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Bioengineering Program

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Incorporation of recombinant fibronectin into genetically engineered elastin-based polymers

2009-11-17 , Balderrama, Fanor Alberto

Cardiovascular disease is the main cause of death in the United States. Many of these conditions require the grafting or bypassing of compromised blood vessels. To this effect, biological vascular grafts (autografts and allografts) are the first line of action. However, when the patient lacks vasculature suitable for grafting use, several synthetic grafting options are available. The search for an inert biomaterial for vascular grafts has proven to be unsuccessful. This makes the interaction taking place on the blood-biomaterial interface critical for the success of the grafts. This thesis introduces a new bio-inspired approach to tackle the mechanical and biological challenges of vascular material design. The hypothesis of this research is that recombinant fibronectin protein can be stably incorporated onto elastin-mimetic polymers to increase endothelialization. Recombinant elastin, designed to recreate the mechanical properties of natural elastin as a candidate material for vascular graft fabrication, was used as a model surface. Recombinant fibronectin-functionalized elastin-mimetic polymer displayed significant improvement in cell adhesion. Quantification of surface bound recombinant fibronectin verified the concentration dependence of this cell adhesive behavior. Modified elastin-mimetic polymer also demonstrated an enhanced ability to support endothelial cell proliferation. Furthermore, the stability of recombinant fibronectin-modified polymers was assessed. These studies provide the foundation for fabricating elastin-mimetic vascular grafts with improved endothelialization and subsequent biological performance.

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Stucture and thermomechanical behavior of nitipt shape memory alloy wires

2009-04-10 , Lin, Brian E.

The objective of this work is to understand the structure-property relationships in a pseudoelastic composition of polycrystalline NiTiPt (Ti-42.7 at% Ni-7.5 at% Pt). Structural characterization of the alloy includes grain size determination and texture analysis while the thermo-mechanical properties are explored using tensile testing. Variation in heat treatment is used as a vehicle to modify microstructure. The results are compared to experiments on Ni-rich NiTi alloy wires (Ti-51.0 at% Ni), which are in commercial use in various biomedical applications. With regards to microstructure, both alloys exhibit a <111> fiber texture along the wire drawing axis, however the NiTiPt alloy's grain size is smaller than that of the Ni-rich NiTi wires, while the latter materials contain second phase precipitates. Given the nanometer scale grain size in NiTiPt and the dispersed, nanometer scale precipitate size in NiTi, the overall strength and ductility of the alloys are essentially identical when given appropriate heat treatments. Property differences include a much smaller stress hysteresis and smaller temperature dependence of the transformation stress for NiTiPt alloys compared to NiTi alloys. Potential benefits and implications for use in vascular stent applications are discussed.

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Microstimulation and multicellular analysis: A neural interfacing system for spatiotemporal stimulation

2008-05-19 , Ross, James

Willfully controlling the focus of an extracellular stimulus remains a significant challenge in the development of neural prosthetics and therapeutic devices. In part, this challenge is due to the vast set of complex interactions between the electric fields induced by the microelectrodes and the complex morphologies and dynamics of the neural tissue. Overcoming such issues to produce methodologies for targeted neural stimulation requires a system that is capable of (1) delivering precise, localized stimuli a function of the stimulating electrodes and (2) recording the locations and magnitudes of the resulting evoked responses a function of the cell geometry and membrane dynamics. In order to improve stimulus delivery, we developed microfabrication technologies that could specify the electrode geometry and electrical properties. Specifically, we developed a closed-loop electroplating strategy to monitor and control the morphology of surface coatings during deposition, and we implemented pulse-plating techniques as a means to produce robust, resilient microelectrodes that could withstand rigorous handling and harsh environments. In order to evaluate the responses evoked by these stimulating electrodes, we developed microscopy techniques and signal processing algorithms that could automatically identify and evaluate the electrical response of each individual neuron. Finally, by applying this simultaneous stimulation and optical recording system to the study of dissociated cortical cultures in multielectode arrays, we could evaluate the efficacy of excitatory and inhibitory waveforms. Although we found that the proximity of the electrode is a poor predictor of individual neural excitation thresholds, we have shown that it is possible to use inhibitory waveforms to globally reduce excitability in the vicinity of the electrode. Thus, the developed system was able to provide very high resolution insight into the complex set of interactions between the stimulating electrodes and populations of individual neurons.

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Bayesian based risk stratification of atrial fibrillation in coronary artery bypass graft patients

2007-05-22 , Wiggins, Matthew Corbin

Roughly thirty percent of coronary artery bypass graft (CABG) patients develop atrial fibrillation (AF) in the five days following surgery, increasing the risk of stroke, prolonging hospital stay three to four days, and increasing the overall cost of the procedure. Current pharmacologic and nonpharmacologic means of AF prevention are suboptimal, and their side effects, expense, and inconvenience limit their widespread application. An accurate method for identifying patients at high risk for postoperative AF would allow these methods to be focused on the patients on which its utility would be highest. The main objective of this research was to develop a Bayesian network (BN) which could model/predict/assign risk of the occurrence of atrial fibrillation in CABG patients using retrospective data. A secondary objective was to develop an integrated framework for more advanced methods of feature selection and fusion for medical classification/prediction. We determined that the naïve Bayesian network classifier used with features selected by a genetic algorithm is a better classifier to use, given our cohort. The naïve BN allows for reasonable prediction despite being presented with patients with missing data points as might occur in the hospital. This classifier achieves a sensitivity of 0.63 and a specificity of 0.73 with an AUC of 0.74. Furthermore, this system is based on probabilities that are well understood and easily incorporated into a clinical environment. These probabilities can be altered based on the cardiologists prior knowledge through Bayesian statistics, allowing for online sensitivity analysis by doctors, to perceive the best treatment options. Contributions of this research include: - An accurate, physician-friendly, postoperative AF risk stratification system that performs even under missing data conditions, while outperforming the state of the art system, - A thorough analysis of previously examined and novel pre- and postoperative clinical and ECG features for postoperative AF risk stratification, - A new methodology for genetic algorithm-built traditional Bayesian network classifiers allowing dynamic structure through novel chromosome, operator, and fitness definitions, and - An integrated methodology for inclusion of doctor s expert knowledge into a probabilistic diagnosis support system.

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Long-term patency of a polymer vein valve

2009-07-08 , Midha, Prem Anand

Chronic Venous Insufficiency (CVI) is a condition in present in almost 27% of adults in which an insufficient amount of blood is pumped back to the heart due to damaged or poorly apposed one-way valves in the leg veins. During forward flow, vein valves allow blood to return to the heart while posing very little resistance to the flow. During gravity-driven reverse flow, normal valves close and prevent blood from flowing backward through the valve. Incompetent, or damaged, vein valves cannot prevent this reverse flow and lead to a pooling of blood at the feet. CVI is a painful disease presents itself in various ways, including varicose veins, ulcerations of the lower extremities, and severe swelling. Current therapies and treatments include compressive stockings, destruction or removal of affected veins, valve repair, and valve transplants. The implantation of prosthetic vein valves is a future treatment option that does not require an invasive surgery, human donor, or lengthy hospital stay. While no prosthetic vein valves are currently commercially available, this thesis describes the design, verification, and validation of a novel prosthetic vein valve. Verification tests include CFD simulations, functional tests, mechanical tests, and in vitro thromogenicity tests. The validation of the device was done through an animal study in sheep external jugular veins. CFD analysis verified that shear rates within the valve support its lower thrombogenicity as compared to a previous vein valve. Benchtop tests demonstrate superiority in short-term patency over a previous polymer valve. In a sheep study, patency was shown at 6 weeks, surpassing many autograft valves and showing great potential to meet the goal of 3 month patency in sheep.

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Development of a visualization and information management platform in translational biomedical informatics

2009-04-06 , Stokes, Todd Hamilton

Translational Biomedical Informatics (TBMI) is an emerging discipline expanding beyond traditional bioinformatics, with a focus on developing computational technologies for real-world biomedical practice. The goal of my Ph.D. research is to address a few key challenges in TBI, including: (1) the high quality and reproducibility required by medical applications when processing high throughput data, (2) the need for knowledge management solutions that allow molecular data to be handled and evaluated by researchers, regulators, and doctors collectively, (3) the need for near real-time, efficient access to decision-oriented visualizations of integrated data and data processing results, and (4) the need for an integrated solution that can evolve as medical consensus evolves, without requiring retraining, overhaul or replacement. This dissertation resulted in the development and adoption of concrete web-based application deliverables in regular use by bioinformaticians, clinicians, biologists and nanotechnologists. These include: the Chip Artifact Correction (caCORRECT) web site and grid services, the ArrayWiki community microarray repository, and the SimpleVisGrid visualization grid services (including eGOMiner, nanoDRIVE, PathwayVis and SphingoVisGrid).

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Development of a small animal model to study tissue engineering strategies for growth plate defects

2007-07-10 , Coleman, Rhima M.

The growth plate is a cartilaginous tissue responsible for the longitudinal growth of long bones. It is a complex tissue composed of chondrocytes whose maturation and proliferation is tightly regulated by a biochemical feedback loop. Injury to this tissue can result in a limb length discrepancy or angular deformity that may lead to life long disability. Given the recent rise in the number of growth plate injuries and the variability in success of current therapies, there is a significant need for a greater understanding of growth plate injury pathology and the development of improved treatment strategies. Cartilage tissue engineering strategies offer an attractive alternative to regenerating growth plate tissue and restoring growth function. Bone marrow-derived stem cells (BMSCs) have been shown to be able to undergo chondrogenic differentiation and in vitro and in vivo and therefore offers an appealing and abundant cell resource for developing tissue engineering strategies for the treatment of growth plate defects. However, the dependence of chondrogenic differentiation and matrix accumulation on monolayer expansion protocols and three-dimensional (3D) culture environment has received little attention. Prior to developing treatment strategies for growth plate injury repair, it is essential to first understand the interconnection between alterations in growth plate morphology and subsequent limb deformities. To that end, we have established a surgical defect model of growth plate injury in Sprague Dawley rats and developed a novel technique to quantitatively monitor growth plate morphology in health and disease using microcomputed tomography (micro-CT) imaging. In an effort to develop a tissue engineering treatment strategy for growth plate injury, the role of monolayer expansion, 3D scaffold, and growth factor regimen in the chondrogenic differentiation of rat BMSCs was also examined. This research study has demonstrated the utility of micro-CT as a non-invasive imaging modality for assessing growth plate injury and repair. This work has also provided an improved understanding of the interrelationship of monolayer expansion, 3D culture environment, and growth factor regimen in BMSC chondrogenic differentiation. Finally, this work suggests that an injectable in situ gelling hydrogel is a feasible method for decreasing limb length discrepancies, however, neither implantation of agarose alone into the defect nor the inclusion of BMSCs fully corrects growth disruption.

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Quality control for translational biomedical informatics

2009-07-02 , Moffitt, Richard Austin

Translational biomedical informatics is the application of computational methods to facilitate the translation of basic biomedical science to clinical relevance. An example of this is the multi-step process in which large-scale microarray-based discovery experiments are refined into reliable clinical tests. Unfortunately, the quality of microarray data is a major issue that must be addressed before microarrays can reach their full potential as a clinical molecular profiling tool for personalized and predictive medicine. A new methodology, titled caCORRECT, has been developed to replace or augment existing microarray processing technologies, in order to improve the translation of microarray data to clinical relevance. Results of validation studies show that caCORRECT is able to improve the mean accuracy of microarray gene expression by as much as 60%, depending on the magnitude and size of artifacts on the array surface. As part of a case study to demonstrate the widespread usefulness of caCORRECT, the entire pipeline of biomarker discovery has been executed for the clinical problem of classifying Renal Cell Carcinoma (RCC) specimens into appropriate subtypes. As a result, we have discovered and validated a novel two-gene RT-PCR assay, which has the ability to diagnose between the Clear Cell and Oncocytoma RCC subtypes with near perfect accuracy. As an extension to this work, progress has been made towards a quantitative quantum dot immunohistochemical assay, which is expected to be more clinically viable than a PCR-based test.

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Study of early signaling events in T cell activation enabled through a modular and multi-time point microfluidic device

2008-11-19 , Rivet, Catherine Aurelie

Binding of the antigen receptor on T cells initiates a rapid series of signaling events leading to an immune response. To fully understand T cell mediated immunity, underlying regulatory properties of the receptor network must be understood. Monitoring dynamic protein signaling events allows for network analysis. Unfortunately, dynamic data acquisition is often extremely time-consuming and expensive with conventional methods; the number of proteins monitored at the same time on the same sample is limited. Furthermore, with conventional, multi-well plate assays it is difficult to achieve adequate resolution at sub-minute timescales. Microfluidics is a capable alternative, providing uniformity in sample handling to reduce error between experiments and precision in timing, an important factor in monitoring phosphorylation events that occur within minutes of stimulation. We used a two-module microfluidic platform for simultaneous multi-time point stimulation and lysis of T cells to investigate early signaling events with a resolution down to 20 seconds using only small amounts of cells and reagents. The device did not elicit adverse cellular stress in Jurkat cells. The activation of 6 important proteins in the signaling cascade upon stimulation with a soluble form of α-CD3 in the device was quantified and compared under a variety of conditions. First, in comparison to manual pipetting, the microdevice exhibits significantly less error between experiments. Secondly, a comparison between Jurkat cells and primary T cells shows similar dynamic trends across the 6 proteins. Finally, we have used the device to compare properties of long-term vs, short-term cultured primary T cells. As expected, older cells present a much weakened response to antigenic cues, as measured with TCR response markers. This modular microdevice provides a flexible format for investigating cell signaling properties through the use of soluble cue stimuli.

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Coated microneedles and microdermabrasion for transdermal delivery

2007-07-09 , Gill, Harvinder Singh

The major hurdle in the development of transdermal route as a versatile drug delivery method is the formidable transport barrier provided by the stratum corneum. Despite decades of research to overcome the stratum corneum barrier, limited success has been achieved. The objectives of this research were to develop and characterize two different strategies to overcome the stratum corneum barrier for transdermal delivery of biopharmaceuticals and vaccines. In the first strategy, coated microneedles (sharp-tipped, micron-sized structures) were developed to enable delivery of drugs directly into the skin by bypassing the stratum corneum barrier. In the second strategy, instead of bypassing the barrier, microdermabrasion was used to selectively abrade stratum corneum with sharp microparticles for topical drug application. Coated microneedles For developing painless microneedles, the first detailed study was performed to characterize the effect of microneedle geometry on pain caused by microneedle insertions in human volunteers. This study demonstrated that microneedles are significantly less painful than a 26-gage hypodermic needle and that decreasing microneedle length and numbers reduces pain. Next, the first in-depth study of microneedle coating methods and formulations was performed to (i) develop a novel micron-scale dip-coating process, (ii) test the breadth of compounds that can be coated onto microneedles, and (iii) develop a rational basis to design novel coating formulations based on the physics of dip-coating. Finally, a plasmid DNA-vaccine was coated onto microneedles to immunize mice, to provide the first evidence that microneedle-based skin immunization can generate a robust in vivo antigen-specific cytotoxic-T-lymphocyte response using similar, or lower, DNA doses on microneedles as when using the gene gun or intramuscular injection. Microdermabrasion We demonstrated for the first time that microdermabrasion in monkeys and humans can selectively, yet completely remove the stratum corneum layer. Using a mobile mode of microdermabrasion, an increase in the number of treatment passes led to greater tissue removal. Furthermore, topical application of Modified Vaccinia Ankara virus after microdermabrasion induced virus-specific antibodies in monkeys. In conclusion, both coated microneedles and microdermabrasion were developed to enable delivery of biomolecules into the skin, indicating their potential for transdermal delivery of a wide range of biopharmaceuticals and vaccines.

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