Biostatistics Commons^™

Combining Chicken Retina Rna-Seq Data Across Studies To Strengthen Biomarker Detection, Sarah Szvetecz

Senior Honors Projects, 2010-2019

Various studies have identified the chicken embryo (Gallus gallus) as a useful model to study the retinogenesis process in humans. This project uses data from two specific RNA sequencing (RNA-seq) studies to investigate retina developmental biology. These studies are done in two different labs using different protocols, as such they cannot be compared directly. Study 1 contains chicken retina samples from embryonic day 3, 5 and 8; while study 2 has retina samples from embryonic day 8, 16, and 18 of developmental age. We apply a normalization method on both studies to account for differences in the two …

Tdp-43 Proteinopathy In Aging: Associations With Risk-Associated Gene Variants And With Brain Parenchymal Thyroid Hormone Levels, Peter T. Nelson, Zsombor Gal, Wang-Xia Wang, Dana M. Niedowicz, Sergey C. Artiushin, Samuel Wycoff, Angela Wei, Gregory A. Jicha, David W. Fardo

Pathology and Laboratory Medicine Faculty Publications

TDP-43 proteinopathy is very prevalent among the elderly (affecting at least 25% of individuals over 85 years of age) and is associated with substantial cognitive impairment. Risk factors implicated in age-related TDP-43 proteinopathy include commonly inherited gene variants, comorbid Alzheimer's disease pathology, and thyroid hormone dysfunction. To test parameters that are associated with aging-related TDP-43 pathology, we performed exploratory analyses of pathologic, genetic, and biochemical data derived from research volunteers in the University of Kentucky Alzheimer's Disease Center autopsy cohort (n = 136 subjects). Digital pathologic methods were used to discriminate and quantify both neuritic and intracytoplasmic TDP-43 pathology …

Health Disparities Among Sexual And Gender Minorities, Jennifer Keeley

UNLV Theses, Dissertations, Professional Papers, and Capstones

Decades of research has shown that sexual and gender minorities (SGMs) experience adverse health and mental health outcomes to a greater extent than their heterosexual peers. The need to better understand and eliminate health disparities in the SGM population was recognized by the National Institute on Minority Health and Health Disparities (NIMHD) at NIH. The Secretary of Health at the Department of Health and Human Services approved the designation of the SGM population as a health disparities population in 2016 and called for SGM studies to examine the health needs of the SGM population across SGM subgroups via large representative …

Effects Of Perioperative Hyperglycemia In Patients With Diabetes Compared To Patients Without Diabetes: A Retrospective Study Of Treatment And Outcomes, Matthew Anderson

Capstone Experience: Master of Public Health

The main goal of this project was to examine the differences in perioperative hyperglycemia treatment received by patients with a diagnosis of diabetes mellitus (DM) and patients without a diagnosis of diabetes (NDM); and how these treatment differences can affect the length of hospital stay. Studies have revealed that, when comparing DM and NDM patients with the same degree of perioperative hyperglycemia, NDM patients suffer worse outcomes. It has been suggested in previous research that this may be because NDM patients receive treatment that does not measure up to the standard of care treatment that DM patients receive. In this …

Contributions To Mcmc Methods In Constrained Domains With Applications To Neuroimaging, Sharang Chaudhry

UNLV Theses, Dissertations, Professional Papers, and Capstones

Markov chain Monte Carlo (MCMC) methods form a rich class of computational techniques that help its user ascertain samples from target distributions when direct sampling is not possible or when their closed forms are intractable. Over the years, MCMC methods have been used in innumerable situations due to their flexibility and generalizability, even in situations involving nonlinear and/or highly parametrized models. In this dissertation, two major works relating to MCMC methods are presented.

The first involves the development of a method to identify the number and directions of nerve fibers using diffusion-weighted MRI measurements. For this, the biological problem is …

Telomeres, Nutrition And Mortality: Risk Factors For The Rate Of Telomere Length Decline And The Associations Between Telomere Length, Nutrition And Mortality, Saruna Ghimire

UNLV Theses, Dissertations, Professional Papers, and Capstones

Introduction: Telomeres are nucleoprotein structures located at the ends of eukaryotic chromosomes, thought to protect the DNA from damage. As a person experiences stressors, harmful exposures, and other diseases throughout their life, telomeres are thought to become damaged and their length shortened, decreasing their ability to protect the DNA. Nutrition is an important aspect of healthy aging. Preservation of telomere length (TL) is thought to be one of the mechanisms by which good nutrition can delay or prevent the development of chronic disease and death. Recent evidence of preservation of TL with good nutrition is promising. Thus, the aim of …

The Effects Of Injury On Running Status And Gait Biomechanics, Kristyne Wiegand

UNLV Theses, Dissertations, Professional Papers, and Capstones

Over the past several decades, endurance running has grown steadily as a popular form of physical activity. Running is easily accessible, does not require expensive equipment, and can be performed without specific skill training. Individuals who run also experience health benefits like increased cardiovascular health and reduced risk of all-cause morbidity. Despite these benefits, running is also associated with high rates of musculoskeletal injury. Although researchers have attempted to identify injury risks and mitigate the incidence of running injury, there is still no consensus as to why runners become injured. Research has also attempted to identify biomechanical movement patterns that …

An Analysis Of Postmastectomy Breast Reconstruction Due To Breast Cancer In Nevada And The United States From 2008-2013, Jenna Webb

UNLV Theses, Dissertations, Professional Papers, and Capstones

Background: In the United States, female breast cancer was the leading cause of new cancer cases from 2011-2015. Since the Women’s Health and Cancer Act of 1998 (WHCRA), the federal government mandates employee and private health insurance providers to cover breast reconstruction if they cover mastectomies. Postmastectomy breast reconstruction (PBR) rates increased after the WHCRA, but these rates have remained relatively low throughout recent years. Objective: The objective of this study was to determine factors associated with women having PBR due to breast cancer in Nevada and the United States from 2008 to 2013. Methods: Using two HCUP database, NIS …

Incorporating Pathway Information Into Feature Selection Towards Better Performed Gene Signatures, Suyan Tian, Chi Wang, Bing Wang

Biostatistics Faculty Publications

To analyze gene expression data with sophisticated grouping structures and to extract hidden patterns from such data, feature selection is of critical importance. It is well known that genes do not function in isolation but rather work together within various metabolic, regulatory, and signaling pathways. If the biological knowledge contained within these pathways is taken into account, the resulting method is a pathway-based algorithm. Studies have demonstrated that a pathway-based method usually outperforms its gene-based counterpart in which no biological knowledge is considered. In this article, a pathway-based feature selection is firstly divided into three major categories, namely, pathway-level selection, …

Spatio-Temporal Cluster Detection And Local Moran Statistics Of Point Processes, Jennifer L. Matthews

Mathematics & Statistics Theses & Dissertations

Moran's index is a statistic that measures spatial dependence, quantifying the degree of dispersion or clustering of point processes and events in some location/area. Recognizing that a single Moran's index may not give a sufficient summary of the spatial autocorrelation measure, a local indicator of spatial association (LISA) has gained popularity. Accordingly, we propose extending LISAs to time after partitioning the area and computing a Moran-type statistic for each subarea. Patterns between the local neighbors are unveiled that would not otherwise be apparent. We consider the measures of Moran statistics while incorporating a time factor under simulated multilevel Palm distribution, …

Randomization Analysis Driven Software, Steph-Yves Louis

Theses and Dissertations

The application of a method of randomization for a clinical trial frequently summarizes to using Simple Randomization. Even though the latter method provides favorable characteristics, if the collected sample is not large enough, it still presents the highest chance of imbalance both marginally in the treatment groups and locally in terms of the covariates. Methods of Permuted Block Randomization, Urn Randomization, Stratified Permuted Block Randomization, and Minimization represent popular alternative methods that one should consider depending on the goal of the study. A comparison of the previously mentioned methods is carried to evaluate their performance with samples that are not …

Beach Composition Preferences For Nesting Populations Of Leatherback Sea Turtles (Dermochelys Coriacea), Armila Beach, Guna Yala Comarca, Scott Campbell

Independent Study Project (ISP) Collection

Sea turtles play a critical role in marine ecosystems all over the world, including the Caribbean Sea. However, many sea turtle species are under threat due to anthropogenic impacts, such as habitat destruction and fisheries bycatch. This has caused significant declines in sea turtle populations around the world, which in turn has impacted marine ecosystems where sea turtles play critical roles in proper ecosystem functioning. A crucial part of the sea turtle life cycle that has been threatened by anthropogenic factors is nesting. Sea turtles rely on unspoiled beaches with particular physical characteristics for laying their eggs. One of the …

Avian Upsloping In The Tropics: Myioborus Miniatus And Myioborus Torquatus Abundance In Different Altitudinal Ranges In Boquete, Chiriquí, Panama, Julie Yoon

Independent Study Project (ISP) Collection

Direct and indirect effects of warming global temperatures due to climate change are known to cause upwards shifts of the altitudinal ranges of some avian species. Most susceptible to this trend and at risk of riding the “escalator to extinction” are endemic species in tropical montane cloud forests, such as Myioborus torquatus. There are abiotic factors, like temperature, and biotic interactions, such as the presence of its altitudinal neighbor Myioborus miniatus, that limit the altitudinal range of this bird species in the Neotropics. This study measured abundance of M. miniatus and M. torquatus populations at different altitudinal ranges by point …

A Survey Of Beetle Diversity (Order Coleoptera) On Lizard Island, John Mccormack

Independent Study Project (ISP) Collection

The beetles (order Coleoptera) of Lizard Island, a small granitic island on the mid shelf of the Great Barrier Reef, have never been assessed in the scientific literature. Prior to our work, only a single beetle genus had been documented on the island (Caryotrypes Decelle, 1968), based on a single specimen collected in 1993 (Reid & Beatson 2013). We conducted a survey of Lizard Island in April 2019 to determine which beetle families are present on the island and which families are the most diverse. The survey also assessed the beetle diversity in different habitats on the island and two …

Tobacco Smoking And Dementia In A Kentucky Cohort: A Competing Risk Analysis, Erin L. Abner, Peter T. Nelson, Gregory A. Jicha, Gregory E. Cooper, David W. Fardo, Frederick A. Schmitt, Richard J. Kryscio

Epidemiology and Environmental Health Faculty Publications

Tobacco smoking was examined as a risk for dementia and neuropathological burden in 531 initially cognitively normal older adults followed longitudinally at the University of Kentucky’s Alzheimer’s Disease Center. The cohort was followed for an average of 11.5 years; 111 (20.9%) participants were diagnosed with dementia, while 242 (45.6%) died without dementia. At baseline, 49 (9.2%) participants reported current smoking (median pack-years = 47.3) and 231 (43.5%) former smoking (median pack-years = 24.5). The hazard ratio (HR) for dementia for former smokers versus never smokers based on the Cox model was 1.64 (95% CI: 1.09, 2.46), while the HR for …

Feature Selection For Longitudinal Data By Using Sign Averages To Summarize Gene Expression Values Over Time, Suyan Tian, Chi Wang

Biostatistics Faculty Publications

With the rapid evolution of high-throughput technologies, time series/longitudinal high-throughput experiments have become possible and affordable. However, the development of statistical methods dealing with gene expression profiles across time points has not kept up with the explosion of such data. The feature selection process is of critical importance for longitudinal microarray data. In this study, we proposed aggregating a gene’s expression values across time into a single value using the sign average method, thereby degrading a longitudinal feature selection process into a classic one. Regularized logistic regression models with pseudogenes (i.e., the sign average of genes across time as predictors) …

Unified Methods For Feature Selection In Large-Scale Genomic Studies With Censored Survival Outcomes, Lauren Spirko-Burns, Karthik Devarajan

COBRA Preprint Series

One of the major goals in large-scale genomic studies is to identify genes with a prognostic impact on time-to-event outcomes which provide insight into the disease's process. With rapid developments in high-throughput genomic technologies in the past two decades, the scientific community is able to monitor the expression levels of tens of thousands of genes and proteins resulting in enormous data sets where the number of genomic features is far greater than the number of subjects. Methods based on univariate Cox regression are often used to select genomic features related to survival outcome; however, the Cox model assumes proportional hazards …

Data Analytics Pipeline For Rna Structure Analysis Via Shape, Quinn Nelson

UNO Student Research and Creative Activity Fair

Coxsackievirus B3 (CVB3) is a cardiovirulent enterovirus from the family Picornaviridae. The RNA genome houses an internal ribosome entry site (IRES) in the 5’ untranslated region (5’UTR) that enables cap-independent translation. Ample evidence suggests that the structure of the 5’UTR is a critical element for virulence. We probe RNA structure in solution using base-specific modifying agents such as dimethyl sulfate as well as backbone targeting agents such as N-methylisatoic anhydride used in Selective 2’-Hydroxyl Acylation Analyzed by Primer Extension (SHAPE). We have developed a pipeline that merges and evaluates base-specific and SHAPE data together with statistical analyses that provides confidence …

Influence Of Decentralization And Type Of Patient On Loss To Follow-Up Among Multidrug-Resistant Tuberculosis Patients In Indonesia From 2014 To 2015, Noerfitri Noerfitri, R. Sutiawan, Tri Yunis Miko Wahyono, Pratiwi Ayuningtyas Hartono

Kesmas

Drug-resistant tuberculosis (TB) patients have a greater risk of loss to follow-up (LTFU) than drug-sensitive TB patients, due to their longer treatment duration. This study aimed to determine the influence of decentralization and patient type on LTFU among multidrug-resistant TB (MDR-TB) patients in Indonesia. A retrospective cohort study was conducted at all MDR-TB treatment healthcare facilities in Indonesia from 014 to 2015. Using total sampling technique, 961 patients were examined and sampled. Of these patients, 86.03% were decentralized. Patients were classified into types as follows: 35.17% were “relapse” patients, 5.52% were “new,” 13.94% were classified as “after LTFU” patients, 23.10% …

Knowledge And Practice In Household Waste Management, Agnes Fitria Widiyanto, Suratman Suratman, Nisrina Alifah, Tri Murniati, Oktafiani Catur Pratiwi

Kesmas

Declining environmental quality is one of population caused by household consumption behavior. Some of the highest contaminant contributions are domestic waste, waste, and company waste. Waste contamination will lead to dead fish, decreased water quality and disease transmission. Community approach can be done to solve the waste problem, especially at the household level. This study uses quantitative methods to analyze the effect of intervention and waste management training on changes in household waste management knowledge and practices. This type of research uses quasi experiment with one group of pre and post test design. The results showed that there was an …