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Undergraduate Research Opportunities Program

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Now showing 1 - 10 of 936
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    Progress towards Co-crystalization of the E. coli Membrane Protein Intimin with Engineered Peptide-specific Antibody Fragments
    (Georgia Institute of Technology, 2016-01-25) Heaner, David Prince ; Lieberman, Raquel L. ; Schmidt-Krey, Ingeborg ; School of Chemistry and Biochemistry ; College of Sciences ; Undergraduate Research Opportunities Program ; Chemistry and Biochemistry
    The determination of membrane protein structures is critical for the development of new pharmaceutical agents. Conventionally, membrane proteins are solubilized by the use of mild detergents. However, due to the lack of hydrophilic residues available to make crystal contacts and interference by the large detergent micelle, the quality of diffraction and resolution level needed for de novo structure determination is usually not obtained. In addition to the conventional detergent method, a new method using engineered single chain antibody fragments (scFv) and a Fab antibody fragment have been developed for use as crystallization chaperones. The scFv and Fab fragment interact with the membrane protein of interest via the EYMPME (EE) tag, which is selectively mutated into a hydrophilic loop of the protein. The membrane protein-antibody fragment complex may enter crystallization trials with the antibody fragment driving the complex nucleation through the formation of numerous, strong crystal contacts. Such a co-crystallization method with anti-EE scFv and Fab fragments provides the protein crystallographer with a “crystallization toolbox” that can be used for any crystallographic study of a protein of interest. Through size exclusion chromatography and SDS-PAGE analysis, complexation of the β-barrel membrane protein intimin harboring the EE tag with scFv/EE and Fab/EE has been shown to occur, from which crystallization trials have ensued. Formation of a co-crystal has proven to be difficult, which can be explained in part through molecular dynamics simulations of the mutated intimin L4 loop. This thesis work will present results and conclusions for this novel co-crystallization method.
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    AdventumRL: A Quest-Based Reinforcement Learning API
    (Georgia Institute of Technology, 2021-05) Singh, Kushagr ; Riedl, Mark ; Gombolay, Matthew ; College of Computing ; School of Computer Science ; Undergraduate Research Opportunities Program ; Computer Science
    We propose AdventumRL, a framework to facilitate complex, quest-based reinforcement learning in Minecraft, a 3D first person sandbox video game. We define a set of encodings on top of tools provided by Malmo, an open-source Minecraft reinforcement learning framework. We define a grammar framework for encodings states, actions, transitions, and goals that can represent quests in a reinforcement learning scenario. Proof of concept reinforcement learning agents are provided: a tabular Q-learning agent, utilizing a table to determine the best action to take from a given state, and two different deep Q- learning agents, which utilize a neural network instead of a table to determine the best action to take from a given state. One of the deep Q-learning agents solely utilizes the camera feed from Minecraft to determine its location, while the other directly uses positional and coordinate information instead. We demonstrate that the addition of our grammar framework allows the agents to complete a locked room quest that they could not complete without it.
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    Automated Forensics Analysis Final Report
    (Georgia Institute of Technology, 2019-08) Harper, Grace ; Lee, Wenke ; College of Computing ; School of Computer Science ; Undergraduate Research Opportunities Program ; Computer Science
    RAIN [2] is a system which has the ability to record and replay system call events at the process level as well as perform dynamic information flow tracking (DIFT) on-demand during replay. This project’s goal is to utilize RAIN to more efficiently determine the entrypoint of an attack as well as its effects on the victim’s system. Specifically, this project attempts to use the low-level information recorded by RAIN to determine potential entry points of the attack.
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    (Georgia Institute of Technology, 2021-05) Brashear, Jillian ; Snell, Terry ; Weigel , Emily ; Goodisman , Michael ; College of Sciences ; School of Biological Sciences ; Undergraduate Research Opportunities Program ; Biology
    Rotifers are sensitive indicators of environmental conditions and serve as model organisms for assessing toxicity. It is understood that rotifer cysts (diapausing eggs) are convenient for toxicity assessment because they remove the need to maintain animal cultures, reduce variability in tests, and can be stored for on-demand use. Indeed, cyst-based toxicity tests for the rotifer Proales similis have helped to fill a need for an additional marine animal model to the rotifer Brachionus plicatilis in ecotoxicology. A challenge to implementing tests is the need for readily- available P. similis diapausing eggs, which need to be reliably preserved and hatched on demand. This study explores preservation methods to extend the viability of P. similis eggs. We explore factors including storage temperature, salinity, and the addition of ascorbic acid to measure their effects independently and combined. We found that storing the diapausing eggs at approximately 4℃ in the presence of 20µM ascorbic acid and a 220ppt salinity is effective for extending egg viability. With longer viability, P. similis diapausing eggs are more readily available and thereby valuable as a tool in toxicity assessments.
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    Novel technology & techniques to study long-term neural dynamics of living neural networks cultured in-vitro
    (Georgia Institute of Technology, 2013-05-08) Ghosh, Ushnik ; Wallace H. Coulter Department of Biomedical Engineering ; Undergraduate Research Opportunities Program ; College of Engineering ; Biomedical Engineering
    The fundamental mechanisms of information processing and storage, and network plasticity for in-vitro LNNs are studied by monitoring extracellular electrochemical neuronal activity via a Multi-Electrode Array (MEA). MEAs monitor action potentials, and enable observing morphological activities of in-vitro dissociated LNNs at the network level. Cortical neurons (extracted from 18-day old rat embryos) are dissociated and plated onto a grid of 59 electrodes on the center of an MEA culture dish. Once plated, the neurons reform synaptic connections with one another to become a single functional network, displaying highly correlated activity among constituent neurons. MEAs can be used as two-way interface between the outside world and LNNs. In-vitro LNNs serve as excellent models for long-term experiments studying the development of network circuitry. This specific investigation focused on designing novel technologies aimed at studying a specific form of neural network plasticity: synaptic scaling in homeostatic plasticity. This endeavor is broken into 3 thrusts: Thrust I: Cell Incubation System: The Hotbox is a custom-built environmental control device that modulates temperature, CO₂, and humidity levels inside a custom built environmental enclosure. Temperature is monitored with thermocouple, and a PID controller is used to drive heating elements. CO₂ monitored with CO₂ sensors; bang-bang controller is used to turn CO₂ air supply on/off. Thrust II: Electrophysiology—Alleviating Bursting in LNN: Attempts to scale short-term Burst-Inhibiting phenomena to longer time scales and induce more pronounced and permanent network modifications were successful. However, the integrity of LNN health was compromised at 17 DIV; thus this experiment can only serve as a preliminary experiment for future experiments attempting to demonstrate Burst-Inhibiting and Synaptic Scaling phenomena. Thrust III: Enabling Two-Photon Microscopy Imaging—Transfection Protocols Electroporation: based transfection techniques were assessed for their effectiveness for fluorescent microscopy imaging cases. Although some electroporation parameters yielded successful transfections, all treatments yielded low transfection efficiency and low cell viability.
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    Fighting on Facebook: Political Conversations Between Strong and Weak Ties
    (Georgia Institute of Technology, 2023-01-18) Bernstein, Lily ; Bruckman, Amy ; Joyner, David ; College of Computing ; School of Computer Science ; Undergraduate Research Opportunities Program ; Computer Science
    Most Facebook users have observed a heated disagreement on the site, or been involved in such a disagreement themselves. Why do we get into these disagreements and who are we fighting with? Are we learning anything from the disagreements we have online? In this research, we interviewed eighteen regular Facebook users about their experiences with conflict on the site. We found that people get into disagreements online because their \textit{expectations} about how the people in their network will react were violated. Conflict was often a result not of disagreement, but of breach of expectations. When conflict ensued, participants sometimes dissolved their relationship with their argument counterpart, and sometimes did not. We review strategies used for relationship maintenance. Weak-tie relationships were more susceptible to being dissolved, and strong-tie relationships were often salvaged by "agreeing to disagree" or ceasing political discussion. Participants report sometimes learning from these hard conversations, but not often. We follow-up with design recommendations for social media platforms that could help mitigate disagreements or give people access to tools that help them have productive, hard conversations.
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    Platelet Adhesion and Mechanosensing on Collagen Coated Substrates
    (Georgia Institute of Technology, 2015-08-18) Kee, Matthew ; Lam, Wilbur ; Barker, Thomas ; Behravesh, Esfandiar ; Wallace H. Coulter Department of Biomedical Engineering ; Undergraduate Research Opportunities Program ; College of Engineering ; Biomedical Engineering (Joint GT/Emory Department)
    Platelets play a critical role in maintaining homeostasis of the body. In order to protect the body from significant injury, platelets adhere to the vascular wall preventing critical vascular system failure. When the collagen is exposed on damaged endothelial cells, platelets adhere to the exposed protein and spread, increasing the size of the clot and preventing further damage to the body. For hemostatic diseases, biomechanical properties of platelets are an area of research critical to helping understand arterial diseases while also furthering the treatment of them. Platelet clot formation relies on the biomechanical aspects of the platelet surroundings as they adhere to the cell wall. It is hypothesized that an increase in the substrate stiffness on which platelets adhere to will increase the spreading area of the platelet in both static and dynamic environments. This paper shows a novel approach to better comprehend biomechanical properties of platelets relating to adhesion and spreading on varying substrate stiffness of collagen-coated polyacrylamide gels.
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    Analysis of Deviant Opioid Addiction Treatment Communities on Reddit
    (Georgia Institute of Technology, 2018-05) Zampieri, Francisco Alejandro ; De Choudhury, Munmun ; Bruckman, Amy ; College of Computing ; School of Interactive Computing ; Undergraduate Research Opportunities Program ; Interactive Computing
    As the opioid epidemic in the US continues, many addicts turn to clinically unverified, non-mainstream, deviant recovery methods to ameliorate the symptoms of withdrawal. In this study, we analyze discussion on the social media site Reddit surrounding these treatments. We apply transfer learning methods to train a classifier highly sensitive to recovery-related posts. Based on network analysis of Reddit communities (known as “subreddits”), we generate a list of subreddits where discussion of deviant addiction treatment methods is taking place. Using word embeddings and the testimony of a practicing opioid addiction clinician, we identify potential alternative opioid addiction treatment methods. Applying the classifier to subreddit post data, we generate a dataset consisting of recovery-related discourse. When applied to these posts, topic modeling methods, such as Latent Dirichlet Allocation (LDA), reveal topics discussed within the context of recovery, such as the lifestyle changes associated with kratom use.
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    Development of a Polyethylene Glycol Hydrogel Delivery System for Interleukin-10
    (Georgia Institute of Technology, 2017-12) Jiang, Huige ; Babensee, Julia ; Pai, S. Balakrishna ; Behravesh, Esfandiar ; Wallace H. Coulter Department of Biomedical Engineering ; Undergraduate Research Opportunities Program ; College of Engineering ; Biomedical Engineering (Joint GT/Emory Department)
    Multiple Sclerosis (MS) is an autoimmune disease where the patient’s own immune system attacks the myelin cover of his nerves, causing communication problems between the brain and the rest of the body. Currently there is no cure for MS, however treatments can slow down the progression of MS by reducing the frequency and severity of attacks and the development of new brain lesions. Dr. Babensee’s lab aims to relive effects and symptoms of MS by utilizing interleukin-10 (IL-10), an anti-inflammatory cytokine to induce immunosuppressive tolerogenic dendritic cells (DCs). The purpose of this study is to design a delivery system of IL-10 with high loading efficiency and allows for adjustable release profile. Ovalbumin (OVA), a main protein found in egg white, was chosen as a less costly model for IL-10 for this project due to its similar physical and chemical properties to IL-10. Early stages of this study focused on creating an OVA incorporated 4-arm polyethylene glycol maleimide (PEG-4MAL) by chemically attaching OVA to the molecule’s maleimide group. A variety of molar ratios of PEG-4MAL and OVA were examined to determine the ratio that provides the highest loading efficiency. Results have shown that a 3:1 molar ratio of PEG-4MAL and OVA offers the highest loading efficiency. Later stages of the study focused on designing a IL-10 attached PEG-4MAL microgel, which allows for more control over the release profile of IL-10. The microgels are created using a microfluidic device with flow-focusing geometry in the Garcia Lab at Georgia Tech. The anticipated outcome of this project is to create a IL-10 incorporated microgel system that allows for less invasion, more targeted release of IL-10 and more control over the release profile of IL-10 to provide an immunosuppressive environment for DCs. This microgel system can act as a potential treatment for MS.
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    Review study on left atrial appendage occlusion and current implant devices
    (Georgia Institute of Technology, 2014-05-05) Moon, Young Suk ; Jang, Seung Soon ; Vidakovic, Brani ; Wallace H. Coulter Department of Biomedical Engineering ; Undergraduate Research Opportunities Program ; College of Engineering ; Biomedical Engineering (Joint GT/Emory Department)
    Stroke and heart-related diseases are one of the leading causes of deaths in United States. There are many factors that may cause stroke, and left atrial appendage coagulation is one of them. Left atrial appendage coagulation is a coagulation of blood inside the left atrial appendage caused by atrial fibrillation, not rhythmical contraction of your heart muscle. For left atrial appendage, not like other heart defects, anti-coagulant currently is only solution to solve this problem. There isn’t any implant device solution specific for left atrial appendage occlusion. However, there are some devices that are currently going through FDA approval process. These are Watchman and Lariat. According to interviews performed with cardiac specialists throughout Atlanta, they are emphasizing three major factors. They are stability, customizability, and full occlusion. Limitations of Watchman and Lariat are customizability and full occlusion. To satisfy all three factors and to improve from Lariat and Watchman, Flow Medical has come up with innovative left atrial appendage occlusion balloon.