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Evaluation Of Multiple Interventions Using A Stepped Wedge Design, Vivian H. Lyons, Lingyu Li, James Hughes, Ali Rowhani-Rahbar 2017 University of Washington - Seattle Campus

Evaluation Of Multiple Interventions Using A Stepped Wedge Design, Vivian H. Lyons, Lingyu Li, James Hughes, Ali Rowhani-Rahbar

UW Biostatistics Working Paper Series

Background: Stepped wedge cluster randomized trials are a class of unidirectional crossover studies that have historically been limited to evaluating a single intervention. This design is especially suitable for pragmatic trials where the study feasibility can be improved with a phased introduction of the intervention. We examined variations of stepped wedge designs that would support evaluation of multiple interventions. Methods: We propose four different design variants for implementing a stepped wedge trial with two interventions: concurrent design, supplementation, replacement, and factorial designs. Analyses were conducted comparing the precision of the estimated intervention effects for the different designs. Results: Concurrent, supplementation ...


Randomized Clinical Trial To Evaluate The Pathogenicity Of Bibersteinia Trehalosi In Respiratory Disease Among Calves, Christy Jo Hanthorn, Reneé Dewell, Vickie L. Cooper, Timothy S. Frana, Paul J. Plummer, Chong Wang, Grant A. Dewell 2017 Iowa State University

Randomized Clinical Trial To Evaluate The Pathogenicity Of Bibersteinia Trehalosi In Respiratory Disease Among Calves, Christy Jo Hanthorn, Reneé Dewell, Vickie L. Cooper, Timothy S. Frana, Paul J. Plummer, Chong Wang, Grant A. Dewell

Grant A. Dewell

Bibersteinia trehalosi causes respiratory disease in ruminants particularly in wild and domestic sheep. Recently, there has been an increased number of B. trehalosi isolates obtained from diagnostic samples from bovine respiratory disease cases. This study evaluated the role of B. trehalosi in bovine respiratory disease using an intra-tracheal inoculation model in calves. Thirty six cross bred 2–3 month old dairy calves were inoculated intra-tracheally with either leukotoxin negative B. trehalosi, leukotoxin positive B. trehalosi isolate, Mannheimia haemolytica, a combination of leukotoxin negative B. trehalosi and M. haemolytica or negative control. Calves were euthanized and necropsy performed on day 10 ...


Denoising Tandem Mass Spectrometry Data, Felix Offei 2017 East Tennessee State Universtiy

Denoising Tandem Mass Spectrometry Data, Felix Offei

Electronic Theses and Dissertations

Protein identification using tandem mass spectrometry (MS/MS) has proven to be an effective way to identify proteins in a biological sample. An observed spectrum is constructed from the data produced by the tandem mass spectrometer. A protein can be identified if the observed spectrum aligns with the theoretical spectrum. However, data generated by the tandem mass spectrometer are affected by errors thus making protein identification challenging in the field of proteomics. Some of these errors include wrong calibration of the instrument, instrument distortion and noise. In this thesis, we present a pre-processing method, which focuses on the removal of ...


Effect Of Immediate Initiation Of Antiretroviral Therapy On Risk Of Severe Bacterial Infections In Hiv-Positive People With Cd4 Cell Counts Of More Than 500 Cells Per Μl: Secondary Outcome Results From A Randomised Controlled Trial., Jemma O'Connor, Michael J Vjecha, Andrew N Phillips, Brian Angus, David Cooper, Fred Gordin, +several additional authors 2017 George Washington University

Effect Of Immediate Initiation Of Antiretroviral Therapy On Risk Of Severe Bacterial Infections In Hiv-Positive People With Cd4 Cell Counts Of More Than 500 Cells Per Μl: Secondary Outcome Results From A Randomised Controlled Trial., Jemma O'Connor, Michael J Vjecha, Andrew N Phillips, Brian Angus, David Cooper, Fred Gordin, +Several Additional Authors

Medicine Faculty Publications

BACKGROUND: The effects of antiretroviral therapy on risk of severe bacterial infections in people with high CD4 cell counts have not been well described. In this study, we aimed to quantify the effects of immediate versus deferred ART on the risk of severe bacterial infection in people with high CD4 cell counts in a preplanned analysis of the START trial.

METHODS: The START trial was a randomised controlled trial in ART-naive HIV-positive patients with CD4 cell count of more than 500 cells per μL assigned to immediate ART or deferral until their CD4 cell counts were lower than 350 cells ...


Adaptive Non-Inferiority Margins Under Observable Non-Constancy, Brett S. Hanscom, Deborah J. Donnell, Brian D. Williamson, Jim Hughes 2017 Fred Hutchinson Cancer Research Center

Adaptive Non-Inferiority Margins Under Observable Non-Constancy, Brett S. Hanscom, Deborah J. Donnell, Brian D. Williamson, Jim Hughes

UW Biostatistics Working Paper Series

A central assumption in the design and conduct of non-inferiority trials is that the active-control therapy will have the same degree of effectiveness in the planned non-inferiority trial as it had in the prior placebo-controlled trials used to define the non-inferiority margin. This is referred to as the `constancy' assumption. If the constancy assumption fails, the chosen non-inferiority margin is not valid and the study runs the risk of approving an inferior product or failing to approve a beneficial product. The constancy assumption cannot be validated in a trial without a placebo arm, and it is unlikely ever to be ...


A Comparison Of The Quality Of Informed Consent For Clinical Trials Of An Experimental Hookworm Vaccine Conducted In Developed And Developing Countries., David J. Diemert, Lucas Lobato, Ashley Styczynski, Maria Zumer, Amanda Soares, Maria Flávia Gazzinelli 2017 George Washington University

A Comparison Of The Quality Of Informed Consent For Clinical Trials Of An Experimental Hookworm Vaccine Conducted In Developed And Developing Countries., David J. Diemert, Lucas Lobato, Ashley Styczynski, Maria Zumer, Amanda Soares, Maria Flávia Gazzinelli

Microbiology, Immunology, and Tropical Medicine Faculty Publications

Informed consent is one of the principal ethical requirements of conducting clinical research, regardless of the study setting. Breaches in the quality of the informed consent process are frequently described in reference to clinical trials conducted in developing countries, due to low levels of formal education, a lack of familiarity with biomedical research, and limited access to health services in these countries. However, few studies have directly compared the quality of the informed consent process in developed and developing countries using the same tool and in similar clinical trials. This study was conducted to compare the quality of the informed ...


A Predictive Probability Interim Design For Phase Ii Clinical Trials With Continuous Endpoints, Meng Liu 2017 University of Kentucky

A Predictive Probability Interim Design For Phase Ii Clinical Trials With Continuous Endpoints, Meng Liu

Theses and Dissertations--Epidemiology and Biostatistics

Phase II clinical trials aim to potentially screen out ineffective and identify effective therapies to move forward to randomized phase III trials. Single-arm studies remain the most utilized design in phase II oncology trials, especially in scenarios where a randomized design is simply not practical. Due to concerns regarding excessive toxicity or ineffective new treatment strategies, interim analyses are typically incorporated in the trial, and the choice of statistical methods mainly depends on the type of primary endpoints. For oncology trials, the most common primary objectives in phase II trials include tumor response rate (binary endpoint) and progression disease-free survival ...


Update On Schizophrenia And Bipolar Disorder: Focus On Cariprazine, Rona Jeannie Roberts, Lillian Jan Findlay, Peggy El-Mallakh, Rif S. El-Mallakh 2016 University of Louisville

Update On Schizophrenia And Bipolar Disorder: Focus On Cariprazine, Rona Jeannie Roberts, Lillian Jan Findlay, Peggy El-Mallakh, Rif S. El-Mallakh

Nursing Faculty Publications

Schizophrenia and bipolar disorder are severe psychiatric disorders that are frequently associated with persistent symptoms and significant dysfunction. While there are a multitude of psychopharmacologic agents are available for treatment of these illnesses, suboptimal response and significant adverse consequences limit their utility. Cariprazine is a new, novel antipsychotic medication with dopamine D2 and D3 partial agonist effects. Its safety and efficacy have been investigated in acute psychosis of schizophrenia, bipolar mania, bipolar depression, and unipolar depression. Efficacy has been demonstrated in schizophrenia and mania. It is unclear if cariprazine is effective in depression associated with unipolar or bipolar illness. Adverse ...


Is The Force Awakened? Publication Trends In Oncology Big Data As Phase Ii Cancerlinq Is Launched, Hind Rafei, Benjamin Viernes, Angelike P. Liappis, Dalia Abdelaziz Mobarek 2016 George Washington University

Is The Force Awakened? Publication Trends In Oncology Big Data As Phase Ii Cancerlinq Is Launched, Hind Rafei, Benjamin Viernes, Angelike P. Liappis, Dalia Abdelaziz Mobarek

GW Research Days 2016 - Present

Background: The American Society of Clinical Oncology launched CancerLinQ project in 2010 to provide real-time data collection, mining and visualization, clinical decision support, and quality feedback. Creation of a big data software platform is currently underway to power the CancerLinQ in the phase II of the project. This would allow for evidence driven practice and rapid learning for cancer care providers. Additionally, adequate knowledge about the utility of Big Data to encourage provider utilization in high Impact Factor (IF) journals is needed. We aimed to assess trends and quality of Big Data published in Oncology.

Methods: Peer-reviewed English papers published ...


Randomized Clinical Trial To Evaluate The Pathogenicity Of Bibersteinia Trehalosi In Respiratory Disease Among Calves, Christy Jo Hanthorn, Reneé Dewell, Vickie L. Cooper, Timothy S. Frana, Paul J. Plummer, Chong Wang, Grant A. Dewell 2016 Iowa State University

Randomized Clinical Trial To Evaluate The Pathogenicity Of Bibersteinia Trehalosi In Respiratory Disease Among Calves, Christy Jo Hanthorn, Reneé Dewell, Vickie L. Cooper, Timothy S. Frana, Paul J. Plummer, Chong Wang, Grant A. Dewell

Paul Plummer

Bibersteinia trehalosi causes respiratory disease in ruminants particularly in wild and domestic sheep. Recently, there has been an increased number of B. trehalosi isolates obtained from diagnostic samples from bovine respiratory disease cases. This study evaluated the role of B. trehalosi in bovine respiratory disease using an intra-tracheal inoculation model in calves. Thirty six cross bred 2–3 month old dairy calves were inoculated intra-tracheally with either leukotoxin negative B. trehalosi, leukotoxin positive B. trehalosi isolate, Mannheimia haemolytica, a combination of leukotoxin negative B. trehalosi and M. haemolytica or negative control. Calves were euthanized and necropsy performed on day 10 ...


Models For Hsv Shedding Must Account For Two Levels Of Overdispersion, Amalia Magaret 2016 University of Washington - Seattle Campus

Models For Hsv Shedding Must Account For Two Levels Of Overdispersion, Amalia Magaret

UW Biostatistics Working Paper Series

We have frequently implemented crossover studies to evaluate new therapeutic interventions for genital herpes simplex virus infection. The outcome measured to assess the efficacy of interventions on herpes disease severity is the viral shedding rate, defined as the frequency of detection of HSV on the genital skin and mucosa. We performed a simulation study to ascertain whether our standard model, which we have used previously, was appropriately considering all the necessary features of the shedding data to provide correct inference. We simulated shedding data under our standard, validated assumptions and assessed the ability of 5 different models to reproduce the ...


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 2016 Shionogi & Co., Ltd.

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 ...


Missing Data In Clinical Trial: A Critical Look At The Proportionality Of Mnar And Mar Assumptions For Multiple Imputation, Theophile B. Dipita 2016 Georgia Southern University

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

Electronic 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 ...


Hyperoxia Increases Arterial Oxygen Pressure During Exercise In Type 2 Diabetes Patients: A Feasibility Study, Robert Rozenberg, Robert T. Mankowski, Luc van Loon, Janneke G. Langendonk, Eric J. G. Sijbrands, Anton H. van den Meiracker, Henk J. Stam, Stephan F. E. Praet 2016 Australian Catholic University

Hyperoxia Increases Arterial Oxygen Pressure During Exercise In Type 2 Diabetes Patients: A Feasibility Study, Robert Rozenberg, Robert T. Mankowski, Luc Van Loon, Janneke G. Langendonk, Eric J. G. Sijbrands, Anton H. Van Den Meiracker, Henk J. Stam, Stephan F. E. Praet

Faculty of Health Sciences Publications

Objective: The study investigated the feasibility and potential outcome measures during acute hyperoxia in type 2 diabetes patients ( DM2 ). Methods: Eleven DM2 patients ( 7 men and 4 women ) were included in the study. The patients cycled ( 30 min at 20 % Wmax ) whilst breathing three different supplemental oxygen flows ( SOF, 5, 10, 15 L min−1 ). During hyperoxic exercise, arterial blood gases and intra-arterial blood pressure measurements were obtained. Results: Arterial pO2 levels increased significantly ( ANOVA, p < 0.05 ) with SOF: 13.9 ± 1.2 ( 0 L min−1 ); 18.5 ± 1.5 ( 5 L min−1 ); 21.7 ± 1.7 ( 10 L min−1 ); 24.0 ± 2.3 ( 15 L min−1 ). Heart rate ( HR ) and pH increased significantly after terminating administration of hyperoxic air. Conclusions: An SOF of 15 L min−1 appears to be more effective than 5 or 10 L min−1. Moreover, HR, blood pressure, blood lactate and pH are not recommended as primary outcome measures.


Simulations Of A New Response-Adaptive Biased Coin Design, Aleksandra Stein 2015 University of Nebraska-Lincoln

Simulations Of A New Response-Adaptive Biased Coin Design, Aleksandra Stein

Dissertations and Theses in Statistics

Modern medical experiments accrue and treat patients--hence obtain treatment response data--throughout a trial. Designs which prospectively plan to modify patient allocation by leveraging accumulating data are response-adaptive randomization (RAR) designs. Many such designs attempt to balance the desire to bias assignment proportions towards a treatment which is performing better against the need to maintain randomization in the face of continued equipoise.

This dissertation consists of simulated investigations into frequentist and ethical properties of an new RAR biased coin design. Chapter 2 proposes a new adaptive design for phase III clinical trials, a modification of the 2001 Bandyopadhyay and Biswas biased ...


C-Learning: A New Classification Framework To Estimate Optimal Dynamic Treatment Regimes, Baqun Zhang, Min Zhang 2015 Renmin University of China, School of Statistics

C-Learning: A New Classification Framework To Estimate Optimal Dynamic Treatment Regimes, Baqun Zhang, Min Zhang

The University of Michigan Department of Biostatistics Working Paper Series

Personalizing treatment to accommodate patient heterogeneity and the evolving nature of a disease over time has received considerable attention lately. A dynamic treatment regime is a set of decision rules, each corresponding to a decision point, that determine that next treatment based on each individual’s own available characteristics and treatment history up to that point. We show that identifying the optimal dynamic treatment regime can be recast as a sequential classification problem and is equivalent to sequentially minimizing a weighted expected misclassification error. This general classification perspective targets the exact goal of optimally individualizing treatments and is new and ...


Simultaneously Optimizing Dose And Schedule Of A New Cytotoxic Agent, Thomas Braun, Peter Thall, Hoang Nguyen, Marcos de Lima 2015 University of Michigan

Simultaneously Optimizing Dose And Schedule Of A New Cytotoxic Agent, Thomas Braun, Peter Thall, Hoang Nguyen, Marcos De Lima

Peter F. Thall

Traditionally, phase I clinical trial designs determine a maximum tolerated dose of an experimental cytotoxic agent based on a fixed schedule, usually one course consisting of multiple administrations, while varying the dose per administration between patients. However, in actual medical practice patients often receive several courses of treatment, and some patients may receive one or more dose reductions due to low-grade (non-dose limiting) toxicity in previous courses. As a result, the overall risk of toxicity for each patient is a function of both the schedule and the dose used at each adminstration. We propose a new paradigm for Phase I ...


Assessing Usual Care In Clinical Trials, Judith A. Erlen, Lisa K. Tamres, Nancy Reynolds, Carol E. Golin, Marc I. Rosen, Robert H. Remien, Julie W. Banderas, Neil Schneiderman, Glenn Wagner, David Bangsberg, Honghu Liu 2015 University of Pittsburgh School of Nursing

Assessing Usual Care In Clinical Trials, Judith A. Erlen, Lisa K. Tamres, Nancy Reynolds, Carol E. Golin, Marc I. Rosen, Robert H. Remien, Julie W. Banderas, Neil Schneiderman, Glenn Wagner, David Bangsberg, Honghu Liu

OHSU-PSU Joint School of Public Health Faculty Publications and Presentations

Researchers designing clinical trials often specify usual care received by participants as the control condition expecting that all participants receive usual care regardless of group assignment. The assumption is that the groups in the study are affected similarly. We describe the assessment of usual care within the 16 studies in MACH 14, a multi-site collaboration on adherence to antiretroviral therapy. Only five of the studies in MACH 14 assessed usual care. Assessment protocols varied as did the timing and frequency of assessments. All usual care assessments addressed patient education focused on HIV, HIV medications, and medication adherence. Our findings support ...


A Novel Multi-Tissue Rna Diagnostic Of Healthy Ageing Relates To Cognitive Health Status, Sanjana Sood, Iain J. Gallagher, Katie Lunnon, Eric Rullman, Aoife Keohane, Hannah Crossland, Bethan E. Phillips, Tommy Cederholm, Thomas E. Jensen, Luc J. C. van Loon, Lars Lannfelt, William E. Kraus, Philip J. Atherton, Robert Howard, Thomas Gustafsson, Angela Hodges, James A. Timmons 2015 Australian Catholic University

A Novel Multi-Tissue Rna Diagnostic Of Healthy Ageing Relates To Cognitive Health Status, Sanjana Sood, Iain J. Gallagher, Katie Lunnon, Eric Rullman, Aoife Keohane, Hannah Crossland, Bethan E. Phillips, Tommy Cederholm, Thomas E. Jensen, Luc J. C. Van Loon, Lars Lannfelt, William E. Kraus, Philip J. Atherton, Robert Howard, Thomas Gustafsson, Angela Hodges, James A. Timmons

Faculty of Health Sciences Publications

Background: Diagnostics of the human ageing process may help predict future healthcare needs or guide preventative measures for tackling diseases of older age. We take a transcriptomics approach to build the first reproducible multi-tissue RNA expression signature by gene-chip profiling tissue from sedentary normal subjects who reached 65 years of age in good health. Results: One hundred and fifty probe-sets form an accurate classifier of young versus older muscle tissue and this healthy ageing RNA classifier performed consistently in independent cohorts of human muscle, skin and brain tissue ( n = 594, AUC = 0.83–0.96 ) and thus represents a biomarker ...


The Effect Of Exercise Training On The Course Of Cardiac Troponin T And I Levels: Three Independent Training Studies, Noreen van der Linden, Lieke J. J. Klinkenberg, Marika Leenders, Michael Tieland, Lex B. Verdijk, Marijke Niens, Jeroen D. E. van Suijlen, Lisette C. P. G. M. de Groot, Otto Bekers, Luc J. C. van Loon, Marja P. van Dieijen-Visser, Steven J. R. Meex 2015 Australian Catholic University

The Effect Of Exercise Training On The Course Of Cardiac Troponin T And I Levels: Three Independent Training Studies, Noreen Van Der Linden, Lieke J. J. Klinkenberg, Marika Leenders, Michael Tieland, Lex B. Verdijk, Marijke Niens, Jeroen D. E. Van Suijlen, Lisette C. P. G. M. De Groot, Otto Bekers, Luc J. C. Van Loon, Marja P. Van Dieijen-Visser, Steven J. R. Meex

Faculty of Health Sciences Publications

With the introduction of high-sensitive assays, cardiac troponins became potential biomarkers for risk stratification and prognostic medicine. Observational studies have reported an inverse association between physical activity and basal cardiac troponin levels. However, causality has never been demonstrated. This study investigated whether basal cardiac troponin concentrations are receptive to lifestyle interventions such as exercise training. Basal high-sensitive cardiac troponin T ( cTnT ) and I ( cTnI ) were monitored in two resistance-type exercise training programs ( 12-week ( study 1 ) and 24-week ( study 2 ) ) in older adults ( ≥65 years ). In addition, a retrospective analysis for high sensitive troponin I in a 24-week exercise controlled trial ...


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