Cross-Reference Visualizations

Bible Cross-References: The bar graph that runs along the bottom represents all of the chapters in the Bible. Books alternate in color between white and light gray. The length of each bar denotes the number of verses in the chapter. Each of the 63,779 cross references found in the Bible is depicted by a single arc - the color corresponds to the distance between the two chapters, creating a rainbow-like effect.

This is a pretty cool visualization of bible cross-references that was developed by Chris Harrison to show bible cross references throughout the length of the bible. I can’t help but think of how interesting this could be for genome visualization: the cross references could be based on genes that are transcription factors for other genes. (activate or deactivate those genes). Chris has lots of other fascinating visualization projects to look at, and is very stimulating to browse it.

Are Genius and Madness Even Closer Than we Think?

“no great genius was without a mixture of insanity”
- Aristotle

“They say madness runs in our family. Some even call me mad! And why? Because I dared to dream …of my own race of atomic monsters! Atomic supermen with octagonal-shaped bodies that suck blood out of…”
-Prof. Hubert Farnsworth

To be clear, by genius I mean the ability for humans to think at the level we do. And by madness, I mean madness. A recent study suggests that we have our big brains at a high price: schizophrenia. It comes down to the massive metabolism needs that our brains have. A team led by evolutionary biologist Philipp Khaitovich of the Shanghai Institutes for Biological Sciences and the Max Planck Institute for Evolutionary Anthropology created an experiment to see how much genes that are involved in schizophrenia have evolved since humans split from chimpanzees.

Searching for Text in Images

We (my lab, http://krauthammerlab.med.yale.edu) recently published on our new image search engine for biomedical images, called YIF, or Yale Image Finder. From our blog post on our web site:

We have recently released a new biomedical image search engine we call YIF. You can access it at:

http://krauthammerlab.med.yale.edu/imagefinder

You can search the actual image content of over 34,000 Open Access articles from PubMed Central. We use OCR with different levels of image correction (article and corpus) for highly accurate image text extraction.

For more details about our algorithms, we have a paper in Bioinformatics titled “Yale Image Finder (YIF): a new search engine for retrieving biomedical images“.

Double Arm Transplant in Germany Considered Success

15 hours and 40 doctors later, a farmer has two new arms. The surgery replaced both limbs of a farmer who lost his arms in an accident in 2002. He lost both arms below the shoulder. From the Guardian article:

Christoph Höhnke, a surgeon on the transplant team, said that the complicated procedure was completed without any unforeseen problems. It involved a team of 40 doctors, nurses and assistants working together, attaching one arm and then the other. “The whole thing went according to script,” he said.

With a surgery as complicated as this, though, many things can go wrong. The patient can reject the transplants, although close matching of blood and other immunological factors can minimize this, along with drugs that can dampen the immune system’s reaction to foreign bodies. The bones may not completely graft together. It’s like recovering from two severely broken arms on top of everything else.

Nerve regeneration has come a long way, however. The man who received a single arm transplant in 2006 was able to write with the transplanted hand within a year.

“nerve regeneration” at Yale Image Finder.