Category Archives: Writing


Dissertation Update: 171 pages

Today’s status:

  • 21,241 words
  • 171 pages
  • 31 floats (images/tables

Today I incorporated another study, and at one point the page count nearly hit 200. However, I realized that my (long) figure captions were severely bloating the list of figures, so I cut them out and did some other editing. That eliminated between twenty and thirty (!) pages. There remains now only one more study to be incorporated, although I still have to do the writing for that study. I also have to write bits and pieces throughout the dissertation and do some massive editing, but it’s nice to feel like I’m picking up some positive momentum on this thing. It’s also much easier to cut and rearrange than it is to generate text, so that part should be easier.

The Dissertation: It’s back on

The dissertation was set on the back burner for a few months while I worked on something else, but now it’s back on the front.

Today’s status:

  • 16,112 words
  • 139 pages
  • 20 floats (images/tables)

I added 17 of those floats today.

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:

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.

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