Cornell BME Summer Immersion 2017

As I am ending my internship in NYC, all I can say is that I will never forget the past 7 weeks here. I've learned a tremendous deal regarding what goes on in a hospital environment, which will be invaluable to my work in Ithaca. I spent the first half of my week with the Clinical Microbiology laboratory team, participating in rounds with the residents & fellows. Also, I was able to have a great discussion with Dr. Westblade, PhD and Associate Director of the Clinical Microbiology lab. Speaking with physicians has been essential to my experience here, but speaking with a PhD gave me additional insight to the opportunities available to me should I pursue clinical work. The training for an MD is entirely different than one for a PhD and both require different skill sets. I've been told time and time again here that medicine is more of an art and diagnosis for certain diseases can be subjective. The PhD, on the other hand, will perhaps be more analytical. Both are essential

This is the last week of being immersed resulting in a final push in finishing the data collection. This week was focusing on gathering the last of the pathology results to finish the database the team and I have been building this summer. We fortunately did that this week, but due to the amount of time it took, we have not been able to do any analysis on it yet. Therefore, for this final post I primarily want to thank everyone that I have worked with this summer. From Dr. Hu and Dr. Margolis who provided the mentorship for the project to the medical students and residents that helped gather all this data. Without them this summer would have been much less informing and entertaining. Also without them I would not have been able to find most of the places I ate at through the summer as they made so many suggestions. With that I will end this post and conclude this blog series. It was a lot of fun New York and I will be back to visit some time soon.

During my last week, I was able to segment and analyze the rat tendon MRI scans for T2* values. As I mentioned last week, I used ITK-SNAP for segmentation and a custom MATLAB code for T2* quantification of each pixel in the segmented area. The resulting maps showed mean T2* relaxation times similar to those seen in fresh and frozen rabbit patellar tendons. These results suggest that UTE scans of rat tendons could be used to further investigate tendon injury and healing. Future tests could include comparing T2* values of healthy and diseased tendons. This would be potentially useful in a clinical setting, as there are currently no methods to detect tendon degeneration or healing in vivo . After returning to Ithaca, I will hopefully be able to continue contributing to this work by better characterizing our fatigue loading model of tendinopathy and sending additional rat specimens.

For my last week in the OR, I observed a procedure that was the first of its kind in the country. In this case, the patient had previously received a sternum resection due to cancer. Although an implant was placed in place of the missing sternum, it needed to be replaced. To this end, the physicians on the case called for a custom designed 3D printed titanium implant to replace the sternum. This implant was created using CT scans of the patient’s own anatomy, ensuring that this artificial sternum would be tailored to the patient and fit perfectly. The surgery itself involved cutting through the chest wall and removing the previous implant. After removing some of the soft tissue on the rib cage, the implant was fit into place and securely screwed in. Dr. Spector’s part of the surgery was to reconstruct the chest wall by bringing muscle flaps over the implant. In the research front, we have made multiple technical adjustments to the SMF platform to bring us closer to being able to r

It is hard to conceptualize the impact that the Summer Clinical Immersion Program has had in my life as a graduate student and future contributor to the field of biomedical engineering. These past weeks have served as a catalyst to rediscover my passion for the advancement of medicine and science. I feel extremely thankful for being able to experience clinical research in ways that were impossible to envision before coming to Weill Cornell Medical College. The professionalism, compassion, and willingness of medical doctors, scientist, and engineers to share their knowledge and expertise have been an instrumental part of the journey. Furthermore, being immersed in the hospital setting for six consecutive weeks gave me the opportunity to be exposed to the entire spectrum of the medicine. By shadowing Dr. Stein on the clinic, I learned about the importance of preventive healthcare and the impact that personalized medicine could have in patients worldwide in the future. Although my in

I spent my week analyzing my flow cytometry data and preparing a presentation for HSS's weekly Orthopedic Soft Tissue Research group meetings. This gave me the chance to learn how to use the analysis software, FlowJo, which will be instrumental for my work back at Cornell. I hope to keep this project going as a collaboration by having surgical discards shipped from HSS to Cornell, where I can expand cells and do analysis there. I also finished building the new multiphoton stage, which allows for live imaging of a mouse patellar tendon with enough room between the objective lens and the animal. Although my stage works great, unfortunately the settings on the microscope were wrong and none of the students knew how to change it, so we could not actually image the tendon that day. However, with the redesigned stage, new students who will join the lab can take over the project. I taught the other summer students in the lab how to use some power tools and design and adjust the stage pa

With the end of our summer immersion approaching, I feel sad to say goodbye to all the persons I've met in the hospital during this summer. The past 7 weeks has been very fulfilling and exciting to me, and I will never forget my experience here. As a student will electrical engineering background, I never thought that I can be able to go to a real operation room in the hospital and observe doctors operating on surgeries. But in the past 7 weeks, I was able to go to OR every week, and there's always surgery techniques that are impressing to me. Beside clinical experience, I also had a research project, automatic segmentation of zebra fish neuron images. As I have presented in my previous bloggers, for my project, I have tried several different algorithms. The first is simple thresholding. It is usually used as a preprocessing step in image analysis. The second method is watershed algorithm. It works pretty well, but, it's very sensitive to noise, resulting in over segmenta

During last couple of weeks at HSS, I have learned a lot of eye opening experiences. First of all, as a graduate student in BME, chances to look at up-to-date biomedical device gave me some ideas about how to approach to improve existing device. Those are hard to come by without observing clinic fields in the first place. Also, developing new surgical procedures requires basic scientific knowledge. For example, quite recently, HSS introduced Lipogems' product for adipose tissue derived messnchymal strm cells treatment. Firstly, the therapeutic effect of adipose drived-MSC was demonstrated. However. Due to the difficulty in purifying MSCs and several biomolecules, the application of them in short time was delayed, which was resolved by the effort of researchers in BME. These sorts of experience made me clear about how to utilize what I will have learned through my PhD program. with Dr. John G. Kennedy and Dr. Yoshiharu Shimozono.  Second, personally I did not realize how hard c

This week I was able to go to OR and shadowed a couple surgeries. Some of them were really impressing to me. The first surgery was to remove a tumor near spinal cord. In order not to touch the nerve system in spinal cord, the doctors put screws in the vertebra. Also, they partly stimulated the neurons and put them on EMG to make sure those neurons are not effected during the surgery. The second surgery was to drill a hole through nose to remove a big brain tumor. As I saw from MRI images. the brain tumor was really a big one. In order to get rid of it, the surgeons had to cut it into pieces, and then took them out piece by piece. Besides surgery shadowing, there are also some updates on my project. As I have mentioned in my previous bloggers, watershed algorithms work the best for my project, automatic image segmentation of zebra fish neuron images. However, this algorithm is very sensitive to noise, resulting in over segmentation in regions with low SNR. In order to overcome this pr

As my immersion experience comes to an end, I am extremely grateful to have spent this summer with the rising second-year PhD students in NYC. The early mornings spent observing Neuroscience ICU rounds provided me with invaluable clinical exposure to patient care while learning directly from world-class neurocritical care fellows and attendings. Outside of the Neuroscience ICU, I shadowed surgeries, attended hospital seminars, and talked with various physicians about their research. These opportunities have drastically changed my perception of clinical research and physicians. After seeing the day-to-day activities that Dr. Mangat and other individuals undertake in addition to their research and patients, I now have a much greater appreciation for those who dedicate their lives to work in this field. With only 7 weeks to define and conduct a project, it was difficult not being overly critical of myself whenever my code was not working properly. Despite all the roadblocks and unfor

Tibra Wheeler Seven weeks down, zero to go. Here we are at the end of the road. This point of the summer came waaaaay too fast. Over the weekend, I went to Queens to celebrate national cheesecake day at the Cheesecake Factory with half price slices. I also enjoyed catching up with old friends and exploring the lower east side of Manhattan. This week was mostly spent wrapping things up in lab as well as checking more things off my “things to do while in NYC” list. Monday was a very laid back day. That morning, I worked more on the segmentations in ITK-Snap. Once I got to a stopping point with the segmentations, Kirsty gave me the RNA expression data that we collected last week so that I could make different plots in Graph Pad Prism (this really nice software that allows you to create really pretty graphs of your data). Our plots graphed the Ct value ratios of the housekeeping gene we chose against the particular gene of interest for each of the groups. The Ct value is the cycle t

Although this summer came and went, I don’t think my time here is finished just yet. This week, I continued to work on my project regarding seminal vesicle dilatation in patients with autosomal dominant polycystic kidney disease. I finally finished measuring the seminal vesicle volume and lumen diameter of the 90 patients in our PKD study, and met with our collaborators Dr. Jon Blumenfeld, a nephrologist, and Stephanie Donahue, a nurse practitioner, at the New York-Presbyterian Hospital to collect the renal, hepatic, biochemical, and genetic information on each patient. By obtaining this information, I can now start the statistical analysis that is necessary to determine if there is a significant correlation between ADPKD patients with a specific pathogenic mutation and seminal vesicle size. Apart from compiling the quantitative data for my project, I also spent a lot of time selecting and formatting figures for my research paper, which is probably one of my favorite parts of research

This week I had lots of opportunities to attend lectures and meetings related to lymphoma. On Tuesday I went to the thesis defense of a student who works in one of our collaborators' labs. His thesis was entitled "Epigenetic Silencing in Humoral Immune Response and Lymphomagenesis". In a nutshell, the PhD candidate studied the relevance of DNA methylation on the turning on and off of genes that lead to B cell immunity and separately to B cell lymphomas. His work was focused in both germinal center B cell and activated B cell diffuse large B cell lymphomas, the latter of which is typically more aggressive and harder to keep at bay. Despite my background in lymphoma research, I will admit that I had a difficult time keeping up with his thesis points. His training was in computational biology, something I am only remotely familiar with, which definitely contributed to the complexity. Even though I didn't understand much of the talk, I am glad I went. I think every opport

These seven weeks of immersion have come and gone so quickly! As distant as I am from truly understanding pathology, I was able to get the fundamental ideas, and I loved learning new things every day! This has been an amazing opportunity to experience the clinical world in a very unique way. When I started, I was completely unfamiliar with pathology, but now I know a lot more. It was great to learn some anatomy, and I enjoyed seeing the process of diagnosis. Everything was new and exciting, but the main take-away was the understanding of how physicians interact and communicate. This immersion program has shown me what is important to physicians, and has provided a different perspective for requirements of good medical innovation. I also had no idea what medical school was like or what residency was until I met the twenty-some pathology residents here, so I gained a better idea of their training and careers as well. This week (the last week of immersion L ), I got to see two

 Guy Scuderi Well, just like that, my immersion experience is complete. These past seven weeks have surely flown bye. I cannot believe it is already over. This experience as a whole is going to be something I look back on for a long time. I am beyond happy with how my experience went as I explored all around the city and learned more than I could have ever imagined in the clinical setting. All my expectations of how this immersion term was going to be were met and I am highly satisfied with the outcome of this experience. This past week basically involved me finishing up my clinical research project. After extracting all the data from the 22 included articles, I went forward and computed some basic calculations on the overall reoperation characteristics of the entire meta-analysis cohort, as shown in Table 1 below. This initial data was pretty interesting. If you recall, the main research question Dr. Gaudino and Dr. Weinsaft wanted to look at through this meta-analysis wa