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Rachel Yerden- Week 6

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...
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BME Immersion - Sixth week 6

 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...
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Week 6 - Alikhan Fidai

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!
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Week 6 - Alexandra Roberts

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  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.
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Week 6

     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...
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Week 6: Allison [A Letter from the Student]

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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 ...
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Week 6: Juan Boza - The End

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 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...
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Week 6

  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...
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Rich Hoff Immersion Week 6 - Bye NYC

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 ...
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In Retrospect

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A beautiful view of the Queensboro Bridge, the East River, and Queens. Looking at this reminds me of the first few words form J. Cole's Change  - "My intuition is telling me there'll be better days." I'll just leave it at that. Six weeks is a lot of time. 42 days, or 1008 hours, or 60,480 minutes. In an almost cruel twist, it passes like no time at all. Of course, this is the duality of time; both lengthy and fleeting in a single experience. I look back and see that through this immersion, I've gotten to witness many cases, work day in and day out with physicians, and work through my project. Before I started, I was interested and enthusiastic about MRI - learning about T2 and other image weighting. Now, I have some of the basics of scanner operations down, and I was even able to perform a scan on a phantom just this week! I didn't really know what ablation was, and I got to watch two procedures in the past two weeks. I've learned a lot, and there is a...
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Week 6- Au revoir!

As this is my final week, I find it just to reflect on my experiences during this immersion. From day 1 to day 42, there were a lot of ups and downs. However, I am glad I made the decision to come in the end When I started this term, I had no idea about what could be achieved in these six weeks. Thankfully, with the guidance of Dr. Dadhania, Dr. Westblade, and Dr. Chughtai, I was able to learn a lot about conditions and procedures that would be either foreign or hear say. Research wise, it is unfortunate not to have more time to continue working on the current projects while in proximity to the clinicians.  However, I hope to continue what I started in Ithaca. Although it took me a while to get the logistics and understand what I was to to, I am happy I got to do some actual data analysis.
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Week 6 - Samantha Bratcher

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The final week! This week I watched a kidney biopsy and ablation and a bone biopsy. Biopsy involves getting small cores of tissues from a tumor or mass. Ablation is a technique used to destroy tumors. This can be done with heat or cold. Thermal ablation can further be accomplished using radio frequency or microwaves. However, when heat is used, the doctor must also account for "burn back." Heat is difficult to control precisely and will diffuse to surrounding healthy tissues/organs back along the probe. Hydrodissection injects saline to push organs away from the burn area, protecting them. The craziest part, though, is that they do this with the patient awake (but sedated) and insert a long needle through the torso. The bone biopsy was similar, but a drill had to be used to go through the bone and cut a small cylinder out of the suspicious area. For my last weekend in NYC, I went to Luna Park and the Coney Island beach. Personally, the ticket price for Luna Park wasn't wo...
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Week 6 - Shuofei

For clinical experience, I shadowed one flap surgery and two wound cleaning surgeries with Dr. Spector. The patient with flap surgery had a huge hold in her mouse due to tumor removal, and the plan was to harvest a muscle from the wrist to patch up that hole. Two fellows were making incisions on the patient's neck to access the oral cavity while Dr. Spector was harvesting the muscle flap. Then, microsurgery was performed to anastomose the arteries and veins of the muscle slap to that of the neck, and the muscular flap was sutured on top of the hold in the mouth. Meanwhile, a layer of skin was harvested using a dermatome to cover up the wound on the wrist. Overall, I was impressed by how efficiently the medical team worked together to perform multiple parts of the surgeries simultaneously. For the wound cleaning surgeries, one was for the back of a foot and another was for the spinal fusion metal implant. Both patients had serious infections that halted wound healing, therefore Dr. ...
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Week 6 - Austin Bunce

Clinical:     As I wrapped up my time at Weill Cornell, I spent most of my time working on deliverables for our program.  I did get into surgery on Thursday though to watch a tumor removal.  The main reason I went in was so that Robert, another student in the  program, could come with me.  He had not seen a surgery at all yet so it was good that we were able to get in for one.  I know what to expect from tumor removal surgeries by now so it was mostly the same, but there are always some new things to pick up during every surgery.  Usually some new brain anatomy and how the surgery has to be individualized based on the certain location of the tumor.       Research:     I had finish up most of my research so that I could present on earlier today (07/31).  I have been done with my app for a few weeks now, so all I had to do with that was put what I did into a few slides for the presentation.  My secon...
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Week 6 - Jon Albo

 It's crazy to think that immersion is over and it's already been 6 weeks. It feels like just yesterday we were all debating how many clothes to bring and how many suitcases we'd be allowed to take on the bus. Although one suitcase was enough for my clothes, I'm glad I had an extra duffle bag to bring some bagels back with me. I came into this experience with very little expectations and not a clear path of what I wanted to learn and take away. I knew I wanted to make connections and meet different research labs in case we wanted to collaborate in the future, but other than that it was more or less an open slate. I chose to dive into learning about lymphoma and stem cell transplants since cancer research has always been interesting to me, but I've never worked anywhere where this was an option. Dr. Leonard and other lymphoma clinicians graciously took me under their wing and taught me an incredible amount about lymphoma and how patients are treated. I saw some patie...
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