Remember those first few days where none of us had internet at Olin Hall? I was just in the same scenario when I got back to Ithaca--having to wait for the Time Warner Cable guy to show up to my apartment. Anyway...
My last week of the summer immersion was spent working on my project on carotid endarterectomies (CEA), which I described in an earlier blog. We are trying to find differences in outcomes between men and women who have this procedure performed, most importantly during peri-op. We are also looking to see which treatment is better for men or women: CEA or carotid stenting (CAS). So far I've pulled up data and charts on over 100 patients and have them organized in a ginormous spreadsheet. I've also quantified the number of men and women had complications after their respective operations. I now just have to do some statistical analysis and then you'll get to see my results in my presentation in September.
Other than working on the project, I visited the OR and saw two surgeries. One I've already seen so I won't describe that, but the other was a fem-fem bypass. In this procedure, a graft is placed between the two femoral arteries so that blood from the healthy femoral artery can reach the unhealthy artery. It was a very straightforward procedure. Dr. Vouyouka and her fellow cut open both groins and then "tunneled" underneath the belly. A graft was threaded through this tunnel and then sewed onto both femoral arteries.
I also followed Dr. Vouyouka and a cardiothoracic resident by the name of John around the Cornell Surgical Associates clinic. There weren't that many interesting cases, mainly because I've seen most everything. It just shows that in all of six weeks I've learned an enormous amount about the clinic and various vascular diseases and procedures to diagnose and treat those diseases. Dr. Vouyouka treated me to breakfast at Le Pain Quotidien on the final day of the immersion term and we said our goodbyes. She said she knows that I have no intention of ever becoming a medical doctor, and she is 100% correct in her assessment.
In the end, I believe I've experienced something very unique. I finally got to see what it is like to be the doctor and not the patient. I've learned an incredible amount of clinical knowledge, and maybe one day this knowledge will help me develop novel research questions. One thing is for sure--I will have fond memories of the NY Presbyterian hospital. Many thanks to all those involved in making this summer possible.
Friday, August 8, 2008
Wrapping up
Now that it's all said and done, it feels like the immersion term went by far too quickly. There is just too much to learn and too many projects in the medical field to be done in only seven weeks. With that said, my project is finally nearing completion. (Miraculously taking only slightly longer than the seven week term!) I'm currently tying up some loose ends with the data analysis I did for Dr. Schwartz.
The last week and a half was a massive attempt to finish my project on time, so I wasn't able to see any surgeries or tag along with Dr. Schwartz. Regardless, I'm having great success with the optical imaging data I'm supposed to analyze. In my last post, I mentioned difficulties adjusting the gain of each pixel in the data so that it accurately represents truth. I was able to do this using a slick variance minimization method I found in an estimation and detection book. I also wrote matlab code that computes various blood flows (total, oxygenated and deoxygenated) to a certain region of the brain, based on the optical data. The hope is that I will be able to determine some sort of correspondence between a type of electrical stimulus and the blood flow response. Although the data is only taken in rats, it brings us one step closer to understanding the relationship between electrical activity and blood flow response, which is not currently understood on a microscopic scale.
In all, the summer immersion experience, though challenging at times, was incredibly unique and enriching. My medical vocabulary expanded by orders of magnitude, and I was given the privilege of seeing things that are usually exclusive to only medical students and clinicians. On top of it all, I had an interesting and medically useful project. I only hope that I was a fraction as helpful to my clinician, Dr. Schwartz as he was to me. I'd like to thank him along with Dr. Wang and Dr. Frayer and Belinda and all the other people behind the scenes who made the immersion term possible.
The last week and a half was a massive attempt to finish my project on time, so I wasn't able to see any surgeries or tag along with Dr. Schwartz. Regardless, I'm having great success with the optical imaging data I'm supposed to analyze. In my last post, I mentioned difficulties adjusting the gain of each pixel in the data so that it accurately represents truth. I was able to do this using a slick variance minimization method I found in an estimation and detection book. I also wrote matlab code that computes various blood flows (total, oxygenated and deoxygenated) to a certain region of the brain, based on the optical data. The hope is that I will be able to determine some sort of correspondence between a type of electrical stimulus and the blood flow response. Although the data is only taken in rats, it brings us one step closer to understanding the relationship between electrical activity and blood flow response, which is not currently understood on a microscopic scale.
In all, the summer immersion experience, though challenging at times, was incredibly unique and enriching. My medical vocabulary expanded by orders of magnitude, and I was given the privilege of seeing things that are usually exclusive to only medical students and clinicians. On top of it all, I had an interesting and medically useful project. I only hope that I was a fraction as helpful to my clinician, Dr. Schwartz as he was to me. I'd like to thank him along with Dr. Wang and Dr. Frayer and Belinda and all the other people behind the scenes who made the immersion term possible.
Thursday, August 7, 2008
Weeks 6 & 7: Great experience
I've decided to post the manuscript of the uncut version of my immersion presentation, as I will not be able to present this in Ithaca.
Well, here it is:
[This photo was taken at the Fourth of July Fireworks in South Street Seaport, at the bottom tip of the Manhattan Island.]
My Immersion assignment was with my mentor, Dr. Jonathan Weinsaft, in the Cardiology Department. As the primary focus of my immersion experience, I consulted Jonathan to have my immersion experience revolve around noninvasive aspects of the cardiovascular system.
Here is what I learned from the first few weeks of my immersion program:
When patients visit the Cardiology department complaining of chest pain, one of the first scans done is the Echocardiography. This is a standard procedure that uses ultrasound, in which the technologist acquires different 2D ultrasonic images, ranging from Triscupid valve Apical 4 and 2-Chambers. I was told that there are about 70 or more Echos done every day at the NYP.
Of particular note is the transesophageal ECHO, which gave out much nicer ultrasound images compared to standard ECHO. The above photo you see is that of the transesophageal probe, which is about a meter long, and that which a patient sedated for a couple of hours had to swallow.
I also got to see several CATH Labs, in which I observed the insertion of catheters for performing x-ray angiography. There are about 20 of these each day.
Nuclear stress tests are associated with SPECT imaging, and they are used to examine myocardial perfusion. Most of what I saw were the three different kinds of stress tests;
Treadmill, Adenosine, and Dobutamine
I followed Jonathan in the Clinical ICUs, and learned a lot about the importance of spending time examining the cases of each patient. As this is the intensive care unit, the patients are among those who have the most critical cardiac conditions. While I got to ask many questions to the fellows, residents, and medical students about the various instruments, terminologies, and tasks that are done in the ICU, it was also tough to see some patients pass away during the week that I followed Jonathan in the rounds.
Here is a slide that I pulled off from Google; it shows a CT angiography, in which we see a clear extension of the coronary artery in this specific case. In addition to seeing Jonathan examine these on the workstation, I got to learn from one of the fellows how to read CTs. This was a very interesting experience, as CT reading seems to be more of an art, than a systematic task that can be automated by a computer.
Finally, I got to do a bit of Magnetic Resonance Imaging. This is a photo from a scanner on 70th Street. Shawn, a fellow Immersion student, is in the scanner and was my first human volunteer for MRI scanning. At one point during Shawn's brain scan, as I was getting used to the different scanning parameters on the computer control screen, I completely forgot to press the scan button for quite a while. Shawn was unknowingly in the scanner for over 20 minutes without anything happening, and experienced a long and tiring scan due to the ineffective performance of a novice scan technician. (sorry Shawn) However, we did get some cool images.
I’d like to now describe my project, which revolves around the Cinematic (CINE) imaging of the left ventricle.
First, the left ventricle is perhaps the most important of the four chambers in the cardiac system, as it is the primary chamber that pumps the blood to the body. From what I have experienced, most of the coronary angiography, stress perfusion/myocardial performance, and diagnostic imaging focuses on the examination of this chamber.
CINE imaging refers to the cinematic imaging, and cine-CMR (SSFP) provides high spatial resolution imaging and is widely accepted as a diagnostic standard for assessment of left ventricular systolic function and chamber volumes.
In order to use this as an effective tool, the workstations are equipped with a software called ReportCARD, which has a manual tracing feature, which is widely applied for quantification of cine-CMR. This software is used to segment the left ventricle chamber and myocardium at systole and diastole. However, there are limitations to manual tracings.
The major Limitations of Manual Tracing are: that it is time consuming. That reproducibility is variable. That it eliminates data; because of time constraints, only end-systolic and end-diastolic volumes are quantified, so all other cardiac phases are ELIMINATED.
I watched Jonathan perform time trials of these tracings for an upcoming paper, and he took on average about 5 to 7 minutes, and sometimes 10 minutes for each case.
The big question we asked is Can we do better? And the answer is Yes.
The LV METRIC segmenter is a program developed by Mr. Noel Codella of WCMC, and it is an automated system that can quickly segment the CINE images saved as SA FIESTA on the workstations, and acquire volumetric data in a lot less than 5 minutes per case. Citing the performance of the segmenter from Mr. Codella’s paper, we know that this tool demonstrates robust performance in getting an accurate volumetric data of the chamber. Our project will take advantage of the segmenter's ability to perform full volumetric assessment. This opens up new possibilities of not only examining the LV chamber contraction (i.e. systole, ejection fraction) but also the patterns of LV chamber relaxation (i.e. diastole).
Now let us talk about diastole. Is diastolic function important? Yes, for
- prognosis
- treatment
- etiology of heart failure
Q. How do we typically assess diastolic function?
A. MUGA, which stands for Multiple Uptake Gated Acquisition, is an Nuclear study that measures the derivative of pressure; dP/dt. We can also use Echo and look at mitral inflow patterns. The MRI has been used for assessment of diastolic function as well; for example with tagging.
Well, here it is:
[This photo was taken at the Fourth of July Fireworks in South Street Seaport, at the bottom tip of the Manhattan Island.]My Immersion assignment was with my mentor, Dr. Jonathan Weinsaft, in the Cardiology Department. As the primary focus of my immersion experience, I consulted Jonathan to have my immersion experience revolve around noninvasive aspects of the cardiovascular system.
Here is what I learned from the first few weeks of my immersion program:
When patients visit the Cardiology department complaining of chest pain, one of the first scans done is the Echocardiography. This is a standard procedure that uses ultrasound, in which the technologist acquires different 2D ultrasonic images, ranging from Triscupid valve Apical 4 and 2-Chambers. I was told that there are about 70 or more Echos done every day at the NYP.
Of particular note is the transesophageal ECHO, which gave out much nicer ultrasound images compared to standard ECHO. The above photo you see is that of the transesophageal probe, which is about a meter long, and that which a patient sedated for a couple of hours had to swallow.I also got to see several CATH Labs, in which I observed the insertion of catheters for performing x-ray angiography. There are about 20 of these each day.
Nuclear stress tests are associated with SPECT imaging, and they are used to examine myocardial perfusion. Most of what I saw were the three different kinds of stress tests;Treadmill, Adenosine, and Dobutamine
I followed Jonathan in the Clinical ICUs, and learned a lot about the importance of spending time examining the cases of each patient. As this is the intensive care unit, the patients are among those who have the most critical cardiac conditions. While I got to ask many questions to the fellows, residents, and medical students about the various instruments, terminologies, and tasks that are done in the ICU, it was also tough to see some patients pass away during the week that I followed Jonathan in the rounds.
Here is a slide that I pulled off from Google; it shows a CT angiography, in which we see a clear extension of the coronary artery in this specific case. In addition to seeing Jonathan examine these on the workstation, I got to learn from one of the fellows how to read CTs. This was a very interesting experience, as CT reading seems to be more of an art, than a systematic task that can be automated by a computer.
Finally, I got to do a bit of Magnetic Resonance Imaging. This is a photo from a scanner on 70th Street. Shawn, a fellow Immersion student, is in the scanner and was my first human volunteer for MRI scanning. At one point during Shawn's brain scan, as I was getting used to the different scanning parameters on the computer control screen, I completely forgot to press the scan button for quite a while. Shawn was unknowingly in the scanner for over 20 minutes without anything happening, and experienced a long and tiring scan due to the ineffective performance of a novice scan technician. (sorry Shawn) However, we did get some cool images.
I’d like to now describe my project, which revolves around the Cinematic (CINE) imaging of the left ventricle.First, the left ventricle is perhaps the most important of the four chambers in the cardiac system, as it is the primary chamber that pumps the blood to the body. From what I have experienced, most of the coronary angiography, stress perfusion/myocardial performance, and diagnostic imaging focuses on the examination of this chamber.
CINE imaging refers to the cinematic imaging, and cine-CMR (SSFP) provides high spatial resolution imaging and is widely accepted as a diagnostic standard for assessment of left ventricular systolic function and chamber volumes.
In order to use this as an effective tool, the workstations are equipped with a software called ReportCARD, which has a manual tracing feature, which is widely applied for quantification of cine-CMR. This software is used to segment the left ventricle chamber and myocardium at systole and diastole. However, there are limitations to manual tracings.
The major Limitations of Manual Tracing are: that it is time consuming. That reproducibility is variable. That it eliminates data; because of time constraints, only end-systolic and end-diastolic volumes are quantified, so all other cardiac phases are ELIMINATED.
I watched Jonathan perform time trials of these tracings for an upcoming paper, and he took on average about 5 to 7 minutes, and sometimes 10 minutes for each case.
The big question we asked is Can we do better? And the answer is Yes.The LV METRIC segmenter is a program developed by Mr. Noel Codella of WCMC, and it is an automated system that can quickly segment the CINE images saved as SA FIESTA on the workstations, and acquire volumetric data in a lot less than 5 minutes per case. Citing the performance of the segmenter from Mr. Codella’s paper, we know that this tool demonstrates robust performance in getting an accurate volumetric data of the chamber. Our project will take advantage of the segmenter's ability to perform full volumetric assessment. This opens up new possibilities of not only examining the LV chamber contraction (i.e. systole, ejection fraction) but also the patterns of LV chamber relaxation (i.e. diastole).
Now let us talk about diastole. Is diastolic function important? Yes, for- prognosis
- treatment
- etiology of heart failure
Q. How do we typically assess diastolic function?
A. MUGA, which stands for Multiple Uptake Gated Acquisition, is an Nuclear study that measures the derivative of pressure; dP/dt. We can also use Echo and look at mitral inflow patterns. The MRI has been used for assessment of diastolic function as well; for example with tagging.
The problem with tagging is, it requires additional dedicated imaging (adding to exam time, more breath-holds, inability to analyze large datasets), and the computational analysis of change in myocardial thickness by tagging is nontrivial, as it needs to thoroughly account for spatial and temporal geometry.
Let me explain a little more about the Left Ventricle Diastole. With a full volume curve, we can make the following plot, as in the above. We can then identify the diastole region to the peak of the filling curve. One parameter we are interested is the volume change over time; ie. taking the derivative. Now let's zoom in to the derivative of the diastole region.
In the derivative of the diastole region, we observe that the following is analogous to the Mitral Inflow pattern obtained from Echo. In a healthy case, (above) we can observe the E-wave being larger than the A-wave.
In the following diseased case, we see some abnormality, where the E and the A wave profiles look clearly different. We note that our full-volume assessment is able to generate the same curves as the Mitral Inflow patterns.
Here's an illustrative example of why our study is important. Let us consider the following cases:
Consider two cases with TPFR is the “time to peak filling rate”, and is measured from the end of systole to the time of peak filling; in other words, to the moment with the largest slope value.
Notice that for each of the two cases, the TPFR is quite different; but the traditional ejection fraction method would identify these cases to be both healthy.
For the PFR, the peak filling rate taken by the maximum value of the derivative curve, we notice a substantial difference between the two volumetric curves. This would be a likely misdetection case had we used the Ejection Fraction method to diagnose the cardiac condition.
In order to analyze this data, my project was to develop a software that efficiently sorted, filtered out any private information, and would allow easy analysis of all the cases to be examined for an upcoming study. In MATLAB environment, I developed a Graphical User Interface called LV Analyzer.
Here is what the block panel of the Graphical User Interface LV Analyzer looks like. This runs on MATLAB, and feeds in the raw data from the workstation, processes and sorts the data accordingly, displays the features necessary for the study, and saves it as an output file that can be opened by a spreadsheet program, like Excel.
I will continue to develop the LV-Analyzer after the Summer Immersion program, and plan on using the software to analyze data for an upcoming study.
I'd like to finish my presentations by thanking the following people who have made my immersion experience truly a great one.
Let me explain a little more about the Left Ventricle Diastole. With a full volume curve, we can make the following plot, as in the above. We can then identify the diastole region to the peak of the filling curve. One parameter we are interested is the volume change over time; ie. taking the derivative. Now let's zoom in to the derivative of the diastole region.
In the derivative of the diastole region, we observe that the following is analogous to the Mitral Inflow pattern obtained from Echo. In a healthy case, (above) we can observe the E-wave being larger than the A-wave.
In the following diseased case, we see some abnormality, where the E and the A wave profiles look clearly different. We note that our full-volume assessment is able to generate the same curves as the Mitral Inflow patterns.
Here's an illustrative example of why our study is important. Let us consider the following cases:Consider two cases with TPFR is the “time to peak filling rate”, and is measured from the end of systole to the time of peak filling; in other words, to the moment with the largest slope value.
Notice that for each of the two cases, the TPFR is quite different; but the traditional ejection fraction method would identify these cases to be both healthy.
For the PFR, the peak filling rate taken by the maximum value of the derivative curve, we notice a substantial difference between the two volumetric curves. This would be a likely misdetection case had we used the Ejection Fraction method to diagnose the cardiac condition.In order to analyze this data, my project was to develop a software that efficiently sorted, filtered out any private information, and would allow easy analysis of all the cases to be examined for an upcoming study. In MATLAB environment, I developed a Graphical User Interface called LV Analyzer.
Here is what the block panel of the Graphical User Interface LV Analyzer looks like. This runs on MATLAB, and feeds in the raw data from the workstation, processes and sorts the data accordingly, displays the features necessary for the study, and saves it as an output file that can be opened by a spreadsheet program, like Excel.
I will continue to develop the LV-Analyzer after the Summer Immersion program, and plan on using the software to analyze data for an upcoming study.
I'd like to finish my presentations by thanking the following people who have made my immersion experience truly a great one.Wednesday, August 6, 2008
That's All She Wrote
Well, after taking time to mull over my final week at Weill, I can finally offer some parting thoughts on my immersion experience. Incredible. The opportunity that we were presented with is so unique and so beneficial that I can still hardly believe what I just spent the past 7 weeks doing. As a chemical engineer by training, all of my medicinal knowledge has been fairly limited to almost a decade’s worth of time as an
What I’ve truly come to realize is that this 7 week crash course in medicine has exponentially increased my knowledge in my newly adopted field. The awareness of new terminology, treatments, and the field of medicine in general has come so far from my first week to my final weeks that I can hardly believe it. I also have had enough OR time to make any first or second year medical student jealous. It is still as mind boggling to me about the things surgeons can do in the OR as it was 6 weeks ago. This is why I find one of the final cases I was able to observe seems an appropriate way to end my blog posts.
On my final day I was privy to really see the advances in biomedical technology and how it is one of the largest driving forces shaping the medical field. The case I’m speaking about was that of a patient who had previously had an extensive hemangioma tumor removed from their brain. This type of tumor, while benign, can grow and cause severe problems (as one can imagine) if not treated. This patient had undergone surgery some time ago to remove part of the tumor and, due to its extensiveness, had to have part of their skull removed at the time. This missing portion of the skull was replaced by a mesh frame which sadly got infected shortly thereafter and had to be removed. For the past number of months the patient lived normally expect with a giant depression where their skin met their brain without any hard protective barrier. It was at this juncture in the patient’s care that I met them and watched as the original neurosurgeon reopened the skull to try to resect more of the tumor and then fit them with a new biomedical device. What was truly amazing here was how much the technology had already improved in such a short period of time. This meant that instead of a mesh cage molded to fit the patient’s head shape during surgery, a polymer made of Poly(methyl methacrylate) would be custom built beforehand using a rapid prototyper to make the 3d replica. This device was then anchored into the patient’s remaining skull and Dr. Spector made some very precise incisions to move the skin over to cover the new device. After watching this surgery and imaging the improvement in this patient’s quality of because such a device exists really brought the whole experience full circle.
In the end summer immersion had its ups and downs, its ridiculously long days (more than I would like to count), but when all is said and done it was an experience I wouldn’t trade for anything. Good luck to all the incoming 1st year PhDs, I hope you find the same fulfillment with your immersion experience at Weill as I did, because your time there is really what you choose to make out of it.
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