Engineering Commons^™

Using Pareto Fronts To Evaluate Polyp Detection Algorithms For Ct Colonography, Adam Huang, Jiang Li, Ronald M. Summers, Nicholas Petrick, Amy K. Hara

Electrical & Computer Engineering Faculty Publications

We evaluate and improve an existing curvature-based region growing algorithm for colonic polyp detection for our CT colonography (CTC) computer-aided detection (CAD) system by using Pareto fronts. The performance of a polyp detection algorithm involves two conflicting objectives, minimizing both false negative (FN) and false positive (FP) detection rates. This problem does not produce a single optimal solution but a set of solutions known as a Pareto front. Any solution in a Pareto front can only outperform other solutions in one of the two competing objectives. Using evolutionary algorithms to find the Pareto fronts for multi-objective optimization problems has been …

Loss Of Hdmx Leads To Alterations In Gene Expression And Inhibition Of Cell Growth In Tumor Cells With Wild-Type P53, Katherine Ann Heminger

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Mutations in the p53 tumor suppressor gene are among the most prevalent molecular abnormalities in human cancer. While half of all human tumors possess p53 mutations, inactivation of wild-type p53 can also occur through a variety of mechanisms that do not involve p53 gene mutation or deletion. This dissertation focuses on human tumor cell lines harboring wild-type p53 protein and elevated levels of HdmX and/or Hdm2, two critical negative regulators of p53 function. My hypothesis is that loss of HdmX in tumor cells with wild-type p53 and over-expressed HdmX, will activate p53 and induce p53 target genes leading to growth …

Optimal Eeg Channels And Rhythm Selection For Task Classification, Vikramvarun Kannan Adikarapatti

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The Primary Objective of this research is to implement an automatic method for selecting the most optimal EEG channels for task classification purposes. The secondary objective of this research is to choose the most optimal EEG rhythm from which the optimal EEG channels would be selected automatically. The automatic selection of the optimal channels is enabled by implementing the Common Spatial Patterns algorithm (CSP). Common spatial analysis is performed on the data recorded. By choosing the channels with high spatial pattern values the optimal channels are chosen. The optimal frequency bands are chosen by splitting the data from a single …

Structural And Signaling Elements Important For The Efficient Degradation Of Bhmt Through Macroautophagy, Carol A. Mercer

Browse all Theses and Dissertations

Healthy cells maintain a dynamic and responsive intracellular environment that is marked by the synthesis and degradation of proteins, complex macromolecules and organelles. Autophagy, literally "self-eating," is a mechanism that delivers cellular cargo to the lytic compartment for digestion. Defects in the regulation of autophagy have been implicated in pathologies such as cancer and neurodegenerative disease, making the study of its regulation compelling. However, few studies have looked at the regulation of mammalian autophagy as a function of a specific cargo protein. Previous studies had indicated that the metabolic enzyme betaine homocysteine methyltransferase (BHMT) is degraded through an autophagic mechanism. …

Biochemical Characterization Of Htrf1 And Htep1, Two Proteins Involved In Telomere Maintenance, Kambiz Tahmaseb

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Telomeres are the structures that protect the ends of linear chromosomes from fusion and degradation. The telomere consists of tandem repeated DNA sequences that can range from hundreds of bases to kilo-bases depending on the organism. As the cells of an organism replicate their DNA, these repeats are lost due to the end replication problem, where the ends of linear DNA cannot be fully replicated. As the telomeres are shortened through each round of replication, they eventually reach a critical point. Once the telomeres are too short and the cell risks losing coding sequences, a signaling pathway is initiated that …

Investigating The Role Of Subunit Iii In The Structure And Function Of Rhodobacter Sphaeroides Cytochrome C Oxidase, R. Ryan Geyer

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The role of subunit III (SIII) in cytochrome c oxidase structure and function was investigated using enzyme isolated from the bacterium Rhodobacter sphaeroides. Energy minimization calculations suggested that in the absence of SIII, subunit I (SI) adopted a more open conformation. This observation was tested through the use of limited proteolysis using, á-chymotrypsin. The results showed that in the absence of SIII the solution structures of wild-type and I/II oxidase were not significantly different, and that proteolysis occurred exclusively at the N and C-termini of SI. Upon inactivation of I/II oxidase by catalytic turnover, and subsequent digestion with the protease …

Functional Interplay Between Subthreshold Ion Channels In Preautonomic Neurons Of The Hypothalamic Paraventricular Nucleus In Health And Disease Conditions, Patrick M. Sonner

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Under normal conditions, blood pressure is tightly regulated through autonomic tonic and reflex mechanisms. However, when the set-point for blood pressure is chronically elevated, hypertension occurs. Hypertension if untreated can lead to further complications including heart failure, stroke and kidney failure. Elevated sympathetic outflow is known to contribute to the development and/or maintenance of hypertension, and while the hypothalamic paraventricular nucleus (PVN), a preautonomic center, has been implicated in the elevation of sympathetic activity during hypertension, the precise pathophysiological mechanisms underlying sympathoexcitation remain unclear. Subthreshold ion channels, including the A-type K ⁺(I _A) and the T-type Ca ^{2+ …}

Fabrication And Testing Of Scaffolds For Cell Growth From Ionic Liquid Solubilized Fibroin, Maneesh Kumar Gupta

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The advent of tissue engineering has spurred research into developing materials to act as scaffolds for tissue growth. These scaffolds require materials capable of mimicking the in vivo conditions so that tissues can be grown effectively in vitro. Silk is an attractive biomaterial for use in tissue engineering applications because of its slow degradation, excellent mechanical properties, and biocompatibility. The major objective of the research in this thesis is to demonstrate a simple method to cast films directly from silk fibroin dissolved in an ionic liquid. The films cast from the silk ionic liquid solution were found to support normal …

A “Sprinkler” Vegetative Treatment System, Jason Gross, Chris G. Henry

Department of Agricultural and Biological Systems Engineering: Presentations and White Papers

Vegetative Treatment Systems have historically been a practice for the treatment and utilization of open lot livestock wastes. Use of these systems has been rejuvenated in recent years. A “sprinkler” vegetative treatment area (VTA) has been designed and developed as a proof of concept for addressing challenges experienced with small and medium Animal Feeding Operations. The focus of this paper is to report on the design, economics, challenges and the lessons learned on the development of this system. Cost data shows the cost of a “sprinkler” VTS to range between $31 to $63/head, compared to $51 to $170/head for a …

Sharing Distance Education Courses Among Universities, Leon Schmacher, Thomas Brumm, John Slocombe, Jack L. Schinstock

Department of Agricultural and Biological Systems Engineering: Presentations and White Papers

Four universities collaborated to develop mechanized systems management (agricultural systems management, agricultural systems technology, etc.) courses to be shared via distance education. Funded by a USDA Higher Education Challenge Grant, these undergraduate and graduate courses were initially offered to students at Iowa State University, Kansas State University, the University of Missouri, and the University of Nebraska-Lincoln. This effort is affiliated with the Great Plains Interactive Distance Education Alliance (Great Plains IDEA).

The objectives of this cooperative effort were to: (1) develop a collaborative, multi-state educational effort to add depth and breadth to each university’s instructional program in mechanized systems management; …

Energy And Environmental Contributions Of Corn-Ethanol, Adam Liska, Kenneth Cassman, Haishun Yang

Adam Liska Papers

Rapid development of regulatory mechanisms to mitigate greenhouse gas (GHG) emissions requires that the biofuel industry employ standard methods to evaluate biofuel systems comprising both crop production systems and biorefineries. Biofuel systems associated with a variety of organic feedstocks have a range of performance capabilities, and recent life-cycle assessment studies of these different systems have used inconsistent methods, leading to confusion about biofuel energy efficiency and GHG mitigation. Hence, there is a critical need for well documented life-cycle metrics for consistent biofuel evaluation that are established and supported by a national or international governing body. Standardization of net energy and …

Pyrene Mineralization By Mycobacterium Sp. Strain Kms In A Barley Rhizosphere, R. Child, C. Miller, Y. Liang, Ronald C. Sims, A. J. Anderson

Biological Engineering Faculty Publications

To determine whether the soil Mycobacterium isolate KMS would mineralize pyrene under rhizosphere conditions, a microcosm system was established to collect radioactive carbon dioxide released from the labeled polycyclic aromatic hydrocarbon. Microcosms were designed as sealed, flow-through systems that allowed the growth of plants. Experiments were conducted to evaluate mineralization of ¹⁴C-labeled pyrene in a sand amended with the polycyclic aromatic hydrocarbons degrading Mycobacterium isolate KMS, barley plants, or barley plants with roots colonized by isolate KMS. Mineralization was quantified by collecting the ¹⁴CO₂ produced from ¹⁴C-labeled pyrene at intervals during the 10-d incubation period. Roots …

Temperature Effect On Tert-Butyl Alcohol (Tba) Biodegradation Kinetics In Hyporheic Zone Soils, M. H. Greenwood, Ronald C. Sims, J. E. Mclean, W. J. Doucette

Biological Engineering Faculty Publications

Background

Remediation of tert-butyl alcohol (TBA) in subsurface waters should be taken into consideration at reformulated gasoline contaminated sites since it is a biodegradation intermediate of methyl tert-butyl ether (MTBE), ethyl tert-butyl ether (ETBE), and tert-butyl formate (TBF). The effect of temperature on TBA biodegradation has not been not been published in the literature.

Methods

Biodegradation of [U ¹⁴C] TBA was determined using hyporheic zone soil microcosms.

Results

First order mineralization rate constants of TBA at 5°C, 15°C and 25°C were 7.84 ± 0.14 × 10^-3, 9.07 ± 0.09 × 10^-3, and 15.3 ± 0.3 …

Theory And Application Of Landfarming To Remediate Pahs And Mineral Oil Contaminated Sediments: Beneficial Reuse, J. Harmsen, W. Rulkens, Ronald C. Sims, P. Ritjema, A. Zweers

Biological Engineering Faculty Publications

When applying landfarming for the remediation of contaminated soil and sediment, a fraction of the soil-bound contaminant is rapidly degraded; however, a residual concentration may remain, which slowly degrades. Degradation of polycyclic aromatic hydrocarbons (PAHs) and mineral oil can be described using a multi-compartment model and first-order kinetics, in which three degradable fractions are distinguished; (1) rapid, (2) slowly, and (3) very slowly degradable. Using this model populated with data from long-term experiments (initiated in 1990), it is shown that time frames from years to decades can be necessary to clean the soil or sediment to obtain a target below …

Licenses, Leases And Other Contractual Arrangements For The Exploration And Production Of Petroleum A Comparative Study Between Nigeria And The United States, Omolara Elumelu

LLM Theses and Essays

Much has been written about Oil and Gas leases. This paper focuses on the various Oil and Gas leases and other contractual arrangements for oil and gas exploration and production in Nigeria and the United States. The paper examines the origin, structure, development and mode of operations in both jurisdictions and concludes with a comparative analysis of both jurisdictions.

Validating Pareto Optimal Operation Parameters Of Polyp Detection Algorithms For Ct Colonography, Jiang Li, Adam Huang, Nicholas Petrick, Jianhua Yao, Ronald M. Summers, Maryellen L. Giger (Ed.), Nico Karssemeijer (Ed.)

Electrical & Computer Engineering Faculty Publications

We evaluated a Pareto front-based multi-objective evolutionary algorithm for optimizing our CT colonography (CTC) computer-aided detection (CAD) system. The system identifies colonic polyps based on curvature and volumetric based features, where a set of thresholds for these features was optimized by the evolutionary algorithm. We utilized a two-fold cross-validation (CV) method to test if the optimized thresholds can be generalized to new data sets. We performed the CV method on 133 patients; each patient had a prone and a supine scan. There were 103 colonoscopically confirmed polyps resulting in 188 positive detections in CTC reading from either the prone or …

Design Of An Electrospun Type Ii Collagen Scaffold For Articular Cartilage Tissue Engineering, Catherine Pemble Barnes

Theses and Dissertations

Traumatic defects in articular cartilage can lead to joint disease and disability including osteoarthritis. Because cartilage is unable to regenerate when injured, the field of tissue engineering holds promise in restoring functional tissue. In this research, type II collagen was electrospun, cross-linked, and tested as scaffolds for supporting chondrocyte growth. The mechanical, biochemical, and histological characteristics of the engineered tissue were assessed as a function of the electrospinning solution concentration (i.e. scaffold fiber diameter and pore properties) and as a function of the time in culture (evaluated at 2, 4, and 6 weeks). Fiber diameter had a linear relationship with …

The Development Of A Multi-Directional Wear Apparatus And The Characterization And Correlation Of Biomechanical And Biotribological Properties Of Bovine Articular Cartilage, Kelly J. Shields

Theses and Dissertations

A multi-directional wear apparatus was developed to simulate the kinematic motion of diarthrodial joints. A comprehensive evaluation including biotribological and biomechanical characterization of articular surfaces was performed with concomitant translational and oscillating rotational motion similar to that experienced in vivo. Various system parameters were evaluated in the designed experiments including normal load magnitude (high/low), surface quality (defect/no defect), and wear pattern (with/without rotation). Biomechanical characterization was achieved through stress relaxation and dynamic cyclical testing. Quasi-linear viscoelastic theory was used to curve-fit the stress relaxation data, while the dynamic data was used to determine the dynamic properties through Fast Fourier Transform …

Development And Validation Of A Computational Musculoskeletal Model Of The Elbow Joint, Justin Paul Fisk

Theses and Dissertations

Musculoskeletal computational modeling is a versatile and effective tool which may be used to study joint mechanics, examine muscle and ligament function, and simulate surgical reconstructive procedures. While injury to the elbow joint can be significantly debilitating, questions still remain regarding its normal, pathologic, and repaired behavior. Biomechanical models of the elbow have been developed, but all have assumed fixed joint axes of rotation and ignored the effects of ligaments. Therefore, the objective of this thesis was to develop and validate a computational model of the elbow joint whereby joint kinematics are dictated by three-dimensional bony geometry contact, ligamentous constraints, …

Quantifying Kinematics Of Purposeful Movements To Real, Imagined, Or Absent Functional Objects: Implications For Modelling Trajectories For Robot-Assisted Adl Tasks, Kimberly J. Wisneski, Michelle J. Johnson

Biomedical Engineering Faculty Research and Publications

Background

Robotic therapy is at the forefront of stroke rehabilitation. The Activities of Daily Living Exercise Robot (ADLER) was developed to improve carryover of gains after training by combining the benefits of Activities of Daily Living (ADL) training (motivation and functional task practice with real objects), with the benefits of robot mediated therapy (repeatability and reliability). In combining these two therapy techniques, we seek to develop a new model for trajectory generation that will support functional movements to real objects during robot training. We studied natural movements to real objects and report on how initial reaching movements are affected by …

Development Of Fast, Distributed Computational Schemes For Full Body Bio-Models And Their Application To Novel Action Potential Block In Nerves Using Ultra-Short, High Intensity Electric Pulses, Ashutosh Mishra

Electrical & Computer Engineering Theses & Dissertations

An extremely robust and novel scheme for computing three-dimensional, time-dependent potential distributions in full body bio-models is proposed, which, to the best of our knowledge, is the first of its kind. This simulation scheme has been developed to employ distributed computation resources, to achieve a parallelized numerical implementation for enhanced speed and memory capability. The other features of the numerical bio-model included in this dissertation research, are the ability to incorporate multiple electrodes of varying shapes and arbitrary locations. The parallel numerical tool also allows for user defined, current or potential stimuli as the excitation input. Using the available computation …

Elastic Degradable Polyurethanes For Biomedical Applications, Changhong Zhang

All Theses

Several series of polyurethanes were synthesized with linear or crosslinked structures by using different synthesis routes. Two studies are mentioned: (1) the synthesis of degradable polyurethanes with linear structure and the investigation of the elasticity and cytophilicity of the materials as function of the chain extender, and (2) the synthesis and the investigation of the biocompatibility, degradation, hydrophilicity and mechanical properties of the polyurethane-based hydrogels with crosslinked structure.

Validation Of An Inertial Sensor System For Quantifying Knee Function, Aaron Koslin

All Theses

Gait analysis has become a useful tool for clinicians in evaluating the progression of pathologies through functional analysis. The high cost and dedicated laboratories associated with the traditional camera-based motion analysis systems present the need for an alternative system. Direct measurement of kinetic parameters using inertial sensors (gyroscopes and accelerometers), in place of indirect calculations from position data obtained using cameras, has been shown effective in resolving important gait parameters.
In order to directly compare gait parameters obtained using inertial sensors and a camera system, data was simultaneously collected from both systems for seven test subjects during normal gait. Three …

Tannic Acid Crosslinked Collagens And Potential For Breast Tissue Engineering, Cheryl Parzel

All Theses

The purpose of this study was to develop and assess a potential key feature in a minimally-invasive breast reconstruction device and to collect information for an in vitro tissue test system. Tannic acid is a hydrolysable plant tannin, and it has been determined that tannic acid functions as a collagen crosslinking agent through both hydrogen bonding mechanisms and hydrophobic effects. Additionally, current research suggests that tannic acid may have anti-tumor properties. Therefore, it has been proposed that tannic acid can be used as an agent to induce apoptotic processes in any transplanted adult stem cells that are inclined to spontaneously …

Development Of A Cellular Fiber Spinning Technology For Regenerative Medicine, Willie Jones

All Theses

In order to prove that our textile hollow fiber spinning apparatus was adequate for cellular encapsulation, we confirmed the viability and metabolic activity of green fluorescent protein (GFP) labeled bovine mammary epithelial cells (MAC-Ts) that were encapsulated in either the wall or lumen of alginate fibers. After a 21 day in vitro macroscopic evaluation, no decrease in fluorescence was observed; and it was determined that MAC-Ts encapsulated under both methods produced lactic acid and consumed glucose. Histomorphological analyses revealed that the diameter of the MAC-Ts increased under both encapsulation scenarios, with little to no evidence of cell cluster propagation. Based …

Tribological Systems For The Evaluation Of Supercritical Carbon Dioxide Sterilized Ultra-High Molecular Weight Polyethylene, John Desjardins

All Dissertations

Polymeric biomaterials are especially susceptible to changes in mechanical and surface material properties as a result of sterilization processes that involve heat, moisture and/or irradiation. This is problematic for polymeric materials used in total joint replacement bearings, as these constructs must retain their superior mechanical and tribological properties over their expected 10-20 years of implantation. A younger more active patient population has now exacerbated this longevity issue with service lifetimes of 20+ years now being expected. Supercritical phase carbon dioxide (SC-CO2) is an industrial solvent that has shown great promise as a sterilizing agent in the food industry. Recently, SC-CO2 …

Stabilization Of Vascular Elastin By Treatment With Tannins, Jason Isenburg

All Dissertations

Elastin is an important component of the extracellular matrix that endows cardiovascular tissue with the ability to extend and recoil repetitively. It has been shown that elastin may be vulnerable to enzymatic degradation and calcification in certain pathological cases. As a result, elastin degeneration may be associated with the failure of tissue-derived cardiovascular devices, such as bioprosthetic heart valves, as well as the development and progression of aortic aneurysms, a disease associated with progressive connective tissue degeneration of the arterial wall. Therefore, an elastin stabilizing agent may be beneficial for both applications. As such, our objectives for elastin stabilization are …

Soccer Headgear Effects On Impact Profiles During A Heading Scenario, Ryan Posey

All Theses

The risk of head injuries in the sport of soccer has recently become a topic of concern, particularly with youth players whom may suffer long-lasting or even permanent effects from a severe head injury. In response to these worries, headguards have been developed specifically for use in soccer. These headguards have been studied using crash test dummy heads mounted with various electronic instruments - accelerometers, gyroscopes, etc. The headgear-mounted dummy heads have been struck with various objects (soccer ball, another dummy head, pole, etc) to test for changes in head acceleration response.
Testing of soccer headgear has previously been limited …

Spectroscopic Characterization Of Biliary Tract Tissues In-Vivo To Assist Laparoscopic Cholecystectomy, Sarita Kommera

Bioengineering Theses - Archive

Laparoscopic Cholecystectomy is a surgical method for removal of gallbladder when it is diseased with gall stones. Almost 750,000 people are affected with this disease annually in USA. Gall bladder is removed by placing an incision on the cystic duct. This duct is totally embedded in fat (which is a few mm thick) in most of the cases and it becomes a huge problem decreasing the visual capability of the surgeon to distinctly locate the duct. Near Infrared Spectroscopy (NIRS) can solve the fuzziness as it penetrates in a few mm thick tissues. NIRS is one of the simplest techniques …

Novel Intraocular Drug Delivery System For The Prevention Of Posterior Capsule Opacification, Brett Thomes

Bioengineering Dissertations - Archive

Posterior capsule opacification (PCO) is a major complication associated with the implantation of intraocular lens (IOLs). Evidence suggests that PCO formation is caused by abnormal lens epithelial cell (LEC) migration/proliferation. We hypothesize that pharmacologic agents must target inflammatory cells in addition to LECs to inhibit PCO formation. To successfully target both inflammatory cells and LECs, a novel intraocular drug delivery system (DDS) was developed for implantation in the lens capsular bag. Such a system permits direct delivery of anti-inflammatory and anti-proliferative drugs in the lens capsule for extended periods of time resulting in reduced PCO formation. A lubricious polyurethane coating …