Computer Sciences Commons^™

G-Cimp Status Prediction Of Glioblastoma Samples Using Mrna Expression Data, Mehmet Baysan, Serdar Bozdag, Margaret C. Cam, Svetlana Kotliarova, Susie Ahn, Jennifer Walling, Jonathan K. Killian, Holly Stevenson, Paul Meltzer, Howard A. Fine

Mathematics, Statistics and Computer Science Faculty Research and Publications

Glioblastoma Multiforme (GBM) is a tumor with high mortality and no known cure. The dramatic molecular and clinical heterogeneity seen in this tumor has led to attempts to define genetically similar subgroups of GBM with the hope of developing tumor specific therapies targeted to the unique biology within each of these subgroups. Recently, a subset of relatively favorable prognosis GBMs has been identified. These glioma CpG island methylator phenotype, or G-CIMP tumors, have distinct genomic copy number aberrations, DNA methylation patterns, and (mRNA) expression profiles compared to other GBMs. While the standard method for identifying G-CIMP tumors is based on …

On Lattices Of Varieties Of Restriction Semigroups, Peter R. Jones

Mathematics, Statistics and Computer Science Faculty Research and Publications

The left restriction semigroups have arisen in a number of contexts, one being as the abstract characterization of semigroups of partial maps, another as the ‘weakly left E-ample’ semigroups of the ‘York school’, and, more recently as a variety of unary semigroups defined by a set of simple identities. We initiate a study of the lattice of varieties of such semigroups and, in parallel, of their two-sided versions, the restriction semigroups. Although at the very bottom of the respective lattices the behaviour is akin to that of varieties of inverse semigroups, more interesting features are soon found in the …

The Sense-Isomorphism Theoretical Image Voxel Estimation (Sense-Itive) Model For Reconstruction And Observing Statistical Properties Of Reconstruction Operators, Iain P. Bruce, M. Muge Karaman, Daniel B. Rowe

Mathematics, Statistics and Computer Science Faculty Research and Publications

The acquisition of sub-sampled data from an array of receiver coils has become a common means of reducing data acquisition time in MRI. Of the various techniques used in parallel MRI, SENSitivity Encoding (SENSE) is one of the most common, making use of a complex-valued weighted least squares estimation to unfold the aliased images. It was recently shown in Bruce et al. [Magn. Reson. Imag. 29(2011):1267-1287] that when the SENSE model is represented in terms of a real-valued isomorphism,it assumes a skew-symmetric covariance between receiver coils, as well as an identity covariance structure between voxels. In this manuscript, we show …

Mathematical Problem Posing As A Measure Of Curricular Effect On Students' Learning, Jinfa Cai, John Moyer, Ning Wang, Stephen Hwang, Bikai Nie, Tammy Garber

Mathematics, Statistics and Computer Science Faculty Research and Publications

In this study, we used problem posing as a measure of the effect of middle-school curriculum on students' learning in high school. Students who had used a standards-based curriculum in middle school performed equally well or better in high school than students who had used more traditional curricula. The findings from this study not only show evidence of strengths one might expect of students who used the standards-based reform curriculum but also bolster the feasibility and validity of problem posing as a measure of curriculum effect on student learning. In addition, the findings of this study demonstrate the usefulness of …

Analyzing Multiple-Probe Microarray: Estimation And Application Of Gene Expression Indexes, Mehdi Maadooliat, Jianhua Z. Huang, Jianhua Hu

Mathematics, Statistics and Computer Science Faculty Research and Publications

Gene expression index estimation is an essential step in analyzing multiple probe microarray data. Various modeling methods have been proposed in this area. Amidst all, a popular method proposed in Li and Wong (2001) is based on a multiplicative model, which is similar to the additive model discussed in Irizarry et al. (2003a) at the logarithm scale. Along this line, Hu et al. (2006) proposed data transformation to improve expression index estimation based on an ad hoc entropy criteria and naive grid search approach. In this work, we re-examined this problem using a new profile likelihood-based transformation estimation approach that …

On Order Statistics For Gs-Distributions, M. M. Mohie El-Din, M. M. Amein, Gholamhossein Hamedani

Mathematics, Statistics and Computer Science Faculty Research and Publications

In this article, a class of distributions is used to establish several recurrence relations satisfied by single and product moments of order statistics and progressive Type-II right censoring. The recurrence relations for moments of some specific distributions including uniform (a;b); exponential (λ); generalized exponential (α;λ;ν); beta (1;b); beta (b;1); logistic (α;β) and other distributions from order statistics and progressive Type-II right censoring can be obtained as special cases. A short explanation of GS-distribution can be found in reference [27]. As an example, means, variances and covariances for standard exponential distribution of progressive Type-II right censored order statistics are computed. Various …

H-Coloring Tori, John Engbers, David Galvin

Mathematics, Statistics and Computer Science Faculty Research and Publications

For graphs G and H, an H-coloring of G is a function from the vertices of G to the vertices of H that preserves adjacency. H-colorings encode graph theory notions such as independent sets and proper colorings, and are a natural setting for the study of hard-constraint models in statistical physics. We study the set of H-colorings of the even discrete torus View the MathML source, the graph on vertex set {0,…,m−1}d (m even) with two strings adjacent if they differ by 1 (mod m) on one coordinate and agree on all others. This is a bipartite graph, with bipartition …

Bayesian Analysis Of Hypothesis Testing Problems For General Population: A Kullback–Leibler Alternative, Naveen K. Bansal, Gholamhossein Hamedani, Ru Sheng

Mathematics, Statistics and Computer Science Faculty Research and Publications

We consider a hypothesis problem with directional alternatives. We approach the problem from a Bayesian decision theoretic point of view and consider a situation when one side of the alternatives is more important or more probable than the other. We develop a general Bayesian framework by specifying a mixture prior structure and a loss function related to the Kullback–Leibler divergence. This Bayesian decision method is applied to Normal and Poisson populations. Simulations are performed to compare the performance of the proposed method with that of a method based on a classical z-test and a Bayesian method based on the …

Involvement Of Microrna Families In Cancer, Stefan Wuchty, Dolores Arjona, Serdar Bozdag, Peter O. Bauer

Mathematics, Statistics and Computer Science Faculty Research and Publications

Collecting representative sets of cancer microRNAs (miRs) from the literature we show that their corresponding families are enriched in sets of highly interacting miR families. Targeting cancer genes on a statistically significant level, such cancer miR families strongly intervene with signaling pathways that harbor numerous cancer genes. Clustering miR family-specific profiles of pathway intervention, we found that different miR families share similar interaction patterns. Resembling corresponding patterns of cancer miRs families, such interaction patterns may indicate a miR family’s potential role in cancer. As we find that the number of targeted cancer genes is a naı¨ve proxy for a cancer …

Simplified Models Of Vector Control Impact Upon Malaria Transmission By Zoophagic Mosquitoes, Samson S. Kiware, Nakul Chitnis, Sarah J. Moore, Gregor J. Devine, Silas Majambere, Stephen Merrill, Gerry F. Killeen

Mathematics, Statistics and Computer Science Faculty Research and Publications

Background

High coverage of personal protection measures that kill mosquitoes dramatically reduce malaria transmission where vector populations depend upon human blood. However, most primary malaria vectors outside of sub-Saharan Africa can be classified as “very zoophagic,” meaning they feed occasionally (

Methods and Findings

We extended a published malaria transmission model to examine the relationship between transmission, control, and the baseline proportion of bloodmeals obtained from humans (human blood index). The lower limit of the human blood index enables derivation of simplified models for zoophagic vectors that (1) Rely on only three field-measurable parameters. (2) Predict immediate and delayed (with …

H-Colouring Bipartite Graphs, John Engbers, David Galvin

Mathematics, Statistics and Computer Science Faculty Research and Publications

For graphs G and H, an H-colouring of G (or homomorphism from G to H) is a function from the vertices of G to the vertices of H that preserves adjacency. H-colourings generalize such graph theory notions as proper colourings and independent sets. For a given H, k∈V(H) and G we consider the proportion of vertices of G that get mapped to k in a uniformly chosen H-colouring of G. Our main result concerns this quantity when G is regular and bipartite. We find numbers 0⩽a−(k)⩽a+(k)⩽1 with the property that for all such G, with high probability the proportion is …

Human Gene Copy Number Spectra Analysis In Congenital Heart Malformations, Aoy Tomita-Mitchell, Donna K. Mahnke, Craig Struble, Maureen E. Tuffnell, Karl D. Stamm, Mats Hidestrand, Susan Harris, Mary A. Goetsch, Pippa Simpson, David P. Bick, Ulrich Broeckel, Andrew N. Pelech, James S. Tweddell, Michael Mitchell

Mathematics, Statistics and Computer Science Faculty Research and Publications

The clinical significance of copy number variants (CNVs) in congenital heart disease (CHD) continues to be a challenge. Although CNVs including genes can confer disease risk, relationships between gene dosage and phenotype are still being defined. Our goal was to perform a quantitative analysis of CNVs involving 100 well-defined CHD risk genes identified through previously published human association studies in subjects with anatomically defined cardiac malformations. A novel analytical approach permitting CNV gene frequency “spectra” to be computed over prespecified regions to determine phenotype-gene dosage relationships was employed. CNVs in subjects with CHD (n = 945), subphenotyped into 40 …

Genomic Analysis Of Immune Response Against Vibrio Cholerae Hemolysin In Caenorhabditis Elegans, Surasri N. Sahu, Jada Lewis, Isha Patel, Serdar Bozdag, Jeong H. Lee, Joseph E. Leclerc, Hediye Nese Cinar

Mathematics, Statistics and Computer Science Faculty Research and Publications

Vibrio cholerae cytolysin (VCC) is among the accessory V. cholerae virulence factors that may contribute to disease pathogenesis in humans. VCC, encoded by hlyA gene, belongs to the most common class of bacterial toxins, known as poreforming toxins (PFTs). V. cholerae infects and kills Caenorhabditis elegans via cholerae toxin independent manner. VCC is required for the lethality, growth retardation and intestinal cell vacuolation during the infection. However, little is known about the host gene expression responses against VCC. To address this question we performed a microarray study in C. elegans exposed to V. cholerae strains with intact and deleted hlyA …

K-8 Preservice Teachers’ Inductive Reasoning In The Problem-Solving Contexts, Marta Magiera

Mathematics, Statistics and Computer Science Faculty Research and Publications

This paper reports the results from an exploratory study of K-8 pre-service teachers’ inductive reasoning. The analysis of 130 written solutions to seven tasks and 77 reflective journals completed by 20 pre-service teachers lead to descriptions of inductive reasoning processes, i.e. specializing, conjecturing, generalizing, and justifying, in the problem-solving contexts. The uncovered characterizations of the four inductive reasoning processes were further used to describe pathways of successful generalizations. The results highlight the importance of specializing and justifying in constructing powerful generalizations. Implications for teacher education are discussed.

Mathematical Dispositions And Student Learning: A Metaphorical Analysis, Jinfa Cai, Victoria Robison, John Moyer, Ning Wang, Bikai Nie

Mathematics, Statistics and Computer Science Faculty Research and Publications

No abstract provided.

A Cautionary Note On Generalized Linear Models For Covariance Of Unbalanced Longitudinal Data, Jianhua Z. Huang, Min Chen, Mehdi Maadooliat, Mohsen Pourahmadi

Mathematics, Statistics and Computer Science Faculty Research and Publications

Missing data in longitudinal studies can create enormous challenges in data analysis when coupled with the positive-definiteness constraint on a covariance matrix. For complete balanced data, the Cholesky decomposition of a covariance matrix makes it possible to remove the positive-definiteness constraint and use a generalized linear model setup to jointly model the mean and covariance using covariates (Pourahmadi, 2000). However, this approach may not be directly applicable when the longitudinal data are unbalanced, as coherent regression models for the dependence across all times and subjects may not exist. Within the existing generalized linear model framework, we show how to overcome …

A Common Framework For Restriction Semigroups And Regular *-Semigroups, Peter R. Jones

Mathematics, Statistics and Computer Science Faculty Research and Publications

Left restriction semigroups have appeared at the convergence of several flows of research, including the theories of abstract semigroups, of partial mappings, of closure operations and even in logic. For instance, they model unary semigroups of partial mappings on a set, where the unary operation takes a map to the identity map on its domain. This perspective leads naturally to dual and two-sided versions of the restriction property. From a varietal perspective, these classes of semigroups–more generally, the corresponding classes of Ehresmann semigroups–derive from reducts of inverse semigroups, now taking a to a⁺=aa⁻¹ (or, dually, …

Physiologic Noise Regression, Motion Regression, And Toast Dynamic Field Correction In Complex-Valued Fmri Time Series, Andrew D. Hahn, Daniel B. Rowe

Mathematics, Statistics and Computer Science Faculty Research and Publications

As more evidence is presented suggesting that the phase, as well as the magnitude, of functional MRI (fMRI) time series may contain important information and that there are theoretical drawbacks to modeling functional response in the magnitude alone, removing noise in the phase is becoming more important. Previous studies have shown that retrospective correction of noise from physiologic sources can remove significant phase variance and that dynamic main magnetic field correction and regression of estimated motion parameters also remove significant phase fluctuations. In this work, we investigate the performance of physiologic noise regression in a framework along with correction for …

Categoricity And Topological Graphs, Paul Bankston

Mathematics, Statistics and Computer Science Faculty Research and Publications

Let X be a topological graph, with arcs joined only at end points. If Y is any locally connected metrizable compactum that is co-elementarily equivalent to X, then Y is homeomorphic to X. In particular, X and Y are homeomorphic if some lattice base for one is elementarily equivalent to some lattice base for the other.

Protection By 20-5,14-Hedge Against Surgically-Induced Ischemia Reperfusion Lung Injury In Rats, Irshad Ali, Stephanie Gruenloh, Ying Gao, Anne V. Clough, John R. Falck, Meetha Medhora, Elizabeth R. Jacobs

Mathematics, Statistics and Computer Science Faculty Research and Publications

Background

We previously reported that the cytochrome P450 product 20-hydroxyeicosatetraenoic acid has prosurvival effects in pulmonary artery endothelial cells and ex vivo pulmonary arteries. We tested the potential of a 20-hydroxyeicosatetraenoic acid analog N-[20-hydroxyeicosa-5(Z),14(Z)-dienoyl]glycine (20-5,14-HEDGE) to protect against lung ischemic reperfusion injury in rats. Furthermore, we examined activation of innate immune system components, high mobility group box 1 (HMGB1) and toll-like receptor 4 (TLR4), in this model as well as the effect of 20-5,14-HEDGE on this signaling pathway.

Methods

Sprague-Dawley rats treated with 20-5,14-HEDGE or vehicle were subjected to surgically induced, unilateral lung ischemia for 60 minutes followed by reperfusion …

Generalizing Amdahl’S Law For Power And Energy, Rong Ge, Kirk W. Cameron

Mathematics, Statistics and Computer Science Faculty Research and Publications

Extending Amdahl's law to identify optimal power-performance configurations requires considering the interactive effects of power, performance, and parallel overhead.

Characterizations Of Certain Continuous Univariate Distributions Based On The Conditional Distribution Of Generalized Order Statistics, M. Ahsanullah, Gholamhossein Hamedani

Mathematics, Statistics and Computer Science Faculty Research and Publications

The problem of characterizing probability distributions is an interesting problem which has recently attracted the attention of many researchers. Various characterization results have been established in different directions as reported in the literature. We present here, various characterizations of certain univariate continuous distributions based on the conditional distribution of generalized order statistics.

A Direct D-Bar Reconstruction Algorithm For Recovering A Complex Conductivity In 2d, Sarah J. Hamilton, C. N. L. Herrera, J. L. Mueller, A. Von Herrmann

Mathematics, Statistics and Computer Science Faculty Research and Publications

A direct reconstruction algorithm for complex conductivities in W^{2, ∞}(Ω), where Ω is a bounded, simply connected Lipschitz domain in R² , is presented. The framework is based on the uniqueness proof by Francini (2000 Inverse Problems 6 107–19), but equations relating the Dirichlet-to-Neumann to the scattering transform and the exponentially growing solutions are not present in that work, and are derived here. The algorithm constitutes the first D-bar method for the reconstruction of conductivities and permittivities in two dimensions. Reconstructions of numerically simulated chest phantoms with discontinuities at the organ boundaries are included.

Modeling Temporal Pattern And Event Detection Using Hidden Markov Model With Application To A Sludge Bulking Data, Naveen K. Bansal, Xin Feng, Wenjing Zhang, Wutao Wi, Yuanhao Zhao

Mathematics, Statistics and Computer Science Faculty Research and Publications

This paper discusses a method of modeling temporal pattern and event detection based on Hidden Markov Model (HMM) for a continuous time series data. We also provide methods for checking model adequacy and predicting future events. These methods are applied to a real example of sludge bulking data for detecting sludge bulking for a water plant in Chicago.

Various Characterizations Of Modified Weibull And Log Modified Distributions, Gholamhossein Hamedani

Mathematics, Statistics and Computer Science Faculty Research and Publications

Various characterizations of the well-known modified Weibull and log-modified Weibull distributions are presented. These characterizations are based on a simple relationship between two truncated moments; on the hazard function and on functions of the order statistics.