Physical Sciences and Mathematics Commons^™

A Survey On Online Matching And Ad Allocation, Ryan Lee

Theses

One of the classical problems in graph theory is matching. Given an undirected graph, find a matching which is a set of edges without common vertices. In 1990s, Richard Karp, Umesh Vazirani, and Vijay Vazirani would be the first computer scientists to use matchings for online algorithms [8]. In our domain, an online algorithm operates in the online setting where a bipartite graph is given. On one side of the graph there is a set of advertisers and on the other side we have a set of impressions. During the online phase, multiple impressions will arrive and the objective of …

Bayesian Estimation Of The Intensity Function Of A Non-Homogeneous Poisson Process, James Jensen

Theses

In this paper we explore Bayesian inference and its application to the problem of estimating the intensity function of a non-homogeneous Poisson process. These processes model the behavior of phenomena in which one or more events, known as arrivals, occur independently of one another over a certain period of time. We are concerned with the number of events occurring during particular time intervals across several realizations of the process. We show that given sufficient data, we are able to construct a piecewise-constant function which accurately estimates the mean rates on particular intervals. Further, we show that as we reduce these …

Comparison Of Longitudinal Changes In Resting State Functional Magnetic Resonance Imaging Between Alzheimer’S And Healthy Controls, Berk Can Yilmaz

Theses

Resting State Functional Magnetic Resonance Imaging (rs-fMRI) is a technique that is widely used for analyzing brain function using different approaches and methods. This study involves rs-fMRI analysis of Blood Oxygenation Level Dependent (BOLD) signals acquired from Alzheimer’s disease (AD) Patients and Healthy Controls (HC). Each subject in the study had both functional and anatomical images with at least one rs-fMRI scan with their Anatomical (T1) scans. Previous rs-fMRI studies have demonstrated that AD shows differences in Amplitude of Low Frequency (<0.1 Hz) Fluctuations (ALFF), and Regional Homogeneity (ReHo) measures according to HCs.

The aim of the study is to investigate individual and group level differences using ReHo and mALFF related …

Analysis Of Gameplay Strategies In Hearthstone: A Data Science Approach, Connor W. Watson

Theses

In recent years, games have been a popular test bed for AI research, and the presence of Collectible Card Games (CCGs) in that space is still increasing. One such CCG for both competitive/casual play and AI research is Hearthstone, a two-player adversarial game where players seeks to implement one of several gameplay strategies to defeat their opponent and decrease all of their Health points to zero. Although some open source simulators exist, some of their methodologies for simulated agents create opponents with a relatively low skill level. Using evolutionary algorithms, this thesis seeks to evolve agents with a higher skill …

The Primary Volatile Composition Of Comet C/2015 Er61 (Panstarrs), Aaron Butler

Theses

In the outer edges of the solar system exist two regions: the Kuiper belt and Oort cloud. These two regions have a high amount of icy bodies (comets) orbiting the Sun. Comets located within the Oort cloud and Kuiper belt contain an ancient codex to the solar systems contents, before the formation of our solar system. Presented are near-infrared, high-resolution (λ/Δλ ~40000) data obtained from the immersion-grating echelle spectrograph iSHELL at the 3m NASA Infrared Telescope Facility (IRTF) in Maunakea, Hawaii of the Oort cloud comet C/2015 ER61 (PANSTARRS). Observations took place on April 15 and 17 in 2017 while …

Habitat Preferences Of Blue Marlin (Makaira Nigricans) And Black Marlin (Istiompax Indica) In The Eastern Pacific Ocean, Nima Farchadi, Michael G. Hinton, Andrew R. Thompson, Zhi-Yong Yin

Theses

Overexploitation and climate change can reduce the abundance and shift the spatial distribution of marine species. Determining the habitat suitability of a mobile pelagic species, such as Makaira nigricans (BUM) and Istiompax indica (BLM), can help describe their spatiotemporal distribution patterns over a broad spatial scale, which is a crucial need for fisheries management. Using 14 years (1997-2010) of Inter-American Tropical Tuna Commission (IATTC) catch data from purse-seine vessels in the eastern Pacific Ocean (EPO), we modeled the dynamic habitat suitability of BUM and BLM in response to environmental variables within the EPO using a species distribution model (MaxEnt) with …

Bubble Stream Production By Belugas (Delphinapterus Leucas), Megan Slack

Theses

Bubble stream production in belugas has been poorly characterized and its function is not well understood. I examined behavioral states when producing bubble streams (“bubbling”), and when bubbling calls, to determine whether bubbling was significantly associated with a particular call category or behavioral state. Using 19 hours of video and audio recordings collected over a two-day period, I quantified bubble streams of a 4-month old calf and an unrelated adult female housed together. Based on the overall activity budgets and pool of vocalizations for both animals, I calculated the expected counts of bubble streams with and without vocalizations, assuming that …

Network Exploration Of Correlated Multivariate Protein Data For Alzheimer's Disease Association, Matthew J. Lane

Theses

Alzheimer Disease (AD) is difficult to diagnose by using genetic testing or other traditional methods. Unlike diseases with simple genetic risk components, there exists no single marker determining as to whether someone will develop AD. Furthermore, AD is highly heterogeneous and different subgroups of individuals develop the disease due to differing factors. Traditional diagnostic methods using perceivable cognitive deficiencies are often too little too late due to the brain having suffered damage from decades of disease progression. In order to observe AD at early stages prior to the observation of cognitive deficiencies, biomarkers with greater accuracy are required. By using …

Ranking Single Nucleotide Polymorphisms With Support Vector Regression In Continuous Phenotypes, Seif Shahidain

Theses

Support vector machines (SVM) have been used to improve the ranking of single nucleotide polymorphisms (SNPs) over traditional chi-square tests in disease case studies [2]. In this investigation, ranking SNPs with support vector regression (SVR) was compared to the Wald test in predicting continuous phenotypes. SVR-ranked SNPs consistently outperformed the Wald test-ranked SNPs to provide a more accurate prediction of the phenotype with fewer SNPs across several methods of prediction.

Rna Genome Annotation With A Focus On T. Brucei, Brett Bucci

Theses

The goal of this project is to identify untranslated regions (UTRs) and UTR-indicating patterns in the genome of T. brucei. T. brucei is an interesting organism, and as the cause of African sleeping sickness -- which infects 300,000-500,000 people and a significant number of cattle annually -- is currently the subject of considerable research. Using existing algorithms, several patterns have been found that may lead to more complete UTR annotations in the T. brucei genome. The most encouraging sequence is the 11-base sequence GAGGGIICG]TGGGG, which appears in five hypothetical genes near the tail. Discovery of several such sequences could guide …

Utr Prediction Programs For Trypanosoma Brucei, Maria Moutafis

Theses

In the past few years, the field of bioinformatics has seen a rapid increase in the need for use of various sequence analysis tools. As we advance in the fields of science and technology, new programs and software are constantly being developed in this field. Rapidly expanding gene sequence databases and rapidly evolving sequence analysis tools are providing researchers with ways to search for highly similar query sequences whether they are nucleotide, protein, or gene databases. This thesis will focus on sequence alignment tools, specifically concentrating on tools that help determine/predict non-coding regions of sequences also known as untranslated regions …

Network Activity Arising From Optimal Diameters Of Neuronal Processes, Juliane Gansert

Theses

Electrical coupling provides an important pathway for signal transmission between neurons. In several regions of the mammalian brain electrical synapses have been detected, and their role in the synchronization of neural networks and the generation of oscillations has been studied theoretically. Recently, it has been found that the amplitude of the postsynaptic potential is maximized for a specific diameter of the postsynaptic fiber.

In this thesis, the impact of the fiber's diameter on the success or failure of the action potential initiation and propagation is studied theoretically. Systems of two coupled neurons, as well as small networks, are investigated. The …

Comparative Analysis Of Parametric, Nonparametric And Permutation Methods For Differential Expression, Rahul Patil

Theses

DNA microarrays permit us to study the expression of thousands of genes simultaneously. They are now used in many different contexts to compare mRNA levels between two or more samples of cells. Microarray experiments typically give us expression measurements on a large number of genes. Increasing popularity of microarray technology has resulted in a number of tests being proposed to detect differentials expression.

The purpose of study is to compare the parametric, non parametric and permutation tests when applied to microarray data for differential expression analysis. t test (parametric), Mann Whitney test (nonparametric) and Significance of analysis (permutation ) test …

A Data Gathering Toolkit For Biological Information Integration, Munira Lokhandwala

Theses

SYSTERS is a biological information integration system containing protein sequences from many protein databases such as Swiss-Prot and TrEMBL and also protein sequences from complete genomes available at Ensembl, The Arabidopsis Information Resource, SGD and GeneDB. For some protein sequences their encoding nucleotide sequences can be found in their corresponding websites. However, for some protein sequences their encoding nucleotide sequences are missing.

The goal of this thesis is to. collect all nucleotide sequences for the protein sequences in SYSTERS and store them in a common database. There are two cases. The first case is that if the nucleotide sequences can …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

Comparative Molecular Field Analysis (Comfa) Of Protonated Methylphenidate Phenyl-Substituted Analogs, Kathleen Mary Gilbert

Theses

Protonated methylphenidate (pMP) and several phenyl-substituted pMP analogs were analyzed using Comparative Molecular Field Analysis (CoMFA) to develop a pharmacophore for dopamine transporter (DAT) binding. This research is a part of an interdisciplinary study on using methylphenidate (MP) analogs to block the binding of cocaine to the DAT as a treatment for addiction.

A random search conformational analysis using key pMP torsional angles was performed to create conformer families representing possible bioactive conformations. The lowest energy pMP conformer of each family was used as a template to create phenyl-substituted pMP analogs.

Partial least squares analysis was used to determine the …