Author Archives: Brock Tice

Online Biomedical Articles, Reviewed

The author of HubMed (an alternative and nicer interface to PubMed‘s database) recently posted an online journal review on his blog. While he prefers PDFs (as do I, for now), there are various aspects of articles-in-HTML that make them more or less useful and easy to read. All of the major publishers of online biomedical texts are scored. From the post:

HubLog: The state of online biomedical full text articles

I carried out a survey of HTML fulltext pages from the major publishers with the aim of identifying a) problems with usability and b) recurring themes in semantic markup of article elements (which will hopefully lend itself to a microformat recommendation for scientific, or at least biomedical, articles).

This is an issue on which the publishers are way behind. There’s little competition, and therefore little impetus for them to improve.

This Sunday is Darwin Day

Darwin’s theory of evolution via natural selection (which has since been found to be fact) revolutionized biology. That fact that is name is practically reviled by creationists and that his work is so misunderstood among the general public is a tragedy.

Darwin’s accomplishments are on the order of those of Newton, Galileo, Euler, and maybe even Einstein. Sunday is the day to celebrate it.

Darwin Day Celebration

Darwin’s 200th Birthday will occur on February 12, 2009; it will also be the 150th Anniversary of the publication of his famous book On The Origin of Species. So, together we have time to evolve a truly International Celebration to show our appreciation for the enormous benefits that scientific knowledge, acquired through human curiosity and ingenuity, has contributed to the advancement of humanity.

Classes vs. Research

Classes have been hogging my attention lately, generating a lot of reading and homework. I have hardly touched my research projects in a month. Today I got the ball rolling again, completing a few “Next Actions” from each project.

It felt great.

It’s nice that, with GTD, I can just jump back into my projects as if they were the only thing that has been on my mind.

Study finds no heart/cancer benefit to low fat diet

After years of hearing, “lower fat, lower fat” from dieticians, a new authoratative study finds that a diet low in fat doesn’t decrease your chances of heart disease or cancer (if you’re female). I lost my weight by reducing refined sugars and flour… I never really paid attention to fat content.

Chances a low-fat diet will help? Slim and none – Health & Science – International Herald Tribune

The largest study ever to ask whether a low-fat diet reduces the risk of getting cancer or heart disease has found that the diet has no effect.

Wednesday Article Review: Unpinning of a Rotating Wave in Cardiac Muscle by an Electric Field

For the past few weeks, I’ve made Wednesday “Article Review” day. I’ll still post reviews that I deem pertinent on other days, but the goal is to post one each Wednesday at a minimum.

The Hubmed page for today’s article is here: Unpinning of a Rotating Wave in Cardiac Muscle by an Electric Field by Alain Pumir and Valentin Krinsky

Tachycardia (fast heart beat) is commonly caused by a rotating wave of activation in the heart. The study of rotating waves of this type has years of legacy in theoretical and chemical dynamics studies. Today’s article covers rotating waves pinned to anatomical obstacles such as valve openings in the heart. Rotating waves circle a core, which can be functional (a property of the wave shape and dynamics) or anatomical (an obstacle). In the case of an anatomical obstacle, the wave can be eliminated by ablation, which is commonly used in the atria, electrical defibrillation, or possibly unpinning / antitachycardia pacing (ATP). Ablation is typically invasive, requiring catheterization, and defibrillation requires an external shock, or surgery to implant an ICD. Defibrillation, either externally or internally, damages the heart, is painful, and often causes loss of consciousness. Antitachycardia pacing and electrical unpininning open the possibility of elimination of tachycardia with small shocks.

The principle of electrical unpinning, proposed by Huyet et al. (1998) and Krinsky et al. (1995), is that when a localized stimulus is applied in a certain part of the wave tail, it may move the core of the rotating wave. It’s difficult to place a stimulus in a particular place at a particular time in a patient’s heart, but it turns out that when an electrical field is applied over an obstacle, areas of depolarization (positive change) and hyperpolarization (negative change) manifest on the borders of the obstacle.

The paper by Pumir and Krinsky details how a small electrical field may be applied at a specific timing relative to wave rotation in order to create such a depolarization on an obstacle that will unpin a wave attached to that same obstacle. They used simplified models of cardiac action potentials, including the Beeler-Reuter and Fitzhugh models. Since the method deals with the dynamics of a spiral wave, and not with particulars of ionic currents, it’s a safe bet that the methods will apply in more complex models and cardiac tissue.

I won’t repeat the article’s simple and logical explanation of how it works — go read it. It’s only 9 pages, the figures are clear, and the math is mercifully simplified in a way that (ostensibly) doesn’t undermine the results.