Undergraduate Papers

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  • AutoEpiCollect, a Novel Machine Learning-Based GUI Software for Vaccine Design: Application to Pan-Cancer Vaccine Design Targeting PIK3CA Neoantigens
    Samudrala, Madhav; Dhaveji, Sindhusri; Savsani, Kush; Dakshanamurthy, Sivanesan (MDPI, 2024-03-27)
    Previous epitope-based cancer vaccines have focused on analyzing a limited number of mutated epitopes and clinical variables preliminarily to experimental trials. As a result, relatively few positive clinical outcomes have been observed in epitope-based cancer vaccines. Further efforts are required to diversify the selection of mutated epitopes tailored to cancers with different genetic signatures. To address this, we developed the first version of AutoEpiCollect, a user-friendly GUI software, capable of generating safe and immunogenic epitopes from missense mutations in any oncogene of interest. This software incorporates a novel, machine learning-driven epitope ranking method, leveraging a probabilistic logistic regression model that is trained on experimental T-cell assay data. Users can freely download AutoEpiCollectGUI with its user guide for installing and running the software on GitHub. We used AutoEpiCollect to design a pan-cancer vaccine targeting missense mutations found in the proto-oncogene PIK3CA, which encodes the p110ɑ catalytic subunit of the PI3K kinase protein. We selected PIK3CA as our gene target due to its widespread prevalence as an oncokinase across various cancer types and its lack of presence as a gene target in clinical trials. After entering 49 distinct point mutations into AutoEpiCollect, we acquired 361 MHC Class I epitope/HLA pairs and 219 MHC Class II epitope/HLA pairs. From the 49 input point mutations, we identified MHC Class I epitopes targeting 34 of these mutations and MHC Class II epitopes targeting 11 mutations. Furthermore, to assess the potential impact of our pan-cancer vaccine, we employed PCOptim and PCOptim-CD to streamline our epitope list and attain optimized vaccine population coverage. We achieved a world population coverage of 98.09% for MHC Class I data and 81.81% for MHC Class II data. We used three of our predicted immunogenic epitopes to further construct 3D models of peptide-HLA and peptide-HLA-TCR complexes to analyze the epitope binding potential and TCR interactions. Future studies could aim to validate AutoEpiCollect’s vaccine design in murine models affected by PIK3CA-mutated or other mutated tumor cells located in various tissue types. AutoEpiCollect streamlines the preclinical vaccine development process, saving time for thorough testing of vaccinations in experimental trials.
  • Transfusion with Blood Plasma from Young Mice Affects rTg4510 Transgenic Tau Mice Modeling of Alzheimer's Disease
    Hernandez, Carlos M.; Barkey, Rachel E.; Craven, Kristen M.; Pedemonte, Karin A.; Alisantosa, Bernadette; Sanchez, Jonathan O.; Flinn, Jane M. (MDPI, 2023-05-23)
    Alzheimer’s disease (AD) is characterized by the buildup of plaques and tangles in the brain. Tangles are formed when the stabilizing protein, tau, becomes hyperphosphorylated and clumps together. There are limited treatments for AD; therefore, the exploration of new treatments is warranted. Previous research showed that plasma transfusion from young donor mice improved spatial memory and increased synaptic proteins in old transgenic APP/PS1 mice, suggesting a remediation of memory and synaptic function. In the current study, plasma was transfused from 2–3-month-old young wildtype mice (WT) to 8-month-old rTg4510 mice expressing human tau (Tau). One week after the transfusions, behavior and tau pathology were examined. We found that Tau mice injected with plasma had lower expression of phosphorylated tau (ptau) in the brain, accompanied by fewer tau tangles in the cortex and CA1 region of the hippocampus and smaller tau tangles in the cortex, when compared to Tau mice injected with saline. Despite no improvement in behavior, the decreased level of ptau and tangles open the door to future studies involving plasma transfusions.
  • Weather Research and Forecasting — Fire Simulated Burned Area and Propagation Direction Sensitivity to Initiation Point Location and Time
    DeCastro, Amy; Siems-Anderson, Amanda; Smith, Ebone; Knievel, Jason C.; Kosović, Branko; Brown, Barbara G.; Balch, Jennifer K. (MDPI, 2022-04-28)
    Wildland fire behavior models are often initiated using the detection information listed in incident reports. This information carries an unknown amount of uncertainty, though it is often the most readily available ignition data. To determine the extent to which the use of detection information affects wildland fire forecasts, this research examines the range of burned area values and propagation directions resulting from different initiation point locations and times. We examined the forecasts for ten Colorado 2018 wildland fire case studies, each initiated from a set of 17 different point locations, and three different starting times (a total of 520 case study simulations). The results show that the range of forecast burned area and propagation direction values is strongly affected by the location of the initiation location, and to a lesser degree by the time of initiation.
  • Identifying Candidate Biomarkers of Ionizing Radiation in Human Pulmonary Microvascular Lumens Using Microfluidics—A Pilot Study
    Millet, Larry J.; Giannone, Richard J.; Greenwood, Michael S.; Foster, Carmen M.; O’Neil, Kathleen M.; Braatz, Alexander D.; Davern, Sandra M. (MDPI, 2021-07-29)
    The microvasculature system is critical for the delivery and removal of key nutrients and waste products and is significantly damaged by ionizing radiation. Single-cell capillaries and microvasculature structures are the primary cause of circulatory dysfunction, one that results in morbidities leading to progressive tissue and organ failure and premature death. Identifying tissue-specific biomarkers that are predictive of the extent of tissue and organ damage will aid in developing medical countermeasures for treating individuals exposed to ionizing radiation. In this pilot study, we developed and tested a 17 µL human-derived microvascular microfluidic lumen for identifying candidate biomarkers of ionizing radiation exposure. Through mass-spectrometry-based proteomics, we detected 35 proteins that may be candidate early biomarkers of ionizing radiation exposure. This pilot study demonstrates the feasibility of using humanized microfluidic and organ-on-a-chip systems for biomarker discovery studies. A more elaborate study of sufficient statistical power is needed to identify candidate biomarkers and test medical countermeasures of ionizing radiation.
  • Ceres Regolith Simulant Material Property Testing
    Becker, Nicole; Holley, Dustin; Lerman, Allie; Odok, Selim; Ofsa, Max; Puppo, Mark; Srivastava, Surahbi; Stefan, Todd; Waters, Raeven (2021-05)
    The dwarf planetoid Ceres is the interest of space agencies like NASA for the unique geomorphology available. Questions concerning the early formation of planets in our solar system as well as the potential migration of Ceres from the outer solar system could be better understood from the exploration of this planetoid. Currently there are no available samples of Ceres surface to perform testing upon. Therefore, spacecraft hardware and proposed mission applications require the use of regolith simulants as an analog. This experiment outlines the procedures to test Ceres-like simulants for compressive, impact, and tensile strength. Using guidance from other simulant studies, two primary procedures are used in sample creation. The first sample intends to account for the dry sublimated surface of Ceres while the second sample is intended to mimic the frozen clay-like subsurface found immediately under the dry crust. We report the physical properties of these two sample types and compare their differences. The intent of this experiment is to provide base properties that may be used as guidelines for the creation of spacecraft intended to travel to Ceres.
  • VTDITC: Hip Hop Studies at Virginia Tech and COVID-19
    Weiss, Jasmine (2021)
    VTDITC: Hip Hop Studies at Virginia Tech has a heavy focus on community-based learning, we make sure to support our communities’ interest in Hip Hop, and facilitate spaces where people can recognize Hip Hop as a scholarly practice. We have a variety of programs we offer including a monthly seminar, weekly studio hours, media literacy workshops, and live DJ mixes. COVID-19 emerged across the United States around March 2020 and directly impacted everyone's life in various ways. VTDITC programing has had to adjust because of our country’s new norms.
  • Parent Involvement Is Essential for Child’s Academic Development
    Jayakumar, Srinidhi (2020)
    In the paper I compare the views of media and research studies on whether parent Involvement Is essential for child’s academic development. The paper concludes whether parent Involvement Is essential for child’s academic development by using media view, research studies and theories of psychologists such as Skinner and Piaget. The paper also talks about why parent involvement is essential, how parent involvement can have a negative effect and factors that affect parent involvement in child's education
  • Effects of a Low-Fat Vegan Diet on Gut Microbiota in Overweight Individuals and Relationships with Body Weight, Body Composition, and Insulin Sensitivity. A Randomized Clinical Trial
    Kahleova, Hana; Rembert, Emilie; Alwarith, Jihad; Yonas, Willy N.; Tura, Andrea; Holubkov, Richard; Agnello, Melissa; Chutkan, Robynne; Barnard, Neal D. (MDPI, 2020-09-24)
    Diet modulates gut microbiota and plays an important role in human health. The aim of this study was to test the effect of a low-fat vegan diet on gut microbiota and its association with weight, body composition, and insulin resistance in overweight men and women. We enrolled 168 participants and randomly assigned them to a vegan (n = 84) or a control group (n = 84) for 16 weeks. Of these, 115 returned all gut microbiome samples. Gut microbiota composition was assessed using uBiome Explorer™ kits. Body composition was measured using dual energy X-ray absorptiometry. Insulin sensitivity was quantified with the predicted clamp-derived insulin sensitivity index from a standard meal test. Repeated measure ANOVA was used for statistical analysis. Body weight decreased in the vegan group (treatment effect −5.9 kg [95% CI, −7.0 to −4.9 kg]; p < 0.001), mainly due to a reduction in fat mass (−3.9 kg [95% CI, −4.6 to −3.1 kg]; p < 0.001) and in visceral fat (−240 cm3 [95% CI, −345 to −135 kg]; p < 0.001). PREDIcted M, insulin sensitivity index (PREDIM) increased in the vegan group (treatment effect +0.83 [95% CI, +0.48 to +1.2]; p < 0.001). The relative abundance of Faecalibacterium prausnitzii increased in the vegan group (+5.1% [95% CI, +2.4 to +7.9%]; p < 0.001) and correlated negatively with changes in weight (r = −0.24; p = 0.01), fat mass (r = −0.22; p = 0.02), and visceral fat (r = −0.20; p = 0.03). The relative abundance of Bacteroides fragilis decreased in both groups, but less in the vegan group, making the treatment effect positive (+18.9% [95% CI, +14.2 to +23.7%]; p < 0.001), which correlated negatively with changes in weight (r = −0.44; p < 0.001), fat mass (r = −0.43; p < 0.001), and visceral fat (r = −0.28; p = 0.003) and positively with PREDIM (r = 0.36; p < 0.001), so a smaller reduction in Bacteroides fragilis was associated with a greater loss of body weight, fat mass, visceral fat, and a greater increase in insulin sensitivity. A low-fat vegan diet induced significant changes in gut microbiota, which were related to changes in weight, body composition, and insulin sensitivity in overweight adults, suggesting a potential use in clinical practice.
  • Indian Culture and Age Impacts on Mental Health Treatment
    Jayakumar, Srinidhi (Virginia Tech, 2020-07-02)
    The paper is a research paper on Indian Culture and Age Impacts on Mental Health Treatment. I conducted the research for 3 weeks under the assistance of teaching assistant Sadie Giles. I used a convenience sample and found out that those who are older (30+ age) and stick more to the Indian culture have more negative views towards mental health treatment compared to younger (below 30) individuals and those who didn't stick much to the Indian culture.
  • Linking Health and Nature: Implications for the Physical Therapy Field
    Ichoku, Chioma (2015-12-15)
    Nature is often overlooked in the health field, and more specifically the physical therapy field. There is evidence that contact with nature has healing effects both psychologically and physically. When it comes to physical therapy, incorporating nature into the regime may provide added benefits. Perhaps it is time that physical therapy consider a research agenda to explore the link. Once benefits are clearly established and outcomes assessed, the field should then consider the best ways to incorporate nature into practices.
  • Promoting Forest Conservation in the Peruvian Amazon: A Stakeholder Analysis of Incentive Mechanisms
    Daman, Sarah (2014-04-09)
    The Madre de Dios region of Peru is significant for its wealth of biodiversity and natural resources that sustain the local economy and provide ecosystem services. Current demand for extractive land uses (e.g., gold mining) favors land conversion over conservation, leading to questions about how to sustain this ecosystem. The purpose of this study was to understand the relationship between landholder preferences for land use and evaluate the potential to motivate landholders to support forest conservation. Using secondary data from a household survey of 400 landholders, we examined relationships between landholder characteristics and willingness to conserve for cash and services (e.g., healthcare, education). Additionally, respondents ranked preferences for these services. The population was generally not well-educated and lacked health insurance and bank accounts. Most landholders expressed a willingness to participate in forest conservation in exchange for payments (78%) and for services (76%). Of the three main types of livelihoods examined, farmers ranked education and health insurance higher than Brazil nut harvesters. Wood harvesters did not differ significantly in their preferences. Landholders demonstrated very little practical differences in their preferences for services indicating that the potential for successful forest conservation programs in the region exists, despite the increased demand for extractive land uses. Although financial payments are common tools used to promote conservation, the high preferences for health insurance and education indicate that social outcomes may be an effective inducement for conservation programs. However, additional research is required to understand factors that influence participation in such programs.
  • To Can or Not to Can? Feasibility Study for a Cannery in Scott County
    Fields, Damara; Green, Cindy; Pollard, Rachel (2002)
    In Scott County, a community cannery has been proposed. This cannery would allow current canners to continue canning more efficiently at a lower cost, and would likely draw new people to canning. In this study, the economic feasibility of the cannery was studied and a plan for further study and an action plan based on the data collected to this point were developed. Although canning activities are on the decline, canning is likely still prevalent in the area due to the large population over the age of 55. Through a survey, the likely usage of the cannery can be determined, which is necessary to determine the ideal size for the cannery. Based on the data collected on likely usage and the county’s economy, a cooperative seems to be the best form of management for the cannery.
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