Physical Sciences and Mathematics Commons^™

Computational Analysis Of Metabolomic Toxicological Data Derived From Nmr Spectroscopy, Benjamin J. Kelly

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Nuclear magnetic resonance (NMR) spectroscopy is a non-invasive method of acquiring metabolic profiles from biofluids. The most informative metabolomic features, or biomarkers, may provide keys to the early detection of changes within an organism such as those that result from exposure to a toxin. One major difficulty with typical NMR data, whether it come from a toxicological, medical or other source, is that it features a low sample size relative to the number of variables measured. Thus, traditional pattern recognition techniques are not always feasible. The "curse of dimensionality" is an important consideration in selecting appropriate statistical and pattern recognition …

Investigation And Quantification Of Codon Usage Bias Trends In Prokaryotes, Amanda L. Hanes

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Organisms construct proteins out of individual amino acids using instructions encoded in the nucleotide sequence of a DNA molecule. The genetic code associates combinations of three nucleotides, called codons, with every amino acid. Most amino acids are associated with multiple synonymous codons, but although they result in the same amino acid and thus have no effect on the final protein, synonymous codons are not present in equal amounts in the genomes of most organisms. This phenomenon is known as codon usage bias, and the literature has shown that all organisms display a unique pattern of codon usage. Research also suggests …

Tyflos: A Wearable Navigation Prototype For Blind & Visually Impaired; Design, Modelling And Experimental Results, Dimitrios Dakopoulos

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The need for assistive devices has, had and will have a large merit in many engineering research arenas. This dissertation deals with the design, modeling, implementation and experimentation of the navigation component of a wearable assistive system for blind and visually impaired people, called TYFLOS (ΤΥΦΛΟΣ) which is the Greek word for "Blind".

The current prototype consists of two mini cameras attached to a pair of conventional eye-glasses, a 2D tactile display vibration array) which consists of 16 vibrating elements arranged in a 4x4 manner, attached to an elastic vest worn on the user's abdomen, a portable computer, an ear-speaker …

A Software Framework For The Design, Testing And Deployment Of Control Systems For Autonomous Robotics, Duane Stanley Bolick Jr.

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Simulation and control of robotic agents are common enough tasks among computer science and engineering researchers that there exists a large variety of software applications, toolkits, and programming frameworks designed to facilitate such research. The intent of this project is to provide an autonomous robotics simulation and control framework with sufficiently useful tools and reference implementations so as to be immediately useful to basic users, as well as easily understood and extended by software developers and robotics researchers.

As such, this document describes the implementation of a general networking toolkit, an autonomous robotics extension framework, and an autonomous robotics simulator …

Burst Scheduling, Grooming And Qos Provisioning In Optical Burst-Switched Networks, Yuqi Fan

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The demand of network capacity has been increasing steadily with more users than ever connected to the Internet through broadband access and the popularity of video based applications, such as YouTube. Optical wavelength division multiplexing (WDM) networks are expected to form the next-generation backbone network and to fulfill the insatiable appetite for bandwidth.

Wavelength routed WDM optical networks offer the granularity of switching at a fiber, waveband, or a wavelength level. The finest granularity offered is at a wavelength level by provisioning lightpaths for different clients/services. All-optical packet switching is still deemed technically infeasible and its competitiveness as a backbone …

A System For Incorporating Time-Based Event-Condition-Action Rules Into Business Databases, Christina Marie Steidle

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Human beings handle time-based events continuously; however the passage of time does not play an active part in most business systems because they are typically driven by interaction from human users or other systems. In order to take an action based upon the passage of time it is necessary to build a framework which will monitor the progression of time and a way to define what events the system should be waiting for. This thesis describes such a system, and shows that the system performs as specified. With this system business users are able to build event-condition-action rules using a …

Improving Remote Homology Detection Using A Sequence Property Approach, Gina Marie Cooper

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Understanding the structure and function of proteins is a key part of understanding biological systems. Although proteins are complex biological macromolecules, they are made up of only 20 basic building blocks known as amino acids. The makeup of a protein can be described as a sequence of amino acids. One of the most important tools in modern bioinformatics is the ability to search for biological sequences (such as protein sequences) that are similar to a given query sequence. There are many tools for doing this (Altschul et al., 1990, Hobohm and Sander, 1995, Thomson et al., 1994, Karplus and Barrett, …

Design And Performance Analysis Of A Secure Proces-Sor Scan-Sp With Crypto-Biometric Capabilities, Raghudeep Kannavara

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Secure computing is gaining importance in recent times as computing capability is increasingly becoming distributed and information is everywhere. Prevention of piracy and digital rights management has become very important. Information security is mandatory rather than an additional feature. Numerous software techniques have been proposed to provide certain level of copyright and intellectual property protection. Techniques like obfuscation attempt to transform the code into a form that is harder to reverse engineer. Tamper-proofing causes a program to malfunction when it detects that it has been modified. Software watermarking embeds copyright notice in the software code to allow the owners of …

Semantic And Role-Based Access Control For Data Grid Systems, Vineela Muppavarapu

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A Grid is an integration infrastructure for sharing and coordinated use of diverseresources in dynamic, distributed virtual organizations (VOs). A Data Grid is an architecture for the access, exchange, and sharing of data in the Grid environment. Distributed data resources can be diverse in their formats, schema, quality, access mechanisms, ownership, access policies, and capabilities. In recent years, several organizations have started utilizing Grid technologies to deploy data-intensive and/or computation-intensive applications. As more and more organizations are sharing data resources and participating in Data Grids, the complexity and heterogeneity of the systems is increasing constantly, but their management techniques are …

A Cryptanalysis Methodology For The Reverse Engineering Of Encrypted Information In Images, Allan Anthony Rwabutaza

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Security is an important issue related to the storage and communication of data and information. In data and information security, cryptography and steganography are two of the most common security techniques. On one hand, there is cryptography, which is the secret communication between two parties by message scrambling on the sender's side and message unscrambling on the receiver's side so that only the intended receiver gets the secret message. On the other hand, there is steganography, which is the hiding of information in a medium in such a way that no one other than the sender or the intended receiver …

Analysis And Transformation Of Post-Conditions, Abhinav Vasikarla

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Software engineers have been trying for years to develop a software synthesis system that can transform a formal specification model to a design model from which executable code can be generated. AFIT wide spectrum object modeling environment (AWESOME) is one result of their research. AWESOME presents a formal model as an abstract syntax tree. This model consists mainly of object class specifications. The methods in these classes are specified using pre and post-conditions. The intent of this thesis is to support the transformation of post-conditions to code statements. A post-condition is first categorized as dependent or independent relative to other …

Extracting, Representing And Mining Semantic Metadata From Text: Facilitating Knowledge Discovery In Biomedicine, Cartic Ramakrishnan

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The information access paradigm offered by most contemporary text information systems is a search-and-sift paradigm where users have to manually glean and aggregate relevant information from the large number of documents that are typically returned in response to keyword queries. Expecting the users to glean and aggregate information has lead to several inadequacies in these information systems. Owing to the size of many text databases, search-and-sift is a very tedious often requiring repeated keyword searches refining or generalizing queries terms. A more serious limitation arises from the lack of automated mechanisms to aggregate content across different documents to discover new …

Object Similarity Through Correlated Third-Party Objects, Ting Sa

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Given a pair of objects, it is of interest to know how they are related to each other and the strength of their similarity. Many previous studies focused on two types of similarity measures: The first type is based on closeness of attribute values of two given objects, and the second type is based on how often the two objects co-occur in transactions/tuples.

In this thesis we study a new behavior-based similarity measure, which evaluates similarity between two objects by considering how similar their correlated third-party object sets are. Behavior-based similarity can help us find pairs of objects that have …

Performance And Complexity Co-Evaluations Of Mpeg4-Als Compression Standard For Low-Latency Music Compression, Isaac Kevin Matthew

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In this thesis compression ratio and latency of different classical audio music tracks are analyzed with various encoder options of MPEG4ALS. Different tracks of audio music tracks are tested with MPEG4-ALS coder with different options to find the optimum values for various parameters to obtain maximum compression ratio with minimum CPU time (encoder and decoder time). Optimum frame length for which the compression ratio saturates for music audio is found out by analyzing the results when different classical music tracks are experimented with various frame lengths. Also music tracks with varying sampling rate are tested and the compression ratio and …

Evolutionary Methodology For Optimization Of Image Transforms Subject To Quantization Noise, Michael Ray Peterson

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Lossy image compression algorithms sacrifice perfect imagereconstruction in favor of decreased storage requirements. Modelossy compression schemes, such as JPEG2000, rely upon the discrete wavelet transform (DWT) to achieve high levels of compression while minimizing the loss of information for image reconstruction. Some compression applications require higher levels of compression than those achieved through application of the DWT and entropy coding. In such lossy systems, quantization provides high compression rates at the cost of increased distortion. Unfortunately, as the amount of quantization increases, the performance of the DWT for accurate image reconstruction deteriorates. Previous research demonstrates that a genetic algorithm can …

A Framework To Support Spatial, Temporal And Thematic Analytics Over Semantic Web Data, Matthew Steven Perry

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Spatial and temporal data are critical components in many applications. This is especially true in analytical applications ranging from scientific discovery to national security and criminal investigation. The analytical process often requires uncovering and analyzing complex thematic relationships between disparate people, places and events. Fundamentally new query operators based on the graph structure of Semantic Web data models, such as semantic associations, are proving useful for this purpose. However, these analysis mechanisms are primarily intended for thematic relationships. This dissertation proposes a framework built around the RDF data model for analysis of thematic, spatial and temporal relationships between named entities. …

Algorithmic Techniques Employed In The Isolation Of Codon Usage Biases In Prokaryotic Genomes, Douglas W. Raiford Iii

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While genomic sequencing projects are an abundant source of information for biological studies ranging from the molecular to the ecological in scale, much of the information present may yet be hidden from casual analysis. One such information domain, trends in codon usage, can provide a wealth of information about an organism's genes and their expression. Degeneracy in the genetic code allows more than one triplet codon to code for the same amino acid, and usage of these codons is often biased such that one or more of these synonymous codons is preferred. Isolation of translational efficiency bias can have important …

Energy Efficient Image Video Sensor Networks, Paul Anthony Bender

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Image Video Sensor Networks are emerging applications for sensor network technologies. The relatively large size of the data collected by image video sensors presents new challenges for the sensor network in terms of energy consumption and channel capacity. We address each of these issues through the use of a high density network deployment utilizing some nodes as dedicated relay nodes.

A high density network allows network nodes to reduce their transmission power. This reduction in transmission power allows each node to conserve power and simultaneously increases the potential for spatially concurrent transmissions within the network, resulting in improved network throughputs. …

Fuel Flow Control Issue In Jet Engines: An Evolvable Hardware Approach, Kshitij S. Deshpande

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Dealing with unexpected dynamic loads in Jet and Turbine engines have always been a matter of concern and an active area of research. This thesis is an initial attempt to apply Evolvable Hardware methods for augmenting classical control methods in a generic turbine engine model. In this work, the Air Force Research Laboratory Generic Turbine Engine Model was converted into C and interfaced with a simulation of a EH VLSI control chip currently under development. The simulated EH device was allowed to evolve to augment the simulated engine's standard FADEC controller so that the whole system could tolerate unexpected, large …

Computational Methods For The Objective Review Of Forensic Dna Testing Results, Jason R. Gilder

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Since the advent of criminal investigations, investigators have sought a "gold standard" for the evaluation of forensic evidence. Currently, deoxyribonucleic acid (DNA) technology is the most reliable method of identification. Short Tandem Repeat (STR) DNA genotyping has the potential for impressive match statistics, but the methodology not infallible. The condition of an evidentiary sample and potential issues with the handling and testing of a sample can lead to significant issues with the interpretation of DNA testing results. Forensic DNA interpretation standards are determined by laboratory validation studies that often involve small sample sizes. This dissertation presents novel methodologies to address …

Classification Of Microarray Data To Predict Toxic Exposure, Tarek A. Seleem

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This thesis presents a software system for the analysis of microarray data. Microarrays are a relatively new technology that can be used to examine the state of the genome of an organism at some instant in time. The challenge is the amount of natural variation in biological systems limits our ability to identify specific genes that may be sensitive to changes in an organism's physiology or its environment. The analysis software consists of three modules. The first module filters microarray data to reduce the complexity of the problem. The second module selects subsets of genes for evaluation using a genetic …

On Optimal Survivability Design In Wdm Optical Networks Under Scheduled Traffic Models, Tianjian Li

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Wavelength division multiplexing (WDM) optical networks are widely viewed as the most appropriate choice for future Internet backbone with the potential to fulfill the ever-growing demands for bandwidth. WDM divides the enormous bandwidth of an optical fiber into many non-overlapping wavelength channels, each of which may operate at the rate of 10 Gigabit per second or higher. A failure in a network such as a cable cut may result in a tremendous loss of data. Therefore, survivability is a very important issue in WDM optical networks. The objective of this dissertation is to address the survivability provisioning problem in WDM …

Xml Integrated Environment For Service-Oriented Data Management, Marwan Younes Maarouf

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The proliferation of XML as a family of related standards including a markup language (XML), formatting semantics (XSL style sheets), a linking syntax (XLINK), and appropriate data schema standards have emerged as a de facto standard for encoding and sharing data between various applications. XML is designed to be simple, easily parsed and self-describing. XML is based on and support the idea of separation of concerns: information content is separated from information rendering, and relationships between data elements are provided via simple nesting and references. As the XML content grows, the ability to handle schemaless XML documents becomes more critical …

Design And Implementation Of Timeline Application For News Documents, Mastan Vali Shaik

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The growing News document archive emphasizes the need for efficient techniques to retrieve and visualize its content. We present a timeline based graphical interface for this purpose. The timeline is a graph of number of documents supporting association between entity (event, country, person, etc) etc and event (entity, country, person, etc) with respect to dates. The query is formulated based on entity, event, country, and person metadata extracted from the text of the News documents by analyzing the documents using proprietary name-entity recognizers. The timeline also provides a means to index and access relevant documents. Associations inferred on the basis …

Comparative Microarray Data Mining, Shihong Mao

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As a revolutionary technology, microarrays have great potential to provide genome-wide patterns of gene expression, to make accurate medical diagnosis, and to explore genetic causes underlying diseases. It is commonly believed that suitable analysis of microarray datasets can lead to achieve the above goals. While much has been done in microarray data mining, few previous studies, if any, focused on multiple datasets at the comparative level. This dissertation aims to fill this gap by developing tools and methods for set-based comparative microarray data mining. Specifically, we mine highly differentiative gene groups (HDGGs) from given datasets/classes, evaluate the concordance of datasets …

A Hybrid Approach To Retrieving Web Documents And Semantic Web Data, Trivikram Immaneni

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The Semantic Web has been evolving into a property-linked web of RDF data, conceptually divorced from (but physically housed in) the World Wide Web of hyperlinked documents. Data Retrieval techniques are typically used to retrieve data from the Semantic Web while Information Retrieval techniques are used to retrieve documents from the Hypertext Web. Conceptually unifying the two webs enables the exploitation of their interconnections resulting in benefits to both data and document retrieval. Towards this end, we present the Unified Web model that integrates the two webs and formalizes the structure and the semantics of their interconnections. We present a …

An Analog Evolvable Hardware Device For Active Control, Saranyan A. Vigraham

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The field of Evolvable Hardware (EH) has recently gained a lot of interest due to the novel methodology it offers for designing electrical circuits and machines. EH techniques involve configuring a reconfigurable hardware platform with the aid of learning engines such as evolutionary algorithms. The EH devices normally act as closed loop controllers with the capability of learning necessary control laws adaptively. Current EH practices have several shortcomings, which have restricted their use as reliable controllers. This dissertation will present an improved EH device based on behavioral reconfigurability that addresses the current open challenges in the field of analog Evolvable …

Summaritive Digest For Large Document Repositories With Application To E-Rulemaking, Lijun Chen

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Large document repositories need to be organized and summarized to make them more accessible and understandable. Such needs exist in many applications, including web search, e-rulemaking (electronic rulemaking) and document archiving. Even though much has been done in the areas of document clustering and summarization, there are still many new challenges and issues that need to be addressed as the repositories become larger, more prevalent and dynamic. In this dissertation, we investigate more informative ways to organize and summarize large document repositories, especially e-rulemaking feedback repositories (ERFRs), so that the large repositories can be managed and digested more efficiently and …

Analysis Of Very Large Scale Image Data Using Out-Of-Core Technique And Automated 3d Reconstruction Using Calibrated Images, Chandrashekara Hassan Raju

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Analysis of large scale volumetric data sets is very important from the researcher's and technological point of view as it helps in understanding and analyzing the original data. For example, when analyzing volumetric images from cast arteries of pigs, it is essential to apply a suitable segmentation in order to retrieve morphometric data from the scanned image. Due to improved scanning technology, such as MicroCT, these scanned images can get as large as several gigabytes in size. In order to analyze such large scale data sets on common desktop computers is a challenge due to limited main memory. By using …

Gpu-Assisted Rendering Of Large Tree-Shaped Data Sets, Pallavi Ramachandra Mangalvedkar

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Due to their complexity, medical data sets can easily comprise of several gigabytes in size. For example, geometric representations of a coronary arterial tree spanning vessels from the large proximal coronary arteries down to the capillary level consist of 6 gigabytes or more of geometry data, depending on the accuracy of the geometric representation. Visualization of such large data sets using the CPU alone can be inefficient and time consuming since they require special out-of-core techniques due to the size of the data set. The usage of the GPU can help render such data sets faster compared to CPU-based implementations …