Christian Acosta (MMAE)
Project Title: Organophosphorus Nerve Agents: Similarities and Differences
Advisor: Andrey Rogachev
Deborah Adesina (BME)
Project Title: Biosensors for health monitoring
Advisor: Professor Bhushan
I worked with Professor Abhinav Bhushan to create a biosensor for continuous monitoring of Asthma. The project involved putting together a more sensitive and accurate biosensor to help monitor asthma patients continuously. Current methods depend on the use of nitric oxide as the biomarker for asthma but increased levels of nitric oxide in the breath does not always mean that one will have an asthma attack. We researched other biomarkers and found that the measurement of eosinophils in blood is more dependable as it relates to the inflammation of the airways in asthmatic patients. We plan to develop a biosensor that will measure the levels of this biomarker in a closed loop feedback control system that can administer medication based on the level of biomarkers. This research project gave me an opportunity to learn a lot about how biosensors are dependent on biomarkers and how biosensors work. I was given the chance to choose what disease I wanted to create a biosensor on. This taught me some data gathering and research. Though I could not spend time in the lab, I did learn about the concept of creating a biosensor and hope to put it to reality.
Rediet Adugna (BME)
Project Title: Functional Assessment of Decellularized Extracellular Matrix in Failing Heart Tissue
Advisor: Marcella Vaicik
I worked in Dr. Vaicik’s lab on the Functional Assessment of Decellularized Extracellular Matrix in Failing Heart Tissue. The research focuses on understanding the biomechanical properties of the extracellular matrix (ECM) obtained from myocardial tissue at the time of left ventricular assist device (LVAD) implantation. The purpose of this research is to determine the changes of the mechanical properties that occur in the ECM of failing heart tissue. In this project, I sectioned and decellularized the myocardial tissue obtained after LVAD implantation. I also assisted Dr. Vaicik in rheology test. I then measured the mass of each sample before and after we ran rheology. We analyzed the result obtained from the rheology test and plotted the storage modulus and loss modulus using MATLAB to determine the stress-strain relationship. This project gave me an opportunity to enhance my data science and research skills. It also gave me a chance to learn how to use lab equipment including the rheology machine.
Kanishga Balamurrugarajan (BIOLOGY)
Project Title: Refining Models of Type 2 Diabetes
Advisor: Mudassir M.Rashid
Professor Rashid and I worked on understanding and modeling the pharmacokinetics of anti-diabetic drugs. My focus was investigating the dipeptidyl peptidase 4 (DPP-4) inhibitors and how they affect diabetes. DPP-4 inhibitors are a class of anti-diabetic drugs that reduce the glucose in the bloodstream by inhibiting the enzymes that breakdown the incretin hormone glucagon-like peptide-1 (GLP-1). We found that DPP-4 inhibitors cause glucose to decrease by increasing the amount of GLP-1 in the bloodstream, which stimulates insulin secretion and suppresses glucagon production. We studied the DPP-4 inhibitor drugs currently available on the market and compared the various side effects and pharmacokinetics of the drugs on patients who suffer from end-stage renal disease or liver failure. We found literature describing pharmacokinetic parameters and attributes of the DPP-4 inhibitor drugs. We worked on developing a mathematical model of the DPP-4 inhibitor drugs and its effect on patients who suffered from diabetes or liver/kidney disease in Matlab. Future work will involve integrating the models with other models of diabetes and incorporating the pharmacodynamics of the drugs in the models. Overall, this experience was enlightening because it was my first research experience at Illinois Tech. Through this ResMatch experience, I learned how to analyze the pharmacokinetics of drugs and how to quantify it appropriately in a research setting. In conclusion, this experience has given me a better idea of how to do mathematical modeling and in general, how to draw conclusions from the research based on literature findings and reported data.
Monica Bhagavan (BME)
Project Title: Clinical Decision Support System for Type 2 Diabetes
Advisor: Mudassir M. Rashid
I was able to utilize the skills I’ve learned in my engineering courses to a real-world application. Working under Dr. Mudassir Rashid in the Engineering Center for Diabetes Research and Education at Illinois Tech, I learned how to analyze and think critically about a problem and actually did not have the exact right answer. The project I worked on was an extension of an ongoing project to learn more about the relationship between exercise and glucose levels in Type 2 diabetic patients. This relationship is incredibly important for the algorithm behind the lab’s larger project: a model that can advise patients how much insulin to take or when to take antidiabetic medication based on their current status. Using previously obtained data from patients in the Chicago-land area, we attempted to model the data in MATLAB to analyze trends within the data set. Personally I learned what considerations and important factors go into the pre-processing of data such as data-cleaning, interpolation, extracting meaningful features and information from the data, analyzing the trends and patterns in the data, and compiling the right sets of data. We used MATLAB to process the data and prepare the data set for more complex analysis where relationships between physical activity and glucose trends can be quantified in Type 2 diabetic people. I also learned so much more about MATLAB, a platform software regularly used in higher-level courses. I enjoyed learning so from Dr. Rashid as he was very open to explaining and answering all and any questions along the way. He also pushed me to think more critically about the problems we were solving as we attempted to model the data. In the end, although cut short, I was very appreciative of getting an opportunity to learn more about modeling data sets and understanding trends especially in a field where I hope to someday make a difference in.
Dristi Chaudhuri (BME)
Project Title: Ex Vivo Validation MR and US Elastography for the Brain
Advisor: John G. Georgiadis
Alec Diraimondo (CSCI)
Project Title: Mapping Brain Disease
Advisor: Boris Gutman
Annah Elligson (BIOLOGY)
Project Title: A view from inside of cancer cells
Advisor: Jialing Xiang
I was selected by Jialing Xiang to do research on cancer cells. Her project was focused on the effects of artificial sweeteners on cancer cells in culture. It is well known that cancer cells divert a lot of energy in order to fuel their uncontrolled growth. In this study we wanted to see if sweetness had any bearing on their growth or the cells themselves since artificial sugars typically do not contain any calories and are many hundreds of times sweeter than regular sugars. Cell culture is a demanding skill that requires precision to keep your cells happy and healthy. In the first part of my RES-MATCH experience, I went through very rigorous training before I was allowed to work with any actual cells. I went through one week of pipette training which was verified by a spectrophotometer to measure my precision. After I passed this part of my training, I was taught how to change cell culture media. I needed to memorize the protocol and pass a practical before I was approved to work with cells. After I passed my practical, I was given a culture of cells to split so I could grow enough cultures to start my experiments. I maintained a culture of cells for one week, changing the media every two days. In this time I collected multiple kinds of artificial sweetener packets to use for my experiments. After one week, I began splitting my cultures to more plates so I could do my experiments. The day I was meant to start experimenting, the academic buildings were closed off to undergraduates (due to COVID-19), so I was instructed to kill my cultures with bleach and take pictures of them as they were dying. After this, the academic buildings have not been open, so I have been continuing my work at home by doing literature research on each of the artificial sweeteners I have in order to design the experiments that I was meant to do in the lab for this project.
Katia Flores (PHYSICS)
Project Title: Intra-operative Lymph Node Biopsy
Advisor: Kenneth Tichauer
I was part of a team of six undergraduate students working with Professor Kenneth Tichauer on his cancer research project. My personal project was named “lymph node in vivo”, and consisted of studying different imaging agents used in mice that have been infected with cancerous cells. My tasks were often very hands on and required lab work and preparations. They involved culturing the cancer cells and taking care of the cell cultures, and producing the medium necessary to keep the cells alive. A lot of this lab work was done side by side with a Graduate student also working with Professor Tichauer, and watching the dissection of mice to study the cancerous lymph nodes in an “in vivo” scenario, which is the eventual goal of the project. As everything shifted online, I took on a coding based approach for the project. My tasks have revolved around understanding the absorption of the imaging agent by the lymph node when compared to a cancerous cell. For this, I have been doing different models using MatLab that allow us to visualize the changes that occur in both the lymph node and the spheroid over time, by coding them as darker or lighter colors depending what is needed. Although I would have loved to be able to continue the hands on lab work, I have thoroughly enjoyed being part of this project, and have learned enormously from it. I hope to be able to work with Professor Tichauer and his team again in the future.
Alexandra Georgopoulos (BIOLOGY)
Project Title: Investigating the mechanism of functional selectivity in the D2 dopamine receptor
Advisor: David Minh
Andre J. Guardia (PHYSICS)
Project Title: Spinal cord modeling
Advisor: Omar Tawakol
My project consisted of the Development of a Surrogate Spinal Cord for evaluation of Wireless Floating Microelectrode Arrays (WFMA) used in Intraspinal Microstimulation (ISMS). A Thorough review of the mechanical properties of spinal cord parenchyma, pia mater and its structure was conducted. For the Pia mater an Elastic Modulus of 1.5MPa was found, whereas for the Spinal cord parenchyma an Elastic Modulus of 90kPa and a Poisson’s ratio of 0.455 were found. After this, the literature was reviewed to find a suitable material whose elastic properties could be fine-tuned to obtain these values. For the Pia mater the options were: Sylgard 184, RTV81111, QM Skin. For the Spinal Parenchyma: 12wt% of gelatin powder in water and formaldehyde crosslinker. After this a mold for the surrogate spinal cords was designed and manufactured. In addition to this, a physical testing system was also designed and manufactured. This system consisted of a microcontroller, a feedback rod linear actuator, a 5A motor controller, rails and anchors for the surrogate cords. Finally a 3D computational model was developed to quantify the amount of Von-Mises Stress each electrode tip exerted on the surrounding parenchyma. Physical testing was halted by the COVID-19 crisis. In conclusion, I would say the RES-MATCH program has taught me the importance of thinking like a researcher. Through the RES-MATCH program I learned how to properly structure my findings and how to strategically plan a project.
Abigail Gunderson (CHBE)
Project Title: Assessment of Renal Autoregulation
Advisor: Professor Williamson
Chandrika Haldar (BME)
Project Title: ADEPT Cancer Imager: Dry Lab
Advisor: Kenneth Tichauer
The project I worked on was based on a standard tissue simulation using a Monte Carlo (MC) based system matrix, where I depth testing for tumor found in the throat. This was done to gain a clear understanding of cancer margin around a tumor found in a patient, then according to imaging the decision is made to operate or treat with certain kinds of chemotherapy or radiation therapy as per requirement. To obtain a full understanding of MC based on MATLAB, I ran simulations for standard tissue as well as for fluorescence imaging. For the depth simulation, a block of "standard tissue" (absorption coefficient = 1, scattering coefficient = 100, anisotropy factor = 0.9) is illuminated by a pencil beam (infinitely thin beam). When the pencil beam is launched at x = y = 0 and travels straight down, it travels along a well-defined center column of voxels (the middle of the 51st column). The ratio of images of open (11.2% of incident light was absorbed within the cuboid) and closed aperture (31.3% of incident light was absorbed within the cuboid) gives us the depth profile of the imaged tissue after binding potential normalization. It was tested that the simulation time could be reduced from 100 min to 5 min, i.e., reducing the rate of photons per minute without any significant change in the color profile or 3D surface image. Hence, now I am further testing what changes can be seen when there is blood on the tissue surface by changing the absorption coefficient from 1 to that of oxygenated blood at ~780-800 nm. Future questions to be explored are the effect of change in refractive index when flat surface is not assumed, as well as when the tissue is not considered homogeneous anymore.
Patrick Hamilton (AMAT)
Project Title: Development of customized high resolution 3D microscopy for connective tissue biopsy samples
Advisor: Joseph Orgel
Working in Dr. Orgel’s lab provided an abundance of opportunities. I was able to work closely with his research in the structure of the junction between chordae tendineae and papillary muscle. We dissected hearts and put harvested samples through stress testing. Through the Res-Match program, I was able to work with a team in the construction of a 3D microscope. The first priority was to get our mechanism up and running, which took some time to order parts and fix up some materials. We then faced challenges in configuring the stepper motor, which rotates the sample, and coding in python to capture images as the sample is rotated. We had to consider the lighting, not just in the angles, but the frequency as well. One of the more complex challenges we faced was that of reconstructing the images into a usable 3-dimensional model. This is one of few things that has been manageable during the covid-19 outbreak. Although we were no longer meeting in the lab, Dr. Orgel reached out via video chat to the team to ensure we were all doing well. Although the project was discussed to some degree, it was clear that Dr. Orgel was also laying the foundation for a means of open communication so that the group could get a little socialization during this period of isolation. I was able to work on some incredibly interesting projects, but what’s more is I was able to build connections with incredibly knowledgeable people and collaborate with them on a collective goal.
Min Kyoung Kang (CSCI)
Project Title: Early Detection of Diabetic Retinopathy
Advisor: Kenneth Tichauer
Although my major was in computer science, I chose to work on Professor Tichauer’s diabetic retinopathy project with a grad student Elif Kayaalp Nalbant to learn about the disease and to utilize my programming knowledge to contribute in advancing the current research progress. For the first part of the research, Elif provided me with published articles that contained information about one of the methods called tracer kinetic modeling, which was used to quantitatively map the vascular permeability from fluorescein videoangiography from patients diagnosed with diabetic retinopathy. Although there were many technical terms that were beyond the scope of my knowledge in biology, I tried my best in understanding the material by doing more research about the background but also keeping in mind that my focus is to work on the coding part of the mapping of the data on MATLAB. In addition, Professor Tichauer held a weekly meeting in which he went over basic terminology of the overall topic of my project and answered specific questions that I had from reading the articles. The meetings helped me greatly in grasping the bigger picture of the project and allowing me to advance further on to the next topic. I also met up with Elif every week or so in which she went over the MATLAB program that contained the code for analyzing the data of the blood flow gathered from patients and producing a statistical graph from the data analyzed. Although I wished I could have worked on the MATLAB program longer, due to the stay-at-home order, I was not able to find a way to continue working on the code (I tried remotely connecting to a lab computer at Illinois Tech to run the program but it was too slow and the files were too huge to support the program) so after talking about the matter with Professor Tichauer, we thought that it would be best to take a different approach. He provided me with a published article that focused on myocardial blood flow quantification, since it was still very much relevant to my project and the same information could be applied to contribute to the original code. Currently, I am in the process of finishing up the reading and writing up a report on how the article could contribute to the code we have written previously. Overall, from my RES-MATCH experience, I can say that I’ve learned so much that I thought I would never get to learn since my major is in computer science rather than in a biomedical-related field.
Eunjin Kwon (BME)
Project Title: Development of Machine Learning Systems Framework for Fast Heart MRI Disease Detection with Safeguards against Clinically Embedded Errors
Advisor: Keigo Kawaji
My project was focused on detecting heart disease and diabetes using an AI algorithm. Before I started this project, I learned the concept of AI, supervised and unsupervised learning, and python environment. Utilizing representation learning makes a system automatically to find relevant features for a given task. I performed a 4-class classification of the heart image using Deep Neural Network. I wrote the code to run the program on the 16x16 data of heart image. Not only heart disease, but we also distinguish diabetes with enormous data. I used the data of capillary blood glucose(cbg), time, and bolus to detect mealtimes and hypoglycemia. To find the hypoglycemia, find every hypoglycemic event onset when cbg is less than 3.9 mmol/L in the patient's "cbg_imputed" data. And for the mealtime, I used the bolus as a meal marker and extracted the mealtime from the continuous data. With these simple codes, it was easy to figure out when the blood sugar falls to the levels below normal.
Tran Le (BME)
Project Title: Biomaterial scaffold design for cartilage regeneration
Advisor: Georgia Papavasiliou
I was paired with professor Papavasiliou to assist with a current project her lab is working on which is Biomaterial Scaffold Design for Cartilage Regeneration. When I first attended the RES-MATCH introduction event, it was interesting and informative to have the professors introduce their projects first before students could discuss with them right after the presentations. While working with professor Papavasiliou, I get to utilize my Cell & Tissue related knowledge as well as acquire more hands-on experience with cell cultures and hydrogel fabrication processes. Even though COVID-19 emerged quite rapidly and unexpectedly, our lab still communicates effectively to adapt and make progress. I was partially responsible for Live/Dead quantitative image analysis and I was able to do it from home. I greatly appreciate the support and guidance from Illinois Tech and especially BME faculty during the pandemic. Although I am unable to dive deeper into the study for the time being, I believe we all have done a good job coping and making progress in such a situation. I am looking forward to seeing more progress being made in the project as soon as the lab is opened again. I am grateful for Dr. Papavasiliou, Dr. Troyk, Pritzker Institute, and the BME Department at Illinois Tech to have held another meaningful program that helps students gain more experience in researching fields. Not only do I get to work with great people and learn from them, but I also gain the sense of being able to contribute and work toward a better cause which gives me the most meaning out of this researching opportunity. RES-MATCH is an ideal place for ambitious people to start their journeys to become successful and to help make the world a better place. I hope that this program will continue to thrive in the future.
Ruth Negru (BME)
Project Title: Sustained Silencing of Laminin Alpha 4 as Targeted Therapy for Weight Loss Maintenance
Advisor: Marcella Vaicik
In this project, we are studying the disruption of laminin alpha 4 expression to modify fat tissue cell phenotype from white adipocyte cells that store energy as lipid to beige adipocyte cells that burn energy. The hypothesis is that converting some of a human’s white fat into beige fat could help patients maintain their weight after successfully losing weight as a treatment of obesity. With obesity rates reaching all-time highs and causing a myriad of health issues, this project could be vital in the persistent race towards health and wellness. Using drug delivery strategies with the siRNA drug to disrupt the laminin alpha 4 gene expression, and therefore hindering white fat lipid storage, is the ultimate goal of this research project. Though the semester came with unexpected circumstances that hindered long-term hands-on research, I was able to begin some work in culturing human adipose-derived stem cells and studying their differentiation process. I learned how to seed cells for culturing, maintain an appropriate environment for cell growth, passage cells, and count the cell population. I read various articles and protocols on cell viability, staining, culturing adipose in hydrogels, and differentiating pre-adipocyte cells. The next steps for me in this project are differentiating the human cells into adipocytes and evaluating siRNA delivery effectiveness. We are in the process of developing standardized protocols for culture, differentiation, and drug delivery to human adipocyte cells to do repeated and robust data collection. I look forward to the future of this project, have been inspired by the research already performed, and am excited to collect and analyze the results from future experiments.
Sophia Nelson (BME)
Project Title: ADEPT Cancer Imager: Wet Lab
Advisor: Kenneth Tichauer
I have thoroughly enjoyed my time working as an undergraduate researcher in Dr.Tichauers ADEPT Imaging Lab within the Pritzker Institute at Illinois Tech. I think the hardest part about getting involved with research is finding what lab interests you and how you can apply your skills to their lab. RES-match creates an amazing opportunity for undergraduates looking to get into research because you gain insight into a majority of the faculties work and can reach out with confidence in what you want to do. Working in the ADEPT Imaging Lab I performed a wide range of activities. Within the first week I successfully cultured MDA-MB-231 green fluorescent protein-transfected human breast cancer cells. This process allowed me to become familiar with Fume Hoods, incubators, water baths, optical microscopes, centrifuges, autoclave, and safe handling practices of certain reagents and enzymes. Working with an amazing postgraduate peer, we set a goal in mind to what I want to accomplish and how much time I can dedicate for research. With this I worked alongside my peer in her research to dissected pig lymph nodes that matched the size of that of a humans, and freeze them to further inject a spheroid containing the cultured MDA-MB-231 cancerous cell line. With the dissected lymph nodes, I was then tasked to find a tissue clearing method that could easily and cost effectively implemented with the lymph nodes. To create the spheroids I prepared a protocol and made a methylcellulose solution that would be further used to encapsulate the cancerous cell line. As the impregnated spheroid was then implanted into the lymph node, I used Crytome, a Thermo Scientific device to cut the freeze dried spheroid and prepare slides that would then be used under a fluorescent microscope and pictures where captures of the specific location in which the cancerous cells lie within the lymph node. However as the semester abruptly changed to online, we could not finish our work with compiling the lymph node photos for a 3D model in MATLAB. Overall this experience was very valuable in gaining transferable skills such as critical thinking, independence, and communication for future careers.
Keara Rigg (CHEMISTRY)
Project Title: Opioid Receptor Agonists vs. Antagonists
Advisor: Andrey Rogachev
My RES-MATCH experience was both challenging and rewarding. I got the opportunity to work with Dr. Rogachev in his computational chemistry lab over the course of the semester. My project was to use computational chemistry along with quantum mechanical theories to model carfentanil, a very dangerous narcotic that is adding to the opioid crisis. By knowing the chemistry of carfentanil, scientists will hopefully be able to come up with better treatments for overdose, as well as eventually come up with a database for all of the drug’s derivatives and put a stop to illegal smuggling of opioids. As a chemistry major, I had experience with the theory behind my project, but extremely limited knowledge of coding. There was a large learning curve when it came to me learning the ins and outs of Linux; however, Dr. Rogachev was supportive and understanding of my inexperience with code. I was able to gain a greater understanding and appreciation for code, computational chemistry, quantum mechanics, and the importance of research in coming up with solutions for the opioid crisis.
Jennifer Sabatka (BME)
Project Title: Biomimicry Design
Advisor: Alphonso Peluso
Professor Alphonso Peluso’s project was using biomimicry to create a more efficient and cheaper alternative to the modern prosthetic. Our team put together research on current prosthetic options in the market and focused on cost and comfort for the consumer. We redesigned how the prosthetic was shaped and made it easy to 3D print. We investigated creating a softer and more supportive socket for those who used a transtibial (below the knee) prosthetic. Ultimately, we created a prosthetic that was lighter and easier to produce for the consumer, making it ultimately more cost effective. I was able to see the different approaches from different majors. RES-MATCH also allowed me to gain experience in teamwork and interdisciplinary similarities, seeing that architecture and biomedical engineering aren’t as different as they seem to be at face value.
Angelin Thomas (BIOLOGY)
Project Title: Tumor on a Chip
Advisor: Kenneth Tichauer
My initial assignment was the Tumor on a Chip project. Before the COVID-19 situation, we were able to construct some cell plate devices with a window chamber. However, when the stay-at-home order was mandated, we switched focus to studying the relationship between SUSD2 and the protein Galectin. SUSD2 is a protein commonly found in breast cancer cells. Existing research has found it to be a possible tumor suppressor so I made a diagram on the program BioRender to understand the mechanism behind this. The diagram focused on SUSD2 in cancerous tissue and cancerous tissue without SUSD2. In cancer, SUSD2 shows up in adipocytes in malignant breast tissue. The immune response occurs as normal in which the T-cell receptors recognize the antigen, bind to it, and lead to the destruction of the cancer cells. When SUSD2 is present in the malignant tissue, the normal pathway is mutated. The t-cell recognizes an activated antibody outside the cancer cell, but instead of normal death of the host cell, the T-cell undergoes cell death instead. This tumor evasion is likely because the SUSD2-galectin complex triggers a suspected conformational or gene misactivation change in the T-cell receptor. There is not enough research published to confirm what exactly is the underlying cause for the specific mutation. However, the discovery of this complex has opened the possibility of new drug targeting and immunotherapy for breast cancer.
Jesus Vargas Jimenez (BME)
Project Title: Using Deep Learning to analyze X-ray diffraction patterns from muscle.
Advisor: Thomas Irving
Diana Velasquez (BME)
Project Title: Tumor through a Window
Advisor: Kenneth Tichauer
The project’s title is Tumor on a Window. This animal model consists on growing a tumor on a mouse and implanting a window-like chamber on top of it to visualize the angiogenesis processes (creation of veins and arteries) as well as other factors of tumor growth. In order to visualize these, the correct imaging agents need to be injected at the ideal concentrations before putting the animal in an imaging machine. This is where my project came in. I was tasked with finding these ideal concentrations for the two imaging agents that will be injected in the animals. In order to do so, I did serial dilutions of different concentrations of solutions of the imaging agents and imaged them through a machine that measures fluorescence of substances. During the semester, I worked on calculations and wrote protocols for the project, which I presented in front of Prof. Tichauer’s lab on one of our weekly meetings. I also did the serial dilutions and imaging for the project. However, due to the coronavirus crisis, I could not get my data out from the lab. Instead, I worked in creating some diagrams that explain the whole process and logic of the science behind my project as well as a short paper on it.
Jeannina Villalobos (BME)
Project Title: Mechanical property comparison between acute and chronic demyelinated brain lesions
Advisor: John G. Georgiadis
I met with Dr. Georgiadis and discussed the general idea of the project. We talked about the idea of how traumatic stab injury in the brain is associated with a decrease in the stiffness of the tissue that is recovered after remyeliation, while in contrast, a chronic demyelination results in the increase of stiffness of the tissue. The plan was to work in-vivo with the cortical tissue of the brain, using animal subjects such as rats. I was selected to work directly in the data collection and analysis, while other group of students would apply their programming skills for medical imaging and co-registered histology work. I would have the opportunity to learn from these students and have hands-on experience with a wide team of researchers.