Week 4: MJ

This week, I attended the immersion weekly meetings, where Dr. Mert Sabuncu discussed his research on using AI in radiology. He discussed various algorithms and their progress as well as hopes that these models can be used to diagnose patient cases. I also attended rheumatology journal club, where a paper published the statistics of in/out of network claims and denials. They found that there were over 71 million denials and the most common reason for these denials was "other". The other paper discussed at this journal club studied features of myositis and myasthenia gravis in patients treated with immune checkpoint inhibitors. In the clinic, I shadowed Dr. Fernandez as he saw a wide variety of patients with myositis, lupus, and various connective tissue disorders. One particularly interesting patient was a young patient with a severe case of necrotizing myositis. Dr. Fernandez recommended that he consider CAR-T therapy, which has shown promise in cancers and is not being considered in other immune-related diseases. In the lab, I continued to work on analyzing bulk RNA-sequencing data from cells with specific gene knock-outs that may contribute to disease phenotypes in inclusion body myositis. 

Week 4 : Adil

 This week I was mostly in the lab. I spent time analyzing bulk RNA datasets and selecting samples/datasets suitable for downstream analyses from the ICSBCS biobank. I also compiled the information available on WGS datasets of these samples. The next steps involve selecting samples and datasets best suitable for cross comparison of tumor information from the ICSBCS biobank based on the information from WGS, RNAseq and metadata.

I also attended the MDC tumor board earlier this week. This week's cases ranged from new patients to patients who already had surgeries and were undergoing post operative care. Discussions mostly involved treatment plans coming from surgical oncologists and medical oncologists. Later in the week I attended a presentation by a sub-intern working with Dr. Newman on the key features of breast cancer. We discussed the anatomy, current best practices for diagnosis including breast self exam, best practices in breast cancer care and factors involved in decision making for breast cancer surgery. I also attended a didactic session conducted by Dr. Newman on Inflammatory Breast Cancer (IBC). She discussed the background, diagnosis methods and current treatments available for IBC. It was interesting to learn despite advances in breast cancer care so little is known about IBC. 

Week 4: Aidan

 This week I dove into the world of magnetogenetics and Halbach arrays. Dr. Kaplitt is away, so I've been shadowing his post doc who is studying treatments for pain via magnetogenetics. Magnetogenetics in a nutshell is delivering a magnetic field sensitive transmembrane protein to a target nerve population (i.e., the dorsal root ganglion of the spine or the sciatic nerve) via a viral injection (i.e., Adeno-associated virus) to reduce pain or stimulate activity with external magnetic fields. The transmembrane construct that is currently being used (there are both inhibitory and excitatory versions) uses TRPV1 as the main structure (transmembrane protein found on pain receptors and detects capsaicin, which is what I worked with in the Daniel lab). It also has a region that binds to ferritin, a derivative of iron the body produces endogenously. In response to external magnetic fields, torque is applied to the ferritin tags, opening the TRVP1 transmembrane channel and either flooding Ca2+ or Cl- (depending on inhibitory/excitatory version of the construct). 

So far, this has mostly been performed using MRI to apply a strong and moving magnetic field. However, it would be very useful to be able to perform the behavior experiments without the need for the MRI, such as imaging the DRG. This week I have been leveraging the "engineer" half of biomedical engineer, and researching all things magnets so that I can build a benchtop device that can apply a magnetic field to a mouse. Initially I was looking at Helmholtz coils, but after scaling up to the necessary magnetic field strength and size dimensions, my simulations were suggesting a current draw that would cause significant heating and require a complicated cooling solution. Currently, I'm looking into the idea of Halbach arrays - which are arrangements of polar magnets such that their poles rotate causing constructive interference in one direction and destructive interference in the other. Magnets resist being in this orientation, so I have designed a part for 3D printing that I can press-fit the magnets into while building the array. This coming week I will be ordering/building the device, and the following week we can test out its effectiveness via the Von Frey test. 

Week 4 Meichi

This week, I had the privilege of attending a lecture held by Dr. Newman, where we focused on inflammatory breast cancer (IBC). It was a comprehensive session that provided new insights into the pathophysiology, diagnosis, and treatment of this aggressive form of breast cancer. What stood out to me was the emphasis on personalized treatment plans for IBC patients. The lecture explored the role of neoadjuvant therapy—chemotherapy or hormone therapy given before surgery—to shrink the tumor and improve surgical outcomes. 

We also talked about the history of self assessment of breast cancer in the lecture. While BSEs were initially promoted as a key tool for early detection, the scientific community has since debated their effectiveness. This led to discussions about the limitations of self-assessment and how medical advancements, such as mammography and ultrasound imaging, have taken a more prominent role in breast cancer detection over the years.

Week 4: Arina

 This week included our first hands-on sessions with the two-photon microscope after doing cranial window surgeries. We’re preparing to begin actual data collection from our experimental mice over the next two weeks, and, as we were waiting for the virus, we imaged the practice mice. The Liston Lab setup is slightly different from the one i used back in Ithaca, so it was interesting to see how it works. In addition, in preparation for the data we’ll soon be generating (as long as the imaging quality in experimental mice is acceptable), we also began looking at the analysis pipeline for the calcium imaging videos that we will get. 

On the clinical side, we had the chance to visit Dr. Liston’s TMS clinic. The lab currently has an ongoing clinical trial , so we got to learn more about it. The clinic works with individuals who have treatment-resistant depression, beginning with a psychiatric evaluation to assess their symptoms. Then, depending on their assigned protocol, patients receive transcranial magnetic stimulation in frequent sessions. After completing the course of stimulation, they’re re-assessed to track any changes in symptoms. The success rate of this procedure is about 50%, which I found to be promising, especially in the case of medication-resistent depression. 

Week 4: Teagan

This week, I made good progress on my research project. My project is to make a 3D-printed mouse holder for Faxitron imaging. I obtained a base structure from the Rodeo Lab at HSS and modified it for the amputated mice that are used in the Bostrom Lab to explore the potential of bone regeneration. To do this, I brainstormed structural design ideas with Dr. Yang and Dr. Chen and edited the original structure on Fusion 360 software. I was then able to 3D print my design on the Ultimaker printer in the lab; it took ~4.5 hours to print the structure. The next steps for this design process are to connect all of the components and give it to other members of the lab to image with to test the consistency of the imaging orientation with the device, compared to without the device. I will likely have to use an iterative design process to find the right dimensions and structure for the lab's needs.

This week in the OR was a little slow because there were some surgery cancellations, but I got to watch two total hip replacements. For these surgeries, the plastic shields were not utilized to create a physical sterile zone, so I was able to get a much better view into the hip cavity to observe what Dr. Bostrom was doing. This allowed me to gain a new appreciation for the surgery and better see the similarities between knee and hip replacements. I also went to a couple of talks this week, one at HSS titled The Role of Subchondral Bone in Osteoarthritis Development, which relates to the work the van der Meulen lab does back in Ithaca. As well as the talk by Dr. Denise Howard, who is an obstetrician, who discussed some of the challenges that remain in women's healthcare. 

Week 4: Eleana

This week was very eventful. Over the weekend, I made some biocompatible hydrogels from Alginate in Ithaca and carefully transferred them back to Weil. On Monday, I then functionalized the hydrogels with two antibodies anti-CD3 and anti-CD28. These antibodies are required for T-cell activation and proliferation. Tuesday, we started with a T-cell extraction from the spleen and lymph node extraction from mice. We then isolated our cells, purified them to only have T-cells that expressed CD8+ and plated them on hydrogels. The activation takes three days, during this time they are seated on the gel and on an oscillating shaker to provide mechanical forces during activation which T-cells prefer. During this waiting period, I passaged SB28 glioblastoma cells and let them grow in culture. I transferred them to a plate that would be able to fit within the irradiator. We also had the ability to go to a conference where two people presented their work on prostate cancer and cancer organoids with immunotherapy. It was a very insightful conference and some work was heavily genetic focused while others were focused on the treatment and immunotherapy side. On Thursday and Friday we went back to pathology. During this time in pathology, we saw many patient cases with DCIS (ductal carcinoma in situ) and LCIS (lobular carcinoma in situ). In many patients it was very difficult to tell the origin, that is why pathologists also perform an E-cadherin stain to differentiate the two. There was a classical example of LCIS which looked similar to what I was studying in the textbook and I was happy that I was able to identify the type. Throughout the weeks I have been studying the histologic and pathological differences of the breast cancer subtypes those that are benign and and malignant. I have noticed in an improvement the more I look at the slides to identify atypical features within the tissue. Friday we began irradiation of gliblastoma cells with co-culture of T-cells which was an all day process. We wanted to irradiate the SB28 cells and co-culture them with T-cells to see if the gels were able to prevent T-cell exhaustion as compared to no gels. We will confirm these results next week after co-culture is complete and with flow cytometry.

Week 4: Kirtana

 This week, I worked on annotating abdominal MRIs as part of my clinical mentor's research. I also attended a talk on "Disruptive Research for Women's Health" by Dr. Denise Howard. I found the talk very insightful as my research in Ithaca is based on point of care devices for women's health. I got a few ideas on how to progress with my research after that talk.

For my lung cancer project, I worked on developing the code for Table 1 of the paper. This table includes baseline characteristics of the study cohort as well as parameters used in the PLCO model. Next week, I will be working with Dr. Choi on running the PLCO model on our data as well as constructing a new model based on the incidence of lung cancer by state in India. This week was a good insight into areas of improvement for my coding skills in R. I am hoping that I will be able to achieve this goal through the course of the lung cancer project. 

Week 4: Ben

Today, I started formulating ideas on what research project I should do as part of the Immersion Term program requirement. Because my thesis project involves investigating the crosstalk between pancreatic islets and vasculature, I wanted to see if co-culturing the two in a 3D context alters the function of the islets. With that, my plan is to isolate islets from mice, disassociate them, and re-aggregate them with different densities of human umbilical vein endothelial cells (HUVEC). Endothelial cells secrete out basement membrane components such as laminin and collagen IV that directly interact with the pathways that mediate glucose response and insulin secretion function of islets. That being said, I am hypothesizing that by increasing the cellular density of the HUVECs in these re-aggregated islets will bolster the insulin secretion capacity, which I will measure using glucose stimulated insulin secretion (GSIS). In order to execute this experiment, I am currently coordinating with Dr. Shahin Rafii's research group so that I can use their HUVEC reserves and with the Alonso lab so I can source mice that I can extract islets from.

This week, I wanted to expand on my clinical experiences, so I shadowed in the urology department. Here, I observed a prostatectomy and a cystectomy, which is a full prostate and bladder removal, respectfully. In both cases, there were cancerous lesions. With the prostatectomy, the prostate and the urinary tract were removed, so the urinary tract from the bottom of the bladder and the urethra had to be stitched together. For the cystectomy, the bladder, prostate, and ureters connected to the two kidneys were removed. In this case, the ureters were funneled to an external bag that acted as a bladder, in which urine is collected. In addition, lymph nodes were collected to test if the cancers in the two cases were metastatic, but there was doubt it would be given both cases were early stage. One thing that was cool to see about these surgeries was that they both were robot-assisted using the DaVinci robotic surgery system. It was really cool to see it in action, and I learned that it has revolutionized performing urology surgery, as previously, surgeons would poke holes into the abdomen and thread materials through these holes, which has lots of room for error and would make these surgeries extremely long. Robotics has sped up this process, and made these kind of surgeries efficient to perform.

Moving to next week, I will move forth with my experimental plan, and also try to see if I can get into bariatric surgeries so that I can compare the different clinics that I had observed.

Week 4: Anuj

 This was another interesting week with a few robotic surgeries shadowing, a few cystoscopy visualizations, and more progress on the wide-view cystoscope tip design. A new surgery that I watched was a partial nephrectomy, where a part of the kidney with a tumor was removed. The tumor measured roughly 3cm in diameter, and only this part was dissected, so that approximately 95% of the kidney volume was still left intact and unharmed after the surgery. Another surgery involved prostate removal due to tumor growth. While dissecting the prostate from the bladder side, some tissue was removed and sent to pathology during the surgery. After approximately 30 minutes, while the other end of the prostate connected with the urethra was being cut, the results from the pathology came back positive for sarcoma. This allowed the surgeons to remove more of the bladder mass to get rid of the cancerous area. Confirming the presence of cancer margin spread during the surgery within 30 minutes is fascinating, as it prevents future cancer removal surgeries and gives more confidence in full tumor removal from the patient's body. However, this is another opportunity for developing imaging tools that could potentially scan the tissue/glands/organ surface during the surgery for cancer clusters or cells in high-resolution, so that the cancer removal can be more real-time. For the wide-view cystoscopy project, I worked on some theory to check the working mechanism of the helical scanning system. Some parts arrived, and the other parts are being 3D printed; therefore, I am excited to test the prototype next week. 

Week 4- Zuzanna

This week I shadowed in clinic and it was a little more busy than previous weeks so it was interesting to see a wider range of patients. I saw patients who were finishing up therapies, and also patients who needed to switch to another one due to their circumstances. I learned its quite hard to treat immunocompromised patients, like those with transplants and immunosuppressents, especially using a lot of systemic cancer treatments like immunotherapy, as it can have extra side effects relating to that immunosuppression. I also saw a partial nephrectomy, where a tumor was removed off a kidney. It's interesting that one can function without an entire kidney. Additionally, I was able to observe a robotic prostatectomy which was very interesting as I did not realize how huge the robot is. The actual robotic surgical tools are tiny, and its crazy how much they are able to maneuver inside a patient with the few small incisions needed to place the tools. Watching everything on a screen was fascinating as they were inside the patient with a camera, and I could barely see the patient under that robot, but could see all the details of the maneuvers.

In lab I have further been working on methods to image an organoid system, and also doing some research on an in vitro model to improve Tcell survival, as Tcells usually cannot survive for longer than 2 weeks in vitro, but our lab has some longer treatment models of interest.

Week 4: Adam

 This week I spent a lot of time shadowing in the clinic. I learned about burns and the recovery process on Monday, and also shadowed the closure of a spinal surgery site. Then, on Tuesday, I watched a fibula free flap mandible reconstruction for a squamous cell carcinoma patient. The surgical teams used virtual surgical planning to build a new jaw for the patient using their fibula bone. The most surprising part of the procedure is that they did nothing to add support back to the missing region of the fibula. Apparently, most people don't experience a change in their quality of life after losing a large piece of that particular bone. I watched two skin grafts as well. In the lab, I practiced H&E some more, learned how to mount slides into flow cells for automated immunofluorescence imaging, and also started practicing another immunofluorescent imaging technique using primary and secondary antibody stains. We also started a protocol to isolate collagen from rat tails, which is much more cost effective than purchasing collagen in bulk. 

Week 4: Nina

This week, I watched a liver cyst resection and a liver biopsy robot-assisted surgery. I learned that some of the complications using robot-assisted surgery are the angles by which the arms move/rotate in vivo and limitations by camera angle/direction of the probe. I realized that, while the use of multiple ports allows for more mobility of the tools, it can require some time to figure out what the best orientation is for each surgical function. I also went to Dr. Samstein's clinic on Thursday where I saw patients with cirrhotic livers and varying stages of liver disease. I have been continuing my review on normothermic machine perfusion of livers through reading current articles on immune cell sequencing and metabolic readouts at the cellular level. In the next coming weeks, I hope to make more progress on logistical side for project approval.

Week 4: Orren Shachaf

This week, I attended multiple seminars: Role of Subchondral Bone in Osteoarthritis Development (Dr. Marjolein van der Meulen), Salt Inducible Kinase (SIK) inhibition in mice with long bone fractures (Dr. Mark Bubnovich), and Metabolic Regulation of Muscle Regeneration (Dr. Shihuan Kuang). Additionally, I made some progress on my research—I finally received sectioned samples of human patients from ACL reconstruction, total knee arthroplasty, or total knee arthroplasty revision, which I will be using to study the correlation between patient stiffness, fibrosis, and cellular senescence. I was able to stain the samples with H&E, and will be using a slide scanner (which I got trained on this week!) to image all of the slides next week. Further, I confirmed that my IHC protocol for staining uPAR (a marker of senescence) works on mouse knees, meaning that, once I order and receive an antibody for human uPAR (since there isn’t much cross-reaction between human and mouse uPAR), I will be able to stain the human patient samples. Lastly, I observed an arthroscopic hip surgery with Dr. Stephanie Buza—I am definitely a bigger fan of arthroscopic surgeries compared to open surgeries, since both the blood and smell are a little overwhelming with open surgeries, so this was an awesome experience to see another surgeon operate.

Week 4: Allison

 This week, Eleana and I have started our experiments to investigate the relationship between T cell mechanosensing and susceptibility to radiation-induced exhaustion. Earlier this week, we extracted T cells from mouse spleens and lymph nodes and performed a 3 day activation process. Today, we irradiated glioblastoma cells and are coculturing them with the activated T cells over the weekend. We have also been preparing hydrogels for our experiment next week that will look at the direct impact of radiation on T cell survival and exhaustion and how this is modulated by activating T cells on different substrates, rather than looking at the indirect impacts through coculture with irradiated cancer cells.

I was able to attend the Meyer Cancer Center Basic Research Group Meeting this week and saw two talks that in general described how specific genetic changes in cancer can be targeted to provide personalized treatment in mouse and patient-derived organoid models of cancer. It was very interesting to compare more clinically-focused research seminars to the ones I have attended in Ithaca, specifically with the types of questions clinicians were asking the presenters to make sure the research considered generalizability and patient translation. I spent time Thursday and Friday shadowing in breast pathology and got to see the usual analysis of patient biopsies and lumpectomies. This week had some unusual cases, so it was very interesting to compare to what I saw last time I was shadowing and also to the images in histology/pathology textbooks. It again surprised me how heterogeneous breast tissue is, and how wildly different each case appears even for the same condition.

Week 4: Amelia

This week we were able to practice imaging with the 2P microscope on our first cranial window surgeries, with the intention of imaging to collect data from our experimental mice next week and the week after. I have used 2P microscopes before, but this was my first time doing calcium imaging instead of structural imaging, which was cool to see. We also started working on code to analyze the calcium imaging video data once we have it - this was a new challenge for me, as R is not one of my strong suits. I was also able to tour the TMS (Transcranial Magnetic Stimulation) clinic that Dr. Liston has, which is in the middle of a clinical trial right now. Patients with treatment-resistant depression come in, and are evaluated by one of the psychiatrists to quantify their symptoms. Then, they are put on one of the TMS protocols, in which they receive the transcranial magnetic stimulation once an hour for several hours, so they spend a lot of time in the clinic. Some patients are on a shorter protocol, in which they come in every day for a week, and some a longer protocol. At the end of their TMS protocol, their depression symptoms are reevaluated by a psychiatrist. Some patients also get their EEG data taken before and after TMS, and getting to see the research grade EEG cap was very cool. 

Week 4: Joe

 I've been exploring a few other projects due to the microtome being out of order. Another student in the lab is working on a novel model of tendinopathy. The actual apparatus is shockingly similar to an amusement park's drop tower, with 8 capsules to be loaded with upright mice. The model itself is striving for clinical relevance with the mice essentially being forced to 'jump', generating similar strain and microdamage to athletes and the notorious 'jumper's knee'. I've begun writing some code to modulate how high the tower will rise before dropping based on weight, allowing for a tunable system that would exert the same force across differing sample sizes and mouse weight. I'm utilizing a simple height x weight x gravity equation, in which the weight is inputted by the user and height being a function of weight. I'm looking forward to implementing this code in the following week.

I have also began discussing a blood flow rate (BFR) occlusion model with Dr. Rodeo. Temporary BFR reduction has been shown to improve muscle and tendon remodeling under lower weights, making it ideal for recovering patients who cannot fully weightbear. Another interesting week!

Week 4: Peter

 This week has been pretty interesting. At the lab meeting for Dr. Roth's group on Monday, I got some further context for projects in the lab and got the ball rolling with the histology images. On Tuesday, Adam invited me to a surgery that Dr. Spector was working on. The patient had a squamous cell carcinoma that implicated a large portion of their lower jaw bone. Using some cool 3D printed titanium cutting guides, the plan was to take the patients fibula and reconstruct a jawbone. One thing that really surprised me is that they can just remove the midsection of the fibula, and without adding any extra hardware, the patient will be able to walk fairly normally. To ensure a speedy operation, Dr. Kutler, an ENT surgeon, was going to handle the removal of the jaw while Dr. Spector's team handled the fibula. However as he was working, he found the tumor involved the tongue so an oral surgeon was called in to assist in the total glossectomy. At this point, there were about 20 people in the room with about 15 of them being scrubbed in and actively working on the patient. By the time I left, they had the leg mostly patched back up and had finished the microsurgery in the jaw to reconnect the blood vessels. Overall, it made for a fascinating first surgery to observe. On Wednesday, I was able to zoom into the Hepatobiliary tumor board. While some of the details were definitely going over my head, it was cool to see the discussions between the doctors regarding each patient. I also was provide support for the injection of mice with cytotoxic T lymphocytes and getting the ears labeled on another batch of mice. On Thursday I saw the tumor injections into the mice that had their ears clipped the day prior. Assuming my cells behave, we will be doing flow next week. I'm also working on putting together a rough draft of the histology data to show at lab meeting.

Week 4: Hamilton

This week, I advanced my thesis research by developing a MATLAB simulation to model the release kinetics of a therapeutic peptide from a drug delivery vehicle. This peptide is currently used in both my home lab at Cornell and the host lab at HSS, so the model will serve as a critical tool to compare experimental data across sites and validate theoretical predictions.

Clinically, I observed several surgical procedures, including a robot-assisted total hip replacement using the MAKO system. This procedure integrates preoperative MRI imaging with intraoperative robotic guidance, enabling the system to restrict surgical tools if they deviate from the planned trajectory. The precision and safety offered by this technology reinforced the powerful role of engineering in modern surgical care.

Unfortunately, due to a mechanical issue with the microtome, I was unable to continue histological sample preparation this week. We are planning on sending some sample blocks up to Cornell to have them section slides for us.

Week 4: Brenda

This week I with Christina, one of the lab techs between Dr. Carli and Dr. Bostrom. We prepared screws that have biofilm on them for SEM at NYU. These are screws used on both hip and knee implants and we are trying to see the effects of different cleaning methods on removing biofilm from implant materials. Since the preparation and transportation to NYU took a while, I was not able to attend the clinic with Dr. Carli as per usual. I really enjoyed our weekly meeting given by Dr. Mert Sabuncu, as it is closely related to my PhD research back in Ithaca (in the way that it involves image segmentation and training models). I love the idea of translational research from anatomy to knowledge at different length scales. I learned so much about missing data and what to do, this is an area that I have been exposed to and now I understand an option of what to do. 

I attended the OR with Dr. Carli basically all day on Wednesday (6/25). Here is list of the surgical operations I saw:

1. total hip replacement - posterior left
2. replacement total hip - posterior - mako robotics right
3. arthrotomy knee osteochondral allograft with fresh articular cartilage left MFC
4. left hip replacement total hip posterior mako robotics

I got the see the implementation of mako robotics in the operating room, this technique is used in special cases where precision is required. Here is a definition of it: "Mako surgery involves using a Robotic Arm Interactive Orthopaedic System, known as RIO. This surgeon-controlled robotic arm helps surgeons get a patient-specific image and more precisely place and align the implants used in joint replacement surgery.". I always heard so much about this technique from fellow colleagues, but seeing it in person was amazing. The 3rd surgical operation was actually performed by Dr. Sabrina Strickland, my colleague (Salman) who collects the knees samples used in both of our PhD projects was actually picking up a sample and invited me to this operation. On Thursday I attended a talk given by Dr. Denise Howard on advancing woman's health. Throughout the rest of the day and on Friday I planned the rest of my experiments being done this summer. As I am working with bacteria, I need to plan out days to culture, seed, and clean my tibial base implants. 

Week 4: Anais

This week was a slower week since Dr. Fenster was out of town at the beginning.  Thus, I continued my literature search on pelvic pain and heavy menstrual bleeding and presented on the topic on Tuesday.  I then further read up on papers to ideate how to best improve and implement Dr.Fenster’s device. I also went to Dr.Howard’s seminar on Thursday, where I learned more about the current disparities in obstetrics and how research can help.  It was eye opening to see how the United States lags behind in terms of maternal health.  However, I was also glad to see that doctors like Dr.Howard were actively speaking about these topics and trying to change the system in order to deliver more equitable health care.  I hope I can further help bridge some of the gaps in women’s healthcare in my own research as well. On Friday, I observed an abdominal entrance myomectamy which was once again very interesting to see. This patient in particular had around 28 fibroids so the before and after was quite the stark comparison.

Week 4: Pei Wen

On Tuesday, I shadowed Dr. Fenster at the primary care clinic. As always, the interactions with patients were informative, offering me a glimpse into both doctor and patient experiences. While some of these moments manifest as emotional or frustrating, I continue to be inspired by how warmly Dr. Fenster and her team engage with patients and remain committed to delivering quality care. That same day, Anais and I presented our literature review findings to Dr. Fenster and Dr. Wolf. Our literature review turned out to be quite limited, as the questions we are trying to answer are rather specific. It was disappointing to see how little research exists in the field of women’s health, but this only reinforces the importance of our work and strengthens my motivation to continue. Consequently, Anais and I will focus on developing and refining a prototype for our project. Lastly, on Thursday, we attended Dr. Denise Howard’s talk, who spoke about health disparities and unmet needs in women’s healthcare. Her presentation was incredibly informative and inspiring, since many of the topics she discussed closely align with our research.

Week 4: Wendy Zimmerman

 Last Friday I got to see two reverse shoulder arthroplasties and an arthroscopic debridement in the shoulder done by Dr. Eliasberg. On Monday, I shadow the ultrasounds of mouse patellar tendon done to correlate the ultrasound measurements to histological analysis of tendon properties. On Tuesday, I did some work analyzing some of the RNA Seq data and attended the Research in Progress. On Wednesday, I shadowed Dr. Gulotta in his clinic and planned a shadowing experience next week, and later shadowed Dr. Rodeo in the clinic. Today, I attended lab meeting, an orthopedic talk given Dr. Shihuan Kuang on metabolic regulation of muscle regeneration, and performed RNA isolation on three samples monitored by a member of the lab. I also planned on which samples I will be isolating in the coming weeks and did more work, specifically, analyzing the pathways found in the RNA Seq comparisons using Enrichr-KG. Tomorrow, I will be shadowing Dr. Laura Moore in the OR in the morning, and in the afternoon I will be shadowing a clinic study using ultrasound with Dr. Eliasberg.

Week 3 : Adil

The third week started with attending the MDC tumor board. Doctors from different departments discussed breast cancer cases and came up with treatment plans for each case. One case was particularly interesting - a middle aged male patient was diagnosed with a tumoral mass in his chest. Doctors reviewed his imaging and radiology reports and finalized a seed localized lumpectomy as the treatment plan. Later in the week I shadowed Dr. Newman in the clincic for two patient sessions. These were new cases and Dr. Newman walked them through their treatment plan - localized lumpectomies followed by radiation therapy. I later shadowed Dr. Newman in the OR. I saw five surgeries - two mastectomies , one of which was followed by breast reconstruction and three lumpectomies. The lumpectomies were quite distinct from each other- first was direct removal of a hardened mass through a physical inspection of the breast, second was a seed localized lumpectomy and third was a wire localized bilateral lumpectomy. Finally I attended the 15th ICSBCS didactic lecture by Dr. Mark Robson. Dr. Robson discussed his recent work in treating breast cancers with high rates of genetic predisposition. In the lab, we finally pooled our samples and sent them for sequencing since the QC report for TCR library came back good. I also spent some time preprocessing tumor RNAseq datasets and prepping them for downstream analysis.

Week 3: Eleana

 This week was an eventful one. We started the week shadowing in neuropathology. We got a lesson in different types of brain cancer and anatomy of the brain. On Wednesday our experimental plan was approved and I began by making some alginate gels for our experiment that starts on Tuesday. I then try to autoclaved materials as well. I ended up having to go back to Ithaca to get some materials in order to properly do the experiment for next week. On Monday, I performed a craniotomy on a mouse and a brain dissection for practice. Lastly, I got to work with some imaging software called HALO, to segment some immunofluorescence histology and am working on a new module to segment histology images.

Week 3 - Arina

 This week, we finished working on surgeries for the cohort of our experimental mice. I’m glad I had the chance to do this: at this point I feel significantly more confident as a mouse surgeon than I did at the beginning of June. I also attended another lab meeting and got more context for one of the ongoing projects in the Liston lab. In addition to lab work, this week I got to see a clinical procedure. On Wednesday, I saw a MRI-guided focused ultrasound ablation. It was done in an Alzheimer’s patient to help stabilize tremors. It was remarkable to see just how significantly the patient’s control of motor function improved after. The precision is stunning too. I know that the brain region targeted in this procedure is adjacent to other important regions (e.g. speech-related), so the clinician has to be extra careful about not accidentally damaging those areas. Next week, I am looking forward to getting started on 2P imaging in the Liston lab, and hopefully getting to see some more clinical work. 

Week 3-Meichi

This week, I had the opportunity to engage in discussions with members of Dr. Newman’s lab about the details of the ongoing immersion projects. It was incredibly insightful to hear different perspectives on the project and explore what aspects of it could be particularly interesting and worthy of further investigation. The exchange of ideas with the team sparked new thoughts about the potential avenues for research and also how our my future research could contribute to a deeper understanding of breast cancer treatment.

I also attended the ICSBCS Breast Surgery Didactic Lecture. Dr. Mark Robson’s presentation on the management of women with a monogenic breast cancer predisposition was particularly fascinating. He shared statistical data comparing the effectiveness of different management strategies, providing a picture of how clinical guidelines are developed and tailored for individuals at higher risk for developing breast cancer. This lecture emphasized the importance of preemptive care and early interventions, particularly for those with a genetic predisposition but who have not yet been diagnosed with cancer. Dr. Robson’s approach to developing risk management plans for these patients was eye-opening, highlighting strategies that aim to either prevent cancer or mitigate its effects if it does occur.

Moreover, I attended a breast cancer case discussion conference. It was enlightening to see how doctors collaborate to make clinical decisions regarding patient treatment. The decision engaged many factors ranging from evaluating diagnostic data to discussing treatment options. I found it fascinating to learn about the tools and methodologies that help medical professionals weigh the pros and cons of various treatment options. 

Week 3 Anuj

 This week was another interesting week featuring a few robotic organ removals (prostates and kidneys), several imaging (cystoscopies), and some patient consultation shadowing. Another key feature in robotic surgery that I noticed this week was the rapid temperature sensing and control used in the cauterizing forceps/scissors. The instant heating and cooling of the instrument with real-time audio feedback assist the surgeons in making precise cuts. Besides, I made more progress on the wide-view cystoscope project and completed some preliminary design aspects. I will be ordering the design parts next week and using Weill Cornell's 3D printed services to fabricate a few housing materials for the camera used for the cystoscope. Hopefully, by the end of the week, we will have a decent prototype if all things go well. 

Week 3- Zuzanna

This week I was able to see some surgeries which was very interesting as it was the first time I had observed any. I was able to observe breast cancer related surgeries, including a masectomy and lupectomy.  It was definitely shocking at first to see the surgeries and the removal of tissue, but after watching a few I was able to recognize what the steps were and what they were aiming to do. Each surgery was a little different, due to either the preferences of the patient or the methods of doctors involved. First, I saw a bilateral masectomy, and I was surprised how many people were involved, from nurses to PAs, to pathology and oncology and plastic surgery- it was quite tight in the room! Some patients prefer to have breast reconstruction done, but this patient also had her implants removed and with her specific history, preferred not to reconstruct. Another surgery I saw only removed a mass, but required removal of the nipple due to the proximity. The next one however removed only a mass, but without affecting the nipples. It was really interesting how many methods of removal there are, but even the methods of tumor localization. Some patients had a radioactive seed locating the mass, some had a staples, and some had wires sticking out of their chest locating that. I did not realize how many methods there are for localization but it depends partly on the patient and partly on the radiologists preferred method of marking a tumor. Watching the whole process really gave me an idea of the morphology of the disease and methods of resection. My research in Ithaca concerns making immunotherapeutic hydrogels to place next to tumors to improve immune infiltration, and seeing these surgeries gave me an idea of how realistic applying those may be given various situations.

I also continued to shadow in clinic this week and we had a few very interesting cases where I learned more about how chemotherapy and immunotherapy can be combined, or even given consecutively, but with certain risk factors that can make it difficult for a patient and doctor to decide next steps with the risks and benefits.

In the lab I continued to analyze some cancer organoid images and some next steps in the project.

Week 3: Kirtana

At Dr. Prince's lab this week, I did image segmentation of muscles from abdominal MRIs. This will now be used as training data to improve the AI model used for interpreting MRI scans. I also learnt how to conduct an abdominal MRI which was very cool. I started on a new project to determine poorly segmented images in order to further improve the training data.

With Dr. Choi, I discussed the details of the lung cancer project. We came up with a plan to implement the PLCO model on our data while also trying to form a new model which may be a better fit. I worked on a project proposal this week to solidify my aims and anticipated manuscript timeline.

Overall, it was a productive week with many learning experiences. I am hoping to focus more on the lung cancer project next week and start my data analysis.

Week 3: Anais

This week started off with another OR day.  This time, we got to see two different myomectomy surgeries, one robotic and one abdominal.  I even scrubbed in for the first surgery and was able to see it more closely.  It was very cool to see how the surgical robot was controlled and what went into preparing the incisions. Also interestingly enough, the myomectomies seemed more tricky than the hysterectomies we saw last Friday.  I was also glad to see the surgeries to day side by side and be able to compare them.  This week, I also shadowed Dr.Fenster in her private clinic.  Once again, it was very interesting to see the interactions between doctors, nurses and patients.  Because uterus related problems and fertility can be an emotional topic, I noticed how well they were able to calm down the patient and create a welcoming and safe space.  I also got to see a wide array of different treatment options and discussions.  Pei Wen and I also presented on our literature review updates and discussed ways to apply current methods to the research goals of Dr.Fenster’s and Dr.Wolf’s collaboration.

Week 3: Allison

 Early this week I was able to see how mice with glioblastoma receive radiation therapy. It's a specialized machine for small animal irradiation that first takes a CT scan, so the administration of the x-rays is very precise to the tumor. I also received training on how to extract and process mouse brains for RNA-seq. I was introduced to a resident in neuropathology, who took me to shadow Dr. Liechty for his morning cases as he diagnosed brain tumor biopsies. After being in breast pathology last week, it was very interesting to see the different features of each cancer type and contrast which additional stains are ordered to diagnose cancers from different areas of the body. The rest of my time this week mainly entailed having meetings with Dr. Demaria and Dr. Vanpouille-Box, as well as speaking with people in the lab to finalize experimental plans and make sure we have the supplies to start experiments next week!

Week 3: MJ

This week started off with me being recruited to donate blood to be a healthy control in a Lupus study. The study is interested in microRNAs and other non-coding RNAs, which is a special interest to me because my own research looks at how non-coding RNAs regulate skeletal muscle regeneration. I then went to our weekly meetings, where a professor here presented on using AI in fertility to predict aneuploidy and pregnancy outcomes. I also attended HSS research's weekly seminar, where a visiting professor from Yale presented on treating skin conditions that cause fibrosis in the middle layer of the skin. I also met with members of the Donlin lab to discuss my research project this summer, which involves analyzing bulk RNA sequencing data of CD4/8 mutants to look at specific pathways and genes that are up/down regulated and could be involved in inclusion body myositis. Additionally, I presented a journal club for the Donlin lab on muscle fiber heterogeneity beyond myosin heavy chain isoforms. In the clinic, I shadowed Dr. Fernandez as he saw patients with various muscle disorders, such as dermatomyositis, inclusion body myositis, and rhabdomyolysis. 

Week 3: Brenda

This week, I had the opportunity to meet with my colleague at Cornell, Salman. At Cornell, I work in collaboration with Dr. Bonassar, and through Salman, I receive bone samples taken from the knee joint by Dr. Andreas Gomoll, Dr. Sabrina Strickland, and Dr. Scott Rodeo. Salman took Hamilton and me to observe an arthrotomy knee osteochondral allograft with fresh articular cartilage to the left patella, performed by Dr. Gomoll, essentially a procedure where damaged cartilage and bone on the patella (kneecap) are replaced with a fresh osteochondral allograft from a deceased donor. It was fascinating not only to observe the surgical technique but also to learn how the samples I use in my Ph.D. research are collected.

At the clinic, I also shadowed a particularly interesting case: a patient who had undergone total knee arthroplasty without initial complications, but began experiencing periprosthetic joint infections (PJI) three years post-operation. In the lab, we’ve been revisiting bacterial culture methods for Staphylococcus aureus and E. coli. We prepared bacterial solutions, submerged knee implants in them, and used crystal violet staining to visualize the resulting biofilm. Aside from that, I’ve been reviewing lab protocols and refreshing my technical skills.

Week 3: Pei Wen

This week, I was most astonished by the robot-assisted and open surgery myomectomies, surgical procedure to remove uterine fibroids, we observed early in the week. Coincidentally, both myomectomies were performed on the same day, so it was especially interesting to compare and contrast both strategies for myomectomies. Compared to the minimally invasive hysteroscopic fibroid removals we observed in our first week, these myomectomies were more time-intensive, taking 3-4 hours each and required more precise and deeper cuts as the fibroids were larger in these cases. In the context of the robot-assisted surgery, it was reminiscent of the hysterectomies performed last week where the internal abdomen and uterus were accessed through a small incision at the umbilicus supplemented with additional smaller port sites to accommodate the robotic arms. For the technology itself, I was surprised by the resolution, depth, and precision the robot and associated interface offered. While Dr. Fenster is accustomed to robot-assisted surgeries, she mentioned tactility and pressure sensitivity were features that were lacking for this approach. For the surgery itself, I was surprised by the many layers of tissue of the uterus and how deep the incision needed to be to remove the fibroid in this case. As such, I was unsure about the suturing process, but I learned that, contrary to my initial assumption of a single pass, the closure was performed in multiple passes, beginning with the deepest layer and progressing outward. In the context of the open surgery approach, the process was comparatively more invasive, requiring a few centimeters incision at the abdomen. Surprisingly, there was less bleeding compared to the robot-assisted approach. Dr. Fenster informed us that most patients prefer open surgery, as it was considered more cosmetically pleasing. However, recovery is typically faster in robot-assisted cases. 

Week 3: Adam

 This week I spent some time in Dr. Spector's outpatient clinic shadowing pre-operative planning and post-operative follow-up appointments. In the clinic I also learned more about skin grafting and the wound healing process. This translated well to the OR, since I was able to watch some skin grafts be placed over surgical sites from tumor resections. I also watched a DIEP flap breast reconstruction, which is a very interesting procedure where skin, fat, and blood vessels from the abdomen were used to rebuild a patient's breasts after a bilateral mastectomy. The DIEP reconstruction is a microsurgical procedure, since individual blood vessels in the tissue are reconnected in order to supply blood to the reconstructed breast. They also performed a microneurorrhaphy on the patient, connecting some of the nerves from the abdomen to potentially provide sensation to the reconstructed tissue. This was the first microsurgery I have seen and it was really interesting to watch. In Dr. Spector's lab this week, I learned how to use the microtome to section tissue from paraffin blocks, and also learned how to stain with hematoxylin and eosin to visualize tissue microanatomy. This will be useful to confirm the results of the immunofluorescent staining later. 

Week 3: Teagan

This week, I had a good mix of clinical and research experiences. In the OR, I was again able to watch a total knee replacement and a total hip replacement, along with some total knee revisions. The reason these total knee revisions were needed was due to a recent implant recall that caused many of a company's implants to be faulty as a result of improper packaging. This improper packaging degraded the polyethylene in the implants, causing osteolysis in patients' bones. Each of the three knee revisions was slightly different; one was particularly difficult for the surgical team because the bone was especially osteoporotic. This situation is far from being resolved as Dr. Bostrom continues to have pre-operative appointments discussing the need to move forward with revision surgery as a result of this recall with other patients, I saw some of these during my time at the clinic this week. Another experience that I had in the clinic was that I sat in on a consultation for a patient who, through surgical intervention (double hip and knee replacement), would regain the ability to walk. It was inspiring to see the impact that these implants can have on patients' lives. 

On the research side, I completed my mouse training, which now grants me access to the Faxitron imaging equipment. I also purchased all the necessary materials to 3D print the jig that will hold the mouse's limbs during imaging. I also got the mouse femurs that I dissected earlier this summer Faxitron imaged by a member of the lab, and I analyzed them in ImageJ to better scale the design of my device. I also attended a meeting about Qupath and how to effectively utilize that technology as a model for the lab's experimental analysis. The person training us was informative on how the system can be utilized at a lower level as a tool that can only be used by the person who trained the data, vs. optimizing the training and code to be a model whose technology can be used across people in the lab since the programing is more robust. Qupath is a program that could be of potential use to my lab work back in Ithaca as well!

Week 3: Joe

Hamilton and I performed more sectioning and H&E staining for the collagenase-based model of tendinopathy. We were able to visualize the patellar tendon in embedded mouse knees, taking photos to begin preparing for ImageJ analysis. I applied for a grant to work on a research project across Ithaca and HSS, making use of HSS' excellent resources for musculoskeletal research. 

I spent more time in the clinic this week, watching two arthroscopic procedures in the knee and a shoulder joint replacement. Both arthroscopic procedures involved the use of two unique tools: one to shave down large chunks of fibrotic tissue and a cauterizing device used to smooth the surface. Notably, two Stryker employees were present for the shoulder joint replacement to guide the on-site construction/customization of the shoulder implant. I'm looking forward to the next week of research and surgeries!

Week 3: Hamilton

This week, I observed a partial patellar allograft replacement surgery. The procedure addressed significant cartilage degradation by replacing nonfunctional tissue with donor graft material. I was struck by the precision and adaptability involved—surgeons used an array of tools resembling those in a mechanical workshop, including carts of rods, sizing guides, drills, and bone saws to tailor the donor tissue to the recipient site. The hands-on, tool-driven nature of the procedure highlighted the intersection of engineering principles and surgical practice.

On the research side, I successfully prepared several murine patellar tendon sections using a microtome, which will be used for downstream H&E staining to evaluate tissue structure and morphology. 

Week 3: Orren Shachaf

This week, both clinical and research work picked up. During Dr. Moore’s Medicaid clinic—which she holds once a month—I saw some particularly difficult cases, including one 49-year-old woman with bilateral frozen shoulder (also called adhesive capsulitis), which is characterized by joint stiffness and subsequent pain that results in limited motion, either through stiffness or as a pain response.  Another one of these cases was a 21-year-old male who had had acute lymphoblastic leukemia and, as a result of his sustained use of steroids (which decrease immune system activity), developed avascular necrosis in his knee and got a total knee replacement; at the clinic—two years after his knee replacement—his knee was nearly double the width of this calf, and he had about 10-15 degrees of motion, making it extremely difficult for him to walk and perform other normal, daily tasks. He had been referred to Dr. Moore, since she performs arthroscopic knee surgeries for fibrotic tissue cleanup, but the amount of scar tissue in his knee joint would be too time-consuming for her to perform arthroscopically; further, Dr. Moore noted some calcification behind his patella (heterotopic calcification), which was most likely the biggest factor inhibiting his motion. Ultimately, he will likely need to get a fully new total knee replacement, which was a really unfortunate conclusion. In addition to in-clinic patient interactions, I observed three arthroscopic knee surgeries, which were all cleaning up fibrotic tissue formation following prior knee surgeries. 

Week 3: Aidan

This week I observed more MR guided focused ultrasound ablation cases, as well as two more surgical procedures. The focused ultrasound cases are so exciting every time - they are able to precisely ablate a 3mm sphere of brain tissue called the Ventral Intermediate Nucleus (VIM) of the thalamus. This helps reduce/eliminate tremors permanently. This weeks cases were bilateral - meaning that it was the second MRgFUS procedure, targeting the other half of the brain (patients receive their first treatment 9-15 months prior). Symptom relief is immediate, with the only known side-effect being temporary nausea and in rare cases some numbness in fingertips/facial regions. Recurrence of tremors occurs is ~10% of patients, and is theorized to be due to an incomplete ablation of the VIM, but little is understood about what causes the recurrence. Recently, Dr. Kaplitt submitted a paper to JAMA regarding bilateral MRgFUS. Many in the field are cautious about the side effects of performing symmetrical ablation. However, Dr. Kaplitt has found that in his patients, performing the procedure bilaterally improves patient symptoms without any additional consequences to unilateral ablation.  

Week 3: Amelia

This week I continued my mouse surgeries, and we're making good progress towards a group of 20 mice with cranial windows for 2P imaging. I also attended another lab meeting, and this provided more excellent context for me about the Liston Lab's previous and ongoing work, specifically related to how depression may be related to systemic and chronic inflammation. This week I was also able to see the clinical side of the hospital for the first time. I observed two of Dr. Kaplitt's procedures: one was MRI-guided focused ultrasound (MRgFUS) ablation targeting the ventral intermediate nucleus of the thalamus for helping with tremors. The other was a bilateral implantation of a deep brain stimulator (DBS) into the globus pallidus internus (GPI), for advanced Parkinson's disease. In both of these procedures, the patient is awake so that their tremors can be assessed as the protocol goes on, and it was incredible to see the extent to which tremors decreased throughout these procedures. 

Week 3: Nina

In the third week of immersion, I got to see my first robot-assisted surgery. I saw a living donor liver transplant surgery using the Da Vinci 5 surgical robot. It was really amazing seeing how the machine looks and operates in real life. While I have seen videos of the robot being used, I was shocked at how fine the resolution of the camera was and how precise each of the probes were in removing tissue. I also was surprised by the incorporation of multiple surgical tools into one robotic probe. The Da Vinci forceps attachment could cauterize and cut tissue, which decrease the amount of tool switching the surgeon had to do. It was really fascinating seeing how sealing tissue via stapling and suturing was done using the robotic arms. The vacuum pressure and gas exchange system incorporated into the machine, like the cauterizing and stapling tool, were also configured with audible cues to alert the surgeon to errors. I found that the auditory feedback helps the surgeon determine how long to use tools and allows them to monitor the success of failure of an intervention. One of the issues for this machine is that it the camera probe often had to be pulled out and cleaned manually. Stray tissue, bleeds, and system pressure/temperature can all contribute to build-up on the camera lens. Therefore, I think some optimization could be used clear the lens in-vivo and prevent time being spent on monitoring the state of the lens. Later this week, on Friday, I will see another liver resection. Together, experiencing clinic and surgeries has allowed me to see the importance of pre-transplant organ preservation and understand the value of surgical time when performing a transplant surgery. Up to this point, Dr. Samstein, my thesis advisor, Dr. Schwartz, and I have been finalizing the aims for the research collaboration that will ensue this summer. As liver transplantation involves human subjects, we have been careful to examine logistic hurdles to ensure the safety, de-identification, and consent of all involved parties before starting any research. My project will focus on examining the technique of normothermic machine perfusion used to preserve donor livers before transplant. More specifically, I will try to expand readouts for organs before transplant to better understand organ viability and predict graft success in patients. 

Week 3: Wendy Zimmerman

 On Monday and Thursday this week I shadowed sham and shoulder impingement surgeries on young and aged mice. This procedure is used to create a tendinopathy model in the rotator cuff. The RNA sequencing data that I have been examining is from this same experiment, but with smaller cohorts. Four mice per group were used in those earlier experiments and for the procedures I shadowed there were 15 mice per group. It was very interesting getting to see the process of placing the clip in the subacromial space to cause the impingement, and it was very nice getting to talk more with Dr. Eliasberg and the postdoc with whom I am working. On Tuesday, I learned the RNA isolation procedure used by the lab. I will be helping with the processing of the tissue samples over the course of the summer for the shoulder impingement and ACL models. My lab back in Ithaca has done some RNA isolation, so learning this technique will be helpful for my future work. On Friday I will finally get to shadow my first human surgery with Dr. Eliasberg. Next week, I will be shadowing procedures on mice using ultrasound to look at tendon properties. I am excited for this as some of my previous research used focus ultrasound for therapeutic delivery, so I am interested in seeing other ways it can be used in research. Additionally, I also finally received Dr. Rodeo's schedule and will be shadowing him in the clinic and in surgery. In July, I have also schedule a couple of days where I will get to shadow Dr. Eliasberg in the clinic. I am very much looking forward to getting to do more on the clinical side of this program.

Week 3: Ben

For my third week in NYC, I did a lot of wet lab research and clinical shadowing. To start off my week, I got to practice the islet extraction protocol that the Alonso lab performs routinely. I was given post mortem mice to practice the procedure, in which I cut open the abdomen of the mice, carefully remove the ribcage and remove the heart so I have easy access to the gallbladder. I then clamped the small intestine where it meets the bile duct, then through the gallbladder, I inject collagenase to disassociate the pancreas. I then excise the pancreas and further digest it, and centrifuge it to isolate the islets (Image 1). The following day, I picked out the intact islets that survived overnight incubation and further disassociated them onto a 24-well plate (Image 2). After, typically the lab performs different assays to assess its insulin and glucose responsiveness or treats them with an inhibitor, but the mice I performed the procedure on were practice mice with genomic defects in its insulin secreting gene INS. Thus, it was not worth the time and resources to perform further analysis, and I discarded them. However, this was valuable practice that I will keep doing throughout the summer so that I can master it. This will be an essential skill to take back with me to Ithaca.

Image 1: Islets after isolation from mice.

Image 2: Islets after disassociation and plating.

I also engaged in talks with a potential collaborator that can contribute a lot to the success of my project. I talked to Dr. Shahin Rafii, whose expertise is in organ-specific endothelial cells and their function. They recently published a paper in Cell about using an engineered adaptable endothelial cell line that vascularized and promoted the function of islets. Their work and ongoing efforts align with what I am trying to do, and working with them will definitely mutually benefit both of us. Dr. Rafii has invited me to present my research at their lab meeting, and I will get a more comprehensive view on how exactly we can help each other out, and what areas we can collaborate in.

Finally, I got the opportunity to shadow surgeries. Through my friends in my cohort, I was connected to Dr. Lisa Newman, who is a oncology surgeon specializing in breast cancer. During my time shadowing her clinic, I saw five surgeries. Two of them where mastectomies, which are full breast removal, and three of them were lumpectomies, which are partial breast removal. For the mastectomies, one procedure was a single breast removal, while the other was a double breast removal. For both procedures, the nipple was not preserved. For the lumpectomies, different strategies were used. One strategy used was a pellet-guided tumor extract, in which a radioactive pellet was injected near the site of the tumor pre-op. During the procedure, a probe that detects radioactive activity was used to detect the position of the pellet, and it was them excised. This strategy is used when the tumor is deep into the breast tissue and cannot be definitively felt by hand. Another strategy used was a guide free approach. In this case, the patient was able to feel the lump in her breast, and the tumor was located on the posterior of the areola and felt very defined. In this case, they simple added a metal clip which was inserted as part of a routine mammogram. Due to the easy access and physical identification of the tumor, no further guided strategy was needed. Finally, a wire-guided approach was used, where a metal wire is inserted into the site of the tumor pre-op using a mammogram as a visual guide. Similarly to the pellet-guided strategy, this was used for difficult to feel and access tumors, but it is typically offered as an alternative strategy if the patient is uncomfortable with radioactive material being inserted into their body. Also, the strategy depends on the radiologist on the case and which strategies they prefer. However, this strategy can be invasive, as needle will be sticking out of the breast. It was very cool to see clinical practice and the thought processes that go into the decision making on how to remove a breast tumor from a patient.

This week was very productive, and I not only made strives in getting resources that will directly help me drive my thesis back in Ithaca, but I also got valuable insight on clinical practice and the decision matrix that goes on there. Moving on to next week, I wish to learn more protocols related to islet biology, further establish potential collaborations, and continue to observe clinical practice in other surgery areas.

Week 3: Peter

 This week didn't have a ton going on with Juneteenth and all that. My cells were slow to grow last week so we are postponing my Flow Cytometry experiment. In the meantime, I've started up a histology project. There are a number of TMA's from lymphoma patients that have been stained for EBER, EBNA2, LMP1. Using HALO, I'll be determining the number of cells positive for these markers for each biopsy. The software has been pretty quick to learn and I hope to meet with a pathologist next week to confirm my results. I should be shadowing my first surgery next week so I'm pretty excited for that.

Week 2-Meichi

This week, I had the opportunity to observe several breast cancer surgeries under the guidance of Dr. Newman. Witnessing these procedures firsthand was an eye-opening experience that deepened my understanding of the complexities involved in the surgical management of breast cancer. Dr. Newman thoughtfully walked us through each procedure, explaining the decision-making process and addressing our questions in detail.

One of the most fascinating aspects was the use of tumor localization techniques, such as breast seed localization and needle localization. These methods involve placing a small marker or seed near the tumor, enabling the surgeon to precisely target and remove malignant tissue while preserving as much healthy tissue as possible.

I also observed a variety of advanced surgical tools that assist in real-time intraoperative decision-making. These tools not only help guide precise excisions but also provide critical feedback, enhancing surgical accuracy and safety.

Overall, this is a profound learning experience for me and I hope to contribute to advancements that further enhance the precision and effectiveness of cancer treatments.

Week 2: Arina

 This week, we started diving into more lab work and learning new techniques. I got a chance to do a couple of surgeries and try a viral injection. Although I have performed those before in a different lab during my undergrad, the equipment we used was completely different, so it’s a bit of an adjustment. I also got to do some tissue work — specifically, slice some paraffin-embedded brains on a cryostat. Here, I experienced similar emotions: I’ve only used a cryostat a couple of times before, and the rest of my undergraduate I only worked with a vibratome. It’s curious to approach those familiar-but-not-quite techniques with better awareness. I am beginning to notice just how much improvement can take place even with something you think you’re somewhat comfortable with, and how many little hacks you can learn from other people. For example, someone mentioned using biopsy punches for marking the location of a future cranial window. This wasn’t something I thought of before, but it worked pretty well!

We also got to attend the lab meeting where one of the students in the lab practiced their A-exam. I haven’t seen an A-exam before, so it was informative to see what is typically being prepared, what the format is, and what the ratios of background and experimental content are. 

Week 2 : Adil

This week was heavy in the clinic and OR. We started out with attending the weekly multidisciplinary tumor board on Monday. Doctors discussed treatment plans for several patients. Doctors from surgical oncology, medical oncology and radiation oncology discussed treatment plans for several cases, depending on the grade of tumor, previous tumor and treatment history etc. It was very interesting to see oncologists specializing in different fields discuss and customize treatment plans for each patient individually.

Tuesday, I was fortunate to shadow Dr. Newman in clinic. Dr. Newman saw 7 patients. Most of them were either follow-up consultations who had surgeries in the last few weeks or newly diagnosed breast cancer patients who came in to discuss their treatment plans with Dr. Newman. It was amazing how Dr. Newman patiently discussed treatment options and plans with each patient and answered all of their questions. On Wednesday and Thursday, I shadowed Dr. Newman in the OR. She performed several surgeries ranging from bilateral mastectomies, radioactive seed localized lumpectomies to sentinel lymph node biopsies (to test for invasiveness of the cancer). One of these surgeries was particularly interesting, a wire guided lumpectomy instead of a radioactive seed to track the location of the tumor and calcifications. On Friday, Dr. Newman conducted a didactic session wherein she discussed Ductal Carcinoma In Situ (DCIS) and the COMET (Comparing an Operation to Monitoring, With or Without Endocrine Therapy) clinical trial for DCIS. In the lab, we had to redo a few steps for the TCR library preparation as the QC report from last week's TCR library was not great. We have submitted the new sample to the genomics core facility and will go ahead with the sequencing if the QC results come back positive!

Week 2: Kirtana

 This week I started shadowing Dr. Martin Prince and working with Dr. Eunji Choi as my research mentor. It was a wonderful, fast-paced week with a lot of learning. With Dr. Prince, I had a chance to evaluate MRIs of polycystic kidney disease. I learnt the anatomy of the abdominal cavity and more about the AI model used to automatically annotate each organ. I also learnt about how the model could be improved and started contributing to a research project to improve the performance metrics of the model. As a BME student with some background in AI, I found this very interesting and informative. I am excited to continue contributing towards the project and learning more about patient cases from Dr. Prince. 

I had a meeting with Dr. Eunji Choi on Monday to discuss my research project on lung cancer. We will be looking at the susceptibility to lung cancer in LMICs based on data from Demographic Health Surveys. We will then compare it to existing risk prediction models and the incidence of lung cancer in India. The hope is to publish some of our results as a report. I am very excited to get started on this project and hope to have more updates on this next week.

Week 2: Anais

  On my second week of immersion, I was able to witness several more surgeries ad got to sit in on very interesting meetings. On Monday, I shadowed Dr.Fenster on to hysteroscopy surgeries conducted to remove and take biopsies of polyps.  One patient had a surprise cyst, which was also removed during the surgery.  Pei Wen and I also presented on our previous literature review from last week.  This meeting proved quite informative and Dr. Wolf suggested meeting again next week to further discuss the protocols and methods briefly mentioned during the meeting.  On Tuesday, I thus started off on creating my slides for the meeting.  On Wednesday, Pei Wen and I sat in on a few of Dr.Fenster’s meetings. The first meeting of the day was a meeting to discuss in detail steps toward applying for an IRB.  This meeting is particularly relevant for a project idea Dr. Fenster and Dr.Wolf are hoping to collaborate on.  The next meeting of the day was a fibroid center conference meeting, where several doctors and practitioners discussed particularly interesting fibroid cases.  Dr.Schiffman, was particularly helpful in describing and explaining each MRI presented and stoping to further elaborate on what they were talking about.  I found this session really cool and loved learning more about how patients are diagnosed and how doctors collaborate to decide how to best move forward with each case.  On Thursday, I continued to work on the presentation and joined in on a few meetings.  We had another meeting regarding Dr. Fenster and Dr. Wolf’s collaboration, this time they discussed prototyping and initial animal trials.  I ended the week by observing two more surgeries on Friday.  Specifically, they were laparoscopic hysterectomies.

Week 2: Amelia

This week, research got very busy very quickly. Monday, Tuesday, Thursday, and Friday were spent doing cranial windows and GCaMP injections in mice for a study in the Liston lab. These mice will be imaged in three weeks with a 2 photon microscope. I enjoyed the problem-solving of merging techniques from each of our labs. I got to see different methods of doing cranial windows and learn how to do the injections solo. I also attended my first lab meeting on Wednesday, which was a practice talk for a thesis proposal, which was well timed as it gave me some great context about the lab's previous and current work. I also got to try brain slicing on a Cryostat, which I had previously only done on a Vibratome. 

Week 2 : Zuzanna

This week I went into clinic with my clinician and shadowed as he saw patients. He sees patients in urological oncology, so I saw many cancer patients. It was interesting to see the different types of patients he sees, from people who are in chemo and immunotherapy, as well as people who are getting prepped for surgery. It was interesting to learn the different combinations of therapies used to treat patients, and even with these less invasive treatments, surgical intervention is often included. I learned removal of the entire bladder is still standard even if it has a tumor removed as it still has relapse risk. In my Ithaca campus lab I am making immunotherapeutic hydrogels so it can be interesting to see how to combine those with current standards. In lab, I currently have been analyzing cancer organoid images, so that can be a useful skill for some imaging I want to do in my Ithaca campus lab as well.

While my clinician mainly has male patients due to the predominance of males affected with the cancer he treats, there was a female patient that had previously had a cancer treated by my clinician, but came back with what was a uterine benign tumor, where it was optional for her to remove it, and was sent to an OB/GYN as they further specialize in uterine tumors. It is interesting to see the clinical flow of further consults and treatments, but also see the emotional affect it has on patients, as the clinician must remain professional and think of the treatment option, while also consoling a distressed patient. I may see some surgeries in the next few weeks.

Week 2: MJ

I started this week by attending lab meeting for the Donlin lab at HSS, where various lab members gave small research updates on their work. The research spanned from nuclei isolation troubleshooting to using machine learning algorithms to predict protein structure. I also attended a research in progress talk at HSS for a visiting scientist in the Rodeo lab, who presented on his work trying to characterize the biomarkers for predicting outcomes after meniscus tear and subsequent surgical repair. I similarly attended the rheumatology department's journal club at HSS, where two papers were presented on the association of treating kawasaki disease with various doses of asprin and coronary heart aneurisms, as well as the efficacy of using AI for identifying Raynaud's disease. This week, I also shadowed Dr. Fernandez in his clinic, where he treated many patients with various forms of myositis, such as dermatomyositis, which is an autoimmune disease that causes inflammation of the skin and skeletal muscle and presents with various symptoms. Dr. Fernandez is working with Donlin lab and other institutions to build a myositis registry from patient samples, so I also saw what those patients look like and shadowed a member of the Donlin lab as the blood sample was processed to isolate peripheral blood mononuclear cells.  

Week 2: Eleana

This week was an exciting week full of looking at pathological samples and learning new information. Allison and I started the week off with presenting our research to the Dr. Demaria and Dr. VanPouille-Box labs. It was a very long presentation, but we were able to share the research we do back in Ithaca with them and get their input on our work that we do, and the project proposal we have for them to work on this Summer. From the initial meetings, they approved our project and they thought that it will be exciting to work on. We spent the next few days working on protocol development, and figuring out what materials that we would need to start the project off. During the beginning of the week we also viewed a mice craniotomy where, mice were being implanted with glioblastoma and will then undergo radiation treatment. Thursday and Friday we then shadowed Dr. Demaria in the Breast Anatomical Pathology lab and got to sit in as they viewed cases and their slides to determine a diagnosis of the patient. We had a tour of the grossing lab and saw a lumpectomy being grossed by one of the residents. We were showed around the lab and saw the microtomy, and special stains room. Friday, we were in pathology again and viewed cases and later attended a grossing conference where residents had to identify what kind of tumor they had. Finally, on both days we attended conferences where the slides and cases are reevaluated in a group to get a consensus.  

Week 2: Allison

 On Monday, I was able to see craniotomies and stereotactic injections of glioblastoma cells into mouse brains to establish models that will be used for radiation and immunotherapy in the coming weeks. On Tuesday, Eleana and I presented our research and an immersion project proposal at a joint meeting for the labs of Dr. Demaria and Dr. Vanpouille-Box, and we have been working with members of the labs to create experimental plans and get materials together. I have spent the past two days in the anatomical pathology department shadowing Dr. Demaria and a resident and fellow in breast anatomical pathology. In the mornings, I have seen how histology slides of breast, lymph node, and skin biopsies/lumpectomies are analyzed to diagnose cancer. I have also been able to attend multiple conferences, including consensus conferences to see how more complex cases are discussed between clinicians to agree on a final diagnosis, and a grossing conference to walk through uncommon incidences of kidney cancer and a brain cancer autopsy. I went on a tour of the histology and immunohistochemistry labs to understand how a tissue sample goes from a patient in the OR to a slide for diagnosis, and was able to shadow the process of preparing a lumpectomy for histological staining. Overall, I have been able to learn a significant amount about how cancer is diagnosed, and I have a much better understanding of what tumors actually look like in the body.

Week 2: Ben

This week, I continued to shadow in the Alonso lab. I learned more about their projects in expanding beta cell mass to recover insulin secretion capacity and treat diabetes. I observed their FSIVGTT protocol in action for the first time, and also shadowed the staining and imaging of pancreatic tissue for a few of the ongoing projects. Also, I followed Dr. Alonso on Thursday to her outpatient clinic, where I observed her rounds in checking in with diabetic patients. From this, I learned a lot of things about diabetes care and the field. First, it was really interesting to see how widespread Dexcoms (continuous glucose monitors) are in the clinic. They were user friendly, simple to use, but very robust in their measurement of blood glucose, which provides lots of use for the clinician to make recommendations in their treatment regiments.  Second, it was interesting to see how normalized Ozempic and other GLP-1 agonists are in diabetes care. At this point, much of my knowledge of Ozempic came from the media and its usage by celebrities to lose weight, and it is from media where my perception of it is controversial. It was really insightful to see how useful it was in the clinic in diabetes management as it decreases hunger and caloric intake of diabetes patients to prevent high glucose spikes. As per my clinician's words, GLP-1 agonists have been a game changer in diabetes management, as it helps lower blood glucose while decreasing weight gain, which is a drawback of increasing insulin content in bolus injections. Finally, I learned about the intersection of lifestyle changes and pharmacological intervention in diabetes care, and how endocrinologists have to navigate this line. A lot of their recommendations depends on what the patient ultimately wants, but they need to be able to communicate medicine and science to them effectively if they believe pharmacological intervention is absolutely needed, which is often the case in patients with dangerously high levels of chronic blood glucose, ketones, hemoglobin A1C, and triglycerides which need to be brought down immediately in which lifestyle changes cannot do. Moving to next week, I will be presenting my research to the lab to introduce them to my research in organ-on-chip models, and I will be practicing the islet isolation protocol for the first time. Also, I plan to shadow in the bariatric division to observe surgeries. Finally, I have plans to talk to the Shahin Rafii group, whose work revolves around engineered adaptable endothelial cells and co-culturing them with tissues such as pancreatic islets and cancer cells to study how they adapt to them. Their research complements mine, and I aim to engage in a discussion to see how we can collaborate and help me drive my project back when I go back to Ithaca.

Week 2: Aidan

 Another very busy procedure week. Two very exciting cases. One involved awake brain surgery with two electrodes inserted to treat Parkinson’s disease, and listening to the brain circuits converted into sound was a fascinating experience. The other type of procedure (3 this week) involves inserting two flexible electrodes into the spinal cord, which can directly stimulate the spine. I have to learn more about the technology/how these work to treat Parkinson’s. Something interesting about the implantation surgeries is that there is always a company rep from the device manufacturer, who is trained in the specific device. In these electrode implants they use live x-ray to carefully thread the electrode up the spine, so there is a very minimal incision area along the spine. 

Week 2: Adam

This week was much lighter in the OR than last week, but I observed the placement of a patient-derived skin graft, as well as a mastectomy and tissue expander placement. Mini lessons in the OR this week included the history of the mastectomy and how to calculate the maximum safe dose of local anesthetic for patients. I also spent a lot of time in the outpatient clinic, where I was able to observe follow-up visits for patients that I had seen in the OR so that Dr. Spector and his team could monitor the healing process. We also saw a patient that was recovering from a traumatic injury to the ear, and it was informative to learn how the reconstructive process changes from reconstruction that is a planned part of surgery to reconstruction after a traumatic injury. I also learned a lot about scar tissue formation and scar revision. We are planning on doing some fluorescent imaging of patient-derived adipose tissue, so I started laying the groundwork for those experiments.