Biomedical Engineering and Bioengineering Commons^™

Hyperspectral Tomographic Ftir Imaging Using Two Illumination Geometries For Polymer Phantoms, Zahrasadat Alavi

Theses and Dissertations

The purpose of this dissertation is to carry out non-destructive 3D imaging by applying Fourier Transform Infrared (FTIR) spectro-microtomographic techniques, and develop corresponding methods of data analysis. This is done by collecting 3D synchrotron-based and lab-based (Thermal) FTIR hyper spectral data at the Synchrotron Radiation Center (SRC) for the first time. Despite other 2D imaging techniques, this does not manipulate the sample, and suppresses the need to microtome 3D biological, material or biomedical samples into slices to study by spectroscopic imaging techniques. Spectro-micro-tomography is applicable for scientific, industrial, energy, biomedical samples such as stem cell characterization and materials such as …

Scattering Correction Methods Of Infrared Spectra Using Graphics Processing Units, Asher Imtiaz

Theses and Dissertations

Fourier transform infrared (FTIR) microspectroscopy has been used for many years as a technique that provides distinctive structure-specific infrared spectra for a wide range of materials (e.g., biological (tissues, cells, bacteria, viruses), polymers, energy related, composites, minerals). The mid-infrared radiation can strongly scatter from distinct particles, with diameters ranging between 2-20 micrometer. Transmission measurements of samples (approximately 100 micrometers x 100 micrometers x 10 micrometers) with distinct particles. will be dominated by this scattering (Mie scattering). The scattering distorts the measured spectra, and the absorption spectra appear different from pure absorbance spectra. This thesis presents development and implementation of two …

Biomechanical Joint Demands And Functional Outcomes During Manual Wheelchair Use In Pediatric Patients With Spinal Cord Injury, Christine M. Aurit

Theses and Dissertations

The biomechanical demands of the upper extremities (UEs) during pediatric manual wheelchair (MWC) use have not been fully explored. Children who use MWCs for mobility engage in a range of functional activities that may place large biomechanical demands on the UEs leading to a high risk on overuse injuries. This study aims to analyze the kinematics and kinetics of pediatric manual wheelchair use during propulsion, starting, stopping and weight relief tasks. Fourteen pediatric patients with spinal cord injury were recruited and data were collected using a 14-camera Vicon MX motion analysis system (Oxford Metric Group, Oxford, UK) and a SmartWheel …

An Optogenetic Brain-Machine Interface For Spatiotemporal Neuromodulation, Ryan Andrew Baumgartner

Theses and Dissertations

Direct neural stimulation has recently become a standard therapy for neurological disorders such as Parkinson's Disease, Essential Tremors, and Dystonia. Currently, deep brain electro-stimulation and neuro-pharmaceutical treatments are the dominant therapeutic options available to the public. As our understanding of brain function and neurological diseases improves, we are able to develop more advanced neuromodulation techniques. These methods could become viable treatment solutions for treating brain dysfunction. Optogenetics, first introduced by a research team led by Karl Deisseroth at Stanford University, has proved to be a versatile technique with remarkable potential to be used in treatments for brain disorders, dysfunction, and …

Role Of Sensation In Altered Phalanx Grip Force In Persons With Stroke, Leah R. Enders

Theses and Dissertations

Many individuals experience hand impairment after stroke leading to decreased ability to perform daily living activities. Previous research studies have investigated how stroke survivors' pinch grip control differs from healthy individuals, even though many individuals can only grasp with power grip after stroke. Furthermore, many stroke survivors experience tactile sensory deficit in their paretic limb in addition to motor deficit. It is currently unknown how stroke induced tactile sensory deficit affects power grip force directional control, which is important in terms of preventing object slippage and power grip normal force generation. Additionally it is unknown if power grip could be …

Cryoimaging-Microscopy Implementation For 3d Optical Imaging, Mohammad Masoudimotlagh

Theses and Dissertations

The structures and biochemistry properties of biological tissues are mostly affected by diseases. The visualization of organ structure and biochemistry helps in early detection and progression monitoring of diseases.

Although, 2D imaging has traditionally been used to gain information from the tissue, it does not accurately represent many of the structures and functions. There currently exists a need for sensitive and specific methods to show detailed information about the structure of the tissue with high resolution and in 3D. The potential advantage of the high resolution 3D images is the ability to accurately probe structural and biochemical properties of the …

Effect Of Junction Geometry On Monodispersed Microdroplet Generation In Microfluidic Aqueous Two-Phase Systems, Young Gyu Nam

Theses and Dissertations

Aqueous two-phase system (ATPS) consists of two immiscible water-based solutions of polymers, which can form phase partitioning. Dextran and polyethylene glycol I used in this thesis is the one of common components of aqueous two-phase system give a reliable and incompatible environment for purification of biomedical products and cellular macromolecules. Recently, ATPS have received increasing attention as a separation method in microfluidic device due to the advantages of biocompatibility, unlimited combination, and low interfacial tension. Hence, it became an important to discover researches related to ATPS microfluidic device.

Microdroplets produced in microfluidic device are a largely interesting phenomenon for various …

Monitoring Changes In Hemodynamics Following Optogenetic Stimulation, Seth Thomas Frye

Theses and Dissertations

The brain is composed of billions of neurons, all of which connected through a vast network. After years of study and applications of different technologies and techniques, there are still more questions than answers when it comes to the fundamental functions of the brain. This project aims to provide a new tool which can be used to gain a better understanding of the fundamental mechanisms that govern neurological processes inside the brain. In order for neural networks to operate, blood has to be supplied through neighboring blood vessels. As such, the increase or decrease in the blood supply has been …

Citefinder: A System To Find And Rank Medical Citations, Seyed Soheil Moosavinasab

Theses and Dissertations

This thesis presents CiteFinder, a system to find relevant citations for clinicians' written content. Inclusion of citations for clinical information content makes the content more reliable through the provision of scientific articles as references, and enables clinicians to easily update their written content using new information. The proposed approach splits the content into sentences, identifies the sentences that need to be supported with citations by applying classification algorithms, and uses information retrieval and ranking techniques to extract and rank relevant citations from MEDLINE for any given sentence. Additionally, this system extracts snippets from the retrieved articles. We assessed our approach …

Optical Studies Of Oxidative Stress In Lung Tissue: Rodent Models, Reyhaneh Sepehr

Theses and Dissertations

Objectives: There currently exists a need for reliable measurements of tissue metabolic state at cellular levels. The objective of this research was to study tools capable of evaluating cellular redox states in intact tissue. To meet this goal, three different instruments (cryoimager, fluorometer, and fluorescent microscope) were used to study the metabolism and functions of the mitochondria at different levels and regimes (cryo, ex vivo, in vivo and in vitro).

Introduction: Through optical monitoring of autofluorescent mitochondrial metabolic coenzymes, as well as exogenous fluorophores, the state of mitochondria can be probed in real time in many intact organs and in …

Extracting The Structure And Conformations Of Biological Entities From Large Datasets, Ali Dashti

Theses and Dissertations

In biology, structure determines function, which often proceeds via changes in conformation. Efficient means for determining structure exist, but mapping conformations continue to present a serious challenge. Single-particles approaches, such as cryogenic electron microscopy (cryo-EM) and emerging "diffract & destroy" X-ray techniques are, in principle, ideally positioned to overcome these challenges. But the algorithmic ability to extract information from large heterogeneous datasets consisting of "unsorted" snapshots - each emanating from an unknown orientation of an object in an unknown conformation - remains elusive.

It is the objective of this thesis to describe and validate a powerful suite of manifold-based algorithms …

Patient-Oriented Evidence-Based Treatment Decision Support System (Treatquest®) For Lung Cancer, Danqing Hu

Theses and Dissertations

Involving patients in healthcare decisions makes a significant and enduring difference to healthcare outcomes. One challenge for patients is the lack of evidence-based information and tools to support their decision making. Although patients have access to significant information through internet and other sources, it is not personalized for their specific situation. This dissertation attempts to help patients acquire evidence-based information relevant to their own situation, so they can make a more informed decision in co-operation with their physicians. Lung cancer has been selected as a focus for this study because lung cancer presents very complex decision making situation and is …

Angiography And Monitoring Of Hemodynamic Signals In The Brain Via Optical Coherence Tomography, Alana Mauluidy Soehartono

Theses and Dissertations

The brain is a complex network of interconnected neurons with each cell functioning as a nonlinear processing unit. Neural responses to stimulus can be described by activity in neurons. While blood flow changes have been associated with neural activity and are critical to brain function, this neurovascular coupling is not well understood. This work presents a technique for neurovascular interrogation, combining optogenetics and optical coherence tomography.

Optogenetics is a recently developed neuromodulation technique to control activity in the brain using light with precise spatial neuronal control and high temporal resolution. Using this method, cells act as light-gated ion channels and …

Extraction And Classification Of Drug-Drug Interaction From Biomedical Text Using A Two-Stage Classifier, Majid Rastegar-Mojarad

Theses and Dissertations

One of the critical causes of medical errors is Drug-Drug interaction (DDI), which occurs when one drug increases or decreases the effect of another drug. We propose a machine learning system to extract and classify drug-drug interactions from the biomedical literature, using the annotated corpus from the DDIExtraction-2013 shared task challenge. Our approach applies a two-stage classifier to handle the highly unbalanced class distribution in the corpus. The first stage is designed for binary classification of drug pairs as interacting or non-interacting, and the second stage for further classification of interacting pairs into one of four interacting types: advise, effect, …

Efficient Computation Of K-Nearest Neighbor Graphs For Large High-Dimensional Data Sets On Gpu Clusters, Ali Dashti

Theses and Dissertations

The k-Nearest Neighbor Graph (k-NNG) and the related k-Nearest Neighbor (k-NN) methods have a wide variety of applications in areas such as bioinformatics, machine learning, data mining, clustering analysis, and pattern recognition. Our application of interest is manifold embedding. Due to the large dimensionality of the input data (<15k), spatial subdivision based techniques such OBBs, k-d tree, BSP etc., are not viable. The only alternative is the brute-force search, which has two distinct parts. The first finds distances between individual vectors in the corpus based on a pre-defined metric. Given the distance matrix, the second step selects k nearest neighbors for each member of the query data set.

This thesis presents the development and implementation of a distributed exact k-Nearest Neighbor Graph (k-NNG) construction method. The proposed method uses Graphics Processing Units (GPUs) and exploits multiple levels of parallelism for distributed computational systems using GPUs. It is scalable for different cluster sizes, with each compute node in the cluster …

Continuum Deformation Model For Drug-Eluting Stent (Des) Medical Devices Using Finite Element Analysis (Fea), Solki Lee

Theses and Dissertations

The development of coronary stent medical devices was originally considered as a major advance in the treatment of obstructive cardiovascular disease. The implantation of stent, however, involves clinical adverse effects such as re-narrowing of arterial wall after stenting. Drug-eluting stents (DES) have been developed to prevent such adverse effects by slowly delivering anti-proliferative and/or anti-inflammatory drugs from coating composites of drug-containing polymers. One of the major issues in DES implantation is, however, that the coatings comprised of drug and polymer composite phases are often fractured or delaminated during the deployment of stent, which can lead to more serious clinical complications. …

Density Functional Theory (Dft) Study On The Hydrolysis Behavior Of Degradable Mg/Mg Alloys For Biomedical Applications, Marjan Nezafati

Theses and Dissertations

Magnesium-based (Mg and/or Mg alloys) materials possess many advantageous physicochemical/biological characteristics such as good biocompatibility and similarity of the mechanical properties to the human bone tissue, which renders this material a promising candidate for the biomedical and implant applications. One of the most attractive features of Mg-based materials is the degradability in the physiological environment. With the burst of research on the biodegradable materials for the healthcare device applications, Mg and its alloys attracted a strong attention in the bioengineering field in recent years. However, the major limitation of applying Mg-based materials to biomedical applications is the fast degradation/corrosion rate …

Fibrinogen-Conjugated Gold-Coated Magnetite Nanoparticles For Antiplatelet Therapy, Evan Schuerer Krystofiak

Theses and Dissertations

Ischemic stroke is the world's second leading cause of death and accounts for 2-4% of total worldwide healthcare costs. Ischemic stroke is caused by the occlusion of arteries responsible for supplying blood to the brain, which can result in disability or death. Arterial blood clots consist of aggregates of activated platelets wrapped in a mesh of fibrin. Tissue plasminogen activator, the only current FDA-approved treatment for ischemic stroke, functions by lysing fibrin in a blood clot. Unfortunately, tissue plasminogen activator significantly increases bleeding risks, which restricts its use. Alternatively, targeting and disrupting platelets within a clot could improve stroke outcome. …

Development Of A Novel Revison Total Hip Arthroplasty Method For Femoral Component Extraction, Michael Kevin Keenan

Theses and Dissertations

Revision total hip arthroplasty is an expensive, arduous procedure where a femoral implant must first be removed and then replaced. The most difficult part of this procedure is the removal of the hip implant, without damaging the host bone. To make this process easier, it is proposed that a device could utilize an implant's natural frequency to propagate cracks in the bone cement used to bond the implant to the host bone. The foci of this thesis is to (i) determine the natural frequency of an implant, (ii) design a device that can be easily used in a surgical setting …

Dc And Microwave Analysis Of Gallium Arsenide Field-Effect Transistor-Based Nucleic Acid Biosensors, John K. Kimani

Theses and Dissertations

Sensitive high-frequency microwave devices hold great promise for biosensor design. These devices include GaAs field effect transistors (FETs), which can serve as transducers for biochemical reactions, providing a platform for label-free biosensing. In this study, a two-dimensional numerical model of a GaAs FET-based nucleic acid biosensor is proposed and simulated. The electronic band structure, space charge density, and current-voltage relationships of the biosensor device are calculated. The intrinsic small signal parameters for the device are derived from simulated DC characteristics and used to predict AC behavior at high frequencies.

The biosensor model is based on GaAs field-effect device physics, semiconductor …

Accelerating Mri Data Acquisition Using Parallel Imaging And Compressed Sensing, Haifeng Wang

Theses and Dissertations

Magnetic Resonance Imaging (MRI) scanners are one of important medical instruments, which can achieve more information of soft issues in human body than other medical instruments, such as Ultrasound, Computed Tomography (CT), Single Photon Emission Computed Tomography (SPECT), Positron Emission Tomography (PET), etc. But MRI's scanning is slow for patience of doctors and patients. In this dissertation, the author proposes some methods of parallel imaging and compressed sensing to accelerate MRI data acquisition. Firstly, a method is proposed to improve the conventional GRAPPA using cross-sampled auto-calibration data. This method use cross-sampled auto-calibration data instead of the conventional parallel-sampled auto-calibration data …

Optical Cryoimaging Of Celular Redox In Kidneys From Diabetic Mice, Sepideh Maleki

Theses and Dissertations

Diabetic Nephropathy (DN) is the major single cause of end stage renal diseases (ESRD) in the United States. Diabetes is the third leading fatal disorder after cancer and heart disease. It is affecting 8.3% of the residents of the United States, with a total healthcare cost of $174 billion/yr by 2010.

There currently exists a need for a sensitive and specific diagnosis for temporal detection of oxidative stress (OS) in cellular metabolic levels, which plays an early role in the development of DN. The objective of this research is to use a fluorescence optical imaging technique in order to delineate …