Week 6 : Adil

This week I continued working with the ICSBCS sequencing datasets. We also got access to the docker image of the deconvolution package we plan to use for immune cell fraction analysis. We still have few WGS and RNAseq datasets to analyze. We shortlisted a few samples which have both WGS and RNA datasets for own downstream analyses. We are also interested to integrate H&E stained image data in our data analysis. So I spent sometime with Dr. Newman's group members trying to identify the samples which already have H&E data and samples for which we need to capture the H&E images. On the experimental front we are trying to collect more samples to run trovo experiments wherein we capture, isolate and culture T cells and tumor cells. We then run sequencing experiments to understand T cell activity in these samples (the TCR seq library we submitted for sequencing a few days back is also a part of this analysis). Overall it was a heavy week in the lab!

Week 6: Pei Wen

On Monday, Anais and I observed Dr. Fenster performing several laparoscopic polypectomies and myomectomies in the OR. It has been a while since we saw these procedures and were reminded how quick each case took. Compared to the polypectomies done in the clinic, I can understand why some patients would choose to have it done in the OR with anesthesia compared to the availability and accessibility offered by the clinic. In most cases where polypectomies were done in the clinics, patients often felt discomfort and pain despite the administration of a nerve blocker. Moreover, it seems that the resolution and visibility with the equipment in the clinic was lower than that in the OR. At the same time, for other patients, having the procedure done in the clinic is optimal as it is quick and recovery time is significantly less. On Tuesday, we presented our findings in the methodology and pelvic pain neuromodulation to Dr. Fenster and Dr. Wolf. I find these presentations and literature reviews to be helpful and informative in learning about the technology and extent of our knowledge in women’s health research broadly. We concluded the week by working on our final presentation for the summer immersion program and shadowing more surgeries.

Week 6-Meichi

This week, I dedicated my time to working on my immersion research project. As the immersion program draws to a close, I find myself reflecting on the incredible journey I've had over the past weeks. This experience has been an opportunity for me to learn and grow, both personally and professionally. I feel I have gained a deeper understanding of the intersection between clinical practice and engineering, and how the two fields can collaborate to improve patient care.

One of the most valuable aspects of this immersion was the chance to observe and understand how clinicians work on a day-to-day basis. It was fascinating to see the tools and technologies that doctors use to assist in surgeries and decision-making processes. From tumor localization techniques to surgical planning tools, it was inspiring to witness firsthand how these innovations directly contribute to improving patient outcomes. This exposure has made me realize just how essential it is for engineers to think about the practical applications of their work in a clinical setting. Understanding the challenges and needs of clinicians can lead to the development of technologies that truly make a difference in patient care.

In addition to observing the technical aspects, I also learned a great deal about the human side of medicine. It was enlightening to see how breast cancer surgeries are performed and how clinicians explain treatment options to patients. I was particularly moved by how doctors take the time to walk patients through their surgery and treatment options, discussing the pros and cons of each. I also gained a better understanding of how multidisciplinary teams collaborate to make informed decisions about the best course of action for each patient. This collaborative approach emphasizes the importance of clear communication, empathy, and shared decision-making in healthcare.

Week 6- Zuzanna

This week in the clinic I saw some patient that I had seen previously that were following up on their consultations and coming in for treatments, so it is interesting to see the process of cancer treatments and observe the patient's journeys, from starting treatment and also following up on just how they are feeling post-treatments- one patient had to pause treatment for a while as chemo was causing too much exhaustion. In the OR I observed a bladder resection and reconstruction, and I think that was the most complex surgery I have thus far seen. The patient had been on chemo for bladder cancer and as a precautionary measure it is standard to follow with the removal of the bladder- I had heard of this in clinic but many patients receive a bag in place of the bladder- I did not realize they can also construct a new bladder using the colon and appendix. First they robotically removed the bladder, and then cut open into the patient to construct another bladder. There was a lot of moving parts- simply put, they cut the colon in half and attach part of it to the appendix, while repositioning the urethra there and sewing the remaining colon back to allow it to function properly.

In lab I have been do some more image analysis on some cocultured methods for organoids, and trying light sheet microscopy to image those organoids.

Week 6: Teagan

This week was well balanced between OR, clinic, and research experiences. I spent both Monday and Wednesday in the OR watching hip and knee replacement surgeries. However, some cases this week were slightly different than those in previous weeks. I observed a case involving the removal of previously installed and unrelated hardware before the total knee replacement, and saw how they dealt with the extra factors due to this hardware. Additionally, I observed a surgery on a woman with underlying conditions that made her joints particularly stiff and how they navigated that environment differently than those in people who have typical joint environments. The last new thing I observed in the OR was a patella resurfacing, which is a type of knee revision surgery that involves only altering the patella button of the implant. The importance of this type of revision is in removing excess discomfort from movements like walking up stairs. It's fascinating to see the impact that such a small component can have on the overall success of a joint replacement! 

On Tuesday, I went to the clinic, where most of the appointments were follow-ups. In these appointments, Dr. Bostrom assesses the patient's joint flexion, extension, and overall ease of movement. There is a variation in results dependent on how well the patients are adhering to the rehabilitation plans. Thursday and Friday were spent researching; I added the edits I had previously discussed to my 3D printed device, adding more femur support and moving components further up the board to fit the dimensions of female mice. Lastly, on Friday, I also attended a presentation by the HSS Biomechanics department titled: "Quantitative Knee Laxity Post TKA and its relation to Patient Reported Outcomes". This presentation was very insightful for determining the correlation between patient-reported outcomes in PROM questionnaires with actual laxity in the implanted joint. 

Week 6: Anais

On Monday I observed several hysteroscopies. After having observed the myomectamies and hysterectomies over the past few weeks, I was now able to appreciate the simplicity of the hysteroscopy compared to when I had first seen the surgery.  I was also able to observe how shaggy the endometrium gets during menstruation compared to patients that were not menstruating, as Dr. Fenster pointed out.  Though this makes sense, it is still interesting seeing the visual characteristics.  In one of the other cases, the fibroid was in the fundus of the uterus which was apparently harder to get, thus they were not able to get all of the fibroid. I noted how there were some limitations in regards to the device camera and the liquid circulation during the operation.  Another patient had fibroids that had been previously ablated, making the material properties easier to work with.  Apparently based on such observations Dr. Fenster had previously conducted a study and proposed a device that ablated and resected tissue at the same time.  I also attended Dr.Fenster's clinic on Tuesday, which I feel always provides good context for the surgeries we see and how they actually affect people. I was particularly lucky enough to shadow her while she had post-operation conversations with two of the surgeries I had observed in the past few weeks.  I was very glad to be able to see how quick their recovery has been and it was amazing to see how much better they felt after having these fibroids removed.   Pei Wen and I also presented on some studies we had previously found last week in regards to cervical stimulation of contraction.  On Friday, we also got to shadow Dr. Fenster in the OR.  Both surgeries were hysterectomies and ran pretty smoothly.  

Week 6: Hamilton

This week, I continued clinical shadowing with a focus on orthopedic procedures, including meniscectomies and knee reconstructions. These surgeries provided more valuable insight into the structural complexities of the knee joint and the surgical techniques used to restore stability and function. I additionally worked on the powerpoint that will be used in the Tuesday presentation.

On the research side, I resubmitted murine knee samples for a second round of sectioning, as the initial cuts did not adequately capture the region of interest. The new sections will be stained with H&E and analyzed to evaluate the histological progression of tendinopathy in our injury model.