Computer Sciences Commons^™

Non-Invasive Prenatal Detection Of Trisomy 21 Using Tandem Single Nucleotide Polymorphisms, Sujana Ghanta, Michael Mitchell, Mary Ames, Mats Hidestrand, Pippa Simpson, Mary Goetsch, William Thilly, Craig Struble, Aoy Tomita-Mitchell

Mathematics, Statistics and Computer Science Faculty Research and Publications

Background: Screening tests for Trisomy 21 (T21), also known as Down syndrome, are routinely performed for the majority of pregnant women. However, current tests rely on either evaluating non-specific markers, which lead to false negative and false positive results, or on invasive tests, which while highly accurate, are expensive and carry a risk of fetal loss. We outline a novel, rapid, highly sensitive, and targeted approach to non-invasively detect fetal T21 using maternal plasma DNA.

Methods and Findings: Highly heterozygous tandem Single Nucleotide Polymorphism (SNP) sequences on chromosome 21 were analyzed using High-Fidelity PCR and Cycling Temperature Capillary …

On Circulant And Two-Circulant Weighing Matrices, K. T. Arasu, I. S. Kotsireast, C. Koukouvinos, Jennifer Seberry

Mathematics and Statistics Faculty Publications

We employ theoretical and computational techniques to construct new weighing matrices constructed from two circulants. In particular, we con- struct W (148, 144), W (152, 144), W (156, 144) which are listed as open in the second edition of the Handbook of Combinatorial Designs. We also fill a missing entry in Strassler’s table with answer “YES”, by constructing a circulant weighing matrix of order 142 with weight 100.

Impact Of Interdisciplinary Undergraduate Research In Mathematics And Biology On The Development Of A New Course Integrating Five Stem Disciplines, Lester Caudill, April L. Hill, Kathy Hoke, Ovidiu Z. Lipan

Biology Faculty Publications

Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a …

Impact Of Interdisciplinary Undergraduate Research In Mathematics And Biology On The Development Of A New Course Integrating Five Stem Disciplines, Lester Caudill, April L. Hill, Kathy Hoke, Ovidiu Z. Lipan

Department of Math & Statistics Faculty Publications

Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a …

Economic Optimization Of Offshore Wind Farms Using The Geometric Algorithm, Mahidhar Nandigam

Electrical & Computer Engineering Theses & Dissertations

The research project related to this thesis focuses on the optimization of electrical systems for offshore wind farms for a given capacity. The optimal design and planning is a critical issue for developing cost effectively Offshore Wind Farms in energy systems. The Geometric Optimization Algorithms approach has been adopted to develop an optimization program, where the main components of the electrical system of an offshore wind farm and key technical specifications are used as parameters to be optimized for a minimum cost with necessary constraints. The effectiveness of the optimization program can be evaluated with real-time comparison between offshore wind …

Bioinformatics Across The Sciences, Nigel Yarlett

Cornerstone 3 Reports : Interdisciplinary Informatics

No abstract provided.

Quantitative Analysis Of Arterial Spin Labeling Fmri Data Using A General Linear Model, Luis Hernandez-Garcia, Hesamoddin Jahanian, Daniel B. Rowe

Mathematics, Statistics and Computer Science Faculty Research and Publications

Arterial spin labeling techniques can yield quantitative measures of perfusion by fitting a kinetic model to difference images (tagged-control). Because of the noisy nature of the difference images investigators typically average a large number of tagged versus control difference measurements over long periods of time. This averaging requires that the perfusion signal be at a steady state and not at the transitions between active and baseline states in order to quantitatively estimate activation induced perfusion. This can be an impediment for functional magnetic resonance imaging task experiments. In this work, we introduce a general linear model (GLM) that specifies Blood …

A Methodology For Engineering Collaborative And Ad-Hoc Mobile Applications Using Syd Middleware, Praveen Madiraju, Srilaxmi Malladi, Janaka Balasooriya, Arthi Hariharan, Sushil K. Prasad, Anu Bourgeois

Mathematics, Statistics and Computer Science Faculty Research and Publications

Today’s web applications are more collaborative and utilize standard and ubiquitous Internet protocols. We have earlier developed System on Mobile Devices (SyD) middleware to rapidly develop and deploy collaborative applications over heterogeneous and possibly mobile devices hosting web objects. In this paper, we present the software engineering methodology for developing SyD-enabled web applications and illustrate it through a case study on two representative applications: (i) a calendar of meeting application, which is a collaborative application and (ii) a travel application which is an ad-hoc collaborative application. SyD-enabled web objects allow us to create a collaborative application rapidly with limited coding …

A Class Of Models For Uncorrelated Random Variables, Nader Ebrahimi, Gholamhossein Hamedani, Ehsan S. Soofi, Hans Volkmer

Mathematics, Statistics and Computer Science Faculty Research and Publications

We consider the class of multivariate distributions that gives the distribution of the sum of uncorrelated random variables by the product of their marginal distributions. This class is defined by a representation of the assumption of sub-independence, formulated previously in terms of the characteristic function and convolution, as a weaker assumption than independence for derivation of the distribution of the sum of random variables. The new representation is in terms of stochastic equivalence and the class of distributions is referred to as the summable uncorrelated marginals (SUM) distributions. The SUM distributions can be used as models for the joint distribution …

Processing Induced Voxel Correlation In Sense Fmri Via The Ammust Framework, Daniel B. Rowe, Iain P. Bruce

Mathematics, Statistics and Computer Science Faculty Research and Publications

No abstract provided.

Automated Theorem Prover Axiom Management, Ashley T. Holeman, Ewen Denney

STAR Program Research Presentations

Automated Theorem Provers (ATPs), are computer programs that use collections of axioms,which are logical statements assumed to be true, in order to prove conjectures. NASA uses these programs to verify safety and functional requirements in domains like Guidance, Navigation, and Control. There are about 30 axioms on each major topic including the theory of coordinate systems, elementary arithmetic and linear algebra. These axioms have been created over the duration of many projects and combined into a single file. One task is to manage the axioms by arranging them into logical sections, deleting unnecessary ones and rewriting some into a more …

Discrete Groups And The Complex Contact Geometry Of Sl(2, C), Brendan Foreman

Mathematics and Computer Science

We investigate the vertical foliation of the standard complex contact structure on Γ \ Sl(2, C), where Γ is a discrete subgroup. We find that, if Γ is nonelementary, the vertical leaves on Γ \ Sl(2, C) are holomorphic but not regular. However, if Γ is Kleinian, then Γ \ Sl(2, C) contains an open, dense set on which the vertical leaves are regular, complete and biholomorphic to C ∗. If Γ is a uniform lattice, the foliation is nowhere regular, although there are both infinitely many compact and infinitely many nonclosed leaves.

Acm/Springer Mobile Networks And Applications (Monet) Special Issue On “Advanced Mobile Applications And Intelligent Multimedia Systems For Ubi-Com”, Jong Hyuk Park, Shu-Ching Chen, Mieso Denko, Sheikh Iqbal Ahamed

Mathematics, Statistics and Computer Science Faculty Research and Publications

No abstract provided.

A Formal Context Specific Trust Model (Ftm) For Multimedia And Ubiquitous Computing Environment, Sheikh Iqbal Ahamed, Munirul M. Haque, Nilothpal Talukder

Mathematics, Statistics and Computer Science Faculty Research and Publications

In order to ensure secure sharing of resources in an ad-hoc network of handheld devices in a multimedia and ubiquitous computing environment, mutual collaboration is essential. However, the limitations, such as poor storage and computational capability of these multimedia and ubiquitous devices stand as the bottleneck for effective sharing of resources. As a result of this drawback, the adversaries are obtaining access to the new doors for security breaches. Mutual Trust is the weapon used to combat security violations by restricting malicious devices from participating in any interaction in such an open and dynamic environment. In this paper, we present …

Noise Assumptions In Complex-Valued Sense Mr Image Reconstruction, Daniel B. Rowe, Iain P. Bruce

Mathematics, Statistics and Computer Science Faculty Research and Publications

In fMRI, brain images are not measured instantaneously and a volume of images can take two seconds to acquire at a low 64x64 resolution. Significant effort has been put forth on many fronts to decrease image acquisition time including parallel imaging. In parallel imaging, sub-sampled spatial frequency points are measured in parallel and combined to form a single image. Measurement time is decreased at the expense of increased image reconstruction difficulty and time. One significant parallel imaging technique known as SENSE utilizes a complex-valued regression coefficient estimation process with transposes replaced by conjugate transposes. However, in SENSE the noise structure …

Dnagents: Genetically Engineered Intelligent Mobile Agents, Jeremy Otho Kackley

Dissertations

Mobile agents are a useful paradigm for network coding providing many advantages and disadvantages. Unfortunately, widespread adoption of mobile agents has been hampered by the disadvantages, which could be said to outweigh the advantages. There is a variety of ongoing work to address these issues, and this is discussed. Ultimately, genetic algorithms are selected as the most interesting potential avenue. Genetic algorithms have many potential benefits for mobile agents. The primary benefit is the potential for agents to become even more adaptive to situational changes in the environment and/or emergent security risks. There are secondary benefits such as the natural …

On Folding A Polygon To A Polyhedron, Joseph O'Rourke

Computer Science: Faculty Publications

We show that the open problem presented in "Geometric Folding Algorithms: Linkages, Origami, Polyhedra" [DO07] is solved by a theorem of Burago and Zalgaller [BZ96] from more than a decade earlier.

Fastmedusa: A Parallelized Tool To Infer Gene Regulatory Networks, Serdar Bozdag, Aiguo Li, Stefan Wuchty, Howard A. Fine

Mathematics, Statistics and Computer Science Faculty Research and Publications

Motivation: In order to construct gene regulatory networks of higher organisms from gene expression and promoter sequence data efficiently, we developed FastMEDUSA. In this parallelized version of the regulatory network-modeling tool MEDUSA, expression and sequence data are shared among a user-defined number of processors on a single multi-core machine or cluster. Our results show that FastMEDUSA allows a more efficient utilization of computational resources. While the determination of a regulatory network of brain tumor in Homo sapiens takes 12 days with MEDUSA, FastMEDUSA obtained the same results in 6 h by utilizing 100 processors. Availability: Source code and documentation of …

On Flat Polyhedra Deriving From Alexandrov's Theorem, Joseph O'Rourke

Computer Science: Faculty Publications

We show that there is a straightforward algorithm to determine if the polyhedron guaranteed to exist by Alexandrov's gluing theorem is a degenerate flat polyhedron, and to reconstruct it from the gluing instructions. The algorithm runs in O(n³) time for polygons whose gluings are specified by n labels.

Star Unfolding Convex Polyhedra Via Quasigeodesic Loops, Jin-Ichi Itoh, Joseph O'Rourke, Costin Vîlcu

Computer Science: Faculty Publications

We extend the notion of star unfolding to be based on a quasigeodesic loop Q rather than on a point. This gives a new general method to unfold the surface of any convex polyhedron ℘ to a simple (nonoverlapping) planar polygon: cut along one shortest path from each vertex of ℘ toQ, and cut all but one segment of Q.

The Yao Graph Y6 Is A Spanner, Joseph O'Rourke

Computer Science: Faculty Publications

We prove that Y₆ is a spanner. Y₆ is the Yao graph on a set of planar points, which has an edge from each point x to a closest point y within each of the six angular cones of 60^◦ surrounding x .

Convergence Of The Sinc Method Applied To Volterra Integral Equations, M. Zarebnia, J. Rashidinia

Applications and Applied Mathematics: An International Journal (AAM)

A collocation procedure is developed for the linear and nonlinear Volterra integral equations, using the globally defined Sinc and auxiliary basis functions. We analytically show the exponential convergence of the Sinc collocation method for approximate solution of Volterra integral equations. Numerical examples are included to confirm applicability and justify rapid convergence of our method.

The Teaching Of Equation Solving: Approaches In Standards-Based And Traditional Curricula In The United States, Jinfa Cai, Bikai Nie, John Moyer

Mathematics, Statistics and Computer Science Faculty Research and Publications

This paper discusses the approaches to teaching linear equation solving that are embedded in a Standards-based mathematics curriculum (Connected Mathematics Program or CMP) and in a traditional mathematics curriculum (Glencoe Mathematics) in the United States. Overall, the CMP curriculum takes a functional approach to teaching equation solving, while Glencoe Mathematics takes a structural approach. The functional approach emphasizes the important ideas of change and variation in situations and contexts. It also emphasizes the representation of relationships between variables. The structural approach, on the other hand, requires students to work abstractly with symbols and follow procedures in a systematic way. …

Time Series Models For Computing Activation In Fmri, Daniel W. Adrian, Ranjan Maitra, Daniel B. Rowe

Mathematics, Statistics and Computer Science Faculty Research and Publications

No abstract provided.

Pre-Service Teachers’ Knowledge Of Algebraic Thinking And The Characteristics Of The Questions Posed For Students, Leigh A. Van Den Kieboom, Marta Magiera, John Moyer

Mathematics, Statistics and Computer Science Faculty Research and Publications

In this study, we explored the relationship between the strength of pre-service teachers’ algebraic thinking and the characteristics of the questions they posed during cognitive interviews that focused on probing the algebraic thinking of middle school students. We developed a performance rubric to evaluate the strength of pre-service teachers’ algebraic thinking across 130 algebra-based tasks. We used an existing coding scheme found in the literature to analyze the characteristics of the questions pre-service teachers posed during clinical interviews. We found that pre-service teachers with higher algebraic thinking abilities were able to pose probing questions that uncovered student thinking through the …

Pre-Service Middle School Teachers’ Knowledge Of Algebraic Thinking, Marta Magiera, John Moyer, Leigh A. Van Den Kieboom

Mathematics, Statistics and Computer Science Faculty Research and Publications

In this study we examined the relationship between 18 pre-service middle school teachers’ own ability to use algebraic thinking to solve problems and their ability to recognize and interpret the algebraic thinking of middle school students. We assessed the pre-service teachers’ own algebraic thinking by examining their solutions and explanations to multiple algebra-based tasks posed during a semester-long mathematics content course. We assessed their ability to recognize and interpret the algebraic thinking of students in two ways. The first was by analyzing the preservice teachers’ ability to interpret students’ written solutions to open-ended algebra-based tasks. The second was by analyzing …

M-Refinable Extensions Of Real Valued Functions, John Meuser, Tian-Xiao He, Faculty Advisor

John Wesley Powell Student Research Conference

No abstract provided.

Detecting Malicious Javascript, Matthew F. Der

Honors Theses

The increased use of the World Wide Web and JavaScript as a scripting language for Web pages have made JavaScript a popular attack vector for infecting users' machines with malware. Additionally, attackers often obfuscate their code to avoid detection, which heightens the challenge and complexity of automated defense systems. We present two analyses of malicious scripts and suggest how they could be extended into intrusion detection systems. For our analyses we use a sample of deobfuscated malicious and benign scripts collected from actual Web sites. First, using our malicious sample, we perform a manual analysis of attack signatures, identifying four …

Importance Sampling For Dispersion-Managed Solitons, Elaine T. Spiller, Gino Biondini

Mathematics, Statistics and Computer Science Faculty Research and Publications

The dispersion-managed nonlinear Schrödinger (DMNLS) equation governs the long-term dynamics of systems which are subject to large and rapid dispersion variations. We present a method to study large, noise-induced amplitude and phase perturbations of dispersion-managed solitons. The method is based on the use of importance sampling to bias Monte Carlo simulations toward regions of state space where rare events of interest—large phase or amplitude variations—are most likely to occur. Implementing the method thus involves solving two separate problems: finding the most likely noise realizations that produce a small change in the soliton parameters, and finding the most likely way that …

Volume 03, Cheryl Peck, Charles Hoever, Longwood Theater Department, Brittany Anderson, J. Ervin Sheldon, Richard Hayden, Yuri Calustro, Candice Fleming, Rebecca Franklin, Ashley Yocum, Danielle M. Jagoda, Cristina M. Valdivieso, Jameka Jones, Amy Ellis, Ashley Maser, Erikk Shupp, Jamie Yurasits, Joshua Davis, Alexander Leonhart, Kenny Wolfe, Sally Meadows, J. Haley, Amy Jackson, Morgan Howard, Adrienne Heinbaugh, Melissa Dorton, Ciarra Stalker

Incite: The Journal of Undergraduate Scholarship

Introduction from Dean Dr. Charles Ross

Little Shop of Horrors by Longwood Theater Department

Who Has the Hottest Hotsauce in Farmville: A Quantitative Comparison of Sauces from Local Restaurants by Cheryl Peck and Charles Hoever

Precipitation Effects on the Growth of White Oaks and Virginia Pines on the Mt. Vernon Plantation by Brittany Anderson

Design and Synthesis of Novel Ion Binding Molecules for Self-Assembly and Sensing Applications by J. Ervin Sheldon

A Statistical Analysis of Algorithms for Playing SameGame by Richard Hayden

Intersecting Cylinders at Arbitrary Angles by Yuri Calustro

Putting a Foot in the Revolving Door: Strategies for Reducing …