Digital Commons Network^™

Gene Order Phylogeny Of The Genus Prochlorococcus, Haiwei Luo, Jian Shi, William Arndt, Jijun Tang, Robert Friedman

Faculty Publications

Background
Using gene order as a phylogenetic character has the potential to resolve previously unresolved species relationships. This character was used to resolve the evolutionary history within the genus Prochlorococcus, a group of marine cyanobacteria.

Methodology/Principal Findings
Orthologous gene sets and their genomic positions were identified from 12 species of Prochlorococcus and 1 outgroup species of Synechococcus. From this data, inversion and breakpoint distance-based phylogenetic trees were computed by GRAPPA and FastME. Statistical support of the resulting topology was obtained by application of a 50% jackknife resampling technique. The result was consistent and congruent with nucleotide sequence-based and gene-content based …

Monitoring Tissue Engineering Using Magnetic Resonance Imaging, Huihui Xu, Shadi F. Othman, Richard L. Magin

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Assessment of tissue regeneration is essential to optimize the stages of tissue engineering (cell proliferation, tissue development and implantation). Optical and X-ray imaging have been used in tissue engineering to provide useful information, but each has limitations: for example, poor depth penetration and radiation damage. Magnetic resonance imaging (MRI) largely overcomes these restrictions, exhibits high resolution (approximately 100 μm) and can be applied both in vitro and in vivo. Recently, MRI has been used in tissue engineering to generate spatial maps of tissue relaxation times (T₁, T₂), water diffusion coefficients, and the stiffness (shear moduli) of …

Quantitative Rrna-Targeted Solution-Based Hybridization Assay Using Peptide Nucleic Acid Molecular Beacons, Xu Li, Eberhard Morgenroth, Lutgarde Raskin

Department of Civil and Environmental Engineering: Faculty Publications

The potential of a solution-based hybridization assay using peptide nucleic acid (PNA) molecular beacon (MB) probes to quantify 16S rRNA of specific populations in RNA extracts of environmental samples was evaluated by designing PNA MB probes for the genera Dechloromonas and Dechlorosoma. In a kinetic study with 16S rRNA from pure cultures, the hybridization of PNA MB to target 16S rRNA exhibited a higher final hybridization signal and a lower apparent rate constant than the hybridizations to nontarget 16S rRNAs. A concentration of 10 mM NaCl in the hybridization buffer was found to be optimal for maximizing the difference between …

Biogeography-Based Optimization, Daniel J. Simon

Electrical and Computer Engineering Faculty Publications

Biogeography is the study of the geographical distribution of biological organisms. Mathematical equations that govern the distribution of organisms were first discovered and developed during the 1960s. The mindset of the engineer is that we can learn from nature. This motivates the application of biogeography to optimization problems. Just as the mathematics of biological genetics inspired the development of genetic algorithms (GAs), and the mathematics of biological neurons inspired the development of artificial neural networks, this paper considers the mathematics of biogeography as the basis for the development of a new field: biogeography-based optimization (BBO). We discuss natural biogeography and …

Development And Characterization Of Moisture- And Heat- Activated Oxygen Scavenging Nanoparticle, Youngjae Byun

All Dissertations

Alpha-tocopherol and a transition metal, iron, mixture was evaluated as a possible oxygen scavenger. The effects of moisture, amount of transition metal, and thermal processing on oxygen scavenging capability were also investigated. Results showed that alpha-tocopherol and transition metal had 6.72 cc oxygen per gram of oxygen scavenging capacity and 0.11 cc oxygen per gram per day of oxygen scavenging rate.
Nanoencapsulation technology was adopted for the possible oxygen scavenging activation system. Alpha-tocopherol-loaded poly caprolactone (PCL) nanoparticles were prepared by oil in water (O/W) emulsion solvent evaporation with ultrasonification. The effects of PCL concentration, solvent in oil phase, and ultrasonification …

Ecm Stabilization Strategies For Bioprosthetic Heart Valves For Improved Durability, Devanathan Raghavan

All Dissertations

Abstract
Approximately 85,000 heart valve replacement surgeries are performed every year in United States and about 300,000 surgeries worldwide. It is estimated that half of them are mechanical valve replacements and the other half bioprosthetic valve replacements. The use of bioprosthetic heart valves is slowly increasing. Bioprosthetic heart valves are made from porcine aortic valves or bovine pericardium. Commercially these bioprostheses are currently crosslinked using glutaraldehyde (GLUT) to prevent tissue degradation and reduce tissue antigenicity. GLUT crosslinks these bioprostheses by stabilizing the collagen present in the tissue via a Schiff base reaction of the aldehyde with the hydroxylysine / lysine …

High Speed Wavelength Tuning Of Sgdbr Lasers For Optical Coherence Tomography Applications, Benjamin Maher

Master's Theses

The application of Sample Grated Distributed Bragg Reflector (SGDBR) wavelength tunable lasers for swept-wavelength Optical Coherence Tomography (OCT) is explored. OCT is a method of measuring reflectivity versus distance into samples under test with a focused infrared light source. Swept wavelength OCT requires a laser light source that is capable of sweeping its wavelength quickly over the entire wavelength range of the tunable laser. Fast sweeping of the laser's wavelength enables real-time imaging of a wide surface area of the surface under test. This thesis will show that SGDBR lasers can be designed to meet the fast wavelength ramp speeds …

Measuring And Modeling Of Plant Root Uptake Of Organic Chemicals, Erik Dettenmaier

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Determining the root uptake of xenobiotic organic chemicals into plants is critical for assessing the human and ecological health risks associated with the consumption of plants growing in contaminated environments. Root uptake of xenobiotic organics occurs passively in conjunction with transpiration and the transport from root to shoot is ultimately controlled by passage through one or more lipid root membranes. The transpiration stream concentration factor (TSCF), the ratio between the concentration of a chemical in the xylem to that in the solution used by the roots, is used to describe the relative ability of an organic chemical to be passively …

A Three-Dimensional, Time-Dependent Circulation Model Of Utah Lake, Eric V. Callister

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Spatial and temporal variations of Utah Lake’s flow field were modeled using the Estuary Lake and Computer Model from the Centre for Water Research (CWR-ELCOM) at the University of Western Australia as part of an effort to increase understanding of the lake’s natural processes in order to restore the lake to its pristine, clear-water state and preserve the habitat of the June sucker, an endangered species. The model was validated using temperature measurements taken by sensors in 2007. The water temperature was a strong function of air temperature and incident short wave radiation, and was influenced to a lesser degree …

Estimating Total Phosphorus And Total Suspended Solids Loads From High Frequency Data, Amber Spackman Jones

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Frequently measured turbidity was examined as a surrogate for total phosphorus (TP) and total suspended solids (TSS) loads at two locations in the Little Bear River, Utah, USA. Using regression techniques, equations were developed for TP and TSS as functions of turbidity. The equations accounted for censored data, and additional explanatory variables to represent hydrological conditions were considered for inclusion in the equations. By using the resulting surrogate relationships with high frequency turbidity measurements, high frequency estimates of TP and TSS concentrations were calculated. To examine the effect of sampling frequency, reference loads were determined from the concentration records for …

Hydrogen Production By Anaerobic Fermentation Using Agricultural And Food Processing Wastes Utilizing A Two-Stage Digestion System, Reese S. Thompson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Hydrogen production by means of anaerobic fermentation was researched utilizing three different substrates. Synthetic wastewater, dairy manure, and cheese whey were combined together at different concentrations under batch anaerobic conditions to determine the optimal hydrogen producing potential and waste treatment of each. Cheese whey at a concentration of 55% was combined with dairy manure at a concentration of 45% to produce 1.53 liters of hydrogen per liter of substrate. These results are significant because the control, synthetic wastewater, which was a glucose-based substrate, produced less hydrogen, 1.34 liters per liter of substrate, than the mixture of cheese whey and dairy …

Distributed Control For Robotic Swarms Using Centroidal Voronoi Tessellations, Shelley Rounds

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This thesis introduces a design combining an emerging area in robotics with a well established mathematical research topic: swarm intelligence and Voronoi tessellations, respectively. The main objective for this research is to design an economical and robust swarm system to achieve distributed control. This research combines swarm intelligence with Voronoi tessellations to localize a source and create formations. Extensive software coding must be implemented for this design, such as the development of a discrete centroidal Voronoi tessellation (CVT) algorithm.

The ultimate purpose of this research is to advance the existing Mobile Actuator and Sensor Network (MASnet) platform to eventually develop …

Student Achievement And Affective Traits In Electrical Engineering Laboratories Using Traditional And Computer-Based Instrumentation, Matthew D. Lammi

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Distance education has the ability to transcend distance and time, reaching students anywhere at any time, particularly those underrepresented in engineering. Engineering is a practice-oriented profession requiring an interweaving of scientific theory and applied hands-on activities. Despite the need for distance education in engineering, few studies have systematically investigated the impact of student achievement and attitude in distance engineering laboratories. This quasi-experimental research addressed that need by studying the cognitive and affective domains of achievement in engineering laboratories while employing computer-based and traditional oscilloscopes. The students from two courses, electrical engineering for nonmajors and electronic fundamentals, were randomly assigned into …

Evaluation Of Arrayed-Field Concentration Measurements And U. S. Epa-Regulatory Models For The Determination Of Mixed-Source Particulate Matter Emissions, Derek Jones

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

With the continued population growth and the blurring of the urban and rural interface, air quality impacts associated with agricultural particle-producing processes are becoming increasingly important. There is a lack of emission rate data from these source types and no prescribed measurement technique available to the agricultural and regulatory communities. One technique that has shown promise is combining field measurements with inverse modeling. This approach was used herein to examine particulate emissions from an almond harvesting operation, a cotton ginning facility, and comparative emissions from conservation versus conventional tillage practices. EPAapproved models ISCST3 and AERMOD were used with AirMetrics samplers. …

'Fabrication And Characterization Of Polymer Blends And Composites Derived From Biopolymers', Suraj Sharma

All Dissertations

This research focuses on fabricating blends and composites from natural polymers especially from proteins and natural epoxy, and describing the properties of plastics made from them. Specifically, plastic samples from partially denatured feathermeal and bloodmeal proteins, derived from the animal co-products (rendering) industry, were successfully produced through a compression molding process. The modulus (stiffness) of the material obtained was found to be comparable with that of commercial synthetic materials, such as polystyrene, but was found to have lower toughness characteristics, which is a common phenomenon among plastics produced from animal and plant proteins. Therefore, this study explored blending methods for …

Characterization Of Vascular Smooth Muscle Cell Mechanical And Frictional Properties Using Atomic Force Microscopy, Jason Hemmer

All Dissertations

A working hypothesis within the Laboratory of Vascular Research is that mechanical loading on vascular smooth muscle cells (VSMCs), especially due to solid contact from endovascular devices, contributes to the development of restenosis. In order to better understand the role of mechanical loading on VSMCs in vascular disease development, it is imperative to understand the mechanical properties of VSMCs themselves. To measure the viscoelastic and frictional properties of living VSMCs in an in vitro setting, an atomic force microscope (AFM) was utilized, thereby allowing for mechanical testing of living cells in a fluid environment. In the first phase of research, …

Human Microvasculature Fabrication Using Thermal Inkjet Printing Technology, Xiaofeng Cui

All Dissertations

The current tissue engineering paradigm is that successfully engineered thick tissues must include vasculature. As biological approaches alone such as VGEF have fallen short of their promises, one may look for an engineering approach to build microvasculature. With the advent of cell printing, one may be able to build precise human microvasculature with suitable bio-ink. Human Microvascular Endothelial Cells (HMVEC) and fibrin were studied as bio-ink for microvasculature construction. Endothelial cells are the only cells to compose the human capillaries and also the major cells of blood vessel intima layer. Fibrin has been already widely recognized as tissue engineering scaffold …

Effect Of Clinically Relevant Mechanical Forces On Smooth Muscle Cell Response In Model Of Balloon Angioplasty, Kara Acampora

All Dissertations

Restenosis remains a common problem affecting the patency of endovascular intervention such as balloon angioplasty and stent placement as treatments for atherosclerosis. Denudation of the endothelial layer and the increased injury from balloon deployment can cause phenotypic changes in surrounding vascular smooth muscle cells (SMCs) in vivo. The presented work modeled this mechanical environment in vitro to investigate the role of the altered mechanical environment on the phenotypic response of SMCs. Through the system design and CFD channel characterization, a six-independent-channel system providing low oscillating wall shear stress (WSS) was manufactured to apply concurrent shear and tensile forces with uniform …

Modeling And Control Of Piezoactive Micro And Nano Systems, Saeid Bashash

All Dissertations

Piezoelectrically-driven (piezoactive) systems such as nanopositioning platforms, scanning probe microscopes, and nanomechanical cantilever probes are advantageous devices enabling molecular-level imaging, manipulation, and characterization in disciplines ranging from materials science to physics and biology. Such emerging applications require precise modeling, control and manipulation of objects, components and subsystems ranging in sizes from few nanometers to micrometers. This dissertation presents a comprehensive modeling and control framework for piezoactive micro and nano systems utilized in various applications.
The development of a precise memory-based hysteresis model for feedforward tracking as well as a Lyapunov-based robust-adaptive controller for feedback tracking control of nanopositioning stages are …

Vascular Tissue Engineering: The Creation Of Living, Non-Thrombogenic, Functional Blood Vessels Based On Elastin Scaffolds, Aditee Kurane

All Dissertations

Cardiovascular diseases are the leading cause of death worldwide. Blood vessel replacement is a common treatment for vascular diseases such as atherosclerosis, restenosis and aneurysm, with over 300,000 bypass procedures performed each year. However, vein grafts are limited due to their availability. Although synthetic vascular replacements have been successful for large diameter arteries, they have shown minimal success in arteries with diameters <6mm. This is because most synthetic materials induce thrombus formation which, within a few months of implantation, causes failure of the vascular graft due to occlusion. Tissue engineering is a promising approach to the fabrication of non-thrombogenic vascular grafts, but a reliable and expandable cell source for tissue-engineered vascular graft (TEVG) has not been established.
The work presented here is motivated by the current unavailability of an ideal tissue engineered blood vessel replacement. Our overall goal is to create a living tissue engineered vascular graft that is biodegradable, non-thromobogenic, presents low antigenicity and …

Experimental And Modeling Studies For Optimizing Flocculant-Aided Sediment Retention Ponds, Byung Joon Lee

All Dissertations

Attempts to control sediment-containing runoff and associated water quality problems have involved the establishment of many small to medium sediment retention ponds and the injection of nonionic and anionic polyacrylamide (PAM) flocculants to enhance colloid removal. However, to date use has been driven more by practicing engineers and trial-and-error approaches than by logical and consistent design approaches. Therefore, the purpose of this research was to optimize colloidal clay removal in PAM-aided sediment retention ponds by applying experimental and theoretical methodologies.
Initially, simple measurement techniques for the molecular weight (MW) and charge density (CD) of various PAMs were tested and their …

Green Roofs For A Green Town: Possibilities Of Green Roof Implementation In The Town Of Normal, Lindsey Sihau, '09

Outstanding Senior Seminar Papers

Green roofs have been growing in popularity throughout the world. Scientists have been studying them since the 1980’s. This research project reviews the literature regarding both the benefits and barriers to green roof construction and management. Policies around the nation are then examined and analyzed. Suggestions are made regarding possible additions to the local Stormwater Management Policy that would emphasize the importance of sustainable building techniques such as green roofs, and hopefully offer incentive to their implementation.

Solutions In Folded Geometries, And Associated Cloaking Due To Anomalous Resonance, Graeme W. Milton, Nicolae-Alexandru P. Nicorovici, Ross C. Mcphedran, Kirill Cherednichenko, Zubin Jacob

Birck and NCN Publications

Solutions for the fields in a coated cylinder where the core radius is bigger than the shell radius are seemingly unphysical, but can be given a physical meaning if one transforms to an equivalent problem by unfolding the geometry. In particular, the unfolded material can act as an impedance matched hyperlens, and as the loss in the lens goes to zero finite collections of polarizable line dipoles lying within a critical region surrounding the hyperlens are shown to be cloaked having vanishingly small dipole moments. This cloaking, which occurs both in the folded geometry and the equivalent unfolded one, is …

Design And Testing Of A Pumpless Microelectromechanical System Nanoinjector, Quentin Theodore Aten

Theses and Dissertations

A deeper understanding of human development and disease is made possible partly through the study of genetically modified model organisms, such as the common mouse (Mus musculus). By genetically modifying such model organisms, scientists can activate, deactivate, or highlight particular characteristics. A genetically modified animal is generated by adding exogenous (foreign) genetic material to one or more embryonic cells at their earliest stages of development. Frequently, this exogenous genetic material consists of specially engineered DNA, which is introduced into a fertilized egg cell (zygote). When successfully introduced into the zygote, the exogenous DNA will be incorporated into the …

Median Crossover Crashes In The Vicinity Of Interchanges On Utah Interstates, Katherine Elaine Winters

Theses and Dissertations

While not accounting for a significant proportion of overall crashes, median crossover crashes in the state of Utah do account for a significant proportion of interstate fatalities. Due to the seriousness of median crossover crashes in the state of Utah, the need exists to evaluate the impact of median crossover crashes in the state, to identify locations where median crossover crashes may be occurring at particularly high rates, and to identify methods to help mitigate these crashes. Previous research has noted that median crossover crash rates appear to increase in the vicinity of interchanges. The purpose of this research, therefore, …

Improving Reversal Median Computation Using Commuting Reversals And Cycle Information, William Arndt, Jijun Tang

Faculty Publications

In the past decade, genome rearrangements have attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. Methods for reconstructing phylogeny from genome rearrangements include distance-based methods, MCMC methods, and direct optimization methods. The latter, pioneered by Sankoff and extended with the software suites GRAPPA and MGR, is the most accurate approach, but is very limited due to the difficulty of its scoring procedure—it must solve multiple instances of the reversal median problem to compute the score of a given tree. The reversal median problem is known to be NP-hard and all …

Acuta Enews November 2008, Vol. 37, No. 11

ACUTA Newsletters

In This lssue

From ACUTA Headquarters: FCC lssues Rules to lmplement NET 91 1 ACT........ Jeri Semer, CAE, Exec. Dir

Tech Talk: For Most, the Big Change on Campus ls Wireless.............Kevin Tanzillo, Dux PR

DC Update.............. Dove Ostrom, Washlngton State University

Nominate Now for ACUTA Board of Directors

Be a State/Province Coordinator

Teflon:A Dangerous Part of a High-Risk World.................Frank Bisbee, Wireville USA

Thanks to Exhibitors for 2008

lnfo Links ............. Randy Hayes, Univ. of Northern lowa

Board Report, October....................... Riny Ledgenuood, San Diego State Univ.

Welcome New Members

Check lt Out: RFls/RFPs, Job Postings, Press Releases

Design And Optimization Of A Blood Vessel Mimic Bioreactor System For The Evaluation Of Intravascular Devices In Simple And Complex Vessel Geometries, Sara M. Leifer

Master's Theses

Coronary artery disease affects millions of people and the ability to detect and treat the disease is advancing at a rapid rate. As a result, the development of intravascular technologies is the focus of many medical device manufacturers. Specifically, coronary stent implantation is being performed in an increasing number of patients and a number of new stent designs have been introduced to the market, resulting in the need for improved preclinical testing methods. An in vitro tissue engineered “blood vessel mimic” (BVM) system has previously been established and its feasibility for the initial testing of newly emerging intravascular technology has …

2008 Scholars And Artists Bibliography, Rajshehkar G. Javalgi Dr., Michael Schwartz Library, Cleveland State University, Friends Of The Michael Schwartz Library

Scholars and Artists Bibliographies

This bibliography was created for the annual Friends of the Michael Schwartz Library Scholars and Artists Reception, recognizing scholarly and creative achievements of Cleveland State University faculty, staff and emeriti. Dr. Rajshekhar Javalgi was the guest speaker.

System And Technique For Retrieving Depth Information About A Surface By Projecting A Composite Image Of Modulated Light Patterns, Laurence G. Hassebrook, Daniel L. Lau, Chun Guan

Electrical and Computer Engineering Faculty Patents

A technique, associated system and program code, for retrieving depth information about at least one surface of an object. Core features include: projecting a composite image comprising a plurality of modulated structured light patterns, at the object; capturing an image reflected from the surface; and recovering pattern information from the reflected image, for each of the modulated structured light patterns. Pattern information is preferably recovered for each modulated structured light pattern used to create the composite, by performing a demodulation of the reflected image. Reconstruction of the surface can be accomplished by using depth information from the recovered patterns to …