Bayesian Hierarchical Modeling based on Multi-Source Exchangeability

University of Minnesota Ph.D. dissertation. July 2017. Major: Biostatistics. Advisor: Joseph Koopmeiners. 1 computer file (PDF); xiii, 135 pages.Progress in medical practice traditionally takes place over a sequence of clinical studies which are designed to establish clinical efficacy, identify the safety profile, and seek regulatory approval for a novel treatment strategy. These trials in humans can be expensive and present numerous challenges in their implementation. While some challenges may be addressed by the development of innovative trial designs, it may also be advantageous to incorporate supplemental sources of information, which are typically ignored in traditional approaches to analysis. In this dissertation, we introduce Multi-Source Exchangeability Models (MEMs), a general Bayesian hierarchical approach that integrates supplemental data arising from multiple, possibly non-exchangeable, sources into the analysis of a primary source. We first describe the proposed framework and prove some desirable asymptotic properties that show the consistency of posterior estimation. Simulation results illustrate that MEMs incorporate more supplemental information in the presence of homogeneous supplemental sources and exhibit reduced bias in the presence of heterogeneous supplemental sources relative to competing Bayesian hierarchical modeling strategies. Next, we illustrate how MEMs can be used to design a more efficient sequential platform design for Ebola virus disease by sharing information across trial segments. When compared to the standard platform design, we demonstrate that MEMs with adaptive randomization improved power by as much as 51% with limited type-I error inflation. We conclude by extending our work with model averaging to the estimation of multiple mixture distributions in the presence of a hypothesized biological relationship between groups to identify non-compliance in a regulatory tobacco clinical trial. The results of this dissertation illustrate that MEMs yield favorable characteristics across a variety of scenarios and motivates further research to extend the MEM framework to other settings, as well

Intrathecal enzyme replacement for Hurler syndrome: biomarker association with neurocognitive outcomes.

PurposeAbnormalities in cerebrospinal fluid (CSF) have been reported in Hurler syndrome, a fatal neurodegenerative lysosomal disorder. While no biomarker has predicted neurocognitive response to treatment, one of these abnormalities, glycosaminoglycan nonreducing ends (NREs), holds promise to monitor therapeutic efficacy. A trial of intrathecal enzyme replacement therapy (ERT) added to standard treatment enabled tracking of CSF abnormalities, including NREs. We evaluated safety, biomarker response, and neurocognitive correlates of change.MethodsIn addition to intravenous ERT and hematopoietic cell transplantation, patients (N = 24) received intrathecal ERT at four peritransplant time points; CSF was evaluated at each point. Neurocognitive functioning was quantified at baseline, 1 year, and 2 years posttransplant. Changes in CSF biomarkers and neurocognitive function were evaluated for an association.ResultsOver treatment, there were significant decreases in CSF opening pressure, biomarkers of disease activity, and markers of inflammation. Percent decrease in NRE from pretreatment to final intrathecal dose posttransplant was positively associated with percent change in neurocognitive score from pretreatment to 2 years posttransplant.ConclusionIntrathecal ERT was safe and, in combination with standard treatment, was associated with reductions in CSF abnormalities. Critically, we report evidence of a link between a biomarker treatment response and neurocognitive outcome in Hurler syndrome

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LEGEND-1000 Preconceptual Design Report

We propose the construction of LEGEND-1000, the ton-scale Large Enriched Germanium Experiment for Neutrinoless $\beta \beta$ Decay. This international experiment is designed to answer one of the highest priority questions in fundamental physics. It consists of 1000 kg of Ge detectors enriched to more than 90% in the $^{76}$Ge isotope operated in a liquid argon active shield at a deep underground laboratory. By combining the lowest background levels with the best energy resolution in the field, LEGEND-1000 will perform a quasi-background-free search and can make an unambiguous discovery of neutrinoless double-beta decay with just a handful of counts at the decay $Q$ value. The experiment is designed to probe this decay with a 99.7%-CL discovery sensitivity in the $^{76}$Ge half-life of $1.3\times10^{28}$ years, corresponding to an effective Majorana mass upper limit in the range of 9-21 meV, to cover the inverted-ordering neutrino mass scale with 10 yr of live time

The noise-lovers: cultures of speech and sound in second-century Rome

This chapter provides an examination of an ideal of the ‘deliberate speaker’, who aims to reflect time, thought, and study in his speech. In the Roman Empire, words became a vital tool for creating and defending in-groups, and orators and authors in both Latin and Greek alleged, by contrast, that their enemies produced babbling noise rather than articulate speech. In this chapter, the ideal of the deliberate speaker is explored through the works of two very different contemporaries: the African-born Roman orator Fronto and the Syrian Christian apologist Tatian. Despite moving in very different circles, Fronto and Tatian both express their identity and authority through an expertise in words, in strikingly similar ways. The chapter ends with a call for scholars of the Roman Empire to create categories of analysis that move across different cultural and linguistic groups. If we do not, we risk merely replicating the parochialism and insularity of our sources.Accepted manuscrip

Approaches to analyzing binary data for large-scale A/B testing

An industry-academic collaboration was established to evaluate the choice of statistical test and study design for A/B testing in larger-scale industry experiments. Specifically, the standard approach at the industry partner was to apply a t-test for all outcomes, both continuous and binary, and to apply naïve interim monitoring strategies that had not evaluated the potential implications on operating characteristics such as power and type I error rates. Although many papers have summarized the robustness of the t-test, its performance for the A/B testing context of large-scale proportion data, with or without interim analyses, is needed. Investigating the effect of interim analyses on the robustness of the t-test is important, because interim analyses rely on a fraction of the total sample size and one should ensure that desired properties are maintained when a t-test is implemented not just at the end of the study, but for making interim decisions. Through simulation studies, the performance of the t-test, Chi-squared test, and Chi-squared test with Yate's correction when applied to binary outcomes data is evaluated. Further, interim monitoring through a naïve approach with no correction for multiple testing versus the O'Brien-Fleming boundary are considered in designs that allow early termination for futility, difference, or both. Results indicate that the t-test achieves similar power and type I error rates for binary outcomes data with the large sample sizes used in industrial A/B tests with and without interim monitoring, and naïve interim monitoring without corrections leads to poorly performing studies

Sublingual Sufentanil vs. Intravenous Fentanyl for the Treatment of Acute Postoperative Pain in the Ambulatory Surgery Center: A Randomized Clinical Trial

Objectives. Sublingual sufentanil is a novel opioid medication to treat moderate to severe pain postoperatively. This study’s aim was to determine if a single dose of a sublingual sufentanil tablet (SST) is as efficacious as a single dose of intravenous (IV) fentanyl in readiness to discharge from ambulatory surgery. Methods. This was a two-arm, parallel group, randomized prospective outcomes study conducted at a single, free-standing ambulatory surgery center. Patients aged 18–80 undergoing general anesthesia who developed a postoperative pain score of ≥ 4 were enrolled and randomized to receive either 30 mcg SST or 50 mcg IV fentanyl. After their initial randomized dose, rescue IV fentanyl followed by oral oxycodone if needed. Recovery length of stay from arrival in the postanesthesia care unit until readiness to discharge criteria was met based on phase 2 discharge criteria. Results. 75 patients were analyzed. Readiness to discharge from the recovery room was not significantly different between either group (IV fentanyl median 65 minutes; IQR 56–89; SST 73 min, IQR 58–89; p=0.903). There was no significant difference in the amount of morphine equivalents (MME) of rescue opioids needed (IV fentanyl median rescue MME of 22.5, IQR 13.1–23.4; SST median rescue MME of 15.0, IQR 7.5–30.0; p=0.742). The change in pain from PACU initially, and on discharge was not significantly different (IV fentanyl initial pain minus pain on discharge median 3, IQR 2–4; SST initial pain minus pain on discharge median 4, IQR 2–5.5; p=0.079). There was no difference in the six-item screener and the Overall Benefit of Analgesic Survey Score. Discussion. In conclusion, patients who received a sublingual sufentanil 30 mcg tablet had no significant differences in PACU length of stay or rescue analgesic usage when compared to intravenous fentanyl 50 mcg

Diagnostic performance of salivary pepsin for gastroesophageal reflux disease.

Uncertain diagnostic performance has limited clinical adoption of salivary pepsin, a noninvasive diagnostic tool for gastroesophageal reflux disease (GERD). This study aimed to assess diagnostic performance of salivary pepsin, and test validity of thresholds in an external cohort of patients with or without GERD. This two-phase prospective study conducted at two centers enrolled adult asymptomatic volunteers, patients with symptoms of GERD undergoing reflux monitoring, and patients with Barretts esophagus (BE). Fasting saliva samples were processed for pepsin concentration using Peptest. Phase 1 compared pepsin concentration between No GERD (volunteers/functional heartburn) and GERD (erosive reflux disease/nonerosive reflux disease (NERD)/BE). Phase 2 tested validity of the diagnostic thresholds identified from Phase 1 among external functional heartburn and NERD cohorts. Of 243 enrolled subjects, 156 met inclusion criteria. Phase 1 (n = 114): Pepsin concentrations were significantly higher in GERD (n = 84) versus No GERD (n = 30) (73.8 ng/mL vs. 21.1 ng/mL; P < 0.001). Area under the curve for pepsin concentration was 0.74 (95% CI 0.65, 0.83). A salivary pepsin threshold of 24.9 ng/mL optimized the true negative rate and 100.0 ng/mL optimized the true positive rate. Phase 2 (n = 42): Pepsin concentrations were significantly higher in NERD (n = 22) versus Functional Heartburn (n = 20) (176.0 ng/mL vs. 53.3 ng/mL, P < 0.001). Applying Phase 1 thresholds in this external cohort, salivary pepsin 24.9 ng/mL was 86% sensitive (64%, 97%) and 100.0 ng/mL was 72% specific for distinguishing NERD from functional heartburn. Given modest sensitivity and specificity for GERD, salivary pepsin may have clinical utility as a noninvasive office based diagnostic screening tool for GERD