Adaptive Pre-Specification In Randomized Trials With And Without Pair-Matching,
2015
Division of Biostatistics, University of California, Berkeley - the SEARCH Consortium
Adaptive Pre-Specification In Randomized Trials With And Without Pair-Matching, Laura B. Balzer, Mark J. Van Der Laan, Maya L. Petersen
U.C. Berkeley Division of Biostatistics Working Paper Series
In randomized trials, adjustment for measured covariates during the analysis can reduce variance and increase power. To avoid misleading inference, the analysis plan must be pre-specified. However, it is unclear a priori which baseline covariates (if any) should be included in the analysis. Consider, for example, the Sustainable East Africa Research in Community Health (SEARCH) trial for HIV prevention and treatment. There are 16 matched pairs of communities and many potential adjustment variables, including region, HIV prevalence, male circumcision coverage and measures of community-level viral load. In this paper, we propose a rigorous procedure to data-adaptively select the adjustment set …
Double Robust Estimation Of Encouragement-Design Intervention Effects Transported Across Sites,
2015
Johns Hopkins Bloomberg School of Public Health
Double Robust Estimation Of Encouragement-Design Intervention Effects Transported Across Sites, Kara E. Rudolph, Mark J. Van Der Laan
U.C. Berkeley Division of Biostatistics Working Paper Series
We develop double robust targeted maximum likelihood estimators (TMLE) for transporting intervention effects from one population to another. Specifically, we develop TMLE estimators for three transported estimands: intent-to-treat average treatment effect (ATE) and complier ATE, which are relevant for encouragement-design interventions and instrumental variable analyses, and the ATE of the exposure on the outcome, which is applicable to any randomized or observational study. We demonstrate finite sample performance of these TMLE estimators using simulation, including in the presence of practical violations of the positivity assumption. We then apply these methods to the Moving to Opportunity trial, a multi-site, encouragement-design intervention …
Stochastic Optimization Via Forward Slice,
2015
University of Washington - Seattle Campus
Stochastic Optimization Via Forward Slice, Bob A. Salim, Lurdes Y. T. Inoue
UW Biostatistics Working Paper Series
Optimization consists of maximizing or minimizing a real-valued objective function. In many problems, the objective function may not yield closed-form solutions. Over many decades, optimization methods, both deterministic and stochastic, have been developed to provide solutions to these problems. However, some common limitations of these methods are the sensitivity to the initial value and that often current methods only find a local (non-global) extremum. In this article, we propose an alternative stochastic optimization method, which we call "Forward Slice", and assess its performance relative to available optimization methods.
Using Capture-Mark-Recapture Techniques To Estimate Detection Probabilities & Fidelity Of Expression For The Critically Endangered James Spinymussel (Pleurobema Collina).,
2015
James Madison University
Using Capture-Mark-Recapture Techniques To Estimate Detection Probabilities & Fidelity Of Expression For The Critically Endangered James Spinymussel (Pleurobema Collina)., Alaina C. Esposito
Masters Theses, 2010-2019
The critically endangered James Spinymussel (Pleurobema collina) is a species of freshwater mussel endemic to Virginia’s James and Dan River basins. In the last 20 years, P. collina has experienced a substantial decline in numbers and currently occupies approximately 10% of its original habitat; however, little information is known about this species to assist in conservation. A 230-meter reach of transitional habitat in Swift Run was selected for repeat observations to estimate detection probabilities using a Capture-Mark-Recapture framework. In June 2014, visual scouting began to locate and tag P. collina (including other mussels in the community) with PIT …
Distance Correlation Measures Applied To Analyze Relation Between Variables In Liver Cirrhosis Marker Data,
2015
Malabar Cancer Centre
Distance Correlation Measures Applied To Analyze Relation Between Variables In Liver Cirrhosis Marker Data, Atanu Bhattacharjee Dr.
COBRA Preprint Series
Distance Correlation is another newer choice to compute the relation between variables. However, the Bayesian counterpart of Distance Correlation is not established. In this paper, Bayesian counterpart of Distance Correlation is pro- posed. Proposed method is illustrated with Liver Chirrhosis Marker data. The relevant studies information about relation between AST and ALT is used to formulate the prior information for Bayesian computation. The Distance Correlation between AST and ALT (both are liver performance marker) is computed with 0.44. The credible interval is observed with (0.41, 0.46).Bayesian counter- part to compute Distance correlation is simple and handy.
Genetics Of Obesity In Starr County, Texas Mexican Americans,
2015
The University of Texas Graduate School of Biomedical Sciences at Houston
Genetics Of Obesity In Starr County, Texas Mexican Americans, Heather M. Highland
Dissertations and Theses (Open Access)
Currently, over two-thirds of Americans are classified as over-weight or obese. Obesity increases risk for many other diseases including type 2 diabetes, heart disease, stroke, and cancer, making obesity the largest public health problem in America and most other Westernized nations. Hispanics have a higher rate of both obesity and type 2 diabetes, making them a particularly interesting population in which to study obesity. For the last 33 years, the Starr County Health Studies has collected an array of phenotypes and biological samples from residents of Starr County, along Texas-Mexico border. This study includes 825 subjects who were not known …
Optcluster : An R Package For Determining The Optimal Clustering Algorithm And Optimal Number Of Clusters.,
2015
University of Louisville
Optcluster : An R Package For Determining The Optimal Clustering Algorithm And Optimal Number Of Clusters., Michael N. Sekula
Electronic Theses and Dissertations
Determining the best clustering algorithm and ideal number of clusters for a particular dataset is a fundamental difficulty in unsupervised clustering analysis. In biological research, data generated from Next Generation Sequencing technology and microarray gene expression data are becoming more and more common, so new tools and resources are needed to group such high dimensional data using clustering analysis. Different clustering algorithms can group data very differently. Therefore, there is a need to determine the best groupings in a given dataset using the most suitable clustering algorithm for that data. This paper presents the R package optCluster as an efficient …
Summary Of Survival Analysis With Sas Procedures.,
2015
University of Louisville
Summary Of Survival Analysis With Sas Procedures., Derek Duane Childers 1990-
Electronic Theses and Dissertations
The research conducted for this thesis was performed to summarize some of the most commonly used survival analysis techniques as well as to create one macro that will provide the solutions for these techniques. Some of the techniques that this thesis focuses on are survival and hazard functions, mean and median survival times, life table, log rank test, proportional hazards/model building, and competing risk. To further analyze these survival analysis techniques I will use the Bone Marrow Transplantation for Leukemia dataset. This trial consists of either acute myelocytic leukemia (AML 99 patients) or acute lymphoblastic leukemia (ALL 38 patients). There …
Novel Applications Of And Extensions To Linear Regression Methods For The Biomedical And Materials Sciences.,
2015
University of Louisville
Novel Applications Of And Extensions To Linear Regression Methods For The Biomedical And Materials Sciences., Joe Bible
Electronic Theses and Dissertations
In this work we present three topics, each of which centered on either the application or modification of various linear regression methods. Our work with respect to the “Materials Genome” project while undermined by oversimplification and data integrity issues in its early stages, provides a sound platform from which the project can proceed successfully. Building upon a growing body of knowledge around the use of Weighted Generalized Estimating Equations (WGEE), our second investigation proposes an extension to that framework intended to address the inherent bias present in the analysis of clustered longitudinal data with potentially informative cluster sizes and temporal …
Adaptive Enrichment Designs For Randomized Trials With Delayed Endpoints, Using Locally Efficient Estimators To Improve Precision,
2015
Johns Hopkins University, Johns Hopkins Bloomberg School of Public Health, Department of Biostatistics
Adaptive Enrichment Designs For Randomized Trials With Delayed Endpoints, Using Locally Efficient Estimators To Improve Precision, Michael Rosenblum, Tianchen Qian, Yu Du, Huitong Qiu
Johns Hopkins University, Dept. of Biostatistics Working Papers
Adaptive enrichment designs involve preplanned rules for modifying enrollment criteria based on accrued data in an ongoing trial. For example, enrollment of a subpopulation where there is sufficient evidence of treatment efficacy, futility, or harm could be stopped, while enrollment for the remaining subpopulations is continued. Most existing methods for constructing adaptive enrichment designs are limited to situations where patient outcomes are observed soon after enrollment. This is a major barrier to the use of such designs in practice, since for many diseases the outcome of most clinical importance does not occur shortly after enrollment. We propose a new class …
Simulation Of Semicompeting Risk Survival Data And Estimation Based On Multistate Frailty Model,
2015
Harvard University
Simulation Of Semicompeting Risk Survival Data And Estimation Based On Multistate Frailty Model, Fei Jiang, Sebastien Haneuse
Harvard University Biostatistics Working Paper Series
We develop a simulation procedure to simulate the semicompeting risk survival data. In addition, we introduce an EM algorithm and a B–spline based estimation procedure to evaluate and implement Xu et al. (2010)’s nonparametric likelihood es- timation approach. The simulation procedure provides a route to simulate samples from the likelihood introduced in Xu et al. (2010)’s. Further, the EM algorithm and the B–spline methods stabilize the estimation and gives accurate estimation results. We illustrate the simulation and the estimation procedure with simluation examples and real data analysis.
Association Between Nutritional Awareness And Diet Quality: Evidence From The Observation Of Cardiovascular Risk Factors In Luxembourg (Oriscav-Lux) Study,
2015
University of South Carolina
Association Between Nutritional Awareness And Diet Quality: Evidence From The Observation Of Cardiovascular Risk Factors In Luxembourg (Oriscav-Lux) Study, Ala'a Alkerwi, Nicolas Sauvageot, Leoné Malan, Nitin Shivappa, James R. Hébert
Faculty Publications
This study examined the association between nutritional awareness and diet quality, as indicated by energy density, dietary diversity and adequacy to achieve dietary recommendations, while considering the potentially important role of socioeconomic status (SES). Data were derived from 1351 subjects, aged 18–69 years and enrolled in the ORISCAV-LUX study. Energy density score (EDS), dietary diversity score (DDS) and Recommendation Compliance Index (RCI) were calculated based on data derived from a food frequency questionnaire. Nutritional awareness was defined as self-perception of the importance assigned to eating balanced meals, and classified as high, moderate, or of little importance. Initially, a General Linear …
Test On Existence Of Histology Subtype-Specific Prognostic Signatures Among Early Stage Lung Adenocarcinoma And Squamous Cell Carcinoma Patients Using A Cox-Model Based Filter,
2015
Jilin University, China
Test On Existence Of Histology Subtype-Specific Prognostic Signatures Among Early Stage Lung Adenocarcinoma And Squamous Cell Carcinoma Patients Using A Cox-Model Based Filter, Suyan Tian, Chi Wang, Ming-Wen An
Biostatistics Faculty Publications
BACKGROUND: Non-small cell lung cancer (NSCLC) is the predominant histological type of lung cancer, accounting for up to 85% of cases. Disease stage is commonly used to determine adjuvant treatment eligibility of NSCLC patients, however, it is an imprecise predictor of the prognosis of an individual patient. Currently, many researchers resort to microarray technology for identifying relevant genetic prognostic markers, with particular attention on trimming or extending a Cox regression model. Adenocarcinoma (AC) and squamous cell carcinoma (SCC) are two major histology subtypes of NSCLC. It has been demonstrated that fundamental differences exist in their underlying mechanisms, which motivated us …
Impact Of Population Stratification On Family-Based Association In An Admixed Population,
2015
Cincinnati Children’s Hospital Medical Center
Impact Of Population Stratification On Family-Based Association In An Admixed Population, T. B. Mersha, L. Ding, H. He, E. S. Alexander, X. Zhang, B. G. Kurowski, V. Pilipenko, L. Kottyan, L. J. Martin, David W. Fardo
Biostatistics Faculty Publications
Population substructure is a well-known confounder in population-based case-control genetic studies, but its impact in family-based studies is unclear. We performed population substructure analysis using extended families of admixed population to evaluate power and Type I error in an association study framework. Our analysis shows that power was improved by 1.5% after principal components adjustment. Type I error was also reduced by 2.2% after adjusting for family substratification. The presence of population substructure was underscored by discriminant analysis, in which over 92% of individuals were correctly assigned to their actual family using only 100 principal components. This study demonstrates the …
The Stability Of The Iris As A Biometric Modality,
2015
Purdue University
The Stability Of The Iris As A Biometric Modality, Benjamin Wright Petry
Open Access Theses
In this thesis, the question of the stability of a group of individual subjects' irises is examined and answered. This stability is examined in regards to the time scale of the month range. The covariate for this research was time. Images collected during one month of separation between captures were examined. The genuine and impostor scores for these images were calculated and then interpreted using the stability score index. This index produced a quantifiable value for the stability of iris match scores over the months of the examination. ^ Additionally, a new framework for collecting and analyzing time in biometrics …
Zero-Inflated Models To Identify Transcription Factor Binding Sites In Chip-Seq Experiments,
2015
Old Dominion University
Zero-Inflated Models To Identify Transcription Factor Binding Sites In Chip-Seq Experiments, Sameera Dhananjaya Viswakula
Mathematics & Statistics Theses & Dissertations
It is essential to determine the protein-DNA binding sites to understand many biological processes. A transcription factor is a particular type of protein that binds to DNA and controls gene regulation in living organisms. Chromatin immunoprecipitation followed by highthroughput sequencing (ChIP-seq) is considered the gold standard in locating these binding sites and programs use to identify DNA-transcription factor binding sites are known as peak-callers. ChIP-seq data are known to exhibit considerable background noise and other biases. In this study, we propose a negative binomial model (NB), a zero-inflated Poisson model (ZIP) and a zero-inflated negative binomial model (ZINB) for peak-calling. …
Targeted Estimation And Inference For The Sample Average Treatment Effect,
2015
Division of Biostatistics, University of California, Berkeley - the SEARCH Consortium
Targeted Estimation And Inference For The Sample Average Treatment Effect, Laura B. Balzer, Maya L. Petersen, Mark J. Van Der Laan
U.C. Berkeley Division of Biostatistics Working Paper Series
While the population average treatment effect has been the subject of extensive methods and applied research, less consideration has been given to the sample average treatment effect: the mean difference in the counterfactual outcomes for the study units. The sample parameter is easily interpretable and is arguably the most relevant when the study units are not representative of a greater population or when the exposure's impact is heterogeneous. Formally, the sample effect is not identifiable from the observed data distribution. Nonetheless, targeted maximum likelihood estimation (TMLE) can provide an asymptotically unbiased and efficient estimate of both the population and sample …
Spectral Gene Set Enrichment (Sgse),
2015
Dartmouth College
Spectral Gene Set Enrichment (Sgse), H Robert Frost, Zhigang Li, Jason H. Moore
Dartmouth Scholarship
Gene set testing is typically performed in a supervised context to quantify the association between groups of genes and a clinical phenotype. In many cases, however, a gene set-based interpretation of genomic data is desired in the absence of a phenotype variable. Although methods exist for unsupervised gene set testing, they predominantly compute enrichment relative to clusters of the genomic variables with performance strongly dependent on the clustering algorithm and number of clusters. We propose a novel method, spectral gene set enrichment (SGSE), for unsupervised competitive testing of the association between gene sets and empirical data sources. SGSE first computes …
Model Pengendalian Faktor Risiko Stunting Pada Anak Bawah Tiga Tahun,
2015
Jurusan Kesehatan Masyarakat Fakultas Ilmu-Ilmu Kesehatan Universitas Jenderal Soedirman
Model Pengendalian Faktor Risiko Stunting Pada Anak Bawah Tiga Tahun, Erna Kusumawati, Setiyowati Rahardjo, Hesti Permata Sari
Kesmas
Stunting merupakan masalah gizi, terbukti data pemantauan status gizi Kabupaten Banyumas 2012 prevalensi stunting sebesar 28,37% dan prevalensi tertinggi (41,6%) di Puskesmas Kedungbanteng. Tujuan penelitian untuk menganalisis faktor risiko terkait faktor anak, ibu, lingkungan terhadap stunting bawah tiga tahun (batita) agar dapat dikembangkan model pengendaliannya. Penelitian menggunakan desain kasus kontrol, populasi adalah seluruh anak usia 6 sampai 36 bulan di Puskesmas Kedungbanteng Kabupaten Banyumas selama enam bulan tahun 2013. Sampel kasus adalah 50 batita stunting, sampel kontrol adalah 50 batita status normal. Teknik pengambilan sampel kasus diambil dari tujuh desa yang terbanyak stuntingnya, sedangkan kontrol adalah batita normal tetangga terdekat …
Determinan Perilaku Tes Hiv Pada Ibu Hamil,
2015
Jurusan Kebidanan Politeknik Kesehatan Kementerian Kesehatan Yogyakarta
Determinan Perilaku Tes Hiv Pada Ibu Hamil, Nanik Setiyawati, Niken Meilani
Kesmas
Human immunodeficiency virus (HIV) dan Acquired immune deficiency syndrome (AIDS) merupakan salah satu sorotan dalam pencapaian target Millenium Development Goals (MDGs). Ibu hamil dengan HIV akan berisiko menularkan kepada bayinya. Tes HIV merupakan gerbang pembuka status HIV yang sangat penting dilakukan pada ibu hamil. Penelitian ini bertujuan untuk menentukan determinan perilaku tes HIV pada ibu hamil yaitu tingkat pendidikan, tingkat pengetahuan, persepsi kerentanan diri tertular HIV, sikap, Provider-Initiated Testing and Counselling (PITC) dan ketersediaan sumber informasi (keluarga dan kader kesehatan). Jenis penelitian adalah potong lintang dengan metode survei. Penelitian ini dilakukan di Puskesmas Mantrijeron dan Puskesmas Sleman yang telah memiliki …
