Week 7 – Garrett Beeghly

Clinical Immersion Week Seven

Garrett Beeghly

It is hard to believe that the last week of my clinical immersion term with Dr. Jason Spector in Plastic and Reconstructive Surgery at Weill Cornell Medicine has come to an end. In the OR, we observed the removal of a large pilar cyst from a patient’s scalp. She had developed this cyst over the course of several years. While the cyst did not present a direct threat to her health, it had become large enough to be painful and uncomfortable. In addition, the fibula flap procedure that I mentioned previously was also scheduled for this past Tuesday. However, the case was aborted after putting the patient under anesthesia for a number of reasons. First, the patient quickly became hypotensive and acidotic after being put under anesthesia before subsequently developing supraventricular tachycardia. This gave Dr. Spector and the other surgeons involved with the case pause given that the procedure would normally take eight to ten hours and result in substantial blood loss. Thus, the patient was ordered to receive a full cardiac evaluation to ensure he is fit enough to withstand the surgery, which has been tentatively rescheduled for the middle of August.

In clinic, we saw the patient with tissue expanders in his neck for a follow-up visit. Dr. Spector assessed the increase in skin created by the expanders and further inflated them within saline. In one to two more sessions, Dr. Spector hopes that the patient will have enough excess skin to graft over his facial burns. This week, we also debrided an insufficiently vascularized foot wound in an attempt to promote the formation of granulation tissue and observed an initial consult for breast reconstruction following mastectomy. In lab, I finished embedding and sectioning all the patient adipose tissue samples I processed over the summer. Once I am back at Cornell, I will analyze these samples via histology and immunohistochemistry.

Outside of the hospital, Spector Lab hosted a farewell lunch for us at Felice 64. We were able to meet previous members of the lab and say goodbye to the current members who helped us throughout the summer. We will miss you Ishani, Mariam, and Runlei! In addition, our Ph.D. class took a group photo and had our end of immersion dinner with the program coordinators at Petaluma on Thursday night. On Friday, we went out for drinks to celebrate the end of a productive and enjoyable immersion term. Now, back to Ithaca!

Spector Lab and friends gather for a farewell celebration at Felice 64.

Week 7 - Leigh

Having been in NYC for such a short time, I am remarkably glad to be going back to Ithaca. While some of the reasons for my happiness in returning to Ithaca stem from feelings toward the city itself, I also have a much different perspective on my normal day-to-day coming out of this program. Seeing how much of the medical system functions, both from the perspective of medical students, and of clinicians, has made me evaluate what aspects of my life I prefer, and which I'd be okay with swapping with someone in the medical field. Of course, if I were to conclude that I'd rather swap most things in favor of the medical student's life, perhaps I would reconsider my career in research. Surely, some people, after going through this program, will start looking at how involved the applications are to various medical programs, weighing their options, seeing how they might transition out of their doctoral work into medical school, or some related discipline. At least as of now, I would not count myself a part of that camp, which is to say I still think I prefer my choice to pursue a doctoral degree.

Week 7 - Xieyue Xiao

This week is very packed but also most exciting because I starting following the rounds! My clinician let me join the afternoon rounds with fellows and residents instead of morning rounds. Every afternoon, we meet in the office first and talk about each case one by one. Doctors will go through their cases, either old or new, and come up with their solutions. Dr. Satlin will be ready to answer any questions and comment on their treatment plans. If we have some time left, Dr. Satlin will give some small lectures. Last time he talked about the different generations of cephalosporin antibiotics, including their coverage and efficacy towards specific microorganisms. 

After all the case presentation, we will go to the hospital and see the patients still with questions. Dr. Satlin will ask them a set of questions. Sometimes I found some questions seem to be irrelevant, but they have the correlation. For instance, we have a patient with very severe back pain and we found the abscess in his liver from scanning. When we went to check he,  he was asked about any recent dental experiences and oral conditions. The reason is our mouth is colonized with a large flora of microorganisms and some times they can get into the bloodstream through a tiny wound, and maybe get into the liver from the bloodstream and form abscess finally. 

What I have learned are not only medical knowledge. I also found working as a doctor is not only about diseases itself, a large part of it is how to communicate and deal with patients. Everyone has a unique personality and it is very important to work with them in the correct way. And, with patience, always. 

Week 6 - Xieyue Xiao

This week we finally confirmed the 11 isolates by MALDI (Matrix Assisted Laser Desorption/Ionization) which detects the differences in 16S ribosomes. In our lab in Ithaca, we usually use 16S sequencing to finally identify the species. But here we have a much faster and less complicated way to do it. To set up MALDI, we just need to smear a proper amount of colonies on each spot, resuspend with the matrix provided and put it into the machine. It will firstly map in the clinical database and then the research database and finish the reports in less than 10 min!
As for the results, all of our 11 isolates are confirmed as Pseudomonas aeruginosa. However, they belong to at least three different strains of P. aeruginosa. It would be very interesting investigating how different are they at the genomic level. This will be revealed after I process all the samples and sequence all the isolates when I get back to Ithaca.

Week 7- Grant

And that’s a wrap. Sorry for the late post but moving from New York City back to Ithaca has occupied most of my time. Seven weeks went by extremely quickly, but I learned so much from a clinical perspective about mechanical circulatory support (MCS) devices. My work at Cornell in Ithaca, which mostly concerns clotting in these devices, presents itself as only a subset of issues plaguing the MCS industry. I learned about everything from right heart failure and pulmonary hypertension to non-surgical ways to manage patients with potential adverse events.

My project at Montefiore Hospital completed the enrollment and 15-day follow-up of a third patient in the Sildenafil to Prevent (STOP) Clots study. Again, the patient takes either Sildenafil or a placebo, and a device measures the patient’s response to vasodilation/nitric oxide release. My project will be presented as a case report as this is only the third enrollee of a potential 62. Stay tuned for future insight from Dr. Saeed’s group.  

It was great having an end of the year celebration with Kelly and Dr. Prince. In between good food and conversation, we all shared our most interesting experience during the summer immersion. It was great to see people who had an intellectually stimulating summer both through their clinical rounds and through their research projects. We were also able to see where our projects overlapped, and I can most definitely see the potential for collaborations between lab groups in Ithaca as well as potential new collaborations at Weill. I’d like to extend my gratitude to the BME Department, my advisor, Kelly, and Dr. Prince for allowing us all to participate in such a rewarding program.      

Week 7 - Daniella

Week 7: July 22-26, 2019

Last week of Immersion! This summer has gone by so quickly and has been such a whirlwind of experiences. From living in NYC to shadowing surgeries and patient visits to conducting novel clinical research, I have grown not only as a researcher but as a person as well. In general, this clinical immersion experience has provided greater depth and perspective to my doctoral research back in Ithaca. My interactions with clinicians and researchers in a hospital setting has pushed me to take greater initiative and be more persistent in achieving the goals I set forth.

As a culmination to my immersion project, I presented twice at the beginning of this week, once at a joint osteoimmunology meeting at HSS and once at Dr. Ivashkiv’s lab meeting. Yet, my immersion experience was not yet over as I still had additional samples to collect, process, and analyze in addition to shadowing surgeries. On my last day of immersion, I was able to shadow an ACL reconstruction surgery for which I was able to collect healthy patellar tendon for same day processing in the lab. Although I had already seen this type of surgery once before, this patient opted for a tendon autograft as opposed to a cadaveric allograft. Therefore, the first step was to harvest the appropriate amount of patellar tendon from the patient in an open procedure. I found it quite fascinating how the autograft tendon was prepared by the physician assistant on the side, measuring, sawing, cutting, and sewing the tissue to the appropriate length, width and shape. It is also somewhat surprising how much force is required to pull the tendon autograft through the knee joint to replace the ACL, which is done by pulling strings weaved through small incision holes above and below the knee. I am very glad that I was able to maximize my time not only on my last day but also throughout my summer immersion experience.

Once I return to Ithaca, I will complete data analysis for flow cytometry and prepare an abstract for submission to the annual Orthopedic Research Society (ORS) Conference. The skills and techniques that I have gathered as well as the preliminary data I have collected during immersion will directly benefit me in my doctoral research and will help jumpstart my first aim.

Tyler McNeill - Week 7

It’s hard to believe that our time in New York City has come to an end as we finished the last week of our Clinical Immersion Term! During this week, I was able to shadow Dr. Bostrom in the operating room for one last day and was able to shadow him in clinic for the first time before he left the city to attend a conference in Memphis. I really enjoyed the time during clinic, not only because it was extremely rewarding to see patients make postoperative progress, but also because I was able to see the full journey of the surgical procedure. During clinic, Dr. Bostrom met with new patients that were coming for initial evaluation to see if they would be good candidates for joint replacement surgeries. It was really intriguing to see some of the different concerns that patients have when deciding if they want to move forward with surgery. One new patient asked about being able to get on her knees and touch her nose to the ground so that she would be able to pray following total knee replacement surgeries. I had never considered how different backgrounds and lifestyles could result in specific concerns for patients, so this was really eye-opening for me.

This week in the OR, I was able to see my first primary joint replacement surgeries. Compared to the revision surgeries that I saw last week in the OR, the primary joint replacement surgeries seemed much more straight forward to my untrained eye. Getting to see some of the minor precautions taken during surgery to best ensure that patients will not require revision surgeries was really fascinating. I think that these precautionary efforts—which seem so routine to the surgeon—have a huge impact on the surgical outcomes. This could explain why, based on some articles that I’ve looked over, it seems that orthopedic surgeries generally have a higher success rate compared to other types of surgeries.

Overall, the Immersion Term has been an incredible experience! It gave me a new appreciation for the impact that my work in lab can have over a longer term. Though it’s sad to be leaving New York City, I’m excited to head back to Ithaca and get back into lab!

Week 7 - Aaron LaViolette

The last week of summer immersion has come, so this means the last blog post!

This week was mostly involved in shadowing Dr. Prince. While I was watching Dr. Prince read cases this week, I realized that I have come a long way in terms of how to read an image. When I first started watching images being read, I was really only certain of the modality of the image and the general anatomy (i.e. I could identify the organs). Now that I have reached the end of the immersion, I am now able to pick up that something is “right or wrong” with a particular organ. I am now also thinking differently. I am now asking myself questions like, is the lesion big or dark on T1?, T2?, does is show restriction on DWI?, was contrast given?, does it enhance with contrast? Indeed, this week Dr. Prince brought up a case on the computer and let me comment on what I saw. I used these questions to try to gain some insight. The image had a mass in the liver. I was able to see it was T2 bright, but not super bright like a cyst, and T1 dark. I was also able to see it was well circumscribed. The lesion was a hemangioma. When Dr. Prince told me what it was, it made sense based on the clues I was seeing.

Although I did not know all the vocabulary to describe what I was seeing necessarily and was not able to say what the lesion was, I was able to use clues to eliminate things the lesion wasn’t (such as a cyst). This is certainly an improvement over when I first started immersion. This made me realize that it is simple to train a person and given time they can learn. After all, in a short time of watching people, I was able to look for and determine clues as to what is going on, and if I was given a full rigorous training, I’m sure my results would be better. It also made me realize why it is simpler to train people instead of computers. Simply put people can learn things faster and with less examples, as compared to a deep learning algorithm. More importantly, people can do something a computer can’t: think. This reminds me that anytime computers are employed to help “find” a pathology, the radiologist should always be able to verify and override the computer’s answer if necessary.

Along these same lines, I also got to measure organ volumes for a few ADPKD cases and the T2* for a few liver iron studies (all verified by an MD of course). This week I was getting very close numbers to either Dr. Prince or Dr. Yin. This also emphasized the point that it is easy to train a person.

This week in the reading room Dr. Prince also made a couple of interesting comments about cancer. The first was that cancer is more likely among organs that are able to regenerate after trauma, such as the liver. This explained why many cases that where the patient had liver trauma (particular from hepatitis) in the past were being monitored. The idea that new growth has a better chance of becoming cancer is not particularly eye opening. However, it emphasized the importance of having a scan if you suspect any disease may be likely to occur, because early diagnosis is the best way to treat a disease. This is especially true with techniques such as MR, because there is no ionizing radiation.

The second point Dr. Prince made about cancer is was in the context of a skinny patient. On the MR scans we could see over time how the patient had lost weight, and just how skinny the patient was now, due the patient’s cancer. They are likely so skinny due to the cancer requiring so much energy. However, Dr. Prince mentioned how some people just simply eat more and are able to live for a quite a bit of time with the cancer, but how others simply lose the will to eat and die much sooner. This is an interesting point I did not realize, but it makes sense. It goes to show me the power of the mind. If they cannot overcome their negative thoughts and lose the will to eat, things turn bad quick.

The only trouble with MR, is if you have metal or magnets. Dr. Prince is often reading cases for breast reconstruction. In these cases, the patient wishes to have fat removed from them and placed where a breast use to be. Blood supply is important, and the surgeons want to know where the perforator vessels (vessels running into the fat) exist and how they interact with the muscle under the fat. Hence an MR scan is done to map the vessels. These patients many times have tissue expanders, which contain magnets.

This is a safety concern because the magnet in the expander will align with the magnet in the MRI, so the tissue expander will flip 90 degrees. However, Dr. Prince mentioned generally the 90 degree flip causes issues for the following reason. This is noticeable to the patient if they are laying on their back (because they can see it), but if they are laying on their stomach, they can’t see it only feel it. So, in his experience people tend to scream in the machine because they see something strange happening. In addition to this generally the higher the amount of fluid in the expander, the harder it is for the patients to notice the flip by feeling it happen.

However, sometimes these safety concerns as minimal compared to the risk associated with not being scanned, particular if the patient is worried about metastasis or new cancer. This week Dr. Prince had to clear a lady to enter the magnet with the expanders due to concern over metastasis to the brain. After the risks were explained to the lady she agreed to enter the scanner. The lady reported that she could feel the expanders flip 90 degrees when was near the magnet, and flip back when away from the magnet, but had no pain. Even with the flip, there was not much of an issue. Latter Dr. Prince commented that a lot of MR safety is based on extreme cases. This makes sense to me because like anything you design for the worst-case scenario. I learned that this design for the worst cases scenario principle is not different in the “design” of MR safety.

This week Dr. Prince also did some more research scanning, but this time with a phantom. A phantom is simply a large plastic tube containing fluid and other elements that should be able to be resolved on the scanner. Dr. Prince mentioned how this is used for periodic quality control. Because no one was in the scanner this time, Dr. Prince also used this as a teaching session to show a resident how to operate the scanner. Dr. Prince would suggest changing certain parameters to see what would happen to the image quality. This provided a great learning opportunity for me and really generated intuition on what happens to an image if a parameter is changed. I think hands on learning is particularly useful. Dr. Prince decided to go ahead and continue to train residents weekly as a sort of informal class in how to scan. I am disappointed I will not get to see more of these.

Week 7 - Nathaniel Wright

The final week is a good time to focus not only on what you have learned but also what you hope to achieve in future work. This past week I had the chance to finish review all of my cases, then to review them with Dr. Kim before they were finalized for the paper that we have been working on. The week which started with more data analysis ended with more paper writing as there was a push to submit the paper or at least get approval from the co-authors on the paper that will be submitted to journals. My finalization of the strain analysis was mainly focused on ensuring that the strain data corresponded to physiologically relevant results, the atrial volumes. The strain analysis also yields other values such as ejection fractions and atrial volumes. This is useful to ensure that the strain that is calculated is physiologically relevant and correlated with prior data that is gathered from cardiologists who read the echo. The strain analysis is done from annulus (where the leaflets meet the wall of the heart) down the chamber and back to the other side of the annulus. The trace must be made of the wall of the heart but due to the nature of echocardiagram often containing artifacts. This can make it challenging and it requires experience to fully visualize all the parts of the heart on echo accurately and quickly.
In addition to the work with strain, this past week I have taken more time to learn more about cardiac MRI. MRI provides a useful diagnostic tool that has several advantages over other common imaging modalities such as x-ray. One advantage is that there is no exposure to radiation for the techs or the patients. Additionally, the images that can be gathered are much more informative in some aspects about the soft tissues of the body that an x-ray will not be able to pick up. MRI improves as time goes on with improved techniques and also the additional power that computers are now able to compute. As time moves forward MRI becomes a much better diagnostic tool that is more commonly used. Cardiac MRI is an interesting case where the more powerful MRI machines do not necessary translate into better quality images. As MRIs work on the basis that things are able to remain in place for measurement after the excitation the heart is always moving and the blood is always flowing. Both of these aspects can cause artifacts to be present in the best case scenario. The anatomy of the human body makes so the patient must hold their breath in order to take a cardiac MRI. This does mean not everyone who should get an MRI will get one due to the difficulty of holding ones breath for certain individuals. In the end it is still the best option as a diagnostic tool.
The immersion experience has been a great chance to meet many individuals, to work with them and to learn from them. I have enjoyed many of the different procedures that I have shadowed, I have also seen many of the different ways in which doctors work. I have enjoyed all the chances that I have had during this immersion term and I am grateful for the opportunity to come to Cornell Hospital in New York City.

Week 7 - Ben

The last week! As I said goodbye to friends and colleagues this week, I realized how quickly I grew close to the scientists I worked with. The atmosphere of intensity and communal intellectuality makes it easy to build strong connections. I also realized that I will remember  The City fondly. Again, there's a sense of purpose that pervades everything and infects me, which is both exciting and stressful. 

This week I shadowed Dr. Michael Cross through knee and hip replacements. Dr. Cross was both highly personable and shockingly knowledgable, which made for an excellent experience. He was able to narrate much of the knee procedure as an experienced Fellow did most of the procedure. He explained that the Fellow was about to move and start his own practice. Another key point of Dr. Cross’ minimal involvement was that the procedure precisely followed Dr. Cross’ established technique, and he could be completely sure of the quality of the operation. It was shocking to me how much the procedure resembled carpentry. There were power saws, cutting guides, rasps, and drills. I was particularly interested by the electro-cauterization tool, which was grounded to the patient and hence could not deliver a charge to the operator as they cut through soft tissue. The sheer number of tools used and the necessity for absolute sterility was impressive. The technician in charge of delivering tools to the surgeon’s hands had to be completely sure of the procedure in order to preempt the needs of the operation. The method of selecting and purchasing the implant was also interesting. The sales representative for the company, a younger man, would provide information and recommendations, then the doctor would select dimensions for the implant and a technician would purchase the items, unwrap them, and deliver them to the sterile area. Due to the number of joint replacements, the company keeps a complete stock of inventory at the hospital at all times. 

This week I spent a lot of time taking images of synovial samples. I worked out some good positive controls for the method and was able to confirm the baseline efficacy of the technique. One important step was the establishment of a connection with a group generating a mouse model for PJI. Incredibly, they are able to implant a tiny prosthetic in the knee of a mouse, then inject  S. aureus to model an acute infection. That was exciting for me and bodes well for the continuation of this project beyond the summer. In that line of thinking, I also set up a plan with Dr. Donlin to exchange samples and keep pushing the project forward when I return to Ithaca. All in all, summer research was great for establishing connections to exchange samples and expertise. 

S. aureus (pink) infecting mouse muscle.

Week 6 - Ben

This week I realized how soon the summer immersion term will be over! It is surprising how little time there is left. As such I have been trying to make slides and take as many images as I can. Unfortunately this week I ran into trouble because the microscope I have been using was broken. I frantically searched for another microscope to use and set up several meetings, but right before my first training, the microscope got fixed! It is interesting how connected all the different hospitals are for use of cores like imaging facilities. In my search for other microscopes, I was able to contact and get potential use of facilities at Weill Cornell (I have been in the HSS research building). Using various connections, I was also able to make contact with imaging centers at Rockefeller and Memorial Sloan Kettering. It seems that the ability to work with various researchers and use various facilities is a major strength of the concentrated academic and medical campuses here. However, in spite of the willingness of people to collaborate, the bureaucratic hurdles are considerable. Each institution uses a different system for registering, tracking, and approving access where each system requires a series of convoluted steps that are largely unclear to new (and even experienced) users. Doubtless this is an inevitability when each institution is independent, but perhaps it would be worthwhile to make efforts to ease collaboration. 

E. coli embedded in a synovial tissue sample and labeled with fluorescent oligonucleotide probes (stain is Alexa 488).

I had an interesting meeting with a researcher in the histopathology core discussing the issues involved with immuno-histochemistry. Since I am trying to develop an analogous technique, it was incredibly informative to be taught by someone with extensive experience in various staining methods. She mentioned that paraffin embedding leftover is often the cause of most sample autofluorescence, which was new for me! Cryostat sectioning seems to be a better option, but requires extensive expertise and is quite costly. It also seems that antibodies must be specifically designed to be robust to alterations caused by fixation techniques. This makes me wonder what sort of alterations are happening in the ribosomal RNA due to formalin cross-linking. The lab I've been working in has recently started using a fixative that preserves DNA and RNA much better than formalin and I am interested in comparing hybridization results between the two methods. 

This week I also got a closer look at the inner workings of the histopathology core. The machines used for fixation, dehydration, clearing, and embedding are very efficient and produce reliable results. Although the system is efficient, there is potential for contamination with (dead) microbes that may force me to use my own fixation-embedding technique. Furthermore, the issue of communication between the doctor taking a human sample, the person carrying it to lab, the person who fixes it, and the person who analyzes is incredibly difficult and convoluted. Even being on hand to ask questions, the confusion involved is considerable. This makes collaboration between campuses intimidating to say the least, but it will be very helpful for me to have been here this summer to establish the face to face relationships that will allow such collaboration to be successful. 

Week 6 - Alex

This week I began work on developing a neural net that can detect premature ventricular contractions from an ECG.

The clinical research project that I’m working on requires that we identify, from 24 hour ECG data, whether a patient with PVCs is indicated for treatment with Adenosine. Currently, there is no known way to distinguish between patients with different PVC mechanisms. Some groups posit that the variance of the coupling interval between the previous QRS complex and the PVC could indicate an underlying mechanism: 

• Patients with a low variance in their coupling interval are thought to have PVCs originating from modulated parasystole
• Patients with a high variance are thought to have ectopic PVCs, originating in the right ventricular outflow tract

The clinical trial hypothesizes that adenosine will be an effective treatment for patients in the latter group. This hypothesis is based on an assumption that RVOT PVCs are mechanistically similar to ventricular tachycardias, which is treated by Adenosine.

I have implemented a neural net that is able to identify PVCs in ECGs downloaded from the MIT-BIH ECG database. Since I am able to find the location of the PVCs, I can determine the coupling interval for all the PVCs in a 24 hour time sequence. I will pursue two approaches for clustering patient data:

1. Calculate the coupling interval variance for all PVCs in each patient
2. Perform a principal component analysis on PVCs from each patient to determine if there is a principal component that clusters patients into two different groups.

In addition to these approaches, I will soon begin work with a Dr. Peter Oken and Professor Olivier Elemento on a project for analyzing ECG data using machine learning approaches. My hope is that I can apply these methods to make insights into the ECG data.

Week 6 - McKellar

The main project I have been working on in New York City is the analysis of a large set of single-cell RNA sequencing data in collaboration with Laura Donlin (Hospital for Special Surgery Research Institute). The data sets were collected using a low-cost Drop-seq set up that was developed by the Satija Lab, down at the New York Genome Center at NYU. They are more well-known for their software development (Seurat, https://satijalab.org/seurat/), but this Drop-seq set up boasts a tiny price tag, compared to commercial systems. The 3D-printed device (pictured below) as well as a small subset of the data sets that I have been working with were published in Nature Communications last year (https://www.nature.com/articles/s41467-017-02659-x).

(Stephenson et al, Nat Comm, 2018)

The data sets I am looking at are dissociated synovial membrane tissue (some with matched PBMCs) that came from 4 different types of patients- healthy, osteoarthritis, psoriatic arthritis, and rheumatoid arthritis. They were collected from four different joints- knee, elbow, shoulder, and hip. In total, after some quality filtering, the total data set contains roughly 130,000 cells. Below is a plot that shows each cell as a dot. The cells are plotted along two dimensions that are defined by dimensionally reducing the 130,000 by 29,000 gene expression matrix (130,000 cells by 29,000 genes) using principal component analysis and uniform manifold approximation and projection, or UMAP (https://www.nature.com/articles/nbt.4314). I am going to hold off on labeling any cell populations, or even to say how many cell populations there actually are, because I am not yet done with the analysis. I can say that there is a lot of interesting biology to be learned from this data and a lot of fun work left to be done!

  

This is a relatively large data set, that is spread across 4 disease states, 5 tissue types, and perhaps most importantly 38 different sample collections/preparations. There is a lot of room for technical differences between these samples, and that can easily skew analyses. There have been many methods proposed to integrate data sets and remove technical biases, but I am not sure if anyone has been able to conclusively show that their methods maintain biological differences after that integration (at least by my own standards). One important point of my analysis will be to benchmark a few of these methods (Seurat’s CCA, SCTransform, Scanorama, and Harmony to start with) and come up with a more quantitative way to measure the changes that these methods impart on our data.

We have a lot more fun ideas to combine computational methods with clinical data. This work won’t end next week when I return to Ithaca, but it will continue on for the foreseeable future. The Donlin Lab, De Vlaminck Lab, and Cosgrove Lab will begin working on a new project to study myositis at single-cell resolution and I am looking forward to coming back to NYC as soon as I can!

Week 6- Chase Webb

This past week provided me with an interesting opportunity to learn more about medical education. Around the beginning of July, many of the fellows in cardiology I had come to know completed their fellowships and moved on to their new careers as attending physicians. In their place, a new batch of fellows arrived to start their specialization in some field of cardiology. During this transition, I got to see the change from people who had spent up to three years working in this hospital, honing their skills in the cath lab or clinic alongside the attendings, to ones who did not know where the supplies were kept or what number to call to let the EP lab know someone was coming. While this did not reduce the level of care the patients received, the nurses and attendings made sure of that, it did slow down some procedures and result in many more questions and hesitations than I had been accustomed to. Before this happened, I did not think that much about how fellows and residents learn the on the job skills that cannot learn in the classroom or by reading papers. Things like what a guidewire feels like as it goes an atrium, getting a patient to swallow a TEE probe when they just don’t feel like they are able, and the nuances of holding an ultrasound prove so that it’s in just the right position for the image you are trying to take. It was during this time that I felt like I best saw what it means for Weill Cornell to be a teaching hospital. It also made me reflect on my own experience this summer and the kinds of things I could not have learned about medicine without being here to observe them first hand. I hope that going forward I retain this information and am able to apply it to the work I do. I think it is a great advantage to more holistically approach research because understanding what patients care about, and that those considerations affect medical decisions far more than studies and clinical trial data, will help me design therapies that will not only help people but that patients want to choose. Being able to do this will make my work more attractive, and by extension help both improve patient usage (hopefully for the better if I am able to make treatments that are better than what is currently available) and open the door for other innovative work in the field of regenerative medicine and cardiology.

Week 6- Mariela

We're on the final stretch!


This week, I essentially established how I was going to wrap up my experiments before I leave. It looks like I should be able to complete collecting and sorting samples but that I won't be able to see it through to RNA-seq. I'll still be sure to keep tabs on the project as it continues to progress. Despite the original lack of association with my usual research interests, I've grown an affinity to the project. I think I've really taken ownership of the project, taking it as my own. And I've learned quite a lot about prostate cancer!

While preparing the presentation this week, I was pleasantly surprised to find that I was able to communicate my research project effectively despite learning most of the information so recently. I have a lab presentation coming up that I'm somewhat nervous about since my clinician mentor would be present. Recently, he has been wanting to get into research more, so I hope I'm able to ease in his transition back into the lab (and not disappoint him!).

Fun in NYC: I was able to go to a taping of the Late Night with Seth Meyers, and we got seats almost at the front! I was also able to ask him a question, which was more nerve-wracking than it should have. Also, underrated museum: the Cooper Hewitt Smithsonian Design Museum. It so happens that they had an exhibit on the connections between nature and design. There were plenty of exhibits on biology, medicine, biotechnology, sustainability, biofuturism... very good for a bunch of BME PhDs!

week 6-Emily

              This week shadowing Dr. Spector was filled with some new patients as well as follow-ups of many of the patients we have come to know over the summer. It has really been a unique experience getting to see the patients in surgery and then follow their progression throughout the summer. One patient we saw a lot this summer was the one who had the Achilles heal surgery which ended up infected. After many weeks of debridement and use of the wound vacuum device, he ended up needing surgery to put a skin graft over the wound once it had sufficient granular tissue. This past week we saw the patient after that surgery. During the surgery there was a complication with the “twilight anesthesia” where the patient had a reaction and began coughing and vomiting. The patient had to be intubated and then put under general anesthesia. During this office visit, the patient complained about pain in his throat and jaw which Dr. Spector said was likely due to the process of intubation. This had made me think if there are ways to make the process of intubation simpler and less damaging to the patient.

              In addition, the patient who had squamous cell carcinoma removed on his head was back again to check on the wound left from the excision of the cancer. This patient has been back each week to check on the progress of the wound healing. Each time, Dr. Spector does debridement and cuts away at the wound to remove dead tissue and reveal bleeding, healthy tissue. This is a common theme in all of the patients with wound healing issues. You want to cut away at the calloused, dead tissue until you get to bleeding tissue, which is healthy tissue. In this patient, Dr. Spector used a matrix made by ACell to help facilitate healing of the wound. After a couple weeks of using the product on this patient, Dr. Spector thinks it was helping with the regeneration and this patient is improving each week we see him.

              There are some cases where unfortunately other conditions the patient has leads to complications with the surgeries we see. There was one patient who came in this week who had an infection of a hernia mesh implant. Unfortunately, this patient also has rheumatoid arthritis and was on Humira which had altered the immune system of the patient, likely contributing to the infection of the mesh. The patient is currently off of Humira to try and help with the infection, but suffering from rheumatoid arthritis as a result. In another case, the patient had developed keloids which are raised scars where the skin has healed after surgery. The keloids can grow to be much larger than the original scar which was the case for this patient. The keloids are more fibrotic and can be more tender and painful when the skin stretches. To fix this condition, the patient needs to have surgery to remove the fibrotic scarred tissue and then take precautions to ensure this type of scarring does not occur again. Dr. Spector said steroids can be used to prevent scar formation, however the downside to this is steroids will alter the healing process and could prolong the process since they act in an anti-inflammatory way.

              Another key moment from this past week was seeing the patient who had oral cancer and needed to use the forearm flap to repair the defect from the tumor resection. We have been following this patient’s progress for the past few weeks. This week, she came in and presented Dr. Spector with a plaque thanking him for everything he had done for her. The plaque thanked him for changing her life and giving her a “sweet lisp”. This moment really touched me to see how important health is to someone and how medical care makes so much of a difference in the lives of patients.

              Outside of shadowing and lab work, this week was filled with some great NYC exploring. Tuesday was my birthday and as a gift, my friends got me tickets to see Wicked on Broadway.

Week 6 - Charlie

The summer is almost gone- only one week left. I'm going to miss the city! In terms of my clinical research, I think I have hit a bit of a wall that I won't have time to climb over in my remaining week. I believe I have achieved my initial goal- a program that calculates precision and accuracy of rTMS- but I haven't confirmed that the program works with empirical data. Ideally, I would want to use fMRI and perhaps EMG to confirm that an M1 stimulation marked as successful in my program is indeed successful. I think experimental confirmation of this would take well over a month at least, which is time I do not have.Therefore, my final week here will be occupied with documentation. I want to leave the clinicians here with all of the information they need to operate my software, as well as understand how it works and how I based my ideas. Dr. Marei is talking about writing a paper on my project. The prospect is intimidating considering I only have a week here, but I suppose anything is possible!

Week 6 - Leigh Slyker

 It is at this point in immersion, as we are preparing to head back to Ithaca, that I am realizing just how desensitized I have already become. While I was not particularly squeamish going into this program, the number of operations I have seen has had a significant impact. Things to which I used to react so viscerally now do not have such an effect. This is of course not to say that I'm losing interest in the things I'm seeing. In many ways, I am more interesting in the goings on during surgery. Since the initial shock value of surgery has faded, I find we are able to ask better questions, pay better attention during the most important parts of the procedures. Still, with this amount of desensitization in such a short time frame, I can't imagine how a medical student must feel after so many more hours in the operating room.

On a more personal note, this week my mom had a lipoma, a benign tumor made of fat, removed from her hand. She was worried about the procedure, of course, and I was worried for her. Yet our concerns where wholly different from each others. She was most concerned about the procedure itself. Worries about the anesthesia, about the surgeon, about the pain medication they were going to give her, and whether she would need it in the first place. On the other hand, I had no concerns about the administration of local anesthesia to her hand, nor the removal of a small subcutaneous tumor from an easily accessible area.  Besides, I was confident that the surgeon, who specializes in operating in the wrist and hand,  would not incur any additional complications.

After seeing so many patients through the clinic, OR, and back in the clinic, the things I have most often seen as lasting issues are infections due to issues in post-operative care. As such, I was most worried that my mom would not be given adequate instruction in caring for her wound as it healed. That is the main reason I am glad I could be present, both at the time of the operation, to make sure I understood what needed to be done after the operation, but at home to help her work around only having one hand. I cannot deny that a nice aspect of immersion has been being close to home, especially if it means I can keep my mom happy and healthy after some small health issues.