BME Summer Immersion 2026

 This week is the final week of the clinical immersion experience! It still surprises me how fast these past two months have gone. From surgeries to long days in the lab, this experience has taught me the "dance" of the operating theater, how physicians interpret imaging (and piece together multiple modalities), and given me ideas for how I can maybe address some clinical pain points in my future research.  This week, I was focused on wrapping up my three research projects. For the calcification project, I completed selecting our control group cases and segmented QSM scans with Dr. Pablo Villar-Calle and Angela Deng. After doing a brief analysis of our newly segmented cases, we have found that our QSM moments of the mitral annular region strongly correlate to the gold standard volumetric calcification score in CT (r=0.9)! This was very exciting to see, and we plan on having future meetings to look at other trends we find in the data.  For my QSM oxygenation literature rev...

 Jada Okaikoi | Clinician Mentor: Dr. Jiwon Kim My final week of immersion was spent collecting functional measurements from echocardiograms that will later be used to validate our computational model of right ventricular function following tricuspid valve intervention. This work complemented the CT-based analyses by providing functional data that can be compared against the model predictions, reinforcing the importance of integrating multiple imaging modalities in cardiovascular research. Looking back on the past several weeks, this immersion experience provided valuable exposure to both the clinical and research sides of cardiology. From observing electrophysiology procedures, structural heart interventions, pediatric cardiac surgery, and radiology to conducting research on right ventricular remodeling after tricuspid valve interventions, I gained a deeper appreciation for how engineering and medicine work together to improve patient care. I also developed new technical skills in...

 This was a productive final week of immersion, which I was so grateful to experience. I took so many things away that I wouldn't have had in any other program; it was truly a one of a kind experience. This week consisted of my last trial of OCA staining for mitochondria and live/dead chondrocytes. The mitochondrial stains once again gave me tons of trouble, but the live/dead stains confirmed the patterns we had been seeing: the chondrocytes stay mostly alive even after widespread and harsh treatment such as holding and drilling the cadaveric joint. This is still surprising to see deep within the tissue, but what is not surprising is the fact that the cells may not be performing at their highest capability.  I was also able to shadow Dr. Scott Rodeo in his arthroplasty technique. This was something I was highly looking forward to because Dr. Gomoll only conducts arthroplasties using the MAKO robotic software, whereas Dr. Rodeo typically does it the "old-school" way, using...

How is it that it's already been 8 weeks? This last week consisted of more preliminary analysis on structural connectivity/functional connectivity differences in MS, peri and post menopause. Last week, I was hitting some walls with this analysis (which is still obviously preliminary since I have no menopause data, so I'm using age as a proxy for now), but this week, I tried a few methods that look promising for now.  The first was a partial regression between structural disconnectivity scores for each of the 86 brain regions and age, run separately for female and male datapoints, controlling for disease duration. This showed 13 regions with statistically significant age-related increases in disconnectivity in the female model, compared to 0 in the male model. The fact that the effect was specific to women, despite controlling for disease duration and equalizing sample sizes, is (very) preliminary evidence of a sex-specific aging pattern in structural connectivity that could be ...

 I fully enjoyed the last week in NYC. Had the wonderful opportunity to present my work with Dr. Kim on Tuesday. Also, I shadowed Dr. Mema yesterday to shadow some breast imaging diagnoses: stereotactic. I did not have the chance to shadow a biopsy in person that day as there were cancelled cases. Neverthelessless, she taught me the theory behind stereotactic and ulstrasound-guided biopsies. She also showed me a biopsy needle inperson, where she demonstrated how it is typically dislodged. It was a great way to understand the theory behind the biopsies that I have shadowed previously. Lastly, the project for Dr. Kim is nearly complete. Just helping them with running the rest of the patient cases.

Bladder Image Collection and Classification Model Explanation                   Figure 1: Some screenshots of bladder images segmented and classified (81 Images Total) During the final week of the immersion, I was able to coordinate access to the bladder images collected with the Histolog system and begin using them for analysis. Using ImageJ, I selected and segmented regions representing high-grade, low-grade, and normal bladder tissue. These classifications were confirmed in collaboration with the pathology department using corresponding H&E-stained sections and discussions. In addition, during a prostate removal multiport robotic surgery this Wednesday, Dr.Scherr was able to extract additional normal bladder tissue that I was missing and imaged them in the operating room with the SamanTree histolog scanner. From the bladder specimens imaged over the previous two weeks, I generated 28 high-grade, 22 low-grade, and 28 normal ti...

Preparing for this Summer Immersion experience, I wasn't really sure what to expect. My research focus is biomedical engineering education and my personal interests, while within healthcare, focus more on the interactions and dynamics between intangible designed systems such as departments and surgical teams. My interest isn't focused on the technical implementation of a device but rather the integration of that designed item within a larger system of people, dynamics, and cultural influences. As such, I had to create my own path in this program.  Now that the program has come to an end, I can say that I accomplished my goal. I followed my curiosity and pursued many different avenues to engage in observations (i.e., interviews, surgeries, clinical days, ground rounds, and lots of informal questions). I've learned a lot and I look forward to bringing it back to Ithaca to incorporate into my dissertation and senior design. 

I can't believe how quickly the past two months have gone by. This week was spent completing the final stages of data collection for the mini longitudinal study I described in earlier posts, which examines changes in kidney volume after transplant.  As part of this process, we also had to exclude a number of patients who didn't have enough scans to reliably calculate a growth rate, or who had acute kidney events that would confound any trend we measured. Among the patients who did meet criteria, we identified a small number who went on to develop chronic kidney failure following transplantation, and our initial observations suggest that their kidney volumes increased after an initial period of decline and subsequent stabilization following transplantation. It's a small but interesting signal that warrants  further investigation. One leading explanation for native kidney shrinkage after transplant has been immunosuppressive drugs, since several act on the same mTOR pathway i...

 Alexandra Kot | Dr. Sandra Demaria 2026.07.20: Today was less for lab work and more to prepare for my presentation tomorrow. I was also able to take ELISA samples for the MAVS knockout.  However, over the weekend, Dr. Shahbandi and I ran the timecourse ELISA for the two MLKL knockouts. The results of the assay are shown below in Figure 1.  Figure 1: Timecourse ELISA results for MLKL KO's #13 and #14 tracking interferon production in days after radiation. Plotted against the control ELISA from the TS/A cell line with no knockout.  These were some very exciting results. We did not know how much contribution the necroptosis pathway had toward the production of interferon, so to see a dramatic difference was very exciting. This change does make sense, as necroptosis is a very inflammatory form of cell death.  2026.07.21: I presented! The first of the deliverables for the summer immersion program is finished. It was great to get everything together ahead of time and...

  This week was the eighth and final week of immersion and I have continued to experience a variety of opportunities this week. For research this week, I continued to mark the anatomical landmarks used in the robotic surgery plan. From these anatomical landmarks, the femurs will be cut to mimic those made during surgery and then will be analyzed for BMD.  During the clinic this week, I saw a wide array of patients including bone health work-ups, pain follow-ups, post-ops, and others. One case that stood out to me this week was a metabolic bone health follow-up. This particular patient had a history of 13 years of Fosamax, an atypical femur fracture, and breast cancer. The atypical femur fracture is a known risk associated with usage of bisphosphonates (e.g. Fosamax) and the risk is known to increase with prolonged usage. Due to this history, the patient was hesitant about using a bisphosphonate type drug again, but needs one to come off of the current anabolic treatment. Witho...

  Alessandra Coogan | Clinical Mentor: Dr. Scott Rodeo      My final week consisted of one last day in the operating room, completing my SOP, planning future collaborations, and writing thank-you cards to the people who made this experience so meaningful.      On Tuesday, I invited Manav to observe one of Dr. Rodeo’s total knee arthroplasty cases because he had not yet seen a TKA performed using traditional bone guides and saws. He explained that Dr. Andreas Gomoll, whom he has been shadowing, uses a computer-assisted approach in which the bone resections are guided by measurements determined through both computer modeling and surgeon input. In contrast, Dr. Rodeo uses the more manual technique I described in my Week 7 post. It was interesting to compare how two different surgical approaches can be used to achieve the same goal.      We also observed an osteochondral allograft transplantation. During the procedure, the surgical team harv...

  And just like that, we have reached the end of our Summer Immersion experience! The whole summer flew by, full of engaging and educational opportunities in the hospital and lab, and plenty of adventuring in our time off.  This week was actually much lighter in terms of shadowing, as Dr. Spector was out of the office on Tuesday and Thursday, meaning we ended up having just one clinic day and one OR day. The clinic day was relatively uneventful, mostly seeing patients for pre-operative consultations. I was definitely able to notice how much I have learned this summer, as conversations about procedures that just two months ago I barely understood I was able to completely follow along and understand (I think I could probably discuss breast reconstruction and Moh’s procedures with patients if I was ever to work in a hospital). In the OR, we saw the same patient I have discussed at length in my previous two posts, with extensive facial damage from head and neck cancer-related comp...

I can't believe how quickly the past two months have gone by. At the beginning of this week, I was focused on completing the final stages of data collection and conducting the last round of statistical analyses in preparation for my presentation. The presentation went very well, and after spending so much time preparing, it was rewarding to share the work I had been dedicated to throughout the summer with my cohort. Following the presentation, I spent the remainder of the week assisting with additional data collection for the broader study. This experience highlighted the scale of the project, as the total number of cases being collected is approximately twice the number I worked with over the summer. Contributing to this larger effort allowed me to continue developing my research skills while supporting the overall progress of the study.

 This week was one of my favorite weeks of immersion; I got to do research and shadow two different physicians outside of cardiology! Starting with shadowing, on Monday, I had the pleasure of shadowing Dr. Arzu Kovanlikaya in Pediatric Radiology. Here, I got to see her and her residents read through a few abdominal echo and X-rays. With pediatric patients, reading echos is difficult as the patients move around a lot and bowel gas is high (especially with patients between 0-2). X-ray imaging is the preferred modality as it is quick, and can usually give radiologists an idea of lung and bone pathologies quickly. After watching them read scans, I got a chance to see a voiding cystourethrogram on a two-year-old patient. This patient had a history of recurrent urinary tract infections, which prompted her physician to order this test to see if there is any urine backflow to the kidneys. After catheterization and contrast injection, successive X-rays were taken to see the bladder fill wit...

Much of this seventh week was spent polishing my analysis of pancreatic neuroendocrine tumor (PNET) spatial transcriptomic data. Compared to the earlier weeks of Immersion, when I had no idea where to start, I have become much more comfortable with the analysis workflow with the help of my fellow lab members. After annotating various clusters by cell type, a process that can be pretty subjective and ends up resulting in multiple ways of annotating too choose from, I was able to see how tumor regions, fibrotic regions, and non-tumor regions differ by their cell-type and genetic makeup. Some of the major data points of this analysis include cell type/region fraction by pathology, top expressed genes by sample and pathology, and enriched gene ontology biological processes based on pathology and the presence of vascular invasion. Over the next few weeks, I will be continuing to refine my cell type annotations and performing literature review into potential gene driver candidates of metasta...

 This week, I had the opportunity to shadow Dr. Girardi's, cardiothoracic surgeon, Aortic Valve Repair procedure. This was an open heart surgery where the patient's heart would stop, so that the clinician can replace the diseased aortic valve with an artificial valve along with a graft. When the patient's heart is stopped, the perfusionist work with the Heart-Lung machine to ensure that circulation is maintained through the rest of the organs. The surgery required a lot of precise suturing technique to ensure that the artificial valve stays in place. Afterwards, the patient's heart starts back up to ensure that there is adequate circulation.  As for research, I was able to make a lot of progress in optimizing the delay. I needed to switch to a different method, called Grid Search, where the model is given several timepoints, and it needs to guess which timepoint provides an optimized delay. We made a lot of headway in the code, and this weekend, I will be bulk running t...

Name: Pooja Nair Clinical Mentor: Dr. Jason Spector   Last week, we observed the closure of a spine surgery. During the procedure, we saw the use of Bovie electrocautery, which uses high-frequency electrical current to cut tissue while simultaneously achieving hemostasis by coagulating and sealing blood vessels. A grounding pad was placed on the patient to safely complete the electrical circuit. The procedure concluded with layered closure of the paraspinal muscles, followed by closure of the skin. We also observed a complex head and neck reconstruction. The patient had previously undergone resection of a neck tumor at another hospital, and the resulting defect had been reconstructed with a free flap harvested from the thigh. Although the reconstruction initially healed well, the patient returned approximately one year later with exposed bone. During surgery, the ENT team first debrided the wound and drilled the exposed bone to remove nonviable tissue. Dr. Spector and his t...

This week, I presented at the Tuesday meeting. While this presentation was focused on some of the analysis I've been doing using the entire MS dataset (890 patients), I've recently started looking more into grouping patients by age and sex and running analyses on subsets. I don't currently have menopause data in the dataset I have, but if an MS-menopause grant goes through, this data will be collected and I should get access to it (it's kind of crazy that there are only about 10 papers on MS and menopause total, given that MS affects women 2-3x more often than men and a lot of women are going through menopause right around the age when disease progression tends to accelerate). In the meantime, I was hoping to use age as a proxy for menopause status with the dataset I currently have. I know it's a longshot, and as you'll see below, the proxy doesn't really hold up. But here's what I tried and what worked and what didn't. I grouped patients into fo...

This week, I got to sit in on a lead pacemaker removal procedure. Normally, these procedures are pretty quick, but the one I observed was anything but normal. What was expected to take about 30 minutes ended up lasting almost four hours because of complications during the extraction. While Dr.Cheung was removing the pacemaker, one of the leads broke off. Since the device had been implanted about 20 years ago, a lot of scar tissue had grown around it, causing it to become embedded in the heart. Dr. Cheung tried several different techniques to remove the remaining lead, but it proved to be extremely difficult. Even after multiple attempts, it would not come out safely. In the end, the decision was made to leave it in place for the time being. It was really interesting to watch how the team worked through such an unexpected complication, but it was also pretty nerve-racking since they were dealing directly with the heart. Later in the week, I had the chance to shadow Dr. Gerardi during a ...

This week was spent mainly on continued segmentation work and the early stages of data visualization. Working with Dr. Prince, I continued segmenting kidneys on CT and MRI images across our patient cohort to calculate kidney volumes and began generating longitudinal plots tracking individual patients' kidney volumes over time, aligning each patient's data with their transplant date to compare pre-   and   post-surgery   changes   in   volume . Seeing the data take shape on a per-patient basis was a helpful checkpoint, as it has allowed us to begin identifying patterns and any outliers ahead of the broader analysis across the full ADPKD patient cohort included in our longitudinal study. It has also been genuinely rewarding to watch weeks of segmentation work finally come together into a  visual ,  interpretable result. I look forward to continuing to build out these plots in the coming week as segmentation on the remaining patients is completed.

  It’s hard to believe that we only have one week left here for our immersion term, but week 7 has been productive and engaging, both in shadowing and in the lab. We got to check in on the head and neck cancer patient undergoing treatment for lost/damaged facial tissue, both in rounds and in a follow-up procedure in the OR, and in the lab I was able to significantly improve on my primary adipose IF staining with the use of a confocal microscope and the arrival of dialysis tubing I had ordered. The patient that I introduced at the end of last week’s post, with extensive damage on the right half of their face from complications associated with head and neck cancer, a failed skin graft, and side effects of radiation therapy, spent a week in the hospital after their operation last Wednesday. Checking in on them on Monday, they had a good amount of energy and were in an upbeat mood, and Dr. Spector decided he would bring the patient back to the OR this week to check the progress of the ...

General Update Unfortunately, Dr. Scherr was away this week, so I was unable to shadow any operations. However, the week was still very active, with additional presentations, discussions with SamanTree specialists and employees, and extensive coding. In addition to presenting on Tuesday, I was given two more opportunities to present my work to members of the SamanTree Histolog team and discuss the next steps for the final week of immersion. We are currently working to determine how the images acquired with the Histolog scanner can be exported and made available for my research. In the meantime, I identified confocal image data showing high-grade cancer, low-grade cancer, and healthy tissue in the inner lining of the bladder. Using a dataset of 48 images, I developed a preliminary computer model that examines each image, selects one of the three tissue categories, and provides a score indicating how strongly the image matches each category. Model Changes and Features Because the dat...

This week entailed a lot of planning and logistics for next week and the months ahead.  I planned out my last OCA experiment that is happening early next week, and I am hopefully going to get to see an old school total knee arthroplasty. This is unlike the TKAs and UKAs that I've seen Dr. Gomoll has done thus far. Dr. Gomoll is a huge proponent for the MAKOplasty, which is the robotic knee surgery in which patient MRI and CT data is calibrated for the surgery. This results in Dr. Gomoll shaving away small layers of articular cartilage and the underlying osseous component in order to then make holes to drill and fill in metal implants. This means that there is no intact articular cartilage left after the surgery. On the other hand, if done the classical way, a TKA is done using surgical guides to remove entire portions and chunks of cartilage with bone attached. This, after the surgery, results in a tissue portion, straight out of the patient right after surgery, that is similar in ...

  This week was the seventh week of immersion and I have continued to experience a variety of opportunities this week. For research this week, I started marking the anatomical landmarks used in the robotic surgery plan. From these anatomical landmarks, the femurs will be cut to mimic those made during surgery and then will be analyzed for BMD.  During the clinic this week, I saw a wide array of patients including bone health work-ups, pain follow-ups, post-ops, and others. One case that stood out was a twice failed THA. This particular patient had a THA and a THA revision following an implant failure. Specifically, this patient previously received radiation treatment to the pelvis for gynecologically related cancer. Due to this radiation, the pelvic bone has significantly weakened as evidenced by two THA failures. The acetabular components have sunken into the pelvic cavity. This bone weakening significantly impacts possible treatment options for the patient. The potentia...

Alexandra Kot | Dr. Sandra Demaria  2026.07.13: After growing my suspected MAVS KO TS/A cells over the weekend with a control TS/A, they needed to be irradiated to activate MAVS production. The cells underwent 3 minutes of irradiation, for a total delivery of 8 Gy. In two days, the cells will be processed again for a Western blot.  2026.07.14: Today was the first day of clinical immersion presentations, with most presentations coming from the bone-centric and computational students. It was really interesting to hear about Manav's presentation, focusing on graft deterioration over the extensive testing period required before implantation. Manav looked at both life-dead cell staining and mitochondria depolarization. Pooja's alloplastic ear reconstruction project was also very interesting. I hope the Spector lab can use her work to make an ear replacement.  I was able to catch the second half of the Demaria lab meeting and listened to Dr. Elisa's presentation. She is a visit...