Category Archives: Medicine

Medicine

ECG (or EKG for the Germans) Learning Tools

Clinical Cases and Images has a nice post up with a set of links to and explanations of various ECG/EKG learning tools. They are introduced as follows:

To provide some background, I am a teaching attending at Cleveland Clinic and have multiple rotations during the year with our residents and medical students. We record all topics discussed during a particular rotation on this blog and I know from the feedback which one the residents and students like the best. This month it was the session about using 2 mnemonics as a systematic approach to interpreting EKGs and web-based tools for EKG training.

Mind/Brain Duality (or lack thereof)

What is the mind? Is it a product of the brain, or does it come from somewhere else? Is there a ghost in the machine?

A number of things have brought this source of controversy to my mind recently. One is that I just finished the second season of Ghost in the Shell: Stand Alone Complex (not as good as the first season). The Ghost in the Shell franchise is largely an exploration of the implications of mind/brain duality and how it may actually become a reality as technology improves. Another is that I’m still reading Gödel, Escher, Bach: An Eternal Golden Braid by Douglas Hofstadter, a book that (among many other things) is largely about the origin of consciousness. Yet another is that there was a great party at the Mind/Brain Institute here at Hopkins last Friday. The final thing is that over the weekend I have gotten into some arguments with anti-choice people on YouTube (I know, bad move).

First, a disclaimer — here are the things that I believe, after a lot of reading and thinking:

  • The mind exists as a result of things that happen in the brain.
  • As it stands now, the mind cannot exist without the brain.
  • It is conceptually possible that the mind could be ‘liberated’ from the physical hardware of the brain, but it would require some other equivalent physical hardware. The most computationally difficult and brute-force version of this would be to accurately simulate a physical brain on a computer.
  • Humans are not the only conscious animals on this planet.
  • Not all humans have the same level of consciousness. For instance, a baby in the womb or even a newborn is not likely conscious in the sense that adults or older children are. Probably many animals are more conscious than a one-year-old.

The alternative view, as far as I can discern it, is that the mind is something special that sort of “sits on” the brain, but can be liberated from it should the brain fail (read: die). This consciousness (or “ghost”) can then go on to lead an afterlife. This is an extremely common perception, though it’s highly unlikely, and it is the basis of some very common and heated controversies. It leads to statements of belief (contrasted with mine above) like this:

  • As soon as a zygote is formed, it has a soul and is a person. It has feelings and cries out in pain if aborted, thinking “Why does my mommy not love me?“
  • Humans have a soul and are special. Animals do not, and are not essentially ‘special’.
  • When the body dies, the soul lives on. Its future can contain things like heaven, hell, joining with the universal consciousness from whence it originally came, and so on.

This is why anti-choicers insist that abortion is murder. They will swear up and down to you that abortion is taking a “life”, but try to pin them down on what “life” is and why it’s more valuable than the life of the mildew in their shower or the pregnant woman, and they start to stutter and dive into circular logic. We can pose some difficult questions that will reveal this:

  • What is an aborted foetus’s soul like in Heaven? Does it remain always a baby? Does it grow into an adult?
  • Do people with life-long brain dysfunction on earth (say, from Down’s Syndrome) become different, more intelligent, and function better when relieved of their physical brain?
  • Do people who have suffered head injuries on earth that allow them to survive but damage their ability to function, or people who have survived a stroke regain full function in the afterlife?

These questions are designed to bring attention to conflicting beliefs held within the same mind. That is, if one believes that a head injury causes its mental effects via damage to the brain, and not because it allows a demon into the soul, the rest of the ghost-in-the-machine belief system comes into question. The latter explanation is still accepted by some uneducated people (think rural west Africa) and crazy people in the developed world. The questions make it harder for people to rest assured that they hold reasonable beliefs on the nature of the brain and that these beliefs do not jeopardize their religious convictions.

What are your views on the subject? Do you disagree with me? Can you think of similar and better questions to bring out this sort of thing?

Five years in the lab: looking back, then forward

About this time five years ago, I was a nervous junior undergraduate studying Biomedical Engineering at Tulane University. I had just been accepted as an undergraduate member of Dr. Natalia Trayanova’s computational cardiac electrophysiology lab. The goal at that time was to complete a research project for my undergraduate thesis.


So very many things have happened since then. Here are the highlights:

  • 2002: Started learning the ropes of the lab
  • 2003: Continued to familiarize myself with the computers and code in use in the lab. The most powerful machine in our possession was an SGI with 8 processors (the Origin 300 listed here). There was almost always a wait to use those processors. Spent my summer vacation working in the lab. This was the first time I was paid to to research. Some time during this year (I think) I created the lab wiki using MoinMoin. By this time I was administering the lab computers and was sick of answering the same questions over and over. In desperation I created a wiki and started putting answers on it, referring people to the wiki when I was asked a question. The wiki is now (as of November 2007) huge, and contains basically all of the documentation of everything used in the lab, as well as gigabytes upon gigabytes of attached models, data, and images.
  • 2004: Graduated from Tulane with my Bachelor of Science in Engineering (BSE) degree. Joined the lab as a graduate student. Sometime in 2004 (I think), Tulane acquired a Linux Networx cluster, and we owned 20 nodes in that cluster.
  • 2005: Shortly after returning from my trip to Niger, Katrina struck New Orleans. The lab was scattered. Few people in the lab had access to their data. A few lab members actually snuck past armed guards to get our file servers and some workstations from our lab at Tulane. We took up residence in St.Louis, MO for two and a half months, aided by our colleagues in the labs of Drs. Yoram Rudy and Igor Efimov at Washington University. By the end of the year, we had returned to a slowly-recovering New Orleans.
  • 2006: Dr. Trayanova accepted a position as a professor at Johns Hopkins University. Almost the entire lab transfered to JHU and moved to Baltimore, MD.
  • 2007: In April, I began discussing a cluster purchase with High Performance Computing (HPC) companies. Around that time, the weather warmed up, the server room could no longer be adequately cooled, and we started limping by on 4 compute nodes. By the end of July, we had placed an order for a new cluster. We moved from Clark Hall into the newly-completed though poorly-named Computational Science and Engineering Building. In mid-November, most of our new cluster arrived, though FedEx dropped and destroyed one rack, and the cluster was not completely set up.

That brings us to the present day. Now, looking forward a little:

In the next two weeks, the cluster set-up will be completed. We will have free rein on 140 compute nodes (20 old, 120 new), all managed from one head node. The new nodes will be connected by the fastest Infiniband interconnects available on the market, and each node will have 8 GB of RAM available, with the potential to hold 64 GB each. There are four 3.0 GHz Opteron cores per node, yielding a total of 480 processors and 960 GB of RAM on the new nodes alone.

To give you some perspective on what that means, let me give you some details about the kinds of models we run. When I joined the lab, our two largest models consisted of a 4mm thick slice of the canine heart, and a very smooth, idealized model of the rabbit heart. These models are composed of 1.6 million and 0.82 million tetrahedral elements, respectively. It took something like an hour of wall clock time per millisecond of simulation time to run these models. (In other words, to get one millisecond worth of simulation data it was necessary to wait about an hour.) We could run one or two simulations at a time, at that speed.

My newest model, and currently the largest model in use in the lab, is composed of 28 million tetrahedral elements. On a cluster similar to our new one (Lonestar on TeraGrid), using 32 processors, it takes about 22 minutes of wall-clock time to simulate one millisecond in the model. Using a crude estimated unit of speed of (minutes real time / millisecond simulation time / tetrahedral element), and focusing only on the number of simulations we can run at once, not the number of CPUs required:

  • Old way: 60 minutes / 1 ms / 0.82 million tets = 73 minutes / ms sim time / million tets
  • New way: 22 minutes / 1ms / 28 million tets = .78 minutes / ms sim time / million tets

We have increased our simulation speed by almost 100 fold. We can run two to four simulations of that size at a time, vs one or two the old way. But that’s not all. We can now run bigger models. Much bigger models. We are now capable of running something the size of a dog heart (we have verified this). More importantly, we now have the technical capacity to run a model the size of the human heart, with a resolution near that of the size of a cardiac cell, and to model contraction in addition to electrical activity. It remains only to develop such models. We are prepared to store the results: the new cluster has a storage capacity of 28 TB online, with the ability to add something like 40 or 50 TB more simply by expanding the existing storage device.

In my time in the lab, I have watched our abilities expand from serial jobs with relatively small models to massively parallel jobs with the capacity to model electrical and mechanical activity in the human heart. We are just beginning a very exciting time in the lab and in the field, and what’s really killing me is that fact that there’s so much more to tell you.

But I can’t just yet.

(This post was partly inspired by a conversation with Maria and Amanda)

Device handles chest compression part of CPR

Thanks to my grandma Tice for sending me this article:

The Lucas system runs on high-pressure air from either a compressed air tank or an air wall outlet in a hospital. The device is indicated for treating adults who have acute circulatory arrest – meaning they lack spontaneous breathing and pulse – as well as loss of consciousness.

Mechanical compression allows medical personnel to provide other therapies, the company said. The machine also should provide quality chest compressions for a longer period of time than a human can.

A 1995 study found that fatigue makes it difficult for even well-trained medical personnel to provide more than one minute’s worth of effective chest compressions, said Anne Devine, a Medtronic spokeswoman.

“Clearly these devices do much better compressions than humans do,” said Dr. Charles Lick, medical director of Allina Medical Transportation in Minneapolis.

Sounds kind of difficult to use, but apparently the EMTs like them enough that they’re putting them in ambulances.