FundScience Blog

Laplacianoid animations

02.2.12 by worden

Laplacianoid eigenmatrices

02.2.12 by worden

Notes on MediaWiki extension programming with API actions and Ajax calls #wpsfhack

01.21.12 by worden

wikipedia hackathon

01.20.12 by worden

new paper in progress: Reflexive graph operations for clustering

01.19.12 by worden

FY 11 Success Rates & Other Stats from the NIH

01.17.12 by Michelle Kienholz

Sally Rockey posted the latest NIH success rate numbers (& other applicant data) today …

Overall success rates for research project grants fell compared to 2010.	18%
Success rates for new investigators were equal to established investigators submitting new applications.	15%
The representation of women NIH investigators remained the same as in 2010.	29%
Women’s success rates were equal to men for new applications.	15%
Our commitment to supporting the individual investigator remains strong, with R01s and R37s representing a significant percentage of all research grants.	60%
The average size of R01-equivalent grants increased slightly compared to 2010.	$408,594
The average size of a center grant fell by 6% compared to 2010.	$1,863,037
Number of institutional training grant applications continued to decline, from a peak in 2005.	686

Sally also notes that the success rate (which is not the same thing as a payline or percentile) dropped from 20% to 18% due in part to an 8% increase in the number of applications received (49,592). In addition, fewer applications were funded in FY11 (8,765) than during any of FYs in the decade prior … the same number were funded in FY00 (though that year, the success rate was 32%).

Update: Sally explains the decline in success rate (more applications, less $ appropriated, increasing award size).

Findings of Research Misconduct x 3

01.10.12 by Michelle Kienholz

Three notices from ORI, the first particularly instructive in terms of guiding ethical behavior (holding the facility director responsible for oversight) …

Notice is hereby given that ORI has taken final action in the following case: Based on an inquiry conducted and written admission obtained by Kansas University and additional analysis conducted by ORI in its oversight review, ORI found that Dr. Gerald Lushington, PhD, Director of the K-INBRE Bioinformatics Core Facility and Director of the Molecular Graphics and Modeling Lab, engaged in research misconduct in research supported by P20RR016475. Specifically, ORI found that Respondent engaged in research misconduct by approving publication of 3 articles and 1 abstract he knew contained significant amounts of plagiarized text without attribution or citation from other writers’ published papers. The specific published documents as well as the relevant source documents are:

• Visvanathan, M., Adagarla, B., Lushington, G., Sittampalam, S., Proceedings of the 2009 International Joint Conference on Bioinformatics, Systems, Biology and Intelligent Computing, 2009, 494-497. Greater than half of the total text was obtained from

  (1) Yang, C.-S., Chuang, L.-Y., Ke, C.-H., Yang, C.-H., International Journal of Computer Science, International Association of Engineers, August 2008 35(3),
  (2) Goffard, N. and Weiller, G., Nucleic Acids Research, 2007, 35L:W176-W181, and
  (3) Chuang, L.-Y., Yang, C.-H., Tu, C.-J., Yang, C.-H., Proceedings of the Joint Conference on Information Sciences, Atlantis Press, October 2006.

  Retracted: Retracted administratively by IEEE on Jan 5, 2011 http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5260432

• Vijayan, A.; Skariah, B. E., Nair, B.; Lushington, G., Subramanian, S., Visvanathan, M., Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine Workshop, 2009, BIBMW2009, 267-271.

  Approximately 15% of the text was plagiarized from Goffard, N. and Weiller, G., Nucleic Acids Research, 2007, 35L:W176-W181.

  Retracted: Retracted administratively by IEEE on Jan 5, 2011 http://www.computer.org/portal/web/csdl/doi/10.1109/BIBMW.2009.5332106

• Visvanathan, M., Netzer, M., Seger, M., Adagarla, B. S., Baumgartner, C., Sittampalam, S., Lushington, G., International Journal of Computational Biology and Drug Design, 2009, 2,236-251.

  A complete paragraph of the text was plagiarized from Goffard, N. and Weiller, G., Nucleic Acids Research, 2007, 35L:W176-W181.

• Adagarla, B., Lushington, G., Visvanathan, M., ISMB International Conference, January 2009; the entire abstract for this poster was obtained by plagiarizing text from Pihur, V., Datta, S., Datta S., Genomics, 2003, 92:400-403.

Dr. Lushington has entered into a Voluntary Settlement Agreement for a period of 2 years, beginning on December 6, 2011:

(1) To have any U.S. PHS-supported research supervised; ORI acknowledges that Respondent’s research is currently being supervised by KU; …

(2) that this annual summary, provided by any institution employing him, shall provide assurance that each application for PHS funds, or report, manuscript, or abstract involving PHS-supported research in which Respondent was involved, was based on actual experiments or was otherwise legitimately derived, that the data, procedures, and methodology were accurately reported in the application, report, manuscript, or abstract, and that the text in such submissions was his own or properly cited the source of copied language and ideas; and

(3) to exclude himself from serving in any advisory capacity to PHS including, but not limited to, service on any PHS advisory committee, board, and/or peer review committee, or as a consultant.

***

Notice is hereby given that ORI has taken final action in the following case: Based on an inquiry conducted and written admission obtained by Kansas University and additional analysis conducted by ORI in its oversight review, ORI found that Dr. Mahesh Visvanathan, PhD, Research Assistant Professor in the K-INBRE Bioinformatics Core Facility, engaged in research misconduct in research supported by P20RR016475. Specifically, ORI found that Respondent engaged in research misconduct by intentionally and knowingly plagiarizing large amounts of text from other writers’ published papers without attribution or citation in the following 3 papers and 1 abstract. (see list above)

Dr. Visvanathan has entered into a Voluntary Settlement Agreement for a period of 2 years, beginning on December 20, 2011:

(1) To have any PHS-supported research supervised; ORI acknowledges that Respondent’s research is currently being supervised by KU; …

(2) That this annual summary, provided by any institution employing him, shall provide assurance that each application for PHS funds, or report, manuscript, or abstract involving PHS-supported research in which Respondent was involved, was based on actual experiments or was otherwise legitimately derived, that the data, procedures, and methodology were accurately reported in the application, report, manuscript, or abstract, and that the text in such submissions was his own or properly cited the source of copied language and ideas; and

(3) To exclude himself from serving in any advisory capacity to PHS including, but not limited to, service on any PHS advisory committee, board, and/or peer review committee, or as a consultant.

***

Notice is hereby given that ORI has taken final action in the following case: Based on the report of an investigation conducted by SUNY, Upstate Medical University and additional analysis conducted by ORI in its oversight review, ORI found that Ms. Jennifer Jamieson, former graduate student, Department of Cell and Developmental Biology, engaged in research misconduct in research supported by R01GM047607-18A1 and R01HL70244-05. ORI found that Respondent engaged in research misconduct by falsifying data that were included in grant application R01 GM047607-18A1, in a manuscript submitted for publication to the Journal of Cell Biology, and in several interdepartmental data presentations. Specifically, ORI found that:

Respondent falsified Figure 1A in a manuscript submitted for publication to the Journal of Cell Biology, by altering immunoprecipitation Western blot data to make this experiment appear that no Vav2 SH2 was associated with PKL 3YF, when in fact it did. In addition, the Respondent falsified five figures depicting Western blots of similar experiments in four laboratory meeting presentations. The purpose of the falsifications was to show that the experimental results were as described when they were not, or to show that the results were of greater significance than they actually were.

Respondent falsified Figure 3I in a manuscript submitted for publication to the Journal of Cell Biology by falsely labeling a Western blot to indicate levels of expression for various Vav2 mutants, when the experimental data were taken from a completely unrelated experiment.

Respondent falsified Figure 6A in an interdepartmental laboratory presentation by falsifying Western blot data to falsely depict Paxillin and Hic-5 expression and phosphorylation levels after siRNA treatment.

Respondent falsified Figure 5 from grant application R01GM047607-18A1 by falsifying Western blot data to support the hypothesis that co-transfection of PKL plus RhoA GEF Vav2 induces RhoA activation and signaling upon plating on fibronectin.

Ms. Jamieson has entered into a Voluntary Settlement Agreement. Ms Jamieson neither admits nor denies ORI’s finding of scientific misconduct nor any particular finding of fact asserted in support of that finding. The settlement is not an admission of liability on the part of the Respondent. Ms. Jamieson has voluntarily agreed for a period of 3 years, beginning on December 20, 2011:

(1) To have her research supervised if employed by an institution that receives or applies for U.S. PHS funding; Respondent agrees that prior to the submission of an application for PHS support for a research project on which the Respondent’s participation is proposed and prior to Respondent’s participation in any capacity on PHS-supported research, Respondent shall ensure that a plan for supervision of her duties is submitted to ORI for approval; the supervision plan must be designed to ensure the scientific integrity of Respondent’s research contribution; Respondent agrees that she shall not participate in any PHS-supported research until such a supervision plan is submitted to and approved by ORI; Respondent agrees to maintain responsibility for compliance with the agreed upon supervision plan;

(2) that any institution employing her shall submit, in conjunction with each application for PHS funds, or report, manuscript, or abstract involving PHS supported research in which Respondent is involved, a certification to ORI that the data provided by Respondent are based on actual experiments or are otherwise legitimately derived and that the data, procedures, and methodology were accurately reported in the application, report, manuscript, or abstract; and

(3) to exclude herself from serving in any advisory capacity to PHS including, but not limited to, service on any PHS advisory committee, board, and/or peer review committee, or as a consultant.

NCRR is Dead, Long Live NCATS … Oops

12.18.11 by Michelle Kienholz

NCRR is not quite dead yet … but on Saturday, Collins jumped the gun in trumpeting this “signal moment for NIH”:

From: Exec Sec1 (NIH/OD)
To: NIH-STAFF@LIST.NIH.GOV
Sent: Sat Dec 17 18:56:52 2011
Subject: Message from the NIH Director – Changes at NIH

To: All NIH Staff
From: Director, NIH
Date: December 17, 2011
Subject: Changes at NIH

The omnibus appropriations bill for FY2012 passed by Congress and signed into law by President Obama today includes provisions that formally establish the National Center for Advancing Translational Sciences (NCATS) as a new component of the NIH. This is an important step forward in our efforts to speed the delivery of new drugs, diagnostics, and medical devices to patients. It was just over a year ago that the Scientific Management Review Board recommended the establishment of this new component of NIH, and the achievement of this complex outcome in this time frame is a testimony to the remarkable diligence of many dedicated individuals, both within and outside of NIH, who have worked together to achieve this goal.

This is a signal moment for NIH. I want to take this opportunity to recognize the rich history of the National Center for Research Resources (NCRR) and pay tribute to the important contributions of its dedicated employees and grantees. Over more than two decades, NCRR has established and administered a remarkably diverse portfolio of research programs, most recently including the re-invention of our nation’s academic clinical research network in the form of the Clinical and Translational Sciences Awards (CTSAs). I am grateful to Acting Director Dr. Louise Ramm and all of the dedicated staff of NCRR, for their devotion to the cause of excellence in NIH research. Although NCRR is now disbanded, its scientific legacy will live on. As former NCRR employees and their programs transition into new homes within NCATS and other Institutes and Centers, please welcome them with open arms and embrace their wealth of expertise and experience.

Change is never easy; however, it often opens doors to unexpected opportunities for personal growth and scientific collaboration. So, even as we look back at the many accomplishments of NCRR, let us also look ahead to NCATS and realizing its vision of transforming translational research.

In this vein of change, I am pleased to designate Thomas Insel, M.D., as the Acting Director of NCATS and Kathy L. Hudson, Ph.D., as Acting Deputy Director of NCATS. Drs. Insel and Hudson will lead the many activities of bringing the Center into being and getting its programs underway, while we conduct a nationwide search for the first NCATS Director. Drs. Insel and Hudson have already been deeply involved in establishing the Center and are natural choices to implement our plans for NCATS. Both of them will continue to serve in their current roles, at NIMH and in the Director’s Office respectively, while serving in these Acting leadership positions.

I very much appreciate Tom’s and Kathy’s willingness to take on these exciting but challenging additional roles, and I know I can count on all of you to join me in giving them as much support as possible.

Francis S. Collins, M.D., Ph.D.

***

From: “Exec Sec1 (NIH/OD)” <EXECSEC1@od.nih.gov>
Date: December 17, 2011 7:59:57 PM EST
To: “NIH-STAFF@LIST.NIH.GOV” <NIH-STAFF@LIST.NIH.GOV>
Subject: Message from the NIH Director — Correction: Please disregard the previous message.
Reply-To: “Exec Sec1 (NIH/OD)” <EXECSEC1@od.nih.gov>

To: All NIH Staff
From: Director, NIH
Date: December 17, 2011
Subject: Correction: Please disregard the previous message.

The President signed a Continuing Resolution until December 23, so nothing is finalized until we have a signed bill. We apologize for any confusion.

Francis S. Collins, M.D., Ph.D.

I hope he was not suggesting we disregard the polite praise for NCRR … which, according to the NIH Almanac, has been serving the biomedical research community quite well for closer to five decades (though only formally as NCRR since 1990).

The FY12 appropriations bill Conference Report includes its own assessment of the process by which NCRR was replaced by NCATS:

The conference agreement includes language to eliminate the NCRR and create the National Center for Advancing Translational Sciences (NCATS).

NCATS will study steps in the therapeutics development and implementation process, consult with experts in academia and the biotechnology and pharmaceutical industries to identify bottlenecks in the processes that are amenable to re-engineering, and develop new technologies and innovative methods for streamlining the processes. In order to evaluate these innovations and new approaches, NCATS will undertake targeted therapeutics development and implementation projects. In all of these efforts, the conferees expect that NCATS will complement, not compete with, the efforts of the private sector.

While the conferees welcome the creation of NCATS, they were disappointed by the way the administration requested it. The President’s proposed budget for fiscal year 2012 included a vague description of NCATS but did not formally request funding for the restructuring or provide any details about which components of NIH would be consolidated into the new Center. The failure to do so caused unnecessary uncertainty about the proposal and contributed to the impression that it was being rushed. The conferees are also aware of concerns that the NIH process for evaluating the merits of the NCATS reorganization did not comply with the NIH Reform Act of 2006 with respect to the role of the Scientific Management Review Board (SMRB).

The decision to create NCATS might have been rushed?

NIH FY12 Appropriations – UPDATED

12.16.11 by Michelle Kienholz

With an agreement finally reached on an appropriations bill, the news for the NIH is better than if we had continued the CR with its 1.5% cut all year. Looking at the House Appropriations Committee’s marked up bill (H.R. 3671, see pp 50-56) and FY11 appropriation levels, I initially read slight decreases (except where NCRR funds move to new ICs), with any new money earmarked for specific programs (see notes below). Science and The Chronicle of Higher Education highlighted a slight overall increase for the NIH, which is true but relative (more below). Either way, not much change, up or down.

Biggest bonus surprise: anyone who applied to an IDeA FOA this past year certainly hit the jackpot: this program will have an extra ~$46M+ to hand out by September 30th … not sure if they’ll just reach farther down their payline or whip up a new solicitation in time for review & funding by the end of the FY. This is now NIGMS’ call, with the unfortunate dissolution of NCRR in the same appropriations bill.

I originally used dollar amounts from the marked up HR 3671 and the FY11 $s from what was signed into law. However, the Conference Report (see table at pp 31-34) helpfully provides $s for FY11 enacted that take into account Public Law 112-10‘s 0.2% across-the-board cut in discretionary spending plus an extra $210M cut to the NIH (spread across the ICs) … so the NIH is getting a small increase, though it does not quite offset what was lost last year (i.e., by the 0.2% + $210M additional cuts). I’ll leave all the numbers up as a reminder of how complicated this can get …

NCI: $5,103,388,000 FY11 (PL)/$5,058,577 (Conf) vs $5,081,788,000 FY12

NHLBI: $3,096,916,000 FY11 (PL)/$3,069,723 (Conf) vs $3,084,851,000 FY12

NIDCR: $413,236,000 FY11 (PL)/$409,608,000 (Conf) vs $411,488,000 FY12

NIDDK: $1,808,100,000 FY11 (PL)/$1,792,224,000 (Conf) vs $1,800,447,000 FY12

NINDS: $1,636,371,000 FY11 (PL)/$1,622,003,000 (Conf) vs $1,629,445,000 FY12

NIAID: $4,518,275,000 (after $300M to global fund) FY11/$4,478,668,000 (Conf) vs $4,499,215,000 FY12 (no global fund transfer)

NIGMS: $2,051,798,000 FY11 (PL)/$2,033,782,000 (Conf) vs $2,434,637,000 FY12 (includes $ for NCRR programs transferred to NIGMS … and “provided that not less than $276,480,000 is provided for the IDeA program”)

NICHD: $1,329,528,000 FY11 (PL)/$1,317,854,000 (Conf) vs $1,323,900,000 FY12

NEI: $707,036,000 FY11 (PL)/$700,828,000 (Conf) vs $704,043,000 FY12

NIEHS: $689,781,000 FY11 (PL)/$683,724,000 (Conf) vs $686,869,000 FY12

NIA: $1,110,229,000 FY11 (PL)/$1,100,481,000 (Conf) vs $1,105,530,000 FY12

NIAMS: $539,082,000 FY11 (PL)/$534,349,000 (Conf) vs $536,801,000 FY12

NIDCD: $418,833,000 FY11 (PL)/$415,155,000 (Conf) vs $417,061,000 FY12

NINR: $145,660,000 FY11 (PL)/$144,381,000 (Conf) vs $145,043,000 FY12

NIAAA: $462,346,000 FY11 (PL)/$458,286,000 (Conf) vs $460,389,000 FY12

NIDA: $1,059,848,000 FY11 (PL)/$1,050,542,000 (Conf) vs $1,055,362,000 FY12

NIMH: $1,489,372,000 FY11 (PL)/$1,476,294 (Conf) vs $1,483,068,000 FY12

NHGRI: $516,028,000 FY11 (PL)/$511,497,000 (Conf) vs $513,844,000 FY12

NIBIB: $316,582,000 FY11 (PL)/$313,802,000 (Conf) vs $338,998,000 FY12 (includes $ for NCRR programs transferred to NIBIB)

NCRR: $1,268,896,000 FY11 (PL)/$1,257,754,000 (Conf) vs $0 FY12 (these $ are all redistributed to other ICs & OD)

NCCAM: $128,844,000 FY11 (PL)/$127,713,000 (Conf) vs $128,299,000 FY12

NIMHD: $211,572,000 FY11 (PL)/$209,714,000 (Conf) vs $276,963,000 FY12 (includes $ for NCRR programs transferred to NIMHD)

FIC: $70,051,000 FY11 (PL)/$69,436,000 (Conf) vs $69,754,000 FY12

NLM: $339,716,000 FY11 (PL)/$336,733,000 (Conf) vs $338,278,000 FY12

NCATS: $0 FY11 vs $576,456,000 FY12 ($10M for CAN, $487,767,000 for CTSA, rest for other NCRR programs)

OD: $1,177,300,000 FY11 (PL)/$1,166,963,000 (Conf) ($544,109,000 for Common Fund) vs $1,461,880,000 ($545,962,000 for Common Fund)

Buildings and facilities: $100,000,000 FY11 vs $125,581,000 FY12

If anything changes in the language of the final bill signed into law, I will update this post accordingly.

In the meantime, the Conference Report includes a few other items of interest:

• The conferees affirm the critical importance o f new and competing RPGs to the mission of NIH and are concerned that in the past few years, NIH has failed to support the number of new, competing RPGs that it estimated
  would be awarded in its annual congressional budget justifications.
• NIH should also establish safeguards to ensure the percentage of funds used to support basic research across NIH is maintained.
• While the conferees welcome the creation of NCATS, they were disappointed by the way the administration requested it. The President’s proposed budget for fiscal year 2012 included a vague description of NCATS but did not formally request funding for the restructuring or provide any details about which components of NIH would be consolidated into the new Center. The failure to do so caused unnecessary uncertainty about the proposal and contributed to the impression that it was being rushed. The conferees are also aware of concerns that the NIH process for evaluating the merits ofthe NCATS reorganization did not comply with the NIH Reform Act of 2006 with respect to the role of the Scientific SMRB.
• Lessons learned with NCATS should guide NIH as it considers another proposed restructuring, one that would involve consolidating NIDA, NIAAA and components of other ICs into a new Institute devoted to research on substance use, abuse and addiction. The conferees understand that NIH plans to adopt a more deliberate approach in evaluating the need for this Institute. The conferees strongly recommend that this approach should include full consideration by the SMRB and that if the administration ultimately decides to seek such a restructuring, it should provide sufficient details in a formal budget request to Congress.

NSF Broader Impacts Broadened

12.15.11 by Michelle Kienholz

UPDATE: According to Science Insider, in addition to not listing specific broader impacts, the NSB recommended in its report, NSF Merit Review Criteria: Review and Revisions, flexibility in how these are measured (and by whom):

NSB notes that assessing the effectiveness and impact of outcomes of these activities one project at a time may not be meaningful, particularly if the size of the activity is limited. Thus, assessing the effectiveness of activities designed to advance broader societal goals may best be done at a higher, more aggregated, level than the individual project. Large, campus-wide activities or aggregated activities of multiple PIs could lend themselves to assessment, which should be supported by NSF.

According to Mervis, the changes should be incorporated in the January 2013 version of the Grant Proposal Guide.

Last summer, NSF sought input on merit review criteria for intellectual merit and broader impacts. Nature News now reports that the task force assigned to tweaking these presented its final report, which “kept the wording for the two criteria essentially the same as before” (i.e., no list of specific activities), to the National Science Board, which is likely to approve the recommendations. Another good outcome: NSF Director Subra Suresh indicated that “One thing that remains to be done is finding the right balance in shouldering the responsibility of broader impacts between principal investigator and institution.” Here-here.

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