Biostatistics Commons^™

Spatially Refined Time-Varying Reproduction Numbers Of Covid-19 By Health District In Georgia, Usa, March–December 2020, Chigozie A. Ogwara, Arshpreet Kaur Mallhi, Xinyi Hua, Kamalich Muniz-Rodriguez, Jessica S. Schwind, Xiaolu Zhou, Jeffery A. Jones, Joanne Chopak-Foss, Gerardo Chowell, Isaac Chun-Hai Fung

Biostatistics, Epidemiology & Environmental Health Sciences: Faculty Publications

This study quantifies the transmission potential of SARS-CoV-2 across public health districts in Georgia, USA, and tests if per capita cumulative case count varies across counties. To estimate the time-varying reproduction number, Rt of SARS-CoV-2 in Georgia and its 18 public health districts, we apply the R package ‘EpiEstim’ to the time series of historical daily incidence of confirmed cases, 2 March–15 December 2020. The epidemic curve is shifted backward by nine days to account for the incubation period and delay to testing. Linear regression is performed between log10-transformed per capita cumulative case count and log10-transformed population size. We observe …

Theranostic Applications Of Sirna Bioconjugates In Cancer Detection And Treatment, Sunil S. Shah

Seton Hall University Dissertations and Theses (ETDs)

Abstract

The emerging field of RNA nanotechnology has led to rapid advances in the applications of RNA in chemical biology, medicinal chemistry, and biotechnology. At the forefront of its utility is the ability to self-assemble multiple siRNAs into nanostructure formulations capable of targeting selected oncogenes and potentiating the gene therapy of malignant tumors. Self-assembled siRNA integrates multiple siRNAs within a single molecular platform for silencing multiple oncogenic mRNA targets with high precision and efficacy to potentially induce cancer cell apoptosis through the RNA interference (RNAi) pathway. Furthermore, the conjugation of siRNA self-assemblies with bio-active probes results in multi-functional theranostic (therapy+diagnostic) …

Differences In ​The Proportion Of Children Meeting Behavior Guidelines ​Between Summer ​And School By Socioeconomic Status And Race, Ethan T. Hunt, Lauren Von Klinggraeff, Alexis Jones, Sarah Burkart, Roddrick Dugger, Bridget Armstrong Ph.D., Michael Beets Ph.D., Gabrielle Turner-Mcgrievy Ph.D., Rd, Marco Geraci, Robert Glenn Weaver Med, Phd

Faculty Publications

Objective

Children who fail to meet activity, sleep, and screen-time guidelines are at increased risk for obesity. Further, children who are Black are more likely to have obesity when compared to children who are White, and children from low-income households are at increased risk for obesity when compared to children from higher-income households. The objective of this study was to evaluate the proportion of days meeting obesogenic behavior guidelines during the school year compared to summer vacation by race and free/reduced priced lunch (FRPL) eligibility.

Methods

Mixed-effects linear and logistic regressions estimated the proportion of days participants met activity, sleep, …

A Highly Predictive Microrna Panel For Determining Delayed Cerebral Vasospasm Risk Following Aneurysmal Subarachnoid Hemorrhage, Wang-Xia Wang, Joe E. Springer, Kevin Xie, David W. Fardo, Kevin W. Hatton

Sanders-Brown Center on Aging Faculty Publications

Approximately one-third of aneurysmal subarachnoid hemorrhage (aSAH) patients develop delayed cerebral vasospasm (DCV) 3–10 days after aneurysm rupture resulting in additional, permanent neurologic disability. Currently, no validated biomarker is available to determine the risk of DCV in aSAH patients. MicroRNAs (miRNAs) have been implicated in virtually all human diseases, including aSAH, and are found in extracellular biofluids including plasma and cerebrospinal fluid (CSF). We used a custom designed TaqMan Low Density Array miRNA panel to examine the levels of 47 selected brain and vasculature injury related miRNAs in CSF and plasma specimens collected from 31 patients with or without DCV …

Differences In Effectiveness And Use Of Laparoscopic Surgery In Locally Advanced Colon Cancer Patients, M. Schootman, Matthew Mutch, T. Loux, Jan M. Eberth Ph.D., N. O. Davidson

Faculty Publications

Patients with locally advanced colon cancer have worse outcomes. Guidelines of various organizations are conflicting about the use of laparoscopic colectomy (LC) in locally advanced colon cancer. We determined whether patient outcomes of LC and open colectomy (OC) for locally advanced (T4) colon cancer are comparable in all colon cancer patients, T4a versus T4b patients, obese versus non-obese patients, and tumors located in the ascending, descending, and transverse colon. We used data from the 2013–2015 American College of Surgeons’ National Surgical Quality Improvement Program. Patients were diagnosed with nonmetastatic pT4 colon cancer, with or without obstruction, and underwent LC (n …

Species In Vernal Pools: Anova, Lisa Manne

Open Educational Resources

A one-way analysis of variance exercise using data on species diversities from vernal pools.Data are from vernal pools in Willowbrook Park (adjacent to College of Staten Island's campus) in spring.

The typical ANOVA gives a straightforward result (significant anova, easily-interpreted Tukey-Kramer analysis). This data set requires more nuanced interpretation, as the ANOVA is marginally significant, and Tukey-Kramer yields one significant pairwise comparison between groups. Relative lack of variation within groups explains this apparent enigma.

The Hybridizing Ions Treatment (Hit) Method Development And Computational Study On Sars-Cov-2 E Protein., Shengjie Sun

Open Access Theses & Dissertations

Fast and accurate calculations of the electrostatic features for highly charged biomolecules such as DNA, RNA, highly charged proteins, are crucial but challenging tasks. Traditional implicit solvent methods calculate the electrostatic features fast, but they are not able to balance the high net charges in the biomolecules effectively. Explicit solvent methods add unbalanced ions to neutralize the highly charged biomolecules in molecular dynamic simulations, which require more expensive computing resources. Here we developed a novel method, the Hybridizing Ions Treatment (HIT) method, which hybridizes the implicit solvent method with the explicit method to realistically calculate the electrostatic potential for highly …

Estimating Cumulative Incidence Rate On Interval Censored Data In An Illness-Death Model., Chen Qian

Electronic Theses and Dissertations

Phase IV clinical trials are designed to monitor long-term side effects caused overtime by the medical treatment. For instance, in advanced primary cancer treatment, childhood cancer survivors are often at risk of developing undesired events, such as cardiotoxicity, during their adulthood. Such problems could be due to their cancer or the treatment they received for their cancer such as radiation or intensive chemotherapy. Cardiotoxicity can be diagnosed with electrophysiology with measurements of fraction shortening, afterload, etc. Often the primary focus of a study could be on estimating the cumulative incidence of a particular outcome of interest such as cardiotoxicity. However, …

Observational Studies In Group Testing And Potential Applications., Alexander Christopher Noll

Electronic Theses and Dissertations

The use of group testing to identify individuals with targeted outcomes in a population can greatly improve the efficiency, speed, and cost effectiveness of testing a population for an outcome, or at least for identifying the prevalence of an outcome in a population. The implementation of causal inference techniques can provide the basis for an observational study that would allow an investigator to gather estimates for treatment effectiveness if group testing was conducted on the population in a certain way. This thesis examines a simulation of the above outlined principles in order to demonstrate a potential application for determining treatment …

Gene Selection And Classification In High-Throughput Biological Data With Integrated Machine Learning Algorithms And Bioinformatics Approaches, Abhijeet R Patil

Open Access Theses & Dissertations

With the rise of high throughput technologies in biomedical research, large volumes of expression profiling, methylation profiling, and RNA-sequencing data are being generated. These high-dimensional data have large number of features with small number of samples, a characteristic called the "curse of dimensionality." The selection of optimal features, which largely affects the performance of classification algorithms in machine learning models, has led to challenging problems in bioinformatics analyses of such high-dimensional datasets. In this work, I focus on the design of two-stage frameworks of feature selection and classification and their applications in multiple sets of colorectal cancer data. The first …

Association Between Dietary Inflammatory Index, Dietary Patterns, Plant-Based Dietary Index And The Risk Of Obesity, Yoko B. Wang, Nitin Shivappa, James R. Hébert Scd, Amanda J. Page, Yohannes Adama Melaku

Faculty Publications

Evidence on the association between various dietary constructs and obesity risk is limited. This study aims to investigate the longitudinal relationship between different diet indices and dietary patterns with the risk of obesity. Non-obese participants (n = 787) in the North West Adelaide Health Study were followed from 2010 to 2015. The dietary inflammatory index (DII®), plant-based dietary index (PDI) and factor-derived dietary pattern scores were computed based on food frequency questionnaire data. We found the incidence of obesity was 7.62% at the 5-year follow up. In the adjusted model, results from multivariable log-binomial logistic regression showed that a prudent …

Diet Quality And Risk Of Lung Cancer In The Multiethnic Cohort Study, Song-Yi Park, Carol J. Boushey, Yurii B. Shvetsov, Michael David Wirth Msph,Ph.D., Nitin Shivappa Ph.D., James R. Hébert Sc.D., Christopher A. Haiman, Lynee R. Wilkens, Loic Le Marchand

Faculty Publications

Diet quality, assessed by the Healthy Eating Index-2015 (HEI-2015), the Alternative Healthy Eating Index-2010 (AHEI-2010), the alternate Mediterranean Diet (aMED) score, the Dietary Approaches to Stop Hypertension (DASH) score, and the Dietary Inflammatory Index (DII®), was examined in relation to risk of lung cancer in the Multiethnic Cohort Study. The analysis included 179,318 African Americans, Native Hawaiians, Japanese Americans, Latinos, and Whites aged 45–75 years, with 5350 incident lung cancer cases during an average follow-up of 17.5 ± 5.4 years. In multivariable Cox models comprehensively adjusted for cigarette smoking, the hazard ratios (95% confidence intervals) for the highest vs. lowest …

Association Between Appendicular Skeletal Muscle Index And Leukocyte Telomere Length In Adults: A Study From National Health And Nutrition Examination Survey (Nhanes) 1999-2002, Lingzhi Chen, Nitin Shivappa Mbbs, Mph, Ph.D., Xiuxun Dong, Jinjing Ming

Faculty Publications

Background

A higher body mass index (BMI) is associated with shorter telomeres. The loss of muscle mass with aging is associated with adverse outcomes. The appendicular skeletal muscle index (ASMI) is currently used to quantify muscle mass.

Objective

We investigated the association of the ASMI with leukocyte telomere length in adult Americans.

Methods

This cross-sectional study used the National Health and Nutrition Examination Survey (NHANES) 1999–2002 dataset. Body composition was measured by dual-energy X-ray absorptiometry. Low muscle mass was defined using sex-specific thresholds of the appendicular skeletal muscle mass index (ASMI). The telomere-to-single-copy gene ratio (T/S ratio) was converted to …

Does Social Support Moderate The Association Between Income And Food Security Status Among Seniors Living In Southern Nevada?, Adugna Teka Siweya

UNLV Theses, Dissertations, Professional Papers, and Capstones

Background: Income is the strongest predictor of food insecurity among seniors, and social support also an essential factor to help mitigate the effects of food insecurity. However, little is known about the potential role that social support may play as a moderator of the association between income and food insecurity. Thus, we aim to examine social support as a moderator for the relationship between income and food insecurity among seniors. Methods: Logistic regression models were used to analyze data collected in 2019 from seniors residing in Southern Nevada. Predictors of food insecurity, sociodemographic factors, social support variables, and income and …

Mixture Model Approaches To Integrative Analysis Of Multi-Omics Data And Spatially Correlated Genomic Data, Ziqiao Wang

Dissertations and Theses (Open Access)

Integrative genomic data analysis is a powerful tool to study the complex biological processes behind a disease. Statistical methods can model the interrelationships of the involved gene activities through jointly analyzing multiple types of genomic data from different platforms (vertical integration), or improve the power of a study through aggregating the same type of genomic data across studies (horizontal integration). In this dissertation, we propose statistical methods and strategies for integrative multi-omics data in association analysis of disease phenotypes, with an emphasis on cancer applications.

We develop a new strategy based on horizontal integration by leveraging publicly available datasets into …

Food Insecurity And Adiposity Among Children And Adults Nhanes 2015-2016, Denise Vidal

UNLV Theses, Dissertations, Professional Papers, and Capstones

Background: Obesity is a preventable disease that has been associated with many adverse health outcomes. A possible factor that may influence adiposity development is food insecurity. Although several epidemiological studies have been conducted examining the association between food insecurity and adiposity among children and adults, results have been inconsistent. Objective: This cross-sectional study investigates the relationship between food insecurity and adiposity among children and adults using recent data from a representative sample of the US population. Methods: We examined 3,391 adults and 2,837 children from the National Health and Nutrition Examination Survey (NHANES) 2015-2016. Household food insecurity was assessed using …

Epigenome-Wide Association Study Of Kidney Function Identifies Trans-Ethnic And Ethnic-Specific Loci, Charles E. Breeze, Anna Batorsky, Mi Kyeong Lee, Mindy D. Szeto, Xiaoguang Xu, Daniel L. Mccartney, Rong Jiang, Amit Patki, Holly J. Kramer, James M. Eales, Laura Raffield, Leslie Lange, Ethan Lange, Peter Durda, Yongmei Liu, Russ P. Tracy, David Van Den Berg, Nhlbi Trans-Omics For Precision Medicine (Topmed) Consortium, Topmed Mesa Multi-Omics Working Group, Kathryn L. Evans, William E. Kraus, Donna K. Arnett

Epidemiology and Environmental Health Faculty Publications

BACKGROUND: DNA methylation (DNAm) is associated with gene regulation and estimated glomerular filtration rate (eGFR), a measure of kidney function. Decreased eGFR is more common among US Hispanics and African Americans. The causes for this are poorly understood. We aimed to identify trans-ethnic and ethnic-specific differentially methylated positions (DMPs) associated with eGFR using an agnostic, genome-wide approach.

METHODS: The study included up to 5428 participants from multi-ethnic studies for discovery and 8109 participants for replication. We tested the associations between whole blood DNAm and eGFR using beta values from Illumina 450K or EPIC arrays. Ethnicity-stratified analyses were performed using linear …

Maternal Methylmercury Exposure Through Rice Ingestion And Child Neurodevelopment In The First Three Years: A Prospective Cohort Study In Rural China, Sarah E. Rothenberg, Susan A. Korrick, Jihong Liu, Yanfen Nong, Chuan Hong, Eva P. Trinh, Xu Jiang, Fred J. Biasini, Fengxiu Ouyang

Faculty Publications

Background

Rice is an important dietary source for methylmercury; however, rice does not contain the same beneficial nutrients as fish. Our main objective was to assess associations of prenatal methylmercury exposure through rice ingestion with child neurodevelopment in rural China.

Methods

Eligible peripartum women were enrolled (n = 391), provided peripartum hair samples, and children’s neurodevelopment was assessed at 12 months (n = 264, 68%) and 36 months (n = 190, 48%) using the Bayley Scales of Infant Development, 2nd Edition, including the Mental Developmental Index (MDI) and the Psychomotor Developmental Index (PDI). Associations between prenatal methylmercury …

Associations Between Family-Based Stress And Dietary Inflammatory Potential Among Families With Preschool-Aged Children, Valerie Hruska, Nitin Shivappa Mbbs, Mph, Ph.D., James R. Hébert Scd, Alison M. Duncan, Jess Hines, David W. L. Ma

Faculty Publications

Chronic stress is known to influence dietary choices, and stressed families often report poorer diet quality; however, little is known about how family-based stress is linked with dietary patterns that promote inflammation. This study investigated associations between family-based stress and the inflammatory potential of the diet among preschool-aged children and their parents. Parents (n = 212 mothers, n = 146 fathers) and children (n = 130 girls, n = 123 boys; aged 18 months to 5 years) from 241 families participating in the Guelph Family Health Study were included in the analyses. Parents reported levels of parenting distress, depressive symptoms, …

An Ensemble Of The Icluster Method To Analyze Longitudinal Lncrna Expression Data For Psoriasis Patients, Suyan Tian, Chi Wang

Internal Medicine Faculty Publications

BACKGROUND: Psoriasis is an immune-mediated, inflammatory disorder of the skin with chronic inflammation and hyper-proliferation of the epidermis. Since psoriasis has genetic components and the diseased tissue of psoriasis is very easily accessible, it is natural to use high-throughput technologies to characterize psoriasis and thus seek targeted therapies. Transcriptional profiles change correspondingly after an intervention. Unlike cross-sectional gene expression data, longitudinal gene expression data can capture the dynamic changes and thus facilitate causal inference.

METHODS: Using the iCluster method as a building block, an ensemble method was proposed and applied to a longitudinal gene expression dataset for psoriasis, with the …