Week 3

This week is kind of busy for me. People in the lab have come back from ISMRM conference last weekend, and they have brought a bunch of new ideas in terms of MRI research field. So for this week, I spend half of the time doing my PhD research based on their new ideas, and the other half of the time practicing immersion.

On Monday, Aaron led me to the operating room to watch Dr. Schwartz's surgery. They were extracting pituitary tumor out of the patient's brain through her nose. This was my first time to enter into the operating room and watch surgery at such close location. Before Dr. Schwartz arrived, assistants helped Dr. Schwartz to clean the nose and dig a small hole though which tumor can be caught out of the brain. This process took around one and a half hour until Dr. Schwartz came and started to work on the critical part of this surgery. This main procedure is essential to complete the whole surgery successfully, and Dr. Schwartz was quite skilled to finish this part. They caught a small pituitary tumor from patient's brain and after that, post cleaning and processing steps were done by assistants again.

After watching the clinical surgery, I joined Dr. Gauthier's daily appointments with her patients and watched their conversations on Wednesday. Dr. Gauthier invited me to watch and learn, which was quite a meaningful experience for me to get immersed in doctor's daily work. The first patient was a young pregnant woman with potential multiple sclerosis lesions. This was her second appointment with doctor and back to her first one in February, she was already pregnant. She was in good condition after inquiry and physical exam, so hopefully she could get cured soon. The second patient, a 74-year-old woman, was not that lucky. Because of her age, she had several symptoms such as high  blood pressure, dizzying and blurred vision. Dr. Gauthier was so patient to communicate with her and ask about the medication she had been taken for the last half year.

As for my research, people in the lab shared their experience on Friday's lab meeting. The hottest topic was 'machine learning in MRI'. A lot of posts and talks have come out during ISMRM which caught our attention successively. Dr. Wang wanted me to do some research on combining machine learning with QSM inversion problem. I'm thinking of this direction this days and some of the preliminary results have come out. I'll show some of the results in future's lab meeting. Let's catch up with this trend.

Week 3

6/29/2018

This week has been a slow one. I submitted a revision for my IACUC protocol to address some logistic questions the reviewers asked. With the speed of things has been moving, I am starting to worry if the protocol can be approved by the end of July. Nevertheless, the practices on cadavers continued from last week and I got the chance to practice suturing techniques.

I spent majority of my time this week going through the iterations of my PTOA loader design. The goal of this loader is to have a motorized uniformed linear motion with control force and displacement, and optimally with a way of aligning the direction of the force with the femur. The alternative opinion in the lab is to induce the ACL rupture manually with a load cell monitoring the force exerted and discard the animals of which the measured force is high than a certain threshold. The alternative method, though it requires more skilled animal users, is much easier to develop than the motorized loader. Thus, the time on the loader design and prototype is very tight, as well as the budget. My initial design can successfully achieve motorized linear motion with displacement control and force monitoring. However, because of the simple crankshaft design, the uniform linear motion cannot be accomplished. As a matter of fact, as long as the slider is doing a piston motion (that is, all the variation of the crankshaft design) it is bound to accelerate and decelerate thus not able to move in a uniformed linear motion. Unfortunately, our budget does not allow us to get a linear actuator unless there is absolutely no other way. To solve this problem, I am trying a method of varying angular velocity of motor rotation, as a function of crankshaft arm angle and time, to obtain a uniform linear velocity. Luckily the displacement needed to induced ACL rupture is very small and can be achieved within the first quarter of the crankshaft arm rotation, making this method of controlling linear velocity possible. These are all still on paper, I finished printing all my parts today and the testing should begin next Monday.

Due to Dr. Rodeo’s schedule and other scheduling issues, I have still yet to be able to observe in clinic or OR. I am actively trying to resolve this.

(figure: 3D printed parts under UV light)   

Week 3: Dog in the PET scan?

Week three started off a bit slower compared to week 2. I learned more about what texture analysis is and the different methods for quantifying the “texture” of an image. One way to think about texture is to look at the frequency of the same pixel throughout the image, rather than the pixel intensities that are present in a scan. For example, in a picture of a tomato and an apple, both the fruits might have similar coloring, and the shape might be different, but the pattering of the apple skin will be different than that of the tomato. Although the human eye is good at identifying the difference in texture between these two fruits, it is not able to quantify that difference. However, with texture analysis, the difference in the patterns can be quantified, by looking at the standard deviation, range, spread or relation to the nearest neighbor of the segmented pixel intensities. These are just a few examples of the different types of texture analyses that are possible. The applications of texture analysis are in identifying diseased tissue from healthy tissue and finding similarities in output information from different biomedical imaging modalities. This has the potential for increasing the efficiency of the diagnosis process, by allowing the patient to take only one set of scans, rather than multiple ones.

I also learned about the physical theory behind how a positron emission tomography (PET) scan works. A radioactive isotope, germanium-68, is injected into the patient, which gives off gamma rays. When the gamma rays interact with the electrons in the patient’s body, they undergo a process called Compton scattering. During this scattering, part of the energy of the gamma ray is absorbed by a valence electron, emitting a lower energy electron and gamma ray. The electron is absorbed in the scintillator, which converts the electrical energy into photons. The scintillator is then connected to a photomultiplier tube, which absorbs the photons and progressively increased the electron output causing a high output signal. Although there are more complex procedures that take place, this is my understanding of the imaging modality so far. Next week, I hope to have more data so that I can test whether our hypothesis will be disproved or not.

Week 3

This week will probably be my most unusual during Immersion. I was in the city on Monday and worked to finalize the dataset for the manuscript that the lab is working to submit. I was able to fill out the dataset and make sure that it was ready for statistical analysis. At the end of the day I got one the bus and went back to Ithaca to run our labs 4-H career outreach program for high schoolers.

For the outreach program we ran a variety of activities and lectures that were intended to teach the students about what cardiac engineering is and the kinds of things that we do in the lab. I had been helping to organize the activities leading up until this week and I was also developing new activities that I would run when I returned to Ithaca. My activities were mechanical testing and development of bioinks. For the mechanical testing, I cut pieces of pig hearts that we were using for dissection into rectangles. I had the students test valve leaftlets, aortic sections, and myocardium. The myocardium tore for almost each group and they didn't like that very much, but the leaflet and aortic sections stretched well. They were able to get data points but I don't think they quite understood the purpose of the testing. I will probably try to further develop this activity and reuse it in future years.

The other activity that I ran was making bioinks similar to the ones that I use in the bioprinter for my research. I think they enjoyed messing around with the crosslinkable materials, but again, it took a lot of explaining to get them to understand why I was having them make it. Overall, I enjoyed the program and felt like the students enjoyed it and learned a lot. I took the bus back to the city on Thursday night.

Friday, I was able to help start doing the statistical analysis on the patient data. This came with some issues because I needed to take out outliers. I was able to have the fellow work with me to show me the echocardiograms of the outlier patients. They had unusually large values for heart measurements and we wanted to see if they were typos or if they actually were as large as their reports said. It turns out they were all true values and it was a good teaching lesson for me because I would have assumed that they were false values. The pathologies that those patients were suffering from was a good clinical lesson and I definitely learned more about the limits of the human heart.

Week 3

    This week I read through some paper about building microvascular model and use them to help perfusion imaging, especially arterial spin labeling. I found some open source dataset about kidney and brain vessel model. Basically, I didn't find any model about human, but I found mice brain gray matter vessel sliced data and statistic data of mice kidney, showing the diameter and length of different orders of vessels. This is maybe enough to build a kidney model, because the vessel structure of kidney is simpler, like a uniform tree model. But this is not enough to build a brain vessel model, because brain vessel is much more complicated, including different parts such as gray matter and white matter. Also, I met with some problems in data acquisition as Dr. Ajay Gupta doesn't run ASL routinely, I may need to use T1 DCE or angiography data instead.
    I tried to build some vessel model by myself. I finished a tree like vessel model for kidney, and I am working on brain vessel model now.
    I also talked about how this can be used in cerebral metabolic rate of oxygen estimation with another PhD in Dr.Wang's lab. We found that a good vessel structure can help to determine the orientation of white matter of brain, and the white matter orientation may influence the diffusion of water and the MR signal. Also, a good vessel structure can help with the estimation of cerebral blood volume.
    I didn't go to see the surgery with Aaron this week because of time conflict, and I will go and see the surgery next week.

Week 3

I spent this week immersed in clinical practice. I saw numerous patients with Drs. Knisely, Sanfilippo, and Ng covering brain, lung, head and neck, breast, prostate, and GI cancers and saw patients with early staged, advanced, and metastatic disease. I was able to see patient consults, simulations, treatments, and follow-ups and developed a more comprehensive picture of the standards of care for each patient’s condition.

With Dr. Knisely, I saw a patient that had a moderately sized WHO II astrocytoma that had a partial MGMT mutation and was IDH1 negative (both prognostic indicators). He was 40 years old, which is important because patients with grade II’s who are 40 and over have a different prognosis than patients under 40, thus potentially changing the prescribed treatment. This patient presented at their ophthalmologist with migraine-like visual defects and was referred to a neurologist for an MRI brain scan after their eye exam was unremarkable. He reported no other neurological symptoms, but did recall one episode of “Alice in Wonderland” syndrome around 20 years prior. This syndrome causes the patient’s perception of their surroundings to change, causing everything around them to appear very big or very small relative to their body. This suggests that the mass may have been growing slowly over the last two decades. The mass was resected, and the question was whether to do chemo/radiotherapy (RT) or just watch the area, saving radiotherapy for a possible recurrence. In patients under 40, the recurrence average is 15 years.

The patient was told about two clinical trials which show that in patients with WHO II oligodendrogliomas, patients that receive adjuvant RT, then PCV chemo have the best outcomes in terms of survivability. Because this patient has an astrocytoma, the data are not clear about what will produce the best outcomes, so he must weigh what he hears from Medical Oncologist and Radiation Oncologist about treatment vs. close following and make a decision about possible lifestyle changes caused by upfront RT/chemo vs. the likelihood of recurrence and subsequent inability to retreat a previously irradiated area with RT.

With Dr. Ng, I saw a 4-dimensional, adaptive simulation and treatment of a patient with pancreatic cancer on the Viewray, an MR guided linear accelerator. The technicians and Dr. Ng spent approximately 45 minutes with the patient on the table and the MRI running while they contoured the patient in the MR images and synced that contour to the treatment plan. The patient was simulated during a breath-hold, so the machine only turned the beam on when they took a deep breath and held it, aligning the target area with the contoured plan. If they exhaled or the target area shifted outside the boundary, the beam shut off immediately.  This process is completely automated in the software. Such a high level of accuracy enables Radiation Oncologists to use higher dosages of radiation since they do not have to worry as much about toxicity to the surrounding tissue. This was truly amazing to see in real-time. Dr. Ng believes that higher dosage will be the key to seeing better results in pancreatic cancer, which is hard to treat without MR-guidance because the pancreas is surrounded by the radiation sensitive bowel and moves substantially as the patient breathes.

Week 3

Transitioning away from the purely clinical aspect of my previous weeks, I spent the majority of this 3rd week learning about my research project, which deals with pneumothorax (lung collapse) during percutaneous lung biopsies under CT guidance, and how we can try and predict the incidence of pneumothorax as a function of how we insert the biopsy probe. This is an area of interest in the interventional radiology department, as these biopsies are some of the most frequent procedures performed (in this hospital, they see hundreds of patients a year for lung biopsies).

This provided both an opportunity for me to both use and improve my quantitative skills. For a case like this (binary output in response to large set of parameters), a common method to try and infer the importance of individual parameters is a logistic regression model. I’ve seen applications of this before but have never had the chance to explore the nitty-gritty details, so a couple of the days this week were devoted to understanding some of the underpinnings of the math. Already in reviewing some of the papers attempting to explore similar issues with the same methodology, I’ve noted some errors in conceptual understanding as what I suspect are clinicians use statistics software without properly preparing their data. For example, the misuse of categorical variables. Commonly, when categorical data is used in this type of data, it’s actually separated into n (one-hot) or n-1 (dummy variable) binary variables if the categorical data is not ordinal. This removes the bias of relative valuation – for example, if we imagine the categorical variable to be eye colour, assigning a value of 1 to brown, and 2 to blue, we’ve now explicitly valued blue eyes to have “twice” the value of brown eyes, which is a nonsensical relationship for what we’re interested in exploring.

In addition, I was able to explore some common tools in the machine learning toolbox – a particular example being the gradient descent function to minimize the cost function. What I found to be neat was to be able to learn about this method through linear regression – an algorithm that has a definite solution that we can use to compare gradient descent to so as to be able to see how it can be applied more generally.

All in all, while I don’t have access to the full data set yet, I’ve been able to get a model up and running using randomized data, so when I get access, I’m hoping to be able to learn something interesting with respect to previously undiscovered relationships!

Next week, I’ll be spending the majority of the week expanding the dataset we need for the project. This will involve compiling information about 1000! lung biopsies (but considering the scarcity of this type of data at all, this represents an incredible opportunity to work on something novel) so it’ll likely be the most monotonous work week I have, but I’ve scheduled a couple of other nice bits of clinical shadowing to be a part of my experience to try and break up the week. Of particular interest is a morbidity and mortality meeting, where I’ll be able to learn about how systems level errors affect procedural outcomes.

Week 3

Week 3 felt like it flew by! I cannot believe that we are almost halfway done with immersion already. This week, I saw three more CABGs, two TAVRs, and a thoracic surgery performed using cameras. One of the CABG’s that I saw this week was a re-operation. Performing open heart surgery for a second time is very challenging because scar tissue forms around the heart after the first surgery, and can be difficult to work around. Furthermore, after open heart surgery the heart can stick to the sternum, making it dangerous to re-open the chest in the conventional way. Because of this, Dr. Worku, one of Dr. Tranbaugh’s colleagues, used a special oscillating saw to cut through the sternum. The grafting of this surgery was also more difficult than normal, because some of the grafts typically used for CABG had already been used for the patient’s first CABG procedure. Additionally, I saw a CABG of a diabetic patient this week. The patient had significant calcification in their radial arteries that were used for the bypass. Though the patient still had an intact right internal mammary artery that may have been in better condition, Dr. Tranbaugh said that it is better to leave one internal mammary artery intact because diabetics have a higher risk of chest infection.

This week, I also had a long discussion with Dr. Tranbaugh about pressure measurements and catheters. In order to measure pulmonary arterial pressure, a Swan Ganz catheter is used. These catheters are able to travel through the heart using a balloon that floats with the blood. The balloon and catheter travel with the blood through the superior vena cava, right atrium, right ventricle, and pulmonary artery until they reach a small arteriole. The pressure here can be read by the catheter, and it is called the “wedge pressure”. Additionally, many of these catheters are equipped with a thermister, which can be used to measure cardiac output. Cardiac output, along with the patient’s body surface area, is used to measure their cardiac index, which must be kept minimally above 2 liters/min/m^2. Cardiac output can be measured by the thermister on the catheter if a cold saline solution is injected into the heart. The integral of the change in temperature with time can be used along with some other factors as an approximation of the output, or blood flow. Some of these concepts were a bit complicated to understand- I want to do a little more reading next week on pressure measurements and cardiac output, as we could potentially use this in our rat in-vivo MI models in the fall.

I also was able to see a camera-guided thoracic surgery with Dr. Reyes. The patient had significant fluid buildup in the lungs, and the procedure was to drain the fluid and attach the lungs to the chest cavity, preventing lung collapse. The entire procedure was performed thoracoscopically using cameras and a few small incisions, and took only an hour to complete. Dr. Reyes pointed out many anatomical structures of the lungs on the camera during the procedure- it was amazing how much could be seen by one or two small incisions!

One interesting concept that I learned about medicine this week was from a doctor I met while watching the TAVR cases, whose name escapes me. He said that in surgery, the enemy of “good” is “better”. This means that taking the time or the necessary steps to make a good procedure better can often put the patient at higher risk. This higher risk may come from increased time spent in the procedure or additional steps added. I am not used to this way of thinking, as my main experiences with clinical products have been on the R&D end, when I worked at GSK. There, it was always crucial that every step of manufacturing was perfect no matter the extra time or steps required. I carry this same mentality in my PhD research now. The doctor that I spoke with said these two ways of thinking are very different, but it is important for us, as engineers, to make our devices as perfect as possible. 

Week 3: New Platinum Eye(lid)wear and pearl earrings

I bet a good portion of you reading this have gotten eyewear to correct vision problems, and I bet all of you have experienced the feeling of closing your eyes to go to sleep at the end of a long day. For a patient with a partial facial paralysis and the inability to close their eye, a different kind of hardware for the eye is required to give them the ability to close their eyes. Eye weights are weighted pieces of gold or platinum which can be implanted within the eyelid to make it heavy enough to close.  I watched the implantation of platinum eye weights into a patient who had nerve damage to the facial nerve and could not close their eye, However,they had an undamaged cranial nerve allowing them to open their eye. The idea of the eye weight is that is makes the eye lid heavy enough that when it starts to close the weight will cause the eyelid to close the rest of the way. I watched this operation last week and during the procedure the eyelid was cut open and the layers were separated. The thin platinum weight was placed in the eyelid and sutured into place near the lash line. The eyelid was closed back up and sutured. This week in clinic I got to see the patient 1 week post-op for a suture removal. The patients eye was still swollen but they were able to close it partially with a better closure possible when the swelling goes down. 

Another interesting case spanning last week and this week involved pearl earrings that are both functional and pretty.  Last week keloids were removed from the patients ears and to prevent re-occurrence she had compression earrings put on this week to reduce swelling. The magnetic earrings with broad flat backs apply pressure to the incision site by compressing the earlobe.  I thought these were a cleaver medical device because they were functional while also looking nice to increase patient compliance.

I have been fortunate to see a wide variety of patients in clinic and in the OR. I saw things ranging from Botox to hypertrophic scar removal to full abdominal wall reconstructions after hernias. Most things go very well but I have also seen less ideal situations such as infected wound sites which had to be re-opened and flushed with bleach based solution. To clean the wound, stitches were removed to open it up and it was irrigated with a bleach based solution to remove the puss. Cultures were sent to determine the best antibiotics to give the patient.  

Before this experience, I never realized the potential of plastic surgeons to use pieces of the body to replace other parts to regain structure and function.  Also in clinic this week I saw a patient who had to have 90% of their tongue removed. The plastic surgery team was able to harvest a muscle flap and skin from the thigh to create a new tongue. The patient was able to regain the ability to eat and speak with this newly reconstructed tongue.

In lab, I am working with adipose samples to decellularize them. This is a lengthy 2 week process but the first round from the first adapted protocol is ready to be analyzed. This week I was trained on tissue fixation, processing, paraffin embedding, and sectioning and I am excited to be able to start using these new techniques next week. I am also in the process of testing and developing other protocols.

Beyond the walls of the hospital, I saw Phantom of the Opera last weekend and have been humming the music ever since. I've been enjoying the wide variety of food that New York has to offer and have been balancing the food intake with evening walks with friends through central park, along the river. or through the city.

Week 3: Optimizing MRI for better quality images

This week's routine was similar to my first week here. On Tuesday and Wednesday we went to Columbia to evaluate cases with Dr. Prince. Most of them have to do with lesions in the liver or the kidney. The ones that we are most familiar with are hepatocellular carcinoma and polycistic kidney disease. We go to meetings with other radiologists and pathologists to assess the nature of tumors and evaluate the possibility for a liver transplant for a determined patient. We also evaluate tons of cases everyday which has trained me enough to know at least where are the different organs of the body. It still difficult for me to read MRI images, but I think I have improved through time.

On my project side, I have completed the analysis of patients with tissue expander (TE) who have chest deformity. I calculated total volume of chest deformity, angle of deflection of the sternum, amount of fat in the back and the front, and imaging parameters. We have a total of 39 patients with TE and around 55 with breast implants, the last one to see if the chest deformity resolves after the implant has been positioned.
Today we got to image two patients with TE. This was great because it allowed us to play with the MRI parameters to get the best image possible and reduce the image artifact. We succeeded! We still need to refine our method to get better quality images so that is why we are also doing experiments with phantoms in which we varied bandwidth, slice thickness and frequency encoding matrix. We have seen that the bandwidth has a significant effect in the size of the artifact provoked by the magnet (it actually distorts the whole image if we decrease it), while the other two parameters don't change much the image quality. We performed this experiments with one type of TE phantom but we still need to do the same experiments with the other two left (we have three commercial models). I will also probably get into the MRI to serve as a control (healthy patient with no expander), that should
be really exciting since it would be my first time inside a MRI!

On the fun side, I got to see Phantom of the Opera on broadway. It was such an amazing experience! Definitely worth it. Also, my family has come to visit me so I've trying to show them around as much as possible. I was really happy to see them and share my life in NYC with them. Tomorrow we are planning to go to the statue of liberty and on Sunday probably a museum and central park. Hope they enjoy!

Week 3: Welcome to New York

I arrived in New York City! I’m happy I got to meet the Bostrom Lab in person after seeing them in Skype meetings for several months.

After a bit of time getting my IDs and paperwork in order, I was able to start with some lab work. I was introduced to an ongoing project that I will be helping out with this summer. The project is focused on understanding how alterations in the gut microbiome may affect osteointegration in joint replacement implants when an infectious agent is introduced. The gut microbiome is the community of bacteria that lives within the intestines. The gut microbiome is highly involved with digestion, but more and more we are seeing that the gut microbiome has a profound impact on the whole organism. We are particularly interested in how the gut microbiome affects bone growth and immunity because this is important for bone growth around an implant and resistance to infection after implantation. The gut microbiome can vary greatly between individuals, and ultimately we would like to know if there are ways we can alter a person’s gut microbiome that will produce better outcomes for joint replacement.

RNA sequencing is one method we are using to quantify the response of the joint to the implant, infection, and microbiome status. This week I got some training and helped out with the preparation of some RNA samples for a quality check. RNA sequencing gives an idea of what genes are being expressed in a tissue.  Instead of looking at a whole genome sequence like I did last week, this only focuses on the RNA that are currently being transcribed. The genomic data tells you everything about the organism, but the RNA data tells you what is happening in that tissue specifically at that time point. RNA expression varies between tissues such as cortical bone, cancellous bone, and bone marrow, so it is important to carefully separate those samples. I learned that is can be difficult to get clean separation, and the process involves many cleaning steps with buffer solutions.

One of my favorite things I got to see this week was a mouse model for joint replacement. They designed a tiny titanium implant, and the surgeons in this lab perform a miniature total knee replacement on the mice. It’s really impressive to see the precision that have to perform this microsurgery. I appreciate how well they are mimicking a human total knee replacement; it makes the model translational and relevant. In the coming weeks, I may even get to assist on some of the mouse surgeries.

Week 3: Molecular Pathology and Fancy Equipment

You ever wonder how geneticists get their super detailed information about mutations for each individual patient? Well, this is where molecular pathology comes into play. When people generally think of pathology, they picture tissue stains and tumor observations. But on the molecular scale, visual cues become a lot trickier as you cannot exactly see a genetic mutation under a microscope. Even cytogenetic screening that I mentioned last week cannot pick up the minute base pair changes seen in cases of leukemia or genetic disorders of all kinds. A collaborative mindset that combines molecular biology, bioinformatics, genetics, tissue anatomy, etc. all encompass what a molecular pathologist does.

How does this relate to a biomedical engineer like myself? Beyond simple data analysis skills, the emphasis on cross-discipline knowledge is something easily relatable to me and the techniques used by molecular pathologists in a clinical sense are also being used in basic science research such as my own. This provided an interesting perspective on how robust some of the biological techniques in the lab are and how differently they are used in the clinical setting versus the scientific setting. Funny enough, molecular pathologists use an extensive amount of PCR (Polymerase Chain Reaction) as the mutations they are looking for need to be seen in a clear way. Therefore, the best way to do that is to amplify the amount of DNA present within their clinical samples. My project back in Ithaca uses the same logic applied in cell culture to elucidate some of the genetic changes in cells exposed to stimulus. It’s fascinating to see how precision medicine like this is directly applied.

Another thing to note about this week is that clinical pathologists must use very fancy equipment with robotic arms and enclosed cages that look quite expensive. The amount of work that must go into designing the workflow around these machines is quite daunting and I respect the people who do this kind of work. Also, its fun watching a robotic arm perform a very meticulous task with ease and improve the process. That is engineering at it’s finest.

Week 3

This week has been stupendous! Last week, we started stability tests of radiolabeled nanoparticles in various solutions; the particles were incubated in PBS, mouse serum, and human serum. The week-long experiment finished this Wednesday, and I analyzed the data. We are going to rerun these experiments because we suspect that the human serum we used was old.

We also performed two more tumor resections from mice that had NSCLC tumors. One mouse was injected with nanoparticle drug conjugates, while the other mouse was given free drug via gavage. The tumors were each halved and one half was frozen for sectioning while the other half was stored in buffer for later analysis.

I also had the opportunity to passage an avian cell line, which I learned is very different from all the mammalian cell culturing that I have done in the past. These cells are weakly adherent, unlike many mammalian cancer cell lines, which I did not know beforehand. I quickly learned that I had to be gentler than I am used to when washing the cells. Due to their low adhesion strength, it was faster and easier to detach them for splitting.

In terms of clinical experience, I hope to start shadowing several radiologists at Weill Cornell Imaging in the next couple weeks. They perform mammograms, diagnose breast cancer, and perform biopsies at their outpatient center.

Outside of lab, I got to see the Phantom of the Opera, which was one of the greatest experiences I have ever had! I also got to see a disco-gospel concert in Central Park and tried Turkish food for the first time.

Week 3: The Start of Two Projects

This week I spent most of my time working on my project which involves analyzing data from Dry Eye disease patients. I also have another project, which is in collaboration with Dr. Starr who is another ophthalmologist, which is to test whether sodium fluorescein eye drops have an effect on the topography of the eye.

The data analysis project involves ranking the loss of patient's Meibomian glands as either mild, moderate, or severe. The Meibomian glands, which are located in the eyelids, replenish the oil layer of the tear film which has a mucin, water, and an oil layer. When patients Meibomian glands stop functioning and disappear they do not grow back, which can lead to Dry Eye disease. Technicians are able to image patient's Meibomian glands by using a machine called LipiView. There are also other tests that they do for patients who have Dry Eye disease such as a tear osmolarity and a matrix metallopeptidase 9 (MMP-9) test. After ranking the patients' Meibomian glands, I will see if there is a correlation between their rankings and their results for the tear osmolarity and MMP-9 exams, as well as with their demographics. So far I have created a spreadsheet with the names of the Dry Eye disease patients and I am in the process of entering all of this data for each patient into the spreadsheet.

The other project involves determining whether there are any changes in the topography of the eye with sodium fluorescein drops. To see the dry spots on patient's eyes, doctors put sodium fluorescein into both eyes and then look at them through a microscope with a cobalt blue light. Some doctors think that it is better to measure the topography of the patient's eyes before the sodium fluorescein is administered because it might change the eye topography. We are hoping to recruit some volunteers for eye testing next week! ( P.S. If interested, please contact me! :))

I am having a great time in the city so far and am learning a lot from Dr. Brissette as well as the other ophthalmologists. I cannot believe three weeks here have already passed by, but I am thankful to still have four weeks left here to learn more and continue to explore the city.

Week Three: Babysitting in the ER: How did I get here?

On Tuesday afternoon, I stood in the hallway of ER Bay C discussing octopus stickers with an 8-year-old girl, trying to keep both of us out of the way of passing beds containing patients returning from surgery and imaging. So how did I end up babysitting in this hectic environment? One of the Emergency Room (ER) doctors was nice enough to let me shadow her on this day. When a young mother required a vaginal exam for severe pain and swelling caused by her IUD, she was hesitant to leave her kids but also hesitant to have them in the room. I thought: “This is my chance to do something helpful rather than just being a fly on the wall!” So, I stepped up and offered to stay with her two kids instead of going into the exam room.

The ER is a busy and crowded place with 2 beds per small room and beds lining the hallways, but most of these people are not in immediate danger. When people first come into the hospital they go through triage, either through the walk-in door or the ambulance bay and then they are sorted between three ER sections, mostly by random. Most of the patients I saw were experiencing pain in their abdomen or back or had bad flu like symptoms. I learned a few things during my time there: 1) There is a well-organized method to the madness 2) Most people in the ER are not dying 3) ER shows really must go looking for the drama to make it interesting 4) All hospital personal, especially those in ER, deserve the utmost respect for their effort and patience 5) I am not sure what to talk to kids about after we after we have named every animal sticker in the book.  

While I was in the ER, I took some time to talk to the Point of Care Technician. Point of care diagnostics is my area of research for my PhD back in Ithaca. Point of care means something that can be used anywhere, especially at a patient’s bedside or in developing countries. Typically, these devices work very fast and do not require a full-scale laboratory but may not be as accurate as typical testing. There are many of these devices on the market and in development, but this ER largely only used devices for blood nutrients (Figure 1), troponin for heart function, a blood clotting panel, a UTI detector, and a rapid pregnancy test. The largest gap in the ER and in the various ICUs seems to be diagnosing infectious disease. A positive diagnosis usually only comes from direct identification of a pathogen in a sample from a patient, which can take days if not weeks of culturing and testing. I am more motivated than ever to continue my work back home in point of care diagnostics for infectious diseases.

Figure 1. Alere EPOC Blood Analysis system used in the New York Presbyterian ER to measure pH, carbon dioxide, oxygen, sodium, calcium, potassium, glucose, lactate, and creatine in less than 3 min

I also had the opportunity to sit in on a patient visit for the Research in Old Adults with HIV (ROAH) project. The first part of the study involves the volunteer filling out a questionnaire for about an hour, but I had the chance to read the questionnaire and it got me thinking about how much work goes into designing a clinical research study like this. The phrasing of the question can influence the volunteer’s responses which is especially problematic when the questions are asking about emotions, as this one was. I look forward to getting the data from the clinic trial soon, so I can start analyzing it to see if what interesting correlations appear.

The rain kept me largely inside this week, but I have enjoyed walking on nice evenings. From the roof of my building I saw a lovely New York sunset between buildings (Figure 2). I look forward to attending a Broadway show soon. This weekend, I intend to lay in Central Park with a nice book I got from the library.

Figure 2. New York City sunset from the rooftop

Figure 3. Look Mom! New Coat! 

Bonus Facts:

•         Up to 1/4 of the worldwide population has latent or active Tuberculosis.
•         Tuberculosis is the leading cause of death in HIV patients.
•         Patients with tuberculosis and other infectious disease are kept in negative pressure rooms which suck air in, so the infectious agent doesn’t spread into the hallway.
•        Patients lacking an immune system may be kept in positive pressure rooms which only blow air out of their room, so that infectious agents don’t get into their room.
•         One HIV positive patient can have many different strains of the HIV virus in their system at any time.
•         Only one person, the Berlin Patient, has ever been cured of HIV. It was a happy accident and doctors and scientist haven’t been able to repeat the results, yet.