Biostatistics Commons^™

Sexual Behaviors Associated With Online Partner-Seeking Among Men Who Have Sex With Men From Small/Midsized Towns Or Rural Areas In Kentucky, Vira Pravosud

Theses and Dissertations--Epidemiology and Biostatistics

The HIV epidemic remains one of the most significant public health issues in the United States, particularly among men who have sex with men (MSM). New avenues for partner-seeking have emerged over the past three decades, including through the Internet, social media, and geosocial networking applications. Consisting of three cross-sectional studies, this dissertation research aimed to determine associations between the use of various online tools for partner-seeking (hereafter collectively referred to as “apps”) and HIV-related sexual behaviors among 252 young adult MSM residing in small/midsized towns or rural areas in Central Kentucky, a group that has been under-represented in the …

Innovative Statistical Models In Cancer Immunotherapy Trial Design, Jing Wei

Theses and Dissertations--Statistics

A challenge arising in cancer immunotherapy trial design is the presence of non-proportional hazards (NPH) patterns in survival curves. We considered three different NPH patterns caused by delayed treatment effect, cure rate and responder rate of treatment group in this dissertation. These three NPH patterns would violate the proportional hazard model assumption and ignoring any of them in an immunotherapy trial design will result in substantial loss of statistical power.

In this dissertation, four models to deal with NPH patterns are discussed. First, a piecewise proportional hazards model is proposed to incorporate delayed treatment effect into the trial design consideration. …

The Causes And Control Measures Of Extended Spectrum Beta-Lactamase Producing Enterobacteriaceae In Long-Term Care Facilities, Ismaila Olatunji Sule

Walden Dissertations and Doctoral Studies

Due to extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE), infections among residents are increasing in long-term care facilities (LTCFs), resulting in high rate of morbidity and healthcare costs. ESBL-PE resists empirical antibiotics and reduces treatment options, and a designated infection control team is unavailable to prevent the prevalence of the disease. Ecological theory guided this study. A systematic review and meta-analysis were conducted to characterize the causes of ESBL-PE and evaluate the infection control strategies within LTCFs. Multiple regression analysis (MRA) was included as supplementary statistical analysis to identify relationships between LTCFs, geographical locations, infection control measures (ICMs), and ESBL-PE. A systematic search …

Spatio-Temporal Modelling Of Tick Life-Stage Count Data With Spatially Varying Coefficients, Thabo Lephoto, Henry Mwambi, Oliver Bodhlyera, Holly Gaff

Biological Sciences Faculty Publications

There is a vast amount of geo-referenced data in many fields of study including ecological studies. Geo-referencing is usually by point referencing; that is, latitudes and longitudes or by areal referencing, which includes districts, counties, states, provinces and other administrative units. The availability of large geo-referenced datasets for modelling has necessitated the development and application of spatial statistical methods. However, spatial varying coefficients models exploring the abundance of tick counts remain limited. In this study we used data that was collected and prepared by researchers in the Department of Biological Sciences from the Old Dominion University, Virginia, USA. We modelled …

Construction And Analysis Of Genetic Regulatory Networks With Rna-Seq Data From Arabidopsis Thaliana, Tessa Kriz

Dissertations, Master's Theses and Master's Reports

Reconstruction of gene regulatory networks (GRNs) is a fundamental aspect of genetic engineering and provides a deeper understanding of the biological processes of an organism. Two methods were implemented to reconstruct the gene regulatory networks of Arabidopsis thaliana under two treatments: methyl jasmonate (MeJa) and salicylic acid (SA). The Joint Reconstruction of multiple Gene Regulatory Networks (JRmGRN) method was utilized to construct a joint network for identifying hub genes common to both conditions in addition to networks specific to each condition. The Differential Network Analysis with False Discover Rate Control method constructed a network of connections unique to only one …

Nutritional Approach For Increasing Public Health During Pandemic Of Covid-19: A Comprehensive Review Of Antiviral Nutrients And Nutraceuticals, Vahideh Ebrahimzadeh-Attari, Ghodratollah Panahi, James R. Hébert Scd, Alireza Ostadrahimi, Maryam Saghafi-Asl, Neda Lotfi-Yaghin, Behzad Baradaran

Faculty Publications

Background: The novel coronavirus (COVID-19) is considered as the most life-threatening pandemic disease during the last decade. The individual nutritional status, though usually ignored in the management of COVID-19, plays a critical role in the immune function and pathogenesis of infection. Accordingly, the present review article aimed to report the effects of nutrients and nutraceuticals on respiratory viral infections including COVID-19, with a focus on their mechanisms of action.

Methods: Studies were identified via systematic searches of the databases including PubMed/ MEDLINE, ScienceDirect, Scopus, and Google Scholar from 2000 until April 2020, using keywords. All relevant clinical and experimental studies …

The Need To Incorporate Communities In Compartmental Models, Michael J. Kane, Owais Gilani

Faculty Journal Articles

Tian et al. provide a framework for assessing population- level interventions of disease outbreaks through the construction of counterfactuals in a large-scale, natural experiment assessing the efficacy of mild, but early interventions compared to delayed interventions. The technique is applied to the recent SARS-CoV-2 outbreak with the population of Shenzhen, China acting as the mild-but-early treatment group and a combination of several US counties resembling Shenzhen but enacting a delayed intervention acting as the control. To help further the development of this framework and identify an avenue for further enhancement, we focus on the use and potential limitations of compartmental …

Principal Components Analysis Corrects Collider Bias In Polygenic Risk Score Effect Size Estimation, Nathaniel S. Thomas, Peter B. Barr, Fazil Aliev, Sally I. Kuo, Danielle M. Dick, Jessica E. Salvatore

Graduate Research Posters

BACKGROUND: Genome-wide polygenic scoring has emerged as a way to predict psychiatric and behavioral outcomes and identify environments that promote the expression of genetic risks. An increasing number of studies demonstrate that the effects of polygenic risk scores (PRS) may be biased by the inclusion of heritable environments as covariates when the environment is influenced by unmeasured confounding variables, an example of collider bias. Inclusion of the principal components of observed confounders as covariates may correct for the effect of unmeasured confounders.

METHODS: A simulation study was conducted to test principal components analysis (PCA) as a correction for collider bias. …

Addressing The Ecological Fallacy With Lagrangian Inference, Michael Schwob

Calvert Undergraduate Research Awards

Most epidemiologists elect to use statistical models that use population-level data to make inference on the spread of some virus or disease. This has become commonplace in the fields of epidemiology and biostatistics since most data used to construct and verify epidemic models are recorded at the population-level. Obtaining inference from a population-level model may be beneficial in studying the spread of disease in a homogeneous population, but the use of such models to describe a heterogeneous population results in inadequate inference. The inaccuracy of these models is further amplified when one tries to make individual-level inference from these population-level …

Statistical Methods In Genetic Studies, Cheng Gao

Dissertations, Master's Theses and Master's Reports

This dissertation includes three Chapters. A brief description of each chapter is organized as follows.

In Chapter 1, we proposed a new method, called MF-TOWmuT, for genome-wide association studies with multiple genetic variants and multiple phenotypes using family samples. MF-TOWmuT uses kinship matrix to account for sample relatedness. It is worth mentioning that in simulations, we considered hidden polygenic effects and varied the proportion of variance contributed by it to generate phenotypes. Simulation studies show that MF-TOWmuT can preserve the type I error rates and is more powerful than several existing methods in different simulation scenarios, MFTOWmuT is also quite …

Ensemble Protein Inference Evaluation, Kyle Lee Lucke

Graduate Student Theses, Dissertations, & Professional Papers

The Protein inference problem is becoming an increasingly important tool that aids in the characterization of complex proteomes and analysis of complex protein samples. In bottom-up shotgun proteomics experiments the metrics for evaluation (like AUC and calibration error) are based on an often imperfect target-decoy database. These metrics make the inherent assumption that all of the proteins in the target set are present in the sample being analyzed. In general, this is not the case, they are typically a mix of present and absent proteins. To objectively evaluate inference methods, protein standard datasets are used. These datasets are special in …

Impact Of Case Management On Childhood Lead Exposure In Marion County, Indiana, Maliki Yacouba

Walden Dissertations and Doctoral Studies

The Centers for Disease Control and Prevention recently declared that no amount of childhood blood lead level (BLL) is safe. The purpose of this quantitative study with a retrospective cohort design was to evaluate the effectiveness of case management intervention on children diagnosed with elevated BLL (EBLL; ≥ 5 μg/dL) in Marion, County, Indiana. The health belief model was used as the theoretical foundation for the study. A data set of 160 lead exposure case management records was analyzed to find whether: (a) BLL at post-case-management time significantly differ from BLL at baseline (b) BLL at post-case-management time is affected …

Modeling Time Series With Conditional Heteroscedastic Structure, Ratnayake Mudiyanselage Isuru Panduka Ratnayake

Doctoral Dissertations

"Models with a conditional heteroscedastic variance structure play a vital role in many applications, including modeling financial volatility. In this dissertation several existing formulations, motivated by the Generalized Autoregressive Conditional Heteroscedastic model, are further generalized to provide more effective modeling of price range data well as count data. First, the Conditional Autoregressive Range (CARR) model is generalized by introducing a composite range-based multiplicative component formulation named the Composite CARR model. This formulation enables a more effective modeling of the long and short-term volatility components present in price range data. It treats the long-term volatility as a stochastic component that in …

A Model For Inhalation Of Infectious Aerosol Contaminants In An Aircraft Passenger Cabin, Bert A. Silich

International Journal of Aviation, Aeronautics, and Aerospace

Aerosol contamination of an aircraft cabin by infectious passengers is a concern of passengers, aircrew and the aviation industry. This may be especially important during a pandemic, such as COVID-19, where the full extent of aerosol transmission is not well understood. A statistical method to determine the number of infectious passengers on board along with a mathematical model estimating the contaminant concentration of aerosols in the cabin and the number of inhaled infectious particles by passengers is presented. An example is used to demonstrated how the results can be estimated during normal operations and emergency conditions with malfunctions of the …

Prognostic Modeling Of Recovery Following Stem Cell Transplantation, Brielle A. Forsthoffer

Theses and Dissertations

Predicting the trajectory of lymphoid recovery following myeloablative hematopoietic stem cell transplantation (SCT) can help guide subsequent therapeutic decisions, since poor recovery has been associated with graft-versus-host disease (GVHD), relapse and mortality. Previous attempts at classifying patients depended on absolute criteria being set prior to modeling absolute lymphocyte counts (ALCs) over time. Having an empirical clinical decision support tool for objectively determining the trajectory an individual might take during their recovery would be advantageous. We propose using growth-based trajectory modeling (GBTM) and growth mixture modeling (GMM), which utilize machine learning algorithms to empirically identify latent groupings of data. Due to …

Bayesian Techniques For Relating Genetic Polymorphisms To Diffusion Tensor Images Of Cocaine Users, Tmader Alballa

Theses and Dissertations

Past investigations utilizing Diffusion Tensor Imaging (DTI) have demonstrated that cocaine use disorder (CUD) yields white matter changes. We proposed three Bayesian techniques in order to explore the relationship between Fractional Anisotropy (FA), genetic data, and years of cocaine use (YCU). CUD participants exhibit abnormality in different areas of the brain versus non-drug using controls, which is measured by DTI. This dissertation is motivated by a neuroimaging genetic study in cocaine dependence, which found that there were relationships between several genes such as GAD and 5-HT₂R and CUD subjects.

In the first chapter, there is background on the …

Methods For Developing A Machine Learning Framework For Precise 3d Domain Boundary Prediction At Base-Level Resolution, Spiro C. Stilianoudakis

Theses and Dissertations

High-throughput chromosome conformation capture technology (Hi-C) has revealed extensive DNA looping and folding into discrete 3D domains. These include Topologically Associating Domains (TADs) and chromatin loops, the 3D domains critical for cellular processes like gene regulation and cell differentiation. The relatively low resolution of Hi-C data (regions of several kilobases in size) prevents precise mapping of domain boundaries by conventional TAD/loop-callers. However, high resolution genomic annotations associated with boundaries, such as CTCF and members of cohesin complex, suggest a computational approach for precise location of domain boundaries.

We developed preciseTAD, an optimized machine learning framework that leverages a random …

Analyzing Electronic Health Records With Time-To-Event Endpoints: Propensity Scores And Semiparametric Approaches, Jonathan W. Yu

Theses and Dissertations

For analyzing large electronic health records (EHR) with time-to-event endpoints, such as in kidney transplantation, a major challenge is to provide an accurate risk analyses, while accounting for a multitude of epidemiological and statistical complexities. Motivated by a right-censored kidney transplantation EHR dataset derived from the United Network of Organ Sharing (UNOS), this dissertation, through a culmination of two interrelated yet distinctly different projects, focuses on developments of novel statistical procedures and methodologies to address some pressing issues arising in EHR-based research. In the first project, we aim to decouple the causal effects of treatments (here, studying subgroups, such as …

Dach1 Mutation Frequency In Endometrial Cancer Is Associated With High Tumor Mutation Burden, Mckayla J. Riggs, Nan Lin, Chi Wang, Dava W. Piecoro, Rachel W. Miller, Oliver A. Hampton, Mahadev Rao, Frederick R. Ueland, Jill M. Kolesar

Obstetrics and Gynecology Faculty Publications

OBJECTIVE: DACH1 is a transcriptional repressor and tumor suppressor gene frequently mutated in melanoma, bladder, and prostate cancer. Loss of DACH1 expression is associated with poor prognostic features and reduced overall survival in uterine cancer. In this study, we utilized the Oncology Research Information Exchange Network (ORIEN) Avatar database to determine the frequency of DACH1 mutations in patients with endometrial cancer in our Kentucky population.

METHODS: We obtained clinical and genomic data for 65 patients with endometrial cancer from the Markey Cancer Center (MCC). We examined the clinical attributes of the cancers by DACH1 status by comparing whole-exome sequencing (WES), …

Bayesian Semi-Supervised Keyphrase Extraction And Jackknife Empirical Likelihood For Assessing Heterogeneity In Meta-Analysis, Guanshen Wang

Statistical Science Theses and Dissertations

This dissertation investigates: (1) A Bayesian Semi-supervised Approach to Keyphrase Extraction with Only Positive and Unlabeled Data, (2) Jackknife Empirical Likelihood Confidence Intervals for Assessing Heterogeneity in Meta-analysis of Rare Binary Events.

In the big data era, people are blessed with a huge amount of information. However, the availability of information may also pose great challenges. One big challenge is how to extract useful yet succinct information in an automated fashion. As one of the first few efforts, keyphrase extraction methods summarize an article by identifying a list of keyphrases. Many existing keyphrase extraction methods focus on the unsupervised setting, …