Honors Theses

Permanent URI for this collectionhttps://hdl.handle.net/2152/13341

This is a collection of undergraduate honors theses completed by UT Austin students. There is not a requirement for students to submit their thesis to Texas ScholarWorks, so the collection only includes those students who have opted in. If you are interested in submitting your honors thesis to this collection, please complete this form and send it along with the file for your thesis to tsw@utlists.utexas.edu. Please make sure to remove any signatures from your document before sending it.

If you are looking for a Plan II honors thesis, please see the Plan II Honors Theses collection.


Recent Submissions

Now showing 1 - 20 of 639
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    Effects of executive control on memory integration and inference in adults
    (2021) Quesada, Lauren L.; Preston, Alison R.
    Expanding knowledge in the face of associated and potentially competitive information depends on memory integration. Prior research shows evidence of memory integration in associative learning tasks, which is often correlated with prefrontal activation. While prefrontal regions are implicated in executive control, there’s little evidence of the causal role of executive control on integration. In the present research, adults (N=12) completed a well-established associative learning task in which they learned a series of character-object AB pairs followed by overlapping object-object BC pairs. Following learning, integration of the overlapping pairs was assessed through inference task performance, in which they were tested for knowledge of the novel AC pairs. Critically, half of the overlapping BC pairs were learned while completing a divided attention task in which participants were asked to count simultaneously presented sounds, whereas the other half of BC pairs were incidentally encoded as in prior research, thus serving as a within-participant baseline performance comparison. The divided attention manipulation was designed to engage executive control processes, thus preventing utilization of such processes for additional tasks, namely for formation of the relation between AB and BC pairs online during overlapping learning. Retrieval of direct pairs learned in the divided attention condition was worse compared to pairs in the control condition, suggesting that the manipulation impaired attentional resources. Moreover, adults demonstrated decreased inference accuracy and increased response times for AC items learned under the divided attention condition relative to pairs learned in the control condition, even when direct AB and BC memory was controlled. These results demonstrate how targeting executive processes results in decreased integration, thus providing direct evidence for the role of executive control in flexible memory integration.
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    Stroke Awareness and Proposed Stroke Health Campaign in Mombasa, Kenya
    (2021) Meghani, Kinza; Garcia, Alexandra
    Stroke is the second leading cause of death and a significant source of disability worldwide. With two-thirds of stroke mortalities occurring in Sub-Saharan Africa, there is a need for researchers to comprehend the current understanding of stroke and its related factors in this region. Since stroke knowledge in the general public has been shown to mitigate the incidence of stroke and improve timely treatment-seeking behavior, the purpose of this thesis is to conduct 1) a stroke awareness assessment in Mombasa County, Kenya, and 2) a literature review of stroke interventions and health campaigns. The stroke awareness assessment surveyed 155 community members, collecting demographic data, perceptions, and knowledge about risk factors, warning signs, and response for stroke. Chi-square tests and odds ratios were used to analyze significant associations between knowledge of stroke and demographic characteristics. Findings from this study were that generally, the respondents were aware that stroke risk can be increased by poor lifestyle habits and that stroke needs to be treated at a hospital; however, their understanding of stroke and its warning signs and specific risk factors were fairly low. Majority of this sample had completed higher education but still scored low on awareness thus counties surrounding Mombasa County with lower proportions of high education may have substantially less stroke knowledge. These findings demonstrate a need to improve response time and outcomes of stroke, while reducing its prevalence. A review of the literature on stroke campaigns highlighted four main types of prevention methods that have been implemented in various countries and regions: mass media campaigns, educational presentations, health screenings, and multi-modal community programs. Through exploration of these campaigns, an optimal stroke prevention campaign for Mombasa would combine elements of a multi-modal community approach and a mass media campaign due to the intensive and wide-spread nature of these methods.
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    Identifying Novel Inhibitors Against Klebsiella pneumoniae carbanepenamse-2 Enzymes Found in Carbapenem-Resistant Bacteria Through Structure-Based Small Molecule Virtual Screening
    (2024-05-02) Vu, Madison; Beckham, Josh T.
    Several nosocomial infections in the hospital setting are caused by Klebsiella pneumoniae, a gram-negative bacterium that causes diseases ranging from pneumonia to infected bodily lesions. K. pneumoniae has recently exhibited the production of a hydrolase enzyme identified as Klebsiella pneumoniae carbapenemase-2 (KPC-2), which confers resistance against “last line of defense” carbapenem antibiotics derived from the beta-lactam drug class. In these experiments, high-throughput ligand docking programs GOLD and ICM were employed to identify novel compounds for potential inhibition against KPC-2. Structure-based screening of small molecule libraries revealed that ligands ZINC23337780 and ZINC12003014 exhibited a strong binding affinity for KPC-2, indicating a potential for inhibition of enzymatic activity via conformational protein changes. Physiochemical changes associated with substrate binding were analyzed in wet-lab trials comprised of differential scanning fluorimetry (DSF) and chromogenic substrate (Nitrocefin) assays. This allowed for both a quantitative and qualitative analysis of inhibition against KPC-2 by comparing biochemical activity between the apoenzyme and the enzyme in complex with a screened novel inhibitor. By coupling physical assays with the aforementioned high-throughput screening techniques, the analysis of two small molecules against KPC-2 introduces the possibility for further development of these compounds into viable drug therapeutics that uphold the efficacy of carbapenem antibiotics used in clinical treatment plans.
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    Cross-Species Analysis of YTH Domain Proteins from H. sapiens and A. ricinus
    (2024) Fang, Janssen; Contreras, Lydia
    RNAs are known to undergo a large number of post-synthesis chemical modifications that can alter their function and structure. Current studies are uncovering the significance of modified RNAs by delineating their associations with RNA-binding proteins, known as “readers.” One such family of protein readers contains a YTH RNA-binding domain, which is widely conserved and involved in recognizing N6-Methyladenosine (m6A) modifications found in eukaryotic mRNA. More recently, the YTH domain proteins have been found to recognize other RNA modifications, such as N1‐Methyladenosine (m1A) and 5-Methylcytosine (m5C). However, the “rules” that govern the YTH domain protein interactions with other modifications still remain unclear. In this study, we explored the biochemical characteristics of the YTH domain identified in Acarus ricinus via sequence and structural alignment. This particular YTH domain contains a sequence insertion akin to that observed in YTHDC1, which we hypothesize will impact the affinity and specificity for RNA modifications like m1A and m5C when compared to the human YTHDF1. In addition to sequence-based analysis, we validated protein expression of these domain proteins with SDS-PAGE. We also performed microscale thermophoresis binding assays to compare the binding affinities of YTHDF1 with m6A-containing RNA and unmodified RNA. These experiments lay the groundwork for future comparison of the YTHDF1 YTH domain with the A. ricinus YTH domain.
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    No Money, No Opinion: The Conflict Zones of Power and Capital in Hallyu Fandom Networks
    (2021) Oon, Celeste; Lai, Chiu-Mi
    In the age of Web 2.0 and particularly since the early 2010s, social media platforms have served as spaces for fans around the world to connect with one another in “imagined communities” to express joint affect for their beloved objects and texts. However, instead of a utopia-like community, online fandom has become a polarized battleground that fragments by the day. This is not a new phenomenon that has arisen because of the internet, but online networks have enabled fans to reach each other with unprecedented ease and speed, allowing for more opportunities to clash. As these rifts intensify, fans continue to create segregated spheres of fan identity, and must continuously renegotiate their relationships across these axes of power. By conceptualizing groups of fans as subnetworks in a network society as theorized by Manuel Castells, this thesis illustrates how fans wield networking, network, and networked power to coordinate their social interactions. Fans explicitly leverage Bourdieu’s notions of economic, social, and cultural capital to build fan subcultural capital that structures their networks. Ultimately, power is derived from geographic and cultural proximity to the media object, which exacerbates differences between fans’ cultural frameworks. These subnetworks of fans, in turn, have become attached to and identified by their geographic and cultural backgrounds, which creates intense rivalries between domestic and international fans. However, the emergence of COVID-19 and the movement online have illuminated instabilities within these subnetworks, suggesting that fans are not as strongly bound to this framework as they think. Rather than culture as the main subnetwork boundary and determinant of opinion, this thesis proposes a consideration of different “realities” occupied by subnetworks of fans, which have created completely divergent perceptions of investment, reward, and affect among fans. By analyzing discourse in online communities of Hallyu fans, this thesis explores power dynamics and sources of conflict in Asian transnational fandoms. Current scholarship in Hallyu highlights its industry potential and soft power potential, but there is a lack of scholarship exploring relationships between fans and how they negotiate power with respect to capital. Additionally, scholarship about fan power is largely focused on Western fandom and cannot accurately be used to theorize about Asian fandom due to differences in structure and behavior. Hallyu fandom as a case study thus offers an interesting perspective, given that its fixation on East Asian media objects concentrates power in Asia, which contrasts with typical white or Western hegemonic power, and its hyper-consumerist nature places an even larger emphasis on the importance of capitalistic practices. This thesis, then, highlights the unique aspects of power dynamics within non-Western transnational and transcultural fandom, and the ways in which they challenge us to reconsider existing theories of fans, networks, and power.
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    Reimagining Masculinity in Honglou Meng: The Case of Wang Xi-feng
    (2024) McGee, Rachel; Lai, Chiu-Mi
    This thesis is an exploration of how masculinity is reimagined in the 18th c. masterpiece, Honglou meng by Cao Xueqin. A significant contributing factor to the enduring appeal of this 120-chapter novel is a presentation of memorable characters that project a wide spectrum of gendered roles. The thesis argument is focused on the reimagining of masculinity in the case of a principal female character, Wang Xi-feng, who is one of the most famous figures in Chinese fiction. The character is an exemplary case study for how the women in Honglou meng are not defined by Qing Dynasty gendered expectations. In-depth analysis draws from Maram Epstein’s “construction of the authentic self” (2012). This thesis further explores the significant intersection of the embodiment of masculinity and illness, on both physical and metaphysical levels.
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    Effects of Patient-Physician Relationships on Breast Cancer Survivorship
    (2024-05-01) Reichstein, Marisa
    Breast cancer refers to a group of diseases that affect breast tissue, typically resulting from an uncontrolled growth of breast cells. Though men and women can get breast cancer, it continues to be the second leading cause of death for women. The diagnosis and treatment of breast cancer pose threats to psychosocial issues that impact the quality-of-life responses of women. Prior research indicates that effective patient-physician relationships can improve patient healthrelated quality of life, decision-making, treatment adherence, and survivorship outcomes. Furthermore, understanding barriers to physician trust in non-culturally congruent patients can reveal potential interventions to improve health equity and survivorship outcomes across all demographics. These barriers can include access to treatment, loss of patient autonomy, and communication and language differences. Implementing effective health communication and multidisciplinary care, including social workers, primary physicians, and psychologists (in addition to primary oncologists), can pose a solution to combat patient struggles. This thesis analyzes several frameworks for improving health communication and patient-physician relationships in breast cancer oncology, as well as real-world examples of said practices as presented by a panel of physician-interviewees from the field.
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    Factors Affecting the Equitable Development of Healthcare Innovation, A Retrospective Analysis
    (2024) Gandra, Sreya; Brown, Jay
    Healthcare innovation has the potential to transform patient care delivery and address significant public health challenges. However, technological innovations in medicine are met with additional economic, regulatory, and political barriers to entry into healthcare systems. These hurdles tend to be particularly significant in under-resourced settings, exacerbating disparities in access to and adoption of emerging healthcare technologies. By delving into the historical evolution of health innovation, this study aims to define key factors that contribute to their successful adoption. Specifically, this study analyzes the developmental success factors of the healthcare intervention’s cataloged in the Agency for Healthcare Research and Quality’s Innovations Exchange Database. By uncovering these dynamics, these findings are anticipated to inform policymakers, healthcare providers, and industry stakeholders to develop more targeted strategies that foster the successful integration of healthcare innovation in order to more broadly address key public health challenges.
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    A Review of Community-Based Interventions and Educational Initiatives for Overdose Prevention & Treatment for Opioid Use Disorder in the United States
    (2024) Kulkarni, Sachi; Gonzalez, Sonia K.
    Opioid use disorder (OUD) is a major health challenge facing the United States today, with 80,411 people dying from opioid-involved overdoses in 2021, accounting for 75.4% of overdose deaths. OUD disproportionately affects American Indian/Alaska Natives, people who live in rural areas, and young people ages 18-25. Each of these groups requires a distinct approach to reduce overdose deaths and OUD. This literature review included 22 papers to elucidate the specific aspects of successful community-based interventions and educational initiatives for overdose prevention deployed in the United States. Cultural sensitivity, peer involvement, and advancements in technology such as telehealth were found to be crucial next steps and key aspects of successful interventions.
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    Associations Between Social Norms and E-Cigarette Susceptibility and Ever-Use Among a Diverse Sample of 6th Grade Students
    (2024) Attri, Sarina; Kelder, Steven
    As e-cigarette use remains high among US adolescents, research is needed to identify targetable risk factors for intervention. This study explores associations between two social norms constructs (prevalence misperceptions and social acceptability) and risk for becoming an e-cigarette user among a sample of 6th grade students.
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    Using Machine Learning to Identify Risk Factors Associated with Causes of Fetal Deaths in the United States, 2021
    (2024) Balasubramaniam, Jalini; Jørgensen, Stacy
    Fetal deaths are classified as the spontaneous intrauterine death of a fetus at any time during a pregnancy. Fetal death after 20 weeks or more of gestation are also referred to as still births. In the United States, state laws require reporting of fetal deaths, however the gestational restrictions around death reporting can vary from state to state–most states report deaths of 20 weeks or more or 350 grams birth weight. Death reports are published annually by the CDC’s National Center for Health Statistics (NVSS). Five selected causes account for 89.8% of all the reported deaths in 2018-2020: fetus affected by complications of placenta, cord and membranes; fetus affected by maternal complications of pregnancy; fetus affected by maternal conditions that may be unrelated to present pregnancy; and congenital malformations, deformations, and chromosomal abnormalities. The NVSS data provides information on the birth, the mother’s health history, the father’s health history, and potential risk factors during the pregnancy. The objective of this project is to look at causes of death in 2021 and create an accurate machine learning (ML) model to classify cases of fetal death after 20 weeks of gestation. XGBoost (Extreme Gradient Boosting) machine learning algorithm was used to classify deaths across 6 classes. The model was able to classify deaths amongst placental abnormalities, maternal complications, maternal conditions, unspecified cause, and other with 40 percent accuracy. In future work, hyperparameter tuning, SMOTE, and more complex training and testing techniques can be used to increase model fit.
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    Exploring N- and C-terminal Fragment Ion Biases in UV-Photodissociation Mass Spectrometry of Intact Proteins
    (2024) Lam, Raymond; Brodbelt, Jennifer S.
    193 nm UV-photodissociation (UVPD) is a powerful ion activation method in tandem mass spectrometry (MS/MS) for analyzing complex biomolecules and proteins. Sample ions are isolated by their mass-to-charge m/z ratio and exposed to pulsed UV light, causing absorption of UV photons and cleavage along the amide backbone to generate informative fragment ions. The high energy deposition of UVPD and preservation of higher-order structure and modifications makes it particularly appealing for analysis of large, modified, heterogeneous, or multimeric protein states that prove challenging for conventional tandem mass spectrometry methods. It is expected that fragment ions containing the N- and C-terminal ends of each protein ion should be produced and detected equally upon amide backbone cleavage. Data among recent 193 nm UVPD-MS analyses and other MS/MS methods (such as collision-induced dissociation) show bias in the production of N- and C-terminal ions in different m/z mass-to-charge regions of mass spectra. Owing to the development of UVPD for top-down protein analysis, this method was examined in more detail for the N-term/C-term bias and was the focus of the present study. Among a set of six proteins prepared in denaturing solution conditions to generate standard and “supercharged” charge states, fragment ion identifications from proteins with greater numbers of basic residues were biased towards N-terminal ions in lower m/z regions, while proteins with acidic residues biased C-terminus-containing fragment ions in the same region. The backbone sites of generated fragment ions showed precursor charge-state dependence on the degree of ion current bias but remained intrinsically biased towards N/C-terminal fragment ions, while explorations of the charge of fragment ions proved insufficient to provide rationale for the migration of fragment ions into different m/z regions. This promotes further study of biases in top down MS/MS analysis of proteins, particularly as applied to MS techniques attempting to resolve information from spectrally noisy yet information-rich UVPD fragment ions, like proton-transfer charge reduction and internal fragment ion assignment.
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    Exploring the interactions between affective auditory distractions and working memory
    (2024) Koganti, Sannidhi; Lewis-Peacock, Jarrod
    In our daily lives, the ability to focus on tasks while filtering out distractions is crucial. Attention and working memory play pivotal roles in this process, but distractions, particularly emotional stimuli, can still interfere. Working memory is susceptible to impairments when dealing with emotional distractions, which can have implications for emotional regulation and overall well-being. Negative emotional distractions, in particular, have been shown to interfere with cognitive task performance. However, the impact of affective distractions lacks a consensus in terms of how they interact with working memory performance. Further, the range of acoustic stimuli used as affective distractors is limited, often confined to brief, task-irrelevant sounds, which may not always be applicable to real-world scenarios. In the current study, participants were asked to reproduce the colors of three images presented to them in order of their confidence in their ability to successfully reproduce the correct color. Additionally, the research incorporated prolonged exposure to distraction with the presentation of emotional auditory distractions in the form of news reports. Results showed that the presence of auditory distractions increased participant reports of being off-task. Further, memory errors were higher in the distraction conditions when compared to the no distraction conditions during the last response, when participant confidence was low. The findings suggest that there is a relationship between participant confidence and the interference of emotional auditory distractions. This study underscores the need to consider emotional distractions, particularly auditory stimuli, in real-world scenarios to better comprehend their effects on working memory and cognitive functioning.
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    Protein kinase C epsilon regulation of brain-specific serine/threonine-protein kinase 1 kinase activity and nuclear localization
    (2024) Koduri, Ashwin; Messing, Robert O.
    Protein Kinase C epsilon (PKCε) signaling plays a role in a variety of physiological functions, including neurotransmission, cell cycle progression, and responses to ethanol. However, only a few downstream substrates of PKCε that contribute to these functions are known. Investigating PKCε substrates can further reveal the role of PKCε in these processes and provide targets for the treatment of conditions associated with the function of PKCε. Recently, a chemical genetic screen identified brain-specific serine/threonine-protein kinase 1 (BRSK1) as a substrate of PKCε, with phospho-sites at serine 555 (S555) and serine 559 (S559). BRSK1 plays a role in regulating proper neuronal development and neurotransmitter release in mature neurons. Currently, it is not known if PKCε phosphorylation of BRSK1 at these sites regulates BRSK1 activity or cellular function. In this study, we used phospho-mimic and phospho-null mutations at both S555 and S559, as well as in vitro kinase assays to determine the effect of phosphorylation at these sites on BRSK1 kinase activity. Additionally, we used immunofluorescence to determine if these mutations or if pharmacological activation or inhibition of PKCε changes the nuclear localization of BRSK1 in Neuro-2a cells. We found that phospho-mimic and phospho-null mutations at S555 and S559 as well as preincubation of BRSK1 with PKCε resulted in decreased BRSK1 kinase activity. However, these manipulations did not alter BRSK1 localization. These results suggest that PKCε phosphorylation of BRSK1 decreases BRSK1 kinase activity.
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    Developing a Broad-Host-Range Modular Microcin Secretion System to Protect Plants from Bacterial Pathogens
    (2024) Morton, Alexa Kristine; Barrick, Jeffrey
    Agricultural bacterial pathogens present a major threat to the global food supply. New methods of controlling these pathogens are badly needed, as existing methods such as applying chemical pesticides or razing contaminated crops are not sustainable. Though traditional small-molecule antibiotics have received some use in this capacity, they are hardly ideal for wide-scale application due to the ever-looming threat of antibiotic resistance. One emerging solution has been the use of biocontrol strains, beneficial bacteria that naturally kill or otherwise inhibit pathogenic strains. However, the search for new biocontrol strains relies on serendipitously finding bacteria that naturally have anti-pathogen properties. To expedite the production of new biocontrol strains, I helped develop a pipeline for engineering biocontrol strains to secrete antimicrobial peptides known as microcins. Characterized microcins have a greater specificity than other types of antibiotics, primarily targeting close phylogenetic relatives of the bacteria that naturally produce them. In order to rapidly engineer microcin-secreting biocontrol strains, I refactored a two-plasmid microcin secretion system to increase its modularity. Promoters, microcin coding sequences, signal peptides, replication origins, and even secretion systems can be interchanged in this design, allowing for an array of permutations to the system according to the user’s needs. I show that my refactored system can secrete a known microcin, inhibiting growth of its target bacterium, and I map out how broad-host-range plasmid versions of my system can be used to engineer Pseudomonas and Pantoea biocontrol strains to secrete microcins. In the future, this system can be used to test novel microcins against a multitude of pathogen targets and deploy them in diverse bacterial biocontrol chassis to protect susceptible crops.
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    Exploring RBM6 Overexpression: Impact on Cell Division and Gene Splicing in HeLa Cells
    (2024) Rubio, Jennifer; Mackrell, Albert J.
    The RNA-binding motif protein 6 (RBM6) serves as an alternative splicing factor and tumor suppressor gene initially identified as a gene mapped to a lung cancer tumor suppressor gene locus on chromosome 3p21. Sharing structural similarities with RBM5 and RBM10, such as their two RNA recognition motifs (RRM) domains involved in posttranscriptional gene expression, two zinc finger-like regions, a G-patch and an OCRE domain, as well as a YjbI homology domain not found in RBM5 or RBM10. RBM6 is a splicing factor or interacts with other splicing factors based on its localization to IGCs (interchromatin granule clusters), also known as nuclear speckles, nuclear domains enriched in pre-mRNA splicing factors located in the nucleoplasm of mammalian cells. Changes in RBM6 expression have been reported to alter alternative splicing, to alter the cloning efficiency of HeLa cells, and RBM6 was shown to bind preferentially to a consensus sequence. For example, one study showed that decreased expression of RBM6 caused increased exclusion of NUMB exon 9, the opposite of what is observed following depletion of RBM10. It is notable that these effects could only be observed when RBM6 was stably knocked down in cell lines. While changes in RBM6 expression impact pre-mRNA splicing and cell proliferation, its precise mechanism is unclear. We are creating RBM6 cell lines that overproduce the protein in HeLa cells, as well as studying the effect of transient expression of normal and mutated RBM6 proteins. We will determine if overexpression of RBM6 will promote, and whether this correlates with changes in the rate of cell division. Using mutations in the protein we will investigate how the overexpression of RBM6 promotes the exclusion of the gene NUMB exon 9 and alters the splicing of other pro-apoptotic genes.
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    Beilinson-Bernstein Localization
    (2024) Panner, Michael; Ben-Zvi, David
    Take a complex reductive group $G$ and its lie algebra $\mathfrak{g}$. Understanding the representations of $\mathfrak{g}$ is a major problem within mathematics. A key tool in this direction is try and realize any such representation as some type of generalized functions on a space. This would allow geometric tools to be applied in order to understand the representations of $\mathfrak{g}$. This is done so in a theorem of Beilinson and Bernstein where they show that any $\mathfrak{g}$ representation can be realized as the global sections of a twisted $D$-module over the flag variety $G/B$, where $B$ is a Borel subgroup of $G$. This paper will provide an exposition of some topics in the geometry of Lie algebras and groups necessary to prove part of this theorem.
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    Exploring Invariants in Knot Theory
    (2024) Patel, Kaushal; Austin, Jennifer
    This thesis will explore the importance of invariants within the mathematical branch of Knot Theory with an emphasis on polynomial invariants and one interesting invariant within the subfield of tangle theory. The paper will begin by providing a basic foundation of mathematical knots and links that will be essential to understanding the discussion of invariants. The paper will then explain the importance of invariants and how they have and can be used to answer some of the most crucial questions in Knot Theory. This paper will largely focus on the Alexander Polynomial, the Conway Polynomial, the Jones Polynomial, and the HOMFLYPT Polynomial. For each polynomial, the paper will explain how it is calculated for both knots and links, discuss some important qualities, and analyze crucial limitations. At the end of this section, the paper will provide a discussion comparing and contrasting the relative values of each invariant over different types of knots. Furthermore, the paper will transition into Tangle Theory. I will begin by providing the fundamentals of tangles, emphasizing rational tangles, which is necessary for understanding the rest of the paper. Next, the paper will explain exactly how tangles can be transitioned into knots and links to tie the new concepts into the start of the paper. Finally, the paper will explore an interesting link invariant of tangle theory, specifically highlighting how it differs from the polynomial invariants in its bidirectionality. Lastly, the paper will give a short discussion on potential further explorations of invariants, highlighting goals, open questions, and struggles currently faced.
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    Utilizing the auxin-inducible degron to study cell polarity dynamics in C. elegans and mouse embryonic stem cells
    (2024) de Jesus, Bailey; Dickinson, Daniel J.
    During embryogenesis, early developmental events proceed on a tightly coordinated timescale. This is especially true for cell polarization, whereby cells establish molecularly distinct plasma membrane domains that orient asymmetric cell divisions and enable differentiation. Traditional methods of protein perturbation, such as genetic knockouts or RNA interference (RNAi), typically lack the flexibility to target proteins at multiple specific times during development. Therefore, we sought to implement a method that would allow for temporal treatment in order to examine the regulation of cell polarity. The auxin-inducible degron (AID) system enables proteins of interest to be tagged with a short degron sequence, which is recognized and polyubiquitinated by an E3 ligase specifically in the presence of the plant-derived molecule, auxin. The polyubiquitinated protein is then degraded by the proteasome. We first used this system in the C. elegans embryo to degrade the mitotic kinase Aurora A at different times in the cell cycle, which demonstrated that Aurora A temporally regulates polarity establishment through different mechanisms. Next, we were interested in applying the AID system to mouse embryonic stem cells (mESCs) to study the role of the tight junction protein ZO-1 during epithelial polarization. To do this, we used a CRISPR-Cas9-based universal donor system to endogenously tag the ZO-1 locus with the degron, thereby eliminating the previous need to use transgenes and knockdown endogenous loci when working with mammalian cells.We found that depleting ZO-1 increased the proportion of unpolarized clusters, which suggests that ZO-1 is important for polarization. This approach can be applied to other proteins in order to further elucidate the dynamics of epithelial polarity as well as other developmentally important processes.
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    Deep Learning Approach to Simultaneously Localize Acoustic Source and Receiver with a Single Room Impulse Response
    (2024-04) Hanish, Rick; Haberman, Michael
    This report proposes a method of simultaneously estimating the locations of an acoustic source and receiver in a three-dimensional shoe box-shaped room. We use a convolutional neural network-based model where the only input is a single room impulse response with reverberations. We also propose a method of handling the case of degeneracy using a small amount of information about the positions of the source and receiver relative to one another. In contrast to existing methods, we require no additional information or constraints. The model was shown to have effectively learned patterns in the room impulse response signal, achieving average error of 1.401 m which is shown to be better than a random guess. Although error was still large, we view this work as a proof-of-concept, and we expect that future modifications to the model architecture will improve accuracy substantially, and preprocessing the synthetic data used as the model's input would allow it to generalize better to real-world data sets.