Undergraduate Research Day 2020

Permanent URI for this collectionhttp://hdl.handle.net/1903/20158

With students involved in so many research opportunities, Undergraduate Research Day provides the perfect opportunity for them to share their work with the campus community. Held each April, Undergraduate Research Day showcases current research, scholarship, and artistic endeavors.

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Now showing 1 - 10 of 105
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    Simulating Speech Perception in Bilateral Cochlear Implant Users with Asymmetric Input
    (2020) Zukerman, Danielle; Goupell, Matthew; Jaekel, Brittany; Milvae, Kristina
    Understanding speech in noise is difficult for cochlear-implant (CI) users. One potential reason for this difficulty is asymmetrical hearing between the two ears; that is, when one ear can process sound more effectively and clearly than the other ear. Such asymmetry may impair some CI users’ ability to fuse speech signals from both ears into a single stream. One way to test this is with an alternating speech paradigm, which is an experimental simplification of speech moving from talker to talker in a rapid conversation between a group of people. Previous studies have shown CI users perform 40% worse on alternating speech listening than normal-hearing individuals. The present study aims to examine if reduced alternating speech perception is the result of asymmetrical hearing, which could cause a listener to only use their better ear when listening to alternating speech, and to miss out on much of the signal that is present in the poorer ear. Six young normal-hearing participants were tested using a CI simulation with varying levels of signal degradation to simulate both asymmetrical and symmetrical hearing. The hypothesis was that participants will show selective attention to the ear with the clearer, less degraded signal in asymmetrical hearing conditions, and will overall perform worse in this condition compared to the symmetrical hearing condition. The results comparing the “better ear” and the asymmetric condition suggest that there is no evidence of selective attention; therefore we can reject the hypothesis. Future directions include increasing asymmetry across ears by simulating more drastic degradation in the “poorer ear”. Speech perception in noise is one of the most common issues CI users face, and quantifying the contributions of asymmetrical hearing to this problem is important for resolving this issue.
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    Recognition of Aminated Guests by Acyclic Cucurbiturils in Biological Conditions
    (2020) Shah, Rohan; Isaacs, Lyle; Zebaze, Sandra
    The acyclic cucurbituril Motor2 has already been well documented in its binding to several types of molecular guests in phosphate buffer. However, while these tests provide a rough idea of motor2 affinity to different types of guests, they are incomplete in that they do not reflect how motor2 actually binds in body conditions. The human body contains many proteins and macromolecules that can affect the host-guest interactions of motor2, so it is important for new binding constants to be measured for motor2 in body conditions. In order to do this, Isothermal Titration Calorimetry (ITC) was used to measure motor2 binding constants to several different guest types in several different solutions, including albumin and fetal bovine serum. It was found that when tested with cyclic, monoaminated guests, motor2 binding affinity did not decrease significantly from phosphate to protein serum solvents. This retained affinity held across several different ring sizes and shapes. Motor2 binding affinity did suffer greatly in protein serum for guests that were linear, regardless of how many amines they had. The results also indicated that more hydrophobic guests do not bind as well to motor2 once albumin and other proteins ae introduced to solution, while hydrophilic, polar guests have better affinity retention. The ITC testing results indicated that motor2 binding in body conditions is heavily dependent on the shape of the guests it is binding to, and that motor2 would be most effective at its purpose in the human body if it was used to target cyclic amines and similar types.
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    Predicting facial movement using electromyography and machine learning
    (2020) Choi, Theresa; Brustad, Abby; Morales, Santiago; Fox, Nathan
    Video coding participants’ behavior is inherently a subjective and time-consuming process. The purpose of this study is to support traditional video coding methods of facial expressions by using machine learning on available electromyographic (EMG) data. For this, we tested the accuracy across four machine learning algorithms (i.e., decision tree, K-nearest neighbors (KNN), multilayer perceptron (MLP), and linear support vector classifier (SVC)). Specifically, we tested their accuracy in distinguishing between (a) any facial activity versus no movement, and (b) different facial expressions (Fearful, Happy, Neutral). Success was measured by final accuracy on a pre-chosen test set. Results showed that the decision tree and KNN classifiers had the highest potential for detecting facial activity with a test accuracy of 94%. However, after plotting their decision boundaries, both had a risk of overfitting, suggesting that the best classifier could instead be a safer choice of the MLP or SVC algorithms with 84% accuracy. For classifying different facial expressions, the MLP algorithm had the highest accuracy with 88% accuracy. Overall, the conclusion is that with further development, machine learning models could simplify the video coding process. While there were some models with very high accuracies (above 90%), they tended to risk overfitting and not generalize to larger datasets. Thus, the best use of these models would be in tandem with other coding methods, such as by quickly verifying low-accuracy classifications via video coding or by outputting cutoff parameters that can be used to facilitate other analyses.
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    Analysis of RNA Concentration of Influenza and other Respiratory Viruses from Dormitory Air Sampling
    (2020) Khan, Razeen; Bueno de Mesquita, Jacob; Milton, Donald
    Making accurate exposure assessments of airborne disease transmission is an integral part of a proactive response to outbreak events and can help track the pathway of transmission. This study aimed to assess the use of the rebreathed air equation in a dorm room setting and compare the expected exposure provided by the equation with actual viral collection determined by sampling. The study involved quantifying viral aerosol levels in the dormitory rooms of college students infected with influenza and other respiratory infections. NIOSH bioaerosol samplers collected dorm room air overnight and the viral concentration from these samples were compared against the calculated exposure value provided by the rebreathed air equation informed by direct measurements of viral shedding rates from the infected dorm residents ascertained by the Gesundheit-II bioaerosol collector. This comparison was facilitated by the rebreathed-air equation. Air samples were collected from the dormitories of nineteen participants and three participants had influenza. No virus was detected in the NIOSH samples. Data obtained from GII collection on viral shedding was then used in the application of the rebreathed air equation to predict exposure and assess how close the estimate of viral particles was to the actual results. By sampling in the dormitories of students with acute respiratory infections, we can make exposure assessments for roommates of infected students and others living in the dorms with greater accuracy by comparing actual outcomes with theoretical estimates. This work also helps improve understanding of airborne pathogen transmission in dorms and other indoor environments. The outcome of this project and future research like this helps evaluate the use of the rebreathed-air equation in predicting exposure and transmission risk under the assumption of well-mixed air.
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    Reforestation in Peru: Effects of Mercury Contamination
    (2020) AYEBAE, JADA-MERCY; Andrade, Natasha; Rodriguez, Maria
    Jada-Mercy Ayebae1*, Maria Rodriguez1, Dr. Natasha Andrade *Civil and Environmental Engineering Department, University of Maryland, College Park, MD 20742 In the Amazon Rainforest, illegal gold mining leaves water, soil and vegetation contaminated with mercury. This affects the environment and the populations dependent on the land for survival. Experiments to assess the toxicity of mercury on indigenous plant will be performed by UMD researchers next year in the Amazon. Radish and tomato seeds were used to design experiments with the purpose of understanding the effects of mercury on vegetation, specifically during germination. It was hypothesized that the control seeds (non-exposed to mercury) would grow longer and healthier than the others, to be implicated by root elongation. Seeds were treated with various concentrations of mercury (2ppm, 1ppm, 0.5ppm, 0ppm). The results showed that the seeds from the control group and those exposed to 0.5 ppm of mercury had greater root elongation than those exposed to 1 and 2ppm, after three days of germination in radishes. The tomatoes were tested in a weeklong experiment finding that, the control group had a significantly higher root length followed by 0.5 and 2ppm. These results showed that 2ppm (the greatest concentration) stunted root elongation the most in radishes and 1ppm stunted root elongation the most in tomatoes. These results support some of the hypothesis and the worries about mercury deposits in the Amazon rainforest.
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    Linker Domain Size Does Not Impact Bivalent HER3 Targeting Affibody Efficacy
    (2020) Oubaid, Jinan; Schardt, John; Jay, Steven; Jay, Steven; Schardt, John
    The Epidermal Growth Factor (EGF) family of receptors, also called ErbB or HER family, is a group of tyrosine kinase transmembrane proteins that have many regulatory purposes including regulating cell proliferation and survival. Members of the HER family rely on forming dimers upon ligand binding to promote downstream signaling. Gene mutations can result in the deregulation of the HER receptors, further resulting in cancer. HER3, a receptor that is deregulated in many cancers including ovarian, breast, and lung cancer, has been found to be responsible for drug resistance to therapeutics that currently exist to target other members of the HER family. This can occur through increased phosphorylation and overexpression of the HER3 receptor. There are many HER3 targeted therapeutics, including monoclonal antibodies (mAbs), that are currently in phase 1 and 2 of clinical studies; however, no HER3 targeted therapeutics have been approved by the FDA. In addition to this, previous studies have demonstrated that not every patient will respond to a specific treatment plan or therapeutic; therefore, the development of various treatment options is essential. An engineered protein known as the affibody, which in previous studies has shown to be highly soluble, thermally stable, and small in size allowing for effective tissue penetration, has emerged as a potential therapeutic agent for cancer. In this study, it was found that multivalent affibodies, which are affibodies with more than one binding domain, are more effective at inhibiting HER3 activation, also known as phosphorylation, and inducing HER3 downregulation than monovalent affibodies in multiple cell lines. Inhibiting receptor activation can be effective at reducing cell proliferation and survivability. In addition, other modifications were made to optimize the affibodies, such as altering the length of the linker that tethers the binding domains in a multivalent affibody together, and to test for their efficacy. Finally, an albumin binding domain was incorporated into the affibody design to help increase affibody half-life, which would be essential for in vivo testing.
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    Bisexual Women’s Female Friendships: Predictors and Outcomes of Sexual Identity Disclosure
    (2020) Parekh, Nina; Mohr, Jonathan
    This study examined identity-based predictors of bisexual women’s sexual identity disclosure and outcomes of disclosure related to individual and interpersonal well-being. The study assessed hypotheses that Asian bisexual women would be less likely to disclose their sexual minority status to Asian friends and more likely to White friends, as well as less likely to monosexual friends. The study also identified that the act of sexual identity disclosure for all participants, regardless of race/ethnicity would experience stronger interpersonal wellbeing among the friends to which they have disclosed their sexual minority status. A sample of bisexual women completed measures focused on their demographic information, personal self-esteem, self-authenticity, satisfaction with life, and perceived social support, as well as their interpersonal level of outness, validation, trust, intimacy, and overall friendship.
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    Assessing Life History Parameters of Trissolcus japonicus and Anastatus reduvii, Parasitoids of the Brown Marmorated Stink Bug
    (2020) Thomas, Namitha; Dabek, Elizabeth Z.; Shrewsbury, Paula M.; Hooks, Cerruti R. R.
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    COMPARISON OF RIBOSWITCH REPORTER SYSTEMS FOR LIVE CELL IMAGING OF CYCLIC-DI-GMP DYNAMICS IN BACILLUS SUBTILIS POPULATIONS
    (2019) Pierre, Yasmine; Spirito, Catherine
    Fluorescent riboswitch reporters can be used in vivo to monitor metabolite dynamics. Previous work used a fluorescent yfp reporter based on a cyclic di-GMP responsive riboswitch from Bacillus licheniformis to monitor cyclic di-GMP levels in individual Bacillus subtilis cells. The previous study found that cell fates in Bacillus subtilis are not uniform in the presence of varying cyclic di-GMP levels. It is important to further develop tools that enable single-cell imaging in Gram-positive bacteria. Fluorogenic aptamers are single-stranded RNA molecules that have been evolved via in vitro selection to bind strongly and specifically to fluorophore molecules and emit a fluorescent signal. These fluorogenic aptamers can be used instead of fluorescent proteins in riboswitch reporter systems to provide a more dynamic read-out of metabolite dynamics in cells. However, relatively little work has been done to evaluate the use of these fluorogenic aptamers as reporter systems in Gram-positive bacteria. The objective of this project is to evaluate the use of four different fluorogenic aptamers (Mango-III, Broccoli, dimeric Broccoli, and SpinachII) instead of yfp in a cyclic di-GMP responsive riboswitch reporter system in Bacillus subtilis. All plasmids containing the riboswitch reporters were constructed and successfully transformed into E. coli cells. Subsequently, the cyclic di-GMP responsive riboswitch reporter systems were successfully transformed into B. subtilis WT PY79 and a 𝝙pdeH mutant. Future work involves evaluating their performance in vivo in B. subtilis via laser confocal and fluorescence microscopy.
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    Interpretable Deep Learning for Toxicity Prediction
    (2020) Banerjee, Aranya; Boby, Kevin; Lam, Samuel; Li, Jeffrey; Polefrone, David; San, Robert; Schlunk, Erika; Wynn, Sean; Yancey, Colin; Feizi, Soheil
    Team TOXIC (“Understanding Computational Toxicology”) seeks to apply interpretability techniques to machine learning models which predict drug safety. Currently, such models have been developed with relative accuracy and are used in industry for drug development. However, because they are not sufficiently rooted in chemical knowledge, they are not widely used in regulatory processes. To contribute towards a solution, we evaluate existing explanation methods for toxicity predction models trained on open-source data sets. Additionally, we are working towards models involving the usage of more interpretable data representations. Ultimately, we hope to demonstrate a proof-of-concept for an interpretable model for predicting drug safety which can illustrate its reasoning.