BME Summer Immersion 2023

 During this last week of immersion, I spent more time shadowing Dr. Hartl in the clinic. I also watched him perform a microdiscectomy.  I had the opportunity to shadow Dr. Matthew Cunningham at HSS as well. On Monday, I observed Dr. Cunningham in the OR. The patient presented with broken metal rods in her spine from a previous fusion. Her spinal fusion started from the lumbar region to the top of the thoracic spine. The broken rods were in the lumbar spine and most likely were broken by movement. On Thursday I also attended Dr. Cunningham's clinic hours. We saw multiple patients with scoliosis which is a bit different from Dr. Hartls patients. Throughout the summer I mostly saw patients with slight spinal curvature at Dr. Hartls clinic. It was interesting to see the differences between neuro spine surgery and orthopedic spine surgery. 

This was the last week of immersion and I spent my time in the lab working with our mice injected with a  breast cancer cell line. This was week three post-injection, and it was time to resect the tumor sample. Before resection, we imaged the mice, taking note to measure their weight and hydrating their eyes with vaseline as they cannot close their eyes under isoflurane. In collaboration with people at HSS, we also performed a cardiac puncture to gather blood samples, as well as a spine resection. A cardiac puncture is a terminal procedure that is performed by poking a hole in the heart and using a syringe to pull blood. Because the heart still pumps blood for several beats, the previous step is repeated so when the heart refills with blood, it can be extracted accordingly.  This summer has provided me with so much invaluable experiences, from working with small animals to gaining a deeper understanding of how the healthcare system works.  I shadowed clinicians in neurora...

  In this week, Monday I went OR with Dr. Gomoll and all his surgeries were similar of what I’ve seen before. The only different surgery was a partial knee surgery that Dr. Sabrina Strickland was going which I had the chance to shadow. I was collecting the osteochondral allograft samples after the surgery is over. On Tuesday, as usual I attended the summer immersion meeting and listen some of my friends who were presenting their summer experience and then I went to clinic with Dr. Gomoll. On Wednesday, I was again in the OR with Dr. Gomoll who was performing two surgeries and one of them was torn ligament in the shoulder. It was eye opening for me to learn the similarities of shoulder and knee. On Thursday, I attended one last clinic while on Friday I was in biomechanics. The summer immersion was one the best things that ever happen to me.    

 I had to leave the immersion term a few days early due to some unexpected family problems, but looking back this was such an amazing experience and I'm so grateful to have had this opportunity! It's hard to believe that at the beginning of this summer, I never even imagined I would have the chance to watch a live surgery in the operating room, interact with dozens of cancer patients at all stages of treatment and recovery, or watch talented doctors analyze a vast array of medical data to collectively determine patient diagnoses. Yet, I was able to do all these things and more over the course of just a few short weeks. I've learned a great deal from my time at the immersion program. There was a lot that surprised me; I couldn't believe how personal Dr. Chandwani was with his patients, getting to know them as intimately as a family member over the course of months-long treatment regimens. I had vague impressions (as we all do) of how intelligent doctors are, but getting ...

Week 8: 07/24/23-07/28/23 For the final week of summer immersion, I shadowed in the neuro ICU, this time with Dr. Murthy. One int eresting thing I learned more about was ischemic to hemorrhagic conversion. This is where blood vessels rupture after blood flow has been restored following acute ischemic stroke. This information can directly apply to my research because I have been working with a stroke dataset, so quantifying the risk of hemorrhagic transformation is a potential path I could explore.   During our weekly meeting, I gave a short presentation on my clinical and research experiences from the past 8 weeks. I explained my time in the neuro ICU, my time in the radiology reading room, and my research project. It was interesting to hear about the experiences of the other students in the program who also presented on Tuesday, especially since their clinical and research experiences were much different than mine.   For research, I continued my tests with mathematically fitt...

  It’s hard to believe that summer immersion has come to an end.     The past two months were extremely valuable in expanding my knowledge of the clinical aspect of my research. I was able to build relationships with clinicians in the field actively working on clinical trials and allowed me to interact with patients and identify needs that still exist despite all the advancements that have been made in medicine.     I could not have asked for a better clinician to shadow throughout the summer. Dr. Gomez made sure I saw as much as I could not just within bone marrow transplant but with other clinicians in the hematology/oncology department. I remember the first couple of weeks were emotionally challenging because of the severity of the complications that some of the patients experienced. It was very difficult for me to see them and their families struggling but at the same time I could see the medical team fighting and doing everything they could for the patient....

I had a great last week!  I started the week focusing on wrapping up my project. I made some last-minute adjustments to the code I have written and finished a manual explaining how to use the code. My goal was to make the transition process as easy as possible for everyone in the lab. On Monday I had a great conversation with Dr. Cristofanilli and Dr. Reduzzi about continuing this project while in Ithaca which is exciting! I hope to be able to tie this experience into my thesis research, as I want to keep my research as patient focused as possible.  I also spent my last few days in the clinic with Dr. Cristofanilli. I appreciated getting to know the patients over the past eight weeks and it was great to be able to say bye to a few of them. I saw a few new patients this week as well and one was especially impactful. This patient recently had a baby and received her diagnosis in the last month of her pregnancy. She traveled across the country to receive a diagnosis from Dr. Cris...

 07/24/23 - 07/28/23 This last week is a bittersweet moment as we are coming to end one of the greatest experiences I am having in graduate school. The experiences of the past eight weeks were beyond I could have imagined and surely increased my intellectual bandwidth. For this last week, I spent most of it working on gathering the last bit of data results for my research project. My mentor and I encountered a couple of problems with our camera system, but we were able to find a solution and fix in time to gather the calcium activity in both wild-type and mutant mice. Due to time constraints, the project will continue without me but we believe we got to a good point in the research. The project worked as a proof of concept, but in the future we need more mice with window implant to have a greater statistical power analysis. In my clinical rotation, I worked towards delivering more data for our hydroset paper and did some more literature review on hydroxyapatite for endoscopic skull...

 It is hard to believe that this is already the last week! For this final week, I focused on the research part of my experience and finalized some data analysis. I also gave a presentation on my research project at the Orthopedic Soft Tissue Research weekly meeting. I will likely continue this project in some capacity as it moves to the next steps. Over this summer, I found a number of genes and gene pathsways that were altered following traumatic cartilage. I also determined which of these genes/pathways were similarly altered in osteoarthritis and inflammation of the cartilage. Going forward, qPCR will be used to validate some of my findings.  Overall, the summer immersion program has been incredible. I feel so lucky to get to see a clinical environment and especially lucky as I was able to be part of this program at the very start of my PhD. As a person with an engineering and laboratory background, it is easy to forget the end goal of why we are doing the work. In medical ...

 Week 8 - Reflecting on the immersion term Name: Sally Lee Clinician mentor: Thomas J. Fahey As this week marks the last week, I watched presentations of other immersion cohorts who had not presented last week. It was fascinating to observe the diverse range of projects that everyone has been working on during this immersive experience.   Reflecting on my own research project, an exciting milestone was reached on July 27th. I finally received the bulk RNA-seq data of pancreatic neuroendocrine tumors from Dr. Finnerty’s lab, which is also part of the endocrinology department. It was a relief to have the data in hand. Looking ahead, my next step involves requesting preprocessing of the data from the genomics core facility. I am curious to see how the analysis of these samples, integrated to the control single cell RNA-seq data that I have already generated with control human islet data. By performing a pseudo-bulk analysis, I hope to gain valuable insights into the gene expressi...

Tuesday (July 25th, 2023) The Prosthetic Joint Infection (PJI) research groups have weekly meetings at 8am at HSS Research Institute on the 6th floor. The group is led by Dr. Mathias Bostrom and Dr. Alberto Carli. After the meeting, I went to Starr 8A-05 in Weill Cornell Medicine to listen to the rest of my cohort's summer research projects. Afterward, I returned to the HSS Research Institute to start the third round of cement elution studies and collect data for the 1, 2, 4, and 8hr timepoints. We made eight cement coupons using mixing method #1 and submerged them in 1X PBS for the allotted time points. At every time point, the PBS solution was removed for testing and replaced with new PBS. Wednesday (July 26th, 2023) I traveled to The City College of New York (CCNY) to visit Prof. Mitch Schaffler. His office is in the Grove School of Engineering on the 5th floor. Dr. James Boorman-Padgett gave me a tour of the campus and the core facilities that the lab utilizes for its osteocyte...

 Week 8: 07/24/23 – 07/28/23 I spent the final week of Summer Immersion presenting my experience this summer to my cohort. It was a great experience to hear about what other students were doing during the summer and how it related to their research thesis. Throughout the summer, I had the incredible opportunity to work with a diverse group of medical professionals, including doctors, nurses, and engineers. Also, I was able to witness different stages of healthcare from diagnosis to treatment. It was a transformative experience that allowed me to witness firsthand the challenges and rewards of healthcare.   In terms of research, I transferred my data and discussed my results with the lab. The lab will use my data to identify the prognostic utility of RV volume and strain characteristics in patients with coronary artery disease. It was enriching to see the methodologies used in clinical research to explore whether treatments, diagnostic techniques, and medications are safe a...

 This last week, I have spent most of the time finishing up my research project in the lab. Besides the IP’s using the LY19 cells that I reported on in the last post, I also performed the IP’s with the V5-tagged H1E cells that we had, just to compare even though I did not use a V5 antibody for the IP. I ended up with similar results showing that H1C and H1E were unable to be pulled down. For these IP’s however, I was even unable to see a band for H1E in the input or unbound lanes, which I was able to see in the LY19 cell IP’s. I am wondering if the alteration of the V5 tag in the H1E protein may be hindering its expression in some way, and may also be contributing to why the V5 antibody is not working properly. I also checked the two control IP’s that I did using non-specific mouse IgG and rabbit IgG antibodies. For these I was expecting to see only bands in the input and unbound and nothing in the elution, so these worked as expected. Since I identified the antibody conjugation to...

This week I shadowed Dr. Hartl in the OR and clinic.  Monday I was in the OR, and I watched Dr. Hartl perform a TLIF. I also collected a bone marrow and disc sample. The bone marrow was taken to the Spector Lab for further processing, while the disc sample was shipped to the Delco Lab in Ithaca. As for the BM, I used Ficoll to create a density gradient of the different components. I then froze down the middle, white portion of the gradient which contained the nucleated cells. Following freezing, the cells were shipped to Ithaca where they were plated to obtain the mesenchymal stem cells. From the 3ccs of BM I processed we isolated around 600,000 stem cells. This was around the number we were expecting.  Tuesday and Wednesday, I was in the clinic. I also attended a couple of meetings. One of my lab mates and I are planning on writing a review series with Dr. Hartl. Thursday, I spent the day creating an excel file with patient data for our retrospective study. This study is comp...

  In this week, Monday I went OR with Dr. Gomall and all his surgeries were similar of what I’ve seen before. The only different surgery was a shoulder surgery,  it was very cool to learn the anatomy and understand how knee and shoulder are similar in terms on the joint movement but totally different when it comes to anatomical tissues and how they connected to each other. On Tuesday, I presented my Immersion term presentation and did attend clinic with Dr. Gomoll. On Wednesday, I shadowed Dr. Spector and he performed one of the most amazing surgeries that I’ve ever seen. It was Hemglossectomy. grafting of tongue, since the tongue has higher acidity and less blood vessels, using skin grafting will cause the graft to die before it got blood vessels and immune. The patient has tongue cancer, and some part of his tongue was cut, dr Spector take free flap on the hand with blood vessels on it. Then they’ll hook on his neck to get blood vessels. The new flap will have blood ves...

 This week went by so fast! The main thing I worked on this week was continuing to set up my clinical study. I have a lot of paperwork to get on top of and keep track of, and have to set it up so that we have a system before I return to Ithaca. We are trying to recruit more surgeons to be on the IRB so that we can access their patients to potentially add them to the study as well, but their email responses are elusive at the moment! Next week I will have to follow up and try and collect more responses.  I was also working on finishing up a gene analysis study from several years ago with a collaborator here. We met to discuss the data and how to make sense of it, as I haven’t had to interpret these kinds of graphs before. Hopefully we can make a story out of it to present at ORS! Next week I am looking forward to shadowing in the gait analysis lab at HSS – I haven’t ever seen a gait analysis on a human (I have spent the summer learning how to analyze mouse gait), so I am pretty...

 This week I spent more time at the clinical genomics lab working on my summer projects. Because the data analysis I was working on includes patient IDs which are protected information, I have to work on this analysis on the computers available in the lab. In the beginning of the week, I shared some preliminary results with Dr. Solomon who gave me some additional direction on how to continue this project and what my presentation next week and my poster and paper due in the next month should include. He was excited with the results and I am really happy that I was able to work on a project that will be helpful for the bioinformatics team and could be a part of the genomic data analysis pipeline in certain cases. I have also been brainstorming other ways the data from cBioPortal could be used. In the other project which included image analysis of H&E stained microscope slides by implementing a deep learning algorithm we ran into an issue with the need for GPU to run inference on ...

Much like last week, this week I continued observing Dr. Chandwani in both the OR and the clinic. As usual it was wonderful to watch Dr. Chandwani's work as he operated seamlessly to remove cancer and helped his various patients at all stages of the recovery process. While I haven't spent much time discussing it in my blog posts, I also attended some meetings with Dr. Heller's lab and learned more about the many different research projects going on. One interesting ongoing study in his lab is examining whether or not the contents of blood serum can be used as a diagnostic tool for multiple sclerosis. By collecting data from hundreds of MS patients and using artificial intelligence to compare their serum content, this project hopes to make the MS diagnosis process much more reliable, cheap, and efficient. Another amazing experiment happening in Dr. Heller's lab involves the development of a therapy-agnostic cytokine sensor. The measurement of cytokines can be a valuable ...

Week 7: 07/17/23-07/21/23 This week, I joined for rounds in the neuro ICU at WCMC once again, this week with my clinical mentor, Dr. Kamel, who was the attending physician. I learned about the importance of proper monitoring of glucose levels in ICU patients, specifically regarding hypoglycemia because it can lead to neuronal death, making the patients' conditions worse. Also, I learned that increased intracranial pressure can lead to swelling of the optic disc in the eye which is called papilledema. Additionally, I was able to see a patient get extubated which I found interesting. On Tuesday, the weekly summer immersion meeting was dedicated to short presentations talking about summer immersion experiences. It was interesting to learn more about what type of research other students were participating in, as well as the various clinical experiences they got to be a part of while here. I will be presenting my experiences at the weekly meeting next week. For research, I compared the ...

07/17/23 -  07/21/23 This week, I spent most of the week conducting window implant surgeries and working on gathering data from the mice I did surgery last week. My surgical techniques have improved tremendously and I have become even more confident in my ability to conduct the craniotomies.  This week, we also received the mutant mice - mice with a gene RP58 deletion - that we will be studying its brain changes and functional connectivity after the gene deletion. I have conducted a craniotomy and implanted a window in one of our knockout mice. The surgery went well and we will be analysing calcium activity next week.  Last, but not least, this I presented my summer immersion research to our cohort and to the department. It is a bittersweet moment as this experience is coming to an end, but it is also rewarding to see my growth and all the new ideas I have for my research on the Ithaca campus.  These images are preliminary data of the calcium activity at the dif...

 This week I was able to meet with Dr.Avecilla from the cellular therapy lab. In previous weeks I had seen the apheresis machines that collect the samples as well as bone marrow harvest but he was able to discuss more about the process that occurs between collection and then transfusion. Particularly he shared the different sources of  stem cells like the marrow, peripheral blood and cord blood as well which is the most readily available source of hematopoietic progenitor cells. Once in the lab the sample gets processed and cell populations are positively or negatively selected before infusion. For example, Dr.Avecilla described antibody mediated lysis which which depletes T cells in the allogeneic transplant potentially reducing by or preventing the development of GVHD. The product of this bone marrow processing that  is of interest is  called the Buffy coat which is a concentrate of the white blood cells. This part is usually done through centrifugation.  Gene...

 This week I worked msotly on my research project and only shadowed one day in the clinic. On Monday, I worked with Kalle and Tyler to prepare a cadaver knee specimen for testing later in the week. It was interesting to see how the knee is prepared to undergo mechanical testing and the reasoning behind removing certain tissues for ease of handling later on. Most of the muscles were removed from the tissue and the bones were cut to match the length of the testing frame. the bone were later potted in epoxy to ensure fitting into the frame. On Tuesday, I presented to the immersion cohort about my work during the summer, including both the research work and the clinic shadowing. After the presentation, we performed bio mechanical testing of the intact sample and checked that everything was working so we could continue with the rest of the conditions later during the week. On Wednesday, I shadowed Dr. Strickland in the clinic were I saw two patella fractures but the patients had very di...

 This week, I mainly focused on my research project and spent less time in the hospital with clinicians. During small animal scanning in the MRI machine, there are many wires hooking up to the mouse, one of which tracks ECG and respiration. Unfortunately, one of the mice stopped breathing and died shortly after being in the scanner. The scans are repeated weekly in order to track the tumor growth, and will eventually need to be resected when it becomes too large.  This week, I also gave a journal club presentation in Professor Zuo's lab on two papers surrounding the topic of QSM. It was my first time presenting papers that I've read, and it was a great learning experience to test how much of the reading I understood. Because I don't have a background in physics, it was a bit difficult to understand the mathematical concepts used to produce different MRI images. I learned that there are two steps to producing a quantitative susceptibility map: 1) background field removal and...

This week I had the opportunity to work with Dr. Newman, a breast surgeon, and continue working with Dr. Ng, a radiation oncologist. It was very interesting to see the differences between the three different “pillars” of oncology. Dr. Newman spoke very technically with her patients. She usually explained to the patients where she would place her incisions and what possibilities they would have for reconstruction. She also had many in depth conversation about whether a lumpectomy or mastectomy would be best for the patient and how it would affect the patient’s treatment moving forward. This was my second week working with Dr. Ng. He works with patients who have breast cancer and patients who have pancreatic cancer, so it was interesting to see the difference between the two cancers. Coming from an engineering background, I found the physics behind planning the radiation treatments fascinating.  I also continued working with Dr. Cristofanilli in his clinic. Generally, the patients se...

 Week 7: 07/17/23 - 07/21/23 This week I continued to shadow the cardiology fellows in reading cardiac MRI scans, and I had the opportunity to work with a biomedical engineer at General Electric. During this time, new cardiology fellows have joined the Advanced Cardiovascular Imaging Lab to take over the positions of the previous fellows. It was astonishing to see the new fellows become accustomed to the environment and learn how to use the radiology software in a couple of weeks when it took me a whole summer! Additionally, I was able to learn about other cardiovascular imaging programs at other hospitals from the new fellows. As the prevalence of cardiovascular diseases continues to rise globally, it is interesting to see how different hospitals develop their own specialized programs to meet the diverse needs of patients. This has reminded me of the comprehensive training that medical doctors go through to provide the highest quality of healthcare. In addition, I worked with a ...

 This week, I confirmed the IP results with western blots. For each IP, I took three samples for running in the western: input (proteins extracted from the cell lysate), unbound (proteins that did not bind to the antibody-coated beads after overnight incubation), and elution (proteins that bound to the beads and were eluted off of them after overnight incubation). On the western blot image, I was able to see elution bands for the NSD2 and STAT3 IP’s, however I did not see H1 bands in the elution lanes. This means that I was successful in pulling down (i.e. capturing on the beads) the NSD2 and STAT3 proteins, but was not able to capture the H1 isoforms in complex with these target proteins, even though we excepted them to be interactors. The IP’s for H1C and H1E did not work, as there were no elution bands. However, I know that these proteins were present in the samples because there were bands in the input and unbound lanes. Overall, these results imply that all proteins of interes...

 I shadowed Dr. Marx in the clinic and OR again this week. In the OR, he had only ACL reconstructions, but a few surgeries that posed difficulties. In one, there was a radial meniscal tear that did not appear at all on the patient's MRI. The tear was able to be repaired, but was not planned for at the start of the surgery and made the whole process take significantly longer than anticipated.  While in the OR, I talked to one of the nurses in training. She was explaining to me how she had to be proficient both being a scrub tech and being a circulating nurse. That's  a lot of information to know! She also walked me through some of the steps of preparing the room and documenting the surgery process. This summer immersion program is meant to give us a clinical perspective to influence and support our PhD work. A lot of this perspective comes from the surgeon and I have certainly learned a lot from Dr. Marx. In talking with this nurse in training, I also learned how much more...

Week 7 - A journey through my mini project Name: Sally Lee Clinician mentor: Dr. Thomas J. Fahey On Tuesday (7/18), I presented my Immersion mini research project titled 'Generation of scRNA-seq profiles of human islets to study pancreatic neuroendocrine tumors.' The primary focus of this project was to analyze scRNA-seq profiles of pancreatic neuroendocrine tumors (pNET). However, I encountered several challenges to make progress on the project.   One significant obstacle was that I am not yet added to the IRB protocol, which meant I could not collect patient samples myself. This limitation forced me to consider alternative solutions. Moreover, pNET patients are relatively rare, making it difficult to gather a sufficient number of samples for analysis. Another challenge was the lack of available scRNA-seq data in Drs. Fahey and Finnerty’s lab that I could use for comparison with my established control dataset. Fortunately, I had a productive meeting on Thursday (7/19) with Drs...

 This week, I continued my experiences with Dr. Chandwani in both the clinic and the OR. In a grueling 12-hour day at the OR, I first watched Dr. Chandwani complete another laparoscopic pancreatectomy, and then was privileged to observe my first open surgery, a second pancreatectomy that (due to the size and location of the tumor, alongside other factors) could not be performed laparoscopically. I was quite surprised by a variety of things throughout the course of this surgery; first and foremost, as it was my first time seeing the internal organs of a living person, I couldn't believe how mobile everything was! Each organ was pulsing and shifting, and were not locked in a consistent and stable framework as anatomical images had led me to believe. In fact, the surgeons and fellows would frequently pick organs up and move them aside or even hang them over the edges of the incision onto the patient's stomach in order to better access the tumor. I had no idea this was common pract...

  In this week, Monday I went OR with Dr. Gomall and all his surgeries were similar of what I’ve seen before. I was able to collect two allograft samples from two different surgeries that he did perform. On Tuesday, I was working in the Biomechanics lab. While on Wednesday, I shadowed Dr. Jason Spector and Dr. Adam Jacoby.   Breast reduction and liposuction by Spector, the patient consented to breast reduction for both the breast and liposuction. Lipoaspirate was collected and Ashley processed the samples and shipping to Ithaca for further study. Amputation of the front part of the left ring finger by Dr. Jacoby. The patient has a small vascular disease that caused the blood to stop flowing, which caused the tissue to get an infection. Local anesthesia was used for only the amputated finger. Amputation was inevitable and even if the doctor decided to reconstruct the lost tissue, the new tissue will have a higher chance of getting infected. The section of the amputated fin...

Monday I shadowed Dr. Hartl in the OR. I watched him perform a transforaminal lumbar interbody fusion. I also collected bone marrow aspirate concentrate and intervertebral disc tissue that I processed in the lab. This was our first time collecting samples this summer so we were very excited.  Tuesday I joined a couple of Dr. Hartls group meetings and presented at two. I also shadowed him in the clinic where we obtained more patient consents for tissue collection.  Wednesday I joined Dr. Spector in the OR where I observed a liposuction. I also collected lipoaspirate which I processed in the lab. We had our second case for tissue collection from a TLIF surgery Dr. Hartl performed, so I also processed those samples.  Thursday, I joined Dr. Spector's lab meeting and got to hear more about the different projects he has going on. 

 On Monday, I shadowed Dr. Strickland in the OR where she performed a Shoulder Arthroscopy and a Bankart repair which was my first time seeing shoulder surgery. Additionally I watched her performed two common surgeries she does which a re a tibial tubercle osteotomy and a patello-femoral joint replacement. Later during the week, I worked in the biomechanics lab to shadow the meniscal root repair testing. However, during this day, a lot of problems with the testing device arose and troubleshooting keep pushing the start of the experiment. At the end, the joint was not adequately prepared and testing need ed to be rescheduled to next week. Finally, I shadowed Dr Strickland in the clinic on Thursday where a physical therapist was also shadowing. It was interesting to chat with the physical therapist in between patients about how their work complements orthopedic surgeons care and treatment.

Monday (July 17th, 2023) I attended Dr. Carli's clinic on the 7th floor of the Weill Cornell East River Professional Building. Dr. Carli consulted over 20 patients during the clinic with various knee and hip ailments. I left the clinic around 1pm, to attend an animal facility tour at the HSS Research Institute. I have been waiting to take this course for over a month and it was the last training required before I can handle the laboratory mice. I stayed in the lab until 6pm, where I headed over to the HSS OR to shadow a knee revision. The plan was to remove the patient's total knee spacer and insert an articulating spacer. The surgery ended around 11pm and the final treatment plan was the removal of the spacer, addition of antibiotic beads, fasciocutaneous flap, and medial gastric exploration. Tuesday (July 18th, 2023) The Prosthetic Joint Infection (PJI) research groups have weekly meetings at 8am at HSS Research Institute on the 6th floor. The group is led by Dr. Mathias Bost...

 This week I was able to start one of my experiments with a couple of different cell lines to test the menin inhibitor. As I mentioned previously, it is known to work for leukemia but there is potential that it could have an effect on other hematological malignancies. The goal is to then construct a dose-response curve with the different cell lines using Leukemia cells as our control. That took up most of Monday because it was a new protocol but I was glad to be able to start it.  On Tuesday we had our weekly meeting where we had the opportunity to hear a talk about the impact of Chat GPT on health care and the different applications that are emerging with this technology. As interesting and powerful as it is we also discussed some potential ethical implications that we may see as this program continues to grow and develop.  On  Wednesday I shadowed Dr. Jason Spector for his bilateral breast reduction and liposuction procedure along with Ashley and Salman as they col...

 This week has been great, because my IRB is finally approved! I spent this week setting up the protocols and beginning to screen patients. My study is pretty specific, so its going to be a bit of a struggle to find all of the patients for the study, but I am excited to get it started and hopefully get some good data! It has been interesting to see how now that the IRB is approved exactly what you have to do to stay compliant with the consent forms and the information tracking. Each one of the patients in my study has to have a separate form for screening and consent, just to have a paper trail of the record. In addition to that I have to coordinate getting the consent with a clinical researcher, since I cannot obtain the proper consent. This will be a very fun experience! We also had a mentorship lecture this morning that was very interesting. It was a good time to reflect on how I mentor others and a good reminder on how to get the most out of my mentoring relationships. It’s not...

 Week 6: 07/10/23-07/14/23 This week, I joined Dr. Judy Ch'ang in the neuro ICU at WCMC. I saw a variety of patients, including those with intracranial aneurysms, small vessel disease, stroke, and cerebral edema. It was interesting to see the improvements in the medical images for patients who had undergone surgery, especially considering how serious the conditions they are suffering from are. On Tuesday during our weekly meeting, we had a guest presentation by Dr. George Shih regarding the potential impact of large language models in healthcare. Dr. Shih discussed the evolution of large language models, such as ChatGPT, and how they could potentially be used in healthcare. For example, generative AI could produce synthetic patient data that could then be used in research. However, he also warned about the pitfalls of these models, such as hallucinations, that may pose an ethical problem if applied to healthcare. On Friday, I attended a mentorship lecture by Dr. Elizabeth Hecht. Sh...

 This week I spent my time in the molecular pathology lab with the lab technicians. I was able to see how patient samples are handled and processed in the lab from when they are received from surgical pathology to the time that they are placed in the sequencer. It was interesting to see with how much care the samples are being handled by the technicians. Often, tissue samples are very limited so no amount of the sample can be wasted when it comes to getting a successful test that can be confidently interpreted and can provide meaningful diagnostic or prognostic information to the patient's oncologist. Because tissue is received on glass slides and is formalin fixed, technicians can scrape the cells off of the glass slides. Typically, multiple slides are necessary to get to the required extracted DNA concentration. For example, from biopsy samples a rough average of 9 glass slides will be scraped to produce enough DNA for the NGS gene panels available at the lab. After scraping, and...

 07/10/23 -  07/14/23 This week has been the most impactful week during my summer immersion experience. I started the week by doing more surgeries in mice and attempting to implant more window. Unfortunately, not all of my surgeries did not go as expected; however, I was able to learn from my failure and starting to get better doing the craniotomies. Then during clinic hours, I had the honour to see many patients whose brain tumors were removed years ago and there is no case of remission or reoccurrence. It was amazing to see the happiness and satisfaction on their faces. During the hospital rounds with Dr. Schwartz, I got the privilege to see and interact with some of his patients. It was incredible to see one of the patients who had had a procedure done a day before and only after one day post-op, the patient looks extremely well and felt ready to go back home. For the rest of the week, I was able to practice more on my surgical skills and got a perfect craniotomy and window...

This week, I did the immunoprecipitation experiments as planned. Besides NSD2, I also included another histone interactor, STAT3, to further test the capabilities of the IP protocol. Next week, I will be able to perform the western blots to confirm that the IP’s worked properly. The western blots will also help to verify the specificity of the antibodies I used for the IP. For example, I want to make sure that the H1C antibody does not also capture H1E and vice versa. When doing the IP, I was able to confirm that there was an acceptable amount of protein present in the samples after the protein extraction step via a BCA assay, but I was not able to tell if our target histone proteins were included. If the western blot confirms that the IP’s worked properly, then, if time allows, I would like to redo the IP’s with biological replicates, so I can prepare and run them on the mass spectrometer back at my lab in Ithaca. I continued with mouse work this week as well. Within the past 10 day...

Week 6 - Mini project Name: Sally Lee Clinician mentor: Dr. Thomas J. Fahey This week, I have been working on my mini project for the presentation next week. While the objective of my project was to analyze pancreatic neuroendocrine tumors, I was not able to be added on the protocol on time to be able to obtain any tumor samples from the patients. Hence, my project only involved analyzing single cell RNA-seq data from the normal population with healthy pancreas, that could be used as a control when I have the tumor samples to analyze. I was hoping that I could do some analyses that are meaningful, so I searched if there is any publicly available database of sc-RNA data from patients with neuroendocrine tumors. However, I could not find anything useful. The data published in github or archives of the papers on neuroendocrine tumors also needed approval from the writers, and it has been challenging. So, for the scope of the mini project, I decided to stick with only presenting the contro...

 This week, we imaged our mice that were injected with breast cancer cells from last week. We measured their tumor sizes and put them in a Bruker 7T MRI for small animal imaging. A method called intravenous tail vein injection is used for inducing gadolinium. Gadolinium was used for image contrast, IV for hydration, and cyclophosphamide for chemotherapy.  Small Animal Imaging MRI (7T) Additionally, we performed another round of cell culturing on the SCC VII (head and neck) cancer cell line. The cell growth plates are first derived from frozen cells (seeding phase), followed by a passage phase where cells continue to proliferate. It is important that no bubbles are introduced during the plating stage as cells will not grow in those areas.  SCC VII Cell Line under Microscope For the clinic this week, I was able to observe an ACL and total knee repair by Dr. Robert Marx at HSS. Additionally, I also saw an aortic valve replacement & ventricular septal defect repair in the...

This week started off with my research progress presentation in the Cristofanilli Lab meeting. During this presentation I summarized everything I had done thus far and led an open conversation about where and how my work could be applied in the future. We discussed the possibility of continuing this project as a collaboration when I return to Ithaca which I am excited about.  Since the program is nearing the final weeks, I tried to spend as much time in the clinic as possible. I was back to my regular schedule with Dr. Cristofanilli and spent two full days seeing patients with him. We had a few unique patients this week and I appreciated the conversations I had with Dr. Cristofanilli regarding which type of treatment would be best for the patients. Specifically, I saw one patient who had a glycogen storage disease in addition to breast cancer. While I am unfamiliar with glycogen storage diseases, it was intriguing to consider how to balance the patient’s cancer treatment to manage ...