I am a/an:
Laidlaw Cohort Year
Rooms participated in:Columbia University
1. I have found that reading through papers that detail the mathematical modeling methods that supplement my current work gives me essential insight into the specificity of my unique applications. Understanding cell state and composition (part of a sample or cluster) as having a significant role in my analyses has shifted my original extracted data to be more predictive of the outcomes I am measuring. For the regression modeling portion of my project, I had some issues with a tool for obtaining cluster-specific infection severity markers, but I have now amended that by further discriminating the input data. I now plan on constructing separate classifiers for the cell subtypes to get gene signatures that best distinguish among them marked by severity/composition. Then I am implementing a binary elastic-net model using the gene signatures for each cell type by considering a certain cell type as one class and all other cell types as another class given the severity feature.
2. Github issues, Biostars, and the protocol information from related publications/tools have been invaluable for technical troubleshooting and scoping out where and how my results feed into current literature. Additionally, since my use case is often very different from the presented examples, I am prompted to experiment with novel methods detailed in community guides.
Github and stack overflow have also been valuable resources for me while troubleshooting technological issues. Additionally, going through papers with similar goals/experiments has also been really helpful, especially since they often look at similar problems or questions in different way. I really look forward to hearing your presentation today!
While my ultimate long-term goals have not dramatically changed since I first started my research, I have run into a lot of technological issues that have changed the course of my project. I have had some trouble getting software and technology that could improve the quality of my 3d models to work, and a lot of software I have gotten to work does not work as well as I would like it to. These issues have actually taught me a lot about coding and basic computer science, something I have wanted to learn about for a while, so I am partly happy to have run into these problems. However, these delays have some implications on my work, as the flowering season for columbines, the flowers I am working with, is almost over, which means I have to hurry to collect my data and make sure everything is working properly.
2. My graduate student advisor has been really helpful with trouble shooting different kinds of software. He is very knowledgeable about computer science and is always ready to help and explain ways to fix different issues.
1. My current goal is to compose a paper by the beginning of next semester so currently I keep track of all my progress through detailed notes. I am still working to further my primary research questions. What are the molecular mechanisms that underpin clinical evidence of more severe SARS-CoV-2 infection status when a patient has diabetes, and how may dysregulation as a result of SARS-CoV-2 infection instigate the development of diabetes? My aim is to complete a cluster elastic net regression model to identify gene signature predictive of SARS-CoV-2 infection status informed by cell composition and differentially expressed genes. Additionally, I am working on a comparative transcriptomic analysis of SARS-CoV-2 across stages and type 1 and type 2 diabetes. With a clear step-wise pathway I hope to be better equipped to tackle challenges.
2. Patients with diabetes and COVID-19 are at a heightened risk of developing severe complications, such as acute respiratory distress syndrome, multi-organ failure, and death. This increased susceptibility may be attributed to the underlying inflammation associated with obesity, insulin resistance, and other comorbidities typically seen in patients. Patients with hyperglycemia exhibit elevated expression of angiotensin-converting enzyme 2 (ACE2), the cellular receptor for viral entry, which further facilitates viral infection. The pre-existing chronic inflammation, augmented inflammatory response, and increased viral load in diabetic patients contribute to a systemic immune response known as the "cytokine storm," which is strongly associated with the severity of COVID-19. Moreover, SARS-CoV-2 infection can also induce dysregulation of metabolic factors and trigger the onset of diabetes. However, the molecular mechanisms underlying the bidirectional relationship between SARS-CoV-2 infection and diabetes are not fully understood.
Wow, your research sounds amazing and especially relevant, given the fact that we are just emerging from the SARS-CoV-2 pandemic, and now must deal with all the long term implications the virus has on our bodies. I hope I can read your paper once you finish writing it!
My most immediate goal for my research is to write a methods paper on the best way to create and collect data for 3 dimensional models of flowers on the population level. I also hope to continue my research throughout the rest of the summer and the upcoming school year if I can, utilizing the methods I have explored during this program in order to analyze the evolution of these flowers. My end goal is to be able to construct models of what the common ancestors of the flower species that I scanned looked like, which I think brings me to the second question that is asked. I find this project especially interesting because the idea that I can create models of species that no longer exist is something that I never would have thought as possible- it almost feels like time travel. But perhaps more broadly, my project is important because it can serve as an example as to how flowers, and more generally plants, can be studied in the future. Being able to collect enough models to study plants at the population level means that scientists can better explore the complex relationships and interactions between species, and therefore better understand and protect different ecosystems, a critical step in taking action to protect the natural world.
1. One ethical issue I have in my research is always a possible issue in Humanities research, but I find especially when studying modern artists, musicians, etc., it is difficult to not overanalyze them and over-assume their intentions because we have so much information about the context they lived in. It is important as a scholar that I don't mix up what I think their work means to me with what they think about it, so I don't misrepresent them. Especially with still-living artists, you don't want to box them in and be aware of your own biases and background.
2. It's been really interesting at least in the field of music to consider alternative critiques from beyond the Western world of the subjects and concepts that standard Western classical music theory takes for granted. Considering these other thoughts really allows me to realize the complexities of what I am studying, and how it might be more widely relevant.
I find the ethical issues you bring up about studying living artists and interpreting their work really interesting. I have not really given much thought about analyzing music, but I think your description makes it sound similar to analyzing books or other texts. I know it can be difficult not to over analyze books, but more importantly, and a topic that I do not think people spend enough time on, are the biases we all incorporate into our work, no matter the subject.
While my research does not involve any human or animal subjects, it does involve gathering lots of different flower samples, which I have been taking from Riverside park. The first ethical question that comes to my mind about my project is about the collection of flowers from a public space, one where I have no more of a right to pick flowers than anyone else. Of course, if everyone walking through riverside picked flowers, there would be none left for others to enjoy- which I think points to larger questions about the use of our natural resources. Picking flowers in Riverside park seems pretty trivial, but national parks across the globe have been struggling with the fact that everyone wants to collect a piece of nature. Tourism can destroy natural wonders, not just through the pollution it brings, but also because everyone wants to take a piece of what they see with them, eventually completely depleting the resources they have. In the future I am looking to collect flowers from the new york botanical gardens, but for now I will continue collecting samples from the park, which I think is justified as it will help understand (and protect if needed) these flowers better in the long run.
I enjoy hearing about the range of projects that everyone is working on in this cohort. During the school year, my studies were primarily STEM centered (apart from Lit Hum), and that’s what encouraged me to try something different and take on a humanities based research project this summer. The range of projects that people are taking on this summer inspire my research methods and academic interests. During our discussions, we talked a lot about how to begin research and what methods to take based on if we had humanities or STEM projects, and I found a lot of overlap between the disciplines that I could use in my own research that I hadn’t thought about before. Additionally, the range of projects make me curious to learn more about subjects I hadn’t thought much about before, such as linguistics and the overlap of music, which I found really interesting.
One thing that I have kept in mind is the fact that 6 weeks is not a long time at all. I can’t believe we’re almost 2 full weeks into this program. Time has always been difficult for me to manage, and I definitely felt it this week. I wanted to get so many things done for my research, but I only managed to complete about half of what I originally set out to do. Instead of beating myself up about not finishing everything on time, I remembered what was told to our cohort during our first meetings, which was that research is a process that is different for everyone. Every week will look different from the last, and just because I didn’t complete what I initially set out to do doesn’t mean I will have similar problems next week. Now I know that I have to adjust my goals for the week.
I definitely agree on the fact that there is some interesting overlap in STEM and humanities research methods. I found the ethical considerations every researcher must take particularly interesting, especially Dr. Klitzman's various examples of ethical shortcomings in different research projects. I also cannot believe how time flies, and have realized that perhaps my initial goals are a bit too much to complete in only six weeks.
1. As someone who has only really thought about STEM research, I have never fully understood what humanities research looks like, or how it works. Learning about the libraries and zotero, tools that at first felt geared towards humanities work, helped me not only better understand how this kind of research functions, but also ways I could potentially use these tools for my own work. I think engaging with everyone else's projects has opened up my eyes to the various forms research can take, as well as the important similarities of all these different types of research, such as the ethical considerations we all must think about.
2. I think the most applicable lesson I learned from last week was taking and implementing constructive criticism. Lab meeting is a time where everyone shares their latest work, and gets feedback from everyone else in the room about how to possibly improve their project. At first it was a bit stressful to present my project to a lot of knowledgeable researchers, but since then I have realized that the purpose of lab meeting is only to help everyone meet their research goals. In fact these sort of meetings have led me to see the spirit of collaboration in the lab, even when people are working on separate projects.