Category Archives: Biomedical Engineering

Biomedical Engineering

Writing in Jamaica

This trip to Jamaica has been like a mini-sabbatical to work on my paper. Every morning we head into Lucea, and Amanda goes to the clinic. I take a 5 minute walk down the road to the parish library, check my email and so on, and then sit down to work on the paper. I’ve got 2-5 hours straight to just work. To make myself write. If I need a short break, I look out the window and see the ocean. I was worried that this trip would really interfere with my ability to work on the paper, but for the most part, it has been a blessing.

It has been an interesting adjustment not having continuous internet access. On that note, my internet time is up. More later.

Cardiac EP Finding of the Day

I say finding rather than fact, because sometimes a finding is later revealed to be incorrect, or subject to qualifications. Anyway, I read a lot of papers, and sometimes there are little useful nuggets of information that you might not be able to easily find if looking for them.

Here’s today’s.

According to Hearse et al 1977, the specific gravity of the left ventricular tissue of mongrel dogs is about 1.5.

I had no idea what the specific gravity of LV myocardium was. If asked to estimate, I probably would have placed it between 1 and 2, but I couldn’t have been much more specific. This could be useful when, say, someone gives concentrations in terms of wet weight of the myocardium.

Seeking Validation

Progress has continued smoothly on my class project. I’ve done one of the key validation steps in the project, and am just about ready to move on to the meat of the study.

What I did was to current-clamp the two different models, and compare this with the results of the exact same experiment in the paper that the models are taken from. Below, you can see the results:

Current Clamp Comparison

The top row contains snapshots of both types of model from the original paper. The bottom row shows my results for the same conditions. They’re essentially identical, although it’s hard to tell from the pictures in the original paper.

I still have a little more validation to do, but this is a pretty good sign.

I have working neurons!

After noticing a typo (hello missing negative sign!) in the paper, and debugging two typos in my implementation, I have what seem to be two working models (VCN bushy cells Types I-c and II). Here I’m applying a constant 100 pA stimulus to them. Already I see significant differences between the two cell types:

Some AP traces.

Programming + Espresso = Happy Brock

At the moment I’m working on my Models of the Neuron Project #2. In particular, I’m coding a model of ventral cochlear neuron bushy cells, using Octave rather than Matlab.

I’ve also just had another shot of espresso from our new X6, and I’m listening to an all-string-instrument tribute to Radiohead’s OK Computer. It’s so beautiful it’s giving me chills.

This is what I love to do. I feel good. I’m coding something. When it’s done, it will be a useful, functional, scientific model of a biological system. I’m going to use it to examine the effects of input regularity on its output. There are some technical obstacles I need to figure out, but I love doing that. It’s nice to feel like I’m getting somewhere and doing something useful again.

Here’s a bonus plot of excitatory post-synaptic potentials from two different types of bushy cell models! These aren’t anything complicated, they’re just inputs for the cell, but they look like they’re supposed to, so I’m quite happy.

EPSPs