Biostatistics Commons^™

Sample Size Calculations And Normalization Methods For Rna-Seq Data., Xiaohong Li

Electronic Theses and Dissertations

High-throughput RNA sequencing (RNA-seq) has become the preferred choice for transcriptomics and gene expression studies. With the rapid growth of RNA-seq applications, sample size calculation methods for RNA-seq experiment design and data normalization methods for DEG analysis are important issues to be explored and discussed. The underlying theme of this dissertation is to develop novel sample size calculation methods in RNA-seq experiment design using test statistics. I have also proposed two novel normalization methods for analysis of RNA-seq data. In chapter one, I present the test statistical methods including Wald’s test, log-transformed Wald’s test and likelihood ratio test statistics for …

The Role Of Pre-Existing Type 2 Diabetes Mellitus In Colorectal Cancer Stage And Survival In Elderly Americans: A Seer-Medicare Population-Based Study 2002-~2011, Sanae El Ibrahimi

UNLV Theses, Dissertations, Professional Papers, and Capstones

Diabetes is a common comorbid condition among colorectal cancer (CRC) patients, yet its effects in CRC outcomes, particularly stage at diagnosis, risk of death and variations by diabetes severity (complications vs no complications) and Hispanic ethnicity have not been adequately studied. The purpose of this study was to investigate the association between pre-existing T2DM and advanced stage at diagnosis in elderly patients with CRC; to examine whether diabetes is an independent predictor of poor survival from all-cause and CRC-specific mortality; to assess whether variations exist by diabetes severity and to analyze the outcomes for the Hispanic group.

The Surveillance Epidemiology …

The Impact Of Economic Recession On The Health Of Adult Nevadans, Ariana Goertz

UNLV Theses, Dissertations, Professional Papers, and Capstones

Recessions are generally considered to cause negative consequences, but recent studies have provided evidence that some health outcomes improve as the economy deteriorates. The relationship between economic downfalls and health is not straightforward; it is important to look at how health has been impacted in one of the areas hit hardest by the recession. Las Vegas, Nevada was previously considered recession-proof, seemingly unaffected by previous economic downturns exhibited by the rest of the country. However, during the Great Recession of 2007-2009, Las Vegas led the country in highest rates of unemployment and foreclosures. This was quite a collapse for a …

Increasing Use Of Research Findings In Improving Evidence-Based Health Policy At The National Level, Meiwita Budiharsana

Kesmas

In February 2016, the Minister of Health decided to increase the use of research findings in improving the quality of the national health policy and planning. The Ministry of Health has instructed the National Institute of Health Research and Development or NIHRD to play a stronger role of monitoring and evaluating all health programs, because “their opinion and research findings should be the basis for changes in national health policies and planning”. Compared to the past, the Ministry of Health has increased the research budget for evidence-based research tremendously. However, there is a gap between the information needs of program …

The Change In Mental Health Status Of Indonesian Health Care Migrant Worker In Japan, Susiana Nugraha, Yuko Hirano, Honda Sumihisha

Kesmas

Under the Japan – Indonesia Economic Partnership Agreement, more than 1,000 of Indonesian health care workers have migrated to Japan. Social adjustment during the process of migration is linked to mental health changes. This study aimed to figure out the strongest predictor that influences the change in mental health status as a result of migration. Baseline data were collected in Jakarta in 2013 during pre-departure orientation. Follow-up study was conducted one year after the study participants migrated to Japan in 2014. Using longitudinal design, this study employed 92 participants consisting of nurse and certified care worker candidates. The multiple linear …

Husband’S Education Level And Alcohol Drinking Habit As Risk Factors Of Hiv Infection Among Housewives In Pati District, Nurul Aeni, Annemarie Westendorp

Kesmas

Cases of Human Immunodeficiency Virus (HIV) infection in Pati District increase, particularly among housewives. The aim of this study was to analyse the risk factors of HIV infection among housewives in Pati District using case-control study design. The respondents were 90 housewives divided into case and control group. The case group consisted of 30 housewives living with HIV, while the control group comprised 60 housewives living in the similar area of the counterparts. The data collection was focused on demographic, sexual behaviour, and sociocultural variables possessed by housewives and their husbands. The study resulted that the risk factors of HIV …

Implementation Of Cigarette Excise Policy Against Cigarette Consumption Reduction Among Adolescent In Kuningan, Indonesia, Jani Ramjani, Fitri Kurnia Rahim, Icca Stella Amalia, Wahyu Manggala Putra

Kesmas

Indonesia has the highest prevalence of smoking (50.68%) compared to other ASEAN countries. On January 1st, 2017, the Indonesian government raised cigarette excise taxes. The purpose of this study was to analysis the impact of cigarette excise increase on cigarette consumption among adolescents aged 17 to 25 years. The study design used cross-sectional survey. A total of 153 adolescents were recruited in this study through simple random sampling technique. Questionnaires and observation papers were used in this study. A face-to-face interview was conducted to fulfill the data collection through home visit for each respondent. The data were obtained during May …

Spatial Analysis Of Determinants Of Filariasis-Endemic Areas In West Sumatra, Masrizal Masrizal, Fivi Melva Diana, Rosfita Rasyid

Kesmas

West Pasaman District and Agam District are filariasis-endemic areas in West Sumatra with prevalence of 12.40 per 100,000 cases and 11.27 per 100,000 cases respectively. This study aimed to determine risk factors associated with the prevalence of filariasis and mapping the vulnerability of the area in West Sumatra. A case control study design was conducted in the West Pasaman District and Agam District. The study used a sample of 74 cases and 74 controls taken by simple random sampling for the case and purposive random sampling for control. Data analysis used univariate, bivariate, multivariate and spatial. The results in Agam …

Effect Of Health Education On Community Participation To Eradicate Aedes Aegypti-Breeding Sites In Buahbatu And Cinambo Districts, Bandung, Zahratul Elsa, Uun Sumardi, Lia Faridah

Kesmas

Dengue hemorrhagic fever (DHF) is still a major public health problem in many regions in Indonesia including Bandung City. Community participation in implementing Eradication of Mosquito-Breeding Sites is still needed as it is considered the most effective method in controlling the dengue fever. This study aimed to determine the influence of health education towards community participation to eradicate mosquito-breeding sites, which was measured by knowledge level and larva index conducted in Bandung, specifically in two different locations with the highest and the lowest incidence rates of DHF. This study used quasi-experimental method. Samples were 100 people living in Cijawura and …

Maternal Energy Intake At The Sixth Month As Dominant Factor Of Exclusive Breastfeeding Success, Devi Suryanti Sihite, Sandra Fikawati, Ahmad Syafiq

Kesmas

Breastfeeding mothers needed adequate energy intake to provide 6-month exclusive breastfeeding that is necessary for infant growth and development. This study aimed to investigate real intake at the first and sixth month of breastfeeding and determine the dominant factor affecting 6-month exclusive breastfeeding provision. The design of this study was cross-sectional conducted in March-April 2015 among 109 mothers with 6-12- month-old infant living and registered at integrated health care in Kalangan Primary Health Care area. Data were collected through interview using questionnaires. Breastfeeding mothers’ intake was asked using Semi-Quantitative Food Frequency Questionnaire. The study found that 6-month exclusive breastfeeding proportion …

Equity Level Of Health Insurance Ownership In Indonesia, Risky Kusuma Hartono

Kesmas

Social health insurance from government program are expected to be able to reduce inequalities access to health services in the middle of rising of health care cost, while private health insurance is still limited for up and middle class population. This study aimed to analyze the equity level of health insurance ownership including social and private health insurance in Indonesia. This study examined the condition of Indonesia in the middle of entering National Health Insurance (NHI) era. This study used data of Indonesian Socio-Economic Survey 2012. Data were analyzed by using econometric approach through multinomial logit analysis. The results showed …

Clinical Evaluation Of The Cepheid Xpert® Tv Assay For Detection Of Trichomonas Vaginalis With Prospectively Collected Female And Male Specimens., Jane R Schwebke, C A Gaydos, T Davis, J Marrazzo, D Furgerson, S N Taylor, B Smith, L H Bachmann, R Ackerman, T Spurrell, D Ferris, C A Burnham, H Reno, J Lebed, D Eisenberg, P Kerndt, S Philip, J Jordan, N Quigley

Epidemiology Faculty Publications

Trichomoniasis is the most prevalent curable sexually transmitted disease (STD). It has been associated with preterm birth and acquisition/transmission of HIV. Recently, nucleic acid amplification tests (NAAT) have been FDA-cleared in the United States for detection of Trichomonas vaginalis (TV) in specimens from both women and men. This current study reports the results of a multicenter study recently conducted using the Xpert TV Assay to test specimens from both men and women. On-demand results were available in as little as 40 minutes for positive specimens. A total of 1867 women and 4791 men were eligible for inclusion in the analysis. …

Bayesian Inference On Quantile Regression-Based Mixed-Effects Joint Models For Longitudinal-Survival Data From Aids Studies, Hanze Zhang

USF Tampa Graduate Theses and Dissertations

In HIV/AIDS studies, viral load (the number of copies of HIV-1 RNA) and CD4 cell counts are important biomarkers of the severity of viral infection, disease progression, and treatment evaluation. Recently, joint models, which have the capability on the bias reduction and estimates' efficiency improvement, have been developed to assess the longitudinal process, survival process, and the relationship between them simultaneously. However, the majority of the joint models are based on mean regression, which concentrates only on the mean effect of outcome variable conditional on certain covariates. In fact, in HIV/AIDS research, the mean effect may not always be of …

Enrichment Of Putatively Damaging Rare Variants In The Dyx2 Locus And The Reading-Related Genes Ccdc136 And Flnc, Andrew K. Adams, Shelley D. Smith, Dongnhu T. Truong, Erik G. Willcutt, Richard K. Olson, John C. Defries, Bruce F. Pennington, Jeffrey R. Gruen

Psychology: Faculty Scholarship

Eleven loci with prior evidence for association with reading and language phenotypes were sequenced in 96 unrelated subjects with significant impairment in reading performance drawn from the Colorado Learning Disability Research Center collection. Out of 148 total individual missense variants identified, the chromosome 7 genes CCDC136 and FLNC contained 19. In addition, a region corresponding to the well-known DYX2 locus for RD contained 74 missense variants. Both allele sets were filtered for a minor allele frequency ≤0.01 and high Polyphen-2 scores. To determine if observations of these alleles are occurring more frequently in our cases than expected by chance in …

Using Multilevel Outcomes To Construct And Select Biomarker Combinations For Single-Level Prediction, Allison Meisner, Chirag R. Parikh, Kathleen F. Kerr

UW Biostatistics Working Paper Series

Biomarker studies may involve a multilevel outcome, such as no, mild, or severe disease. There is often interest in predicting one particular level of the outcome due to its clinical significance. The standard approach to constructing biomarker combinations in this context involves dichotomizing the outcome and using a binary logistic regression model. We assessed whether information can be usefully gained from instead using more sophisticated regression methods. Furthermore, it is often necessary to select among several candidate biomarker combinations. One strategy involves selecting a combination on the basis of its ability to predict the outcome level of interest. We propose …

Constructing A Confidence Interval For The Fraction Who Benefit From Treatment, Using Randomized Trial Data, Emily J. Huang, Ethan X. Fang, Daniel F. Hanley, Michael Rosenblum

Johns Hopkins University, Dept. of Biostatistics Working Papers

The fraction who benefit from treatment is the proportion of patients whose potential outcome under treatment is better than that under control. Inference on this parameter is challenging since it is only partially identifiable, even in our context of a randomized trial. We propose a new method for constructing a confidence interval for the fraction, when the outcome is ordinal or binary. Our confidence interval procedure is pointwise consistent. It does not require any assumptions about the joint distribution of the potential outcomes, although it has the flexibility to incorporate various user-defined assumptions. Unlike existing confidence interval methods for partially …

Persistent Organic Pollutants And Mortality In The United States, Nhanes 1999-2011., Kristiann Fry, Melinda C Power

Epidemiology Faculty Publications

Background

Persistent organic pollutants (POPs) are environmentally and biologically persistent chemicals that include polybrominated diphenyl ethers (PBDEs), per- and polyfluoroalkyl substances (PFASs), polychlorinated biphenyls (PCBs), and organochlorine (OC) pesticides. Currently, data on the associations between exposure to POPs and the risk of mortality in the U.S. population is limited.

Our objective was to determine if higher exposure to POPs is associated with greater risk of all-cause, cancer, heart/cerebrovascular disease, or other-cause mortality.

Methods

Analyses included participants aged 60 years and older from the 1999–2006 National Health and Nutrition Examination Surveys (NHANES). We included 483 participants for analyses of PBDEs, 1043 …

Systems Biology Approach To Late-Onset Alzheimer's Disease Genome-Wide Association Study Identifies Novel Candidate Genes Validated Using Brain Expression Data And Caenorhabditis Elegans Experiments, Shubhabrata Mukherjee, Joshua C. Russell, Daniel T. Carr, Jeremy D. Burgess, Mariet Allen, Daniel J. Serie, Kevin L. Boehme, John S. K. Kauwe, Adam C. Naj, David W. Fardo, Dennis W. Dickson, Thomas J. Montine, Nilufer Ertekin-Taner, Matt R. Kaeberlein, Paul K. Crane

Biostatistics Faculty Publications

Introduction—We sought to determine whether a systems biology approach may identify novel late-onset Alzheimer's disease (LOAD) loci.

Methods—We performed gene-wide association analyses and integrated results with human protein-protein interaction data using network analyses. We performed functional validation on novel genes using a transgenic Caenorhabditis elegans Aβ proteotoxicity model and evaluated novel genes using brain expression data from people with LOAD and other neurodegenerative conditions.

Results—We identified 13 novel candidate LOAD genes outside chromosome 19. Of those, RNA interference knockdowns of the C. elegans orthologs of UBC, NDUFS3, EGR1, and ATP5H were associated with Aβ …

Increased Birth Weight Is Associated With Altered Gene Expression In Neonatal Foreskin, Leryn J. Reynolds, Rebecca I. Pollack, Richard J. Charnigo, Cetewayo S. Rashid, Arnold J. Stromberg, Shu Shen, John O'Brien, Kevin J. Pearson

Pharmacology and Nutritional Sciences Faculty Publications

Elevated birth weight is linked to glucose intolerance and obesity health-related complications later in life. No studies have examined if infant birth weight is associated with gene expression markers of obesity and inflammation in a tissue that comes directly from the infant following birth. We evaluated the association between birth weight and gene expression on fetal programming of obesity. Foreskin samples were collected following circumcision, and gene expression analyzed comparing the 15% greatest birth weight infants (n = 7) v. the remainder of the cohort (n = 40). Multivariate linear regression models were fit to relate expression levels on differentially …

Comparison Of Adaptive Randomized Trial Designs For Time-To-Event Outcomes That Expand Versus Restrict Enrollment Criteria, To Test Non-Inferiority, Josh Betz, Jon Arni Steingrimsson, Tianchen Qian, Michael Rosenblum

Johns Hopkins University, Dept. of Biostatistics Working Papers

Adaptive enrichment designs involve preplanned rules for modifying patient enrollment criteria based on data accrued in an ongoing trial. These designs may be useful when it is suspected that a subpopulation, e.g., defined by a biomarker or risk score measured at baseline, may benefit more from treatment than the complementary subpopulation. We compare two types of such designs, for the case of two subpopulations that partition the overall population. The first type starts by enrolling the subpopulation where it is suspected the new treatment is most likely to work, and then may expand inclusion criteria if there is early evidence …