Statistics and Probability Commons^™

Weighted Quantile Sum Regression For Analyzing Correlated Predictors Acting Through A Mediation Pathway On A Biological Outcome, Bhanu M. Evani

Theses and Dissertations

Abstract

Weighted Quantile Sum Regression for Analyzing Correlated Predictors Acting Through a Mediation Pathway on a Biological Outcome

By

Bhanu M. Evani, Ph.D.

A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University.

Virginia Commonwealth University, 2017.

Major Director: Robert A. Perera, Asst. Professor, Department of Biostatistics

This work examines mediated effects of a set of correlated predictors using the recently developed Weighted Quantile Sum (WQS) regression method. Traditionally, mediation analysis has been conducted using the multiple regression method, first proposed by Baron and Kenny (1986), which has since …

Application Of The Fisher Dimer Model To Dna Condensation, John C. Baker Iii

Theses and Dissertations

This paper considers the statistical mechanics occupation of the edge of a single helix of DNA by simple polymers. Using Fisher's exact closed form solution for dimers on a two-dimensional lattice, a one-dimensional lattice is created mathematically that is occupied by dimers, monomers, and holes. The free energy, entropy, average occupation, and total charge on the lattice are found through the usual statistical methods. The results demonstrate the charge inversion required for a DNA helix to undergo DNA condensation.

A Multi-Method Exploration Of The Genetic And Environmental Risks Contributing To Tobacco Use Behaviors In Young Adulthood, Elizabeth K. Do

Theses and Dissertations

Tobacco use remains the leading preventable cause of morbidity and mortality in both the United States and worldwide. Twin and family studies have demonstrated that both genetic and environmental factors are important contributors to tobacco use behaviors. Understanding how genes, the environment, and their interactions is critical to the development of public health interventions that focus on the reduction of tobacco related morbidity and mortality. However, few studies have examined the transition from adolescent to young adulthood – the time when many individuals are experimenting with and developing patterns of tobacco use. This dissertation thesis seeks to provide a comprehensive …

Homeolog Specific Expression Bias, Ronald D. Smith

Biology and Medicine Through Mathematics Conference

No abstract provided.

Heterogeneous Responses To Viral Infection: Insights From Mathematical Modeling Of Yellow Fever Vaccine, James R. Moore

Biology and Medicine Through Mathematics Conference

No abstract provided.

Design & Analysis Of A Computer Experiment For An Aerospace Conformance Simulation Study, Ryan W. Gryder

Theses and Dissertations

Within NASA's Air Traffic Management Technology Demonstration # 1 (ATD-1), Interval Management (IM) is a flight deck tool that enables pilots to achieve or maintain a precise in-trail spacing behind a target aircraft. Previous research has shown that violations of aircraft spacing requirements can occur between an IM aircraft and its surrounding non-IM aircraft when it is following a target on a separate route. This research focused on the experimental design and analysis of a deterministic computer simulation which models our airspace configuration of interest. Using an original space-filling design and Gaussian process modeling, we found that aircraft delay assignments …

Non-Conventional Approaches To Syntheses Of Ferromagnetic Nanomaterials, Dustin M. Clifford

Theses and Dissertations

The work of this dissertation is centered on two non-conventional synthetic approaches to ferromagnetic nanomaterials: high-throughput experimentation (HTE) (polyol process) and continuous flow (CF) synthesis (aqueous reduction and the polyol process). HTE was performed to investigate phase control between Fe_xCo_1-x and Co_3-xFe_xO_y. Exploration of synthesis limitations based on magnetic properties was achieved by reproducing M_s=210 emu/g. Morphological control of Fe_xCo_1-x alloy was achieved by formation of linear chains using an H_ext. The final study of the Fe_xCo_1-x chains used DoE to …

Finding The Cutpoint Of A Continuous Covariate In A Parametric Survival Analysis Model, Kabita Joshi

Theses and Dissertations

In many clinical studies, continuous variables such as age, blood pressure and cholesterol are measured and analyzed. Often clinicians prefer to categorize these continuous variables into different groups, such as low and high risk groups. The goal of this work is to find the cutpoint of a continuous variable where the transition occurs from low to high risk group. Different methods have been published in literature to find such a cutpoint. We extended the methods of Contal and O’Quigley (1999) which was based on the log-rank test and the methods of Klein and Wu (2004) which was based on the …

Modeling Spatially Varying Effects Of Chemical Mixtures, Jenna Czarnota

Theses and Dissertations

Cancer incidence is associated with exposures to multiple environmental chemicals, and geographic variation in cancer rates suggests the importance of accommodating spatially varying effects in the analysis of environmental chemical mixtures and disease risk. Traditional regression methods are challenged by the complex correlation patterns inherent among co-occurring chemicals, and the applicability of geographically weighted regression models is limited in the setting of environmental chemical risk analysis. In comparison to traditional methods, weighted quantile sum (WQS) regression performs well in the identification of important environmental exposures, but is limited by the assumption that effects are fixed over space. We present an …

A Weighted Gene Co-Expression Network Analysis For Streptococcus Sanguinis Microarray Experiments, Erik C. Dvergsten

Theses and Dissertations

Streptococcus sanguinis is a gram-positive, non-motile bacterium native to human mouths. It is the primary cause of endocarditis and is also responsible for tooth decay. Two-component systems (TCSs) are commonly found in bacteria. In response to environmental signals, TCSs may regulate the expression of virulence factor genes.

Gene co-expression networks are exploratory tools used to analyze system-level gene functionality. A gene co-expression network consists of gene expression profiles represented as nodes and gene connections, which occur if two genes are significantly co-expressed. An adjacency function transforms the similarity matrix containing co-expression similarities into the adjacency matrix containing connection strengths. Gene …

Provision Of Hospital-Based Palliative Care And The Impact On Organizational And Patient Outcomes, Marisa L. Roczen

Theses and Dissertations

Hospital-based palliative care services aim to streamline medical care for patients with chronic and potentially life-limiting illnesses by focusing on individual patient needs, efficient use of hospital resources, and providing guidance for patients, patients’ families and clinical providers toward making optimal decisions concerning a patient’s care. This study examined the nature of palliative care provision in U.S. hospitals and its impact on selected organizational and patient outcomes, including hospital costs, length of stay, in-hospital mortality, and transfer to hospice. Hospital costs and length of stay are viewed as important economic indicators. Specifically, lower hospital costs may increase a hospital’s profit …

In-Shoe Plantar Pressure System To Investigate Ground Reaction Force Using Android Platform, Ahmed A. Mostfa

Theses and Dissertations

Human footwear is not yet designed to optimally relieve pressure on the heel of the foot. Proper foot pressure assessment requires personal training and measurements by specialized machinery. This research aims to investigate and hypothesize about Preferred Transition Speed (PTS) and to classify the gait phase of explicit variances in walking patterns between different subjects. An in-shoe wearable pressure system using Android application was developed to investigate walking patterns and collect data on Activities of Daily Living (ADL). In-shoe circuitry used Flexi-Force A201 sensors placed at three major areas: heel contact, 1st metatarsal, and 5th metatarsal with a PIC16F688 microcontroller …

Selecting Spatial Scale Of Area-Level Covariates In Regression Models, Lauren Grant

Theses and Dissertations

Studies have found that the level of association between an area-level covariate and an outcome can vary depending on the spatial scale (SS) of a particular covariate. However, covariates used in regression models are customarily modeled at the same spatial unit. In this dissertation, we developed four SS model selection algorithms that select the best spatial scale for each area-level covariate. The SS forward stepwise, SS incremental forward stagewise, SS least angle regression (LARS), and SS lasso algorithms allow for the selection of different area-level covariates at different spatial scales, while constraining each covariate to enter at most one spatial …

Meta-Analytic Estimation Techniques For Non-Convergent Repeated-Measure Clustered Data, Aobo Wang

Theses and Dissertations

Clustered data often feature nested structures and repeated measures. If coupled with binary outcomes and large samples (>10,000), this complexity can lead to non-convergence problems for the desired model especially if random effects are used to account for the clustering. One way to bypass the convergence problem is to split the dataset into small enough sub-samples for which the desired model convergences, and then recombine results from those sub-samples through meta-analysis. We consider two ways to generate sub-samples: the K independent samples approach where the data are split into k mutually-exclusive sub-samples, and the cluster-based approach where naturally existing …

Dimension Reduction And Variable Selection, Hossein Moradi Rekabdarkolaee

Theses and Dissertations

High-dimensional data are becoming increasingly available as data collection technology advances. Over the last decade, significant developments have been taking place in high-dimensional data analysis, driven primarily by a wide range of applications in many fields such as genomics, signal processing, and environmental studies. Statistical techniques such as dimension reduction and variable selection play important roles in high dimensional data analysis. Sufficient dimension reduction provides a way to find the reduced space of the original space without a parametric model. This method has been widely applied in many scientific fields such as genetics, brain imaging analysis, econometrics, environmental sciences, etc. …

The Relationship Between Exercise And Depression And Anxiety In College Students, Joshua Frank, Dr. Amy Adkins, Nathan Thomas, Dr. Danielle Dick

Undergraduate Research Posters

The literature shows an inverse association between exercise and mental disorders. The aim of this study is to further elaborate on this association with regards to exercise and its relationship with anxiety and depression in a college sample. The subject group focused on seniors in the Spit for Science data set which incorporated a total of 821 students. Physical activity was assessed using the International Physical Activity Questionnaire (IPAQ) to estimate the overall metabolic equivalents (MET’s) each student spent in walking, moderate, or vigorous activity levels in the previous week. Sum scores were used to measure depression and anxiety. Overall,the …

Principal Component Analysis And Optimization: A Tutorial, Robert Reris, J. Paul Brooks

Statistical Sciences and Operations Research Publications

No abstract provided.

The Support Vector Machine And Mixed Integer Linear Programming: Ramp Loss Svm With L1-Norm Regularization, Eric J. Hess, J. Paul Brooks

Statistical Sciences and Operations Research Publications

The support vector machine (SVM) is a flexible classification method that accommodates a kernel trick to learn nonlinear decision rules. The traditional formulation as an optimization problem is a quadratic program. In efforts to reduce computational complexity, some have proposed using an L1-norm regularization to create a linear program (LP). In other efforts aimed at increasing the robustness to outliers, investigators have proposed using the ramp loss which results in what may be expressed as a quadratic integer programming problem (QIP). In this paper, we consider combining these ideas for ramp loss SVM with L1-norm regularization. The result is four …

Firing Rate Dynamics In Recurrent Spiking Neural Networks With Intrinsic And Network Heterogeneity, Cheng Ly

Statistical Sciences and Operations Research Publications

Heterogeneity of neural attributes has recently gained a lot of attention and is increasing recognized as a crucial feature in neural processing. Despite its importance, this physiological feature has traditionally been neglected in theoretical studies of cortical neural networks. Thus, there is still a lot unknown about the consequences of cellular and circuit heterogeneity in spiking neural networks. In particular, combining network or synaptic heterogeneity and intrinsic heterogeneity has yet to be considered systematically despite the fact that both are known to exist and likely have significant roles in neural network dynamics. In a canonical recurrent spiking neural network model, …

Proof-Of-Concept Of Environmental Dna Tools For Atlantic Sturgeon Management, Jameson Hinkle

Theses and Dissertations

Abstract

The Atlantic Sturgeon (Acipenser oxyrinchus oxyrinchus, Mitchell) is an anadromous species that spawns in tidal freshwater rivers from Canada to Florida. Overfishing, river sedimentation and alteration of the river bottom have decreased Atlantic Sturgeon populations, and NOAA lists the species as endangered. Ecologists sometimes find it difficult to locate individuals of a species that is rare, endangered or invasive. The need for methods less invasive that can create more resolution of cryptic species presence is necessary. Environmental DNA (eDNA) is a non-invasive means of detecting rare, endangered, or invasive species by isolating nuclear or mitochondrial DNA (mtDNA) from the …

High-Throughput Data Analysis: Application To Micronuclei Frequency And T-Cell Receptor Sequencing, Mateusz Makowski

Theses and Dissertations

The advent of high-throughput sequencing has brought about the creation of an unprecedented amount of research data. Analytical methodology has not been able to keep pace with the plethora of data being produced. Two assays, ImmunoSEQ and the cytokinesisblock micronucleus (CBMN), that both produce count data and have few methods available to analyze them are considered.

ImmunoSEQ is a sequencing assay that measures the beta T-cell receptor (TCR) repertoire. The ImmunoSEQ assay was used to describe the TCR repertoires of patients that have undergone hematopoietic stem cell transplantation (HSCT). Several different methods for spectratype analysis were extended to the TCR …

Considerations For Screening Designs And Follow-Up Experimentation, Robert D. Leonard

Theses and Dissertations

The success of screening experiments hinges on the effect sparsity assumption, which states that only a few of the factorial effects of interest actually have an impact on the system being investigated. The development of a screening methodology to harness this assumption requires careful consideration of the strengths and weaknesses of a proposed experimental design in addition to the ability of an analysis procedure to properly detect the major influences on the response. However, for the most part, screening designs and their complementing analysis procedures have been proposed separately in the literature without clear consideration of their ability to perform …

Comparing Welch's Anova, A Kruskal-Wallis Test And Traditional Anova In Case Of Heterogeneity Of Variance, Hangcheng Liu

Theses and Dissertations

Analysis of variance (ANOVA) is a robust test against the normality assumption, but it may be inappropriate when the assumption of homogeneity of variance has been violated. Welch ANOVA and the Kruskal-Wallis test (a non-parametric method) can be applicable for this case. In this study we compare the three methods in empirical type I error rate and power, when heterogeneity of variance occurs and find out which method is the most suitable with which cases including balanced/unbalanced, small/large sample size, and/or with normal/non-normal distributions.

Graph-Based Regularization In Machine Learning: Discovering Driver Modules In Biological Networks, Xi Gao

Theses and Dissertations

Curiosity of human nature drives us to explore the origins of what makes each of us different. From ancient legends and mythology, Mendel's law, Punnett square to modern genetic research, we carry on this old but eternal question. Thanks to technological revolution, today's scientists try to answer this question using easily measurable gene expression and other profiling data. However, the exploration can easily get lost in the data of growing volume, dimension, noise and complexity. This dissertation is aimed at developing new machine learning methods that take data from different classes as input, augment them with knowledge of feature relationships, …

Meta-Analysis Of Gene Expression Studies, Umaporn Siangphoe

Theses and Dissertations

Combining effect sizes from individual studies using random-effects models are commonly applied in high-dimensional gene expression data. However, unknown study heterogeneity can arise from inconsistency of sample qualities and experimental conditions. High heterogeneity of effect sizes can reduce statistical power of the models. We proposed two new methods for random effects estimation and measurements for model variation and strength of the study heterogeneity. We then developed a statistical technique to test for significance of random effects and identify heterogeneous genes. We also proposed another meta-analytic approach that incorporates informative weights in the random effects meta-analysis models. We compared the proposed …

Controlling For Confounding When Association Is Quantified By Area Under The Roc Curve, Hadiza I. Galadima

Theses and Dissertations

In the medical literature, there has been an increased interest in evaluating association between exposure and outcomes using nonrandomized observational studies. However, because assignments to exposure are not done randomly in observational studies, comparisons of outcomes between exposed and non-exposed subjects must account for the effect of confounders. Propensity score methods have been widely used to control for confounding, when estimating exposure effect. Previous studies have shown that conditioning on the propensity score results in biased estimation of odds ratio and hazard ratio. However, there is a lack of research into the performance of propensity score methods for estimating the …

Realistic Spiking Neuron Statistics In A Population Are Described By A Single Parametric Distribution, Lauren Crow 9370373

Undergraduate Research Posters

The spiking of activity of neurons throughout the cortex is random and complicated. This complicated activity requires theoretical formulations in order to understand the underlying principles of neural processing. A key aspect of theoretical investigations is characterizing the probability distribution of spiking activity. This study aims to better understand the statistics of the time between spikes, or interspike interval, in both real data and a spiking model with many time scales. Exploration of the interspike intervals of neural network activity can provide a better understanding of neural responses to different stimuli. We consider different parametric distribution fitting techniques to characterize …

Application And Extension Of Weighted Quantile Sum Regression For The Development Of A Clinical Risk Prediction Tool, Ghalib Bello

Theses and Dissertations

In clinical settings, the diagnosis of medical conditions is often aided by measurement of various serum biomarkers through the use of laboratory tests. These biomarkers provide information about different aspects of a patient’s health and the overall function of different organs. In this dissertation, we develop and validate a weighted composite index that aggregates the information from a variety of health biomarkers covering multiple organ systems. The index can be used for predicting all-cause mortality and could also be used as a holistic measure of overall physiological health status. We refer to it as the Health Status Metric (HSM). Validation …

A Study Of The Relationship Between Childhood Body Size And Adult Blood Pressure, Cardiovascular Structure And Function, Yangyang Deng

Theses and Dissertations

BACKGROUND: Little is known of the effects of obesity, body size and body composition, and blood pressure (BP) in childhood on hypertension (HBP) and cardiac structure and function in adulthood due to the lack of long-term serial data on these parameters from childhood into adulthood. In the present study, we are poised to analyze these serial data from the Fels Longitudinal Study (FLS) to evaluate the extent to which body size during childhood determines HBP and cardiac structure and function in the same individuals in adulthood through mathematical modeling. METHODS: The data were from 412 males and 403 females in …

R Code To Accompany “Principal Component Analysis And Optimization: A Tutorial”, Robert Reris, J. Paul Brooks

Statistical Sciences and Operations Research Data

This data accompanies "Principal Component Analysis and Optimization: A Tutorial" by Robert Reris and J. Paul Brooks, presented at the 2015 INFORMS Computing Society Conference, Operations Research and Computing: Algorithms and Software for Analytics, Richmond, Virginia January 11-13, 2015.

The data contains R code, output, and comments that follow the examples for principal component analysis in the paper.