Friday, February 8, 2013

Originally posted on retractionwatch.com 2:




This is one of the original retractionwatch.com posts about the Anil Potti retractions which were taken down at wordpress.com due to a fraudulent DMCA violation notice. It will probably take up to 14 days before they will be again available. Therefore I am posting these in the meantime on my blog:

Source: http://webcache.googleusercontent.com/search?q=cache:http://retractionwatch.wordpress.com/2012/06/04/lead-author-of-major-breast-cancer-study-announced-at-asco-co-authored-two-corrected-papers-with-anil-potti/

"Lead author of major breast cancer study announced at ASCO co-authored two corrected papers with Anil Potti

One of the biggest stories so far out of the American Society of Clinical Oncology (ASCO) meeting that just ended in Chicago was that of T-DM1, which, according to Ivan’s Reuters colleagues, “extended the length of time breast cancer patients lived without their disease getting worse.” (The news was even the subject of an embargo break.)
The widely-hailed study of Roche’s drug was led by Duke’s Kimberly Blackwell, who toldThe New York Times:
“We’ve envisioned a world where cancer treatment would kill the cancer and not hurt the patient,” Dr. Kimberly L. Blackwell, a professor of medicine at the Duke Cancer Institute and the lead investigator in the trial, said in an interview. “And this drug does that.”
Blackwell, as Duke watchdog DukeCheck noted over the weekend, published two studies with Anil Potti, the now-former Duke oncologist who has retracted or corrected 17 papers after resigning in the midst of an investigation into his work. Those two studies — one in the Journal of Clinical Oncology, the other in PLoS Medicine — have not been retracted, but both have been the subject of significant corrections.
It didn’t look to us as though Potti was involved in the T-DM1 work, and Blackwell confirmed that was the case. She also confirmed that the now-corrected papers she co-authored with Potti are not related to the T-DM1 work.
We want to be clear: Despite the fact that work by Blackwell and Potti has been found to have flaws, that doesn’t mean everything Blackwell ever works on needs to be scrutinized more carefully, forever. But we think it’s relevant to note the association, and that she was the point person quoted in a press release saying very positive things about one of the now-corrected papers. A selection:
“The breast tumors that arose in younger women shared a common biology, and this discovery was truly remarkable,” Blackwell said. “The genes that regulate things like immune function, oxygen supply and mutations that we know are related to breast cancer, such as BRCA1, were preferentially expressed in the tumors taken from younger women, but when we compared younger women’s tumors to older women’s tumors, we found those same gene sets were not expressed in the ’older’ tumors.”
We also asked Blackwell if, given all of the issues with Potti’s work, whether oncology research at Duke, or Blackwell’s work in particular, was scrutinized more closely before being made public. She tells Retraction Watch:
Duke has learned a great deal from the issues raised by the Potti situation and we now have developed better research oversight that is benefitting Duke researchers and our peers.
"
Source: http://webcache.googleusercontent.com/search?q=cache:http://retractionwatch.wordpress.com/2012/06/04/lead-author-of-major-breast-cancer-study-announced-at-asco-co-authored-two-corrected-papers-with-anil-potti/

Originally posted on retractionwatch.com 1:


This is one of the original retractionwatch.com posts about the Anil Potti retractions which were taken down at wordpress.com due to a fraudulent DMCA violation notice. It will probably take up to 14 days before they will be again available. Therefore I am posting these in the meantime on my blog:

Source: http://webcache.googleusercontent.com/search?q=cache:http://retractionwatch.wordpress.com/2012/10/05/another-retraction-for-anil-potti-with-an-inscrutable-notice/

"Another retraction for Anil Potti, with an inscrutable notice"


We’ve seen a lot of retraction notices for work by Anil Potti — 10, to be precise, along with 7 corrections and one partial retraction notice. As notices go, they tend to be pretty complete. So when we saw one in CHEST for this 2008 abstract, we were expecting something similar.
Instead, we were confused.
Here’s the notice:
We would like to withdraw our abstract “Upregulated Oncogenic Pathways in Patients Exposed to Tobacco Smoke May Provide a Novel Approach to Lung Cancer Chemoprevention,” which appeared in CHEST2 and was presented as a poster on October 29, 2008.
The results reported in this abstract and poster presentation were obtained using chemotherapeutic predictors developed in the Nature Medicine article, “Genomic Signatures to Guide the Use of Chemotherapeutics”1,that have since been shown to be inaccurate, and the article has been retracted.3The authors relied on the results reported by Potti1, and they were not aware of the errors subsequently reported. We apologize for any negative impact on scientific research or clinical care caused by the presentation of our abstract.
1. Potti A, Dressman HK, Bild A et al. Genomic signatures to guide the use of chemotherapeutics. [retracted in: Nat Med. 2011;17(1):135] Nat Med. 2006;12(11):1294-1300.
2. Redman RC, Acharya CR, Anguiano A et al. Upregulated oncogenic pathways in patients exposed to tobacco smoke may provide a novel approach to lung cancer chemoprevention [abstract]. Chest. 2008;134(4):158001S.
3. Potti A, Dressman HK, Bild A et al. Retraction: Genomic signatures to guide the use of chemotherapeutics.Nat Med. 2011;17(1):135.
This was the sentence we found difficult to interpret:
The authors relied on the results reported by Potti1, and they were not aware of the errors subsequently reported.
That’s because “The authors” include Potti, so “they” would seem to include him too. How exactly was he not aware of the errors subsequently reported?
We’ve asked one of the authors, and the journal’s editor, who actually signed the notice, since the journal doesn’t indicate that, and also asked what that sentence meant. We’ll update with anything we learn.
Potti is now working at a cancer center in North Dakota, the state where he completed some of his medical training. On September 8, neighboring Minnesota granted him a medical license, as DukeCheck reported. He had allowed his previous Minnesota license to expire in 2008.

Thursday, February 7, 2013

Retractionwatch.com coverage of the Anil Potti case




In the last 48 hours or so the retractionwatch.com blog has been hit with a DMCA take down notice in regards to ten posts which covered the Anil Potti case (the now infamous Duke University oncologist who was found to have manipulated research findings, resulting in - among other things - the stop of three clinical trials and now pending civil law suits against the university brought up by patients and their families). More after the jump...

Friday, January 18, 2013

Growth of Human Genomic and Exonic DNA Sequences in NCBI's Short Read Archive since 2009

Figure presenting the growth of total number of bases sequenced from human genomic and exonic DNA submitted to the NCBI Short Read Archive since 2009. The plots are based on SRA Run Summary numbers retrieved through the NCBI E-Utilities interface, sorted by year.





http://dx.doi.org/10.6084/m9.figshare.107021

Thursday, November 15, 2012

Fixing the proxy problem in Mendeley Developer preview 1.7 on Ubuntu 12.04 LTS

I am a big fan of Mendeley (www.mendeley.com) as a tool for storing and organizing my references. In particular the pretty robust extraction of bibliographic data from PDFs saves me a couple of steps in the workflow that I was used to when doing this with Endnote.
I recently received my new (proper) workstation and I have switched from running Ubuntu 10.04LTS in a virtual machine to using Ubuntu 12.04LTS as the main OS and rather running a virtual machine instance of Windows 7 for the few remaining pieces of software which need a Windows OS. Since switching over to Linux, I have not been able to use the Linux version of Mendeley, as it steadfastly refuses to connect to the internet via our work proxy server. While it is possible to configure the proxy settings under "Tools/Options/Connection" the connection test (which can be invoked by pressing Ctrl+Shift+D to bring up the debug console - "Test Internet Connection") reported that it wasn't able to provide proxy authentication. I tried several fixes as outlined in the Mendeley support forums (e.g. http://feedback.mendeley.com/forums/4941-general/suggestions/1051563-generic-linux-bug-connecting-through-proxy-does-n) but none of them worked...

Eventually a combination of defining system wide proxy settings as described here:

http://askubuntu.com/questions/150210/how-do-i-set-systemwide-proxy-servers-in-xubuntu-lubuntu-or-ubuntu-studio

and here some GNOME specific settings:

http://developer.gnome.org/ProxyConfiguration/

and setting the "Tools/Options/Connection" settings in Mendeley to

"No Proxy"

have fixed this problem.

Now Mendeley uses the system-wide proxy setting for connecting to the server and nicely syncs my library the way I was used to. Unfortunately I cannot tell which environment variable is relevant to Mendeley, but as I am using a number of applications which need internet access and everyone of them seems to read out different variables the best way seems to be to set all possible PROXY variables with the relevant connection information.


Thursday, October 25, 2012

Installing "mixOmics" under R-2.15.1 - fixing missing dependencies

mixOmics

The package "mixOmics" depends on a nunber of packages which render some of the 3D graphics output, among them "rgl" which in turn needs a OpenGL libraries/header files for successful compilation. These can be installed by issuing following command in a separate terminal window:
sudo apt-get install libglu1-mesa-dev libgl1-mesa-dev
 Once the system packages have been installed, issuing following command in your R session will install the "mixOmics" package:
install.packages("mixOmics")

Installing R-2.15.1 source package on Ubuntu 12.04 LTS

When attempting to install R-2.15.1 from source on a freshly installed Ubuntu 12.04.1 desktop I ran into several problems stemming from unmet dependencies. The by far most challenging to resolve was the missing of "libg2c0" which is required to run mixed C/FORTRAN code.

The error message from running ./configure in the R source directory:
checking whether mixed C/Fortran code can be run... configure: WARNING: cannot run mixed C/Fortan code
configure: error: Maybe check LDFLAGS for paths to Fortran libraries?
 After spending approximately two hours trying to resolve this unmet dependency by several different approaches, the command which brought the solution to this was:
sudo apt-get install cfortran
And some additional packages to resolve issues with HTML and PDF format R manuals:
apt-get install texlive-fonts-extra fig2ps
"fig2ps" in particular will install a lot of dependencies if TEX has not previously been installed on the system.