Survival Analysis Commons^™

Novel R Shiny Tool For Survival Analysis With Time-Varying Covariate In Oncology Studies: Overcoming Biases And Enhancing Collaboration, Yimei Li, Yang Qiao, Fei Gao, Jordan Gauthier, Qiang Ed Zhang, Jenna Voutsinas, Wendy Leisenring, Ted Gooley, Corinne Summers, Alexandre Hirayama, Cameron Turtle, Rebecca Gardner, Jarcy Zee, Qian Vicky Wu

Wills Eye Hospital Papers

PURPOSE: Our study is motivated by evaluating the role of hematopoietic cell transplantation (HCT) after chimeric antigen receptor T-cell (CAR-T) therapy for ALL, a debated topic. Because patients may receive HCT at different times after CAR-T infusion or never, HCT post-CAR-T should be considered as a time-varying covariate (TVC).

METHODS: Standard Cox models and Kaplan-Meier (KM) curves (naïve method) assume that TVC status is known and fixed at baseline, which can yield biased estimates. Landmark analysis is a popular alternative but depends on a chosen landmark time. Time-dependent (TD) Cox model is better suited for TVC although visualizing survival curves …

Modeling Musculoskeletal Combat Casualty Care: Nato Trauma System Performance In Large Scale Combat Operations, Mark P. Cote, Kaitlyn E. Holly, Roman J. Schoenfeld, Matthew R. Bryan, Malina O. Hatton, Mitchel B. Harris, Tracey P. Koehlmoos, Andrew J. Schoenfeld

Department of Orthopaedic Surgery Faculty Papers

BACKGROUND: It is unclear whether the current North Atlantic Treaty Organization (NATO) trauma system will be effective in the setting of Large-Scale Combat Operations (LSCO). We sought to model the efficacy of the NATO trauma system in the setting of LSCO. We also intended to model novel scenarios that could better adapt the current system to LSCO.

METHODS: We developed a discrete-event simulation model for patients with combat musculoskeletal injuries treated within the standard NATO system. The primary outcome of the model was survival. The model's health states were characterized as stable, hypovolemia, sepsis, shock, or death. The model simulated …

Pediatric Renal Cell Carcinoma (Prcc) Subpopulation Environmental Differentials In Survival Disadvantage Of Black/African American Children In The United States: Large-Cohort Evidence, Laurens Holmes, Phatismo Masire, Arieanna Eaton, Robert Mason, Mackenzie Holmes, Justin William, Maura Poleon, Michael Enwere

College of Population Health Faculty Papers

OBJECTIVE: Renal cell carcinoma (RCC) is a rare but severe and aggressive pediatric malignancy. While incidence is uncommon, survival is relatively low with respect to acute lymphocytic leukemia (ALL), AML, lymphoma, ependymoma, glioblastoma, and Wilms Tumor. The pediatric renal cell carcinoma (pRCC) incidence, cumulative incidence (period prevalence), and mortality vary by health disparities' indicators, namely sex, race, ethnicity, age at tumor diagnosis, and social determinants of health (SDHs) as well as Epigenomic Determinants of Health (EDHs). However, studies are unavailable on some pRCC risk determinants, such as area of residence and socio-economic status (SES). The current study aimed at assessing …

Outpatient Fall Prevention In Ambulatory Adults 65 Years Old And Over, Dorothy L. Osborne-White

Doctor of Nursing Practice (DNP) Scholarly Projects - Archive

Background: In the United States (U.S.), falls are the leading cause of injury among adults 65 and over, resulting in 36 million falls yearly (Moreland et al., 2020). According to the Centers for Disease Control and Prevention (CDC, 2023), one in four older adults experiences a fall each year. Falls are the world's second most prominent cause of accidental deaths (World Health Organization [WHO], 2021). Falls are the leading cause of both fatal and non-fatal injuries among older adults (Moreland et al., 2020).

Methods: A quality improvement project that included a fall bundle was implemented in a primary clinic. A …

Applications Of Causal Inference Methods For The Estimation Of Effects Of Bone Marrow Transplant And Prescription Drugs On Survival Of Aplastic Anemia Patients, Yesha M. Patel

Computational and Data Sciences (PhD) Dissertations

This dissertation provides an in-depth exploration into the treatment effectiveness for aplastic anemia using causal inference methods, structured around three pivotal research papers. Each paper contributes to a nuanced understanding of treatment impacts, specifically focusing on bone marrow transplantation (BMT) and prescription drugs, and the identification of optimal treatment strategies.

The first paper, "Causal Inference Analysis for Assessing the Effect of Bone Marrow Transplantation on the One-Year Survival of Adult and Pediatric Aplastic Anemia Patients," sets the foundation. It examines the short-term effectiveness of BMT in both adult and pediatric patients, providing crucial insights into how this treatment affects survival …

Addressing The Analytical And Computational Challenges Using Machine Learning In Biomedical Research, Yizhuo Wang

Dissertations and Theses (Open Access)

In the contemporary healthcare field, professionals are confronted with an ever-growing volume of clinical data stored in electronic health records, alongside the genomic data stemming from laboratory experiments. As a response to this deluge of data, the application of machine learning (ML) techniques is gaining popularity since ML techniques have demonstrated an exceptional proficiency in processing big data and deciphering complex nonlinear patterns that are intrinsic to biomedical research.

My research leverages ML's capabilities to address the computational challenges spanning diverse areas, including adaptive clinical trial designs, survival analysis, and high-dimensional genetic data analysis. Specifically, Chapter 2 focused on the …

Striving For Appropriate Antibiotic Use: A Biomarker Initiative, And Outcomes Associated With Azithromycin Exposure, Amanda Gusovsky

Theses and Dissertations--Pharmacy

The introduction of antibiotics into clinical practice is considered the greatest medical breakthrough of the 20^thcentury. However, the use of antibiotics can contribute to the development of resistance. In the United States (U.S.), approximately 2.8 million people are infected with antibiotic-resistant bacteria each year, and more than 35,000 people die as a result. Moreover, some antibiotics are known to cause cardiac side effects including QT prolongation, hypotension, and ventricular arrythmias. The U.S. Centers for Disease Control and Prevention (CDC) defines appropriate antibiotic use as the effort to use “the right antibiotic, at the right dose, for the right …

Infrastructure Development For Personalized Risk Prediction To Reduce Cardiovascular Disease In Childhood Cancer Survivors, Suman Shrestha

Dissertations and Theses (Open Access)

Although childhood cancer survivors have lengthy life expectancies, they run the risk of experiencing long-term health issues as a result of their treatment. The most frequent non-cancerous cause of morbidity and mortality for these survivors is cardiac disease. Radiation therapy (RT) has been linked in numerous cohort studies to a higher chance of developing a late cardiac disease in these survivors, and this risk rises with higher mean heart doses and increased RT exposure to larger cardiac volumes. Since, the heart is a heterogeneous organ made up of several distinct substructures, RT dose received by the entire heart does not …

Sars-Cov-2 Pandemic Analytical Overview With Machine Learning Predictability, Anthony Tanaydin, Jingchen Liang, Daniel W. Engels

SMU Data Science Review

Understanding diagnostic tests and examining important features of novel coronavirus (COVID-19) infection are essential steps for controlling the current pandemic of 2020. In this paper, we study the relationship between clinical diagnosis and analytical features of patient blood panels from the US, Mexico, and Brazil. Our analysis confirms that among adults, the risk of severe illness from COVID-19 increases with pre-existing conditions such as diabetes and immunosuppression. Although more than eight months into pandemic, more data have become available to indicate that more young adults were getting infected. In addition, we expand on the definition of COVID-19 test and discuss …

Effects Of Perioperative Hyperglycemia In Patients With Diabetes Compared To Patients Without Diabetes: A Retrospective Study Of Treatment And Outcomes, Matthew Anderson

Capstone Experience: Master of Public Health

The main goal of this project was to examine the differences in perioperative hyperglycemia treatment received by patients with a diagnosis of diabetes mellitus (DM) and patients without a diagnosis of diabetes (NDM); and how these treatment differences can affect the length of hospital stay. Studies have revealed that, when comparing DM and NDM patients with the same degree of perioperative hyperglycemia, NDM patients suffer worse outcomes. It has been suggested in previous research that this may be because NDM patients receive treatment that does not measure up to the standard of care treatment that DM patients receive. In this …

Statistical Methods For Two Problems In Cancer Research: Analysis Of Rna-Seq Data From Archival Samples And Characterization Of Onset Of Multiple Primary Cancers, Jialu Li

Dissertations and Theses (Open Access)

My dissertation is focused on quantitative methodology development and application for two important topics in translational and clinical cancer research.

The first topic was motivated by the challenge of applying transcriptome sequencing (RNA-seq) to formalin-fixation and paraffin-embedding (FFPE) tumor samples for reliable diagnostic development. We designed a biospecimen study to directly compare gene expression results from different protocols to prepare libraries for RNA-seq from human breast cancer tissues, with randomization to fresh-frozen (FF) or FFPE conditions. To comprehensively evaluate the FFPE RNA-seq data quality for expression profiling, we developed multiple computational methods for assessment, such as the uniformity and continuity …

Conditional Screening For Ultra-High Dimensional Covariates With Survival Outcomes, Hyokyoung Grace Hong, Jian Kang, Yi Li

The University of Michigan Department of Biostatistics Working Paper Series

Identifying important biomarkers that are predictive for cancer patients' prognosis is key in gaining better insights into the biological influences on the disease and has become a critical component of precision medicine. The emergence of large-scale biomedical survival studies, which typically involve excessive number of biomarkers, has brought high demand in designing efficient screening tools for selecting predictive biomarkers. The vast amount of biomarkers defies any existing variable selection methods via regularization. The recently developed variable screening methods, though powerful in many practical setting, fail to incorporate prior information on the importance of each biomarker and are less powerful in …

Multilevel Analysis Of Individual, Neighborhood, And Health Care Facility Characteristics Associated With Achievement And Maintenance Of Hiv Viral Suppression Among Persons Newly Diagnosed With Hiv In New York City, Ellen W. Wiewel

Dissertations, Theses, and Capstone Projects

Objective

To investigate the effect of individual, health care facility, and neighborhood characteristics on achievement and maintenance of HIV viral suppression, among New York City residents aged 13 years and older diagnosed with HIV between 2006 and 2012.

Methods

I used individual-level data from the New York City HIV surveillance registry and Case Surveillance-Based Sampling, facility-level data from the surveillance registry, and neighborhood-level data from the U.S. Census and American Community Survey. The outcomes of interest were first viral suppression after diagnosis (Aims 1 and 3; ≤400 copies/mL) and virologic failure after first suppression among persons who achieved suppression (Aim …

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 …

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.

The Association Between The Il-1 Pathway, Isaac C. Wun

Dissertations and Theses (Open Access)

Cutaneous malignant melanoma (CMM) is a potentially lethal malignancy that warrants attention and further research, as it is known to that there is an increasing rate of incidence in theUnited States, and it is also known that exposure to UV light is its most crucial risk factor, and family history of melanoma is also an important risk factor. Melanoma is an aggressive and lethal cancer in humans. There are an estimated new 132,000 melanoma cases annually worldwide, and the trend has doubled in the past 20 years. However, attempts to treat melanoma have encountered considerable resistance and remained ineffective. The …

Renal Cryoablation: Investigation Of Periprocedural Visualization To Ols And Treatment Response Quantification, Katherine L. Dextraze

Dissertations and Theses (Open Access)

Cryoablation for small renal tumors has demonstrated sufficient clinical efficacy over the past decade as a non-surgical nephron-sparing approach for treating renal masses for patients who are not surgical candidates. Minimally invasive percutaneous cryoablations have been performed with image guidance from CT, ultrasound, and MRI. During the MRI-guided cryoablation procedure, the interventional radiologist visually compares the iceball size on monitoring images with respect to the original tumor on separate planning images. The comparisons made during the monitoring step are time consuming, inefficient and sometimes lack the precision needed for decision making, requiring the radiologist to make further changes later in …

Evaluation Of The Survival Effect For Various Treatment Modalities Among Stage Ii And Iii Rectal Cancer Patients In California, 1994-2009, Myung Mi Cho

Loma Linda University Electronic Theses, Dissertations & Projects

Background: European trials evaluating the effect of preoperative (PreOP) versus postoperative chemoradiotherapy (PostOP CRT) found no survival benefit. However, the effect of a change from PostOP to PreOP CRT has not been evaluated in a population-based setting. We sought to evaluate multimodal treatment changes and overall survival for perioperative (PeriOP) CRT versus surgery alone and for PreOP versus PostOP CRT from 1994 through 2009 among patients receiving radical surgery for stage II and III rectal cancer (RC).

Patients and Methods: We conducted a nonconcurrent cohort study evaluating demographic predictors of multimodal therapy for stage II and III RC using …

Assessing Association For Bivariate Survival Data With Interval Sampling: A Copula Model Approach With Application To Aids Study, Hong Zhu, Mei-Cheng Wang

Johns Hopkins University, Dept. of Biostatistics Working Papers

In disease surveillance systems or registries, bivariate survival data are typically collected under interval sampling. It refers to a situation when entry into a registry is at the time of the first failure event (e.g., HIV infection) within a calendar time interval, the time of the initiating event (e.g., birth) is retrospectively identified for all the cases in the registry, and subsequently the second failure event (e.g., death) is observed during the follow-up. Sampling bias is induced due to the selection process that the data are collected conditioning on the first failure event occurs within a time interval. Consequently, the …

A Regularization Corrected Score Method For Nonlinear Regression Models With Covariate Error, David M. Zucker, Malka Gorfine, Yi Li, Donna Spiegelman

Harvard University Biostatistics Working Paper Series

No abstract provided.

Threshold Regression Models Adapted To Case-Control Studies, And The Risk Of Lung Cancer Due To Occupational Exposure To Asbestos In France, Antoine Chambaz, Dominique Choudat, Catherine Huber, Jean-Claude Pairon, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

Asbestos has been known for many years as a powerful carcinogen. Our purpose is quantify the relationship between an occupational exposure to asbestos and an increase of the risk of lung cancer. Furthermore, we wish to tackle the very delicate question of the evaluation, in subjects suffering from a lung cancer, of how much the amount of exposure to asbestos explains the occurrence of the cancer. For this purpose, we rely on a recent French case-control study. We build a large collection of threshold regression models, data-adaptively select a better model in it by multi-fold likelihood-based cross-validation, then fit the …

Landmark Prediction Of Survival, Layla Parast, Tianxi Cai

Harvard University Biostatistics Working Paper Series

No abstract provided.

Improving Statistical Analysis Of Prospective Clinical Trials In Stem Cell Transplantation. An Inventory Of New Approaches In Survival Analysis, Aurelien Latouche

COBRA Preprint Series

The CLINT project is an European Union funded project, run as a specific support action, under the sixth framework programme. It is a 2 year project aimed at supporting the European Group for Blood and Marrow Transplantation (EBMT) to develop its infrastructure for the conduct of trans-European clinical trials in accordance with the EU Clinical Trials Directive, and to facilitate International prospective clinical trials in stem cell transplantation. The initial task is to create an inventory of the existing biostatistical literature on new approaches to survival analyses that are not currently widely utilised. The estimation of survival endpoints is introduced, …

Survival Analysis With Error-Prone Time-Varying Covariates: A Risk Set Calibration Approach, Xiaomei Liao, David M. Zucker, Yi Li, Donna Spiegelman

Harvard University Biostatistics Working Paper Series

No abstract provided.

Neurodevelopmental Outcome & Mr Spectroscopy Of Therapeutic Hypothermia After Pediatric Drowning, Sharon Mieras Perugini

Loma Linda University Electronic Theses, Dissertations & Projects

Despite advances in medical treatment and technology, outcome following pediatric drowning can vary widely from mild to severe impairments and death. Prognosis is often difficult to predict given a number of contributing factors. As such, this study examined the relationship between clinical indicators including submersion duration, initial GCS and PRISM scores, and waking time with outcome as well as metabolite ratios based on magnetic resonance spectroscopy. Research stemming from the area of cardiac arrest as well as anecdotal case study reports of cold water drownings suggests that lowering the body temperature may be helpful and protective. As such, the use …

Comparing Risk Scoring Systems Beyond The Roc Paradigm In Survival Analysis, Hajime Uno, Lu Tian, Tianxi Cai, Isaac S. Kohane, L. J. Wei

Harvard University Biostatistics Working Paper Series

No abstract provided.

Analysis Of Randomized Comparative Clinical Trial Data For Personalized Treatment Selections, Tianxi Cai, Lu Tian, Peggy H. Wong, L. J. Wei

Harvard University Biostatistics Working Paper Series

No abstract provided.

Calibrating Parametric Subject-Specific Risk Estimation, Tianxi Cai, Lu Tian, Hajime Uno, Scott D. Solomon, L. J. Wei

Harvard University Biostatistics Working Paper Series

No abstract provided.

Joint Spatial Modeling Of Recurrent Infection And Growth With Processes Under Intermittent Observation, Farouk S. Nathoo

COBRA Preprint Series

In this article we present new statistical methodology for longitudinal studies in forestry where trees are subject to recurrent infection and the hazard of infection depends on tree growth over time. Understanding the nature of this dependence has important implications for reforestation and breeding programs. Challenges arise for statistical analysis in this setting with sampling schemes leading to panel data, exhibiting dynamic spatial variability, and incomplete covariate histories for hazard regression. In addition, data are collected at a large number of locations which poses computational difficulties for spatiotemporal modeling. A joint model for infection and growth is developed; wherein, a …

Nonparametric Regression Using Local Kernel Estimating Equations For Correlated Failure Time Data, Zhangsheng Yu, Xihong Lin

Harvard University Biostatistics Working Paper Series

No abstract provided.