Biomedical Engineering and Bioengineering Commons^™

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 …