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Medical Biomathematics and Biometrics Commons

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A Mathematical Model Of The Inflammatory Response To Pathogen Challenge, Lester Caudill, Fiona Lynch 2018 University of Richmond

A Mathematical Model Of The Inflammatory Response To Pathogen Challenge, Lester Caudill, Fiona Lynch

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Introducing The Fractional Differentiation For Clinical Data-Justified Prostate Cancer Modelling Under Iad Therapy, Ozlem Ozturk Mizrak 2018 Illinois State University

Introducing The Fractional Differentiation For Clinical Data-Justified Prostate Cancer Modelling Under Iad Therapy, Ozlem Ozturk Mizrak

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


The Epidemiology Of Infective Endocarditis Among People Who Inject Drugs In London, Ontario., Brian Hallam 2018 The University of Western Ontario

The Epidemiology Of Infective Endocarditis Among People Who Inject Drugs In London, Ontario., Brian Hallam

Electronic Thesis and Dissertation Repository

Infective endocarditis is an infectious disease that affects the valves of the heart. Injection drug use is currently a leading risk factor among patients with endocarditis. We conducted a prospective study using data from hospital chart records among patients with endocarditis in London, Ontario, which has a relatively high prevalence of people who inject drugs to assess the severity of the issue and the major risk factors of mortality pertaining to this population. This study had a sample size of 353 and included a review of the incidence of admissions of endocarditis, as well as a survival analysis, using both ...


Bayesian Analytical Approaches For Metabolomics : A Novel Method For Molecular Structure-Informed Metabolite Interaction Modeling, A Novel Diagnostic Model For Differentiating Myocardial Infarction Type, And Approaches For Compound Identification Given Mass Spectrometry Data., Patrick J. Trainor 2018 University of Louisville

Bayesian Analytical Approaches For Metabolomics : A Novel Method For Molecular Structure-Informed Metabolite Interaction Modeling, A Novel Diagnostic Model For Differentiating Myocardial Infarction Type, And Approaches For Compound Identification Given Mass Spectrometry Data., Patrick J. Trainor

Electronic Theses and Dissertations

Metabolomics, the study of small molecules in biological systems, has enjoyed great success in enabling researchers to examine disease-associated metabolic dysregulation and has been utilized for the discovery biomarkers of disease and phenotypic states. In spite of recent technological advances in the analytical platforms utilized in metabolomics and the proliferation of tools for the analysis of metabolomics data, significant challenges in metabolomics data analyses remain. In this dissertation, we present three of these challenges and Bayesian methodological solutions for each. In the first part we develop a new methodology to serve a basis for making higher order inferences in metabolomics ...


Effect Of Study Design On Sample Size In Studies Intended To Evaluate Bioequivalence Of Inhaled Short-Acting Β-Agonist Formulations, Yaohui Zeng, Sachinkumar Singh, Kai Wang, Richard C. Ahrens 2018 University of Iowa

Effect Of Study Design On Sample Size In Studies Intended To Evaluate Bioequivalence Of Inhaled Short-Acting Β-Agonist Formulations, Yaohui Zeng, Sachinkumar Singh, Kai Wang, Richard C. Ahrens

Stead Family Department of Pediatrics Publications

Pharmacodynamic studies that use methacholine challenge to assess bioequivalence of generic and innovator albuterol formulations are generally designed per published Food and Drug Administration guidance, with 3 reference doses and 1 test dose (3-by-1 design). These studies are challenging and expensive to conduct, typically requiring large sample sizes. We proposed 14 modified study designs as alternatives to the Food and Drug Administration-recommended 3-by-1 design, hypothesizing that adding reference and/or test doses would reduce sample size and cost. We used Monte Carlo simulation to estimate sample size. Simulation inputs were selected based on published studies and our own experience with ...


Cheating The Cheaters: Spatial Dynamics In The Evolutionary Stability Of Antibiotic Resistance, Devin Akman 2017 University of Illinois at Urbana-Champaign

Cheating The Cheaters: Spatial Dynamics In The Evolutionary Stability Of Antibiotic Resistance, Devin Akman

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Uncertainty Of 1-D Fluid Models In Patients With Pulmonary Hypertension, Mitchel J. Colebank 2017 North Carolina State University

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 2017 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

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

UT GSBS 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 ...


Modeling The Spread Of The Zika Virus At The 2016 Olympics, Triona Matheson, Brian Satterthwaite, Hannah Callender Highlander 2017 University of Portland

Modeling The Spread Of The Zika Virus At The 2016 Olympics, Triona Matheson, Brian Satterthwaite, Hannah Callender Highlander

Mathematics Faculty Publications and Presentations

The Zika Virus is an arbovirus that is spread by mosquitoes of the Aedes genus and causes mild fever-like symptoms. It is strongly associated with microcephaly, a condition that affects development of fetal brains. With the recent emergence of Zika in Brazil, we develop an agent-based model to track mosquitoes and humans throughout the 2016 Olympics in Rio de Janeiro to investigate how the Olympics might affect the spread of the virus. There are many unknowns regarding the spread and prevalence of Zika, with approximately 80% of infected individuals unaware of their infectious status. We therefore discuss results of experiments ...


Mathematical Models Of The Inflammatory Response In The Lungs, Sarah B. Minucci 2017 Virginia Commonwealth University

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. 2016 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

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

UT GSBS 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 ...


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 2016 Leeds Beckett University

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 ...


The Effects Of Scarring On Face Recognition, Kevin J. Chan 2016 Purdue University

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 ...


Snpredict: A Machine Learning Approach For Detecting Low Frequency Variants In Cancer, Vatsal Mehra 2016 Marquette University

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 ...


Mathematical Models Of Hiv And Hpv Coinfection, Samantha Erwin, Meghna Verma, Vida Abedi, Raquel Hontecillas-Magarzo, Stefan Hoops, Josep Bassaganya-Riera, Stanca M. Ciupe 2016 Virginia Polytechnic Institute and State University

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 2016 East Tennessee State Universtiy

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 ...


Power Analysis In Applied Linear Regression For Cell Type-Specific Differential Expression Detection, Edmund Glass 2016 Virginia Commonwealth University

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 ...


Analyzing Direct Effects In Randomized Trials With Secondary Interventions: An Application To Hiv Prevention Trials, Michael Rosenblum, Nicholas Jewell, Mark van der Laan, Steven Shiboski, Ariane van der Straten, Nancy Padian 2015 Johns Hopkins University

Analyzing Direct Effects In Randomized Trials With Secondary Interventions: An Application To Hiv Prevention Trials, Michael Rosenblum, Nicholas Jewell, Mark Van Der Laan, Steven Shiboski, Ariane Van Der Straten, Nancy Padian

Michael Rosenblum MD

The `Methods for improving reproductive health in Africa' trial is a recently completed randomized trial that investigated the effect of diaphragm and lubricant gel use in reducing infection by the human immunodeficiency virus (HIV) among susceptible women. 5045 women were randomly assigned to either the active treatment arm or not. Additionally, all subjects in both arms received intensive condom counselling and provision, the `gold standard' HIV prevention barrier method. There was much lower reported use of condoms in the intervention arm than in the control arm, making it difficult to answer important public health questions based solely on the intention-to-treat ...


Diaphragm And Lubricant Gel For Prevention Of Hiv Acquisition In Southern African Women: A Randomised Controlled Trial, Nancy Padian, Ariane van der Straten, Gita Ramjee, Tsungai Chipato, Guy de Bruyn, Kelly Blanchard, Stephen Shiboski, Elizabeth Montgomery, Heidi Fancher, Helen Cheng, Michael Rosenblum, Mark van der Laan, Nicholas Jewell, James McIntyre 2015 Johns Hopkins University

Diaphragm And Lubricant Gel For Prevention Of Hiv Acquisition In Southern African Women: A Randomised Controlled Trial, Nancy Padian, Ariane Van Der Straten, Gita Ramjee, Tsungai Chipato, Guy De Bruyn, Kelly Blanchard, Stephen Shiboski, Elizabeth Montgomery, Heidi Fancher, Helen Cheng, Michael Rosenblum, Mark Van Der Laan, Nicholas Jewell, James Mcintyre

Michael Rosenblum MD

Background Female-controlled methods of HIV prevention are urgently needed. We assessed the effect of provision of latex diaphragm, lubricant gel, and condoms (intervention), compared with condoms alone (control) on HIV seroincidence in women in South Africa and Zimbabwe. Methods We did an open-label, randomised controlled trial in HIV-negative, sexually active women recruited from clinics and community-based organisations, who were followed up quarterly for 12—24 months (median 21 months). All participants received an HIV prevention package consisting of pre-test and post-test counselling about HIV and sexually transmitted infections, testing, treatment of curable sexually transmitted infections, and intensive risk-reduction counselling. The ...


The Risk Of Virologic Failure Decreases With Duration Of Hiv Suppression, At Greater Than 50% Adherence To Antiretroviral Therapy., Michael Rosenblum, Steven Deeks, Mark van der Laan, David Bangsberg 2015 Johns Hopkins University

The Risk Of Virologic Failure Decreases With Duration Of Hiv Suppression, At Greater Than 50% Adherence To Antiretroviral Therapy., Michael Rosenblum, Steven Deeks, Mark Van Der Laan, David Bangsberg

Michael Rosenblum MD

Background We hypothesized that the percent adherence to antiretroviral therapy necessary to maintain HIV suppression would decrease with longer duration of viral suppression. Methodology Eligible participants were identified from the REACH cohort of marginally housed HIV infected adults in San Francisco. Adherence to antiretroviral therapy was measured through pill counts obtained at unannounced visits by research staff to each participant's usual place of residence. Marginal structural models and targeted maximum likelihood estimation methodologies were used to determine the effect of adherence to antiretroviral therapy on the probability of virologic failure during early and late viral suppression. Principal Findings A ...


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