June 2003 Archives
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senorjosh.comJune 2003
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JNCI paper published
June 26, 2003
Gavin J. Gordon, Roderick V. Jensen, Li-Li Hsiao, Steven R. Gullans, Joshua E. Blumenstock, William G. Richards, Michael T. Jaklitsch, David J. Sugarbaker, and Raphael Bueno. Using Gene Expression Ratios to Predict Outcome Among Patients With Mesothelioma Journal of the National Cancer Institute 95:8 (Apr. 2003): 598-605


We have recently demonstrated that simple ratios of the expression levels of selected genes in tumor samples can be used to distinguish among types of thoracic malignancies. We examined whether this technique could predict treatment-related outcome for patients with mesothelioma. Methods: We used gene expression profiling data previously collected from 17 mesothelioma patients with different overall survival times to define two outcome-related groups of patients and to train an expression ratio-based outcome predictor model. A Student’s t test was used to identify genes among the two outcome groups that had statistically significant, inversely correlated expression levels; those genes were used to form prognostic expression ratios. We used a combination of several highly accurate expression ratios and cross-validation techniques to assess the internal consistency of this predictor model, quantitative reverse transcription–polymerase chain reaction of tumor RNA to confirm the microarray data, and Kaplan–Meier survival analysis to validate the model among an independent set of 29 mesothelioma tumors. All statistical tests were two-sided. Results: We developed an expression ratio-based test capable of identifying 100% (17/17) of the samples used to train the model. This test remained highly accurate (88%, 15/17) after cross-validation. A four-gene expression ratio test statistically significantly (P = .0035) predicted treatment-related patient outcome in mesothelioma independent of the histologic subtype of the tumor. Conclusions: Gene expression ratio-based analysis accurately predicts treatment-related outcome in mesothelioma samples. This technique could impact the clinical treatment of mesothelioma by allowing the preoperative identification of patients with widely divergent prognoses.

Posted by senorjosh at 09:48 PM | Comments (0) | TrackBack (0)
the nuances of trip planning
June 12, 2003
I've spent the better part of the day looking into travel insurance and plane fares for next year. This has been the most boring day of my life. There are two things that have kept me sane. 1) this guy:

and 2) ridiculous exclusions for travel insurance, such as:

Continue reading "the nuances of trip planning"

Posted by senorjosh at 06:15 PM | Comments (5)
on wealth
June 11, 2003
A few weeks ago I wrote about the treacherous path of making money in order to use it for good purposes. Bill Gates, for instance, is doing some mighty good things with his money. Here's what Einstein says:

I am absolutely convinced that no wealth in the world can help humanity forward, even in the hands of the most devoted worker in this cause. The example of great and pure individuals is the only thing that can lead us to noble thoughts and deeds. Money only appeals to selfishness and irresistibly invites abuse... Can anyone imagine Moses, Jesus, or Gandhi armed with the money-bags of Carnegie?

Mein Weltbild, 1934

Posted by senorjosh at 03:39 AM | Comments (0)
overhaul iminent
June 10, 2003
So far, this website has been a disjoint jumble of random thoughts and formal projects. That won't change anytime soon. However, I've decided to do a better job of separating the random thoughts from the formal projects. So, if things aren't where they used to be, that is why. Also, I'm going to follow john's lead (as always) and migrate to movable type in the next couple of weeks, so things could get very ugly for a little while. Lastly, I took a crash course in Flash and threw together an animated itinerary of where I'll be next year, and I'm quite proud. Unfortunately, Flash seems to require quite a bit of patience, which isn't my strong suit, so the map is (and forever will be) sloppy.

Posted by senorjosh at 01:23 AM | Comments (3)
two cool links
June 8, 2003
The Flash Mind Reader, courtesy of Alex, and 20 Questions, thanks to John.

Posted by senorjosh at 11:56 PM | Comments (1)
driving the trans-can
June 6, 2003
After nine days and 4,300 miles, I'm back home in California. in case you were wondering.

...um, anyone know why the animation is so small? It's supposed to be 450 px wide. anyhow, click on the microscopic green button for a demo...

Posted by senorjosh at 12:36 PM | Comments (2)
Putting cancer on the run
E. Coli causes diarrhea, and may fight cancer as well

MANY a stalwart man trembles at the mention of the word “colonoscopy.” Odysseus braved Hades and defied the dreaded Scylla, but never did he confront the neighborhood proctologist. Yet colorectal cancer, the fourth leading cause of cancer worldwide, claims tens of thousands of lives each year, and is not a disease easily wiped aside. Maybe, suggests Dr. GianMario Pitari of Thomas Jefferson University, we can flush it out.

Continue reading "Putting cancer on the run"

Posted by senorjosh at 12:31 PM | Comments (0)

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