Medical Biomathematics and Biometrics Commons^™

Uncertainty Of 1-D Fluid Models In Patients With Pulmonary Hypertension, Mitchel J. Colebank

Biology and Medicine Through Mathematics Conference

No abstract provided.

Detecting And Evaluating Therapy Induced Changes In Radiomics Features Measured From Non-Small Cell Lung Cancer To Predict Patient Outcomes, Xenia J. Fave

Dissertations and Theses (Open Access)

The purpose of this study was to investigate whether radiomics features measured from weekly 4-dimensional computed tomography (4DCT) images of non-small cell lung cancers (NSCLC) change during treatment and if those changes are prognostic for patient outcomes or dependent on treatment modality. Radiomics features are quantitative metrics designed to evaluate tumor heterogeneity from routine medical imaging. Features that are prognostic for patient outcome could be used to monitor tumor response and identify high-risk patients for adaptive treatment. This would be especially valuable for NSCLC due to the high prevalence and mortality of this disease.

A novel process was designed to …

Mathematical Models Of The Inflammatory Response In The Lungs, Sarah B. Minucci

Theses and Dissertations

Inflammation in the lungs can occur for many reasons, from bacterial infections to stretch by mechanical ventilation. In this work we compare and contrast various mathematical models for lung injuries in the categories of acute infection, latent versus active infection, and particulate inhalation. We focus on systems of ordinary differential equations (ODEs), agent-based models (ABMs), and Boolean networks. Each type of model provides different insight into the immune response to damage in the lungs. This knowledge includes a better understanding of the complex dynamics of immune cells, proteins, and cytokines, recommendations for treatment with antibiotics, and a foundation for more …

Assessing The Potential Clinical Impact Of Variable Biological Effectiveness In Proton Radiotherapy, Christopher R. Peeler Ph.D.

Dissertations and Theses (Open Access)

It has long been known that proton radiotherapy has an increased biological effectiveness compared to traditional x-ray radiotherapy. This arises from the clustered nature of DNA damage produced by the energy deposition of protons along their tracks in medium. This effect is currently quantified in clinical settings by assigning protons a relative biological effectiveness (RBE) value of 1.1 corresponding to 10% increased effectiveness compared to photon radiation. Numerous studies have shown, however, that the RBE value of protons is variable and can deviate substantially from 1.1, but experimental data on RBE and clinical evidence of its variability remains limited.

The …

The Effects Of Scarring On Face Recognition, Kevin J. Chan

Open Access Theses

The focus of this research is the effects of scarring on face recognition. Face recognition is a common biometric modality implemented for access control operations such as customs and borders. The recent report from the Special Group on Issues Affecting Facial Recognition and Best Practices for their Mitigation highlighted scarring as one of the emerging challenges. The significance of this problem extends to the ISO/IEC and national agencies are researching to enhance their intelligence capabilities. Data was collected on face images with and without scars, using theatrical special effects to simulate scarring on the face and also from subjects that …

A Comparison Of Stride Length And Lower Extremity Kinematics During Barefoot And Shod Running In Well Trained Distance Runners, Peter Francis, James Ledingham, Sarah B. Clarke Phd, Dj Collins, Philip Jakeman

Journal Articles

Stride length, hip, knee and ankle angles were compared during barefoot and shod running on a treadmill at two speeds. Nine well-trained (1500m time: 3min:59.80s ± 14.7 s) male (22 ±3 years; 73 ±9 kg; 1.79 ±0.4 m) middle distance (800 m – 5,000 m) runners performed 2 minutes of running at 3.05 m·s^-1 and 4.72 m·s^-1 on an treadmill. This approach allowed continuous measurement of lower extremity kinematic data and calculation of stride length. Statistical analysis using a 2X2 factorial ANOVA revealed speed to have a main effect on stride length and hip angle and footwear to …

Snpredict: A Machine Learning Approach For Detecting Low Frequency Variants In Cancer, Vatsal Mehra

Master's Theses (2009 -)

Cancer is a genetic disease caused by the accumulation of DNA variants such as single nucleotide changes or insertions/deletions in DNA. DNA variants can cause silencing of tumor suppressor genes or increase the activity of oncogenes. In order to come up with successful therapies for cancer patients, these DNA variants need to be identified accurately. DNA variants can be identified by comparing DNA sequence of tumor tissue to a non-tumor tissue by using Next Generation Sequencing (NGS) technology. But the problem of detecting variants in cancer is hard because many of these variant occurs only in a small subpopulation of …

Mathematical Models Of Hiv And Hpv Coinfection, Samantha Erwin, Meghna Verma, Vida Abedi, Raquel Hontecillas-Magarzo, Stefan Hoops, Josep Bassaganya-Riera, Stanca M. Ciupe

Biology and Medicine Through Mathematics Conference

No abstract provided.

Strategies Of Balancing: Regulation Of Posture As A Complex Phenomenon, Allison Leich Hilbun

Electronic Theses and Dissertations

The complexity of the interface between the muscular system and the nervous system is still elusive. We investigated how the neuromuscular system functions and how it is influenced by various perturbations. Postural stability was selected as the model system, because this system provides complex output, which could indicate underlying mechanisms and feedback loops of the neuromuscular system. We hypothesized that aging, physical pain, and mental and physical perturbations affect balancing strategy, and based on these observations, we constructed a model that simulates many aspects of the neuromuscular system. Our results show that aging changes the control strategy of balancing from …

Mathematical Modeling Of Blood Coagulation, Joana L. Perdomo

HMC Senior Theses

Blood coagulation is a series of biochemical reactions that take place to form a blood clot. Abnormalities in coagulation, such as under-clotting or over- clotting, can lead to significant blood loss, cardiac arrest, damage to vital organs, or even death. Thus, understanding quantitatively how blood coagulation works is important in informing clinical decisions about treating deficiencies and disorders. Quantifying blood coagulation is possible through mathematical modeling. This review presents different mathematical models that have been developed in the past 30 years to describe the biochemistry, biophysics, and clinical applications of blood coagulation research. This review includes the strengths and limitations …

Power Analysis In Applied Linear Regression For Cell Type-Specific Differential Expression Detection, Edmund Glass

Theses and Dissertations

The goal of many human disease-oriented studies is to detect molecular mechanisms different between healthy controls and patients. Yet, commonly used gene expression measurements from any tissues suffer from variability of cell composition. This variability hinders the detection of differentially expressed genes and is often ignored. However, this variability may actually be advantageous, as heterogeneous gene expression measurements coupled with cell counts may provide deeper insights into the gene expression differences on the cell type-specific level. Published computational methods use linear regression to estimate cell type-specific differential expression. Yet, they do not consider many artifacts hidden in high-dimensional gene expression …

Interaction Of Alu Polymorphisms And Novel Measures Of Discrimination In Association With Blood Pressure In African Americans Living In Tallahassee, Alexis C. Boulter, Jackyn Quinlan, Aida T. Miró-Herrans, Laurel N. Pearson, Nubiana L. Todd, Clarence C. Gravlee, Connie J. Mulligan

Human Biology Open Access Pre-Prints

African Americans are 40% more likely to be afflicted with hypertension in comparison to non-Hispanic, white Americans, resulting in a 30% higher instance of mortality due to cardiovascular disease. There is debate about the relative contributions of genetic and sociocultural risk factors to the racial disparity in hypertension.

We assayed three Alu insertion polymorphisms located in the angiotensin-1-converting enzyme (ACE), tissue plasminogen activator (PLAT), and with no-lysine kinase 1 (WNK1) genes. We also estimated West African genetic ancestry and developed novel measures of perceived discrimination to create a biocultural model of blood pressure among …

Mathematical Modeling And Simulations Of The Pathophysiology Of Type-2 Diabetes Mellitus, Frank K. Nani, Mingxian Jin

Math and Computer Science Faculty Working Papers

The pathophysiology of Type 2 Diabetes Mellitus (T2DM) is modelled using a coupled system of non-linear deterministic differential equations. An attempt is made to construct to a clinically plausible mathematical model that incorporates the homeostasis associated with endocrinological regulation of glucose and glycogen levels in the human body, by the hormones, insulin and glucagon. The model variables include the concentrations of glucose in the venous blood plasma, the concentration of glycogen in the liver/tissues, the concentration of the hormone glucagon, and the concentration of insulin in the venous blood plasma. The physiological interactions between the model parameters are depicted by …

Nonparametric Inference In Hidden Markov Models Using P-Splines, Roland Langrock, Thomas Kneib, Alexander Sohn, Stacy L. Deruiter

University Faculty Publications and Creative Works

Hidden Markov models (HMMs) are flexible time series models in which the distribution of the observations depends on unobserved serially correlated states. The state-dependent distributions in HMMs are usually taken from some class of parametrically specified distributions. The choice of this class can be difficult, and an unfortunate choice can have serious consequences for example on state estimates, and more generally on the resulting model complexity and interpretation. We demonstrate these practical issues in a real data application concerned with vertical speeds of a diving beaked whale, where we demonstrate that parametric approaches can easily lead to overly complex state …

An Association Study Between Adult Blood Pressure And Time To First Cardiovascular Disease, Yongjia Pu

Theses and Dissertations

BACKGROUND: Several studies have demonstrated the association between the time to hypertension event and multiple baseline measurements for adults, yet other survival cardiovascular disease (CVD) outcomes such as high cholesterol and heart attack have been somewhat less considered. The Fels Longitudinal Study (FLS) provides us an opportunity to connect adult blood pressure (BP) at certain ages to the time to first CVD outcomes. The availability of long-term serial BP measurements from FLS also potentially allows us to evaluate if the trend of the measured BP biomarkers over time predicts survival outcomes in adulthood through statistical modeling.

METHODS: When the reference …

Stratified Meta-Analysis To Examine Data Biases In Lung Cancer Studies Of Refinery Workers, Sherman Selix

Yale Day of Data

Petroleum refineries employ a variety of workers who historically experienced different potentials for asbestos exposure depending on job tasks. Associations between petroleum refinery work and lung cancer related to occupational asbestos exposure have been quantified among various locations, corporations, and time periods. To combine the data from several individual refinery studies and examine an overall effect, a systematic review and stratified meta-analysis was employed. Using set search terms among four databases, 112 potential publications were identified, of which 29 qualified for meta-analysis. Risk estimates and confidence intervals were extracted from these publications to construct four separate datasets. Inverse variance weighting …

Dose Expansion Cohorts In Phase I Trials, Alexia Iasonos, John O'Quigley

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

A rapidly increasing number of Phase I dose-finding studies, and in particular those based on the standard 3+3 design, frequently prolong the study and include dose expansion cohorts (DEC) with the goal to better characterize the toxicity profiles of experimental agents and to study disease specific cohorts. These trials consist of two phases: the usual dose escalation phase that aims to establish the maximum tolerated dose (MTD) and the dose expansion phase that accrues additional patients, often with different eligibility criteria, and where additional information is being collected. Current protocols typically do not specify whether the MTD will be updated …

Health Care Information Technology: Securing The Electronic Health Record With Biometric Technology, Alyssa Iacona

The Review: A Journal of Undergraduate Student Research

The principal focus of this paper is to examine the integration of biometric technology into healthcare’s information technology systems. Biometric technology, a rapidly evolving mechanism, analyzes specific anatomical and physiological features of an individual for identity verification (Perrin, 2002). Moreover, as the federal government has mandated all health records to be electronic in 2014, the implementation of biometrics has become a prevalent means of security. In an effort to adhere to the patient privacy laws authorized by the Health Insurance Portability and Accountability Act (HIPAA), biometric recognition is currently used to restrict access to verified health care providers and detect …

Tibial Tubercle Transfer To Correct Bilateral Patellar Tendinopathy In A Collegiate Football Player, Andrew D. Hamstra

Boise State University Theses and Dissertations

Objective: To present a case of a competitive football player with chronic patellar tendinopathy and the associated bilateral tibial tubercle transfer surgeries performed leading to the reduction of pain and return to participation.

Background: A 19 year-old male football athlete (height= 187.96 cm, mass= 112.037 kg) presented with chronic patellar tendinopathy that began in his high school career and continued to worsen with the increased physical demands associated with participation in collegiate sport.

Differential Diagnosis: Chondromalacia patella and Osgood Schlatters disease.

Treatment: After nonsurgical intervention resulted in no decrease of pain, bilateral tibial tubercle transfer surgery was conducted to correct …

Estimating The Impact Of Lost To Follow-Up On Breast Cancer Patients' Disease-Free Survival, Debbie Yan Qun Huang

Statistics

Background The 5-year survival rate for patients with breast cancer is much higher than patients with other types of cancer. Due to this longer survival period, breast cancer patients also tend to have increased rates of lost to follow-up, when compared to other cancers. When a patient becomes lost, the occurrence of distant metastasis cannot be reliably ascertained, unless the patient had a breast cancer-specific (BC) death. The impact of lost patients on recurrence rates and disease-free survival (DFS) was explored in breast cancer patients seen at the City of Hope from 1997 to 2012.

Methods Female breast cancer patients …

A Semantic-Based Method For Extracting Concept Definitions From Scientific Publications: Evaluation In The Autism Phenotype Domain, Saeed Hassanpour, Martin J. O’Connor, Amar K. Das

Dartmouth Scholarship

Background: A variety of informatics approaches have been developed that use information retrieval, NLP and text-mining techniques to identify biomedical concepts and relations within scientific publications or their sentences. These approaches have not typically addressed the challenge of extracting more complex knowledge such as biomedical definitions. In our efforts to facilitate knowledge acquisition of rule-based definitions of autism phenotypes, we have developed a novel semantic-based text-mining approach that can automatically identify such definitions within text.

Results: Using an existing knowledge base of 156 autism phenotype definitions and an annotated corpus of 26 source articles containing such definitions, we evaluated and …

An Epidemiological Model Of Rift Valley Fever With Spatial Dynamics, Tianchan Niu, Holly D. Gaff, Yiannis E. Papelis, David M. Hartley

Biological Sciences Faculty Publications

As a category A agent in the Center for Disease Control bioterrorism list, Rift Valley fever (RVF) is considered a major threat to the United States (USA). Should the pathogen be intentionally or unintentionally introduced to the continental USA, there is tremendous potential for economic damages due to loss of livestock, trade restrictions, and subsequent food supply chain disruptions. We have incorporated the effects of space into a mathematical model of RVF in order to study the dynamics of the pathogen spread as affected by the movement of humans, livestock, and mosquitoes. The model accounts for the horizontal transmission of …

An Algorithm For Facial Expression Recognition To Assist Handicapped Individuals With Eating Disabilities, Anthony Rudolph De La Loza

Theses Digitization Project

The purpose of this thesis is to describe an algorithm and implement a software system based upon facial expression recognition that will accurately determine the specific need of a handicapped individual pertaining to the eating process. Then based upon that need, determine the appropriate action that should be executed. This thesis aims to present a solution to allow a special needs individual to eat more efficienty and foster independence, while providing a platform for further research in the area of feature detection to assist individuals with special needs.

A Computational Framework For Proteome-Wide Pursuit And Prediction Of Metalloproteins Using Icp-Ms And Ms/Ms Data, W. Andrew Lancaster, Jeremy L. Praissman, Farris L. Poole, Aleksandar Cvetkovic, Angeli Lal Menon, Joseph W. Scott, Francis E. Jenney, Michael P. Thorgersen, Ewa Kalisiak, Junefredo V. Apon, Sunia A. Trauger, Gary Siuzdak, John A. Tainer, Michael W. W. Adams

PCOM Scholarly Works

BACKGROUND: Metal-containing proteins comprise a diverse and sizable category within the proteomes of organisms, ranging from proteins that use metals to catalyze reactions to proteins in which metals play key structural roles. Unfortunately, reliably predicting that a protein will contain a specific metal from its amino acid sequence is not currently possible. We recently developed a generally-applicable experimental technique for finding metalloproteins on a genome-wide scale. Applying this metal-directed protein purification approach (ICP-MS and MS/MS based) to the prototypical microbe Pyrococcus furiosus conclusively demonstrated the extent and diversity of the uncharacterized portion of microbial metalloproteomes since a majority of the …

The Cardiac Atlas Project--An Imaging Database For Computational Modeling And Statistical Atlases Of The Heart, Carissa G. Fonseca, Michael Backhaus, David A. Bluemke, Randall D. Britten, Jae Do Chung, Brett R. Cowan, Alan H. Kadish

Office of the President Publications and Research

MOTIVATION: Integrative mathematical and statistical models of cardiac anatomy and physiology can play a vital role in understanding cardiac disease phenotype and planning therapeutic strategies. However, the accuracy and predictive power of such models is dependent upon the breadth and depth of noninvasive imaging datasets. The Cardiac Atlas Project (CAP) has established a large-scale database of cardiac imaging examinations and associated clinical data in order to develop a shareable, web-accessible, structural and functional atlas of the normal and pathological heart for clinical, research and educational purposes. A goal of CAP is to facilitate collaborative statistical analysis of regional heart shape …

Computational Analyses Of The Uptake And Distribution Of Carbon Monoxide (Co) In Human Subjects, Kinnera Chada

University of Kentucky Doctoral Dissertations

Carbon monoxide (CO) is an odorless, colorless, tasteless gas that binds to hemoglobin with high affinity. This property underlies the use of low doses of CO to determine hemoglobin mass (M_Hb) in the fields of clinical and sports medicine. However, hemoglobin bound to CO is unable to transport oxygen and exposure to high CO concentrations is a significant environmental and occupational health concern. These contrasting aspects of CO—clinically useful in low doses but potentially lethal in higher doses—mandates a need for a quantitative understanding of the temporal profiles of the uptake and distribution of CO …

Improving Quantitative Treatment Response Monitoring With Deformable Image Registration, Blake A. Cannon

Dissertations and Theses (Open Access)

Quantitative imaging with 18F-FDG PET/CT has the potential to provide an in vivo assessment of response to radiotherapy (RT). However, comparing tissue tracer uptake in longitudinal studies is often confounded by variations in patient setup and potential treatment induced gross anatomic changes. These variations make true response monitoring for the same anatomic volume a challenge, not only for tumors, but also for normal organs-at-risk (OAR). The central hypothesis of this study is that more accurate image registration will lead to improved quantitation of tissue response to RT with 18F-FDG PET/CT. Employing an in-house developed “demons” based deformable image registration algorithm, …

Cellular Automata Rules Generator For Microbial Communities, Melissa Marie Quintana

Theses Digitization Project

The purpose of this project is to provide a visual representation as program output so that the rules and the radius of effect can be estimated. Currently there is a need for a method that extracts the cellular automata rules which simulate the growth patterns of microbial communities found within extreme environments. Contains source code.

To Live And Die In Ca, Jane Frances Curnutt

Theses Digitization Project

This thesis investigates the nature of elementary cellular automata to better understand their relationship of the models they support to the biological organisms that create the mats and soil crusts found in extreme environments here on earth. Cellular automata have been used to study growth and patterns in forests, arid desert environments, predator-prey problems, and sea shells. It has also been used to study areas of diverse epidemiology and linguistics. Cellular automata have been used as the core of computer games as well. This investigation has led to develop a graphical grammar for simple cellular automata, using L-systems, a grammar …

Reordered Subsets Reconstruction Of Proton Computed Tomography, Wenzhe Xue

Theses Digitization Project

This project investigates the improvement of iterative reconstruction using reordered subsets. Block iterative projection and Ordered Subset reconstruction algorithms are developed to improve the performance of image reconstruction. Contains source code.