Biomedical and Health Informatics Electronic Theses (UMKC)
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The items in this collection are the theses written by students of the Department of Biomedical and Health Informatics. Some items may be viewed only by members of the University of Missouri System and/or University of Missouri-Kansas City. Click on one of the browse buttons above for a complete listing of the works.
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Item Illustrating the clinical landscape of Mucorales infection: a comprehensive examination of demographic characteristics, regional variation, length of stay, and readmission rates of cases in the United States(2025) Jones, Andrew Paul; Allsworth, Jenifer E.Mucormycosis is a rare but devastating fungal infection that primarily afflicts immunocompromised patients including those with hematological malignancy, solid organ and bone marrow transplants, and diabetes mellitus. The objective of this study was to assess the prevalence and clinical burden of mucormycosis among hospitalized patients in the United States. The three studies conducted analyzed the Oracle Health Facts® database, a deidentified electronic health record resource, which includes more than 750 participating healthcare facilities, 500 million unique patient encounters, 69 million patients, and 4.7 billion laboratory results between 2000 and 2018. All inpatient hospitalizations were examined for documentation of mucormycosis using an ICD-9-CM code of 117.7 or ICD-10-CM codes of B46.0-B46.9. In study 1, we estimated the prevalence of mucormycosis-related hospitalizations nationally, by census region and demographic characteristics, and described temporal trends. In study 2, we conducted a matched case-control study design to estimate the association of mucormycosis on length of hospital stay. Controls were matched by facility, year of case, sex and age. Finally, in study 3, we conducted a matched case-control study to estimate readmission rates at 30- and 90-days for mucormycosis patients compared to control patients. Results: The prevalence of mucormycosis-related hospitalizations was estimated as 0.12 per 100,000 discharges during January 2000 to June 2018. The highest prevalence and number of cases occurred in western states (i.e. Alaska, Arizona, California, Colorado, Hawaii, Idaho, Montana, Nevada, New Mexico, Oregon, Utah, Washington, Wyoming). We also found a higher prevalence of mucormycosis among patients with coagulopathy, chronic heart failure, weight loss and cardiac arrythmias. This analysis confirmed prior findings that mucormycosis was more common among patients with diabetes mellitus, hematological malignancies, and fluid and electrolyte disorders. Mucormycosis was associated with longer inpatient stays; the average length of stay for mucormycosis patients was 23 days compared to 6 days for controls matched by facility, year, sex and age. Regression analyses found that mucormycosis was a significant predictor of increased length of hospital stay, adding almost two days on average compared to matched controls. Mucormycosis patients also had a higher rate of readmission than control patients; they had 30-day readmission rates 35 times higher and 90-day readmission rates more than four times that of controls. Conclusions: While mucormycosis is not a common infection documented in US patients, it has a significant impact of patient length of stay and hospital readmission rates. The study provides an estimate of the prevalence and burden of mucormycosis among US hospital patients. The significant clinical and patient burden associated with mucormycosis showcases the importance of surveillance and understanding required to further optimize treatment protocols and protect susceptible US patients.Item The impact of supplemental nutrition assistance participation, and food security on diabetes-related mortality(2025) Basurto-Reyes, Jessica; Allsworth, Jenifer E.Food insecurity has been a rising issue for many people in the United States and is an ongoing public health concern. Every day, food insecurity not only affects diets, it is also associated with increased risk of chronic disease and death. Households facing food insecurity may also experience elevated rates of type 2 diabetes and its health complications. National food assistance initiatives, such as Supplemental Nutrition Program (SNAP) and Special Supplemental Nutrition Program for Women, Infants, and Children (WIC), are programs that help reduce food insecurity. Although these programs exist to help individuals facing food insecurity, it has not been thoroughly studied whether these programs slow diabetes-related mortality. The purpose of this study is to explore the association between food insecurity and food assistance participation with diabetes-related mortality among adults in the United States. This study uses a retrospective design incorporating National Health and Nutrition Examination Survey (NHANES) cycles from 1999 to 2018 with mortality follow-up through linkage to the National Death Index through the end of 2019. Participants aged 18 years and older in NHANES were included in this study. Key variables include household food security status, participation in WIC, and diabetes-related mortality outcomes. Covariates include sex, race/ethnicity, education, income-to-poverty ratio, family size, and health indicators such as body mass index (BMI), hypertension, and glycosylated hemoglobin (HbA1c). Analyses adjusted for complex survey design were performed using the survey and srvyr packages in R. Descriptive statistics were generated to compare participant characteristics between levels of food security and receipt of WIC. Kaplan-Meier survival curves were used to illustrate survival across levels of WIC participation and household food security, and Cox proportional hazards regression models were used to estimate associations with diabetes-related mortality. Preliminary descriptive analyses suggest that food-insecure adults who participate in food assistance programs differ in demographic and health characteristics compared to non-participants. Ongoing analyses will determine whether participation in food assistance is associated with a decrease in diabetes-related mortality, after adjusting for socioeconomic and health factors. The findings will contribute to understanding how public nutrition programs influence chronic disease outcomes and serve as a guide for future strategies to reduce health disparities for vulnerable populations.Item Investigation of HPV16-related genomic alterations in cervical squamous cell carcinoma(2025) Richards, Christopher Thomas; Zeeshan, SamanThis study examined the effects of human papillomavirus genomic integration into the host genome on host gene expression in cervical squamous cell carcinoma (CSCC) tumors. The genomic analysis involved clinical and genomics data analysis using bioinformatics and statistical methods. The Cancer Genome Atlas Program (TCGA) resource was used to download Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma data. Molecular differentiation was performed through differential gene expression (DGE) analysis conducted using R 4.5.1, R Studio, and packages from Bioconductor. Experimental design was created to compare samples with HPV 16 integrated genome with the non-integrated genome. Gene expression involved filtration criteria setting a minimum threshold of 10 counts per gene and 10 samples in each group. The median of ratios method was used to normalize the raw count data, accounting for differences in sequencing depth and RNA composition between samples. A negative binomial distribution model was fitted to the normalized count data for each gene. Statistically significant genes were filtered to an adjusted p-value <= 0.05 and log2 fold change >= 2 yielding upregulated and downregulated genes. Pathway analysis and prognosis assessment identified mechanisms that may have a role in the development of CSCC. Improved insights into the causes and consequences of HPV genomic integration could significantly improve strategies and lead to advancements in the prevention, detection, and treatment of HPV associated cancers.Item A partially-observed Merton's model for financial ultra-high frequency (UHF) data with Bayesian learning via filtering equations(2025) Kridan, Jamila; Zeng, Yong (Professor of Mathematics and Statistics); Cheng, An-LinThis dissertation proposes a new model, referred to as a partially observed Merton model, for financial ultra-high-frequency data. The model is built upon the classical Merton model, which extends the Black-Scholes model by incorporating a jump component to account for abnormal price fluctuations. Both Merton model and Black-Scholes model are widely used in financial economics.The partially observed Merton’s model is constructed to match two features in ultrahigh-frequency (UHF) data: random trading times and trading noises. We develop a Bayesian framework for estimating model parameters and for model selection between two partially observed models. We employ the Bayesian inference, including estimation and model selection, via filtering equations approach to construct efficient recursive algorithms for parameter and model uncertainty quantification. Specifically, adding the jump component in Merton model significantly complicates the related filtering equations, which are stochastic PDEs (SPDEs) that govern the evaluation of the joint posterior and the Bayes Factors. To numerically solve the SPDEs so as to quantify parameter and model uncertainty as data stream in, we apply the related weak convergence theorems, enabling the use of the Markov chain approximation method to construct consistent recursive algorithms via explicit and implicit methods. Due to the positivity of the measure masses, the explicit algorithm suffers from the curse of fine step size. We construct the implicit recursive algorithms involving the iterated Thomas algorithm to overcome the fine-step-size curse and significantly mitigate the computation costs. The implicit recursive algorithms are consistent, easily parallelized, and efficient, with the potential for real-time parameter and model learning. We prove the nonnegativity and convergence of the iterated Thomas algorithm, develop related computer programs, and present preliminary simulation studies.Item Virus-host interactions mediated by pea enation mosaic virus 2 biomolecular condensates(2024) Brown, Shelby L.; May, Jared P.; Bame, Karen J. (Karen Joyce); Gaddis, Monica Louise, 1955-The concept of phase separation applied to biological systems has been rapidly building momentum and interest. Phase separation is the conversion of a single-phase solution into two distinct phases: a dilute phase and a concentrated droplet phase. When applied to cells, the term droplet refers to membraneless organelles or condensates that concentrate biomolecules like proteins and RNA. Viruses can interfere with host condensates, like the nucleolus or stress granules, as well as generate condensates to facilitate viral processes. Our research suggests that electrostatic interactions in the intrinsically disordered region of p26, a movement protein encoded by the +sense RNA plant virus Pea enation mosaic virus 2 (PEMV2), drive p26 phase separation to form viral condensates. We demonstrate co-localization of p26 with host proteins, specifically fibrillarin and G3BP1, into condensates during virus infection and subsequently illustrate the importance of G3BP1 phase separation in the plant anti-viral response. These findings outline a key role for p26 phase separation in the coordination of virus-host interactions, viral ribonucleoprotein (vRNP) formation, and systemic virus movement. This work explores how host- and virus-induced phase separation impacts virus-host interactions to promote or restrict a virus infection.Viral condensate research has predominantly centered around the formation of membraneless replication factories by negative sense viruses. However, the function and composition of cytoplasmic condensates formed by positive sense RNA viruses, which utilize membrane-associated replication factories, has been largely uninvestigated. Mass spectrometry revealed that p26 condensates were enriched with ribosomal proteins and fibrillarin, a host rRNA methyltransferase hijacked by PEMV2 to support virus movement. Our data shows that p26 expression represses global translation >40% in plants. In corroboration, polysome profiling exposed significant defects in monosome formation for p26-overexpression and virus-infected samples, whereas infection with a mutant virus lacking p26 partially rescued monosome formation. Our findings suggest that p26 binds rRNA with a high affinity, yet there was no significant alteration in rRNA abundance, processing, or 2’-O-methylation. Therefore, we propose that p26-mediated sequestration of fibrillarin, mRNA, rRNA, and ribosomal proteins into condensates may serve as a switch to repress translation in favor of virus trafficking, a process incompatible with active translation.