Sunday, November 27, 2011
Monday, November 21, 2011
Clinical Research Oriented Workshop (CROW) Meeting: Nov 17, 2011
Present: Kairn Kelley, Amanda Kennedy, Rodger Kessler, Ben Littenberg, Connie van Eeghen
1. Start Up: Amanda – goal for today is to become fluent in “survival analysis” and why the article (Ridker, Rosuvastatin…, 2008) raises flags about supporting the treatment it advises.
2. Ben: Has been reading “Made to Stick” – a book that indicates that numbers alone are rarely enough to change behavior; the “story” needs to be present too. (Relates back to H. Pylori as the cause of ulcers, with treatment by antibiotics, translated to practice by personal demonstration rather than RCTs.) The interpretation of survival analysis studies is based on the following:
a. Approach like any hypothesis testing exercise, with time involved
b. Two variable outcome: will there be an event and when will it happen?
c. Analytical rules
i. One event (even a non-fatal event) removes the subject from the study
ii. Death for any reason is a cause for removal as well
d. The curves illustrated in the article (placebo and experimental drug) show the cumulative incidence to time “t,” or the rate of events for the entire population up to any time “t” conditional on being at risk in the time period (“time to event” analysis)
e. Kochs figured out how to smooth the step-wise curve; Kaplan-Meier created a log rank, non-parametric test. It is an omnibus test: it tests all comparisons but doesn’t say where any differences lie, just whether they are present.
f. The p value indicates whether the cumulative survival rate over time is (or is not) different.
g. This analysis gets a little more complicated when subjects are recruited over time (they don’t all start at the same time); survival for a “short time” subject isn’t as meaningful as for a “long time” subject. Calendar time survival shows incoming and outgoing subjects throughout the study:
i. Survivors who are short timers are “censored out” of the denominators and numerators. Elapsed time survival “pulls back” new recruits; they don’t have an effect on later time periods because they haven’t been in the study long enough:
ii. K-M calculates the cumulative effect of the probability for each time period within the study
h. Is the graph in the article convincing? Reasons that the difference between 2 groups could exist:
i. Randomness, which is affected by:
1. Sample size
2. Measure of variance
3. Effect size
4. And is measured by p value
ii. Bias – systematic error, sampling bias, or fraud – in general, we never know for sure
iii. Real effect – the difference is a reflection of the truth – and we’ll never know, again
i. Precision: decreases over time, as the number of survivors decreases over time. This is why the “number at risk” should be included below the graph for each time interval.
j. Questions to ask about a study:
i. Is it worth it (to prescribe a drug) if the drug costs $1000/year, which for every 20 out of 100 will have unwelcome effects and 1 will be saved a critical event that would cost ~$50K? Is the effect size worth it?
ii. Is the biology convincing?
iii. Was it funded by a neutral source? Some judgment is required here.
3. Next Workshop Meeting(s): Thursday, 12:30 p.m. – 2:00 p.m., at Given Courtyard Level 4
a. Nov 24: Cancelled – Thanksgiving
b. Dec 1: Connie – data presentation or R03 draft (no Rodger)
c. Dec 8: (no Ben)
d. Dec 15: (no Ben)
e. Dec 22: (no Amanda, Kairn)
f. Dec 29: UVM closed
g. Jan 5: Kairn - update
h. Future agenda to consider:
i. Ben: budgeting exercise for grant applications
ii. Rodger: Mixed methods article; article on Behavior’s Influence on Medical Conditions (unpublished); drug company funding
iii. Amanda: presentation and interpretation of data in articles
iv. Future: Review of different types of journal articles (lit review, case study, original article, letter to editor…), when each is appropriate, tips on planning/writing (Abby)
Recorder: C. van Eeghen
Thursday, November 17, 2011
UVM Publication cited in Boston Globe
Prevalence of limited health literacy and compensatory strategies used by hospitalized patients.
Source
Abstract
BACKGROUND:
OBJECTIVES:
METHOD:
RESULTS:
DISCUSSION:
- PMID:
- 21878798
- [PubMed - indexed for MEDLINE]
- PMCID: PMC3212986
- [Available on 2012/9/1]
Monday, November 7, 2011
Clinical Research Oriented Workshop (CROW) Meeting: Nov 3, 2011
Present: Kim Dittus and guest Dr. O'Brien, Kairn Kelley, Amanda Kennedy, Rodger Kessler, Charlie MacLean
1. Rodger: Rodger is preparing an R01 in which practice demographics could impact outcome. He asked if he should stratify. Clarifying discussion about stratification, block randomization, and block randomization with stratification ended in the conclusion that, for Rodger's current grant, block randomization makes sense but effects of demographics should be looked at during analysis not assumed and stratified for.
2. Kim: Kim shared a power-point presentation describing an oncology rehabilitation program which she would like to see paid for by insurance companies. Dr. Wheeler from BC/BS indicated an interest in the program if it can be shown that "it works." Kim shared successes in getting the program going thus far for breast cancer survivors completing treatment. Ideas for gathering and presenting useful pilot data and future evaluation with comparison groups were discussed.
3. Next Workshop Meeting(s): Thursday, 12:30 p.m. – 2:00 p.m., at Given Courtyard Level 4
a. Nov 10: Amanda: survivor analysis chalk talk
b. Nov 17: Connie: Review of Case Study #2 data
c. Nov 24: Cancelled – Thanksgiving
d. Dec 1:
e. Dec 7:
f. Dec 15: (no Ben)
g. Dec 22:
h. Future agenda to consider:
i. Ben: budgeting exercise for grant applications
ii. Rodger: Mixed methods article; article on Behavior’s Influence on Medical Conditions (unpublished)
iii. Future: Review of different types of journal articles (lit review, case study, original article, letter to editor…), when each is appropriate, tips on planning/writing (Abby)
Recorder: K. Kelley
Saturday, November 5, 2011
Example of Visual Data Points in Nature
http://vimeo.com/31158841
Enjoy...
Thursday, November 3, 2011
New Funding Opportunity for the NIH Director’s Transformative Research Award
This informational webinar will provide information and answer questions about NEW funding opportunity announcements (FOAs) for the HRHR program, specifically for the Transformative Research Award, which is open until January 12, 2012 (5:00 PM local time of applicant organization). The types of questions to be addressed during the webinar include, but are not limited to:
· What types of projects have been funded to date?
· Why don’t there seem to be so many clinical and/or behavioral science projects funded?
· What are the expectations regarding preliminary data?
· What are typical budgets of successful applications?
· What are the most common criticisms?
· What makes a particularly strong application?
· Can you give some examples of projects that might be considered transformative or not transformative?
· What is the review process?
· How are reviewers selected?
· How can applications with such diverse topic areas be reasonably reviewed by a single panel?
Agenda
1:00 PM Welcome
James Anderson, M.D., Ph.D., Director, Division of Program Coordination, Planning, and Strategic Initiatives (DPCPSI), NIH
1:05 PM New Funding Announcement for High Risk-High Reward Program:
NIH Director’s Transformative Research Award
Ravi Basavappa, Ph.D., Program Director, Office of Strategic Coordination, DPCPSI, NIH
1:30 PM Review process for Transformative Research Award applications
John Bowers, Ph.D., Initial Review Group Chief and Scientific Review Officer for the
Transformative Research Award initiative, Center for Scientific Review, NIH
1:40 PM Question and Answer Session
Members of the High Risk-High Reward Working Group will answer questions submitted via Email and phone
2:45 PM Adjourn
Access the webinar via: https://webmeeting.nih.gov/hrhr
The computer system requirements for joining the webinar can be found here: http://webcollaboration.nih.gov/systemRequirements.asp
Please send us your questions in advance or during the program via Email at Transformative_Awards@mail.nih.gov or by phone at 1-800-593-9895, pass code 10699.
The webinar is open to external participants and NIH staff. The webinar is being broadcast from the NIH Bethesda campus, Bldg 31, 6C/7. In-person seating is limited. The webinar will be closed captioned and video archived on the Common Fund website (http://commonfund.nih.gov).
The NIH Common Fund (formerly the NIH Roadmap) encourages collaboration and supports a series of exceptionally high impact, trans-NIH programs. These programs are supported by the Common Fund, and managed by the NIH Office of the Director in partnership with the various NIH Institutes, Centers and Offices. Additional information about the NIH Common Fund can be found at http://commonfund.nih.gov.
The National Institutes of Health (NIH) –“The Nation's Medical Research Agency” – includes 27 Institutes and Centers and is a component of the U. S. Department of Health and Human Services. It is the primary federal agency for conducting and supporting basic, clinical and translational medical research, and it investigates the causes, treatments and cures for both common and rare diseases. For more information about NIH and its programs, visit http://www.nih.gov.
Wednesday, November 2, 2011
American Medical Informatics Association Annual Symposium
UVM (particularly, CTS faculty) had quite a presence with 3 papers, 2 panels, and 1 poster this year – all the papers were up for awards and won 2 of them.
Full-Lenth Papers
Chen ES, Manaktala S, Sarkar IN, Melton GB. A multi-site content analysis of social history information in clinical notes. AMIA Annu Symp Proc. 2011:227-236. [Distinguished Paper Award Winner]
Sarkar IN. A vector space model approach to identify genetically related diseases. AMIA Annu Symp Proc. 2011:1206. [Distinguished Paper Award Winner; under consideration for journal publication]
Ye H, Chen ES. Attribute utility motivated k-anonymization of datasets to support the heterogeneous needs of biomedical researchers. AMIA Annu Symp Proc. 2011:1573-1582. [Student Paper Competition Finalist]
Panels
Bhavnani SK, Bassler K, Sarkar IN, Gundlapalli AV, Shaikh AR. Can Network Visualization and Analysis Accelerate Medical Discoveries? Theoretical, Applied, and Funding Perspectives. AMIA Annu Symp Proc. 2011:2035-2037.
Payne PRO, Sarkar IN. The Joint Summits on Translational Science: Reflections and Aspirations. AMIA Annu Symp Proc. 2011.
Poster
Kost R, Littenberg B, Chen ES. Assessing disease co-occurrences using association rule mining and public health data sets. AMIA Annu Symp Proc. 2011:1841.
Congratulations to Director Neil Sarkar and Associate Director Liz Chen for putting together a remarkable showing in only the second year of the CCTS Biomedical Informatics program.
Tuesday, November 1, 2011
Clinical Research Oriented Workshop (CROW) Meeting: Oct 27, 2011
Present: Kairn Kelley, Amanda Kennedy, Rodger Kessler, Ben Littenberg, and guest Mike Kenny from the Vermont Oxford Network
1. Ben: How to match individual data from two sources without exchanging any PHI
a. Ben described an area for research that attempts to analyze the impact of geographic factors on health outcomes. Ben and his collaborators hope to connect health data with information about geographic factors (“geomarkers”) near subjects’ homes. The health data may come from clinical and research databases registries housed in different health organizations. The challenge discussed today is how to respect the legal and political needs of data partners that collect the protected health information while still gaining enough information to meaningfully link health outcomes with "geomarkers" (geographic factors).
b. Potential research questions would include:
i. What are the best ways to model geomarkers?
ii. What is the relationship between geomarker ‘x’ (e.g., density of commercial real estate, or topographical slope) and health status ‘y’ (e.g., BMI or breast cancer diagnosis)?
iii. What level of analysis (i.e., individual, zip code, county, etc.) shows the strongest association between geomarkers and health status?
c. Recent stories of the consequences of erroneous release of PHI (Protected health Information) have made many organizations nervous about sharing data even for permitted purposes. In order to respond to data security concerns, Ben proposed a number of data sharing strategies that could be offered to potential partners (not all will be offered). The hope is that presenting choices to the data partner will increase trust so the least restrictive option can be selected. At least one of these options is a novel strategy, and Ben may wish to expand this into a paper. For that reason, I am limiting notes to listing the potential strategies by name:
i. Simple transfer
ii. Partner geocoding
iii. Partner geocoding with random error
iv. Partner geocoding with "snap”
v. Remote access
vi. Sneaker net
vii. Partner geocoding and association
viii. ARC model
ix. Triple transfer (name changed from Triple swap due to negative connotations for the word “swap” re: trust)
x. (Amanda also suggested “Trusted Third Party”)
2. Next Workshop Meeting(s): Thursday, 12:30 p.m. – 2:00 p.m., at Given Courtyard Level 4
a. Nov 3: Kim: research/grant opportunity (no Ben)
b. Nov 10: Amanda: survivor analysis chalk talk
c. Nov 17:
d. Nov 24: Cancelled – Thanksgiving
e. Dec 1:
f. Dec 7:
g. Dec 15: (no Ben)
h. Dec 22:
i. Future agenda to consider:
i. Ben: budgeting exercise for grant applications
ii. Rodger: Mixed methods article; article on Behavior’s Influence on Medical Conditions (unpublished)
iii. Future: Review of different types of journal articles (lit review, case study, original article, letter to editor…), when each is appropriate, tips on planning/writing (Abby)
Recorder: K. Kelley