Figure: An early test of our new 3-D agent-based cell model, growing from 10 to 80,000 agents in about 25 days (24-threaded simulation required about 5 hours). Rendered in 3D using POVRAY (with a cutaway view). [Read more ...]

Friday, September 23, 2011

Giving a talk at my alma mater

This is really exciting--I'll be giving a talk at the weekly applied math seminar at the University of California at Irvine in November. (4:00 pm on November 21, 2011) This will be a fun homecoming, and I can't wait to catch up with old friends (and potential collaborators)! Many thanks to John Lowengrub for the invitation!

Here is my current list of upcoming talks in 2011-2012:
  • September 30, 2011 (noon): Millind Tambe's Teamcore group, University of Southern California (not a public talk)
  • October 17, 2011 (Session II): USC PSOC short course: "physical sciences approach to understanding cancer", University of Southern California 
  • November 21, 2011 (4:00 pm): Applied Mathematics Seminar, Department of Mathematics, University of California at Irvine
  • Spring 2012: Mathematics Biology and Ecology Seminar, Centre for Mathematical Biology, University of Oxford (UK)
  • May 18, 2012: USC PSOC seminar, Center for Applied Molecular Medicine, University of Southern California

Monday, September 12, 2011

Ramone's Benefit at Hollywood Forever (Proceeds go to WCC and CAMM!)

David Agus sent word that there will be a special Halloween / Ramone's Benefit for our cancer research center. The proceeds will benefit the Westside Cancer Center and the Center for Applied Molecular Medicine.
(Click on the picture to zoom in)
Drop in if you're in the Los Angeles area--it should be a lot of fun, and the proceeds will help our research towards patient-calibrated cancer modeling!

Wednesday, September 7, 2011

ACP paper accepted

After a few years of work, our big DCIS paper has been accepted at Analytical Cell Pathology. I'll post a preprint soon on the publications page. Major points: 
  • We used my agent model calibration technique, plus a volume-averaging upscaling to calibrate a simplified continuum model of DCIS growth in the breast. 
  • We used the steady-state approximation of the continuum model to estimate the DCIS volume.
  • We applied this technique to 17 cases and found a very good match in predicted vs. pathology volume in 14 of 17 cases. 
  • We also found that the model was a much better predictor of volume than mammographic estimates (although this can vary with how the mammography is processed).
  • We found that the mathematical theory predicted that a single variable A--a ratio of the apoptotic index, the proliferative index, and the estimated intraductal oxygenation--is a better predictor of tumor volume than grade, PI, or AI alone.  
The last finding is significant, because you can AI and PI from fairly standard immunohistochemical stains (cleaved Caspase-3 and Ki-67), and oxygenation can be estimated from histopathologic measurements of the viable rim size when comedonecrosis is present.  These things can likely be done on pre-operative biopsy tissue. 

In the long term, this could prove useful for improved surgical planning. Right now, second surgeries are required in 50% or more DCIS lumpectomies due to inadequate pre-surgical estimates of tumor shape and volume. 

More to come when I post the preprint tonight or tomorrow. 

Edit on Sept. 8, 2011 at 11:22 am PDT:

Preprint is now online: