Week 5: Goose

I seriously started major progress in my project with Dr. Souweidane from this week. I had frequent meetings with a medical student, Peter Morgenstern, to talk about the current techniques related to endoscopically guided third ventriculostomy with regard to prepontine space. I also had meetings with a visiting physician from Greece, Jonathan Roth, who helped me so much with how to use MRI stations and read the images to retrieve the specific information I want. Initially Dr. Souweidane and I had brainstormed many ways to prove his hypothesis. His experience with endoscopic third ventriculostomy hinted him that the entry site of endoscope on the skull relative to the suture shifts depending on age. The results from the study, if proven true, could provide with a more specific guideline for starting physician on what would be the generally accepted endoscopic entry site for the patients. However, this turns out to be a very difficult task as most of patients come with different symptoms such as swollen cortex and ventricles, there is no solid standards of references for measurement. We even had a brief meeting with Dr. Michael Kaplitt who provided some ideas with how to go about measuring the differences that we would see between patients of different age groups. He showed us how to reconstruct a three-dimensional brain structures from plane images and argued that the measurements should not be distances from suture but rather an angle to the target site from the entry site as patients have different skull sizes and slight shifts in the brain anatomy.

Despite all the trouble and difficulties we faced in deciding what the measurement should be, I started organizing the list of patients who underwent endoscopic third ventriculostomy. In the end we had about 70 patients with decent medical records and documentations that I could work on. The range of age at the day of surgery seemed pretty diverse, ranging from 1 day old to the 70s. The etiology of the surgery and results also varied a lot as some patients even had shunts at young age and some other patients had to revise to shunt after an unsuccessful result from the endoscopic third venstriculostomy. Would it be the nature of research in medical practice? The diverse list of patients seemed almost overwhelming for me to do a well controlled analysis.

Week 6: Goose

So finally the entire journey at New York City is over. I actually had to spend some more extra time even after the last day at the city to wrap up my project. Everything turned out nice, though the project seemed too sketchy in the beginning. Dr. Souweidane and I turned in an abstract to the American Association of Neurological Surgeons, a congress of neurological surgeons in October at Seattle, Washington. Of course I would not be able to go to the conference but I am glad that I have contributed to the work Dr. Souweidane does and made it to an abstract. Although the original ideas we had in the beginning seemed to be more attractive and with higher impact, we had to shift our ideas as to it is somewhat more doable. Original intension of the study, that is the dependence of age in hydrocephalus patients in the entry site of endoscope relative to the skull suture for endoscopic third ventriculostomy, was just way too difficult to make legitimate measurements and enough patients with cases that we can do better controlled studies. Instead, we decided to analyze the hydrocephalous patients with cases of diminished prepontine interval space, which can affect the safety and functionality of endoscopic third ventriculostomy. The result showed that functional success rate of patients with obliterated prepontine interval appeared equivalent to historical controls. The diminished success rate was functional success rate was rather apparent in young patients, which is believed that the rapidly growing bodies can soon block the fenestration on the floor of the third ventricle within a few weeks requiring them to have shunts instead.

I much enjoyed the summer immersion program and was really a blast to have a chance to work with a practicing physician. I learned so much in the privilege of meeting patients and witnessing surgeries. The lessons I learned from these experiences not only have taught me that there are endless diseases that need to be more researched, but also that what we are studying as biomedical engineers is truly worth our time and effort. The deprived quality of life that these patients are having can be immensely improved by the breakthroughs we make, and that is for sure my conclusion after the summer immersion program at the hospital.

Week3: Goose

A 4 year old boy had a retina blastoma on the back of his left eye. The left eye was surgically removed and was replaced with a prosthetic eye. To eliminate all the cancer residues, the boy went through radiotherapy. About three years later, when the boy was 7, he was again diagnosed to retina blastoma on his right eye and had to undergo the same procedures.

I met this young patient in clinics in the beginning of my third week, and now he is 14 years old. He came to clinics with several complaints for his headaches and hearing problems. I first did not notice that he was blind but after the brief physical exams Dr. Souweidane performed I realized that he could not see what was in front of him. When I heard the whole story about him, I truly felt sorry for him and his family. He was diagnosed to acoustic neuroma—it was his third cancer occurrence. Dr. Souweidane explained that he had about 50% chance of losing his hearing after the surgery if he opts to remove the tumor mass by surgical methods. As a matter of fact, the tumor mass was already quite large in size and because radiotherapy has seemed to cause more trouble than helping cancer clean up for the patient, Dr. Souweidane decided not to give him any more radiotherapy. The boy was rather calm as Dr. Souweidane explained all the possible etiology, surgical plans, its associated risks, and expected improvements as well as loss after the surgery, but I could certainly see the devastated looks of his parents through their eyes.

The privilege of seeing patients in clinics has given me mixed feelings. Sometimes my adviser Dr. Souweidane would look like a hero, giving relief to patients and even, as a result, saving their lives. Some patients would come to see him with problems which fortunately can be relatively easily treated and would not have much postoperative complication such as chiari malformation. But some other patients have to face diagnosis such as malignant brain tumors with some cases unfortunately occurring at regions of brain that require traumatic craniotomy. Not only that I feel disappointed at current medicine, but also feel responsibility to contribute whichever way I can through things I study. Also, before I tell my friends how cool my experience has been at Cornell hospital seeing patients with all kinds of diseases in clinics and witnessing topnotch surgeries, I should always keep in mind that there are always close friends and family who would weep for these patients.

Week 4: Goose

The 17 year old boy, who had a benign tumor in the middle of his left cortex and had to go through an open brain surgery, came to clinics for follow ups. The surgery the boy went through was the first craniotomy I have ever seen. I was in fact so shocked at how traumatizing the procedure was--perhaps the tears of the boy and his mother before the surgery began had also elevated my emotions. However, today when I saw him, I was quite surprised at the results. Although the boy seemed to be responding somewhat late to the questions Dr. Souweidane asked, he was perfectly normal. He walked straight without a problem with symmetric facial expression as well as full control over every limb. The scar from the surgery has already started healing, though the incision made still looked quite painfully large, and could be somehow covered by hair. However, he seemed to have some change in attitude which I thought it reflected some distrust toward Dr. Souweidane. I still think the surgery was the best solution and decisions Dr. Souweidane could provided based on MRI images to the problems he was having. I guess some patients come with trust and open mind trying their best to have the greatest results, while some other patients come with distrust and doubts towards their physicians and only are disappointed by the results.

During the week I met a patient with neurofibromatosis type 1. Her left eye was covered with a large growing tissue mass, neurofibroma. She had several brownish dime sized freckles on her skin, I could easily notice. The reason why she came to see Dr. Souweidane was her back problems. Apparently, patients with neurofibromatosis type 1 often have abnormal development of spine, termed scoliosis, which can give discomfort while sitting and standing. She did have trouble sitting straight up but was not so severe. Neurofibromatosis is known to be a genetic disorder, having mutation in proteins that control cell production. Neurofibromatosis type 1 is pretty common occurring in 1 in 3000 individual in the United States. I did not know what I would do if I had such problem and what I could say to cheer her up. Sometimes, and every since I came to Weill medical school, I keep realizing that being able to live a normal and healthy life almost seems like a miracle.

Finally.. Internet in Ithaca

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.

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.

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.

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.

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 EMS worker on an ambulance corp. I knew, while useful in small, contained scenario’s, this knowledge wasn’t passable to transform myself into a biomedical engineer. I find it impossible to be a successful biomedical engineer if there is a complete disconnect between one’s studies and one’s field.

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 1^st 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.

End of this story but the beginning of many more

While Summer Immersion term is over, my project most definitely is not. Over the past few weeks I’ve been spending less and less time in the OR and the clinic and more time behind a computer learning statistical methods and doing statistical analysis. My project has been to use a database created by medical research assistants to determine if there is a correlation between the rate of complications after radical cystectomy and the type of cystectomy being performed (robotic vs. open). The crazy thing is that in all my weeks at Weill I had yet to see an open cystectomy. It seems that Dr. Scherr is somewhat defined for his ability and proficiency with robotic cystectomies. Just yesterday I had my first opportunity to see an open cystectomy, so I popped into the OR to see what my analysis was really evaluating. The surgery definitely seemed more difficult without the magnification of the robotic camera, but the reality is that many surgeons still prefer to perform this surgery open because they are more proficient behind the table rather than at a robotic console. The specific case Dr. Scherr was performing was an open cystectomy because the patient had had a partial nephrectomy before and they knew there would be scar tissue to deal with that they were unaccustomed to with the robot.

I say that my research project is definitely not over for a couple of reasons. First, I will continue to analyze and tweak our model over the next few days to see if I can improve the model fit. We had to use multinomial logistic regression to analyze the data because we are looking at a binary outcome (complication or no complication). Additionally many of our predictor values are ordinal or nominal rather than scalar. The five variables we choose to evaluate (we being a few residents and I) are body mass index (BMI), age, Charlson score, ASA score (American Society of Anesthesiologists score) and the type of cystectomy (robotic or open). I first looked for a basic correlation between the type of cystectomy and occurrence of complications using crosstabulation and Pearson chi-squared tests. This showed that there is a significant correlation between the two, but we needed to ensure that was not just an artifact of other factors. For example we needed to prove that it is not just the younger, leaner, healthier patients that are undergoing robotic cystectomies. To show this more rigorously I needed to use multivariate regression but with these nominal and categorical variables. In the end I think I developed accurate models, but only more time and more critical evaluation by the residents will tell. Secondly this project is far from over because our analysis is limited by the fact that we only have around 200 patients. At first I thought this was more than sufficient, but as I continued to do my analysis and needed to categorize these cases the sub-grouping became ever smaller making statistical analysis very difficult. So this evaluation will just be the foundation that they can build upon in years to come as they continue to have a more robust database of cases.

Finally I just want to remark on the miracle of life. Last Friday Jen and I had a wonderful opportunity to observe a C-section. Not only were the patients gracious at having additional people in the room but the surgeon was also keen to teach us. Before we ever entered the OR he had us read-up on why this patient was having a C-section. This woman had a bicornuate bicollis uterus (which is to say she had a septum in her uterus dividing it in two). A C-section was required and might need to be performed along the length of the uterus rather than at the base because her two uteri are narrower than a standard woman’s uterus. In this case though, they were able to get the baby out of the base of pregnant uterus and could even show us the amazing capability of the uterus to expand with a baby since this woman had one pregnant and one non-pregnant uterus. So not only had we walked in to see a C-section, but we also walked in on a high risk pregnancy that had come to full term with a healthy baby. Additionally this was the first child for these parents and they didn’t know the baby’s sex, so it was a very exciting OR!

Yeah!! The Last Week of Summer Immersion

Wrapping up the data I have collected until now and catching the last chance to visit the OR I haven't been before, these two things are basically what I have been doing in the last week. Even though I knew that I won't be able to finish the great plan of website within six weeks a long time ago, even though I knew that there are numerous small miracles and drama happening somewhere in this hospital I wouldn't be able to learn, even though I still have tons of questions and ideas in my mind about the PC measurement, I had to face to fact that: the last week of this summer immersion program is coming to an end.

In retrospect, six weeks is really too short for me to get enough insight into the hospital. This morning when I watched the whole process of C-section for the first time and maybe the last time in my life, the strong contradiction between the bloody scene and the super happy expression on the face of the mother was still a great shock to me. As an undergraduate in biology, I would never be be touched by a bloody experiment and hardly moved by an affecting drama. Because of that, I underestimated the power of the inevitable combination of the two in hospital before I could realize it. Though for many times I reminded myself not be too involved in personal emotion about one single case, I know it is actually very hard. How could one find a simple righteous principle in the mergence area of natural and social science? How could the hybrid of research institution and social facilities be easily judged on right and wrong?

Knowing this, I am very happy that this program could offer me this chance to have a little touch to the knowledge of this super complicated system during the short six weeks under such circumstances. Perhaps many years later, most of the medical terms I learned at this moment would be gradually erased from my memory. Nevertheless, there are definitely some scenes, some people and some words I once came across in this summer would remind me from time to time many different aspects I used to neglect when studying healthcare in the lab. They will also remind me what kind of things I should pay attention to besides the improvement of technology in my career as a bioengineer.

Knowing this, I am not regretful that I have only been here for six weeks. Actually, on the other hand, I found myself can be helpful to someone in hospital right in the last week. When the assistant of doctor came over to me in panic asking about some net questions, when the medical student also came over to ask me some math conceptions in references, I finally felt that I little "nobody" BME PhD could also do "something" here!

All done

Going through 200 patient charts to extract data was very energy consuming. Since all my patients look normal, I had no reasons to take a picture of them to post on the blog, so I decided to post pictures of me with food instead since it's restaurant week.

After data analysis, I found some similarities and differences. For instance, patients who have severe symptoms with minimal Jak2 allele burden tend to have a higher time between first drug treatment and diagnosis. Patients with high Jak2 tends to be about about 10 years younger than patients with low Jak2, etc. All data are being submitted to the statistics department for verification.

John Thomas will have to do

In the last two weeks, I’ve spent most of my time in the clinic and OR. I saw several interesting and pretty nauseating cases. Let’s start in the clinic.

There was a patient with an infected hematoma on his leg. It was pretty disgusting to look at immediately after he took off his bandages. Basically there was a putrid, fleshy black spot on his shin. Dr. Vouyouka had to debride the wound so that it would heal properly, which consisted of surgically removing the dead tissue and irrigating the area. From the patient’s groans and screams—no, he wasn’t put under—the debridement seemed to be an excruciating procedure. Afterwards, gauze was packed into the wound beneath the dermal layer. Moral of the story: take care of your wounds!

In the OR, I saw a thrombectomy that was performed on a woman with a leaky brachial artery in her right arm that resulted in a nasty hematoma. Truthfully, the doctors didn’t really know why her artery was leaky but went and opened her up anyway. I guess they were planning on fixing the artery but found, or maybe even created, a thrombus.

The bloodiest case I saw was a below-the-knee amputation. This was also the most straightforward case I observed during my summer here so far. As you can imagine, Dr. Vouyouka basically cut through all the layers to get to the bone. The bone had to be sawed and any arteries that were cut were tied up. They cut the leg in such a way that the calf muscle was used as a flap to cover everything.

Lastly, I saw a carotid endarterectomy (CEA), which involves the removal of an atherosclerotic plaque from a carotid artery. There are certain complications with this procedure, such as ensuring blood supply to the brain, which is done most often by using a shunt to deliver blood and electroencephalography (EEG) to monitor the brain. To diagnose a stenosed carotid, magnetic resonance angiogram (MRA) or ultrasound is used to determine how much occlusion has developed in the blood vessel.

I wanted to mention CEA last because my summer research project is directly related to this procedure. I am analyzing clinical data and trying to make sense of the differences between men and women in the events leading up to and after their CEA. Some parameters included in my data-mining include: presence of hypertension, high cholesterol, coronary artery bypass graft (CABG), transient ischemic attacks (TIA), cerebrovascular accidents (CVA/strokes), myocardial infarctions (MI), and restenosis.

It looks like I should be able to finish my data collection and analyze everything by the end of this term. I’m also excited about going back to Ithaca and working in the new BME building. One thing I’ll miss about NYC is the Michelin-rated restaurants I’ve been lucky enough to eat at. After eating the hanger steak at JoJo, I can die happy.

Measurement, New Ideas and More Measurement

Last week I put more effort on one of Dr. Prince's new project: comparing the change of portal vein flow before and after meal in normal people and cirrhotic patients. Dr. Prince, me and other two medical students are working on the the pre-experiment part right now. Tons of problems with new ideas poped out, which made this week compact and intense.

It has been a long time that doctors found food intake can cause significant increase of portal blood flow, however, fibrous scar and regenerative nodules generated in cirrhosis can severely affect the liver reserve of this flow change. Studies on the comparison of this flow change between normal volunteers and cirrhotic patients by Doppler measurements started about decades ago. But because of the poor accuracy of Doppler in flow measurements, all the previous studies have many discrepancies, rendering this mecomparison not feasible in the diagnosis for early cirrhosis.

On the other hand, MRI can also do the flow measurement using PC (phase contrast) sequence. So Dr. Prince came up with the idea that whether MR can be used to improve the measurement of the portal flow change. Last week, we first tried out this measurement on him before and after meal. Surprisingly, after several repeated scanning, we found the measurement of the same portal flow can be very different in PC. What may cause the measurement error in PC? If we found them out, is it possible that we can get much better measurement of portal flow using MR?

Aiming for discorvering a better non-invasive diagnosis for early cirrhosis, we thought about many parameters that can be modified to achieve the improvement: resolution, SNR, and tricks to make the contour of portal vein, etc. To test these ideas, we need a proper phantom of human portal vein first. Then we came up with the "U-shape tubing phantom" idea. We connected a tubing bended into U shape to the injector of contrast agent and this could work as a nice continous flow phantom mimicing portal vein within 1 minute. Comparing the flow measurement obtained from both "in" and "out" profile of this tubing, we could get an idea about how sensible the scanning method or how accurate the measurement is with the known flow rate in the phantom.

After a whole week fighting with air bubbles, water leakage and all kinds of problems, we have finally got some very useful preliminary data. I am excited about this and will continue to do more measurement this week after analysing the current data thoroughly. I will keep you guys posted on this~

Projects and Projections

Now that the term is winding down I'm beginning to feel the crunch to finish my project. It will require a fair amount of effort, but I think it can be completed with time to spare. The parameters of my project are pretty simple. Dr. Schwartz is very interested in epilepsy, and specifically methods for treating cases of epilepsy that are refractory to drug therapy. Often in these cases, there is one localized portion of the brain responsible for the epileptic activity. These patients can opt to have this portion of the brain removed (which is where Dr. Schwartz comes into play), thereby eliminating the seizures. But removing a part of somebody's brain is obviously costly, dangerous, and potentially debilitating. Is it possible to do any better? Well maybe. However, first more knowledge needs to be attained about the way depolarization waves spread in the brain.

A medical student working in Dr. Schwartz's lab took massive amounts of data over the course of two years, stimulating rat brains at various frequencies and analyzing the hemodynamic response. One of the things Dr. Schwartz has asked that I do during my stay at Weill is analyze the data in a meaningful way, so that blood flow response can be correlated with the stimulus. As always in biological, medical, and engineering fields, this task is a little more convoluted than it superficially appears. Firstly, it requires sorting through volumes of data to determine which is "good" and which is "bad." Not to be confused with desirable versus undesirable data, there is actually an issue of noise corrupting some of the data to the point that it is totally unusable. In general, the data can be viewed by the equation: data=gain*truth + bias + noise. I'm trying to cleverly extract the truth from this equation so it can be analyzed. In a perfect world, gain would be 1, and bias and noise would be 0, but I don't expect to be so lucky. Fortunately there is a ton of information on estimation and detection methods, which I can use to hopefully solve this problem.

Decisions

As my summer gets more and more immersed I have begun to really enjoy visiting other surgeon’s ORs. I especially enjoy the mobility that I have been allowed by the plastic surgery department. Over the course of the summer I have seen quite a few breast reconstruction cases because of this mobility. It is quite fascinating to see the different techniques each doctor uses and to see which techniques their residents and fellows have started picking up as they learn. I bring this up because last week I was able to stand in on a surgery with a different doctor than my clinician and see a surgery I have been curious about all summer. I’ve seen quite a few skin grafts and flaps, as well as breast reconstructions post mastectomy with tissue expanders, but it is the TRAM flap surgery that I was really intrigued by.

The TRAM flap, or transverse rectus abdominis myocutaneous flap, is a fairly ingenious way to aesthetically correct a traumatic surgery with a patient’s own tissue. I have had quite a bit of contact with pre-op and post-op mastectomy patients during clinic hours and have heard how difficult the decision is for the method of reconstruction. These patients basically have two choices, the choice of using a tissue expander followed by a permanent implant (silicone or saline, which unto itself is a difficult decision) or the TRAM flap procedure. Both require nipple reconstruction afterward (though a few doctors are now working on nipple saving mastectomies), but the consequences of each are hard to decide between. An implant of course is a synthetic material inside your body, but recovery time is much quicker. The TRAM flap involves taking a large portion of abdominal skin, tissue, and part of the rectus abdominis muscles (in lay terms, your abs), and fashioning a new breast out of that in place of the removed one. This is a much longer surgery, a longer recovery, a lifelong weakening of your abdominal muscles with the increased risk of a hernia and the flap does have the possibility of dying, which in term would lead right back to a tissue expander/implant surgery. Though with the TRAM flap surgery you are replacing your lost breast with your own transplanted tissue and you get a tummy tuck out of the entire process. Seriously not a decision I would want to make, ever.

As I mentioned bore, the patient was not one of Dr. Spector’s patients, but the other surgeon was quite accommodating to let me stay for the 6+ hour operation and attempted to ensure I had a view/knew what was going on. The procedure itself was not a free flap procedure, so in this case the rectus muscle wasn’t cut completely off from the blood supply before being sewn to the tissue above for relocation. This complex, known as the pedicle, was then pushed through a tunnel under the skin made from the abdomen diagonally to the affected side of the chest and sewn into place. After discussing the procedure with Dr. Spector, I found that his preference is actually to perform this as a free flap and actually remove the entire muscle and microsurgically re-establish the blood flow that was feeding the flap. Like I mentioned before, every doctor has their own established way to tackle the same problem. This is why it is important to speak to a few doctors when electing to undergo any surgery. Not every surgeon is the right fit for a patient and the ability to hear new ideas and takes on a situation is important when making an informed choice. Regardless, the surgery was immensely fascinating and seeing this shapeless mass of adipose tissue and skin suddenly come together to form a new breast was astounding. I think it is safe to say I will always be constantly amazed at what doctors have pioneered in surgery.

Putting together the Puzzle Pieces

Recently I’ve had the opportunity to widen my horizon further beyond the Urology department. I’ve done rounds with Dr. Cooke in the ICU and followed Dr. Tagawa in the Medical Oncology clinic. Although both of these areas are very different from my general experiences in Urology rounds and clinic, at the same time, they are all related.

In the ICU, I experienced two different types of care. Many patients had come in the night before or the day before with an acute symptom (ie nausea, disorientation, shortness of breath). These patients were quickly being moved through diagnosis, treatment and recovery either in the ICU or in another unit of the hospital. Other patients though had more devastating diagnoses which left them in the ICU for a lengthier period of time. Many of these cases were due to the severity of disease or the patients’ inability to breath on their own.

In the Oncology clinic, we visited with patients who had metastasized cancers generally from the bladder, prostate or kidney. Additionally, many of these patients had been through either a surgical procedure to treat their primary cancer site or had undergone chemo or radiation. In general, the patients were visiting Dr. Tagawa in order to alter chemo, enroll in a clinical trial, start hormonal therapy or get general consultation as to what to do next. I was amazed by the variety of patients he saw and how thorough he was with each patient. Each case definitely required customized care and Dr. Tagawa was able to provide not only the standard options for care, but also the numerous clinical trails that were going on under a variety of clinicians.

So now to putting all the puzzle pieces together… My research project with Dr. Scherr is analyzing data from radical robotic cystectomies. Included in the database is detailed information for each patient which allows us to analyze the outcomes with regards to prior surgeries or treatments and complications that occur afterwards. Having looked at this data for a while now, visiting the ICU brought new life to the complications of re-admittance due to sepsis or pneumonia. As well, visiting the Oncology Clinic gave me an idea of what patients go through if their cancer returns. I had visited patients after their cystectomy in Dr. Scherr’s clinic and often the difficulties are with incontinence at night, but the patients in the Oncology Clinic with recurrence deal with many more challenges as they weigh their options for further treatment.

Finally, I’d just like to make a comment about the many roles I’ve seen Dr. Scherr play over the past few weeks. He is both a physician administering personalized care, a surgeon with technical skills, a researcher always asking questions and even an entrepreneur looking for new developments to change the way treatment in administered. I’ve been amazed to see him put on these different “hats” and even more astonished to see just how well each one fits.

I like mice

Other than going to clinics for 5 hours, I spent my week in the library in front of my laptop. My research project is on polycythemia vera patients who have mild symptoms when they have high JAK2 allelle burden, or severe symptoms with minimal JAK2 positive ratio. Normally, patients with increasing ratio of JAK2 positive burden have increasing phenotypes of the disease. For some reasons, these people have opposite output than what's expected. Several problems I run into during my statistical analysis include: incomplete/unorganized data (missing from different doctors, etc.), very small sample of patients, and not being able to rule out what causes what exclusively since we can't just test things on human patients. I'm not so sure if a publication is going to come out of this, but my fingers are crossed.

Week 5: Rollin'

Finally back to a regular full week's schedule, unobstructed by the national holidays nor other commitments! The last two weeks have been shortened one way or another, so it's great to be immersed for a full week again!

I spent most of the time bouncing around between Floors 0, 2, and 4 of the Starr Building this week, and reinforcing what I have learned about cardiology and different kinds of imaging so far in the program. Got to ask the fellows, nurses, and techs in each department tons of questions, as well as getting a lot more interesting references and resources to read. It was also great to see the end of the tunnel for my immersion project, for which I now have a realistic timeline to complete the study and possibly a paper or an abstract.

This week, I'll write a little bit more about the software that's used in my project, the LVMetric Segmentor, which was developed at WCMC to speed up the segmentation process of cardiac images. Image segmentation provides a lot of important information, such as the chamber volume, blood mass, etc. which can be used as an indicator for certain diseases. In the past, doctors spend an awfully long time on each image case to segment myocardium from the chambers, while taking into account the papillary muscle mass, etc. For each patient's image, it can take anywhere from 4 to 10 minutes for an experienced doctor like Jonathan to segment the image profiles at the systolic and diastolic cardiac phases. LVMetric, on the other hand is very efficient, as it automates this segmentation process using some nifty image transforms and segmentation algorithms, and does it for all 25 or so different cardiac phases; in a matter of few seconds!

In addition to speeding up the process for doctors, the software can get data point at almost every cardiac phase; this allows us to study the temporal aspects of the chamber volume, etc. at each moment in the cardiac phase. We've recently added a new function to the program, so that it can output a decent amount of data from different cases that we examine. The remainder of my project starting Monday will be to organize, process, and analyze the volume curve for a number of these cases (Jonathan said it would be ~20 or so).

From this study, we are hoping to identify a quantitative indicator of certain physiological defects by analyzing quantitative data that I will work with. So it will be time to hit my Statistics textbooks hiding somewhere in my room next week (where are they?!). I'm really looking forward to wrapping up my project.

Finally, I got to follow Dr. Frayer on the rounds in the NICU this morning; I really must resonate Shawn and everybody else's earlier comments: man those babies are cute!

Interesting experience this week

It is never a rare case to see some patients with breast cancer in radiology department. During the past weeks, I have written about two cases with breast cancer or breast cancer history in my post. This week, an especially interesting case came in, and gave me some brand-new insights into healthcare.

This is a 44-year-old breast cancer patient coming in with a bright blue scarf wrapped around head, which is undergoing hair loss due to the radiation therapy. I talked with her for a while she was waiting for the scan. Different from some other patients, I found her very cheerful throughout the short chat. Rattling super happily and proudly on her twins, she almost made me forget she was actually a cancer patient. The surprising thing happened at the time when I found out she actaully came to do an abdomen scan rather than a chest scan. Was this for checking the possible metastasis? I thought this way at first. But things just surprised me more when I gradually noticed the technicians paid more attention to some abdominal blood vessels. At last the most elucidating yet surprising thing came when I was told she was actually doing this scan for the susceptabilty test of a breast reconstruction surgery.

I know this is still confusing so let me explain more. Obviously this optimistic lady had not underwent a surgery to take out the breast cancer yet. She was doing the radiation therapy right now to suppress the cancer cells, so that they won't metastasize so easily post surgery. At the same time, she was also worried that she won't look so good after the excision of breast and DIEP Flap Breast Reconstruction technology came at the right time. Her surgeons planned to carry out two surgeries - mastectomy and breast reconstruction - on her at the same time, but before that, they need to make sure that her perforator vessels are still intact so that they are able to function as the internal mammary blood vessels later. She was very happy to learn the good news that day: her perforator vessels look super good even after the incision in C-section many years ago.

For me, this story totally refreshed my idea about the role of surgery in healthcare. In my old memory, surgery is always related with pain, wound and scar; surgery happens when medicine fails. However, this time just imagining nowadays patients can actually choose to combine resection with orthopaedics, I am totally overwhelmed. You can get cure and beauty at the same time - one stone two birds - isn't it fantastic?

Of course I understand that this technology must also be very controversial. Just like people would even argue whether this is worthy and safe to create an artificial beauty through orthopaedics, DIEP Flap Breast Reconstruction on a cancer patient is also risky. Recovery from two surgeries is definitely slower, not to mention the underlying risk to keep some breast tissues near lesions for better reconstruction. The fact is, ethic problems always come with healthcare. Nevertheless, the hope for benefiting more from medical technology never dies. Medical care is not all about elongating one's life. It also helps improving the quality of life, and the way we look at life and ourselves. There is nothing more important than that patients find health care help their lives and be happy about it. And I think the impressing part of this case just lies in that it teaches me the function of healthcare CAN be not only for physical well-being, but also spiritual welfare.

New Experiences

Last week I got to see deep brain stimulation surgery. I wanted to see as much as possible because I am supposed to be implanting DBS electrodes in rats for my thesis. Of course I tried so hard to see everything that I kept touching the blue sterile surface. The guy got kind of annoyed with me and I felt stupid and useless. My clinician also was telling me that I was getting too close. It is a very serious surgery, so I understood that I need to stay back to some extent. Nonetheless, it was fascinating. They used a lot of trial and error to find the right position and voltage of the electrode to maximize benefit for the treatment of Parkinsonian symptoms without interfering with motor control. They kept asking the guy to speak the days of the week. Sometimes it was muffled, sometimes it wasn't. I guess it varied depending on the positioning of the electrode. They also told him to flex his feet and open/close his hand. The surgery lasted for several hours.

The next day I saw three plastic surgeries. These surgeons were sooo much less serious. They played music, joked around, and the head surgeon played peek-a-boo behind the door. In the first two surgeries there was a lot of manipulation of the skin. In one, the skin would be stretched over time, then excess skin would be used to replace scar tissue. In the other surgery, the woman needed a skin graft. I could see all the exposed muscle that they were covering up. She also had the biggest blister on her heel that I had ever seen. It looked like a giant diabetic blister or something.

Today I saw open heart surgery. They are right, it is intense. They bypassed the heart and lungs so that they could treat an aortic valve inefficiency. The blood went to a machine that acted as a heart. The resident said they would take a blood vessel from the leg and use it to replace one of the aortic vessels. It did not see the whole thing because I had other things to do.

I really want to learn as much about stereotactic surgical techniques from my clinician as possible, specifically on dissecting rats. He had me hook up with a woman in his lab who plans on doing stereotactic surgery. She said she had never done stereotactic surgery either. Not too encouraging. On the other hand, Yi stated clearly that this work is not meant to be for our theses.

I continued to work on the research protocol that Dr.Frayer says is junk. I was too lazy to change what I was doing and figured that at least I am learning a lot about neuroanatomy, something that is important to me in pursuing a neural engineering career. Now that I have learned about the neuroanatomy of drug addiction, I think about the reward circuit when I pop in snack foods and go out for a run. I have finished writing about the rationale now, so I don't know what he will have me do next.