Digital Commons Network^™

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 …

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 …

Geochemical Studies To Assess Marine Oil Pollution Zakum Field, Abu Dhabi, Uae, Bakheet Saeed Al Katheeri

Theses

The present study aims at quantifying and assessing the organic and inorganic pollutants in the offshore sediments of the Zakum Field, Abu Dhabi, UAE. Twenty-six sampling stations were selected to cover the maximum area of the field. Sediments samples were subjected to a variety of analyses including mechanical analysis, Total Organic Carbon (TOC) analysis, Total Petroleum Hydrocarbon (TPH) analysis, twenty congeners of Poly Chlorinated Biphenyls (PCBs) analysis, sixteen different Polycyclic Aromatic Hydrocarbons (PAHs) analysis and eight heavy metals analysis. For a comparison purpose six old marine seabed core samples which collected from Zakum Filed between 1966 and 1978 were analyzed …

Assessment Of Surface Water Runoff And Groundwater Recharge Using Mathematical Models, Khaled Omer Mohamed Haroon

Theses

In arid and semi-arid regions, surface water resources are scarce and, in most cases, groundwater is the only natural resource of freshwater. Pumping of groundwater often exceeds natural recharge. Therefore, groundwater levels are declining and its quality is deteriorating. Sustainable management of groundwater is thus a key issue and requires implementation of appropriate technologies to augment groundwater resources. Artificial recharge augments the natural movement of surface water into the underground formations using some means of construction whereby surface water from streams or lakes is made to infiltrate into the ground.

The UAE is known by its arid conditions and limited …

The Rise And Fall Of Open Market Emissions Trading In New Jersey, Devin Peter Demarco

Theses

On August 2, 1996, the New Jersey Department of Environmental Protection (NJDEP) promulgated rules governing its Open Market Emissions Trading (OMET) program. With a goal to provide industry with a greater degree of flexibility in meeting federal air compliance directives and simultaneously move the state towards the attainment of National Ambient Air Quality Standards (NAAQS), this program is now slated for termination following scrutiny from the federal Environmental Protection Agency (EPA), environmental groups and a new NJDEP administration.

This thesis discusses the basis for this scrutiny and other program flaws discovered through interviews with, and public comments from, NJDEP and …

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 …

Incineration And Environmental Justice : The Case Of Communities Around Connecticut Resource Recovery Facilities, Michael A. Bilheimer

Theses

The current depleting landfill capacity in Connecticut means that resource recovery facilities will be relied on heavily to meet the States' waste disposal needs. This heavy reliance on these facilities will place greater burdens on the host communities of these waste facilities. Therefore it is important to examine the citing of these facilities to determine if these sitings unfairly targeted a particular segment of the population.

To determine if siting has been unjust in Connecticut, this study uses a geographic information system (GIS) to analyze demographic data surrounding each facility in a comparison of demographic data from 1990 and 2000 …

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.

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 …

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 …

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 …

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 …

Environmental Risk Factors Of Bronchial Asthma Among Primary Schoolchildren In Abu Dhabi City, Fareed Hussain Saleh H. Jalabi

Theses

The aim of this study was to describe the current epidemiological pattern of bronchial asthma among the schoolchildren aged 7-12 years old in 60 government primary schools at Abu Dhabi city -UAE.

The analytical cross-section design (ACSD) was chosen as a suitable method to investigate the exposure variables (environmental risk factors) and prevalence of bronchial asthma simultaneously in a representative samples.

A self-administered questionnaire was completed by the parents of the school children to collect information regarding bronchial asthma, other related allergic conditions and family history of respiratory allergy.

Analyses of the effect of the different socio-demographic variables and clinical …

Establishing A Uae Database Using Str Loci, Ibrahim Abdullah Ali Al-Housani

Theses

The analysis of DNA polymorphism has become an indispensable tool in forensic science and criminal cases. Today, the amplification of Short Tandem Repeat (STR) loci using PCR is the perfect method for typing biological evidence found at crime scenes. Forensic laboratories all over the world have been progressively expanding their databases for better discrimination among individuals and suspects of crimes.

The objective of this thesis was to analyze the DNA profile of native and non-native populations, and to study the similarities and dissimilarities among them. Blood samples were collected from three non-natives (Egyptian, Indian and Pakistani) and native populations from …

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 …

Thermochemical Properties Of Small Oxygenated Sulfur Hydrocarbons And Kinetics - Reaction Pathways Of Methylthiomethyl Radical With Oxygen, Fei Jin

Theses

The thermochemical properties on CH₃SCH₂OOH and the corresponding two radicals resulting from loss of H atom: CH₃SCH₂OO and CH₂SCH₂OOH are important to understand the stability, reaction paths and kinetics of reactions of dimethyl sulfide and other sulfur hydrocarbons (sulfides) in the atmosphere and combustion processes. Thermochemical properties for species and transition states in the methylthiomethyl radical (CH₃SCH₂) + O₂ reaction system are analyzed to evaluate reaction paths and kinetics under these conditions. Isodesmic working reaction are employed to determine the enthalpies of formation …

Laboratory Investigation Of Transport And Treatment Of Chromium In Groundwater At Liwa District, Abu Dhabi, Wali-Ur-Rahman Din Badshah

Theses

Groundwater quality is a critical aspect affecting utilization of this source for certain purposes. In the UAE, utilization of groundwater for domestic purposes is well practiced. While the quality of groundwater at some locations does not permit direct utilization of this source, groundwater, in many cases, is mixed with desalinated water at certain proportion before being disinfected and then distributed to customers.

Groundwater of Liwa aquifer contains high level of Cr(VI) which is believed to originate from natural sources. However, little has been done to investigate the fate of this contaminant. Spreading of chromium to nearby aquifers may render the …

The Synthesis And Characterisation Of Diiron And Triiron Carbonyl Cluster Compounds With Sulphur And Phosphine Ligands, Geraldine Gray

Theses

This work is primarily concerned with the synthesis and characterisation of di and triiron carbonyl cluster derivatives which contain sulphur and phosphine ligands.

The first chapter is a review of the literature of such complexes. Included are diiron carbonyl clusters which contain phosphine ligands, those which contain sulphur, and those that contain phosphine and sulphur ligands. Triiron carbonyl clusters which contain phosphine ligands, sulphur ligands and both are also discussed.

Chapter two describes the synthesis of compounds of the type [{Fe₂(SR)₂(CO)₅)₂Ph₂P (CH₂)_nPPh₂] (R = …

Multi-Path Differential Optical Absorption Spectroscopy, John Gerard Murphy

Theses

A number of potential methods for the production of multiple light beams for long- path differential absorption spectroscopy have been considered and analysed. The system deemed most suitable has been designed, constructed and tested over two adjacent measurement paths.

The system was built in Cork Institute of Technology to the west of Cork City, Ireland during the period 2000 - 2004. The system has been tested during the winter period of 2003/2004 and ambient concentrations of SO₂ and NO₂ have been measured and are reported. The measurement of additional gaseous species and suspended particulate matter was excluded from …

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 …

Optimisation Of Heat Transfer And Fluid Flow In The Cooling Of Building Integrated Photovoltaic Facades., Eoin Patrick Hodge

Theses

The aim of this research was to explore the effects of mature and developing technologies from aeronautical industries such as impingement and film cooling, and electronic cooling techniques, in the setting up of different laminar and turbulent flow regimes on PV cooling duct heat transfer rates, with air flow as that brought about with natural buoyancy effects in a vertical building facade. The problem of efficiency losses in PV panels, due to overheating, is one of the factors restricting the development and use of this renewable power source. PV panels can experience very high temperatures, due to the heat input …

A Proposal To Meet The Biofuels Directive In Ireland, Karl Mccarthy

Theses

In 1990 the transport sector accounted for 9,5% of all Irish emissions. By 2010 it is predicted that transport emissions will have increased by 179%, accounting for 18.8% of all emissions. It is predicted that transport emissions will therefore be around 14,000 kt in 2010. This equates to around €370 million pa in carbon taxes if and when the taxation regime is introduced. This €370 million may be used to facilitate a biofuel industry (for example, by reducing excise duty on biofuels).

The proposed carbon tax along with the EU Biofuels Directive aims to encourage the use of renewable transport …

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 …

Influence Of Varying Intensities Of Natural Area On-Site Interpretation On Attitudes And Knowledge, Michael Hughes

Theses

Using interpretation as a means of influencing attitudes and knowledge is a core component of natural area management practice. However, this aspect of on-site interpretation is rarely assessed when evaluating natural area management success. This thesis examined the immediate influence of different intensities of on-site interpretation on attitudes and knowledge of visitors to natural areas. Measuring the immediate (short term) influence of a site experience enables clearer links to be made between survey responses and interpretation used at a specific site, something long term surveys are less able to achieve. Two sites from Western Australia (the Tree Top Walk and …

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 …

Development Of Electrochemical Sensors For Monitoring Glucose, Michael Nesbitt

Theses

The thesis focuses on evaluating calcium alginate as an immobilisation matrix for the oxidase enzyme glucose oxidase for the amperometric determination of glucose. The basic principles of enzymology and enzyme immobilisation is discussed followed by a review of a variety of first, second and third generation type enzyme electrodes. Amperometry as governed by the Cottrell equation and mass transfer models relating to amperometric electrodes are also considered.

Bovine serum albumin (BSA / GOx) enzyme electrode system was employed as a model to evaluate a calcium alginate immobilisation technique for glucose oxidase. The principal methods employed for enzyme immobilisation were:

• …

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 …