The Daily Scan

the Knack

At Aperio, as a company which makes precision instruments, we have a number of people with the knack (MP3). "Oh no!" (via Greg Crandall, VP/Engineering)

Jules Berman on Tumor Classification

Jules J. Berman, of the National Cancer Institute (NCI), has posted a fascinating paper: Tumor Classification: molecular analysis meets Aristotle (PDF):

Traditionally, tumors have been classified by their morphologic appearances. Unfortunately, tumors with similar histologic features often follow different clinical courses or respond differently to chemotherapy. Limitations in the clinical utility of morphology-based tumor classifications have prompted a search for a new tumor classification based on molecular analysis. Gene expression array data and proteomic data from tumor samples will provide complex data that is unobtainable from morphologic examination alone. The growing question facing cancer researchers is, "How can we successfully integrate the molecular, morphologic and clinical characteristics of human cancer to produce a helpful tumor classification?"

This manuscript reviews tumor classification and provides a new and comprehensive classification for neoplasia that preserves traditional nomenclature while incorporating information derived from the molecular analysis of tumors. The classification is provided as an open access XML document that can be used by cancer researchers to relate tumor classes with heterogeneous experimental and clinical tumor databases.

The use of XML schemas to define data for common access is growing in many fields in parallel, medicine not least among them. The challenge is analyzing the fundamentally analog information in medical samples to create digital information from them.

Of course I have to add, the ability to digitally scan entire tissue samples and analyze them with computers will be a boon to Pathologists like Dr. Berman. Aperio's ScanScope and competing devices from other vendors are now commercially available, providing this capability.

Handling Human Samples Is Worth the Risk

Gilbert E. Ellis and Allen F. Sanborn have an interesting article in the latest issue of The Scientist, arguing that "using blood and tissues in undergraduate labs teaches valuable lessons about the real world":

Requiring students to practice precautions in undergraduate laboratories while they are being exposed to potential pathogens provides a foundation for building a career in the health sciences. Returning graduated students tell us that they learned the most in these labs. Perhaps the risks of not knowing, early in one's career, present a greater hazard than identifying those risks and addressing them at the start.

Surgeons Who Play Video Games Err Less

ABC reports Research Shows Playing Video Games Leads to Fewer Mistakes on the Operating Table:

Researchers found that doctors who spent at least three hours a week playing video games made about 37 percent fewer mistakes in laparoscopic surgery and performed the task 27 percent faster than their counterparts who did not play video games.

Kind of like the way playing foosball keeps you sharp for computer progamming :)

DNA Sequencing Costs Continue to Decline

FuturePundit reports Biotech instrumentation company Affymetrix has announced a new instrument for mapping DNA Single Nucleotide Polymorphisms (SNPs) which is much cheaper to operate than previous instruments designed for this purpose. SNPs are locations in the genome where not all humans or all members of another species have the same the DNA letter. The instrument will reportedly lower the cost of human DNA SNP testing to 1 penny per DNA letter. That is amazing!

(There are 2.9B DNA letters in the human genome, so the cost of sequencing for a single person is still $29M.)

If you're interested in human DNA sequencing, check out the Personal Genome blog.

Electronic Prescribing on Medicare Fast Track

Medscape reports: Mark B. McClellan, MD, PhD, the new administrator of the Centers for Medicare and Medicaid Services (CMS), said that removing barriers to electronic prescribing in physician offices is a top priority in implementing Medicare reforms mandated by Congress.

"Under the law, we will have electronic prescribing by 2009. I would like to see it way before that. The only question is when and how much we can accelerate it, and that's what we are focusing on."

Dr. McClellan said the agency will push forward on electronic prescribing standards and pilot programs to help physicians implement systems in their offices.

Electronic prescriptions are an obvious way to streamline patient care, and a part of the overall "electronic medical record." (Of course, digital images, including digital Pathology images via virtual microscopy, are a part as well :)

Losing the war on Cancer?

Fortune magazine recently ran an interesting cover story: Why We're Losing the War on Cancer (PDF). The point of view in the article is that little progress has been made in preventing or curing cancer, despite a huge amount of resource, attention, and effort being focused on the problem. The article argues that researchers, drug developers, and physicians are primarily concerned with treating patients who already have cancer to prolong their lives or improve their quality of life. Additionally, there is a suggestion that much cancer research is unfocused or uncoordinated, and that a centralized effort led by the National Cancer Institute would be a more efficient approach.

An excerpt:

So why aren't we winning this decades-old war on terror—and what can we do now to turn it around?

Virtually all these experts offered testimony that, when taken together, describes a dysfunctional "cancer culture"—a groupthink that pushes tens of thousands of physicians and scientists toward the goal of finding the tiniest improvements in treatment rather than genuine breakthroughs; that fosters isolated (and redundant) problem solving instead of cooperation; and rewards academic achievement and publication over all else.

At each step along the way from basic science to patient bedside, investigators rely on models that are consistently lousy at predicting success—to the point where hundreds of cancer drugs are thrust into the pipeline, and many are approved by the FDA, even though their proven "activity" has little to do with curing cancer.

The author does offer some balance, writing:

And to be sure, cancer is a challenge like no other. The reason is that this killer has a truly uncanny ability to change its identity. A cancer cell's DNA is not fixed the way a normal cell's is. A normal cell passes on pristine copies of its three-billion-letter code to every next-generation cell. But when a cancer cell divides, it may pass along to its daughters an altered copy of its DNA instructions—and even the slightest change can have giant effects on cell behavior.

Personally I think we've made huge progress in the war, and I wouldn't describe this progress as "losing". It is frustrating that more progress hasn't been made, but then "curing" cancer is a tough proposition, and really amounts to solving many problems in parallel, since there are so many kinds of cancer.

I'm curious to know, what do you think? If you have a point of view, please leave a comment. Thanks!

Organic Flexible Displays

Scientific American has a fascinating article about organic flexible displays:

"Light-emitting organic materials offer brighter and more efficient displays than LEDs. And you'll be able to unroll them across a tabletop."

Not only are they bright and flexible, but OLED displays can be made very large. Looks like a fantastic technology for virtual microscopy :)

JPEG2000 primer

Advanced Imaging Magazine recently ran a nice article by Stewart Taylor on the JPEG2000 codec. If you are interested in compression technology you will find it very informative.

One of the key decisions which must be made for medical imaging systems is what type of compression to use. Medical images are large, so some type of compression is desirable, but the resolution and detail of medical images is critical, so image corruption and artifacts must be avoided.

These challenges are present for most types of medical images, but they are especially important for Pathology images obtained with virtual microscopy. A typical microscope slide tissue sample may be 1" x 1/2" in size, or about 30mm x 15mm. A high-resolution scanner like the Aperio ScanScope with a 40X objective generates images with a resolution of about 1/4 micron/pixel, yielding an image of 120,000 x 60,000 pixels. Since there are 3 bytes per pixel, this is 22GB of image data!

JPEG2000 is a great compression technology based on wavelet technology which strikes a great balance between high compression and preserving image quality; compression ratios of 25:1 are often achievable. This reduces the size of a 22GB image to 850MB, still very large but much more manageable. (By comparison, JPEG compression usually yields about 15:1, with more image artifacts.)

JPEG2000 is computationally-intense compression technology, and implementations often rely on dedicated hardware to speed up compression. (Aperio uses the Matrox Morphis board for this purpose.) A nice attribute of JPEG2000 is that the computation requires is asymmetric; far more computation is required for compression than for decompression. As a result, hardware acceleration is really only needed for compression; viewing images can be done with ordinary computer hardware.

An Autism gene is found

FuturePundit reports one of the genes which have variations that contribute to Autism has been discovered:

Researchers at Mount Sinai School of Medicine are first to strongly link a specific gene with autism. While earlier studies have found rare genetic mutations in single families, a study published in the April issue of the American Journal of Psychiatry is the first to identify a gene that increases susceptibility to autism in a broad population.

This is great stuff; the payoff from sequencing the human genome is beginning. What a great time to be a scientist!