BME Summer Immersion 2021

I spent the final week of immersion concluding my research work, setting up future collaborations, and completing a few tasks I wanted to achieve before returning to Ithaca. To conclude my research, I created presentations for Dr. Hartl's group, the Bonassar lab, and our summer cohort. I also had lab members complete the quiz I had created for our MRI grading scale. To continue our collaboration, I set up a sample pipeline, protocols, and paperwork to allow for future data and tissue collection. I established a method for shipping disc tissue so I can co-culture these discs with stem cells upon my return to Ithaca. I established paperwork for collecting measurements for the cannula I am developing. I made excel sheets to organize this data. I spoke with HSS to create a collaboration for future mechanical testing. I worked on a histological report on images used for a study using materials manufactured by our collaborators at 3DBio. Thursday, I shadowed Dr. Spector in the clinic, le...

 Last Days of Immersion: This week was the most exciting of them all. I finally got to see a liver transplant surgery. Liver failure is a common disease in which the immune system attacks liver cells which tends to cause severe inflammations and internal damages. This patient ultimately made it through a successful 12 hour+ surgery. In terms of the immersion deliverables, the imaging patient data that I gathered from Eileen was crucial for the completion of the project. Unfortunately, it was difficult to view the data without having access to the Weill Cornell Medicine account. Therefore, Dr. Shou will be continuing with developing the hospital's ERCP/MRCP protocol.  Overall, I managed to say my goodbye's to the TRAUMA and BURN team. It was bittersweet since I learned to respect and admire the tenacity the team has shown these past few weeks when it comes to patient care. This experience was life-changing since I was able to appreciate the hard work the men and women do behind...

I spent my final week establishing a sample pipeline between Weill Cornell and Cornell Ithaca, so that I can receive and process samples once I'm granted IRB approval. My clinical mentor was out of town for the final week, so we did not have our usual lab meetings. I also spent some time preparing my final immersion term presentation. It was interesting to see all the different projects that folks in the cohort were working on. The topics ranged between artificial intelligence in image processing to regenerative medicine. To wrap up the immersion term, I joined the rest of the cohort at a picnic in central park. The weather was beautiful, and we had pizza to celebrate an unforgettable summer. Working at NY Presbyterian was a unique and formative experience in my PhD. I got to see first hand the reach and impact of the research I do in Ithaca. Thank you so much for this opportunity!

  Last week I shared the network performance on learning the mapping between 7T and downsampled 7T (3T analog) scans. This week I prepared a training dataset of real 3T and 7T scans acquired on a General Electric (GE) scanner. The pre-processing routine includes reconstructing the susceptibility weighted images (SWI) from gradient echo data, registering the 3T dataset to the 7T dataset, and normalizing the intensity of both datasets. In the fused image below, the green pixels indicate similar intensity, and the magenta pixels indicate differing intensity between the registered 3T slice and the 7T slice. Notice most of the difference is around the vessels and what appears to be phase artifact from the 7T.   After these measures, each of the 9 cases was split into 3D patches of size 32x32x32. The new residual is shown below. The residual is now a volume rather than a 2D slice. A sample 3D patch is shown below.

     It comes to the week when we say goodbye to the summer immersion term and everyone met during this incredible experience. We had a reception on Wednesday and a picnic on Friday. I really appreciate every moment that I got to spend with these amazing people. Because of COVID, we didn't have many chances to see and talk to each other in classes and events last year and I saw many of my classmates the first time during the summer immersion. After 6 weeks of bumping into each other in the elevator, on the way to the hospital or late night in the kitchen (unsurprisingly often), we have developed a special relationship. Though we worked in different departments, going through the same thing made we understand each other so much. Unlike in the first few weeks when we talked mostly about the hospital and clinicians, in the last week, we also talked about the future: life in Ithaca next year, research ideas, chances to visit NYC again......Everyone got so much out of this exp...

Dear Dr. Glesby,     I saw an art exhibit at the MOMA the other day: "General Idea’s  Magi© Bullet by AA Bronson". Hundreds of silver pill-shaped balloons filled the expanse of the ceiling lit only from below. When it was installed, at the height of the AIDS epidemic in the 90's, two members of Bronson's art collective had died.  The gallery label was below at eye level.     " Filling the gallery with pill-shaped mylar balloons, Magi© Bullet in part functions as a metaphor for seeking a temporary remedy for an illness—physical or social—rather than examining its root causes. As the balloons’ helium levels decrease, they fall; you are invited to take a deflated balloon home with you. The installation thus gradually disappears over time, evoking the lives needlessly lost to aids because of state abandonment—and prompting comparison to the current global pandemic and the harm it’s wrought on our most vulnerable communities."     Though I looked ...

 The End I can't believe that immersion is over, can you? It feels like these six weeks flew by. I still remember the first day when we were lost and eager to find new memories. So many buildings are part of the hospital - So many elevators - So many opportunities. And well, now we have reached the end... For me, this has been a fantastic experience. I learned so much these past weeks, you wouldn't even understand how this changes a person.   This week was great. I did a lot of the things in the city that I wanted to do. I went again to the Met museum, ate at Empanada Mama, and shared some great moments with friends. What else could I have asked for? what else would you ask for? Anyway, I am not sad that the program is over, I am pretty sure I will see everyone at some point and laugh about our experiences. Plus, now I feel super motivated to come back and work on my projects and get this Ph.D. Here I leave you with my favorite picture, check out the lab coat. Even though...

  Week 6 This week I continued to join the infectious diseases doctors at the clinic and inpatient rounds. One memorable case was an old lady with urinary track infection that has abnormally high white blood cell count. The doctors initially thought it was solely due to the infection, however upon further investigation and consultation, it was suspected that the patient has a specific type of cancer that produces G-CSF, which is a growth factor that stimulates white blood cell production, thus resulting in the insanely high reading while no severe infection was found. During the rounds, Dr. Vielemeyer gave me an important lesson on treating severe cases - instead of reverting all abnormalities to the patient's normal physical state, it is more important to make the transition as gradual as possible, as the body already adapts to the diseased state. Any sudden changes would cause more problem than doing any good. In the case of a alcohol liver disease patient, although t...

This week I was able to wrap up my second project in Dr. Cesarman's lab. One member of the lab attempting to acquire image analysis data from immunohistochemistry-stained nuclei of lymphoma patient cells using a software called HALO. This was done with the intention of developing a scoring system for the gene expression of a particular histone mutation. He and Dr. Cesarman wanted me to develop a strategy for performing the image analysis and acquire some preliminary data for a large set of samples so that they could look for trends in the data that could be relevant to gene expression scoring. I figured out how to use the software and went through both slides acquiring and exporting the data for 200+ samples altogether with the optimized image analysis algorithm. Due to the amount of time it would take to process the large number of exported data files and acquire the desired, categorized summary statistics, I wrote a MATLAB code that would do the task for me, also categorizing by ...