Sunday, June 26, 2016

If you have contributed to a paper that is already published, can you use the same title, abstract, and images for a poster presentation?

'If you have contributed to a paper that is already published, can you use the same title, abstract, and images for a poster presentation?'
Yes, provided you have permission from the other authors of that paper and provided the meeting abstract submission policies allow submission of a published paper. For example, having clarified these two issues, I have presented posters of papers that were under review or already accepted for publication.

'Does it depend on whether I wrote it in the first place?'
No, but the poster that you plan to present should retain the list of authors from the published paper as is, of course, with those authors' permission. On the poster, you could put an asterisk after your name with the explanation of the asterisk noting you as the poster presenter. Under no circumstances should the poster list only your name as the author.

'Do people rewrite this info or just use the info from the paper?I'm guessing it's frowned upon to literally copy/paste the abstract, but I really doubt I could write a better version that says the exact same thing'.
Tending to stricter word limits, usually poster abstracts are shorter compared to those of journal papers so you may not be able to use the exact same abstract anyway. Remember though that if you end up re-writing some phrases or sentences to conform to a strict word limit, you should get approval of the re-worded abstract from all the other authors. Your poster should also indicate that it's based on a published paper by clearly referencing it, i.e., title, list of authors, journal (year, volume, issue, page numbers), on the poster itself.


https://www.quora.com/If-you-have-contributed-to-a-paper-that-is-already-published-can-you-use-the-same-title-abstract-and-images-for-a-poster-presentation/answer/Tirumalai-Kamala


Sunday, June 19, 2016

In 2010-2011, David Koch was asked to leave the National Cancer Institute at NIH for obfuscating the role of formaldehyde in causing cancer. Which scientists did he rely on most for generating doubt?

The question is slightly inaccurate. David Koch sat on the advisory board of the National Cancer Institute (NCI), the largest (by size and budget) permanent institute at the NIH. The NCI has the mandate for identifying and researching human carcinogens.

In the August 30, 2010 issue of the New Yorker, the award-winning journalist Jane Mayer published an investigative piece on the Koch family where, among other things, she reported, 'Koch Industries has been lobbying to prevent the E.P.A. from classifying formaldehyde, which the company produces in great quantities, as a ‘known carcinogen’ in humans' (Covert Operations - The New Yorker).

As Jane Meyer reports further in her piece, 'Scientists have long known that formaldehyde causes cancer in rats, and several major scientific studies have concluded that formaldehyde causes cancer in human beings—including one published last year by the National Cancer Institute, on whose advisory board Koch sits. The study tracked twenty-five thousand patients for an average of forty years; subjects exposed to higher amounts of formaldehyde had significantly higher rates of leukemia. These results helped lead an expert panel within the National Institutes of Health to conclude that formaldehyde should be categorized as a known carcinogen, and be strictly controlled by the government. Corporations have resisted regulations on formaldehyde for decades, however, and Koch Industries has been a large funder of members of Congress who have stymied the E.P.A., requiring it to defer new regulations until more studies are completed'.

Also, 'James Huff, an associate director at the National Institute for Environmental Health Sciences, a division of the N.I.H., told me that it was “disgusting” for Koch to be serving on the National Cancer Advisory Board: “It’s just not good for public health. Vested interests should not be on the board.” He went on, “Those boards are very important. They’re very influential as to whether N.C.I. goes into formaldehyde or not. Billions of dollars are involved in formaldehyde'.

And, 'Harold Varmus, the director of the National Cancer Institute, knows David Koch from Memorial Sloan-Kettering, which he used to run. He said that, at Sloan-Kettering, “a lot of people who gave to us had large business interests. The one thing we wouldn’t tolerate in our board members is tobacco.” When told of Koch Industries’ stance on formaldehyde, Varmus said that he was “surprised'.

Predictably, this piece created a media and activist firestorm around the clear conflict of interest in Koch, whose Koch Industries is the owner of one of the largest manufacturers of formaldehyde, sitting on an advisory board  of such import on public health policy. It was after this piece appeared in print that David Koch left his advisory board position at the NCI, as the New York Times reported on October 27, 2010  (Koch Leaves Federal Cancer Panel as Groups Urge Ethics Probe).

And it was after this piece appeared in print that the US government announced on June 9, 2011, that it was adding formaldehyde to a list of known human carcinogens (U.S. (finally) Labels Formaldehyde "Known Human Carcinogen").

Read Jane Meyer's New Yorker piece to understand how lobbying relevant government agencies such as the EPA (Environmental Protection Agency) was the approach to prevent or delay classifying formaldehyde as a known carcinogen in humans, not relying on specific scientists to create doubt.


https://www.quora.com/In-2010-2011-David-Koch-was-asked-to-leave-the-National-Cancer-Institute-at-NIH-for-obfuscating-the-role-of-formaldehyde-in-causing-cancer-Which-scientists-did-he-rely-on-most-for-generating-doubt/answer/Tirumalai-Kamala


Sunday, June 12, 2016

Is it true that Bill Gates faced trial in India for illegally testing tribal children with vaccines? Source http://articles.economictimes.indiatimes.com/2014-08-31/news/53413161_1_hpv-vaccine-cervarix-human-papilloma-virus

No, that isn't completely accurate.

Who: Bill & Melinda Gates Foundation (BMGF), https://en.wikipedia.org/wiki/PATH_%28global_health_organization%29 (PATH) and Indian Council of Medical Research (ICMR)
The BMGF funds PATH, a Seattle-based NGO and main recipient of BMGF grant money for global public health initiatives. Since 1998, BMGF has funded PATH to the tune of ~$2 billion. The ICMR is the Indian Government's primary agency tasked with conducting biomedical research.

What: A Phase V human papilloma virus (HPV) Phase V vaccine trial in Andhra Pradesh & Gujarat, India
PATH carried out a large  HPV Phase V vaccine trial in India. Phase V means using approved, not test, vaccines. Certain forms of HPV are associated with cervical cancer. The vaccines in question, Gardasil from Merck and Cervarix from GlaxoSmithKline, were granted marketing approval in India in 2008 while the PATH-sponsored trial began in 2009 as a joint project with the ICMR, using donated vaccines.
  • The purpose of the trial was to generate data to support the inclusion of the HPV vaccine in India's Universal Immunization Programme (UIP).
  • Specifically recruiting from low-income rural, largely tribal, households, the trial was conducted on girls aged 10 to 14 using Gardasil in Khammam district of Andhra Pradesh (AP) state (n=13000), and using Cervarix in Vadodara in Gujarat state (n=10000).

The Problems
Public recognition of problems with this trial started with the reported death of 7 girls. This led to immediate suspension of the trial in 2010 even though it was supposed to run until 2011. Investigations showed these deaths weren't directly connected to the vaccines (see table from the initial official investigation report, 1).

However, investigations triggered by these deaths instead uncovered serious violations of the process of informed consent (see official investigation reports below from 1, see also 2). Aged 10 to 15, girls in this trial were obviously below the age of  consent meaning their participation in the trial required the consent of  parents/guardians. In the course of Government of India (GOI)  investigations, the trial investigators 'were asked to submit 100 consent forms, chosen randomly, for both AP and Gujarat for independent verification' (1). These consent forms turned out to have several problems (see reports below from 1).

Investigations (1) revealed that
  • In Andhra Pradesh, 'Signatures of one parent were obtained on 9543 forms, thumb impression of one parent on 1948 forms and signatures of Hostel Warden/Head Master as Guardian in 2763 forms
  • The investigators noted, 'The legality of the signing by the Hostel Warden/Head Master in Andhra Pradesh needs to be examined by an appropriate authority'. 
  • In Gujarat, 'In Gujarat one parent has signed on 6217 forms, has provided thumb impression on 3944 forms and Legal guardian has signed or put thumb impression on 545 forms'.
  • As a newspaper report summarized, signature of ~2800 consent forms had instead been signed by school teachers, principals or hostel wardens, even in cases where the girls had parents (2).

The Indian Parliament's Standing Committee on Health began its investigation in April 2010 and concluded that 'safety and rights of children were highly compromised and violated' (3).

The Committee's report (3) found
  • The girls' consent was not fully informed.
  • Post-vaccination adverse events weren't adequately monitored or reported.
  • PATH and ICMR hadn't sought mandatory permission from the Drug Controller General of India (DCGI) or the Indian National Technical Advisory Group on Immunization (NTAGI).
  • PATH wasn't even a registered legal entity when it began working with the ICMR.
  • DGAI culpable for dereliction of duty.

The Committee's report stated, 'PATH resorted to an element of subterfuge by calling the clinical trial as 'observational studies' or 'demonstration project' and recommended legal action against PATH (3). However, the Union Government of India  decided legal action couldn't proceed based on the its assessment of the country's prevailing laws. Instead in 2014, it issued a warning letter to PATH (4).

PATH's dubious and unconvincing defense was that this wasn't a clinical trial, only an observational study of an already approved vaccine. As such, it argued that neither provision, i.e., informed consent and monitoring/reporting of post-vaccination adverse events, was necessary (5). This is patently incorrect.

Bibliography
  1. http://icmr.nic.in/final/HPV%20P...
  2. The Hindu, May 25, 2011. Editorial. A shockingly unethical trial
  3. Page on preventdisease.com
  4. The Hindu, August 25, 2012. Aarti Dhar. Government warns PATH
  5. LaMontagne, D. Scott, and Jacqueline D. Sherris. "Addressing questions about the HPV vaccine project in India." Lancet Oncology 12.14 (2013): e492; Statement from PATH: cervical cancer demonstration project in India

Further Reading
  1. Kumar, S., and D. Butler. "Calls in India for legal action against US charity. Nature News [Internet]. 2013 Sep 9 [cited 2013 Oct 22]." Calls in India for legal action against US charity
  2. sSharma, Dinesh C. "Rights violation found in HPV vaccine studies in India." The Lancet Oncology 14.11 (2013): e443.

https://www.quora.com/Is-it-true-that-Bill-Gates-faced-trial-in-India-for-illegally-testing-tribal-children-with-vaccines/answer/Tirumalai-Kamala


Monday, June 6, 2016

What are the best ways to write a literature review?


I don't think best way is an appropriate or helpful way of putting it. Rather, literature reviews should be comprehensive, covering the topic’s history, key concepts, influential figures and notable developments. As well, they shouldn't shy away from contentious material. Rather they should attempt to persuasively present data and arguments for or against certain interpretations. This broad umbrella accommodates a variety of writing styles and analytical approaches.

Some examples may help explain the process. For e.g., a while back I wrote an answer about possible human- Mycobacterium tuberculosis co-evolution, Tirumalai Kamala's answer to What if Mycobacterium tuberculosis evolved as a cohabitating organism within the human body?. Like many of my Quora answers, this too took the form of a review so it may be a relevant example.

How to start? Start with what I call a hook. As simple as searching for Human Mycobacterium tuberculosis co-evolution in Home - PubMed - NCBI. In this particular example, I got 24 search results (see screenshot below). Several good leads (outlined in blue), i.e. hooks to get into the subject.


Got those papers, read them, looked up their references, looked up the papers that cited them. Read the abstracts to decide whether to download or not. Doing this builds up a database on the topic rather fast. Once done screening and collating this database, I can sort them into different bins according to subject matter (see screenshots below). In this particular example, I ended up with a database consisting of 9 papers I catalogued as General, 2 as Bottleneck, 15 as Canetti, 4 as Co-evolution, 2 as Deletions, 3 as M. africanum, 7 as M. bovis, 4 as Methods, 15 as Paleopathology, and 3 as Virulence Definitions, for a total of 64 papers. Not a thorough up and down, front and back dredging of source material by any stretch of the imagination. Answer intended only for a general, not specialist, audience after all but this is an example of the basic skeleton required for assembling the database needed for a literature review. As I go through this bunch, the answer starts to shape itself into existence and I start whittling the pile. What's useful? In this particular example, my shorthand for papers I cited have a green dot while ones I found useful for references have a blue dot (see screenshots below).


A similar process attends just about any kind of research I undertake. Cataloging and sorting plus a common file-naming system helps tremendously in gaining control over the reading material, and brings order to what starts out as utter chaos.
Another invaluable helper? Keyword search through a database using Command+F. Helps both with the binning process as well in mining the database for the portion of the answer dealing with a particular keyword.

Process is simple and straightforward in theory. In practice, it requires genuine unflagging interest, and tremendous focus and discipline. Certainly not for the faint-hearted. Especially the citation search. Often papers are cited 100s, even 1000s of times. Trawling though such citations requires a hardy stomach and a spine of steel. Of course, checking each and every citation isn't mandatory nor required for each review. Time and practice helps develop judgment regarding when to pause to pick up another reference or to move on. As well, I tend to read very fast so I can consume relatively vast amounts of information fairly quickly. Plus years of experience doing this. However, reading fast has its perils as well so experience has taught me to go over papers more than once. A gap in time helps plug gaps as fresh eyes bring more value to the task.

I find this general approach very versatile so much so that I use it both for work and elsewhere. For e.g., my hometown of Chennai recently suffered unprecedented floods that marooned the city and relegated it to the medieval age in one stroke. Since I have family there, I spent many waking hours tracking the situation on the ground the best I could on the internet. The material I found doing this formed the basis of my blog post cataloging what happened, why and what it says about the body politic, The 2015 South Indian Floods: The Front Page News Story that Global News Media Wantonly Neglected by Tirumalai Kamala on TK Talk.

Using a similar approach to catalog, collate and bin my starting material (see screenshot below), the post started to shape itself into existence. Again, Command+F is an irreplaceable help. Using it to find keywords such as 'drain', 'police', 'military', 'NDRF', etc., helped me quickly shape a narrative that made sense to my understanding of the situation. Quickly scan, copy-paste the relevant passages, move on. Soon, my post was done. 


So there you have it, a broad brush overview of my approach to review writing. How the review/answer starts to shape itself is the most mysterious aspect of this process. This is where the individual's unique Masala (or alchemy) makes all the difference. A feeling for narrative, bolstering arguments with tangible, verifiable, sometimes testable data, one part of the narrative flowing to the next, these are some of the essential elements. Often arguments in one section will stoke into existence logical questions. These can then serve as bridges connecting one section to the next, or even one para to the next. In this manner, hopefully a cogent narrative emerges, akin to a building, the original database the foundation and the review sections the above-ground structure the foundation makes possible. More comprehensive the database (foundation) that went into researching the review topic, better the review (building) and greater its value.


https://www.quora.com/What-are-the-best-ways-to-write-a-literature-review/answer/Tirumalai-Kamala