Per the SHERPA RoMEO project, it is permitted to self-publish or archive scientific articles from the Heart Rhythm Journal.
As such, I have completed the layout of the only HR article on which I am an author, and published it here. The final version of the article as laid out by Heart Rhythm is available here, if you happen to have access.
Hot on the heels of Rob’s post yesterday, comparing academia with crack dealing, P-Zed Myers over at Pharyngula discusses a recent article in Nature (Check, E (2007) More biologists but tenure stays static. Nature 448:848-849.) on the number of graduate students vs. tenure positions in biology.
The answer to Rob’s question about where the other students are going? In biology, it’s industry. My guess is that in Computer Science, it’s Google.
I noticed today the the PLoS ONE blog is celebrating the first birthday of PLoS ONE. It sounds like things have been going pretty well for them since last August:
On 1st August last year, PLoS ONE opened its doors for submission and so we have decided to call today our official birthday.
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Most importantly of all though, in the last year, or, at least, in the months from December 2006, we have published 695 pieces of original research. All of that research is, of course, Open Access and all of that research can be annotated by users, discussed by users and for the last few weeks rated by users.
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This potential for interaction is unprecedented in any other scientific publication and it is being used to an extremely high standard.
You should go read the whole thing. They have three birthday wishes:
Whenever you write about a published paper, be it in a journal or on a blog, always provide a link to the freely available version of the paper if one exists.
Whenever you read a paper in PLoS ONE, always rate it before leaving.
And most importantly….
Whenever you write a scientific paper, always, always, always publish it Open Access.
I finally signed up today to get notices about articles in PLoS Computational Biology and PLoS Medicine. (Where’s PLoS Computational Medicine, hmm?)
The reason I got into electrophysiology was because I was excited about the potential for electronic prosthetics. It seems the first real one has come to market. It’s still primitive in comparison to what I envision — a prosthetic that hooks directly up to nerves and sends and receives signals — but I’m sure that will come in time.
Kudos to these guys for making it happen!
One of the questions that has been asked before, and which this underlines, is, “when will artificial hands become superior to natural ones, and would you voluntarily switch in that scenario?” This sort of concept is explored in the various Ghost in the Shell movies, and the TV series “GITS: Stand-Alone Complex”.
In my last few posts, I’ve mentioned optical mapping and optical coherence tomography (OCT). Given just the names it’s not actually obvious that they’re entirely different things. Thus, I thought I should explain them.
“Optical Mapping” is short for something like “Optical mapping of voltage on the surface of the heart using fluorescence from potentiometric dyes”. The short version is ambiguous, as it could mean optical mapping of all kinds of stuff, and could in fact be synonymous with OCT. When cardiac electrophysiologists refer to an optical mapping study, what that usually involves is the following.
A heart is mounted in a clear chamber of some kind, and instrumented appropriately for whatever experiment is being done (say, defibrillation). A dye is then injected into the fluid flowing through the heart, typically “Tyrode’s” solution, which is kind of like blood without proteins and blood cells. This dye is fluorescent, meaning that when a certain color of light shines on it, it absorbs that light but then releases light of a different color. The cool (and useful) thing is that the amount of light released depends on the voltage gradient across the dye. It is designed to sit across the membrane of a cell, so by measuring changes in light released, it’s possible to measure changes in the electrical potential across the cell membrane, and to thereby monitor excitation, arrhythmia, and so on without electrodes. Using a fast, high-resolution camera, it is thereby possible to measure electrical activity in the heart from many more points, and at much better resolution, than using a bunch of electrodes. The major downside of optical mapping is that it is essentially limited to surfaces. Electrodes are still needed to probe the depths of the myocardium. Alternatively, optical mapping experiments can be combined with simulation experiments. We contend that if the sufrace activity of the simulation matches the suface activity of the experimental preparation “reasonably” well, the simulated activity within the walls should be a good approximation of what’s going on inside the experimental heart.
Typically referred to as OCT, the easiest way to explain it is that it’s like ultrasound imaging, but with light. In reality it gets a little more complicated. Wikipedia has a pretty good explanation. We’re using it to scan the thin right-ventricular free wall of the rabbit heart, and are then going to make and use computational models based on the resulting data. To do that, we have to segment the images (determine what is tissue, what is not), and then analyze them to create a finite element mesh.