BME Summer Immersion 2024

This was the final week of immersion. I spent Monday working on finalizing my final presentation and literature review which I have been working on this summer. On Tuesday, I gave my presentation along with some of my peers. It was cool to see what all the other cardiac people were working on! On Wednesday, I took the day off work to check off an NYC bucket list item, and went to the Bronx zoo. It was a great trip and I saw lots of cool birds. After that, we returned to the upper east side for our farewell dinner with all the immersion students. We had some great conversations with Dr. Wang about the use of AI, and with Kelly about the organizational aspects of immersion. It was a great conclusion to an exciting and productive summer! 

During the final week of the immersion term, I focused on developing a plan to continue several analysis projects into the Fall. At this point, the data transfers are complete, and I have developed a foundational understanding of the datasets and questions that Dr. Cristofanilli's lab is interested in answering. Throughout the summer, I observed the collection of a multitude of liquid biopsy and clinical data types. By shadowing Dr. Cristofanilli in the clinic, I was able to see when and how these data types provide valuable insights into disease progression and may be used to guide patient care. In addition to the intellectual usefulness of this experience, I am very grateful for the emotional element. Engineers don't often get to see the implementation of the work they do, especially in a medical setting. My experiences this summer were centered around the human experience of the result of biomedical research, something that will motivate me throughout my career.  On Tuesday,

 This was my final week working at HSS. On Monday I spent the entire day working with Dr. Anju Malhotra. Dr. Malhotra is an anesthesiologist and focuses on pain management. For this I was shadowing both the clinic and the procedures that he performed. I was mainly interested in this because of the work I am staring up in Ithaca with a focus in pain. This gave me a great deal of insight in how pain is perceived and how it is managed in a clinical setting and could possibly make it easier to transition my pre-clinical work to the clinical side. On Tuesday I spent time in the clinic and spoke with a design engineer about what they do. This meeting was mainly used as a way to gauge what the design engineers do. Their focus is on designing custom implants for special cases. They work very closely with many of the implant manufacture to create implants. They also work closely with surgeons and research engineers in impact development. Since these engineers have a lot of experience working wi

 My final week of immersion I did some more shadowing in the cath lab and watched more aortic valve replacements following similar procedures as those I had previously witnessed. I also did more work to further refine device development of the catheter device I have been working on with Dr.Chen. after some initial consultation with manufacturers we realized some of the specification were not going to be realistic and as such I redesigned the device to match geometries that are possible with current manufacturing methods. After watching many more catheter procedures I was also able to tweak the design to better fit in with the currently used technology related to the device. This will make its use more accessible and affordable since doctors already have the tools needed to operate it. Overall, this has helped me realize how big an influence device design can have on medical accessibility. The tiny details I learned about through in depth shadowing helped me realize what is truly import

The final week of immersion was similar to week 7 as I continued to shadow/assist Alex Piacentini while he cultured cells and loaded them in a Flexcell in vitro model (shown below).  Once again, I got to see how the final tendon construct is formed and placed under load via vacuum, and how cell viability is measured. This experimental group was placed under a 10% strain and compared to unloaded constructs (pictured). Subsequently, the midsubstance of the tendon was again resected and inflammatory markers were identified via qPCR  to ensure that the tendon was in an overloaded state. Once it is demonstrated that 10% strain causes sufficient overload, another round of experiments will be run with 10% strain controls and 10% strain YAP/TAZ inhibition treatments, to assess how this signaling interruption alters the expression profile of the tendon (measured via transcriptional profiling).  I also saw my peers present their research in our weekly cohort meeting, and got to see some of the o

 This week I implemented another AI to study the lung cancer metastasis predictors. Unlike the sequential model which predicts time until diagnosis, the new random forest model predicts which features are the most impactful for the prediction. I was surprised to see several of the diagnosis predictors, many of which seem largely unrelated, and I am curious how the results will compare to the Cox model Eunji is using for a similar purpose. This is the last blog post I will be making about the project, but I will be continuing to work on it into the academic year with the Tamimi lab.

I collected two intervertebral disc samples from Dr. Roger Hartl's C5/6/7 disc replacement case. We have an ongoing collaboration between Dr. Bonassar's lab and the neurosurgery department to collect these tissue samples. While waiting for the tissue to be collected, I was able to observe the surgery being performed. The anterior cervical discectomy was performed by opening the patient up from the front of the neck and using microsurgery to get to the spine. Two screws were placed across the disc that needed to be replaced. Then, the disc tissue was scraped away, almost looking like cold butter shavings. These were collected into a specimen jar. Vendors from NuVasive were then with guidance on how to use their "Simplify Cervical Disc Tool" that was used to first spread apart the vertebrae, and then put in the spacer that will be used as the replacement. These were all put into the disc space with an impactor/hammer and x-rays were used throughout the insertion to dete

 This week I worked primarily on finishing up my research on the Cardiology Whole Genome Study. I accessed several patient MRI results from the list that I was able to compile last week and extracted some functional numbers such as end diastolic pressure, end systolic pressure, stroke volume, and ejection fraction. I also copied their percentage of scarring and any critical comments listed at the end of their report. I looked over which mutation was the most common among the patients in the genetic testing list and decided to focus on finding similarities in patients with the MYBCP3 mutation which is cardiac myosin binding protein C. Initially, I noticed that most patients had significant scarring reported and moderate to severe dilation of their left ventricle. I also noticed that there were some relatively young patients as well with this mutation, one having had a heart transplant.

    07/22/24 - 07/26/24 Week 8: This week has been quite eventful and productive. On Tuesday, I delivered my summer immersion presentation, summarizing the work I've done over the past few months. The presentation went well, and I received valuable feedback from the audience. Following the presentation, I had an in-depth meeting with Dr. Beecy to discuss my progress on the amyloid project. We reviewed the results of my experiments so far and brainstormed future directions for the research. Dr. Beecy provided insightful feedback and suggestions, which I plan to incorporate into my next steps. I also had multiple meetings with the data team to ensure we have all the necessary data for our ongoing and future experiments. I provided them with detailed specifications and requirements, and we discussed strategies for efficient data management and analysis. These meetings were important for aligning our efforts and ensuring that we have a solid data foundation for our research. Additional

 7/22/2024 - 7/26/2024 This week started with clinicals. There weren't many patients, but it was still a cool last day of clinics. It was also really crowded in the clinic space where Dr. Spector works because, in addition to the usual members of his team, there were two extra people. One was training to be a Physician Assistant (PA). It was really interesting to talk to the PA-in-training because she is in the stage of her program where she is rotating through different medical departments to decide which is the best fit for her. Plastic surgery is her third rotation; her first was psychiatry, and her second was in the colostomy department. She already decided that the colostomy department is not for her, which is completely understandable. She said psychiatry was really cool. I found her stories about her time in the psychiatry department fascinating as it is completely different from anything I have experienced. My sphere of research has always been focused on the physical condi

It's difficult to leave when the projects you've been working on for so long are unfinished, although I suppose there's rarely ever a point in time where the science is wrapped up neatly and shelved for good. ----------------------------- This week, for the alginate hydrogel project with the Khormaee lab, we attempted to re-image some of our prior gels to obtain a later time point. However, we were not able to visualize any cells—whether this is due to some change in the hydrogel over time or something occurred to the cells themselves, we are unsure.  We also received training on using Imaris software for analyzing our cell image stacks. We determined processes within the software to correct for changes in background intensity (which is a frequent problem within our hydrogels), correctly identify cells, and track cell movements over time. As we've previously noted before, cell movement is very minimal within the gels; however, the program picks up on small cell movement

 Week 8 Final Week Blog! This week is the end of my summer immersion research in Dr. Babak Mehrara's lab in MSKCC. To summarize my progress during the past two months, I participated in their lymphedema research to further understand the pathophysiology of cancer related secondary lymphedema. This experience was extremely helpful for my future research. Meanwhile, I learned and practiced some really important in vivo experimental skills, including flow cytometry, tissue staining, protein and RNA isolation, qPCR, western blot, etc.  On Monday, we collected patients' blood samples for isolation of human peripheral mononuclear cells (PBMCs) and to prepare for flow cytometry for memory T cells. After centrifugation,  I observed a clear phase separation of 4 layers as shown in the images: clear plasma on the top, mononuclear cells (buffy coat) in the middle, then a semi-transparent Ficoll-Paque Plus layer, and a red non-transparent layer of granulocytes and erythrocytes at the botto

 Last blog post! I can’t believe the Immersion Term is already over. Overall, I think it was a really positive experience that I learned a lot from. After my first trip to the pathology lab, I realized that I really didn’t understand the anatomy of breast tissue and where breast cancer comes from. With Dr. Demaria’s instruction, I feel I have a much better grasp of these concepts and I’m better prepared to do breast cancer research. I had also never really understood how to interpret histology before coming to Weill. If I saw images of H&E stains in a paper, I mostly just ignored them because I didn’t know what to look for. Now I think I’ll have an easier time reading the literature and I’m interested in potentially doing some histology of our in vitro systems back in Ithaca. Getting to work with the organoids in the Demaria lab was huge for me and my lab. I’m already working on plans with my PI and Dr. Demaria to bring some organoids to Ithaca so we can do our mechanics-focused wo

This week's didactic meeting consisted of a PIP Joint Contracture presentation and Indications Conference for Oral and Maxillofacial Surgery. An interesting case consisted of a patient who received help from the emergency department to repair a glass-shard injury to the third digit. The patient lost some mobility of the digit. A Z-plasty was performed in a follow-up surgery, allowing the patient to regain full joint mobility. Finally, I was attempting to actualize my proposed experiment for a biomimetic breast microenvironment platform that consists of a tumor spheroid, biomimetic/plain collagen layer, and endothelial cell layer. Breast tissue was isolated and everything was prepared for plating. However, upon attempting to plate spheroid-in-collagen solutions into a 96-well plate, I discovered the formation of the meniscus kept pushing the spheroids into the walls of the well, making them unviable for analysis. Troubleshooting this in a second attempt showed that technique in pipe

 This week, I observed some neuroradiology readings with some radiology fellows and saw a variety of scans that looked at the brain structure, as well as the vasculature for abnormalities. Much of the reading involved the reader scrolling through the images and taking notes on findings before having an attending come and look through the images to check for additional findings. They also showed me a website with games and even cases to help teach students how to read different images. For research, I wrapped up my project and presented my findings during the weekly lab meeting. I also met with my clinical mentor and others who I was working with to discuss my immersion experience and give them the data that I got.

Chelsea Loh July 22-26 This week I wrapped up my research project with Dr. Weinsaft's team and presented my research during our weekly Tuesday seminars. I also met with Dr. Narula (cardiology) to read sheep vascular ultrasounds as part of a collaboration between my lab in Ithaca and Dr. Weinsaft's team. Overall, I really enjoyed my experience here in NYC, both personal and clinical. I learned basic MRI and imaging interpretation skills which I hope to use once I start my in vivo studies back in Ithaca.  

 This week, I went in to the OR on Monday and watched a surgery in which they implant stereotacatic depth electrodes in to the patient's brain to map out seizure focus. First, they had the machine moved around patient's head to register locations with the Rosa robot. One the patient's head is registered and is at the correct locations, the robot arm, with a laser guide, will move to locations predesignated for electrode implants. The arm of the robot consists of a laser pointer and a stereotactic guiding device. Once the arm moved to a implantation spot, the surgeon will opens up the skin in that locations, and drill through the skull following the stereotactic guiding device. After drilling through the skull, the surgeon ill put in a holder in to the skull. The surgeon will then put a electric wire through the guiding device, throguh the holder and in to the brain. The wire acts like a monopolar, which will heat up due to the current going through and burn the dura and the

 This week has been a lot of data science and coding. We are trying to integrate traditional statistical models to give more robust and reliable predictions than just the AI alone. Eunji helped me resolve some missing data issues and how to expand our model to other predictors. One such predictor, time from cancer to metastasis, is showing very low error rates in our initial results! Once we integrate more than just diagnosis data for the model features, it will hopefully be a very promising prediction model.

This week I presented my summer immersion YAP/TAZ in vitro research as one of the final program deliverables. Additionally, I worked with the Rodeo lab manager to start the next phase of the YAP study. We ensured tenocyte viability, cultured the cells, then placed them in a Flexcell in vitro model where they were formed into a ribbon-shaped tendon. Once the constructs were properly developed, we put the tendons under 10% strain. Then, the midsubstance of the tendon constructs was harvested and frozen for qPCR. This will determine if inflammatory markers (such as DDR2) are present, simulating injury. Some of the tendon constructs were not loaded, in order to provide controls. Once this model is validated, another YAP inhibition experimental group will assess whether or not YAP inhibition has an effect on the landscape of "injured" tendon constructs. 

 This week we wrapped up the test periods of the NIH behavioral assay and had interesting findings between sex differences. Previous studies and numerous stress based behaviors have notable sex differences, in which males perform to a predicted state of freezing and feeding. As for females, they typically dart around or avoid food in the presence of stress. Our NIH findings with the pilot cohort supported this phenomenon.  Additionally, I concluded surgeries for our other behavioral cohort with more fiber optic implants. Shane and I were able to conclude the summer with over 60 surgeries performed.  Lastly I prepared my presentation for the upcoming week to close out my immersion experience. 

This week had a mix of research work and also clinical shadowing. In terms of research, I started work on the next two batches of Mtb rif-mutants which was almost 50 samples. I went through the same protocol that I refined and described previously; extracting gDNA from the samples, amplifying the rpoB gene through PCR and then cleaning up the PCR products (with some Nanodrop and QuBit quantification steps in between). I aim to sequence these samples and analyze the subsequent data next week. I also shadowed Dr. Schwartz in the OR with Jack where he and his team performed a stereotaxic implantation of electrodes to treat the patient's epilepsy. The surgery started with calibrating the Rosa robot to the patient's head, and then it used a laser to point out implantation sites for the team to mark. The process consisted of using a scalpel to create an opening for a lead and cap to be inserted into, allowing a thin drill to drill deep into the patient's brain. Finally, an electr

 This past week, I began working on a data analysis project focused on differentiating inflammatory from non-inflammatory breast cancer utilizing a liquid biopsy data set. Inflammatory breast cancer (IBC) is a rare, aggressive form of breast cancer (BC) that differs significantly from non-inflammatory BCs in presentation and prognosis. While rare in the general population, IBC is more prevalent in the Ashkenazi Jewish population (of which there is a very large population in NYC). This is partially because Ashkenazi Jewish people are much more likely (~1:40 as opposed to ~1:500 for general pop.) to have germline mutations (BRCA1 and BRCA2) that genetically predispose them to developing more aggressive forms of cancer. However, in the clinic, we are seeing an increased number of patients with Ashkenazi Jewish heritage and IBC, without BRCA1 and BRCA2 mutations. Given that Dr. Cristofanilli employs a variety of liquid biopsy tests in the clinic, our lab has built a large, longitudinal dat

 7/15/2024 - 7/19/2024 The week started with clinicals. One of the patients had a skin graft. I had watched the operation where the patient received their skin graft. The patient was seeing Dr. Spector for their weekly post-surgery follow-up. The patient came in concerned that their skin graft had gotten infected because of how bad it looked. When Dr. Spector checked the graft, he explained that its condition was due to the accumulation of scabs. The graft was in an area that was difficult to clean and had likely not been properly cleaned since the surgery. We also visited a patient in the SICU. This patient had undergone major surgery that required collaboration among multiple surgical teams. While visiting, we saw the result of Dr. Spector's involvement. The patient had a huge flap attached to their body. Dr. Spector explained that the flap would naturally decrease in size over time and would not remain as bulky as it currently was. This was my first time seeing a patient initial

For the femoral head project, I primarily worked on CT image processing and analysis of the femurs, both in their native state and after our testing (including simulating a subchondral bone fracture and performing impaction grafting to repair). One of our desired outcomes for the study is bone density, measured in hounsfield units (HU) both of the native bone and of the fracture/graft region. Higher density in the fracture volume is likely due to improved packing of the graft, i.e. reducing space between grafted osteopearl beads, and may indicate better mechanical strength. This week, I finalized the methodology for calculating HU of the graft region and will be performing the analysis on our 14 samples during our final immersion term week. In short, the image processing methodology involves selecting the defect volume as an ROI, obtaining the average pixel intensity over that region, then performing a linear transform from pixel intensity to HU—using the rescale slope and intercept fr

 Week 7 Summary On Monday I attended a talk presented by Dr. Manuel Esteller on cancer epigenetics and its applications on cancer prediction and diagnosis. He introduced epigenetic hallmarks of cancers. For example, I learned that epigenetic loss of miA ALKBH3 generally leads to poor survival, while NSUN5 epigenetic loss leads to longer overall survival after cancer. Dr. Esteller also discussed his interesting findings on the world longest living person alive, Maria Branyas. The average biological age of her body was much younger than her actual chronological age. In the lab, I helped look into different mast cell knockout mice models to help plan for an experiment. On Tuesday, I helped with the preparation steps for a flow cytometry experiment planned on Wednesday. We collected mice talk skin cells from wild type, PTEN ko, and PI3K ko mice. We stained for macrophages, T cells, LEC, and fibroblasts. The cells were fixed for flow cytometry the next day. On Wednesday, we used the equipme

 This week was spent finalizing some of the literature review I did, and creating my final presentation. I will be presenting on what I learned about this condition clinically, and on some of the background work I did for doing some preclinical investigation back in Ithaca. I also took a brief trip upstate to buy a car, which was successful! Additionally, Anna and I got to shadow an open heart surgery in the OR on Thursday. We got in early to meet Dr. Joshua Goldberg before he started the case, and he and his fellow gave us an intro to the OR (where to stand, who to talk to, etc.), and the case they were doing. The case was a full aortic arch replacement to treat an aortic aneurism proximal to a previously placed bovine aortic graft. The patient's previous surgery presented some difficulty in opening the chest, but it went smoothly. Once the patient was put on cardiopulmonary bypass, the aortic arch was removed, and the new graft was placed. This involved suturing the graft to the

 This week I went to the OR on Monday and Thursday to watch surgeries. On Monday, I saw an endarterectomy on the left carotid artery. The surgeons opened up the left carotid artery of the patient and removed as much of the calcified plaque from the artery wall as they can. The srub tech kindly showed us the plaque samples from the patient. Some of those are already hardened while others being soft and gelatin like. All the plaques are at a decent size where they are blocking the blood flow in the artery. The process of opening up the left carotid artery is really interesting. After doing the incision and preparing the surgery site to expose the artery, the surgeons applied clamps on both sides of the plaque position of the artery to stop the blood flow. The surgeon told us that this clamp can only be on there for at max 45 mins, or the left hemisphere of the brain will start of suffer from the lack of fresh blood supply. To mitigate this lost of the blood supply, the surgeon asked the

This week I was able to get access to Epic in order to access patient health information for the whole genome study. Using the data I merged last week, I was able to copy over MRI results for patients with MYBPC3 mutations in order to combine the results and look for trends in both the structural and functional results. I was then able to combine these results into my presentation about my research on Tuesday. I was also able to see an open heart surgery with Dr. Goldberg, a cardiothoracic surgeon. This surgery was an aortic aneurism repair and involved placing the patient on bypass, removing the aortic arch and the major vessels extending outwards, and then sewing in a graft into the missing places. After each aspect of the graft was attached, the blood flow was restored to that section and Dr. Goldberg searched for leaks. Once all of the sections were attached, blood flow was restored to the heart and chest tubes were inserted to monitor air and fluid buildup in the chest area post o

This week was filled with wrapping up and finalizing research and presentations. I gave both the summer immersion presentation this week as well as a high level quarterly review to a sponsoring company about how the research I'm doing in Dr. Spector's lab connects to the developed technology. In lab I helped India as an extra pair of hands to finalize the bioprinter assembly. On the clinical side, we went to Dr. Spector's clinic hours and observed some patients. One patient was there for a pre-op appointment for a top eyelid removal surgery to reduce the "hooded" eyelid as well as the removal of the fat in the under eye bags. It was interesting to see Dr. Spector talk about the consent form to obtain the special fat from under the eye to use in research and the questions that the patient had about that. Another patient was there for a consult about a very large hernia that they had. We learned that large hernias a more "safe" than small ones, because sma

Week 7 July 15-19 I was mainly in the lab this week continuing to analyze cardiac MRI images to quantify the extracellular volume. I have also been tasked with a smaller project of obtaining the number of cardiac MRI scans patients have undergone, and recording that into our database. I hope to finish both projects by the end of next week. In the meantime, I will be presenting my clinical project to my peers on Tuesday during our weekly seminars, and will start on the term paper due at the start of next semester. This week, I also got the chance to read some carotid ultrasound data with Dr. Narula during her training session with her fellows. I learned some basic vascular anatomy of the chest and next, and how to review images sent by ultrasound technicians. Next week I hope to shadow one or two more clinical cases. 

Dr. Catherine Ly and Dr. Spector presented in this week's didactic meetings. Dr. Catherine Ly is associated with NYPW and has been tasked to build free flaps into the plastic surgery practice up there. She mentioned that it was challenging to start this project from the ground up due to NYPW having no recent memory of free flaps, limited plastic surgery exposure, having no SICU (only an ICU), no residents, and the fact that the OR set up wasn't optimal. Surgical instruments that were standard at her previous locations needed to be factored in-- along with working the team of nurses to prep the OR for microsurgery. She then went into two cases she saw: 1) breast reconstruction after patient dissatisfaction with asymmetry following a DIEP-breast implant procedure, and 2) a lower extremity reconstruction for a foot injury with bone exposure.  Dr. Spector presented on his work with scleroderma patients and reconstructive surgery. He talked about cases where these patients often hav

 This week I spent more time working on my research project. Our device went through several revisions after further consultation and realizations that getting the device to stay in place would be more difficult than expected. I also began running fluid flow simulations mimicking the heart environment in order to determine how the device will react to and influence the blood flow once in position.  I also spent more time shadowing in the catheter lab. I got to witness another TAVR procedure. This time however they interventionist used a different brand heart valve. This valve requires a balloon dilation before the placement of the valve and was designed to meet the needs of the larger patient. After the unique prep they deployed the valve similar to how any other valve is used. It was interesting to see how every company has their own specification when they design valves, and how each variation can fit different patients batter than others. Especially when designing devices this has m

 This week, I observed a carotid endarterectomy, where the surgeons opened the patient's carotid artery to remove plaque build-up. First, the surgeons had to push aside the surrounding structures to create a clear view of the carotid. Once they were ready to occlude the vessel they had the anesthesiologist increase the patient's blood pressure to help compensate and increase blood profusion to the brain and the rest of the the head from other vessels. Once occluded the surgeons had about 45 minutes to work comfortably before there was an increased risk of stroke. To open the carotid, the surgeons first made a small incision into the wall and then used a special pair of scissors to lengthen the cut. Once open, the surgeons began carefully scraping the vessel's walls to remove the plaque, careful not to damage the rest of the opposite wall. The plaque was stiff and had calcified portions that crumbled when scrapped. Once they had finished, they began carefully sewing up the v

 This week stared with me observing some total hip replacements Monday morning. In the afternoon I was finalizing my slides for the final presentation. Tuesday was the day of the presentation. After the presentation i went to the clinic to work with Dr. Bostrom in see patients and plan the surgeries that would take place in the future. On Wednesday I spent time in the lab writing a review about the efficacy of resurfacing the patella vs. keeping the native patella. This review looked at how resurfacing the patella during a total knee replacement can impact the quality of life for patients. Thursday was an interesting day because it started with a meeting with the design engineering team for custom implants. During this meeting we met to talk about special cases and the approaches that will be taken to make implants for these patients. During the meeting Dr. Bostrom and the engineers both gave their thoughts on approaches to take and we had a productive meeting. This meeting was followe

 Last Friday, after I had posted my blog for the week, I spoke to Dr. Demaria about brining some organoids to Ithaca. She’s definitely interested in what our more mechanics-focused lab can do with patient-derived cells. We’ll have to work out some of the details, likely after the immersion term is over, but I’m really hoping to continue working with her lab. I feel so fortunate to have found a clinical mentor who fits my research interests so well and I would love for our labs to continue to collaborate in the long-term. One thing that I’ll have to work on if we do try to use organoids in Ithaca is figuring out how we’ll culture them. The experiment I’m doing right now is sort of an early exploration on whether the methods we use with tumor spheroids are compatible with patient-derived organoids. I was finally able to do the experiment I’ve been trying to get to for weeks on Wednesday. The collagen I ordered still hasn’t arrived in the mail and I can’t conduct the experiment I had pl

 On Monday, I watched a uterine fibroid embolization. The patient had 3 fibroids that needed to be blocked from receiving blood flow without blocking blood flow to the ovaries as the patient still wanted to maybe become pregnant. The anatomy was very difficult to navigate because the vasculature becomes tangled and coiled near the fibroids, so this procedure took a long time just to guide the wire into the correct vessel.  On Tuesday, I watched a pulse electric field ablation which is what my research project is based on. The needle sends electric field pulses into the lesion, causing pores to form in the cell membrane and the cytoplasm, proteins, and other innards begin leaking out. Combined with immunotherapy, this procedure can result in a non targeted effect where lesions that were not directed ablated are also attacked by the immune system. The dying cancer cells release antigens which result in a specific immune response. However, this response is only observed in 20% of patients

  07/15/24 - 07/19/24 Week 7: This week was particularly engaging and productive. I attended a presentation session on Tuesday where half of the students presented their summer projects. The diversity and depth of their work were remarkable, covering various aspects of medical research and technology. It was inspiring to see the innovative approaches and significant progress made by my peers. In addition to attending the presentations, I focused extensively on developing an AI model for cardiac amyloid. This involved working with several data modalities, including CT scans, ECG data, ECHO data and other meta information. I conducted numerous experiments, tweaking the model parameters and incorporating different feature extraction techniques to optimize the performance. The results were promising, indicating that the model has the potential to accurately detect and analyze cardiac amyloid. To further improve the model, I plan to run additional experiments, exploring advanced algorithms

 I got my hands on some new patient data this week. The smoking history data is still being compiled, so I'm seeing what a neural network can do trying to predict brain metastasis from other diagnoses. At first the results were suspiciously high, but after removing the BM diagnoses from the training dataset, it performed well (85.5%) and reached the benchmark for clinical relevance (70%). I also worked on making the figures for my final presentation!

 I spent most of this week reading, focused on vascular contributions to pulmonary hypertension. While I am focused primarily on the microvasculature, I am also looking at some literature looking at pulmonary arterial remodeling in PH. While there are some structural and functional differences between these vessels, I think there is enough overlap to make understanding arterial pathophysiology important for this project.  Arterial-associated PH involves pathological remodeling of the pulmonary arteries, increasing vascular resistance and pulmonary arterial pressure. This remodeling involves all layers of the artery, although the exact progression is unknown. Pulmonary arteries consist of 3 primary layers: the intima, which consists primarily of an endothelial cell barrier; the media which consists of vascular smooth muscle cells; and the adventitia, which consists of fibroblasts. Remodeling of these layers can result in cellular hyperproliferation and phenotypic changes, as well as cha

This week, I spent the majority of my week focused on my research project. I first did a QuBit assay on my Mtb gDNA samples to get a better estimate of their concentration and quality than Nanodrop before I submitted them for sequencing. After preparing my samples, I submitted them for sequencing to Plasmidsaurus and was able to get the data back for these within a day! I then spent the rest of the week on extracting gDNA from the second batch of samples and also analyzing the sequencing results. Interestingly, none of the samples I submitted had the S531L mutation which is by far the most common mutation in Mtb clinical isolates. The SNPs that my samples had in rpoB were also outside of the rifampicin-resistance determining region. 

This week I continued to shadow laboratory work, while gearing up for my final immersion presentation. I learned how to use imaging software to analyze relevant tendon tissue, identified different cell types in tendon, and read about different immunohistochemistry analysis metrics. I also helped members of the Rodeo lab analyze some slides, and discussed dissection methods we use in Ithaca to help students that haven't studied the patellar tendon. It's been really interesting to see how the Rodeo lab assesses tendon health, and I've learned a lot of new methods that I can translate to my research back in Ithaca.  This week, I also learned more about the yes-associated protein tendon inhibition study I have been primarily focused on. Specifically, the initial experimental RNA sequencing results for tendon constructs strained at 4% were analyzed and new experimental plans were mapped out based on those results. I am excited to see the in vitro tendon constructs develop over t

 This week was one focused more in the lab. I was finalizing the annotations for the slides that I had scanned to train an AI model. I met with Dr. Richard Bell, a post-doc in the lab, and we spoke about what the next steps would be. The first step would be to attempt to modify the current model. This is the first step because there are tissue types that the original model was able to distinguish very well so attempting to train the model on the other tissue types could work. Another approach would be to create a whole new model that will only segments the tissues that I have annotated and run it in parallel with the current model and only make the outputs the tissues i want from the better models. This would allow for the current best of both models to be incorporated in the final result. With the two possible approach we will try them the following week and see which one works better. After this is done we will start to implement the grading of the cartilage damage. With these steps

 This week was again filled with mouse surgeries as Shane and I push to complete AAV-injected, fiber optic implantation samples in the female and male mouse cohorts. Each mouse requires an AAV injection to the prefrontal cortex of either CamKII-GFP (Control group) or CamKII-Chronos (Stimulus group), followed by a fiber optic implant to the injection site and a head plate attachment to the skull for future head-fixed behavior assays. We were able to complete 20 surgeries, while also performing the first few days of novelty-induced hypophagia (NIH) on a separate mouse cohort.  The first few days of NIH involve numerous days of handling to allow the mouse to adjust to the experimenter. Handling is used to minimize unintentional stress artifacts by familiarizing the mouse with the handler. Naturally, any behavioral assay will possess handler stress artifacts due to the natural stress that comes with animal work, but our goal is to at least mitigate the size of said artifact. The following

 This past week I spent more time working in the heart catheterization lab watching valve replacements. This week involved some very interesting cases that brought to light some challenges that would be worth looking into in the future for device development work. The one case that really stood out was for a younger patient with aortic valve issues. In older patients the issue would be resolved by simply replacing the valve with a trans catheter prosthetic but in this situation that would be pretty difficult. Since the patient was younger their valve had very little calcium buildup. The failure of the valve was due to congenital malformations instead of stenosis. The lack of calcium meant the valve prosthetic would have less friction to stay in place over time and simply putting a normal valve in would not last. The doctors found a creative solution to this by over sizing a valve and creating ways for a new valve to grip onto the area. This was an interesting way to solve the problem a

 This week, I have tried to shift my focus more towards research while maintaining the amount of OR and clinic experience. I went to OR and clinic to shadow surgery and patient seeing for the first half of the day, and then went to lab to do experiments for the second half. On Wednesday, I was able to see a ventriculoperitoneal shunt replacement followed by a right endoscopic craniopharyngioma resection. On Thursday morning, I went in to Dr. Schwartz surgery in which they were doing a right endoscopic intraventricular tumor biopsy. As the tumor is in the ventricle, the surgeon needed to go though the cortex to access the tumor. While only a tiny hole is made on the skull and the cortex for the endoscope to go in and for it to be less invasive, there were a really limited field of view and a limited room for operation. Surgeons were able to locate the tumor and get a few samples from it. However, a blood vessel near the tumor site ruptures and leads to bleeding into the ventricle space.

For the femoral head impaction grafting project, I began writing methods, results, and some discussion for the manuscript we intend to submit for publication. My parts of this so far include detailing the compressive loading process and subsequent mechanical analysis, such as how we calculated defect region moduli or linear displacement at 800 N, the 3D scanning process and subsequent volumetric analysis of defect volumes, and then the corresponding results. These included toe-region and linear region moduli for the fracture, linear displacement at 800N, and defect and raised volumes at various stages throughout testing—all of these also included a paired t-test analysis comparing each fracture before and after grafting. I began generating figures for this paper, some of which are included below. In order, these show a 3D reconstruction of the Osteopearl graft beads inside the subchondral fracture volume, the linear displacement at 800N before and after grafting, and the fracture's

 Most of this week I was out with Covid. I was really sick, so I wasn’t able to get much done. I did however do some literature searches for Dr. Mcclure’s localized prostate delivery idea and sent him an email with some useful papers and ideas on how to get started.  On Friday, I went back to the hospital and shadowed some procedures with Dr. Pua. He was implementing Mediview’s AR goggles for a biopsy and 2 sclerotherapies for vascular malformations in the limbs. The first procedure ended up being a laparoscopic surgery procedure with Dr. Milsom, but the AR goggles did help to overlay the ultrasound image to guide the initial placement of the ports. The second case was a vascular malformation on the forearm. Due to the setup of the equipment in the room, the image overlay was obstructed, so we weren’t able to use the goggles. The third case is a vascular malformation in the knee, so hopefully we’re able to use the AR headset for that. Here’s a phot of Dr. Pua wearing the headset. 

 My work in the lab this week focused on developing 3D designs and models of custom bioprinter parts. I verified that the parts fit together using my technical drawings and printed them using the lab's 3D printer. I then assembled the printed parts and the hardware parts that I previously ordered. I am still waiting for a few parts to arrive and then I can finish the hardware assembly. Additionally, I attended Dr. Spector's clinic hours with Julia where we observed a variety of consultations and follow ups. These included a post-op follow ups for a tummy tuck, several skin grafts, a patient with calcinosis, and a patient with a jaw reconstruction who was bothered by hair growing in his mouth from the leg flap that had been used for reconstruction.

This week I went in to shadow Dr. Daniel Lu who is an advanced heart failure physician. We saw patients with ischemic heart failure and many of them had this caused or worsened by poorly managed diabetes. I learned that with poor management of diabetes, a patient's blood vessels can stiffen, increasing blood pressure and putting strain on the heart. Dr. Lu often refers patients to endocrinologists for their diabetes management, and nephrologists for kidney function monitoring. I also learned that there is a team of doctors called the "Centralized Heart Failure" team and they will call in to patients at home a few times a week to request their blood pressure and weight measurements. They will then be able to adjust their medications according to any fluctuations in these numbers without the patients having to come into the clinic.  I also worked some more on my research project with the Cardiology Whole Genome study. I searched for patients that we have genetic testing res

In this week's didactic meetings, Dr. Jacoby presented information on hand calls for emergencies and splinting. Dr. Jacoby specializes in taking care of everything below the elbow, ranging from radius and carpal fractures to nerve and soft tissue injuries. He mentioned that every consult gets an x-ray, all infections get labs, and all flexor tendon and digit nerve injuries get Doppler exams. If the injury is not an emergency the Green's textbook on hand surgery apparently has all the answers. He then went on to discuss interesting cases, like Neonatal Forearm Compartment Syndrome, flexor synovitis, and paint injection injury. Overall, it was interesting hearing about the various ways a hand can get injured and the methods to treat them.  In clinic this week, Dr. Spector followed up on a post-op septoplasty patient, who I saw last week in the OR. It was fascinating to see how swollen the nose appeared, but Dr. Spector assured the patient that all the swelling was going away.  In

Week 6 July 8-12 I spent my time this week in the lab and in the OR. I observed a skin graft retrieval from the upper right thigh. The graft was used to reconstruct the upper left arm after amputation. The operation was split into two teams. One team focused on the debridement of the left arm, the other team focused on the skin grafts on the right leg. The doctors used an electric blade to retrieve the skin grafts. It looked like a large razor that had one blade. The blade was pressed down to the skin at an angle to shave off some layers of skin. The graft had a rectangular shape and was quickly put into solution to keep it hydrated. From my position in the OR, I was not able to see the debridement of the amputation site or the tissue transfer.  The rest of my time was spent in the lab where I am still continuing on quantifying the extracellular volume of cardiac MRI data. Next week I hope to spend more time in the lab and shadow in the Electrophysiology lab. I will also be preparing a