Physical Sciences and Mathematics Commons^™

Understanding The Role Of Electrostatics On Protein-Protein Binding, Rooplekha C Mitra

All Theses

Ionized groups carry net charge and thus play a major role in the electrostatic interactions between the ligand and receptor. So understanding the role of electrostatics on protein-protein interactions is crucial for understanding the contribution of ionizable groups to the binding. However, their ionization states depend on many factors including pH of water phase. The complexity comes from the fact that the pKa's of ionizable groups may be quite different from their standard values and even may change due to protein-protein binding. The main difficulty in modeling plausible ionization changes induced by the complex formation arises from the differences in …

Constructed Wetland Treatment Systems For Risk Mitigation Of Energy Derived Waters, Michael Spacil

All Theses

Energy derived waters (EDWs) (e.g. petroleum refinery effluents, produced waters) can contain a variety of constituents [e.g. selenium (Se), arsenic (As), low molecular weight organics (LMWOs)]. The overall objective of this research was to provide an approach for remediation of specific constituents of concern in these waters and to measure a relationship between Se removal and abundance of Se reducing microbes. The specific objectives of this research were to: (1) evaluate removal of Se from simulated refinery effluent (SRE) using a pilot-scale constructed wetland treatment system (CWTS); (2) evaluate removal of Se, As, and LMWOs from a generic simulated fresh …

Impact Of Microsparticle Concentration Levels Upon Toxicity Of Phenol To Artemia, Federico Sinche

All Theses

Plastic pollution constitutes a threat to marine wildlife because of the deleterious impacts ranging from entanglement to ingestion of plastic debris. However, knowledge regarding the impacts of fragmented plastics into micron sizes and their interaction with other toxicants in the marine environment is still limited. In the present study the impact of polystyrene microspheres, 3 µm in diameter, upon toxicity of phenol to the brine shrimp Artemia was investigated in acute toxicity tests. The brine shrimp are employed as a model organism in marine toxicity tests. Phenol is a hydrophobic compound used as an intermediate resin discharged to the environment. …

Extraction Of Pesticides From Contaminated Soil Via Cyclodextrin Complexation, Bertil Nshime, Andrew Lantz

Student Summer Scholars Manuscripts

Cyclodextrins (CDs) were successfully used to extract numerous commonly used pesticides from contaminated soil via cyclodextrin complexation, a more environmentally friendly method compared to surfactants and organic solvents. A combination of five CDs (α-CD, β-CD, γ-CD, hydroxypropyl-β-CD (HP-β-CD), and methylated-β-CD (M-β-CD)) and eight pesticides (2,4-Dichlorophenoxyacetic acid (2,4-D) alachlor, acetochlor, diazinon, dicamba, dimethanamid, metalochlor and propanil) were examined in this study. It was found that a linear relationship exists between the concentrations of the M-β-CD and alachlor, which generally indicates that the amount of pesticide extracted depends on the concentration of the cyclodextrin present. With some pesticide-cyclodextrin combination, it was found …

Structure-Property Correlation In Cyclopolymerization Of New Acrylate-Based Functional Monomers, Huseyin Tas

Dissertations

New ether dimer; (ED-Od) and (ED-Eh) and diester; (ODE) and (EHDE) derivatives of α-(hydroxymethyl)acrylate, each having two octadecyl and 2-ethylhexyl side chains respectively, and an amine-linked di(2-ethylhexyl)acrylate (AL-Eh), having three 2-ethylhexyl side chains, were synthesized and (co)polymerized to evaluate the effects of differences in the structures of the monomers on final (co)polymer properties, particularly glass transition temperature, Tg. The free radical polymerizations of these monomers yielded high molecular weight polymers. Cyclopolymer formation of ED-Od, ED-Eh and AL-Eh was confirmed by 13C NMR analysis and the cyclization efficiencies were found to be very high (~100%). Copolymers of ED-Od, ODE, ED-Eh, EHDE, …

Dnagents: Genetically Engineered Intelligent Mobile Agents, Jeremy Otho Kackley

Dissertations

Mobile agents are a useful paradigm for network coding providing many advantages and disadvantages. Unfortunately, widespread adoption of mobile agents has been hampered by the disadvantages, which could be said to outweigh the advantages. There is a variety of ongoing work to address these issues, and this is discussed. Ultimately, genetic algorithms are selected as the most interesting potential avenue. Genetic algorithms have many potential benefits for mobile agents. The primary benefit is the potential for agents to become even more adaptive to situational changes in the environment and/or emergent security risks. There are secondary benefits such as the natural …

Windows Azure: Using Windows Azure's Service Bus To Solve Data Security Issues, Don Chambers

Theses and Dissertations

Many of the largest technology companies are heavily investing in Cloud Computing technology, making this a major force in the realm of software development. However, this software paradigm brings with it significantdata related security issues. This paper discusses some of these security issues and presents a solution. The solution calls for storing data outside of the cloud, and under the control of the cloud consumer. In addition, the solution provides the ability to manipulate data using only the standard HTTP ports that are typically opened at most locations. This solution is implemented using Microsoft's Windows Azure Cloud Computing operating system. …

Benchmarking And Implementation Of A New Independent Monte Carlo Dose Calculation Quality Assurance Audit Tool For Clinical Trials, Scott E. Davidson

Dissertations & Theses (Open Access)

Introduction Commercial treatment planning systems employ a variety of dose calculation algorithms to plan and predict the dose distributions a patient receives during external beam radiation therapy. Traditionally, the Radiological Physics Center has relied on measurements to assure that institutions participating in the National Cancer Institute sponsored clinical trials administer radiation in doses that are clinically comparable to those of other participating institutions. To complement the effort of the RPC, an independent dose calculation tool needs to be developed that will enable a generic method to determine patient dose distributions in three dimensions and to perform retrospective analysis of radiation …

A Bayesian Approach To Dose-Response Assessment And Drug-Drug Interaction Analysis: Application To In Vitro Studies, Violeta G. Hennessey

Dissertations & Theses (Open Access)

The considerable search for synergistic agents in cancer research is motivated by the therapeutic benefits achieved by combining anti-cancer agents. Synergistic agents make it possible to reduce dosage while maintaining or enhancing a desired effect. Other favorable outcomes of synergistic agents include reduction in toxicity and minimizing or delaying drug resistance. Dose-response assessment and drug-drug interaction analysis play an important part in the drug discovery process, however analysis are often poorly done. This dissertation is an effort to notably improve dose-response assessment and drug-drug interaction analysis.

The most commonly used method in published analysis is the Median-Effect Principle/Combination Index method …

Wind Speed Dependence Of Single-Site Wave-Height Retrievals From High-Frequency Radars, Brian K. Haus, Lynn K. Shay, Paul A. Work, George Voulgaris, Rafael J. Ramos, Jorge Martinez-Pedraja

Faculty Publications

Wave-height observations derived from single-site high-frequency (HF) radar backscattered Doppler spectra are generally recognized to be less accurate than overlapping radar techniques but can provide significantly larger sampling regions. The larger available wave-sampling region may have important implications for observing system design. Comparison of HF radar–derived wave heights with acoustic Doppler profiler and buoy data revealed that the scale separation between the Bragg scattering waves and the peak energy-containing waves may contribute to errors in the single-site estimates in light-to-moderate winds. A wave-height correction factor was developed that explicitly considers this scale separation and eliminates the trend of increasing errors …

A Diagnostic Examination Of Consecutive Extreme Cool-Season Precipitation Events At St. John's, Newfoundland, In December 2008, Shawn M. Milrad, Eyad H. Atallah, John R. Gyakum

Publications

St. John’s, Newfoundland, Canada (CYYT), is frequently affected by extreme precipitation events, particularly in the cool season (October–April). Previous work classified precipitation events at CYYT into categories by precipitation amount and a manual synoptic typing was performed on the 50 median extreme precipitation events, using two separate methods. Here, consecutive extreme precipitation events in December 2008 are analyzed. These events occurred over a 6-day period and produced over 125 mm of precipitation at CYYT. The first manual typing method, using a backward-trajectory analysis, results in both events being classified as “southwest,” which were previously defined as the majority of the …

Simsight: A Virtual Machine Based Dynamic Call Graph Generator, Xueling Chen

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

One problem with using component-based software development approach is that once software modules are reused over generations of products, they form legacy structures that can be challenging to understand, making validating these systems difficult. Therefore, tools and methodologies that enable engineers to see interactions of these software modules will enhance their ability to make these software systems more dependable. To address this need, we propose SimSight, a framework to capture dynamic call graphs in Simics, a widely adopted commercial full-system simulator. Simics is a software system that simulates complete computer systems. Thus, it performs nearly identical tasks to …

Jvm-Based Techniques For Improving Java Observability, Peng Du

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Observability measures the support of computer systems to accurately capture, analyze, and present (collectively observe) the internal information about the systems. Observability frameworks play important roles for program understanding, troubleshooting, performance diagnosis, and optimizations. However, traditional solutions are either expensive or coarse-grained, consequently compromising their utility in accommodating today’s increasingly complex software systems. New solutions are emerging for VM-based languages due to the full control language VMs have over program executions. Existing such solutions, nonetheless, still lack flexibility, have high overhead, or provide limited context information for developing powerful dynamic analyses. In this thesis, we present a VM-based infrastructure, called …

Managing Large Data Sets Using Support Vector Machines, Ranjini Srinivas

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Hundreds of Terabytes of CMS (Compact Muon Solenoid) data are being accumulated for storage day by day at the University of Nebraska-Lincoln, which is one of the eight US CMS Tier-2 sites. Managing this data includes retaining useful CMS data sets and clearing storage space for newly arriving data by deleting less useful data sets. This is an important task that is currently being done manually and it requires a large amount of time. The overall objective of this study was to develop a methodology to help identify the data sets to be deleted when there is a requirement for …

Estimating Teacher Effects Using Value-Added Models, Jennifer L. Green

Department of Statistics: Dissertations, Theses, and Student Work

Value-added modeling is an alternative approach to test-based accountability systems based on the proportions of students scoring at or above pre-determined proficiency levels. Value-added modeling techniques provide opportunities to estimate an individual teacher’s effect on student learning, while allowing for the possibility to control for the effect of non-educational factors beyond a school system’s control, such as socioeconomic status. However, numerous considerations exist when using value-added models to estimate teacher effects and defining what the teacher effects really describe. Chapter 2 provides an introduction to value-added methodology by describing several value-added models available for estimating teacher effects and their respective …

Controlling Reductive Elimination From Novel I(Iii) Salts Using A Secure Method, Joseph W. Graskemper

Department of Chemistry: Dissertations, Theses, and Student Research

Positron Emission Tomography (PET) is a valuable clinical, research, and diagnostic technique for human and animal organ imaging. The current market for PET in the United States is $500 million per year and is projected to be $5.4 billion per year globally by 2015. To synthesize labeled radiotracers, we are most interested in using ¹⁸F as the isotope of choice because it is a nearly ideal positron emitting radionuclide.

Electron-rich aromatic substrates can be particularly difficult to fluorinate. We show that reductive elimination of I(III) diaryliodonium salts provide increased fluorination of electron-rich aromatic substrates. Modest yields of fluorinated product …

High Temperature Rare Earth Compounds: Synthesis, Characterization And Applications In Device Fabrication, Joseph R. Brewer

Department of Chemistry: Dissertations, Theses, and Student Research

As the area of nanotechnology continues to grow, the development of new nanomaterials with interesting physical and electronic properties and improved characterization techniques are several areas of research that will be remain vital for continued improvement of devices and the understanding in nanoscale phenomenon. In this dissertation, the chemical vapor deposition synthesis of rare earth (RE) compounds is described in detail. In general, the procedure involves the vaporization of a REClx (RE = Y, La, Ce, Pr, Nd, Sm, Gd, Tb, Dy, Ho) in the presence of hydride phase precursors such as decaborane and ammonia at high temperatures and low …

Injecting, Controlling, And Storing Magnetic Domain Walls In Ferromagnetic Nanowires, Andrew Kunz, Jonathan D. Priem, Sarah C. Reiff

Physics Faculty Research and Publications

Domain walls in ferromagnetic nanowires are important for proposed devices in recording, logic, and sensing. The realization of such devices depends in part on the ability to quickly and accurately control the domain wall from creation until placement. Using micromagnetic computer simulation we demonstrate how a combination of externally applied magnetic fields is used to quickly inject, move, and accurately place multiple domain walls within a single wire for potential recording and logical operations. The use of a magnetic field component applied perpendicular to the principle domain wall driving field is found to be critical for increased speed and reliability. …

Biosynthesis Of Salinosporamides From Α,Β-Unsaturated Fatty Acids: Implications For Extending Polyketide Synthase Diversity, Yuan Liu, Christopher Hazzard, Alessandra S. Eustáquio, Kevin A. Reynolds, Bradley S. Moore

Chemistry Faculty Publications and Presentations

A new series of coenzyme A-tethered polyketide synthase extender units were discovered in relation to the biosynthesis of the salinosporamide family of anticancer agents from the marine bacterium Salinispora tropica. In vivo and in vitro experiments revealed that the crotonyl-CoA reductase/carboxylase SalG has broad substrate tolerance toward 2-alkenyl-CoAs that give rise to the salinosporamide C-2 substitution pattern.

An Efficient Signcryption Scheme With Key Privacy And Its Extension To Ring Signcryption, Chung Ki Li, Guomin Yang, Duncan S. Wong, Xiaotie Deng, Sherman S. M. Chow

Research Collection School Of Computing and Information Systems

In Information Processing Letters (2006), Tan pointed out that the anonymous signcryption scheme proposed by Yang, Wong and Deng (YWD) in ISC 2005 provides neither confidentiality nor anonymity. However, no discussion has been made on how a secure scheme can be made and there is no secure scheme available to date. In this paper, we propose a modification of YWD scheme which resolves the security issues of the original scheme without sacrificing its high efficiency and simple design. Indeed, we show that our scheme achieves confidentiality, existential unforgeability and anonymity with more precise reduction bounds. We also give a variation …

Automatic Generation Of Semantic Fields For Annotating Web Images, Gang Wang, Tat Seng Chua, Chong-Wah Ngo, Yong Cheng Wang

Research Collection School Of Computing and Information Systems

The overwhelming amounts of multimedia contents have triggered the need for automatically detecting the semantic concepts within the media contents. With the development of photo sharing websites such as Flickr, we are able to obtain millions of images with usersupplied tags. However, user tags tend to be noisy, ambiguous and incomplete. In order to improve the quality of tags to annotate web images, we propose an approach to build Semantic Fields for annotating the web images. The main idea is that the images are more likely to be relevant to a given concept, if several tags to the image belong …

Learning Personal Agents With Adaptive Player Modeling In Virtual Worlds, Yilin Kang, Ah-Hwee Tan

Research Collection School Of Computing and Information Systems

There has been growing interest in creating intelligent agents in virtual worlds that do not follow fixed scripts predefined by the developers, but react accordingly based on actions performed by human players during their interaction. In order to achieve this objective, previous approaches have attempted to model the environment and the user’s context directly. However, a critical component for enabling personalized virtual world experience is missing, namely the capability to adapt over time to the habits and eccentricity of a particular player. To address the above issue, this paper presents a cognitive agent with learning player model capability for personalized …

Semi-Supervised Distance Metric Learning For Collaborative Image Retrieval And Clustering, Steven C. H. Hoi, Wei Liu, Shih-Fu Chang

Research Collection School Of Computing and Information Systems

Learning a good distance metric plays a vital role in many multimedia retrieval and data mining tasks. For example, a typical content-based image retrieval (CBIR) system often relies on an effective distance metric to measure similarity between any two images. Conventional CBIR systems simply adopting Euclidean distance metric often fail to return satisfactory results mainly due to the well-known semantic gap challenge. In this article, we present a novel framework of Semi-Supervised Distance Metric Learning for learning effective distance metrics by exploring the historical relevance feedback log data of a CBIR system and utilizing unlabeled data when log data are …

On Decision Support For Deliberating With Constraints In Constrained Optimization Models, Steven O. Kimbrough, Ann Kuo, Hoong Chuin Lau, David H. Wood

Research Collection School Of Computing and Information Systems

This paper introduces the Deliberation Decision Support System (DDSS). The DDSS obtains heuristically (using a genetic algorithm) solutions of interest for constrained optimization models. This is illustrated, without loss of generality, by generalized assignment problems. The DDSS also provides users with graphical tools that support post-solution deliberation for constrained optimization models. The DDSS and this paper, as befits practical concerns, are focused on deliberation with respect to the constraints of the models being used.

A Framework For Automatically Repairing Gui Test Suites, Si Huang

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Testing is an effective means for assuring the quality of software. In programs with Graphical User Interfaces (GUIs), event sequences serve as test cases for executing system tests. To aid in the test generation process, researchers have developed methods that automatically derive graph models from GUIs, which can then be traversed to create sequences for testing. Recent advances using these graph models incorporate combinatorial interaction testing sampling techniques to generate longer GUI test cases, which exercise more event interactions and have been shown to improve fault detection. However, because the models extracted are only approximations of the actual event interactions, …

Analytical Solutions For Efficient Interpretation Of Single-Well Push-Pull Tracer Tests, Junqi Huang, John A. Christ, Mark N. Goltz

Faculty Publications

Single-well push-pull tracer tests have been used to characterize the extent, fate, and transport of subsurface contamination. Analytical solutions provide one alternative for interpreting test results. In this work, an exact analytical solution to two-dimensional equations describing the governing processes acting on a dissolved compound during a modified push-pull test (advection, longitudinal and transverse dispersion, first-order decay, and rate-limited sorption/partitioning in steady, divergent, and convergent flow fields) is developed. The coupling of this solution with inverse modeling to estimate aquifer parameters provides an efficient methodology for subsurface characterization. Synthetic data for single-well push-pull tests are employed to demonstrate the utility …

Malware Type Recognition And Cyber Situational Awareness, Thomas Dube, Richard A. Raines, Gilbert L. Peterson, Kenneth W. Bauer, Michael R. Grimaila, Steven K. Rogers

Faculty Publications

Current technologies for computer network and host defense do not provide suitable information to support strategic and tactical decision making processes. Although pattern-based malware detection is an active research area, the additional context of the type of malware can improve cyber situational awareness. This additional context is an indicator of threat capability thus allowing organizations to assess information losses and focus response actions appropriately. Malware Type Recognition (MaTR) is a research initiative extending detection technologies to provide the additional context of malware types using only static heuristics. Test results with MaTR demonstrate over a 99% accurate detection rate and 59% …

Toward Using Games To Teach Fundamental Computer Science Concepts, Jeffrey Michael Edgington

Electronic Theses and Dissertations

Video and computer games have become an important area of study in the field of education. Games have been designed to teach mathematics, physics, raise social awareness, teach history and geography, and train soldiers in the military. Recent work has created computer games for teaching computer programming and understanding basic algorithms.

We present an investigation where computer games are used to teach two fundamental computer science concepts: boolean expressions and recursion. The games are intended to teach the concepts and not how to implement them in a programming language.

For this investigation, two computer games were created. One is designed …

Composing Music In Constrained Search Environments, Jeffrey Keene

Electronic Theses and Dissertations

Composing music with computers in constrained search environments adds complexities and problems not present in the traditional problem domain of generative music. The traditional and well researched mechanisms of Markov chains, genetic algorithms and data driven rule based systems do not directly map to a problem domain in which pitch choice and rhythm choice are likely to be highly limited.

We therefore explore several possible solutions to generating rhythms in extremely constrained environments with the goal of generating music that adheres to user specified constraints and is aesthetically pleasing.

Noise Assumptions In Complex-Valued Sense Mr Image Reconstruction, Daniel B. Rowe, Iain P. Bruce

Mathematics, Statistics and Computer Science Faculty Research and Publications

In fMRI, brain images are not measured instantaneously and a volume of images can take two seconds to acquire at a low 64x64 resolution. Significant effort has been put forth on many fronts to decrease image acquisition time including parallel imaging. In parallel imaging, sub-sampled spatial frequency points are measured in parallel and combined to form a single image. Measurement time is decreased at the expense of increased image reconstruction difficulty and time. One significant parallel imaging technique known as SENSE utilizes a complex-valued regression coefficient estimation process with transposes replaced by conjugate transposes. However, in SENSE the noise structure …