Computer Sciences Commons^™

Structure And Dynamics Of Soluble Guanylyl Cyclase, Kentaro Sugino

Theses

Soluble guanylyl cyclase (sGC) is one of the key enzymes involved in many fundamental biological processes including vasodilatation. It can be allosterically activated by synthetic compound such as YC-l. Recently, the 3D structure of adenylyl cyclase (AC), which is a homologue of sGC, was determined. Using AC as template and homology modeling, the 3D structure of sGC is predicted. Prior experimental work has suggested two binding modes of YC- 1. In the current investigation, molecular dynamics simulations (MD) were conducted to seek more detail of molecular mechanism of sGC activation.

From these MD simulations, a tentative mechanism of sGC activation …

2d Quantitative Structure Activity Relationship Modeling Of Methylphenidate Analogues Using Algorithm And Partial Least Square Regression, Noureen Wadhwaniya

Theses

Quantitative Structure-Activity Relationship (QSAR) analysis attempts to develop a predictive model of biological activity based on molecular descriptors. 2D QSAR uses descriptors, such as topological indices, that are independent of molecular conformation. A genetic algorithm - partial least squares (GA-PLS) approach was used to identify the molecular descriptors that correlate to the biological activity (binding affinity) of a set of 80 methylphenidate analogues and to construct a predictive model. The GA code was implemented using the fitness function (1-(n-1)(1-q²)/ (n - c)), where n is the number of compounds, c is the optimal number of components, and q …

Social Indicators In Cleveland's Ward 17, Mark Salling, Sharon Bliss, Joseph Ahern

All Maxine Goodman Levin School of Urban Affairs Publications

No abstract provided.

Mapping Properties Of Co-Existentially Closed Continua, Paul Bankston

Mathematics, Statistics and Computer Science Faculty Research and Publications

A continuous surjection between compacta is called co-existential if it is the second of two maps whose composition is a standard ultracopower projection. A continuum is called co-existentially closed if it is only a co-existential image of other continua. This notion is not only an exact dual of Abraham Robinson's existentially closed structures in model theory, it also parallels the definition of other classes of continua defined by what kinds of continuous images they can be. In this paper we continue our study of co-existentially closed continua, especially how they (and related continua) behave in certain mapping situations.

Bottleneck Analysis Of Cports, Sreekalyana Chakravarthy Kajuluri

Electrical & Computer Engineering Theses & Dissertations

CPortS is a transportation logistics simulation that models the flow of military cargo through a seaport and the interaction of the cargo with the port resources and infrastructure. It provides information about the seaport's capabilities, how the cargo has been handled, how many days the cargo took to clear a particular port area, and the overall throughput of the seaport. The model is highly data intensive since it models the huge traffic in a real seaport.

Bottlenecks reduce system performance. Systems that are traffic intensive or simulations of systems, which are data intensive, encounter bottlenecks, which reduce their performance. In …

Modulation Of Airway Inflammation By Immunostimulatory Cpg Oligodeoxynucleotides In A Murine Model Of Allergic Aspergillosis, Banani Banerjee, Kevin J. Kelly, Jordan N. Fink, James D. Henderson Jr., Naveen K. Bansal, Viswanath P. Kurup

Mathematics, Statistics and Computer Science Faculty Research and Publications

Allergic aspergillosis is a Th2 T-lymphocyte-mediated pulmonary complication in patients with atopic asthma and cystic fibrosis. Therefore, any therapeutic strategy that selectively inhibits Th2 T-cell activation may be useful in downregulating allergic lung inflammation in asthma. In the present study, we developed a CpG oligodeoxynucleotide (ODN)-based immune intervention of allergic inflammation in a mouse model of allergic aspergillosis. Four different groups of mice were used in a short-term immunization protocol. Three experimental groups of animals (groups 1 to 3) were sensitized with Aspergillus fumigatus antigens. Animals in group 1 were immunized with A. fumigatus antigen alone, while those in group …

Deadline Analysis Of Interrupt-Driven Software, Dennis Brylow, Jens Palsberg

Mathematics, Statistics and Computer Science Faculty Research and Publications

Real-time, reactive, and embedded systems are increasingly used throughout society (e.g., flight control, railway signaling, vehicle management, medical devices, and many others). For real-time, interrupt-driven software, timely interrupt handling is part of correctness. It is vital for software verification in such systems to check that all specified deadlines for interrupt handling are met. Such verification is a daunting task because of the large number of different possible interrupt arrival scenarios. For example, for a Z86-based microcontroller, there can be up to six interrupt sources and each interrupt can arrive during any clock cycle. Verification of such systems has traditionally relied …

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 …

Enhancements To Crisp Possibilistic Reconstructability Analysis, Anas Al-Rabadi, Martin Zwick

Complex Systems Faculty Publications and Presentations

Modified Reconstructibility Analysis (MRA), a novel decomposition within the framework of set-theoretic (crisp possibilistic) Reconstructibility Analysis, is presented. It is shown that in some cases while 3-variable NPN-classified Boolean functions are not decomposable using Conventional Reconstructibility Analysis (CRA), they are decomposable using Modified Reconstructibility Analysis (MRA). Also, it is shown that whenever a decomposition of 3-variable NPN-classified Boolean functions exists in both MRA and CRA, MRA yields simpler or equal complexity decompositions. A comparison of the corresponding complexities for Ashenhurst-Curtis decompositions, and Modified Reconstructibility Analysis (MRA) is also presented. While both AC and MRA decompose some but …

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 …

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 …

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 …

Reconstructability Analysis With Fourier Transforms, Martin Zwick

Complex Systems Faculty Publications and Presentations

Fourier methods used in two‐ and three‐dimensional image reconstruction can be used also in reconstructability analysis (RA). These methods maximize a variance‐type measure instead of information‐theoretic uncertainty, but the two measures are roughly collinear and the Fourier approach yields results close to that of standard RA. The Fourier method, however, does not require iterative calculations for models with loops. Moreover, the error in Fourier RA models can be assessed without actually generating the full probability distributions of the models; calculations scale with the size of the data rather than the state space. State‐based modeling using the Fourier approach is also …

A Comparison Of Modified Reconstructability Analysis And Ashenhurst‐Curtis Decomposition Of Boolean Functions, Anas Al-Rabadi, Marek Perkowski, Martin Zwick

Complex Systems Faculty Publications and Presentations

Modified reconstructability analysis (MRA), a novel decomposition technique within the framework of set‐theoretic (crisp possibilistic) reconstructability analysis, is applied to three‐variable NPN‐classified Boolean functions. MRA is superior to conventional reconstructability analysis, i.e. it decomposes more NPN functions. MRA is compared to Ashenhurst‐Curtis (AC) decomposition using two different complexity measures: log‐functionality, a measure suitable for machine learning, and the count of the total number of two‐input gates, a measure suitable for circuit design. MRA is superior to AC using the first of these measures, and is comparable to, but different from AC, using the second.

An Overview Of Reconstructability Analysis, Martin Zwick

Complex Systems Faculty Publications and Presentations

This paper is an overview of reconstructability analysis (RA), a discrete multivariate modeling methodology developed in the systems literature; an earlier version of this tutorial is Zwick (2001). RA was derived from Ashby (1964), and was developed by Broekstra, Cavallo, Cellier Conant, Jones, Klir, Krippendorff, and others (Klir, 1986, 1996). RA resembles and partially overlaps log‐line (LL) statistical methods used in the social sciences (Bishop et al., 1978; Knoke and Burke, 1980). RA also resembles and overlaps methods used in logic design and machine learning (LDL) in electrical and computer engineering (e.g. Perkowski et al., 1997). Applications of RA, like …

Gamma-Set Domination Graphs. I: Complete Biorientations Of Q-Extended Stars And Wounded Spider Graphs, Kim A. S. Factor

Mathematics, Statistics and Computer Science Faculty Research and Publications

The domination number of a graph G, γ(G), and the domination graph of a digraph D, dom(D) are integrated in this paper. The γ-set domination graph of the complete biorientation of a graph G, dom_γ(G) is created. All γ-sets of specific trees T are found, and dom-_γ(T) is characterized for those classes.

Flow And Pressure Distributions In Vascular Networks Consisting Of Distensible Vessels, Gary S. Krenz, Christopher A. Dawson

Mathematics, Statistics and Computer Science Faculty Research and Publications

We examine the influence of vessel distensibility on the fraction of the total network flow passing through each vessel of a model vascular network. An exact computational methodology is developed yielding an analytic proof. For a class of structurally heterogeneous asymmetric vascular networks, if all the individual vessels share a common distensibility relation when the total network flow is changed, this methodology proves that each vessel will continue to receive the same fraction of the total network flow. This constant flow partitioning occurs despite a redistribution of pressures, which may result in a decrease in the diameter of one and …

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 …

Machine Learning Approaches For Determining Effective Seeds For K -Means Algorithm, Kaveephong Lertwachara

Doctoral Dissertations

In this study, I investigate and conduct an experiment on two-stage clustering procedures, hybrid models in simulated environments where conditions such as collinearity problems and cluster structures are controlled, and in real-life problems where conditions are not controlled. The first hybrid model (NK) is an integration between a neural network (NN) and the k-means algorithm (KM) where NN screens seeds and passes them to KM. The second hybrid (GK) uses a genetic algorithm (GA) instead of the neural network. Both NN and GA used in this study are in their simplest-possible forms.

In the simulated data sets, I investigate two …

A Combinatorial Technique For Face Detection Based On Color And Statistical Analysis, Harishwaran Hariharan

Electrical & Computer Engineering Theses & Dissertations

Automatic detection of faces from video sequences is an important task in security applications. The number, location, size and orientation of human faces in a video frame are unpredictable and can vary from frame to frame. A face detection algorithm for color images in the presence of varying lighting conditions and complexity in background relying upon color and statistical analysis is presented in this thesis. The new method detects skin regions over the entire image and then classifies the skin regions as faces and non-faces. Segmentation of skin regions is performed by a novel color space merging procedure named Integrated …

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" …

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 …

Census 2000 Demographic Profile Report Of The Older Adult Population In Cuyahoga, Lake, Geauga, Lorain And Medina Counties, Mark Salling, Sharon Bliss, Mcnamara, Brian

All Maxine Goodman Levin School of Urban Affairs Publications

No abstract provided.

Multi-Level Decomposition Of Probabilistic Relations, Stanislaw Grygiel, Martin Zwick, Marek Perkowski

Complex Systems Faculty Publications and Presentations

Two methods of decomposition of probabilistic relations are presented in this paper. They consist of splitting relations (blocks) into pairs of smaller blocks related to each other by new variables generated in such a way so as to minimize a cost function which depends on the size and structure of the result. The decomposition is repeated iteratively until a stopping criterion is met. Topology and contents of the resulting structure develop dynamically in the decomposition process and reflect relationships hidden in the data.

Support For Statistical Analysis Of The Configurable Port Simulation (Cports), Saurav Mazumdar

Electrical & Computer Engineering Theses & Dissertations

The primary objective of this thesis is to provide support for statistical analysis of CPortS: a transportation logistics simulation, which models the movement of military traffic through seaports and the interaction of the traffic with port infrastructure. By any standards, CPortS is a very large, data intensive simulation. It provides capabilities for analyzing many important issues such as port clearance and throughput. CPortS was classically run in single run mode. Only a single replication of the simulation was performed and conclusions were drawn from the results obtained. Users and analysts of CPortS performed multiple runs only to see the effect …

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 …

Fuzzy Product -Limit Estimators: Soft Computing In The Presence Of Very Small And Highly Censored Data Sets, Kian Lawrence Pokorny

Doctoral Dissertations

When very few data are available and a high proportion of the data is censored, accurate estimates of reliability are problematic. Standard statistical methods require a more complete data set, and with any fewer data, expert knowledge or heuristic methods are required. In the current research a computational system is developed that obtains a survival curve, point estimate, and confidence interval about the point estimate.

The system uses numerical methods to define fuzzy membership functions about each data point that quantify uncertainty due to censoring. The “fuzzy” data are then used to estimate a survival curve, and the mean survival …