Physical Sciences and Mathematics Commons^™

Power In Pairs: Assessing The Statistical Value Of Paired Samples In Tests For Differential Expression, John R. Stevens, Jennifer S. Herrick, Roger K. Wolff, Martha L. Slattery

Mathematics and Statistics Faculty Publications

Background: When genomics researchers design a high-throughput study to test for differential expression, some biological systems and research questions provide opportunities to use paired samples from subjects, and researchers can plan for a certain proportion of subjects to have paired samples. We consider the effect of this paired samples proportion on the statistical power of the study, using characteristics of both count (RNA-Seq) and continuous (microarray) expression data from a colorectal cancer study.

Results: We demonstrate that a higher proportion of subjects with paired samples yields higher statistical power, for various total numbers of samples, and for various strengths of …

Logarithmic Hennings Invariants For Restricted Quantum Sl (2), Anna Beliakova, Christian Blanchet, Alexandra Tebbs

Mathematics and Statistics Faculty Publications

We construct a Hennings-type logarithmic invariant for restricted quantum sl (2) at a 2p^th root of unity. This quantum group U is not quasitriangular and hence not ribbon, but factorizable. The invariant is defined for a pair: a 3–manifold M and a colored link L inside M. The link L is split into two parts colored by central elements and by trace classes, or elements in the 0^th Hochschild homology of U, respectively. The two main ingredients of our construction are the universal invariant of a string link with values in tensor powers of U, and the modified …

Developmental Parameters Of A Southern Mountain Pine Beetle (Coleoptera: Curculionidae) Population Reveal Potential Source Of Latitudinal Differences In Generation Time, Anne E. Mcmanis, James A. Powell, Barbara J. Bentz

Mathematics and Statistics Faculty Publications

Mountain pine beetle (Dendroctonus ponderosae, Hopkins) is a major disturbance agent in pine ecosystems of western North America. Adaptation to local climates has resulted in primarily univoltine generation time across a thermally diverse latitudinal gradient. We hypothesized that voltinism patterns have been shaped by selection for slower developmental rates in southern populations inhabiting warmer climates. To investigate traits responsible for latitudinal differences we measured lifestage-specific development of southern mountain pine beetle eggs, larvae and pupae across a range of temperatures. Developmental rate curves were fit using maximum posterior likelihood estimation with a Bayesian prior to improve fit stability. …

Genome-Wide Association Study For Variants That Modulate Relationships Between Cerebrospinal Fluid Amyloid-Beta 42, Tau, And P-Tau Levels, Taylor J. Maxwell, Chris Corcoran, Jorge L. Del-Aguila, John P. Budde, Yuetiva Deming, Carlos Cruchaga, Alison M. Goate, John S. K. Kauwe, Alzheimer's Disease Neuroimaging Initiative

Mathematics and Statistics Faculty Publications

Background: A relationship quantitative trait locus exists when the correlation between multiple traits varies by genotype for that locus. Relationship quantitative trait loci (rQTL) are often involved in gene-by-gene (G×G) interactions or gene-by-environmental interactions, making them a powerful tool for detecting G×G.

Methods: We performed genome-wide association studies to identify rQTL between tau and Aβ42 and ptau and Aβ42 with over 3000 individuals using age, gender, series, APOE ε2, APOE ε4, and two principal components for population structure as covariates. Each significant rQTL was separately screened for interactions with other loci for each trait in the rQTL model. Parametric bootstrapping …

Remarks On Legendrian Self-Linking, Chris Beasley, Brendan Mclellan, Ruoran Zhang

Mathematics and Statistics Faculty Publications

The Thurston-Bennequin invariant provides one notion of self-linking for any homologically-trivial Legendrian curve in a contact three-manifold. Here we discuss related analytic notions of self-linking for Legendrian knots in R³. Our definition is based upon reformulation of the elementary Gauss linking integral and is motivated by ideas from supersymmetric gauge theory. We recover the Thurston-Bennequin invariant as a special case.

Ensemble Estimation Of Information Divergence, Kevin R. Moon, Kumar Sricharan, Kristjan Greenewald, Alfred O. Hero Iii

Mathematics and Statistics Faculty Publications

Recent work has focused on the problem of nonparametric estimation of information divergence functionals between two continuous random variables. Many existing approaches require either restrictive assumptions about the density support set or difficult calculations at the support set boundary which must be known a priori. The mean squared error (MSE) convergence rate of a leave-one-out kernel density plug-in divergence functional estimator for general bounded density support sets is derived where knowledge of the support boundary, and therefore, the boundary correction is not required. The theory of optimally weighted ensemble estimation is generalized to derive a divergence estimator that achieves the …

Limit Behavior Of Mass Critical Hartree Minimization Problems With Steep Potential Wells, Yujin Guo, Yong Luo, Zhi-Qiang Wang

Mathematics and Statistics Faculty Publications

We consider minimizers of the following mass critical Hartree minimization problem: e_λ(N) ≔ inf{u∈H¹(ℝ^d),‖u‖²₂=N} E_λ(u), where d ≥ 3, λ > 0, and the Hartree energy functional E_λ(u) is defined by E_λ(u)≔∫_R^d|∇u(x)|²dx + λ∫_R^d g(x)u²(x)dx − 1/2∫_R^d∫_R^d {u²(x)u²(y)/|x−y|²} dxdy. Here the steep potential g(x) satisfies 0 = g(0) = inf_ℝ^dg(x) ≤ g(x) ≤ 1 and 1 …

Full Dyon Excitation Spectrum In Extended Levin-Wen Models, Yuting Hu, Alexandra Tebbs, Yong-Shi Wu

Mathematics and Statistics Faculty Publications

In Levin-Wen (LW) models, a wide class of exactly solvable discrete models, for two-dimensional topological phases, it is relatively easy to describe only single-fluxon excitations, but not the charge and dyonic as well as many-fluxon excitations. To incorporate charged and dyonic excitations in (doubled) topological phases, an extension of the LW models is proposed in this paper. We first enlarge the Hilbert space with adding a tail on one of the edges of each trivalent vertex to describe the internal charge degrees of freedom at the vertex. Then, we study the full dyon spectrum of the extended LW models, including …

The Effect Of Warmer Winters On The Demography Of An Outbreak Insect Is Hidden By Intraspecific Competition, Devin W. Goodsman, Guenchik Grosklos, Brian H. Aukema, Caroline Whitehouse, Katherine P. Bleiker, Nate G. Mcdowell, Richard S. Middleton, Chonggang Xu

Mathematics and Statistics Faculty Publications

Warmer climates are predicted to increase bark beetle outbreak frequency, severity, and range. Even in favorable climates, however, outbreaks can decelerate due to resource limitation, which necessitates the inclusion of competition for limited resources in analyses of climatic effects on populations. We evaluated several hypotheses of how climate impacts mountain pine beetle reproduction using an extensive 9‐year dataset, in which nearly 10,000 trees were sampled across a region of approximately 90,000 km², that was recently invaded by the mountain pine beetle in Alberta, Canada. Our analysis supports the hypothesis of a positive effect of warmer winter temperatures on …

Gaps In The Saturation Spectrum Of Trees, Ronald J. Gould, Paul Horn, Michael S. Jacobson, Brent J. Thomas

Mathematics and Statistics Faculty Publications

A graph G is H-saturated if H is not a subgraph of G but the addition of any edge from the complement of G to G results in a copy of H. The minimum number of edges (the size) of an H-saturated graph on n vertices is denoted sat(n, H), while the maximum size is the well studied extremal number, ex(n, H). The saturation spectrum for a graph H is the set of sizes of H-saturated graphs between sat(n, H) and ex(n, H). In …

Feasibility Of Predicting Vietnam’S Autumn Rainfall Regime Based On The Tree-Ring Record And Decadal Variability, Yan Sun, Shih-Yu (Simon) Wang, Rong Li, Brendan M. Buckley, Robert R. Gilies, Kyle G. Hansen

Mathematics and Statistics Faculty Publications

We investigate the feasibility of developing decadal prediction models for autumn rainfall ( R_A ) over Central Vietnam by utilizing a published tree-ring reconstruction of October–November (ON) rainfall derived from the earlywood width measurements from a type of Douglas-fir (Pseudotsuga sinensis). Autumn rainfall for this region accounts for a large percentage of the annual total, and is often the source of extreme flooding. Central Vietnam’s R_A along with its notable autocorrelation and significant cross-correlation with basin-wide Pacific sea surface temperature (SST) variability, to develop four discrete time-series models. The sparse autoregressive model, with Pacific SST as …

Possible Isolation Number Of A Matrix Over Nonnegative Integers, Leroy B. Beasley, Young Bae Jun, Seok-Zun Song

Mathematics and Statistics Faculty Publications

Let ℤ₊ be the semiring of all nonnegative integers and A an m × n matrix over ℤ₊. The rank of A is the smallest k such that A can be factored as an m × k matrix times a k×n matrix. The isolation number of A is the maximum number of nonzero entries in A such that no two are in any row or any column, and no two are in a 2 × 2 submatrix of all nonzero entries. We have that the isolation number of A is a lower bound of the rank of …

Jacobian Elliptic Kummer Surfaces And Special Function Identities, Elise Griffin, Andreas Malmendier

Mathematics and Statistics Faculty Publications

We derive formulas for the construction of all inequivalent Jacobian elliptic fibrations on the Kummer surface of two non-isogeneous elliptic curves from extremal rational elliptic surfaces by rational base transformations and quadratic twists. We then show that each such decomposition yields a description of the Picard-Fuchs system satisfied by the periods of the holomorphic two-form as either a tensor product of two Gauss' hypergeometric differential equations, an Appell hypergeometric system, or a GKZ differential system. As the answer must be independent of the fibration used, identities relating differential systems are obtained. They include a new identity relating Appell's hypergeometric system …

Genetic Variation Determines Which Feedbacks Drive And Alter Predator–Prey Eco-Evolutionary Cycles, Michael H. Cortez

Mathematics and Statistics Faculty Publications

Evolution can alter the ecological dynamics of communities, but the effects depend on the magnitudes of standing genetic variation in the evolving species. Using an eco‐coevolutionary predator–prey model, I identify how the magnitudes of prey and predator standing genetic variation determine when ecological, evolutionary, and eco‐evolutionary feedbacks influence system stability and the phase lags in predator–prey cycles. Here, feedbacks are defined by subsystems, i.e., the dynamics of a subset of the components of the whole system when the other components are held fixed; ecological (evolutionary) feedbacks involve the direct and indirect effects between population densities (species traits) and eco‐evolutionary feedbacks …

Second Order Fully Discrete Energy Stable Methods On Staggered Grids For Hydrodynamic Phase Field Models Of Binary Viscous Fluids, Yuezheng Gong, Jia Zhao, Qi Wang

Mathematics and Statistics Faculty Publications

We present second order, fully discrete, energy stable methods on spatially staggered grids for a hydrodynamic phase field model of binary viscous fluid mixtures in a confined geometry subject to both physical and periodic boundary conditions. We apply the energy quadratization strategy to develop a linear-implicit scheme. We then extend it to a decoupled, linear scheme by introducing an intermediate velocity term so that the phase variable, velocity field, and pressure can be solved sequentially. The two new, fully discrete linear schemes are then shown to be unconditionally energy stable, and the linear systems resulting from the schemes are proved …

Partitioning The Effects Of Eco-Evolutionary Feedbacks On Community Stability, Swati Patel, Michael H. Cortez, Sebastian J. Schreiber

Mathematics and Statistics Faculty Publications

A fundamental challenge in ecology continues to be identifying mechanisms that stabilize community dynamics. By altering the interactions within a community, eco-evolutionary feedbacks may play a role in community stability. Indeed, recent empirical and theoretical studies demonstrate that these feedbacks can stabilize or destabilize communities and, moreover, that this sometimes depends on the relative rate of ecological to evolutionary processes. So far, theory on how eco-evolutionary feedbacks impact stability exists only for a few special cases. In our work, we develop a general theory for determining the effects of eco-evolutionary feedbacks on stability in communities with an arbitrary number of …

Fully Discrete Second-Order Linear Schemes For Hydrodynamic Phase Field Models Of Binary Viscous Fluid Flows With Variable Densities, Yuezheng Gong, Jia Zhao, Xiaogang Yang, Qi Wang

Mathematics and Statistics Faculty Publications

We develop spatial-temporally second-order, energy stable numerical schemes for two classes of hydrodynamic phase field models of binary viscous fluid mixtures of different densities. One is quasi-incompressible while the other is incompressible. We introduce a novel energy quadratization technique to arrive at fully discrete linear schemes, where in each time step only a linear system needs to be solved. These schemes are then shown to be unconditionally energy stable rigorously subject to periodic boundary conditions so that a large time step is plausible. Both spatial and temporal mesh refinements are conducted to illustrate the second-order accuracy of the schemes. The …

Local And Global Dynamic Bifurcations Of Nonlinear Evolution Equations, Desheng Li, Zhi-Qiang Wang

Mathematics and Statistics Faculty Publications

We present new local and global dynamic bifurcation results for nonlinear evolution equations of the form ut + Au = fλ(u) on a Banach space X, where A is a sectorial operator, and λ ∈ R is the bifurcation parameter. Suppose the equation has a trivial solution branch {(0, λ) : λ ∈ R}. Denote Φλ the local semiflow generated by the initial value problem of the equation. It is shown that if the crossing number n at a bifurcation value λ = λ0 is nonzero and moreover, S0 = {0} is an isolated invariant set of Φλ0 , then …