability — are slightly less likely to be reproduced successfully.
They summarize their results in the paper:
The former University of Tokyo endocrinologist recently earned another retraction, for a paper in Archives of Biochemistry and Biophysics that contained image manipulation. As we’ve noted before, Kato resigned from the university in 2012 as it investigated his work for misconduct; in 2013 a Japanese newspaper reported that the investigation had found 43 papers from his lab contained “likely altered or forged materials.”
In addition to the new retraction, we’ve dug up four others for Kato from the past few years, plus one correction. Two of the retraction notices mention an investigation at the University of Tokyo.
First, the retraction note for “Multiple co-activator complexes support ligand-induced transactivation function of VDR,” published in December:
An analysis of more than 50,000 papers submitted to Proceedings of the National Academy of Sciences (PNAS) shows that those published using its “contributed track” — in which academy members can fast-track their own papers by coordinating the peer-review process themselves — have been cited less often than regular submissions, but that gap is shrinking.
Although the overall average difference in citations between contributed and regular submissions was 9%, the yearly difference has declined from 13.6% in 2005 to 2.2% in 2014, according to the new study, posted before peer review on the preprint server bioRxiv by Phil Davis, an independent researcher and publishing consultant based in New York.
Five years ago this month, Swedish pharmaceutical company WntResearch immediately notified shareholders when authors retracted a 2009 Proceedings of the National Academy of Sciences (PNAS) paper on a potential cancer therapy that was key to the company’s business.
At the time, the company’s decision to disclose the retraction hurt its finances, as WntResearch delayed its planned initial public offering for three weeks. It also offered investors and shareholders the opportunity to withdraw their shares of WntResearch stock.
But, aside from one of the paper’s co-authors, “No one did that,” Nils Brünner, WntResearch’s CEO, told us. Since the company’s IPO on December 17, 2010, its stock price has increased from Read the rest of this entry »
Two out of the three authors of a PNAS paper on mutations underlying lung diseases are pulling it after failing to reproduce key findings.
The paper, published in 2012, investigated how mutations in lung surfactant genes induce molecular changes that lead to lung pulmonary fibrosis and lung cancer might work. But follow-up work revealed problems. In the retraction note, last author Christine Kim Garcia and second author Christoper Cano, both at the University of Texas Southwestern Medical Center, write:
Current members of the C.K.G. laboratory are unable to reproduce key findings reported in the paper.
Here’s the retraction note in full: