Computer Sciences Commons^™

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 …

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 …

A Toolkit For Xml-Based And Process-Oriented Application Integration, Volker Münch

Theses

Systems integration is hard work; different architectures with different interfaces and an innumerable amount of Legacy applications with non-standard interfaces exist. However the needs to meet changing business requirements and to implement faster and optimised procedures within an enterprise and in cooperation with other external enterprises mean that there is a continuing demand for such integration strategies and products. Integration was often an activity separate from system development and could not be accomplished without re-involving system designers and developers. Such a process is therefore inefficient and costly. This thesis proposes a process-oriented integration strategy that combines the tasks of integration …

Investigation Of Implementation Techniques For Backpropagation Neural Networks., John Culloty

Theses

Artificial neural networks are biologically inspired computational methods that have the ability to approximate discrete, real and vector valued target functions. For some problem domains this ability makes neural networks a more appealing solution than traditional computational techniques. Such problem domains typically contain a large number of parameters that are interrelated in a complex and often unknown manner. This makes rule based solutions all but impossible. However another feature of such problem domains is the presence of large volumes of real world data that can be used to tram a neural network until it learns the solution.

One of the …

Speech Enabled E-Learning Technology For Adult Literacy Tutoring, Jason Meade

Theses

This research presents the work involved in developing a speech-enabled e-Learning prototype for use in literacy tutoring. As the main objective was to develop an interface for literacy learning, initial research concentrated on establishing a framework for literacy e-Leaming through the use of speech technology. Requirements for best practice e-Learning and the relevance of learning theories to an e-Learning application were also investigated. The technologies to facilitate this, such as text to speech technologies and mark-up languages, were addressed during the implementation of speech-enabled prototypes. Both server-side and client-side prototypes were implemented to investigate speech technology. Testing found the server-side …

Investigation Of Implementation Techniques For Backpropagation Neural Networks, John Culloty

Theses

Artificial neural networks are biologically inspired computational methods that have the ability to approximate discrete, real and vector valued target functions. For some problem domains this ability makes neural networks a more appealing solution than traditional computational techniques. Such problem domains typically contain a large number of parameters that are interrelated in a complex and often unknown manner. This makes rule based solutions all but impossible. However another feature of such problem domains is the presence of large volumes of real world data that can be used to tram a neural network until it learns the solution.

One of the …

Integrating Experiments And Simulators Into A Distributed E-Learning Environment, Frank Koehler

Theses

New information and communication technologies have emerged in the last few years which have made an impact on learning at all levels. At universities, the spectrum of learning support ranges from enriching traditional lectures and courses with multi- media elements to complete web-based interactive learning environments. A special aspect based on the new media technologies is learning within model worlds by use of simulations or real-life experiments. There are normally no links between these applications and the learning content, so it is impossible to tap the full potential of these applications. Research activities in the area of e-learning underline the …

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.

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 …

Feedback Algorithm For Switch Location : Analysis Of Complexity And Application To Network Design, Yuriy S. Polyakov

Theses

An accelerated feedback algorithm to solve the single-facility minisum problem is studied with application to designing networks with the star topology. The algorithm, in which the acceleration with respect to the Weiszfeld procedure is achieved by multiplying the current Weiszfeld iterate by an accelerating feedback factor, is shown to converge faster than the accelerating procedures available in the literature. Singularities encountered in the algorithm are discussed in detail. A simple practical exception handling subroutine is developed. Several applications of the algorithm to designing computer networks with the star topology are demonstrated. Applications of the algorithm as a subroutine for multi-switch …

Uber-Claws : Unsupervised Pattern Classification For Multi-Unit Extracellular Neuronal Burst Extraction, Rama Natarajan

Theses

To further an understanding of how a neuronal population generates patterns of rhythmic activity, the temporal dynamics of the group of neurons must be formalized. Essential to this pursuit, is the ability to reliably detect and separate the classes of single-unit neuronal activity from multi-unit extracellular signals recorded in a single channel. This study proposes a unified approach to automatically detect and classify single-unit bursts, and to observe the precise onset and offset of burst activity. Existing approaches to the problem fundamentally depend on the statistics of spike waveform variability, both extrinsic and intrinsic to the neuron. In contrast, the …

Towards Digital Library Service Integration, Prateek Shrivastava

Theses

Digital Library Service Integration (DLSI) aims to provide a systematic approach in integrating the services and collections of National Science and Digital Library. The National Science and Digital Library collections can share the services among themselves in a totally integrated environinent. Collections as such will require no change to plug into the DLSI architecture. Collections will keep using the services of NSDL in the similar manner as before. These services will in turn pass few parameters to the services of DLSI. With the help of these parameters, wrappers will fetch the details and priority of the users. These wrappers will …

A Method For Developing In-Silico Protein Homologs, Susan Mcclatchy

Theses

Computational methods for identifying and screening the most promising drug receptor candidates in the human genome are of great interest to drug discovery researchers. Successful methods will accurately identify and narrow the field of potential drug receptor candidates. This study details one such method.

The method described here begins with the assumption that novel drug receptors have high sequence similarity to established drug receptors. The similarity search program FASTA3 aligns translated sequences of the human genome to known drug receptor sequences and ranks these alignments by measuring their statistical significance. Query results returned by FASTA3 are assembled into "in-silico proteins" …

Functional Annotation And Dendrogram Representation Of Gene Expression Clustering Results, Antoneta Petkova Vladimirova

Theses

The advances in genomic sciences have created vast amounts of gene expression data. To make sense of the expression information, various techniques have been applied. Clustering is among the unsupervised methods used to group the results according to gene expression level. Dendrogram visualization allows graphical representation of the clustering. The aim of this thesis is to enhance these techniques by adding another layer of functionality, namely, annotating the dendrogram with gene functional information. Presented is an application which visualizes yeast clustering results as a dendrogram along with color-coded gene keyword annotations. Gene keyword information was extracted from a major biological …

Analysis Of Gene Expression Data Using Expressionist 3.1 And Genespring 4.2, Indu Shrivastava

Theses

The purpose of this study was to determine the differences in the gene expression analysis methods of two data mining tools, Expressionistic^TM 3.1 and GeneSpring^TM 4.2 with focus on basic statistical analysis and clustering algorithms. The data for this analysis was derived from the hybridization of Rattus norvegicus RNA to the Affymetrix RG34A GeneChip. This analysis was derived from experiments designed to identify changes in gene expression patterns that were induced in vivo by an experimental treatment.

The tools were found to be comparable with respect to the list of statistically significant genes that were up-regulated by more …

Sip Message Compression Technique For Efficient Multimedia Services In 3g Wireless Communications, Valerie Kenneally

Theses

The direction of the global cellular industry is primarily determined by two standardisation bodies, the 3rd Generation Partnership Project (3GPP) (in Europe and Asia) and 3GPP2 (in North America). Both of these standardisation bodies are currently specifying a core network to deliver IP based multimedia services over 3G wireless networks. One of the fundamental building blocks of this IP based multimedia core network is the use of SIP (Session Initiation Protocol) as the control protocol. The radio resource, that is the available frequency spectrum, in wireless communication systems remains a limiting factor in terms of the bandwidth available to an …

Measuring Software Size For Continuous Process Improvement, Claire O'Sullivan

Theses

This thesis looks at how the size of a software product can be measured. It looks at current software sizing methods (LOC and FPA) and shows that they are not sufficient in today’s rapidly changing environment. The COSMIC-FFP method is introduced and an overview of how it works is given. The hypothesis to be tested in this thesis is whether COSMIC-FFP is an accurate, repeatable sizing method that when applied to any type of software project produces a size measure that can be used to predict the effort required to complete the project.

This thesis investigates the use of the …

Heterogenous Network Management, Kenneth Carey

Theses

Enterprise level system development, integrating a broad range of arctures and legacy systems, has received significant attention over the last few yentegrated chain management, which allows companies to see their full manufactu inventory and sales channels, has driven much of this work. Delivering quality IP 1 wireless access is forcing similar integration in 2.5G and 3G telecom archires. Such integration has resulted in the emergence of multi-protocol heterogeneietworks, combining IP core backbones, legacy databases and switchinghnology. Heterogeneous networks, due to their diversity of equipment and suppoDrotocols, introduce challenges for today's network administrators, particularly ii areas of device configuration and alarm …

Interactive Multimedia In The Teaching Of The Irish Language In Primary School : Design, Implementation And Development., Máire Lynch

Theses

This thesis focuses on interactive multimedia use specifically in the area of vocabulary acquisition in a second language. It addresses the language learning requirements of third class (nine year olds) language learners, in Primary school. The study is based on existing second language acquisition research, computer - assisted language learning and the design and development of educational multimedia and it delivers an interactive application based on them. The study is firmly rooted in the foundations of the Revised Curriculum for Irish Primary Schools most especially in the language teaching methods it recommends and its emphasis on the use of information …

Statistical Image Analysis Of Spotted Arrays, Filippo Posta

Theses

There is a lot of systematic and specific variability in microarray experiments, this variability affects measured gene expression levels, leading to unreliable gene profiling or an heavy load of extra experiment to statistically confirm the data observed in one experiment.

The aim of this work is to systematically analyze, using statistics, the image derived from a cDNA microarray experiment to have a better understanding of this variability and thus a better confidence over the data obtained from an experiment.

Using technologies available at the Center for Applied Genomics, Newark, New Jersey. Selected images derived from different type of microarray experiments …

An Algorithm For Estimating The Quality Of Microarrays, Ajeet S. Sodhi

Theses

Microarray technology is currently one of the most valuable gene expression tools in molecular biology allowing the experimenter to simultaneously quantify the expression of thousands of genes. It is also one of the most difficult tools to use accurately as each microarray produces a large amount of information that needs to be inspected and normalized before analysis. As the size of a microarray or number of replicates increase, the use of manual inspection becomes impractical. The aim of this thesis is to introduce an algorithm that evaluates each feature of a microarray from the scanned data file. A quality score …