Real Numeracy

Currently, the best test to check for organ rejection is a biopsy. This is an invasive procedure that is expensive and can lead to complications. In a biopsy, a probe is inserted to extract a sample of the transplanted organ. The cells in the sample are then stained and viewed under a microscope to see if they are being attacked by the patient’s immune system.

A new noninvasive test has been developed by researchers led by Hannah Valentine, a cardiologist at Stanford University, and published in Proc. Nat. Aca. Sci. Mar 2011. Their test, which is designed for heart transplant patients, relies on the fact that once the immune system begins to attack the transplanted organ, some of the cells in that organ die, are decomposed by the immune system, and carried away in the blood stream. Since the transplanted organ has different DNA than the host, the level of foreign DNA in the patient’s blood will rise. This DNA can be detected and measured using a simple blood test.

Stanford University is applying for a patent for this process and expects to license it. A good description on the development of this test appears in Tech. Rev. Mar 2011. This new test may be used in conjunction with an existing simple blood-based genetic test sold under the trade name AlloMap, that can predict which patients are most likely to have an active immune system that will lead to organ rejection. The combination of the two tests could provide a better guide for clinicians to adjust the types and dosages of immunosuppressant medications to provide transplant patients with the lowest amount needed to avoid rejection. It will also allow faster diagnosis of rejection to so that  treatment can be adjusted as needed.

by George Taniwaki

In a May 2010 blog post, I featured a new social media web site called PatientsLikeMe which allows patients to compare medical notes with each other. It also allows patients to search for each other and provides a forum where they can create a sense of community.

In February, PatientsLikeMe upgraded its site and added a bunch of new features including automatically adding patients to forums with other patients with similar conditions. They’ve also made it easier to measure and track how you are feeling and share that information with others.

If you are a kidney patient, especially a transplant recipient, I encourage you to check out the site.

New condition tracking page. Image from PatientsLikeMe

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One thing that PatientsLikeMe is missing is the ability to communicate with other patients in real-time, using chat. To address this need for instant feedback from fellow patients there is a site called HealCam.

HealCam was developed by a California anesthesiologist named Michael Ostrovsky. Dr. Ostrovsky modeled HealCam on ChatRoulette. The difference is that ChatRoulette seems to be a rather pointless game while HealCam is intended to be a tool to help both participants cope with their condition.

One problem with HealCam is that even though it has been around for almost a year, very few people have heard of it. For instance, when I signed on, I was the only participant. Unless HealCam can increase usage, it will languish. Perhaps it should not be a standalone operation and just become a feature within a site such as PatientsLikeMe.

The HealCam user interface is clean and simple. Image from HealCam

Sue and I visited Paris recently and had a wonderful time (see a Mar 2011 blog post about my visit to the Musée Carnavalet.).

One thing that we found disconcerting was the prevalence of scam artists around the city. Unfortunately, although we took lots of pictures of the city, we failed to take any of these people.

The door blocking musicians

Our first experience with a scam artist was riding the train from the airport to the city center. At a stop after the airport, a young man, who from his complexion I assume to be North African, stepped on the train with a portable amplifier/synthesizer. He blocked the exit door of the train and began singing. When the train pulled to the next stop, he stopped singing and held a tip cup as people moved on or off the train. When the train started moving again, he started singing again. We saw musicians nearly every day while riding the Metro. Unlike the U.S. the musicians were always on the trains, never in the stations. Also, unlike the street musicians I see in the U.S., these people were uniformly untalented.

The school for the deaf

Our second experience occurred a few minutes later as we exited the airport train at Gare du Nord. It is a beautiful building. In front of the station are throngs of teenage girls, all of them deaf (or so they mime), and all of them with long dark hair and brown eyes. I presume they are also North African. They each have a clipboard with note, in English, asking for a donation for their school. They are very persistent, like flies at a picnic. We saw these deaf girls outside all the Metro stations nearest tourist sites and near the Eiffel Tower.

The found ring

Apparently, lots of men drop their gold wedding bands on the ground near museums in Paris. Luckily, there is always a nice gentleman who speaks broken English who will pick it up and ask you if it is yours. When you say “no”, he will ask if you want to buy it and then point to the 14K mark inside the band. Too bad the ring is made of brass. A version of this scam involving a woman is described here.

The woven bracelet

After walking past the hoard of deaf girls at the upper station for the Montmartre funicular , I started walking down the steps. On the way down, I encountered a group of young men who surround me. They are all black, possibly immigrants from West Africa. One of them places a string loop around my wrist and begins weaving it. I get bored with his spiel and move on. The weaver yells down the hill and a second group of young men surround me again and repeat the process. I’m intrigued, but am in a hurry and break away from them. Naturally, they are disappointed that I didn’t stick around to buy a souvenir of my visit to the Basilique du Sacré-Cœur.

Trinket dealers

As you walk toward the Eiffel Tower, there are many people selling souvenirs and toys. There are some selling identical Eiffel Tower key chains (always 12 for 5 Euros) and Eiffel Tower replicas (in several sizes up to a foot tall). Others sell identical wind-up fuzzy dogs. And a final group sells wooden trains with carved letters that you can use to spell your name, or “P-A-R-I-S” or “E-I-F-F-E-L T-O-W-E-R.” Nearly all of the vendors were young men and appeared to be either black or North African.

What’s going on?

I thought it was odd that so many scam artists would use identical techniques. Here are a few ideas that popped into my head.

1. These people are all copying each other because these particular scams have proven to be the money makers. You wouldn’t want to copy a scam that is inefficient.
2. The prevalence of North African and West African immigrants in these scams indicates how hard it is for these people to find regular employment in the French economy. Discrimination forces immigrants and their descendants to live in the margins of society.
3. The tolerance of the French police to these scammers, who prey on tourists and ply their trade in busy public places in broad daylight, indicates a tacit admission by the government that there are no other jobs for these people and to restrict their activities could lead to violent social unrest. Recall the riots in Clichy-sous-Bois and other banlieues in 2005.
4. Some scams, like the musicians are probably independently operated. But others, like the sales of identical toys, and the soliciting for the deaf girl school, indicate that someone may be controlling access to the goods, the forms, and maybe even the prime street locations. These may be pyramid schemes in which the vendors are paying a cut to someone above. These street scam artists may be victimizing tourists. But they may be victims themselves.
5. The girls with the clipboards ask you to complete the “donation” form because this is an easy way for the scam operator to ensure each girl reaches her quota and ensure she isn’t stealing any of the funds.

I recently watched two videos featuring Anthony Atala, a surgeon and researcher at Wake Forest University who works in the Institute for Regenerative Medicine. The first video is from his talk at TEDMed Oct 2009. In it, he talks about creating artificial tissue and organs. His talk also includes video clips showing working urethras and blood vessels made with biopolymers. He also shows a standard ink jet printer modified to print live endothelial cells to form 3D objects such as heart valves. Finally, he shows a functional liver created using a scaffold made from a decellularized cadaver liver.

Artificial organs. Video from TED Med

The second video is from Dr. Atala’s talk at TED Mar 2011. In this newer video he describes the process of creating a scaffold for a kidney. Much of the content in the first eight minutes is a repeat of the previous talk. The exciting part starts at 10:04 into the video where he describes the process of using a 3D ink jet printer to create the kidney scaffold.

Printing kidneys. Video from TED Med

The work of researchers at Wake Forest developing artificial organs was mentioned in an Aug 2010 blog post.

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Also in March, I attended the Annual Faculty Lecture at Univ Washington. The speaker was Buddy Ratner, a professor in the Department of Bioengineering . Mr. Ratner is the Michael L. & Myrna Darland Endowed Chair in Technology Commercialization, the founder of Ratner BioMedical, and a member of the scientific advisory board for Tengion, a firm that has licensed the Wake Forest technology.

His talk, entitled “Regenerate, Rebuild, Restore — Bioengineering Contributions to the Changing Paradigm in Medicine”, described the work he and his graduate students have done in creating biodegradable scaffolds made from biopolymers such as polyHEMA, a common material used commercially for soft contact lenses, using a novel process called 6S.

The 6S process gets its name from the six steps used to make the material. First, polystyrene pellets are sieved to isolate pellets of 35 to 40 microns in diameter. These pellets are shaken to create a close-packed arrangement. The packed material is sintered to create a porous solid. This solid acts as a mold. The desired biomaterial, such as polyHEMA, is poured into the mold and surrounds the sintered pellets. The biomaterial is allowed to solidify. Finally, a solvent is added to dissolve the polystyrene mold, leaving only the biomaterial which contains many pores of 35 to 40 micron diameter. (Pores of this size have been shown to reduce the immune reaction that leads to scarring and infection. The explanation of why is beyond the scope of this blog.)

A company named Healionics was formed to commercialize the 6S process. Mr. Ratner is the chairman of the firm’s scientific advisory board.

Schematic of 6S process. Image from U.S. FDA

After the talk I spoke to Mr. Ratner about artificial kidneys. Unfortunately, he indicated that there are no researchers at Univ Washington working on producing artificial kidneys. I also asked him about the pros and cons of natural and synthetic substrates. He believes that using decellularized organs as the substrate for new artificial organs will prove too difficult except for certain uses and that he expects synthetic substrates, like those created using the ink jet process or the 6S process, to be more likely to lead to successful functional organs.

[Update: Corrected the affiliation of Mr. Ratner with Tengion. He is a member of its scientific advisory board.]

Dante Chinni and James Gimpel, the authors of Our Patchwork Nation: The Surprising Truth About the “Real” America, look at demographic data of the United States at the county level. There are 3,141 counties in the U.S. and though they vary considerably in geographical size and population, using county-level maps to display data provides a convenient way to compare and contrast demographic data.

By mapping demographic data at the county level, you can see how attributes like population density, income, education, attitudes, behaviors, and health are distributed across the U.S.

Unfortunately, the authors take the wonderfully detailed data available from various sources at the county level and use segmentation analysis to group the counties into twelve categories and give them cute names. Ugh.

Our Patchwork Nation. Image from Amazon

Luckily, the authors provide access to the raw county-level data at their website, patchworknation.org. You can view county level chloropleth maps for a wide variety of data. There is even a tool to overlay two maps to do comparisons. The tool doesn’t work very well since you cannot select the colors of the overlays. But overall, the patchworknation site has some of the best U.S. data maps available.

An example of the problem using segments rather than the raw data is illustrated in an article that appears in The Atlantic Apr 2010. The map shown below shows the 12 segments. But the user has to flip back and forth between the legend and the map to determine what each color means.

The 12 states of America. Image from PatchworkNation

The raw data, at the Patchwork Nation website is shown in the three maps below. The first map shows the median household income in 1980. The colors show which quintile each county falls into. The second map shows quintiles for 2010. It is hard to compare the two maps to see how the distribution changes. Going to the Patchwork Nation website and toggling between the two maps makes it easier.

Distribution of median household income by county in 1980. From Patchwork Nation

Distribution of median household income by county in 2010. From Patchwork Nation

The map below shows the change in median income for each county using 2010 adjusted dollars. Notice the counties with large and growing urban populations, mostly on the east and west coasts. They had the highest median incomes in 1980 and in 2010. They also show the highest growth in median income while the remaining counties show smaller gains or a loss. The gap in income distribution in the U.S. is growing.

For more on this story, read the article at the Patchwork Nation website.

Change in median household income by county from 1980 to 2010. From Patchwork Nation

There’s a museum on every street corner in Paris. I’m exaggerating, but it sure feels that way. On Sunday, I took a walking tour of the Marais district of Paris and made a stop at the Musée Carnavalet. Despite the crowded streets, there were only a few visitors in the museum; apparently most people in the Marais district were busy shopping or eating.

The Carnavalet Museum features artwork and furniture that covers the history of Paris. It is housed in two old mansions connected by a corridor on the second floor. Each mansion has a courtyard with a garden, although at this time of year the gardens weren’t on display. The museum is free and photography is allowed.

A rare prerevolutionary statue of Louis XVI in entry courtyard. Photo by George Taniwaki

Each room covers a single time period, but the rooms are not in chronological order. The labels are in French only. It’s all quite confusing unless you bring a guidebook with you. I used Rick Steves’ Paris 2011.

Just for fun, I took a few panorama shots using my iPhone. They are stitched together using Autostitch, an app featured in a Feb 2010 blog post.

90 degree panorama of first floor staircase. Photo by George Taniwaki

180 degree panorama of mural above staircase. Photo by George Taniwaki

I’ll say one thing about France. There sure were a lot of wars there from 1789 to 1945.