Open Access. Powered by Scholars. Published by Universities.®

Biomedical Engineering and Bioengineering Commons

Open Access. Powered by Scholars. Published by Universities.®

Theses/Dissertations

Publicabstract

Articles 1 - 26 of 26

Full-Text Articles in Biomedical Engineering and Bioengineering

Identification Of A Rational, Physiologically Based Early Biomarker And Pathogenic Pathway For Preeclampsia, Mark K. Santillan May 2016

Identification Of A Rational, Physiologically Based Early Biomarker And Pathogenic Pathway For Preeclampsia, Mark K. Santillan

Theses and Dissertations

Preeclampsia is a hypertensive disorder of pregnancy that is diagnosed after the 20th week of gestation. It is defined by the American College of Obstetrics and Gynecology as de novo hypertension of at least 140/90 in a pregnant woman. Proteinuria with the hypertension is sufficient but not required for the diagnosis, especially if a woman displays severe symptoms such as headache, blurry vision, right upper quadrant pain, and low platelet count. Despite significant research, preeclampsia continues to kill 76,000 mothers and 500,000 babies per year worldwide. It causes short and long term consequences such as future metabolic ...


Global Optimization Using Metadynamics And A Polarizable Force Field: Application To Protein Loops, Armin Avdic May 2016

Global Optimization Using Metadynamics And A Polarizable Force Field: Application To Protein Loops, Armin Avdic

Theses and Dissertations

Genetic sequences are being collected at an ever increasing rate due to rapid cost reductions; however, experimental approaches to determine the structure and function of the protein(s) each gene codes are not keeping pace. Therefore, computational methods to augment experimental structures with comparative (i.e. homology) models using physics-based methods for building residues, loops and domains are needed to thread new sequences onto homologous structures. In addition, even experimental structure determination relies on analogous first principles structure refinement and prediction algorithms to place structural elements that are not defined by the data alone.

Computational methods developed to find the ...


Effects Of Mechanical Stimulation On Fibroblast-Guided Microstructural And Compositional Remodeling, Aribet M. De Jesús May 2016

Effects Of Mechanical Stimulation On Fibroblast-Guided Microstructural And Compositional Remodeling, Aribet M. De Jesús

Theses and Dissertations

Many physiological and pathological processes, such as wound healing and tissue remodeling, are heavily influenced by continuous mechanical cell-cell and cell-ECM communication. Abnormalities that may compromise the biomechanical communication between the cells and the ECM can have significant repercussions on these physiological and pathological processes. The state of the mechanical environment and the reciprocal communication of mechanical signals between the ECM and the cell during wound healing and aged dermal tissue regeneration may be key in controlling the quality of the structure and physical properties of regenerated tissue.

This dissertation encompasses a series of studies developed for characterizing the effects ...


Pushing The Boundaries: Feature Extraction From The Lung Improves Pulmonary Nodule Classification, Samantha Kirsten Nowik Dilger May 2016

Pushing The Boundaries: Feature Extraction From The Lung Improves Pulmonary Nodule Classification, Samantha Kirsten Nowik Dilger

Theses and Dissertations

Lung cancer is the leading cause of cancer death in the United States. While low-dose computed tomography (CT) screening reduces lung cancer mortality by 20%, 97% of suspicious lesions are found to be benign upon further investigation. Computer-aided diagnosis (CAD) tools can improve the accuracy of CT screening, however, current CAD tools which focus on imaging characteristics of the nodule alone are challenged by the limited data captured in small, early identified nodules. We hypothesize a CAD tool that incorporates quantitative CT features from the surrounding lung parenchyma will improve the ability of a CAD tool to determine the malignancy ...


Development And Verification Of Medical Image Analysis Tools Within The 3d Slicer Environment, Jessica Leeann Forbes May 2016

Development And Verification Of Medical Image Analysis Tools Within The 3d Slicer Environment, Jessica Leeann Forbes

Theses and Dissertations

Rapid development of domain specialized medical imaging tools is essential for deploying medical imaging technologies to advance clinical research and clinical practice. This work describes the development process, deployment method, and evaluation of modules constructed within the 3D Slicer environment. These tools address critical problems encountered in four different clinical domains: quality control review of large repositories of medical images, rule-based automated label map cleaning, quantification of calcification in the heart using low-dose radiation scanning, and waist circumference measurement from abdominal scans. Each of these modules enables and accelerates clinical research by incorporating medical imaging technologies that minimize manual human ...


Building User Interactive Capabilities For Image-Based Modeling Of Patient-Specific Biological Flows In Single Platform, Liza Shrestha May 2016

Building User Interactive Capabilities For Image-Based Modeling Of Patient-Specific Biological Flows In Single Platform, Liza Shrestha

Theses and Dissertations

In this work, we have developed user interactive capabilities that allow us to perform segmentation and manipulation of patient-specific geometries required for Computational Fluid Dynamics (CFD) studies, entirely in image domain and within a single platform of ‘IAFEMesh'. Within this toolkit we have added commonly required manipulation capabilities for performing CFD on segmented objects by utilizing libraries like ITK, VTK and KWWidgets. With the advent of these capabilities we can now manipulate a single patient specific image into a set of possible cases we seek to study; which is difficult to do in commercially available software like VMTK, Slicer, MITK ...


An Automated Method Of Generating Nurbs Meshes For Patient-Specific Geometries, Moustafa Galal Ibrahim May 2016

An Automated Method Of Generating Nurbs Meshes For Patient-Specific Geometries, Moustafa Galal Ibrahim

Theses and Dissertations

Cardiovascular disease is the number one reason for emergency room visits in the United States. Understanding the different pathologies of the cardiovascular system is crucial when trying to prescribe proper treatment or intervention. In order best understand these issues proper computer simulations would be necessary. Due to the fact that every patient is different. Being able to analysis and properly simulate each patients data individually to better understanding their specific case is necessary for patient specific interventions. In order to achieve such requirement we propose a new method of mesh generation to better map patient specific geometries. This new framework ...


Dual Energy Ct Based Approach To Assessing Early Pulmonary Vascular Dysfunction In Smoking-Associated Inflammatory Lung Disease, Krishna S. Iyer May 2016

Dual Energy Ct Based Approach To Assessing Early Pulmonary Vascular Dysfunction In Smoking-Associated Inflammatory Lung Disease, Krishna S. Iyer

Theses and Dissertations

CT is a powerful method for noninvasive assessment of the lung. Advancements to CT technology have guided the high-resolution structural and functional assessment of lung diseases. This has helped make the transition from characterizing the severity of lung disease to novel phenotyping of disease subtypes. Chronic obstructive pulmonary disease (COPD) is a spectrum of inflammatory lung disease affecting lung parenchyma, airways, and the pulmonary and systemic vasculature. Quantitative CT-based measures have largely focused on quantifying the extent of airway and parenchymal damage with disease. Recently perfusion CT method has been used to assess the pulmonary vascular bed. This technique was ...


Comprehensive Assessment And Characterization Of Pulmonary Acinar Morphometry Using Multi-Resolution Micro X-Ray Computed Tomography, Abhilash Srikumar Kizhakke Puliyakote May 2016

Comprehensive Assessment And Characterization Of Pulmonary Acinar Morphometry Using Multi-Resolution Micro X-Ray Computed Tomography, Abhilash Srikumar Kizhakke Puliyakote

Theses and Dissertations

The characterization of the normal pulmonary acinus is a necessary first step in understanding the nature of respiratory physiology and in assessing the etiology of pulmonary pathology. Murine models play a vital role in the advancement of current understanding of the dynamics of gas exchange, particle deposition and the manifestations of diseases such as COPD, Cystic Fibrosis and Asthma. With the advent of interior tomography techniques, high-resolution micro computed tomography (μCT) systems provide the ability to nondestructively assess the pulmonary acinus at micron and sub-micron resolutions. With the application of Systematic Uniform Random Sampling (SURS) principles applied to in-situ fixed ...


An Automated Tissue Classification Pipeline For Magnetic Resonance Images Of Infant Brains Using Age-Specific Atlases And Level Set Segmentation, Andrew Metzger May 2016

An Automated Tissue Classification Pipeline For Magnetic Resonance Images Of Infant Brains Using Age-Specific Atlases And Level Set Segmentation, Andrew Metzger

Theses and Dissertations

Quantifying tissue volumes in pediatric brains from magnetic resonance (MR) images can provide insight into etiology and onset of neurological disease. Unbiased volumetric analysis can be applied to large population studies when automated image processing is possible. Standard segmentation strategies using adult atlases fail to account for varying tissue contrasts and types associated with the rapid growth and maturational changes seen in early neurodevelopment. The goal of this project was to develop an automated pipeline and two age-specific atlases capable of providing accurate tissue classification despite these challenges.

The automated pipeline consisted of a stepwise initial atlas-to-subject registration, expectation maximization ...


Computational Methods To Model Disease And Genetic Effects On Optic Nerve Head Structure, Mark Allen Christopher Dec 2015

Computational Methods To Model Disease And Genetic Effects On Optic Nerve Head Structure, Mark Allen Christopher

Theses and Dissertations

Glaucoma is a leading cause of blindness throughout the world and is estimated to affect 80 million by 2020. This disease causes progressive loss of vision and, left untreated, can lead to complete blindness. With treatment, however, disease progression can be slowed dramatically. This makes early detection and intervention crucial in preserving the vision of affected individuals.

Onset and progression of glaucoma are associated with structural changes to an anatomical feature known as the optic nerve head (ONH). The ONH is the site of attachment between the retina and the optic nerve that carries all visual information to the brain ...


An Objective Ct-Based Method For Quantifying Articular Fracture Severity : Clinical Application In Multiple Joints, Kevin Nathaniel Dibbern Dec 2015

An Objective Ct-Based Method For Quantifying Articular Fracture Severity : Clinical Application In Multiple Joints, Kevin Nathaniel Dibbern

Theses and Dissertations

Adequately assessing injury severity is critical in treating articular fractures. Severity assessment is used to inform clinical and surgical decision making through anticipation of patient outcomes. The assessments generally involve interpreting radiographs or CT image data. In recognition of the poor reliability of existing clinical severity assessments, objective severity metrics have been developed that are firmly rooted in mechanics and provide capable alternatives for use in research, where reliable data is paramount. Their broader clinical utility remains to be established.

An existing CT-based method for determining the energy expended in a bone fracture was extended to facilitate its use in ...


Applying Vessel Inlet/Outlet Conditions To Patient-Specific Models Embedded In Cartesian Grids, Aaron Matthew Goddard Dec 2015

Applying Vessel Inlet/Outlet Conditions To Patient-Specific Models Embedded In Cartesian Grids, Aaron Matthew Goddard

Theses and Dissertations

Cardiovascular modeling has the capability to provide valuable information allowing clinicians to better classify patients and aid in surgical planning. Modeling is advantageous for being non-invasive, and also allows for quantification of values not easily obtained from physical measurements. Hemodynamics are heavily dependent on vessel geometry, which varies greatly from patient to patient. For this reason, clinically relevant approaches must perform these simulations on patient-specific geometry. Geometry is acquired from various imaging modalities, including magnetic resonance imaging, computed tomography, and ultrasound. The typical approach for generating a computational model requires construction of a triangulated surface mesh for use with finite ...


Characterization Of T1rho Sensitivity To Metabolite And Temperature Changes, Nana Owusu Jul 2015

Characterization Of T1rho Sensitivity To Metabolite And Temperature Changes, Nana Owusu

Theses and Dissertations

Spin-lattice relaxation in the rotating frame (T1ρ) is a relaxation parameter measured in nuclear magnetic resonance studies. This parameter has been found to be sensitive to chemical exchange processes occurring in diseased tissue associated with abnormal metabolism when measured in magnetic resonance imaging (MRI). Metabolic changes in tissue affected by abnormal metabolism can be quantified with good spatial and temporal resolution using T1ρ, better than a similar method of assessment known as CEST and current methods such as spectroscopic (1H- and 31P-MRS) and nuclear medicine (PET) methods used in clinical settings. Though T1ρ has these advantages, there is ...


Feasibility Of Intra-Articular Adeno-Associated Virus-Mediated Proteoglycan-4 Gene Therapy To Prevent Osteoarthritis, Hyeong Hun Choe Jul 2015

Feasibility Of Intra-Articular Adeno-Associated Virus-Mediated Proteoglycan-4 Gene Therapy To Prevent Osteoarthritis, Hyeong Hun Choe

Theses and Dissertations

Lubricin, or proteoglycan 4 (PRG4), is a secreted, glycosylated protein that binds to cartilage surfaces, which functions as a boundary lubricant. The loss of lubricin from cartilage is identified as a major pathogenic factor in post-traumatic osteoarthritis (PTOA) that has now been the aim of therapeutic intervention. Intra-articular injection of PRG4 protein provides short-term benefits that might be extended using sustained delivery methods such as in gene therapy.

Here we describe the development and testing of such therapy using adeno-associated virus (AAV) as a vector for the transfer of PRG4-green fluorescent protein (GFP) fusion gene. Our recombinant PRG4 gene produces ...


Evaluation Of A Low-Cost Aerosol Sensor To Assess Occupational Exposures, Samuel M. Jones Jul 2015

Evaluation Of A Low-Cost Aerosol Sensor To Assess Occupational Exposures, Samuel M. Jones

Theses and Dissertations

A Dylos DC1100 was evaluated to: 1. Establish relationship between low-cost DC1100 and higher-cost pDR 1200; 2. Develop a method to convert DC1100 particle number into mass concentration to compare with respirable and inhalable mass references.

A Dylos DC1100 was deployed in a swine CAFO, along with a pDR-1200 and filter set to collect respirable and inhalable particles. Deployment was conducted from December 2013 through February 2014 in 24 hour intervals. The pDR-1200 and respirable mass concentration was used to convert the DC1100 particle count to mass concentration. Two methods of conversion were used, physical property method (Method 1) and ...


Community Based Air Quality Monitoring Near Proppant Sand Facilities, Ryan James Grant Jul 2015

Community Based Air Quality Monitoring Near Proppant Sand Facilities, Ryan James Grant

Theses and Dissertations

Silica sand is used in the hydraulic fracturing process as a proppant—a material that holds open fissures in a rock formation to allow oil and gas to escape. Due to the increased demand for proppant sand, numerous sand mining and processing facilities have been constructed in the vicinity of small communities. Silica sand contains crystalline silica, which can cause chronic health problems such as silicosis. This study monitored airborne particulate matter at residences within 800 m from the facilities property line, with active mining, processing, and/or transport. Real-time particulate air monitoring with automated acquisition of explanatory variables: sound ...


New Neural Network For Real-Time Human Dynamic Motion Prediction, Mohammad Hindi Bataineh May 2015

New Neural Network For Real-Time Human Dynamic Motion Prediction, Mohammad Hindi Bataineh

Theses and Dissertations

Artificial neural networks (ANNs) have been used successfully in various practical problems. Though extensive improvements on different types of ANNs have been made to improve their performance, each ANN design still experiences its own limitations. The existing digital human models are mature enough to provide accurate and useful results for different tasks and scenarios under various conditions. There is, however, a critical need for these models to run in real time, especially those with large-scale problems like motion prediction which can be computationally demanding. For even small changes to the task conditions, the motion simulation needs to run for a ...


Computational Prediction Of Organic Crystal Thermodynamics Using Molecular Dynamics, Jooyeon Park May 2015

Computational Prediction Of Organic Crystal Thermodynamics Using Molecular Dynamics, Jooyeon Park

Theses and Dissertations

Computation predictions of organic crystal structure and thermodynamics are essential for material design, crystal engineering and drug development. However, accurate computational tools for organic crystal thermodynamics calculations are lacking, and experimental data set for validation of computational methods is limited. Most crystal structure predictions and stability calculations depend solely on potential energy, which is an insufficient representation of thermodynamics. This thesis proposes and validates both absolute and relative free energy calculation of small organic compounds, thus presenting an accurate computational tool that overcomes the shortcomings of potential-energy-based models.

The solubility of organic molecules can be computed from a thermodynamic cycle ...


Optimization-Based Dynamic Simulation Of Human Jogging Motion, Kaustubh Anil Patwardhan May 2015

Optimization-Based Dynamic Simulation Of Human Jogging Motion, Kaustubh Anil Patwardhan

Theses and Dissertations

Mathematical modeling and realistic human simulation of human jogging motion is a very challenging problem. Majority of the current literature is focused on studying walking or running. This work is aimed at bridging the gap in literature due to the lack of research work in three main areas: (1) simulations and experiments on running at speeds lower than 3 m/s, (2) Kinetics of fore-foot strike pattern in jogging and running and (3) the existence of a double support phase in running at slower speeds and its effects. Formulations to simulate natural human jogging are studied and developed. The digital ...


Biophysical Effects Of Ultrasound Therapy For Cartilage Regeneration And Microbubble Mediated Shock Waves And Drug Release Control For Cancer Treatment, Kee Woong Jang May 2015

Biophysical Effects Of Ultrasound Therapy For Cartilage Regeneration And Microbubble Mediated Shock Waves And Drug Release Control For Cancer Treatment, Kee Woong Jang

Theses and Dissertations

Articular cartilage is a complex soft tissue covering the end of moving bones in joints which provide pressure load distribution over the joint surface and smooth lubrication with little friction for establishing movement. Articular cartilage has an intrinsically limited capacity for self-repair when injured due to the lack of nerve and blood supply. Considered that injured cartilage is left untreated, it is likely to undergo progressive cartilage degeneration without pain which may lead to posttraumatic osteoarthritis. Therefore functional and physiologic restoration of injured cartilage back to a normal condition has long been in demand, yet current available repairing methods in ...


Validation And Applications Of Discrete Element Analysis In The Hip Joint, Kevin Charles Townsend May 2015

Validation And Applications Of Discrete Element Analysis In The Hip Joint, Kevin Charles Townsend

Theses and Dissertations

Osteoarthritis is a progressive degenerative joint disease which causes pain, inflammation, and eventual loss of joint function. This debilitating disease affects approximately 3% of U.S. adults over 30 years old, with direct medical costs of over $100 billion each year. Post-traumatic osteoarthritis is a sub-set of osteoarthritis initiated by injuries such as a fracture of the joint surface. When a surgeon reconstructs a fractured joint, there are often residual incongruities on the surface, which can lead to elevated contact stresses. Increased cartilage contact stress has been shown to be a major risk factor for developing post-traumatic osteoarthritis. Computational modeling ...


Feasibility For Spinal Muscles Creating Pure Axial Compressive Load Or Follower Load In The Lumbar Spine In 3-D Postures, Tianjiao Wang May 2015

Feasibility For Spinal Muscles Creating Pure Axial Compressive Load Or Follower Load In The Lumbar Spine In 3-D Postures, Tianjiao Wang

Theses and Dissertations

Previous in-vivo studies showed that compressive force acting on the spine may exceed 2600 N. However, the ligamentous lumbar spine becomes unstable when subjected to compressive loads less than 100 N. It is generally accepted that the ligamentous spine itself is unstable but can be stabilized by muscle forces (MFs) in vivo. Nevertheless, normal spinal muscle contraction patterns remain unknown.

In recent in vitro studies, when the direction of the applied load was controlled along the spinal curvature so that the internal spinal load became perfect compressive follower loads (CFLs) at all lumbar levels, the ligamentous lumbar spine was found ...


Towards An Optimized Low Radiation Dose Quantitative Computed Tomography Protocol For Pulmonary Airway Assessment, Alexandra Lynae Judisch May 2015

Towards An Optimized Low Radiation Dose Quantitative Computed Tomography Protocol For Pulmonary Airway Assessment, Alexandra Lynae Judisch

Theses and Dissertations

Lung disease affects tens of millions of Americans, making it one of the most common medical conditions in the United States. Many of these lung diseases are classified as chronic airway disease. Because of this, it is important to be able to catch the development early so as to begin treatment as soon as possible to delay the progression and subsequently monitor that progression. One method of doing so is the use of quantitative computed tomography (CT). Study of the airway anatomy can be quantified using such measures as minor inner diameter (MinD), major inner diameter (MajD), wall thickness (WT ...


Multimodal Nanoparticles For Image-Guided Delivery Of Mesenchymal Stem Cells In The Treatment Of Myocardial Infarction, Sean Sweeney May 2015

Multimodal Nanoparticles For Image-Guided Delivery Of Mesenchymal Stem Cells In The Treatment Of Myocardial Infarction, Sean Sweeney

Theses and Dissertations

One of the leading causes of death and hospital stays in the United States, myocardial infarction (MI) occurs when coronary blockages lead to downstream ischemia in the myocardium. Following the MI, the heart activates a number of pathways to repair or remodel the infarcted zone. Endothelial cells respond to ischemia by de-differentiating to form neovasculature and myofibroblasts. The resident cardiac differentiable stem cells (CDCs) are recruited via local cytokines and chemokines to the infarct zone where they too differentiate into myofibroblasts. Mesenchymal stem cells (MSCs) of the bone marrow respond to circulating factors by immobilizing to the heart and differentiating ...


Adaptation And Validation Of An Analytical Localized Muscle Fatigue Model For Workplace Tasks, John Maurice Looft Dec 2014

Adaptation And Validation Of An Analytical Localized Muscle Fatigue Model For Workplace Tasks, John Maurice Looft

Theses and Dissertations

Muscle fatigue is universally experienced in daily life, from recreational physical activity to the workplace. However, our ability to estimate fatigue is limited. Several attempts have been made to mathematically model the effects of fatigue, such as how long a muscle contraction may be sustained, known as `endurance time.' However, these simple models of endurance time are limited to static contractions when the body is not moving, but muscles are contracted. This research aims to advance a previously proposed analytical model of muscle fatigue to represent complex tasks such as with rest intervals and dynamic contractions. Multiple methodologies were employed ...