Archive for October, 2010

NIH Budget – Timing & Impact on FY11 Paylines etc.

Right now, traffic on the NIH Paylines & Resources and NIH Discussion pages is all about what does my impact score mean and will I get funded. Most funding decisions are a long way off, though, since 1) the NIH is currently operating under FY10 budget levels; 2) there is a mid-term election coming up (everyone get out & vote!); and 3) results of this election will likely affect whether the NIH gets the recommended 3% increase, a lesser increase, or even a cut in appropriation.

The current Continuing Resolution will keep the federal government operating at FY10 levels through December 3rd. Last year, a non-election year, the omnibus FY10 appropriations bills were passed by Congress and signed by the President in December. However, the CR could well be extended through the start of the new Congress next January. Keep in mind, though, that FY07, which encompassed the 2006 mid-terms, was managed under a CR all year. Not surprisingly, the ICs must be conservative in making funding decisions until they know how much money they have to play with … and will be especially conservative this year with even more unknowns in the equation.

Where do things stand? The Labor/HHS/Education Appropriation Bill, which funds the NIH budget, includes $1B increase for the NIH … but came out of Committee last July along partisan lines (18-12 vote) and has not been considered by the House. The Senate Committee report is of interest in that it lays out Senate interest in specific areas of research at each IC, such as a request to fund liver cancer SPOREs, an increase in funding for stroke research (“The Committee is concerned that the NIH continues to invests only 1% of its budget on stroke research”), and a “networked pediatric research consortia model”. The Report includes only one item under NIGMS that probably would not immediately come to mind for most of us:

The Committee applauds the Institute’s leadership role in the OppNet initiative, which will support basic behavioral science throughout the NIH. The Committee encourages the NIGMS to support basic behavioral research to its fullest potential, and to incorporate basic behavioral training in its forthcoming training plan.

Nature News prepared a series of pieces about the loss of NIH champions in Congress, the threat posed by the deficit on science funding, and the potential ideological (and budgetary) challenges science could face after the mid-term elections. The loss of NIH champions such as Arlen Specter and David Obey, make the NIH appropriation situation even more precarious.

So what about everyone with scored Cycle 1 applications? For applications scored outside the FY10 payline, my advice is to start working on a resubmission (if an A0). For those near or just inside the FY10 payline, decisions will be a long way off in all likelihood, so you might want to discuss a resubmission strategy with your PO (who won’t know about funding either until an appropriation is passed). For those with clearly fundable scores and an encouraging word from your PO, notices will be slow trickling out, so please be patient. And for those of you looking to ICs with no prior payline benchmarks, please be patient with your PO … unless your score is obviously competitive or not, he or she will not know about funding strategies until the NIH appropriation passes, and the advice will likely be to plan on resubmission (assuming you still have your A1 left) or reworking the research for a (legal) new submission.

Update: Oof … from Bloomberg News:

Republicans taking control of the House next year would roll back funding to agencies including NIH to fiscal 2008 levels, according to a proposal by Rep. Eric Cantor, R-Va., who is likely to become the chamber’s majority leader. That would equate to a 4.3% , or $1.3 billion, cut to the agency’s $30.8 billion annual budget.

But then a glimmer of hope …

Some Republican lawmakers in the House and Senate may defy the budget cuts and defend NIH, Zeitzer said. One ally may be Sen.-elect Mark Kirk of Illinois, who now serves on the House Appropriations Committee, which controls discretionary spending. … Other potential Republican supporters include Reps. Brian Bilbray of California and Dave Reichert of Washington and Sen. Richard Shelby of Alabama.

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Peer Review Survey

The Comparative Assessment of Peer Review (who knew?), an NSF-funded project of the Center for the Study of Interdisciplinarity (who knew?) at the University of North Texas, has an online survey that you are all invited (and encouraged) to complete. The CAPR “examines the peer review process at 6 science agencies worldwide: NSF, NIH, NOAA, NSERC, the EU’s 7th Framework Programme, and the Dutch STW.”

Probably not entirely what you might expect, but still an interesting thought exercise with plenty of opportunity to enter free-text comments and input.

The project is also creating a digital repository for the aforementioned science agencies (the sorts of program & policy documents not easily found in one place) and examining the broader impacts criteria for NSF-funded research (other than their own).

And, speaking of peer review & broader impacts, for those of you familiar with the Rocket Boys story (and even more so for those of you who are not familiar with it!), I think you’ll enjoy this adorable little (3’32″) video from the NIH.

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Journal Comment Commentary

Although I appreciated the humor with which Rick Trebino wrote about his effort to publish a comment, I also appreciate the underlying serious sentiments regarding the lack of scientific dialogue-debate in the scientific literature. My post last year about Rick’s tale of woe and intrigue generated a bit of discussion, and I thought it was time to revisit the issue of comments (or attempted comments) on journal articles to engage the scientific community.

I found a recent example in Cell instructive – both the comment itself and the manner in which article commentary is managed. Cell permits online comments, subject to Editor approval, but these are only posted on the journal page, not on ScienceDirect, Elsevier’s online full-text database through which most of their published material is accessed. One would think the best way to stimulate scientific discussion of an article would be to keep approved comments linked to the Websites through which most of the community will access the material.

For comparison, Science (AAAS) allows readers to submit E-letters in response to articles, and Nature invites comments directly, with no prior approval needed, though contributors must agree to the Community Guidelines. Nature also maintains a number of blogs, including Peer-to-Peer, which specifically solicits discussion about journal peer review.

Also, one would assume the involvement of the Editor in approving online comments would make them as rigorous yet more timely than printed letters. Cell does not indicate that comments will be held offline until the authors have had a chance to respond, but a recent case suggests otherwise.

In response to PcrA Helicase Dismantles RecA Filaments by Reeling in DNA in Uniform Steps by Park et al., Khan, Anand, and Leuba submitted a comment on August 23rd that was not displayed online until September 20th (simultaneously with author response). The Khan et al. comment focuses on science:

Dismantling of RecA filaments by PcrA was originally published in 2007 by our lab and collaborators
This paper from the Ha lab shows a “new” activity for the monomeric form of PcrA helicase at the ss/ds junction of DNA substrates. The authors show that PcrA helicase, which is bound to ss/ds junctions, can displace RecA under conditions in which PcrA helicase does not unwind the substrate. The thermophilic homolog of PcrA was used in these studies. Surprisingly, the authors of the current publication do not cite our paper published three years ago (Anand SP, Zheng H, Bianco PR, Leuba SH, Khan SA, J Bacteriol. 2007 Jun;189(12):4502-9. Epub 2007 Apr 20) which demonstrated the displacement of RecA from preformed RecA filaments by PcrA. Until the current publication from Ha and collaborators, our paper was the only one demonstrating the RecA displacement activity of PcrA. We had also presented our results at various international conferences, including the first Gordon Research Conference on Single Molecule Biology in 2006.

Our biochemical experiments on PcrA were prompted by genetic studies in Bacillus subtilis from the Ehrlich lab that showed suppression of a pcrA knock-out by mutations in the recFOR genes (Petit MA, Ehrlich D. EMBO J. 2002 Jun 17;21(12):3137-47). In our paper, we also showed the inhibition of RecA-mediated DNA strand exchange by three different homologs of PcrA (Staphylococcus aureus, Bacillus anthracis and Bacillus cereus). Moreover, using two different mutants of S. aureus PcrA, one of which was completely inactive for ATPase and helicase activities, we also showed that the ATPase and helicase activities are not required for the inhibition of RecA-mediated DNA strand exchange or for the displacement of RecA from either ssDNA or dsDNA. In addition, we showed that displacement of DNA-bound proteins by PcrA or its mutants was specific to RecA, as SSB or gp32 proteins were not displaced from the ssDNA. As a matter of record, ours was the first paper to show RecA displacement by PcrA using biochemical and spFRET-based assays. We believe that the broader implications of the mechanism reported by Park et al. in this publication would have been more thoroughly addressed in the context of our earlier findings.

The authors reply?

Apologies for our oversight
We thank Drs. Leuba, Khan and Anand for pointing out our failure to cite their 2007 paper in the Journal of Bacteriology. We apologize for this unfortunate oversight. Jeehae Park, Tim Lohman and Taekjip Ha

I am not sure a journal would print such an authors’ response.

In fact, the reply raises more questions than the comment. The authors couldn’t be bothered with a cursory literature search? (what about the reviewers?) A PubMed search for the Park et al. paper lists among its suggested Related Citations the earlier article by Anand et al. (and vice versa – search for the Anand paper, and Ha shows up as a Related Citation). Of course, the authors’ “unfortunate oversight” avoided the need to address the potential lack of novelty of their findings, which might have knocked their manuscript out of contention for Cell.

And, coincidentally, Ha was Vice Chair of the 2006 Single Molecule Gordon Research Conference at which the data by Anand et al. were presented.

So, Anand et al. data (biochemical & spFRET) presented at June 2006 Gordon Conference. Anand et al. paper received in March 2007 and accepted and published online in April (print publication in June). Park et al. paper submitted in December 2008, revised in February 2010, accepted in July 2010, and published in August 2010.

Aside from the authors’ economical reply and interesting chronology, there remain the unaddressed scientific issues raised … and the question of what journal article commentary is meant for, if not to launch thoughtful discussion of the underlying science.

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NIH-Wide Data on Impact & Criterion Score Correlations

Ask and ye shall receive … NIH-wide data on the correlation between individual review criterion scores and overall impact score, compliments of Jeremy Berg.

Correlation coefficients between the overall impact score and the five criterion scores for 32,608 NIH applications from the Fiscal Year 2010 October, January and May Council rounds

As he notes, the trends across the ICs mirror what he found at NIGMS. The NIH-wide data also include more mechanisms … whereas Jeremy analyzed 654 R01s from one cycle, these data include all RPG, research center, and SBIR/STTR applications over 3 cycles (Oct-Jan-May Councils). Not sure if we’ll get all his other lovely data at the NIH level, but we can dream. In the meantime, thanks so much for your leadership in disseminating the NIGMS and now these NIH-wide data, Dr. Berg.

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