Statistics and Probability Commons^™

Modelling Subject-Specific Childhood Growth Using Linear Mixed-Effect Models With Cubic Regression Splines, Laura M. Grajeda, Andrada Ivanescu, Mayuko Saito, Ciprian Crainiceanu, Devan Jaganath, Robert H. Gilman, Jean E. Crabtree, Dermott Kelleher, Lilia Cabrera, Vitaliano Cama, William Checkley

Department of Applied Mathematics and Statistics Faculty Scholarship and Creative Works

Background: Childhood growth is a cornerstone of pediatric research. Statistical models need to consider individual trajectories to adequately describe growth outcomes. Specifically, well-defined longitudinal models are essential to characterize both population and subject-specific growth. Linear mixed-effect models with cubic regression splines can account for the nonlinearity of growth curves and provide reasonable estimators of population and subject-specific growth, velocity and acceleration. Methods: We provide a stepwise approach that builds from simple to complex models, and account for the intrinsic complexity of the data. We start with standard cubic splines regression models and build up to a model that includes subject-specific …

Analysis Of The Precipitation Detection Algorithm For The Geonor T-200b Precipitation Gauge To Improve Accuracy, Megan Lerman, Robert K. Goodrich

STAR Program Research Presentations

In an effort to improve the precipitation detection algorithm for the Geonor All Weather Precipitation Gauge, an automated truth algorithm has been created to detect errors in the original algorithm. The original algorithm detects precipitation in real time and uses the rate of precipitation to indicate an event. The automated truth does not detect in real time, and focuses on precipitation accumulation to indicate an event. Since the automated truth is delayed, it is able to consider the data collected before and after the point it is analyzing. The automated truth is already more accurate than the original algorithm but …

Spatiotemporal Meta-Analysis: Reviewing Health Psychology Phenomena Over Space And Time., Blair T. Johnson

CHIP Documents

This supplemental material is meant to support this article:

Johnson, B. T., Crowley, E., & Marrouch, N. Spatiotemporal meta-analysis: Reviewing health psychology phenomena over space and time. Health Psychology Review.

Specifically, it is a database of GDPs per capita for nations in the world between 1800 and 2015. It is archived here to support an online supplement to this article.

GDP per capita

Asymptotic Behavior Of Certain Integrodifferential Equations, Said R. Grace, Elvan Akin

Mathematics and Statistics Faculty Research & Creative Works

This paper deals with asymptotic behavior of nonoscillatory solutions of certain forced integrodifferential equations of the form: (a(t)x'(t))' = e (t) + ∫ ^t_c (t - s)^{α - 1}k(t,s)ƒ(s,x(s))ds, c > 1, 0 < α < 1. From the obtained results, we derive a technique which can be applied to some related integrodifferential as well as integral equations.

Nonoscillation Criteria For Two-Dimensional Time-Scale Systems, Ozkan Ozturk, Elvan Akin

Mathematics and Statistics Faculty Research & Creative Works

We study the existence and nonexistence of nonoscillatory solutions of a two-dimensional system of first-order dynamic equations on time scales. Our approach is based on the Knaster and Schauder fixed point theorems and some certain integral conditions. Examples are given to illustrate some of our main results.

Qualitative Analysis On Differential, Fractional Differential, And Dynamic Equations And Related Topics, Said R. Grace, Taher S. Hassan, Shurong Sun, Elvan Akin

Mathematics and Statistics Faculty Research & Creative Works

This issue on qualitative analysis on differential, fractional differential, and dynamic equations and related topics aims at an all-around research and the state-of-the-art theoretical, numerical, and practical achievements that contribute to this field.

Sneak-Out Principle On Time Scales, Martin Bohner, Samir H. Saker

Mathematics and Statistics Faculty Research & Creative Works

In this paper, we show that the so-called "sneak-out principle" for discrete inequalities is valid also on a general time scale. In particular, we prove some new dynamic inequalities on time scales which as special cases contain discrete inequalities obtained by Bennett and Grosse-Erdmann. The main results also are used to formulate the corresponding continuous integral inequalities, and these are essentially new. The techniques employed in this paper are elementary and rely mainly on the time scales integration by parts rule, the time scales chain rule, the time scales Hölder inequality, and the time scales Minkowski inequality.

Oscillation Criteria For Fourth Order Nonlinear Positive Delay Differential Equations With A Middle Term, Said R. Grace, Elvan Akin

Mathematics and Statistics Faculty Research & Creative Works

In this article, we establish some new criteria for the oscillation of fourth order nonlinear delay differential equations of the form (Equation presented) provided that the second order equation (Equation presented) is nonoscillatiory or oscillatory. This equation with g(t) = t is considered in [8] and some oscillation criteria for this equation via certain energy functions are established. Here, we continue the study on the oscillatory behavior of this equation via some inequalities.

An Efficient Basket Trial Design, Kristen Cunanan, Alexia Iasonos, Ronglai Shen, Colin B. Begg, Mithat Gonen

Memorial Sloan-Kettering Cancer Center, Dept. of Epidemiology & Biostatistics Working Paper Series

The landscape for early phase cancer clinical trials is changing dramatically due to the advent of targeted therapy. Increasingly, new drugs are designed to work against a target such as the presence of a specific tumor mutation. Since typically only a small proportion of cancer patients will possess the mutational target, but the mutation is present in many different cancers, a new class of basket trials is emerging, whereby the drug is tested simultaneously in different baskets, i.e., sub-groups of different tumor types. Investigators not only desire to test whether the drug works, but also to determine which types of …

Variable Selection For Case-Cohort Studies With Failure Time Outcome, Andy Ni, Jianwen Cai, Donglin Zeng

Memorial Sloan-Kettering Cancer Center, Dept. of Epidemiology & Biostatistics Working Paper Series

Case-cohort designs are widely used in large cohort studies to reduce the cost associated with covariate measurement. In many such studies the number of covariates is very large, so an efficient variable selection method is necessary. In this paper, we study the properties of variable selection using the smoothly clipped absolute deviation penalty in a case-cohort design with a diverging number of parameters. We establish the consistency and asymptotic normality of the maximum penalized pseudo-partial likelihood estimator, and show that the proposed variable selection procedure is consistent and has an asymptotic oracle property. Simulation studies compare the finite sample performance …

Leveraging Contact Network Structure In The Design Of Cluster Randomized Trials, Guy Harling, Rui Wang, Jukka-Pekka Onnela, Victor Degruttola

Harvard University Biostatistics Working Paper Series

Background: In settings like the Ebola epidemic, where proof-of-principle trials have succeeded but questions remain about the effectiveness of different possible modes of implementation, it may be useful to develop trials that not only generate information about intervention effects but also themselves provide public health benefit. Cluster randomized trials are of particular value for infectious disease prevention research by virtue of their ability to capture both direct and indirect effects of intervention; the latter of which depends heavily on the nature of contact networks within and across clusters. By leveraging information about these networks – in particular the degree …

Using Validation Data To Adjust The Inverse Probability Weighting Estimator For Misclassified Treatment, Danielle Braun, Corwin Zigler, Francesca Dominici, Malka Gorfine

Harvard University Biostatistics Working Paper Series

The inverse probability weighting (IPW) estimator is widely used to estimate the treatment effect in observational studies in which patient characteristics might not be balanced by treatment group. The estimator assumes that treatment assignment, is error-free, but in reality treatment assignment can be measured with error. This arises in the context of comparative effectiveness research, using administrative data sources in which accurate procedural or billing codes are not always available. We show the bias introduced to the estimator when using error-prone treatment assignment, and propose an adjusted estimator using a validation study to eliminate this bias. In simulations, we explore …

Estimation And Inference For The Mediation Proportion, Daniel Nevo, Xiaomei Liao, Donna Spiegelman

Harvard University Biostatistics Working Paper Series

In epidemiology, public health and social science, mediation analysis is often undertaken to investigate the extent to which the effect of a risk factor on an outcome of interest is mediated by other covariates. A pivotal quantity of interest in such an analysis is the mediation proportion. A common method for estimating it, termed the "difference method'', compares estimates from models with and without the hypothesized mediator. However, rigorous methodology for estimation and statistical inference for this quantity has not previously been available. We formulated the problem for the Cox model and generalized linear models, and utilize a data duplication …

A Cautionary Note On The Effect Of Treatment Misclassification On The Average Treatment Effect, Danielle Braun, Corwin Zigler, Malka Gorfine, Francesca Dominici

Harvard University Biostatistics Working Paper Series

Comparative effectiveness research often relies on large administrative data, such as claims data. Methods to estimate treatment effects assume that treatment assignment is error-free, but in reality the inaccuracy of procedural or billing codes frequently misclassifies patients into treatment groups. Propensity score methods are widely used to analyze observational studies in which patient characteristics might not be balanced by treatment group. We evaluate the impact of treatment misclassification on 1) propensity score estimation; 2) treatment effect estimation conditional on propensity score estimation and implementation. We focus on three common propensity score implementations: subclassification, matching, and inverse probability of treatment weighting …

The Myth Of Making Inferences For An Overall Treatment Efficacy With Data From Multiple Comparative Studies Via Meta-Analysis, Takahiro Hasegawa, Brian Claggett, Lu Tian, Scott D. Solomon, Marc A. Pfeffer, Lee-Jen Wei

Harvard University Biostatistics Working Paper Series

Meta analysis techniques, if applied appropriately, can provide a summary of the totality of evidence regarding an overall difference between a new treatment and a control group using data from multiple comparative clinical studies. The standard meta analysis procedures, however, may not give a meaningful between-group difference summary measure or identify a meaningful patient population of interest, especially when the fixed effect model assumption is not met. Moreover, a single between-group comparison measure without a reference value obtained from patients in the control arm would likely not be informative enough for clinical decision making. In this paper, we propose a …

Moving Beyond The Conventional Stratified Analysis To Estimate An Overall Treatment Efficacy With The Data From A Comparative Randomized Clinical Study, Lu Tian, Fei Jiang, Takahiro Hasegawa, Hajime Uno, Marc Alan Pfeffer, L.J. Wei

Harvard University Biostatistics Working Paper Series

No abstract provided.

A Generalization Of The Difference Of Slopes Test To Poisson Regression With Three-Way Interaction, Melinda Bierhals

Theses, Dissertations and Capstones

Linear regression models involving interaction can use the difference of slopes test to compare slopes for various situations. We will be generalizing this process to develop a procedure to compare rates in a Poisson regression model, allowing us to consider unbounded count data as opposed to continuous data. We will apply this process to an educational data set from a sample of students located in two different Los Angeles high schools. Our model will include a three-way interaction and address the following questions:

• Does language ability impact the relationship between math ability and attendance in the same way for …

Detectable Viral Load In Late Pregnancy Among Women In The Rwanda Option B+ Pmtct Program: Enrollment Results From The Kabeho Study., Michelle M Gill, Heather J Hoffman, Emily A Bobrow, Placidie Mugwaneza, Dieudonne Ndatimana, Gilles F Ndayisaba, Cyprien Baribwira, Laura Guay, Anita Asiimwe

Epidemiology Faculty Publications

There are limited viral load (VL) data available from programs implementing "Option B+," lifelong antiretroviral treatment (ART) to all HIV-positive pregnant and postpartum women, in resource-limited settings. Extent of viral suppression from a prevention of mother-to-child transmission of HIV program in Rwanda was assessed among women enrolled in the Kigali Antiretroviral and Breastfeeding Assessment for the Elimination of HIV (Kabeho) Study. ARV drug resistance testing was conducted on women with VL>2000 copies/ml. In April 2013-January 2014, 608 pregnant or early postpartum HIV-positive women were enrolled in 14 facilities. Factors associated with detectable enrollment VL (>20 copies/ml) were examined …

Male Pattern Baldness In Relation To Prostate Cancer–Specific Mortality: A Prospective Analysis In The Nhanes I Epidemiologic Follow-Up Study, Cindy Ke Zhou, Paul H Levine, Sean D. Cleary, Heather J. Hoffman, Barry I Graubard, Michael B. Cook

Epidemiology Faculty Publications

We used male pattern baldness as a proxy for long-term androgen exposure and investigated the association of dermatologist-assessed hair loss with prostate cancer–specific mortality in the first National Health and Nutrition Examination Survey Epidemiologic Follow-up Study. From the baseline survey (1971–1974), we included 4,316 men who were 25–74 years of age and had no prior cancer diagnosis. We estimated hazard ratios and used Cox proportional hazards regressions with age as the time metric and baseline hazard stratified by baseline age. A hybrid framework was used to account for stratification and clustering of the sample design, with adjustment for the variables …

Privacy And Accountability In Black-Box Medicine, Roger Allan Ford, W. Nicholson Price Ii

Law Faculty Scholarship

Black-box medicine—the use of big data and sophisticated machine learning techniques for health-care applications—could be the future of personalized medicine. Black-box medicine promises to make it easier to diagnose rare diseases and conditions, identify the most promising treatments, and allocate scarce resources among different patients. But to succeed, it must overcome two separate, but related, problems: patient privacy and algorithmic accountability. Privacy is a problem because researchers need access to huge amounts of patient health information to generate useful medical predictions. And accountability is a problem because black-box algorithms must be verified by outsiders to ensure they are accurate and …

How Often Are Antibiotic-Resistant Bacteria Said To “Evolve” In The News?, Nina Singh, Matthew T. Sit, Deanna M. Chung, Ana A. Lopez, Ranil Weerackoon, Pamela J. Yeh

Department of Statistics: Faculty Publications

Media plays an important role in informing the general public about scientific ideas.We examine whether the word “evolve,” sometimes considered controversial by the general public, is frequently used in the popular press. Specifically, we ask how often articles discussing antibiotic resistance use the word “evolve” (or its lexemes) as opposed to alternative terms such as “emerge” or “develop.” We chose the topic of antibiotic resistance because it is a medically important issue; bacterial evolution is a central player in human morbidity and mortality. We focused on the most widely-distributed newspapers written in English in the United States, United Kingdom, Canada, …

Systematic Evaluation Of The Impact Of Chip-Seq Read Designs On Genome Coverage, Peak Identification, And Allele-Specific Binding Detection, Qi Zhang, Xin Zeng, Sam Younkin, Trupti Kawli, Michael P. Snyder, Sündüz Kele

Department of Statistics: Faculty Publications

Background: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments revolutionized genome-wide profiling of transcription factors and histone modifications. Although maturing sequencing technologies allow these experiments to be carried out with short (36–50 bps), long (75–100 bps), single-end, or paired-end reads, the impact of these read parameters on the downstream data analysis are not well understood. In this paper, we evaluate the effects of different read parameters on genome sequence alignment, coverage of different classes of genomic features, peak identification, and allele-specific binding detection.

Results: We generated 101 bps paired-end ChIP-seq data for many transcription factors from human GM12878 and MCF7 cell …

The Impact Of Hair Coat Color On Longevity Of Holstein Cows In The Tropics, C. N. Lee, K. S. Baek, A. Parkhurst

Department of Statistics: Faculty Publications

Background: Over two decades of observations in the field in South East Asia and Hawai‘i suggest that majority of the commercial dairy herds are of black hair coat. Hence a simple study to determine the accuracy of the observation was conducted with two large dairy herds in Hawaii in the mid-1990s.

Methods: A retrospective study on longevity of Holstein cattle in the tropics was conducted using DairyComp-305 lactation information coupled with phenotypic evaluation of hair coat color in two large dairy farms. Cows were classified into 3 groups: a) black (B, >90%); b) black/white (BW, 50:50) and c) white (W, …

Sex-Specific Hippocampal 5-Hydroxymethylcytosine Is Disrupted In Response To Acute Stress, Ligia A. Papale, Sisi Li, Andy Madrid, Qi Zhang, Li Chen, Pankaj Chopra, Peng Jin, Sunduz Keles, Reid S. Alisch

Department of Statistics: Faculty Publications

Environmental stress is among the most important contributors to increased susceptibility to develop psychiatric disorders. While it is well known that acute environmental stress alters gene expression, the molecular mechanisms underlying these changes remain largely unknown. 5-hydroxymethylcytosine (5hmC) is a novel environmentally sensitive epigenetic modification that is highly enriched in neurons and is associated with active neuronal transcription. Recently,we reported a genome-wide disruption of hippocampal 5hmCin male mice following acute stress that was correlated to altered transcript levels of genes in known stress related pathways. Since sex-specific endocrine mechanisms respond to environmental stimulus by altering the neuronal epigenome, we examined …

A Compendium Of Chromatin Contact Maps Reveals Spatially Active Regions In The Human Genome, Anthony D. Schmitt, Ming Hu, Inkyung Jung, Zheng Xu, Yunjiang Qiu, Catherine L. Tan, Yun Li, Shin Lin, Yiing Lin, Cathy L. Barr, Bing Ren

Department of Statistics: Faculty Publications

The three-dimensional configuration of DNA is integral to all nuclear processes in eukaryotes, yet our knowledge of the chromosome architecture is still limited. Genome-wide chromosome conformation capture studies have uncovered features of chromatin organization in cultured cells, but genome architecture in human tissues has yet to be explored. Here, we report the most comprehensive survey to date of chromatin organization in human tissues. Through integrative analysis of chromatin contact maps in 21 primary human tissues and cell types, we find topologically associating domains highly conserved in different tissues. We also discover genomic regions that exhibit unusually high levels of local …

Hiview: An Integrative Genome Browser To Leverage Hi‑C Results For The Interpretation Of Gwas Variants, Zheng Xu, Guosheng Zhang, Qing Duan, Shengjie Chai, Baqun Zhang, Cong Wu, Fulai Jin, Feng Yue, Yun Li, Ming Hu

Department of Statistics: Faculty Publications

Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with complex traits and diseases. However, most of them are located in the non-protein coding regions, and therefore it is challenging to hypothesize the functions of these non-coding GWAS variants. Recent large efforts such as the ENCODE and Roadmap Epigenomics projects have predicted a large number of regulatory elements. However, the target genes of these regulatory elements remain largely unknown. Chromatin conformation capture based technologies such as Hi-C can directly measure the chromatin interactions and have generated an increasingly comprehensive catalog of the interactome between the distal regulatory elements …

A Bayesian Gwas Method Utilizing Haplotype Clusters For A Composite Breed Population, Danielle F. Wilson-Wells, Stephen D. Kachman

Department of Statistics: Faculty Publications

Commercial beef cattle are often composites of multiple breeds. Current methods used to produce genomic predictors are based on the underlying assumption of animals being sampled from a homogeneous population. As a result, the predictors can perform poorly when used to predict the relative genetic merit of animals whose breed composition are different. In part, this is due to the changes in linkage disequilibrium between the markers and the quantitative trait loci as we move from one breed to the next. An alternative model based on breed specific haplotype clusters was developed to allow for differences in linkage disequilibrium across …

Design Of Probabilistic Random Forests With Applications To Anticancer Drug Sensitivity Prediction- 2016, Raziur Rahman, Saad Haider, Souparno Ghosh, Ranadip Pal

Department of Statistics: Faculty Publications

Random forests consisting of an ensemble of regression trees with equal weights are frequently used for design of predictive models. In this article, we consider an extension of the methodology by representing the regression trees in the form of probabilistic trees and analyzing the nature of heteroscedasticity. The probabilistic tree representation allows for analytical computation of confidence intervals (CIs), and the tree weight optimization is expected to provide stricter CIs with comparable performance in mean error. We approached the ensemble of probabilistic trees’ prediction from the perspectives of a mixture distribution and as a weighted sum of correlated random variables. …

A Descriptive Study Of The Effect Of Payer Source On Multiple Longitudinal Outcome Measures Within The Tbi Model Systems National Database Using Longitudinal Hlm Analyses, Melissa Carole Hofmann

Electronic Theses and Dissertations

Using longitudinal data from the TBIMS ND, this study utilized a longitudinal hierarchical linear modeling approach to describe the effect of primary payer source on individual level change in outcomes including the FIM and DRS. To facilitate the use of parametric statistics, Rasch-transformed FIM and DRS scores were utilized; thus approaching an interval level of measurement. The FIM was separated into 3 separate cognitive, mobility, and self-care subscales. In this way, rehabilitation professionals including speech, physical, and occupational therapists for this TBI sample could reference results to inform current clinical practice.

Results indicated that FIM and DRS trajectories were best …

A Comparison Between Propensity Score Matching, Weighting, And Stratification In Multiple Treatment Groups: A Simulation Study, Priyalatha Govindasamy

Electronic Theses and Dissertations

The application of propensity score techniques (matching, stratification, and weighting) with multiple treatment levels are similar to those used in binary groups. However, given that the application of propensity scores in multiple treatment groups is new, factors affecting the performance of matching, stratification, and weighting in multiple treatment groups are less explored. Therefore, this study was conducted to determine the performance of different propensity score techniques with multiple treatment groups under various circumstances. Specifically, the study focused on examining how the three propensity score corrective techniques perform in estimating treatment effects under (1) overt and (2) hidden types of selection …