Computer Sciences Commons^™

Singular Value Decomposition Of Analogs Of Gbr 12909, Anna Fiorentino

Theses

Analogs of GBR 12909 are drugs that could potentially be used to treat cocaine addiction. Singular Value Decomposition (SVD) is a multivariate analysis technique used to show relationships between the data and the variables associated with the data. The input data consists of the conformers of each analog (DM324, 728 conformers; TP250, 739 conformers) along with the eight torsional angles (Al, A2, B1-B6). A novel scaling technique was developed to address the problem of data circularity by subtracting the values of the torsional angles of the global energy minimum conformation from those of each conformer.

In SVD the original data …

Slimsvm : A Simple Implementation Of Support Vector Machine For Analysis Of Microarray Data, Avik Karmaker

Theses

Support Vector Machine (SVM) is a supervised machine learning technique being widely used in multiple areas of biological analysis including microarray data analysis. SlimSVM has been developed with the intention of replacing OSU SVM as the classification component of GenoIterSVM in order to make it independent of other SVM packages. GenolterSVM, developed by Dr. Marc Ma, is a SVM implementation with an iterative refinement algorithm for improved accuracy of classification of genotype microarray data. SlimSVM is an object-oriented, modular, and easy-to-use implementation written in C++. It supports dot (linear) and polynomial (non-linear) kernels. The program has been tested with artificial …

New Techniques For Improving Biological Data Quality Through Information Integration, Katherine Grace Herbert

Dissertations

As databases become more pervasive through the biological sciences, various data quality concerns are emerging. Biological databases tend to develop data quality issues regarding data legacy, data uniformity and data duplication. Due to the nature of this data, each of these problems is non-trivial and can cause many problems for the database. For biological data to be corrected and standardized, methods and frameworks must be developed to handle both structural and traditional data.

The BIG-AJAX framework has been developed for solving these problems through both data cleaning and data integration. This framework exploits declarative data cleaning and exploratory data mining …

Relationship Analysis : Improving The Systems Analysis Process, Joseph Thomas Catanio

Dissertations

A significant aspect of systems analysis involves discovering and representing entities and their inter-relationships. Guidelines exist to identify entities but do not provide a rigorous and comprehensive process to explicitly capture the relationship structure of the problem domain. Whereas, other analysis techniques lightly address the relationship discovery process, Relationship Analysis is the only systematic, domain-independent analysis technique focusing exclusively on a domain's relationship structure.

The quality of design artifacts, such as class diagrams, and development time necessary to generate these artifacts can be improved by first representing the complete relationship structure of the problem domain. The Relationship Analysis Model is …

Efficient Similarity Search In High-Dimensional Data Spaces, Yue Li

Dissertations

Similarity search in high-dimensional data spaces is a popular paradigm for many modern database applications, such as content based image retrieval, time series analysis in financial and marketing databases, and data mining. Objects are represented as high-dimensional points or vectors based on their important features. Object similarity is then measured by the distance between feature vectors and similarity search is implemented via range queries or k-Nearest Neighbor (k-NN) queries.

Implementing k-NN queries via a sequential scan of large tables of feature vectors is computationally expensive. Building multi-dimensional indexes on the feature vectors for k-NN search also tends to be unsatisfactory …

A Discovery And Analysis Of Influencing Factors Of Pair Programming, Kyungsub Steve Choi

Dissertations

The exploration into the underlying psychosocial links of pair programming. a new and unorthodox programming paradigm in which two programmers share one keyboard and monitor during real-time programming sessions, is undertaken. These complex psychosocial relationships, along with cognitive process exchanges, ultimately mold the programming output as well as determine the level of communication, satisfaction. confidence and compatibility. Laying the framework for this research, a through review of traditional and contemporary paradigms with a special focus on their limitations and a list of current software development problems are presented. Next, a detailed summary of pair programming and related agile software paradigms, …

On Ip Over Wdm Burst-Switched Long Haul And Metropolitan Area Networks, Jingxuan Liu

Dissertations

The IP over Wavelength Division Multiplexing (WDM) network is a natural evolution ushered in by the phenomenal advances in networking technologies and technical breakthroughs in optical communications, fueled by the increasing demand in the reduction of operation costs and the network management complexity. The unprecedented bandwidth provisioning capability and the multi-service supportability of the WDM technology, in synergy with the data-oriented internetworking mechanisms, facilitates a common shared infrastructure for the Next Generation Internet (NGJ).

While NGI targets to perform packet processing directly on the optical transport layer, a smooth evolution is critical to success. Intense research has been conducted to …

Studies Of Disk Arrays Tolerating Two Disk Failures And A Proposal For A Heterogeneous Disk Array, Chunqi Han

Dissertations

There has been an explosion in the amount of generated data in the past decade. Online access to these data is made possible by large disk arrays, especially in the RAID (Redundant Array of Independent Disks) paradigm. According to the RAID level a disk array can tolerate one or more disk failures, so that the storage subsystem can continue operating with disk failure(s). RAID 5 is a single disk failure tolerant array which dedicates the capacity of one disk to parity information. The content on the failed disk can be reconstructed on demand and written onto a spare disk. However, …

An Approximate Search Engine For Structure, Huiyuan Shan

Dissertations

As the size of structural databases grows, the need for efficiently searching these databases arises. Thanks to previous and ongoing research, searching by attribute-value and by text has become commonplace in these databases. However, searching by topological or physical structure, especially for large databases and especially for approximate matches, is still an art.

In this dissertation, efficient search techniques are presented for retrieving trees from a database that are similar to a given query tree. Rooted ordered labeled trees, rooted unordered labeled trees and free trees are considered. Ordered labeled trees are trees in which each node has a label …

Enriching And Designing Metaschemas For The Umls Semantic Network, Li Zhang

Dissertations

The disparate terminologies used by various biomedical applications or professionals make the communication between them more difficult. The Unified Medical Language System (UMLS) of the National Library of Medicine (NLM) is an attempt to integrate different medical terminologies into a unified representation framework to improve decision making and the quality of patient care as well as research in the health-care field. Metathesaurus (META) and Semantic Network (SN) are two main components of the UMLS system, where the SN provides a high-level abstract of the concepts in the META.

This dissertation addresses three problems of the SN. First, the SN's two-tree …

Participatory Learning Environment : Requirements And Design Analysis, Vikas Manohar Achhpiliya

Theses

The primary purpose of this thesis is to develop the requirements and model preliminary database and class designs for the Participatory Learning Approach Environment (PLAE). The requirements and the designs will be presented for version 1.0 and 2.0 with version 2.0 supporting an enhanced requirements set.

Participatory Learning Approach Environment (PLAE) is an exercise management tool for the Participatory Learning Approach (PLA) - a pedagogy approach based on the theory of constructivism. The PLAE facilitates and enhances learning among students while easing the administrative burden of the instructor and cognitive overload of the students. The theory and concepts on which …

Electronic Marketplaces And Their Roles In The Staffing Industry : An Explorative Analysis, Vishal Khubani

Theses

This thesis will explore and analyze the role of electronic marketplaces in the staffing industry from the viewpoint of hiring executives, human resources personnel, staffing organizations, and candidates. Using analyses of popular electronic job marketplaces, this paper will establish the efficiency and effectiveness of electronic marketplaces as compared to traditional staffing methods. It will also provide a detailed view of various electronic marketplaces, their financial structure and analysis of their performance. This information will also result in a return on investment estimate for the average hiring organization using electronic marketplaces.

A Clustered Back-Bone For Routing In Ad-Hoc Networks, Delzad Kothawala

Theses

In the recent years, a lot of research work has been undertaken in the area of ad-hoc networks due to the increasing potential of putting them to commercial use in various types of mobile computing devices. Topology control in ad-hoc networks is a widely researched topic; with a number of algorithms being proposed for the construction of a power-efficient topology that optimizes the battery usage of the mobile nodes.

This research proposes a novel technique of partitioning the ad-hoc network into virtually-disjoint clusters. The ultimate aim of forming a routing graph over which power-efficient routing can be implemented in a …

Analysis Of Auf1 Targeted Mrna Sequences, Jiebo Lu

Theses

AUF 1, an A+U rich element (ARE) binding protein, plays an important role in mRNA decay. To identify the mRNAs that interact with AUF 1, mRNA derived from a human cardiac cDNA expression library was purified by AUF 1 affinity chromatography and cloned following RT-PCR. 261 sequences were obtained. The sequences were searched against two protein databases and four nucleic acid databases, and the sequence information and database search results were input into a local Microsoft Access database, BLAST-AUF 1, by Java applets for parsing document. Analysis of protein information by querying BLAST-AUF 1 identified 194 function-known proteins, which were …

Review Of Algorithms For Rna Secondary Structure Prediction With Pseudoknots, Ingrid Helene Nielsen

Theses

Pseudoknots are structures that are formed from the base pairing of an RNA secondary loop structure with a complementary base which lies somewhere outside of the loop. The result is a structure, which plays a vital role in cell structure rigidity, regulation of protein synthesis, and in the structural organization of RNA complexes. Deciphering RNA folding patterns would begin to unravel some of the mysteries surrounding the cell and its functions and open a new world to scientists. Many algorithms have been written in this quest to predict RNA's secondary structure but not many have been very successful.

In this …

Analysis Of Molecular Conformations Using Relative Planes, Deepa S. Pai

Theses

Ring substructures of a drug usually participate actively in binding to the receptor. It is necessary to study the spatial relationship of these molecular recognition features in order to determine the pharmacophore of the drug. This is a particularly difficult problem when the drug is a flexible molecule with many energetically accessible conformations.

In this research an innovative approach to calculate the relative displacement and orientation of every possible pair of rings in a given molecule was designed, tested, and implemented in the "Planes" program. Planes were defined from each of the ring substructures and the displacement and rotation of …

Random Search Conformational Analysis Of Piperazine And Piperadine Analogs Of Gbr12909 : Implicit Aqueous Solvation Effects, William A. Roosma

Theses

The object of this work was to study the effect of solvent on the conformational potential energy surface (PES) of GBR12909 analogs. Local minima on the PES's were found by the Random Search algorithm using the Sybyl molecular modeling package from Tripos, Inc., and an implicit solvent model. Two force-field/charge models were employed in the analysis: the Tripos force field with Gasteiger-Huckel charges and the MMFF94 force field with MMFF94 charges.

The effect of solvent on the location of minima in multi-dimensional torsional angle space was studied by comparison to the vacuum phase results. Minima were plotted in torsional angle …

Systems Integration With Dlsi, Tarun Preet S. Bedi

Theses

Systems integration aims to provide a homogenous view to a system consisting of many heterogeneous systems. Systems integration can be achieved by many means out of which the middleware approach is the most popular. This is because middleware can be built around existing systems thereby reducing the amount of changes needed for the integration. Nowadays many middleware technologies are available to integrate heterogeneous systems. One can chose among them depending upon the requirements. But due to the many technologies available for Middleware, a muddle of middleware exists. To reduce this muddle and to integrate the systems already implemented using different …

Virtual Teams Combining Mobile Devices With Web-Based Communication On Group Decision Making, Hyo-Joo Han

Dissertations

Organizations have moved from a face-to-face team environment to a virtual team environment using communication technology during the last decade. More and more workers use asynchronous tools (including email, discussion groups, information sharing tools, and group calendaring systems), and synchronous tools, such as instant messaging and web-based chatting features, to coordinate and share information with people within and outside of organizations. This empirical study on how virtual teams work, integrating mobile devices with web-based group communication for decision-making tasks, examines which technologies and communication modes are the best for distributed group teamwork, and, mainly, what are the predictive characteristics making …

The Impacts Of Delphi Communication Structure On Small And Medium Sized Asynchronous Virtual Teams, Hee-Kyung Cho

Dissertations

The improvement of Internet technology has motivated distributed work groups to collaborate without meeting face to face. Although asynchronous meetings through Web-based group communications systems enable groups dispersed temporarily and geographically to collaborate more flexibly, parallel and non-linear communication among dispersed members also challenge effective and efficient group coordination. Moreover, the Web-based asynchronous meeting is distinguished not only from the face-to-face meeting but also from the synchronous computer-supported meeting in terms of coordination process. However, previous asynchronous group communications or virtual team research focused more on the comparison of this new type of meeting with the face-to-face meeting. Not many …

An Analysis Of The Periodicity Of The Cell Cycle And Apoptotic Regulatory Proteins In Prostate Xenografts Using Anova And Cosinor Methods, Aleen Hosdaghian

Theses

Circadian rhythms have been found in both plants and animals, in normal tissues as well as in most tumors and human cancers. By following these rhythms in healthy and cancerous tissue, it has been possible to find optimal times to deliver a dose of drug, such that efficacy is maximized and toxicity to normal tissues is minimized. In this study, the periodicity of several cell cycle and apoptotic regulatory proteins were studied in two prostate cancer models against a dietary therapeutic agent, Selenium. The ALVA-3 1 (androgen-independent) and PC-3 (androgen-independent) prostate cancer cell lines were grown in vivo, as a …

Simulation And Mathematical Notation Of Alarms Unit For Computer Assisted Resuscitation Algorithm, Swaroop Malangi

Theses

The Computer Assisted Resuscitation Algorithm [CARA] is a system that is used to drive a high output infusion pump used for infusing saline into patients suffering from conditions that lead to hypotension. The infusion pump infuses saline at a particular rate into the patient depending on the blood pressure of the patient.

The alarms unit of CARA was simulated for the infusion pump in which the occurrence of alarms depends on the various criteria the infusion pump encounters when saline is being infused into patients. Various criteria may vary from an air bubble in the line to varying high and …

Programming Language Trends : An Empirical Study, Yaofei Chen

Dissertations

Predicting the evolution of software engineering technology trends is a dubious proposition. The recent evolution of software technology is a prime example; it is fast paced and affected by many factors, which are themselves driven by a wide range of sources. This dissertation is part of a long term project intended to analyze software engineering technology trends and how they evolve. Basically, the following questions will be answered: How to watch, predict, adapt to, and affect software engineering trends?

In this dissertation, one field of software engineering, programming languages, will be discussed. After reviewing the history of a group of …

Design And Evaluation Of A List Gathering Tool In A Web-Based Collaborative Environment, Yuanqiong Wang

Dissertations

This research focuses on how to build a "list" structure to combine individual items of information into some sort of structure that converts the individual items of information into a structure of knowledge relative to the problem. Software was designed to provide relationships among and comparisons of the contributions in a "list" structure, so that individual members of a group process will be able to understand the contributions of information made by the group as a whole.

A List Gathering Tool was designed and implemented, which is one component in a Web-based Social Decision Support System (SDSS) Toolkit. Then, a …

Design And Evaluation Of A Voting Tool In A Collaborative Environment, Zheng Li

Dissertations

This dissertation researchdesigned, implemented, and evaluated a Web-based Dynamic Voting Toolfor small group decision-making in a collaborative environment.

In this dissertation, theliterature on voting tools in current GDSS research is presented. Variousvoting theories and methods are analyzed, and the advantages and weaknessesare compared, so as to gain a better understanding of how to apply thesedifferent voting methods to diverse decision-making situations. A briefoverview of scaling theories is also given, with an emphasis on Thurstone'sLaw.

The basic features of someweb-based voting tool implementations are reviewed along with a discussionof the pros and cons of Intemet voting. A discussion of Human DynamicVoting …

An Experimental Study On Network Intrusion Detection Systems, Peng Fu

Theses

A signature database is the key component of an elaborate intrusion detection system. The efficiency of signature generation for an intrusion detection system is a crucial requirement because of the rapid appearance of new attacks on the World Wide Web. However, in the commercial applications, signature generation is still a manual process, which requires professional skills and heavy human effort. Knowledge Discovery and Data Mining methods may be a solution to this problem. Data Mining and Machine Learning algorithms can be applied to the network traffic databases, in order to automatically generate signatures.

The purpose of this thesis and the …

Face Recognition Using Principal Component Analysis, Timothy Kevin Larkin

Theses

Current methods of face recognition use linear methods to extract features. This causes potentially valuable nonlinear features to be lost. Using a kernel to extract nonlinear features should lead to better feature extraction and, therefore, lower error rates. Kernel Principal Component Analysis (KPCA) will be used as the method for nonlinear feature extraction. KPCA will be compared with well known linear methods such as correlation, Eigenfaces, and Fisherfaces.

Image Morphological Processing, Vijayalakshmi Gaddipati

Dissertations

Mathematical Morphology with applications in image processing and analysis has been becoming increasingly important in today's technology. Mathematical Morphological operations, which are based on set theory, can extract object features by suitably shaped structuring elements. Mathematical Morphological filters are combinations of morphological operations that transform an image into a quantitative description of its geometrical structure based on structuring elements. Important applications of morphological operations are shape description, shape recognition, nonlinear filtering, industrial parts inspection, and medical image processing.

In this dissertation, basic morphological operations, properties and fuzzy morphology are reviewed. Existing techniques for solving corner and edge detection are presented. …

Image Enhancement Techniques Applied To Solar Feature Detection, Artur J. Kowalski

Dissertations

This dissertation presents the development of automatic image enhancement techniques for solar feature detection. The new method allows for detection and tracking of the evolution of filaments in solar images. Series of H-alpha full-disk images are taken in regular time intervals to observe the changes of the solar disk features. In each picture, the solar chromosphere filaments are identified for further evolution examination. The initial preprocessing step involves local thresholding to convert grayscale images into black-and-white pictures with chromosphere granularity enhanced. An alternative preprocessing method, based on image normalization and global thresholding is presented. The next step employs morphological closing …

An Application In Bioinformatics : A Comparison Of Affymetrix And Compugen Human Genome Microarrays, Milind Misra

Theses

The human genome microarrays from Compugen® and Affymetrix® were compared in the context of the emerging field of computational biology. The two premier database servers for genomic sequence data, the National Center for Biotechnology Information and the European Bioinformatics Institute, were described in detail. The various databases and data mining tools available through these data servers were also discussed. Microarrays were examined from a historical perspective and their main current applications-expression analysis, mutation analysis, and comparative genomic hybridization-were discussed. The two main types of microarrays, cDNA spotted microarrays and high-density spotted microarrays were analyzed by exploring the human genome microarray …