Biostatistics Commons^™

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, …

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 …

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 …

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, …

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 …

Exclusive Breastfeeding And Decrease Of Upper Respiratory Infection Incidence Among Infants Aged 6-12 Months In Kampar District, Riau Province, Musfardi Rustam, Renti Mahkota, Nasrin Kodim

Kesmas

Upper Respiratory Infection (URI) is a major cause of morbidity and mortality of infants and toddlers in developing countries. The high infant morbidity and mortality rates in Indonesia are associated with the low exclusive breastfeeding ability. Breast milk is a natural drink for newborns in the first month of life that is beneficial not only for the babies, but also for mothers. The aim of study was to determine exclusive breastfeeding and decrease in incidence of URI among infants aged 6-12 months. This study was conducted by using case control design. Samples were taken by using cluster random sampling. Subject …

The Consumption Of Fresh Vegetables From Street Food And Sanitation Of Street Stalls At Four Locations In Bogor City, Donna Fujie Rahaditha Utami, Winiati P. Rahayu, Lilis Nuraida

Kesmas

The consumption of fresh vegetables at the stalls needs serious attention. This research aimed to estimate the exposure probability due to fresh vegetables consumption of street food consumers, to measure sanitation level of street stalls that serving fresh vegetables, and to recommend a mentoring program for the stalls at four locations in Bogor City. This research was conducted at 16 stalls located at four locations in Bogor City. The number of respondents surveyed was 293 people and determined by stratified sampling method. Food frequency questionnaire was used as a tool in the survey. The survey showed that men consumed more …

Relationship Model For Occupational Safety And Health Climate To Prevent Needlestick Injuries For Nurses, Ketut Ima Ismara, Adi Heru Husodo, Yayi Suryo Prabandari, Widodo Hariyono

Kesmas

The risk of accidents and disease transmission when working at hospitals is quite high, especially in Indonesia. This study aimed to analyze the relationship model between the Occupational Safety and Health (OSH) climate and behavior intention in OSH performance to prevent needlestick injuries (NSI) based on a theory of planned behavior. A mixed approach using qualitative and quantitative methods was applied. Data were obtained from Structural Equation Model questionnaires, observation, and documentation, and interviews were analyzed qualitatively. The population was 1,042 nurses at Dr. Sardjito General Hospital in Yogyakarta. The sample consisted of 289 respondents determined by purposive random sampling …

Effect Of Condom Utilization On Sexuall Transmitted Infection Among Female Sex Workers, In Tulungagung District, East Java, Indonesia, Ainun Hanifah, Ari Natalia Probandari, Eti Poncorini Pamungkasari

Kesmas

One effective strategy for preventing sexually transmitted infection (STI) incidence and providing protection for female sex workers (FSWs) from their sexual partners is correct and consistent condom use behavior. This study examined the effect of condom use on STI among FSWs in Tulungagung District, East Java. This analytic and observational study using a cohort prospective design was conducted at Ngujang ex- prostitution area and Gunung Bolo prostitution area, Tulungagung District, from November to January 2017. The total sample selected was 90 FSWs. Data was collected through a set of questionnaires and tracking condom use in a diary. Data were analyzed …

Perception Of People Living With Hiv/Aids On Social Stigma Of Hiv/Aids In Sukoharjo District, Titik Haryanti, Wartini Wartini

Kesmas

The stigma of wrong society about HIV / AIDS is one of the obstacles to prevention and control of HIV / AIDS in Sukoharjo District. This study aims to determine the relationship of characteristics, causal factors and duration of HIV / AIDS with the perception of people living with HIV to the stigma of society about HIV / AIDS in Sukoharjo District. The research used is analytical descriptive with cross sectional approach. The population is all people with HIV / AIDS until April 2016 amounted to 256 with a sample of 156 people with sampling technique quota sampling. Bivariate analysis …

Prediction Models For Descreasing Visual Acuity In Wig Makers, Nur Ulfah, Siti Harwanti, Ngadiman Ngadiman

Kesmas

One of the occupational diseases that can arise for workers with high accuracy is a decrease in their visual acuity. Therefore, it is necessary to study the risk factors of decreasing visual acuity in workers with high accuracy, such as in wig makers. This study aimed to examine the correlation between age, working period, lighting intensity, fatigue, and nutritional status with visual acuity, and to observe the main risk factors that can be used as a reference for predicting decreasing visual acuity. This study was an observational study that used a cross-sectional design. The population number for this study was …

Evaluating Trajectories Of Episodic Memory In Normal Cognition And Mild Cognitive Impairment: Results From Adni, Xiuhua Ding, Richard J. Charnigo, Frederick A. Schmitt, Richard J. Kryscio, Erin L. Abner, Alzheimer’S Disease Neuroimaging Initiative

Statistics Faculty Publications

BACKGROUND: Memory assessment is a key factor for the diagnosis of cognitive impairment. However, memory performance over time may be quite heterogeneous within diagnostic groups.

METHOD: To identify latent trajectories in memory performance and their associated risk factors, we analyzed data from Alzheimer's Disease Neuroimaging Initiative (ADNI) participants who were classified either as cognitively normal or as Mild Cognitive Impairment (MCI) at baseline and were administered the Rey Auditory Verbal Learning test (RAVLT) for up to 9 years. Group-based trajectory modeling on the 30-minute RAVLT delayed recall score was applied separately to the two baseline diagnostic groups.

RESULTS: There were …

Impact Of The Affordable Care Act On Colorectal Cancer Screening, Incidence, And Survival In Kentucky, Tong Gan, Heather F. Sinner, Samuel C. Walling, Quan Chen, Bin Huang, Thomas C. Tucker, Jitesh A. Patel, B. Mark Evers, Avinash S. Bhakta

Surgery Faculty Publications

Background

Kentucky ranks first in the US in cancer incidence and mortality. Compounded by high poverty levels and a high rate of medically uninsured, cancer rates are even worse in Appalachian Kentucky. Being one of the first states to adopt the Affordable Care Act (ACA) Medicaid expansion, insurance coverage markedly increased for Kentucky residents. The purpose of our study was to determine the impact of Medicaid expansion on colorectal cancer (CRC) screening, diagnosis, and survival in Kentucky.

Study Design

The Kentucky Cabinet for Health and Family Services and the Kentucky Cancer Registry were queried for individuals (≥20 years) undergoing CRC …

Opioids And Cerebral Physiology In The Acute Management Of Traumatic Brain Injury: A Systematic Review, Joshua Weiner, Amanda Mcintyre, Shannon Janzen, Magdalena Mirkowski, Heather M. Mackenzie, Robert Teasell

Epidemiology and Biostatistics Publications

Background: Following traumatic brain injury (TBI), optimization of cerebral physiology is recommended to promote more favourable patient outcomes. Accompanying pain and agitation are commonly treated with sedative and analgesic agents, such as opioids. However, the impact of opioids on certain aspects of cerebral physiology is not well established.

Objective: To conduct a systematic review of the evidence on the effect of opioids on cerebral physiology in TBI during acute care.

Methods: A comprehensive literature search was conducted in five electronic databases for articles published in English up to November 2017. Studies were included if: (1) the study sample was human …

Gene Co-Expression Networks Analysis Reveal Novel Molecular Endotypes In Alpha-1 Antitrypsin Deficiency, Jen-Hwa Chu, Wenlan Zang

Yale Day of Data

Rationale:Alpha-1 antitrypsin deficiency (AATD) is a genetic condition that predisposes to early onset pulmonary emphysema and airways obstruction. The exact mechanism through which AATD leads to lung disease is incompletely understood.

Objectives: To investigate the effect of AAT genotype and augmentation therapy on bronchoalveolar lavage (BAL) and peripheral blood mononuclear cells (PBMC) transcriptome, while examining the link between gene expression profiles, and clinical features of AATD.

Methods: We performed RNA-Seq on RNA extracted from BAL and PBMC on samples obtained from 89 AATD patients enrolled in the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study. Differential …

A Novel Pathway-Based Distance Score Enhances Assessment Of Disease Heterogeneity In Gene Expression, Yunqing Liu, Xiting Yan

Yale Day of Data

Distance-based unsupervised clustering of gene expression data is commonly used to identify heterogeneity in biologic samples. However, high noise levels in gene expression data and the relatively high correlation between genes are often encountered, so traditional distances such as Euclidean distance may not be effective at discriminating the biological differences between samples. In this study, we developed a novel computational method to assess the biological differences based on pathways by assuming that ontologically defined biological pathways in biologically similar samples have similar behavior. Application of this distance score results in more accurate, robust, and biologically meaningful clustering results in both …

Variance Estimation In Inverse Probability Weighted Cox Models, Di Shu, Jessica G. Young, Sengwee Toh, Rui Wang

Harvard University Biostatistics Working Paper Series

Inverse probability weighted Cox models can be used to estimate marginal hazard ratios under different treatments interventions in observational studies. To obtain variance estimates, the robust sandwich variance estimator is often recommended to account for the induced correlation among weighted observations. However, this estimator does not incorporate the uncertainty in estimating the weights and tends to overestimate the variance, leading to inefficient inference. Here we propose a new variance estimator that combines the estimation procedures for the hazard ratio and weights using stacked estimating equations, with additional adjustments for the sum of non-independent and identically distributed terms in a Cox …

General Approach Of Causal Mediation Analysis With Causally Ordered Multiple Mediators And Survival Outcome, An-Shun Tai, Pei-Hsuan Lin, Yen-Tsung Huang, Sheng-Hsuan Lin

Harvard University Biostatistics Working Paper Series

Causal mediation analysis with multiple mediators (causal multi-mediation analysis) is critical in understanding why an intervention works, especially in medical research. Deriving the path-specific effects (PSEs) of exposure on the outcome through a certain set of mediators can detail the causal mechanism of interest. However, the existing models of causal multi-mediation analysis are usually restricted to partial decomposition, which can only evaluate the cumulative effect of several paths. Moreover, the general form of PSEs for an arbitrary number of mediators has not been proposed. In this study, we provide a generalized definition of PSE for partial decomposition (partPSE) and for …

Comparison Of Long-Term Survival Of Patients With Early-Stage Non–Small Cell Lung Cancer After Surgery Vs Stereotactic Body Radiotherapy, Alexander Chi, Wei Fang, Yeping Sun, Sinjin Wen

Faculty & Staff Scholarship

IMPORTANCE Previous comparisons of surgery and stereotactic body radiotherapy (SBRT) for early-stage (ES) non–small cell lung cancer (NSCLC) did not account for the extent of regional lymph node examination (LNE) during surgery. OBJECTIVE To compare long-term overall survival (OS) of patients with ES NSCLC after surgery vs SBRT when the extent of regional LNE in patients undergoing surgery is thoroughly considered. DESIGN, SETTING, AND PARTICIPANTS Cohort study with survival comparisons using the multivariable Cox proportional hazards model and after propensity score matching. Data from the National Cancer Database were analyzed from October 28, 2018, through April 18, 2019. Patients with …

Controlling For Confounding Via Propensity Score Methods Can Result In Biased Estimation Of The Conditional Auc: A Simulation Study, Hadiza I. Galadima, Donna K. Mcclish

Community & Environmental Health Faculty Publications

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 random in observational studies, comparisons of outcomes between exposed and nonexposed 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 conditional odds ratio and hazard ratio. However, research is lacking on the performance of propensity score methods for covariate adjustment when estimating the …

An Information Theory-Based Approach To Assessing Spatial Patterns In Complex Systems, Tarsha Eason, Wen Ching-Chuang, Shana Sundstrom, Heriberto Cabezas

School of Natural Resources: Faculty Publications

Given the intensity and frequency of environmental change, the linked and cross-scale nature of social-ecological systems, and the proliferation of big data, methods that can help synthesize complex system behavior over a geographical area are of great value. Fisher information evaluates order in data and has been established as a robust and effective tool for capturing changes in system dynamics, including the detection of regimes and regime shifts. The methods developed to compute Fisher information can accommodate multivariate data of various types and requires no a priori decisions about system drivers, making it a unique and powerful tool. However, the …

Saturated Fat Intake Is Associated With Lung Function In Individuals With Airflow Obstruction: Results From Nhanes 2007⁻2012, Kasey Cornell, Morshed Alam, Elizabeth Lyden, Lisa Wood, Tricia D. Levan, Tara M. Nordgren, Kristina L. Bailey, Corrine K. Hanson

Journal Articles: Biostatistics

Nutritional status is a well-recognized prognostic indicator in chronic obstructive pulmonary disease (COPD); however, very little is known about the relationship between lung function and saturated fat intake. We used data from the cross-sectional National Health and Nutrition Examination Surveys (NHANES) to assess the relationship between saturated fatty acid (SFA) intake and lung function in the general US adult population. Adults in NHANES (2007⁻2012) with pre-bronchodilator spirometry measurements and dietary SFA intake were included. Primary outcomes were lung function including forced expiratory volume in one second (FEV₁)

Stretching Hiv Treatment: A Replication Study Of Task Shifting In South Africa, Baojiang Chen, Morshed Alam

Journal Articles: Biostatistics

The Streamlining Tasks & Roles to Expand Treatment and Care for HIV (STRETCH) program was developed to increase the reach of antiretroviral therapy (ART) for HIV/AIDS patients in Sub-Saharan Africa by training nurses to prescribe, initiate, and maintain ART. Fairall and colleagues conducted a cluster-randomized trial to determine the effects/impact of STRETCH on patient health outcomes in South Africa between 2008 and 2010. The purpose of our replication study is to evaluate Fairall and colleagues' findings. We conducted push button and pure replication studies and measurement and estimation analyses (MEA). Our MEA validates the original findings: (1) overall, time to …