Biostatistics Commons^™

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 …

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 …

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 …

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 …

Early Sex Work Initiation And Condom Use Among Alcohol-Using Female Sex Workers In Mombasa, Kenya: A Cross-Sectional Analysis, A. M. Parcesepe, Kelly L'Engle, S. L. Martin, S. Green, C. Suchindran, P. Mwarogo

Nursing and Health Professions Faculty Research and Publications

Objectives Early initiation of sex work is prevalent among female sex workers (FSWs) worldwide. The objectives of this study were to investigate if early initiation of sex work was associated with: (1) consistent condom use, (2) condom negotiation self-efficacy or (3) condom use norms among alcohol-using FSWs in Mombasa, Kenya.

Methods In-person interviews were conducted with 816 FSWs in Mombasa, Kenya. Sample participants were: recruited from HIV prevention drop-in centres, 18 years or older and moderate risk drinkers. Early initiation was defined as first engaging in sex work at 17 years or younger. Logistic regression modelled outcomes as a function …

Missing Data In Clinical Trial: A Critical Look At The Proportionality Of Mnar And Mar Assumptions For Multiple Imputation, Theophile B. Dipita

College of Graduate Studies: Theses & Dissertations

Randomized control trial is a gold standard of research studies. Randomization helps reduce bias and infer causality. One constraint of these studies is that it depends on participants to obtain the desired data. Whatever the researcher can do, there is a possibility to end up with incomplete data. The problem is more relevant in clinical trials when missing data can be related to the condition under study. The benefits of randomization is compromised by missing data. Multiple imputation is a valid method of treating missing data under the assumption of MAR. Unfortunately this is an unverified assumptions. Current practice advise …

Sample Size Estimation For Genomics Experiments With Dependent End Points, Desmond Koomson

Open Access Theses & Dissertations

In typical genomics studies involving numerous association tests of gene mutations with a disease, error rate control via multiplicity adjustment is paramount because even if all genes were to be non-differentially associated, we would still make some false positives. Many methods exist that incorporate the control of multiplicity for normally distributed endpoints in sample size estimation, but none addresses the issue for non-normally correlated endpoints.

One common practice in the literature is to assume an equal correlation among all differentially associated or expressed genes, thereby using the generalized binomial or beta-binomial model to compute the comparison-wise power of detecting these …

Semi-Parametrics Dose Finding Methods, Matthieu Clertant, John O'Quigley

COBRA Preprint Series

We describe a new class of dose finding methods to be used in early phase clinical trials. Under some added parametric conditions the class reduces to the family of continual reassessment method (CRM) designs. Under some relaxation of the underlying structure the method is equivalent to the CCD, mTPI or BOIN classes of designs. These latter designs are non-parametric in nature whereas the CRM class can be viewed as being strongly parametric. The proposed class is characterized as being semi-parametric since it corresponds to CRM with a nuisance parameter. Performance is good, matching that of the CRM class and improving …

The Association Between Osteoporosis And Early Menopause Following Hysterectomy, Mia Meeyaong-Won Botkin

Walden Dissertations and Doctoral Studies

Osteoporosis is considered to be the most adverse public health disease associated with substantial mortality among postmenopausal women. Hysterectomy, surgically induced menopause, contributes to the early onset of menopause. However, there was no evidence of an association between early menopause following hysterectomy and osteoporosis among postmenopausal women. The purpose of this quantitative study was to examine the association between demographic and behavioral factors and the prevalence of osteoporosis among hysterectomized postmenopausal women. The integrated theory of health behavior change theoretical framework guided study. Cross-sectional secondary data from the 2009-2010 National Health and Nutrition Examination Survey were used. Multiple logistic regression …

Statistical Handling Of Medical Data - An Ethical Perspective, Ajay Kumar Bansal Dr

COBRA Preprint Series

Medical Science is a delicate subject and the clinical data generated from the medical trials must be reliable and of good quality. Not only the quality of generated data is important, but the management is also crucial and is to be handled very carefully. In this paper, the ethical aspect of statistical handling of such data is discussed.

Every profession has some set of norms to follow to achieve its objectives. These norms are called professional ethics which shows the essence of human behaviour. Same way, the field of medical research is expected to follow ethical norms, to obtain reliable …

Semi-Parametric Estimation And Inference For The Mean Outcome Of The Single Time-Point Intervention In A Causally Connected Population, Oleg Sofrygin, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

We study the framework for semi-parametric estimation and statistical inference for the sample average treatment-specific mean effects in observational settings where data are collected on a single network of connected units (e.g., in the presence of interference or spillover). Despite recent advances, many of the current statistical methods rely on estimation techniques that assume a particular parametric model for the outcome, even though some of the most important statistical assumptions required by these models are most likely violated in the observational network settings, often resulting in invalid and anti-conservative statistical inference. In this manuscript, we rely on the recent methodological …

Statistical Estimation Of White Matter Microstructure From Conventional Mri, Leah Suttner, Amanda Mejia, Blake Dewey, Pascal Sati, Daniel S. Reich, Russell T. Shinohara

UPenn Biostatistics Working Papers

Diffusion tensor imaging (DTI) has become the predominant modality for studying white matter integrity in multiple sclerosis (MS) and other neurological disorders. Unfortunately, the use of DTI-based biomarkers in large multi-center studies is hindered by systematic biases that confound the study of disease-related changes. Furthermore, the site-to-site variability in multi-center studies is significantly higher for DTI than that for conventional MRI-based markers. In our study, we apply the Quantitative MR Estimation Employing Normalization (QuEEN) model to estimate the four DTI measures: MD, FA, RD, and AD. QuEEN uses a voxel-wise generalized additive regression model to relate the normalized intensities of …

Correction Of Verication Bias Using Log-Linear Models For A Single Binaryscale Diagnostic Tests, Haresh Rochani, Hani M. Samawi, Robert L. Vogel, Jingjing Yin

Biostatistics: Faculty Publications

In diagnostic medicine, the test that determines the true disease status without an error is referred to as the gold standard. Even when a gold standard exists, it is extremely difficult to verify each patient due to the issues of costeffectiveness and invasive nature of the procedures. In practice some of the patients with test results are not selected for verification of the disease status which results in verification bias for diagnostic tests. The ability of the diagnostic test to correctly identify the patients with and without the disease can be evaluated by measures such as sensitivity, specificity and predictive …

A Generally Efficient Targeted Minimum Loss Based Estimator, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

Suppose we observe n independent and identically distributed observations of a finite dimensional bounded random variable. This article is concerned with the construction of an efficient targeted minimum loss-based estimator (TMLE) of a pathwise differentiable target parameter based on a realistic statistical model.

The canonical gradient of the target parameter at a particular data distribution will depend on the data distribution through an infinite dimensional nuisance parameter which can be defined as the minimizer of the expectation of a loss function (e.g., log-likelihood loss). For many models and target parameters the nuisance parameter can be split up in two components, …

Estimated Probability Of Becoming Alcohol Dependent: Extending A Multiparametric Approach, Olga A. Vsevolozhskaya, James C. Anthony

Biostatistics Presentations

Background: United States (US) epidemiological studies suggest that for every 5-8 who start drinking alcoholic beverages, at least one drinker will develop an alcohol dependence (AD) syndrome within the first 10 years after onset of drinking (Lopez-Quintero et al., 2011; Wagner & Anthony, 2002). Recently, we described a multiparametric functional analysis approach for new research to estimate these transition probabilities with a one-dimensional function (1D; Vsevolozhskaya & Anthony, 2015). Here, we demonstrate extension of this analysis to two-dimensional (2D) functions that combine information about number of recent drinking days and number of drinks on the typical drinking day.

Methods: Data …

Inequality In Treatment Benefits: Can We Determine If A New Treatment Benefits The Many Or The Few?, Emily Huang, Ethan Fang, Daniel Hanley, Michael Rosenblum

Johns Hopkins University, Dept. of Biostatistics Working Papers

The primary analysis in many randomized controlled trials focuses on the average treatment effect and does not address whether treatment benefits are widespread or limited to a select few. This problem affects many disease areas, since it stems from how randomized trials, often the gold standard for evaluating treatments, are designed and analyzed. Our goal is to learn about the fraction who benefit from a treatment, based on randomized trial data. We consider the case where the outcome is ordinal, with binary outcomes as a special case. In general, the fraction who benefit is a non-identifiable parameter, and the best …

Factors Impacting Transgender Patients’ Discomfort With Their Family Physicians: A Respondent-Driven Sampling Survey, Greta R. Bauer, Xuchen Zong, Ayden I. Scheim, Rebecca Hammond, Amardeep Thind

Epidemiology and Biostatistics Publications

BACKGROUND: Representing approximately 0.5% of the population, transgender (trans) persons in Canada depend on family physicians for both general and transition-related care. However, physicians receive little to no training on this patient population, and trans patients are often profoundly uncomfortable and may avoid health care. This study examined factors associated with patient discomfort discussing trans health issues with a family physician in Ontario, Canada.

METHODS: 433 trans people age 16 and over were surveyed using respondent-driven sampling for the Trans PULSE Project; 356 had a family physician. Weighted logistic regression models were fit to produce prevalence risk ratios (PRRs) via …

Disability Prevention Programs For Older People: Factors Associated With Medical And Nursing Care Costs, Takaaki Ikeda, Susumu Yanagawa, Kenichi Murakami, Toshiyuki Inoue, Takamasa Tsurumi

Kesmas

Penelitian ini bertujuan untuk mengklarifikasi faktor-faktor yang terkait dengan biaya medis dan perawatan lanjut usia (lansia) yang tinggal di panti sosial serta menyarankan program pencegahan disabilitas yang efektif. Total partisipan dalam penelitian ini adalah 83 orang (29 laki-laki dan 54 perempuan; usia rata-rata 81,2 ± 6,3 tahun) pada 1 November – 28 Desember 2014. Penelitian ini membandingkan biaya medis dan perawatan rata-rata per bulan dengan rata-rata nasional bagi yang berusia ≥ 65 tahun. Uji regresi logistik dilakukan untuk memeriksa keterkaitannya dengan biaya medis dan perawatan. Mereka yang pergi ke luar rumah ≥ 3 kali seminggu tiga kali lebih kecil kemungkinannya …

Pesticide Exposure, Behavior Of Farmer, And Activity Of Cholinesterase Enzyme In Blood Of Fertile Women Farmers, Deni Abdul Rahman, Zakianis Zakianis, Laila Fitria

Kesmas

Petani perempuan usia subur berisiko mengalami penurunan aktivitas kolinesterase akibat pajanan pestisida. Penelitian ini bertujuan untuk menganalisis hubungan antara pajanan pestisida dan perilaku pemajan terhadap aktivitas kolinesterase petani perempuan usia subur di Desa Kedunguter. Penelitian ini menggunakan desain potong lintang pada 94 petani perempuan usia subur tahun 2015. Pengumpulan data dilakukan secara observasi, wawancara, dan uji kolinesterase. Analisis data menggunakan uji kai kuadrat dan hasil analisis menunjukkan hubungan signifikan antara jenis pestisida, waktu kerja, penggunaan sarung tangan, perilaku mencuci tangan terhadap aktivitas kolinesterase petani perempuan usia subur. Hasil analisis pada penelitian ini menunjukkan bahwa variabel waktu kerja memiliki nilai odds …

The Use Of Earthworms And Household Organic Waste Composting Length Of Time, Abdul Khair, Lucky Herawati, Noraida Noraida, Munawar Raharja

Kesmas

Pengomposan dengan cacing tanah merupakan proses pembuatan kompos dengan melibatkan organisme makro cacing tanah. Kerja sama antara cacing tanah dengan mikroorganisme dapat memberi dampak pada proses penguraian yang dilakukan oleh mikroorganisme tersebut dibantu dengan keberadaan cacing tanah. Oleh karena bahan-bahan yang akan diurai oleh mikroorganisme telah diurai lebih dahulu oleh cacing, maka kerja mikroorganisme lebih efektif dan lebih cepat. Penelitian ini bertujuan untuk mengetahui pengaruh penggunaan cacing tanah terhadap lama waktu pengomposan sampah organik dari rumah tangga dengan menggunakan desain penelitian eksperimen. Objek penelitian adalah seluruh sampah organik dari rumah tangga yang diambil secara acak pada satu rumah tangga. Variabel …