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.
Findings of Research Misconduct
11.10.11 by Michelle Kienholz
Notice is hereby given that ORI has taken final action in the following case:
Based on the report of an investigation conducted by UVA and additional analysis conducted by ORI in its oversight review, ORI found that Dr. Jayant Jagannathan, former Resident Physician at UVA Medical Center, engaged in research misconduct by including, in 5 publications, large amounts of text and an illustration that he plagiarized from publications supported by the following NIH grant awards: T32CA09677, P01HL024136, R01HL059157, P50CA090270, M01RR01346, R01CA075979, R01DK064169, R01NS027544, R01NS052406, and K08NS002197 and by intramural funds from the NINDS Surgical Neurosurgery Branch and from NIDCR.
Publications in which Respondent reported plagiarized material were:
1. Jagannathan, J., Li, J., Szerlip, N., Vortmeyer, A.O., Lonser, R.R., Oldfied, E.H., Zhuang, Z. “Application and implementation of selective tissue microdissection and proteomic profiling in neurological disease.’ Neurosurgery 64:4-14, 2009 (to be retracted);
2. Jagannathan, J., Prevedello, D.M., Dumont, A.S., Laws, E.R. “Cellular Signaling Molecules as Therapeutic Targets in the Treatment of Glioblastoma Multiforme.’ Neurosurgical Focus 20(4):E8, 2006 (retracted “due to plagiarism,’ Neurosurgical Focus 30(2):E8r, 2011);
3. Kanter, A.S., Jagannathan, J., Shaffrey, C.I., Ouellet, J.A., Mummaneni, P.V. “Inflammatory and dysplastic lesions involving the spine.’ Neurosurgical Clinics of North America 19(1):93-109, 2008;
4. Jagannathan, J., Dumont, A.S., Prevedello, D.M., Oskouian, R.J., Lopes, B., Jane, J.A. Jr, Laws, E.R. Jr. “Genetics of pituitary adenomas: Current theories and future implications.’ Neurosurgical Focus 19(5):E4, 2005 (retracted “due to plagiarism,’ Neurosurgical Focus 30(2):E4r, 2011);
5. Jagannathan, J. “Role of calcium influx and modulation of local neurotransmitters as hallmarks of pediatric traumatic brain injury.’ Biomarkers Med. 3:95-97, 2009 (retracted online 9/11/ 2010).
Dr. Jagannathan has entered into a Voluntary Settlement Agreement (Agreement) and has voluntarily agreed for a period of 4 years, beginning on October 20, 2011:
(1) To have his research supervised; Respondent agreed to ensure that prior to the submission of an application for U.S. PHS support for a research project on which his participation is proposed and prior to his participation in any capacity on PHS-supported research, the institution employing him must submit a plan for supervision of his duties to ORI for approval; the plan for supervision must be designed to ensure the scientific integrity of his research contribution; Respondent agreed that he will not participate in any PHS-supported research after 60 days from the effective date of the Agreement until a plan for supervision is submitted to and approved by ORI; Respondent agreed to maintain responsibility for compliance with the agreed upon supervision plan;
(2) That any institution employing him must 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 are accurately reported in the application, report, manuscript, or abstract;
(3) To submit a letter to the journal editor for publication 3 (Neurosurgical Clinics of North America) listed above, requesting that the paper be retracted because Respondent had plagiarized portions of text reported in it; the letter must be sent to ORI for approval prior to being sent to the editor; and
(4) 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.
Findings of Research Misconduct
10.28.11 by Michelle Kienholz
Notice is hereby given that ORI has taken final action in the following case:
Based on an inquiry conducted and written admission obtained by the University of Pittsburgh and additional analysis conducted by ORI in its oversight review, ORI found that Ms. Marija Manojlovic, former graduate student, Department of Chemistry, engaged in research misconduct in research supported by P50GM067082, P01CA078039, U54MH074411, and R01AI033506.
ORI found that the Respondent engaged in research misconduct by falsifying and fabricating the synthesis and spectral data that were included in one poster presentation and in one pre-submission draft of a paper to be submitted for publication.
Specifically, ORI found that the Respondent knowingly falsified and fabricated the synthesis and characterization, largely in the form of manipulated 1H- and 13C-NMR spectral data, for 5 intermediate steps and the final product, 9-desmethylpleurotin, and presented these false results in a poster, “Efforts Towards the Total Synthesis of Pleurotin,’ presented at the 2011 National Organic Symposium, and in a manuscript, “Total Synthesis of 9-desmethylpleurotin,’ prepared for submission to Angewandte Chemie International Edition.
Ms. Manojlovic has voluntarily agreed for a period of 3 years, beginning on September 26, 2011:
(1) To have her US PHS-supported research supervised; Respondent agreed that prior to the submission of an application for PHS support for a research project on which her participation is proposed and prior to her participation in any capacity on PHS-supported research, she 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 her research contribution; Respondent agreed that she shall not participate in any PHS-supported research until such a supervision plan is submitted to and approved by ORI; Respondent agreed 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 she 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 are 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.
Findings of Research Misconduct x2
04.29.11 by Michelle Kienholz
My least favorite scenario for my least favorite type of post … as reported last year in Nature and again on Nature’s Great Beyond blog …
Notice is hereby given that ORI has taken final action in the following case:
Based on the findings of an investigation by UMich and additional analysis conducted by ORI, ORI found that Vipul Bhrigu, PhD, former postdoctoral fellow, Department of Internal Medicine, engaged in research misconduct in research funded by R01CA098730-05.
Specifically, ORI found that the Respondent knowingly and intentionally tampered with research materials related to 5 immunoprecipitation/Western blot experiments and switched the labels on 4 cell culture dishes for cells used in the same type of experiments to cause false results to be reported in the research record. ORI also found that the Respondent tampered with laboratory research materials by adding ethanol to his colleague’s cell culture media, with the deliberate intent to effectuate the death of growing cells, which caused false results to be reported in the research record. ORI has concluded that these acts seriously deviated from those that are commonly accepted within the scientific community for proposing, conducting, and/or reporting research.
ORI found that the Respondent’s intentional tampering of his colleague’s laboratory research constitutes research misconduct as defined by 42 CFR part 93. ORI determined that the Respondent engaged in a pattern of dishonest conduct through the commission of multiple acts of data falsification. ORI also determined that the subterfuge in which he freely engaged for several months constitutes an aggravating factor. The Respondent attempted to mislead the UMich police by initially denying involvement in the tampering and refusing to accept responsibility for this misconduct. The Respondent eventually made an admission only after the UMich police informed him that his actions in the laboratory had been videotaped. This dishonest conduct established the Respondent’s lack of present responsibility to be a steward of Federal funds (2 CFR 376 et seq.; 42 CFR 93.408).
The following administrative actions have been implemented for a period of 3 years, beginning on April 7, 2011:
(1) Dr. Bhrigu is debarred from eligibility for any contracting or subcontracting with any agency of the United States Government and from eligibility for, or involvement in, nonprocurement programs of the United States Government, referred to as “covered transactions,’ pursuant to HHS’ Implementation of OMB [[Page 23600]] Guidelines to Agencies on Governmentwide Debarment and Suspension (2 CFR 376 et seq.); and
(2) Dr. Bhrigu is prohibited from serving in any advisory capacity to the U.S. PHS, including but not limited to service on any PHS advisory committee, board, and/or peer review committee, or as a consultant.
And …
Notice is hereby given that ORI has taken final action in the following case:
Based on the report of an investigation conducted by New York Medical College (NYMC) and additional analysis by ORI, the U.S. PHS found that Junghee J. Shin, PhD, former graduate student, NYMC, engaged in research misconduct in research supported by R01 AI048856 and R01 AI043063.
PHS found that the Respondent engaged in research misconduct by falsifying data in Figure 4 of a manuscript submitted to the journal Infection and Immunity (Shin, J.J., Godfrey, H.P., & Cabello, F.C. “Expression and localization of BmpC in Borrelia burgdorferi after growth under various environmental conditions.’ Submitted to Infection and Immunity; hereafter referred to as the “manuscript’) and Figure 5 of a paper published in Infection and Immunity (Shin, J.J. Bryksin, A.V., Godfrey, H.P., & Cabello, F.C. “Localization of BmpA on the exposed outer membrane of Borrelia burgdorferi by monospecific anti-recombinant BmpA rabbit antibodies.’ Infection and Immunity 72(4):2280-2287, April 2004; hereafter referred to as the “paper.’ Retracted in: Infection and Immunity 76(10):4792, October 2008). Specifically, NYMC and ORI found that:
- Dr. Shin falsified microscopic immunofluorescence blank images in Figure 4 of the manuscript (top row, 1st, 2nd, 4th, and 5th panels, and bottom row, 1st panel) and Figure 5 of the paper (top row, 1st and 5th panels, lower 1st panel) by using one blank image from an unknown experiment to falsely represent the preimmunization control conditions (intact cells and methanol fixation) as well as the negative staining of anti-BmpC and anti-FlaB in Figure 4 and anti-FlaB in Figure 5 on intact cells.
- Dr. Shin falsified at least one of two images in Figure 4 of the manuscript and Figure 5 of the paper by using different portions of a green-red pair of microscopic immunofluorescence images (1230036.tif and 1230037.tif) because unfixed cells staining positive for BmpA in the top row, 4th panel, of Figure 5 were the same unfixed cells purportedly positive for OspA in the top row, 3rd panel, of Figure 4.
- Dr. Shin falsified at least one of two images in Figure 4 of the manuscript and Figure 5 of the paper by using different photo cropping from a single microscopic immunofluorescence image (1230039.tif) to represent fixed cells positive for BmpA and labeled with anti-FlaB in the lower row, 5th panel, of Figure 5 and to also represent fixed cells positive for BmpC and stained with anti-FlaB in the lower row, 5th panel, of Figure 4.
Dr. Shin has entered into a Voluntary Settlement Agreement in which she has voluntarily agreed, for a period of 3 years, beginning on April 5, 2011:
(1) That any institution that submits an application for PHS support for a research project on which the Respondent’s participation is proposed or that uses her in any capacity on PHS-supported research, or that submits a report of PHS-funded research in which she is involved, must concurrently submit a plan for supervision of her duties to ORI for approval; the supervisory plan must be designed to ensure the scientific integrity of her research contribution; Respondent agrees that she will not participate in any PHS-supported research until such a supervision plan is submitted to ORI; and
(2) to exclude herself voluntarily from service 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.
Findings of Research Misconduct
02.12.11 by Michelle Kienholz
Notice is hereby given that ORI has taken final action in the following case:
Based on the Wadsworth Center report and the oversight review conducted by ORI, the U.S. PHS found that Meleik Goodwill, PhD, former postdoctoral fellow, Wadsworth Center, NYS Department of Health, engaged in research misconduct in research supported by grant R21 ES013269-02.
Specifically, PHS found that the Respondent engaged in research misconduct by the fabrication of data for growth curves presented in Figure 1 in the 2007 Journal of Neuroimmunology article (183(1-2):125-132), and by the use of composite images of Western-blot bands from unrelated experiments done in 2005 that were falsely labeled as if from different experiments to construct Figure 4A in the 2007 Journal of Neuroimmunology article. Figure 4B of the article also was falsified by use of identical sets of number for different treatments. The 2007 Journal of Neuroimmunology article was retracted in J Neuroimmunol. 2008;197(1):197.
Dr. Goodwill has entered into a Voluntary Settlement Agreement in which she has voluntarily agreed, for a period of 3 years, beginning on January 21, 2011:
- That any institution that submits an application for PHS support for a research project on which the Respondent’s participation is proposed or that uses her in any capacity on PHS-supported research, or that submits a report of PHS-funded research in which she is involved, must concurrently submit a plan for supervision of her duties to ORI for approval; the supervisory plan must be designed to ensure the scientific integrity of her research contribution; Respondent agrees that she will not participate in any PHS-supported research until such a supervisory plan is submitted to ORI;
- That any institution employing her submits, in conjunction with each application for PHS funds, or report, manuscript, or abstract involving PHS-funded research in which she was involved, a certification to ORI that the data provided are based on actual experiments or are otherwise legitimately derived and that the data, procedures, and methodology are accurately reported in the application or report; and
- To exclude herself voluntarily from service 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.
Findings of Research Misconduct
12.15.10 by Michelle Kienholz
Oof … an MD-PhD student who admitted that “Approximately, 60-75% of the PhD research data was changed or falsified.” [at least, I assume there should be a percentage sign there] I’m wondering how he still has the doctorate.
Notice is hereby given that ORI has taken final action in the following case:
Based on the Respondent’s written admission, the NYU School of Medicine and ORI found that Sagar S. Mungekar, PhD, former MD/ PhD student in the Sackler Institute of Graduate Biomedical Sciences at NYUSOM, engaged in research misconduct in research supported by R01GM35769, R01GM55624, T32GM07308, and T32AI007180.
Dr. Mungekar admitted that in his PhD thesis he “increased statistical significance of the calculated means and standards of deviation [sic] of the UV spectrophometic [sic] data presented by discarding certain experimental data and thus presented data that was falsified. In addition, as the repression ratios calculated and conclusions reached based on these data that included falsified data, those values and conclusions are fabricated. Approximately, 60-75 of the [Respondent's] PhD research data was changed or falsified.’ Dr. Mungekar also admitted “while doing these experiments, I did not sequence all of the constructs that I constructed, thus, I could not be certain of the exact identity of the plasmids in question.’
ORI found that Dr. Mungekar engaged in research misconduct (42 CFR 93.103) by fabricating and falsifying data. Specifically, ORI found that Dr. Mungekar falsified 5 tables and 5 figures in his PhD thesis entitled “Autoregulation of Ribonuclease E,’ by discarding certain spectrophotometric data, to increase statistical significance, used to calculate repression ratios and RNA decay rates. Dr. Mungekar also claimed to have constructed 53 different reporter plasmids with RNase E mutants, when sequencing data did not exist to support this claim.
Dr. Mungekar has entered into a Voluntary Settlement Agreement in which he has voluntarily agreed, for a period of 3 years, beginning on November 22, 2010:
(1) That any institution that submits an application for PHS support for a research project on which the Respondent’s participation is proposed or that uses him in any capacity on PHS-supported research, or that submits a report of PHS-funded research in which he is involved, must concurrently submit a plan for supervision of his duties to ORI for approval; the supervisory plan must be designed to ensure the scientific integrity of his research contribution; Respondent agrees that he will not participate in any PHS-supported research until such a supervision plan is submitted to ORI;
(2) that any institution employing him submits, in conjunction with each application for PHS funds, or report, manuscript, or abstract involving PHS-funded research in which he is involved, a certification to ORI that the data provided by the Respondent are based on actual experiments or are otherwise legitimately derived and that the data, procedures, and methodology are accurately reported in the application or report; and
(3) to exclude himself voluntarily from serving in any advisory capacity to the US PHS, including but not limited to service on any PHS advisory committee, board, and/or peer review committee, or as a consultant.
Findings of Misconduct in Science
12.1.10 by Michelle Kienholz
Wow … ORI hardly ever gets someone on plagiarism. I wonder what Columbia does/did about the degree itself.
Notice is hereby given that ORI has taken final action in the following case:
Based on the findings of an investigation by Columbia University and additional analysis conducted by ORI during its oversight review, ORI found that Bengu Sezen, PhD, former graduate student, Department of Chemistry, engaged in misconduct in science in research funded by R01GM60326.
Specifically, ORI made 21 findings of scientific misconduct against Dr. Sezen based on evidence that she knowingly and intentionally falsified and fabricated, and in one instance plagiarized, data reported in 3 papers and her doctoral thesis.
The following administrative actions have been implemented for a period of 5 years, beginning on November 4, 2010:
(1) Dr. Sezen is debarred from eligibility for any contracting or subcontracting with any agency of the US Government and from eligibility or involvement in nonprocurement programs of the US Government…; and
(2) Dr. Sezen is prohibited from serving in any advisory capacity to the US PHS, including but not limited to service on any PHS advisory committee, board, and/or peer review committee, or as a consultant.
Journal Comment Commentary
10.5.10 by Michelle Kienholz
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.
Retraction Overexpression
09.24.10 by Michelle Kienholz
The big news during these Nobel-watching weeks is that Nobel Laureate Linda Buck retracted her 2006 Science paper with Zhihua Zou, who, as also reported in the NYT, did not agree with the retraction of this paper or a 2005 PNAS article but did sign off on a Nature 2008 retraction. Dr. Buck notes the disagreement in her Science retraction:
In the Report “Combinatorial Effects of Odorant Mixes in Olfactory Cortex” (1), we described subcellular patterns of Arc (arg3.1) mRNA expression in anterior piriform cortex neurons after mice had been exposed to odorants. We reported that some cortical neurons express Arc in response to a mix of two odorants but not either odorant alone. My laboratory has been unable to reproduce this finding. I am therefore retracting the Report. I sincerely apologize for any confusion that its publication may have caused. Zhihua Zou declined to sign this Retraction.
Separately, Science Insider and then Science News reported four retractions from the lab of therapy researcher Savio Woo at Mount Sinai School of Medicine. RetractionWatch, which originally reported on these, um, retractions, received a statement from Mount Sinai spokesman Ian Micheals indicating Dr. Woo had not been charged with misconduct but that the case (postdocs) was under investigation in cooperation with ORI. RetractionWatch yesterday reported on two additional retractions. RetractionWatch has it all nicely laid out … no need to replicate everything here … other than to wonder how many cases remain to be uncovered at significant cost in others’ time, $, and careers pursuing pathways of fabricated science.
Findings of Research Misconduct
09.1.10 by Michelle Kienholz
Notice is hereby given that ORI and the Assistant Secretary for Health have taken final action in the following case:
Based on the report of an investigation conducted by the Washington State University and additional analysis by ORI in its oversight review, the US PHS found that Hung-Shu Chang, PhD, former postdoctoral fellow, WSU, engaged in research misconduct in research supported by R01ES012974.
PHS found that the Respondent engaged in scientific (42 CFR 50.102) and research misconduct by fabricating and falsifying data in Figure 3 of a paper published in Endocrinology. Specifically, PHS found that:
Respondent, by not conducting any of the claimed bisulfite sequencing, fabricated the methylation status of CpG sites in 8 candidate genes identified in both Figures 3 and 4 as No. 11, No. 12, No. 13, No. 14, 15, No. 22, No. 26, No. 31, and No. 19, to support the hypothesis that the environmental compound, vinclozolin, induces a permanent alteration in the epigenetic reprogramming of the germline that promotes transgenerational disease states.
Respondent, by conducting only a small fraction of the claimed bisulfite sequencing, and falsifying the results obtained, falsified the methylation status of CpG sites in eight additional candidate genes, identified in Figures 3 and 4 as No. 2, 3, 24, No. 5, 6, 9, No. 8, No. 16, No. 17, 18, No. 27, 28, No. 29, and No. 33.
Dr. Chang has voluntarily agreed, for a period of 3 years, beginning on July 21, 2010:
(1) 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;
(2) that any institution that submits an application for PHS support for a research project on which the Respondent’s participation is proposed or that uses him in any capacity on PHS-support research, or that submits a report of PHS-funded research in which the Respondent is involved, must concurrently submit a plan for supervision of the Respondent’s duties to the funding agency for approval. The supervisory plan must be designed to ensure the scientific integrity of the Respondent’s research contribution while applying for or conducting PHS-supported research. Respondent agrees to ensure that a copy of the supervisory plan is submitted to ORI by the institution for ORI approval. Respondent agrees not to participate in any PHS-supported research until such a supervisory plan is submitted to ORI.
