Category Archives: Science

Science

Extracting text highlighted with Acrobat Pro

As mentioned here and here, I typically do my reading and note-taking-on of academic papers in Acrobat Pro these days. I then typically record my comments in a FreeMind mind map. Until today I’d been creating a content summary in Acrobat, highlighting, and then dragging and dropping each comment individually into the mind map.

Today, while doing this, I noticed that there’s an “Export comments to Data File” option in the Comments menu. “Hmm,” I thought, “I wonder how easy it would be to read this data file?” It turns out that it’s just some ASCII text with a bunch of (to me) useless information, and the highlighted comments in parseable “Contents([highlighted text here])” containers.

I wrote a quick and dirty Perl script that pulls the comments into a text file. I can then just copy and paste that file into FreeMind, and it creates all of the leaves for me. This will save me hours carpal-tunnel-syndrome-inducing mousing and frustration. The perl script, for your perusal (improvements welcome) is available here: extract_comments.pl.

Kindly Let me know if you get any use out of this, and if you find any parsing bugs. It’s in the public domain.

Rabbit Right-Ventricular Free Wall Cross-Eye Stereogram

We deal with 3D models all of the time, and when it’s possible to manipulate them in a viewer program, it’s relatively easy to get a sense of 3D objects from a 2D screen. It’s a lot harder with static images. That’s where cross-eye stereograms come in. All you need to see 3D are images from two perspectives, and your eyes and brain. I’ve mentioned these images before, here, with a link to some nice photographs using the same technique. Today while making some figures, I decided to do this with my very-high-resolution model of the right-ventricular free wall. I think it turned out pretty well.

RV Wall Cross-Eye Stereogram

You’ll want to click on the image and look at the full size rather than using the thumbnail. There’s a really large version that you can download and try here. The idea is just to cross your eyes and make the images line up. Sometimes it helps if you sit back from the computer a bit.

Note, this requires doing the opposite thing with your eyes compared with how you view a random dot stereogram.

Penetration of a Re-entrant Wave From a Distant Pacing Location

The following is an (more or less unedited) excerpt from my dissertation, which is in progress. It continues where this post left off.


ATP Peeling

ATP Peeling

Progressive movement of collision location between two wave sources of different frequencies. Each horizontal line schematically represents the one-dimensional space between two wave sources. Curved lines represent wavefronts. Source B has a more rapid frequency than source A, so the location of collision moves progressively toward A with each iteration of the cycle (N).

In anti-tachycardia pacing, however, it is nearly impossible to target the core of re-entry in this fashion – pacing must be applied from a distant source. The core can therefore only be reached if stimulation is applied at a frequency more rapid than the intrinsic frequency of the re-entrant wave. This principle is illustrated schematically in the figure above. Each line between sources A and B represents the one-dimensional space in which wavefront collisions play out when the sources have different frequencies. In this example, conduction velocity is assumed to be constant, and both sources begin creating wavefronts at the same time for the sake of explanation. The concept holds even if they do not, but the position is shifted in one direction or the other depending on the difference in start time. The iterations (N) move from 1 through 6, indicating the first through sixth wavefront collisions. In this example, source B has a slightly higher frequency than source A. As such, wavefront collision proceeds as follows. On iteration 1, each source produces a wavefront at the same time. The waves travel with equal velocity toward each other, colliding in the middle of the space, and both are terminated. On iteration 2, B initiates a wave slightly before A, and so that wave has a longer period of time to travel before it encounters the wave from A. The region of collision is therefore shifted toward A a bit. On iteration 3, the head start of the wave from B in iteration 2 has been doubled, and so the region of collision is shifted twice as far toward A as it was in iteration 2. This continues in iterations 4 and 5, until in iteration 6, the wavefront reaches source A before it has an opportunity to initiate a wave. In cardiac tissue, this would result in overdrive stimulation of site A, and it would no longer initiate its own waves as long as B continued producing them and they continued to reach A.

Thus, if A is the re-entrant wave and B is the site of anti-tachycardia pacing, the core of the re-entry at A will be reached within 6 paced beats, and re-entry will be terminated. However, if the situation is reversed and B is the re-entrant wave, the site of anti-tachycardia pacing will quickly be overdriven and the therapy will be ineffective. Furthermore, if some region between A and B cannot support the higher frequency of activation produced by a sufficiently-fast anti-tachycardia pacing therapy, the therapy will be blocked from reaching the core of the re-entrant wave. These difficulties with anti-tachycardia pacing can, however, be circumvented while using an electrode distant from the site of re-entry, using the technique of far-field stimulation.


This example was inspired by a conversation with Dr.Valentin Krinsky

Resetting and Termination of Re-entry in a Ring

The following is an (more or less unedited) excerpt from my dissertation, which is in progress.


Resetting and termination in a ring

Resetting and termination in a ring


Gradients run from most recently activated (black) to recovering (grey) to recovered (white). Black dots indicate locations of stimulus application. Black lines indicate propagation of activation from the region of the applied stimulus. Flat line endings mark termination of propagation, while the black arrow represents continued propagation. A: Resetting of re-entry in a ring following stimulus application in the excitable gap. B: Termination of re-entry in a ring following stimulus application in the excitable gap.

The classic model of re-entry is the one-dimensional system of a wave propagating within a ring composed of an excitable medium (see figure above). If the ring is longer than the wavelength of the wave of excitation, there will be an excitable gap between the tail of the wave and the head (white regions in figure). A stimulus applied in that gap can either reset or terminate re-entry. Resetting occurs when the stimulus results in an orthodromic wave (that is, moving in the same direction as the original wave) and an antidromic wave (that is, moving in the opposite direction from the original wave) in the excitable gap and the following happens: the antidromic wave collides with the original wavefront and terminates it, while the orthodromic wave follows the recovering tail of the original wave and becomes the starting point of a new re-entrant wave (figure panel A). If, however, the orthodromic wave collides with the recovering tail of the original wave and terminates, then re-entry will be terminated entirely (figure panel B). Thus, if a stimulus were applied at the appropriate time and position to consume the excitable gap, it would terminate re-entry.


Interesting aside. I was at first stumped on how to make ring gradients like what you see above. I used a combination of what I found here and going back and forth from GIMP to OmniGraffle Pro. They key appears to be the use of an asymmetrical conical gradient in GIMP.