Statistics and Probability Commons^™

A Machine Learning Approach To Post-Market Surveillance Of Medical Devices, Jonathan Bates, Shu-Xia Li, Craig Parzynski, Ronald Coifman, Harlan Krumholz, Joseph Ross

Yale Day of Data

Post-market surveillance is a collection of processes and activities used by product manufacturers and regulators, such as the U.S. Food and Drug Administration (FDA) to monitor the safety and effectiveness of medical devices once they are available for use “on the market”. These activities are designed to generate information to identify poorly performing devices and other safety problems, accurately characterize real-world device performance and clinical outcomes, and facilitate the development of new devices, or new uses for existing devices. Typically, a device is monitored by comparing adverse events in the exposed population to a matched unexposed population. This research considers …

K-Mer Analysis On Developmental And Housekeeping Enhancer Peaks, Yunsi Yang, Anurag Sethi, Mark Gerstein

Yale Day of Data

The regulation of gene expression involves interaction between transcriptional enhancers and core promoters. However, the separation between developmental and housekeeping gene regulation remains unknown. Here, we present a method to detect if different core promoters exhibit specificity to certain enhancers within massively parallel assays for enhancer detection. We use k-mers of various length (3-8bp) as sequence features and compare k-mer frequencies between developmental and housekeeping enhancers. This method shows promoter specificity of enhancers in D. melanogaster.

Addressing Confounding In Predictive Models With An Application To Neuroimaging, Kristin A. Linn, Bilwaj Gaonkar, Jimit Doshi, Christos Davatzikos, Russell T. Shinohara

UPenn Biostatistics Working Papers

Understanding structural changes in the brain that are caused by a particular disease is a major goal of neuroimaging research. Multivariate pattern analysis (MVPA) comprises a collection of tools that can be used to understand complex disease effects across the brain. We discuss several important issues that must be considered when analyzing data from neuroimaging studies using MVPA. In particular, we focus on the consequences of confounding by non-imaging variables such as age and sex on the results of MVPA. After reviewing current practice to address confounding in neuroimaging studies, we propose an alternative approach based on inverse probability weighting. …

Control-Group Feature Normalization For Multivariate Pattern Analysis Using The Support Vector Machine, Kristin A. Linn, Bilwaj Gaonkar, Jimit Doshi, Christos Davatzikos, Russell T. Shinohara

UPenn Biostatistics Working Papers

Normalization of feature vector values is a common practice in machine learning. Generally, each feature value is standardized to the unit hypercube or by normalizing to zero mean and unit variance. Classification decisions based on support vector machines (SVMs) or by other methods are sensitive to the specific normalization used on the features. In the context of multivariate pattern analysis using neuroimaging data, standardization effectively up- and down-weights features based on their individual variability. Since the standard approach uses the entire data set to guide the normalization it utilizes the total variability of these features. This total variation is inevitably …

A Simple Method To Estimate The Time-Dependent Roc Curve Under Right Censoring, Liang Li, Bo Hu, Tom Greene

COBRA Preprint Series

The time-dependent Receiver Operating Characteristic (ROC) curve is often used to study the diagnostic accuracy of a single continuous biomarker, measured at baseline, on the onset of a disease condition when the disease onset may occur at different times during the follow-up and hence may be right censored. Due to censoring, the true disease onset status prior to the pre-specified time horizon may be unknown on some patients, which causes difficulty in calculating the time-dependent sensitivity and specificity. We study a simple method that adjusts for censoring by weighting the censored data by the conditional probability of disease onset prior …

Factors Affecting Dimensional Precision Of Consumer 3d Printing, David D. Hernandez

International Journal of Aviation, Aeronautics, and Aerospace

This paper investigates the factors affecting dimensional precision of consumer-grade 3D printing, attempting to isolate and mitigate sources of error. The focus is on creating engineering prototypes of, tooling for, or finalized instances of mechanical devices. A specific fused deposition modeling printer – the Ultimaker 2 – is analyzed in terms of meeting precise physical dimensions, consistent shapes, and predictable surface finish. Extensive trial and error resulted in removal of several sources of bias, with square test articles exhibiting a lower-than-anticipated mean percentage error of -0.387% (SD = 0.559), a value comparable to other modern manufacturing techniques. A full …

Probabilistic Reasoning In Cosmology, Yann Benétreau-Dupin

Electronic Thesis and Dissertation Repository

Cosmology raises novel philosophical questions regarding the use of probabilities in inference. This work aims at identifying and assessing lines of arguments and problematic principles in probabilistic reasoning in cosmology.

The first, second, and third papers deal with the intersection of two distinct problems: accounting for selection effects, and representing ignorance or indifference in probabilistic inferences. These two problems meet in the cosmology literature when anthropic considerations are used to predict cosmological parameters by conditionalizing the distribution of, e.g., the cosmological constant on the number of observers it allows for. However, uniform probability distributions usually appealed to in such arguments …

Bayesian Inference On Longitudinal Semi-Continuous Substance Abuse/Dependence Symptoms Data, Dongyuan Xing

USF Tampa Graduate Theses and Dissertations

Substance use data such as alcohol drinking often contain a high proportion of zeros. In studies examining the alcohol consumption in college students, for instance, many students may not drink in the studied period, resulting in a number of zeros. Zero-inflated continuous data, also called semi continuous data, typically consist of a mixture of a degenerate distribution at the origin (zero) and a right-skewed, continuous distribution for the positive values. Ignoring the extreme non-normality in semi-continuous data may lead to substantially biased estimates and inference. Longitudinal or repeated measures of semi-continuous data present special challenges in statistical inference because of …

On The Construction Of Restricted Minimum Aberration Designs, Chand Midha, Chung-Yi Suen, Ashish Das

Chand K Midha

Deriving a formula, we show that an optimal moment design has the property that each treatment combination appears as equally often as possible. Modifying the definition of minimum aberration to restricted minimum aberration, we show that the word length pattern of a design is proportional to that of its complement. Many restricted minimum aberration designs are constructed

Critical Assessment Of Outcomes In Acute Aortic Dissection (Type A) At A Community Hospital: A 10 Year Review, Tim S. Misselbeck Md, James K. Wu Md, Stephen Deturk Ba, Michael F. Szwerc Md, Sanjay M. Mehta Md, Theodore G. Phillips Md, Gary W. Szydlowski Md, Raymond L. Singer Md

Raymond L Singer MD

No abstract provided.

Conventional Isolated Aortic Valve Replacement In Octogenarians: A 10-Year Single Center Experience, James K. Wu Md, Justin D. Roberts Do, Gregory S. Troutman Bs, Michael J. Weiss Mph, Sanjay M. Mehta Md, Theodore G. Phillips Md, Michael F. Szwerc Md, Gary W. Szydlowski Md, Tim S. Misselbeck Md, Raymond L. Singer Md

Raymond L Singer MD

No abstract provided.

On Varieties Of Doubly Robust Estimators Under Missing Not At Random With An Ancillary Variable, Wang Miao, Eric Tchetgen Tchetgen

Harvard University Biostatistics Working Paper Series

No abstract provided.

A Pairwise Likelihood Augmented Estimator For The Cox Model Under Left-Truncation, Fan Wu, Sehee Kim, Jing Qin, Rajiv Saran, Yi Li

The University of Michigan Department of Biostatistics Working Paper Series

Survival data collected from prevalent cohorts are subject to left-truncation and the analysis is challenging. Conditional approaches for left-truncated data under the Cox model are inefficient as they typically ignore the information in the marginal likelihood of the truncation times. Length-biased sampling methods can improve the estimation efficiency but only when the stationarity assumption of the disease incidence holds, i.e., the truncation distribution is uniform; otherwise they may generate biased estimates. In this paper, we propose a semi-parametric method for the Cox model under general left-truncation, where the truncation distribution is unspecified. Our approach is to make inference based on …

Alterations In Gene Array Patterns In Dendritic Cells From Aged Humans, Jia-Ning Cao, Anshu Agrawal, Edward Sharman, Zhenyu Jia, Sudhir Gupta

Zhenyu Jia

Dendritic cells (DCs) are major antigen-presenting cells that play a key role in initiating and regulating innate and adaptive immune responses. DCs are critical mediators of tolerance and immunity. The functional properties of DCs decline with age. The purpose of this study was to define the age-associated molecular changes in DCs by gene array analysis using Affymatrix GeneChips. The expression levels of a total of 260 genes (1.8%) were significantly different (144 down-regulated and 116 upregulated) in monocyte-derived DCs (MoDCs) from aged compared to young human donors. Of the 260 differentially expressed genes, 24% were down-regulated by more than 3-fold, …

Topical Rapamycin Systematically Suppresses The Early Stages Of Pulsed Dye Laser-Induced Angiogenesis Pathways, Lin Gao, Sydney Phan, Dawnica Nadora, Margarita Chernova, Victor Sun, Salena Preciado, Brittany Ballew, Zhenyu Jia, Wangcun Jia, Gang Wang, Martin Mihm, J. Nelson, Wenbin Tan

Zhenyu Jia

BACKGROUND: Administration of topical rapamycin (RPM) suppresses the regeneration and revascularization of photocoagulated blood vessels induced by pulsed dye laser (PDL). OBJECTIVE: To systematically elucidate the molecular pathophysiology of the inhibition of PDL-induced angiogenesis by topical RPM in a rodent model. METHODS: The mRNA expression profiles of 86 angiogenic genes and phosphorylation levels of ribosomal protein S6 kinase (P70S6K) in rodent skin were examined with or without topical RPM administration post-PDL exposure. RESULTS: The PDL-induced systematic increases in transcriptional levels of angiogenic genes showed a peak expression at days 3-7 post-PDL in rodent skin. Topical application of 1% RPM significantly …

Transcultural Self-Efficacy Perceptions Of Baccalaureate Nursing Students, Margaret Halter, Faye Grund, Mark Fridline, Sharon See, Lisa Young, Carol Reece

Mark Fridline PhD

Addressing the health care needs of a 21st-century nation that is experiencing increased diversity and disparity will require new models of educating future providers. The cultural competence and confidence model was the guiding framework in a study evaluating the influence of cultural educational offerings on the transcultural self-efficacy (TSE) perceptions in baccalaureate nursing students. The Transcultural Self-Efficacy Tool was used to measure perceived TSE in a pretest (N = 260), posttest (N = 236) study over an academic year. Significant changes were demonstrated in overall self-efficacy and on the cognitive, practical, and affective subscales. A classification and regression …

Embアルゴリズムの新たな応用による多重比率補定(高橋将宜), Masayoshi Takahashi

Masayoshi Takahashi

No abstract provided.

On Partial Identification Of The Pure Direct Effect, Caleb Miles, Phyllis Kanki, Seema Meloni, Eric Tchetgen Tchetgen

Harvard University Biostatistics Working Paper Series

No abstract provided.

Preparedness Of Hospitals In The Republic Of Ireland For An Influenza Pandemic, An Infection Control Perspective, Mary Reidy, Fiona Ryan, Dervla Hogan, Seán Lacey, Claire Buckley

Department of Mathematics Publications

When an influenza pandemic occurs most of the population is susceptible and attack rates can range as high as 40–50 %. The most important failure in pandemic planning is the lack of standards or guidelines regarding what it means to be ‘prepared’. The aim of this study was to assess the preparedness of acute hospitals in the Republic of Ireland for an influenza pandemic from an infection control perspective.

A Gene-Based Association Method For Mapping Traits Using Reference Transcriptome Data, Eric R. Gamazon, Heather Wheeler, Kaanan P. Shah, Sahar V. Mozaffari, Keston Aquino-Michaels, Robert J. Carroll, Anne E. Eyler, Joshua C. Denny, Gtex Consortium, Dan L. Nicolae, Nancy J. Cox, Hae Kyung Im

Bioinformatics Faculty Publications

Genome-wide association studies (GWAS) have identified thousands of variants robustly associated with complex traits. However, the biological mechanisms underlying these associations are, in general, not well understood. We propose a gene-based association method called PrediXcan that directly tests the molecular mechanisms through which genetic variation affects phenotype. The approach estimates the component of gene expression determined by an individual’s genetic profile and correlates ‘imputed’ gene expression with the phenotype under investigation to identify genes involved in the etiology of the phenotype. Genetically regulated gene expression is estimated using whole-genome tissue-dependent prediction models trained with reference transcriptome data sets. PrediXcan enjoys …