All posts by eblake1

Halfway through my Summer at the BG&R Lab

I am excited to say that I have completed (a bit more than) half a summer working with Dr. Miller and her team in the BG&R lab! This summer I have dedicated my time to working as a research assistant with the Women’s Reproductive Team to analyze the mechanical properties of tissue in the women’s reproductive system.

Starting out this summer, I set out to develop my skills on applying computer science to practical scientific problems, how to do experiments, and how to work effectively on a team outside of the classroom. Beyond that, I challenged myself to further my understanding of critical thinking and problem solving in the industry, which this summer would be in academia, and my understanding of the women’s reproductive system and how the mechanical properties in our tissue contribute to our susceptibility to Pelvic Organ Prolapse. I can confidently say that through my experiences this summer I have far surpassed the goals I have set for myself in a very hands on way. When working in a research lab it is important to keep a well documented lab notebook. This allows you to keep track of the goals you accomplish throughout your time in the lab, both personal and professional, and also allows you to look back and see just how much you’ve learned throughout your time. My lab notebook has helped me stay on task, keep track of the things I’ve learned (and the things I haven’t), and build on my research on a daily basis.

In the BG&R lab, I personally am working on developing a plug-in, coded in C++, that will run in conjunction with the software we use to model tissue in silico (which means computationally) called FEBio. Our lab uses biaxial devices to test tissue within the reproductive system of mice to study the behavior and degradation of tissue under different pressures and loadings. Through experimentation, and collaboration with other PIs at different universities, we have worked to develop a constitutive model that models the material parameters of the tissue. This is developed from a strain-energy function that we manipulate to determine the stress and strain on the tissue in different configurations. The plug-in I am working to develop implements this constitutive model as a material type in FEBio. FEBio currently only supports a finite number of materials, so currently modeling tissue in the configuration we have developed takes combining many different smaller configurations with different material types which creates a very complex computational model. Once this plug-in is completed, we will be able to create our shapes in FEBio, assign the material type of our plug-in, and analyze the value of the stress on the tissue which exponentially decreases the complexity of the model. Moving forward, this plug-in could be further developed to create patient-specific models that could be used in clinical testing and analysis within hospitals and other sites in the medical field.

Along with this project, I have been learning the ins and outs of experimentation by observing and partially helping with many different types of testing, including the planar biaxial testing, the opening angle testing, and the pressure diameter tissue testing. I have also been training to handle and properly euthanize the mice we use in accordance with Tulane University Institutional Animal Care and Use Committee guidelines. These skills will help me expand on my further work in the BG&R lab.

The skills I have learned during my summer have helped me develop the steady hand and temperament it takes to be successful in a research lab, and in the field of academia. One thing that takes time and patience to learn is that research is an ongoing process and you have to find success in the small things to keep yourself from going crazy. Between my academics, extracurricular activities, research, and job I have a tendency to live life in a whirlwind, and find comfort in accomplishing tasks I have before me. This summer has taught me that even if you’ve completed the things you’ve put in front of you, there is always more to learn. The intellectual autonomy provided to you during individual research is both intimidating and refreshing, and this summer has given me the opportunity to envelope myself in that idea.

Every day I spend in the lab I realize how strongly the goals of our lab align with the goal to produce driven and fearless female leaders that the Newcomb College Institute has. Women’s health, let alone the women’s reproductive system, is studied by an extraordinarily few number of people in academia. The BG&R lab has felt this in our research efforts, as the studies and data sets to be used for further research in the field are scarce. I see our lab as trailblazers in the field because we really do have to construct our own models, machines, and ideas for ways to solve the issues in front of us. Being a part of this team has helped me train in the skills to be a trailblazer in my own professional development. Going into the field of Biomedical Engineering and Computer Science as a woman is an uphill battle, and working in the BG&R lab is giving me the ammunition needed to go in unafraid of the fight, and I couldn’t be more grateful for this opportunity.

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From Coding to Dissecting: My First Two Weeks in the BG&R Lab

I have officially finished my first two weeks working with Dr. Kristin Miller and her team at the Biomechanics of Growth and Remodeling lab! The BG&R Lab dedicates its time to researching the tissue within woman’s reproductive system, specifically what mechanical properties factor into the deterioration of strength in the pelvic wall. There are multiple projects within this area of study, specifically two focusing on Pelvic Organ Prolapse (POP) and Pre-term Birth. There are also projects that focus on tendons in the leg and aortic dissection, which is a tear in the inner lining of the heart that leads to blood leakage. Basically, what the BG&R lab all boils down to is the study of how the extra-cellular matrix (ECM) of tissue reacts to stress and strain.

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Walking into the lab on the first day, I wasn’t sure what to expect. I worked in the lab a bit this past semester, but I knew the direction of my responsibilities were more than likely to change come summer. I thought that I would probably be another lab hand, helping with some experiments, making solutions, and reading papers. I was more than surprised when I was told by my supervisor Cassie, a PhD student in Biomedical Engineering at Tulane, that I would be working on my own project! I have now undertaken the task of writing the code for a new plug-in being used to model the tissue we use in our experiments.

That probably sounds like jibberish to most people, and it did to me too at first. I soon learned that the software we use to model our experimental data is called FEBio and is used for Finite Element Analysis. Finite element analysis (FEA) is a computerized method for predicting how a product reacts to real-world forces, vibration, heat, fluid flow, and other physical effects. (1) This type of analysis allows us to measure how the tissue we work with should react to different stress and strain values placed on it, and whether it will break, bend, stretch and hold its authenticity, or whether it will lose its strength. As a computer science major, I have experience with many different programming languages, including C++ which FEBio is programmed in. I was surprised to find out that I was the only one in the lab with exposure to this language, and that they needed me to decipher their problem of creating a “plug in.” What a plug in does is allow us to model our tissue in FEBio using the parameters that we know through our experimentation affect our material. This comes in the form of an 8-page constitutive model, which is basically just a long and complex equation that models how the tissue behaves. (It’s as scary as you’re thinking it is, don’t worry I’ve included a picture of the first page below). So I was given the project to take this model, take what we know about FEBio, and figure out a way to write this plug in. Once we have a running plug in, we can then use this in our models by selecting on this plug in as our “Material” in the list of parameters, that way when we apply the different values of stress and strain we will be able to see what should happen to the tissue.

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I was extremely excited to learn that I would be undertaking this project, and that everyone was looking forward to seeing what I could come up with. It definitely puts a lot of pressure on me, but it also makes me feel like I am an integral part of the lab, and a true member of the team. To me, this all seems like a big puzzle, but much more complicated because I don’t have all the pieces, so I have to find them. It’s also nice to be able to help others in the lab understand coding and C++, and makes me feel my studying and skills are really paying off. Now I know this may sound extremely boring to some people, and trust me at times it is. I have also had the chance to see other aspects of the lab, such as touring the surgery rooms and observing how the rats are dissected and their tissue is prepared for loading in our biaxial testing machine (Pictured below). I am very excited for the rest of the summer, and to see what I am capable of accomplishing in terms of determining how to write this plug in. I am also anticipating getting to do some hands on work, such as dissections and tissue testing.

I love the possibilities this internship provides, and am glad that I will get to continue this into the school year. In the Biomedical Engineering curriculum, there is a required course called “Research and Professional Practice,” which basically just means working in a lab underneath a professor and taking on your own project within their lab. It is incredible that I have gotten the opportunity to start building a relationship with the members of this lab, and that I will get to continue my project through my junior and senior year in the same lab. I was fortunate that all of the professors in the BME department are very receptive to undergraduate students joining their labs, so this internship opportunity was not too difficult to find. If you are looking for an internship in research, there are so many opportunities at Tulane that you can take advantage of. Just reaching out to a professor you may enjoy learning from, and doing your own investigating into what they study is the first step in this process. I can promise from experience that it pays off, and hopefully it will lead to an incredible opportunity to grow both academically and professionally.

(1) https://www.autodesk.com/solutions/finite-element-analysis

Beginning a Summer in the Biomechanics of Growth and Remodeling Lab

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Hello! My name is Erin Blake and I am a rising junior majoring in Biomedical Engineering and Computer Science at Tulane University. I am from Mobile, AL, just 2 hours away from New Orleans, but I couldn’t feel more at home than I do at Tulane. I am so fortunate and excited to have the opportunity to stay in New Orleans for the summer, and begin research in the BG&R Lab in the Tulane School of Medicine.

BG&R stands for the Biomechanics of Growth and Remodeling, and is led by Dr. Kristin Miller, principal researcher in the lab and professor in the Tulane Biomedical Engineering Department. The BG&R Lab focuses on studying the extracellular matrix, how it deteriorates and regenerates over time, and how it responds to biochemical stimuli such as aging, pregnancy, disease and injury. This research is done through a combination of experimentation and computational analysis, and focuses specifically on the ECM of the woman’s uterus and cervix. The lab analyzes these properties through two types of biaxial testing, force-length and pressure-diameter testing,  which are then analyzed through a computer programming application called MATLAB.  This summer, I will have the opportunity to work with Dr. Miller and PhD student Cassandra Conway to continue this research, and even begin looking at the soft muscle tissue of the ECM, which is a property the BG&R lab has yet to study. My role will be to assist Cassie in the experiments on the mice that are studied in the lab, along with working with MATLAB to determine the way to factor in the soft muscle tissue to our computational analysis.

Below you’ll find my 5 learning objectives that I plan to focus on in my internship this summer:

  • To learn practical applications for computer science in problem solving in the medical community.
  • To learn the meticulous process of experimental based research.
  • To learn how to effectively work on a team focused in Biomedical Engineering outside of the classroom.
  • To develop my skills of critical thinking and problem solving through practical application rather than just theory.
  • To better understand the inner workings of the woman’s reproductive system, and thus help in the fight for better woman’s reproductive health care.

The opportunity to join Dr. Miller’s lab aligns perfectly with NCI’s mission to “educate undergraduate women for leadership in the 21st century” by providing me the opportunity to dive head first into two male dominated fields, Biomedical Engineering and Computer Science. This internship also focuses on NCI’s mission because Dr. Miller and her team are focusing on research that directly affects women’s health, specifically a condition called Pelvic Organ Prolapse. POP, as it is commonly termed, is a condition where the ECM of the woman’s reproductive system deteriorates and loses its elastic properties and strength. This can cause organs to “fall” into the pelvic cavity, causing extreme discomfort, incomplete bladder emptying, and an overall decrease in the quality of life for women. The most shocking part is that this condition affects 40% of women, and there is no research to this date to show why this condition happens, or proper ways to treat it. The work done in the BG&R lab tackles an issue that affects tons women, but has yet to be studied, which is not only enlightening, but inspiring as I begin my career in this field.

To prepare for my internship this summer, I have been studying the ECM, focusing on collagen, elastin, and soft muscle tissue, the factors we will be focusing on. I have also been reading articles and scientific journals to learn how to read and write scientific papers. I’m very excited to begin my work in the lab, and learn from the brilliant women who work in the BG&R lab. This will be my first experience working full time in a research lab, and this will be the perfect intro into the field of Biomedical Engineering. This will also be a great experience to combine my two fields of study in a practical first-hand way. The research Dr. Miller and her team are doing in the BG&R lab is groundbreaking to say the least, and I cannot wait to become a part of that work this summer.

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