Statistics and Probability Commons^™

Anticancer Peptidylarginine Deiminase (Pad) Inhibitors Regulate The Autophagy Flux And The Mammalian Target Of Rapamycin Complex 1 Activity, Yuji Wang, Pingxin Li, Shu Wang, Jing Hu, Xiangyun Amy Chen, Jianhui Wu, Megan Fisher, Kira Oshaben, Na Zhao, Ying Gu, Dong Wang, Gong Chen, Yanming Wang

Department of Statistics: Faculty Publications

Tumor suppressor genes are frequently silenced in cancer cells by enzymes catalyzing epigenetic histone modifications. The peptidylarginine deiminase family member PAD4 (also called PADI4) is markedly overexpressed in a majority of human cancers, suggesting that PAD4 is a putative target for cancer treatment. Here, we have generated novel PAD inhibitors with low micromolar IC₅₀ in PAD activity and cancer cell growth inhibition. The lead compound YW3-56 alters the expression of genes controlling the cell cycle and cell death, including SESN2 that encodes an upstream inhibitor of the mammalian target of rapamycin complex 1 (mTORC1) signaling pathway. Guided by the …

Sample Size Under Inverse Negative Binomial Group Testing For Accuracy In Parameter Estimation, Osval Antonio Montesinos-López, Abelardo Montesinos-López, Jose Crossa, Kent M. Eskridge

Department of Statistics: Faculty Publications

Background:The group testing method has been proposed for the detection and estimation of genetically modified plants (adventitious presence of unwanted transgenic plants, AP). For binary response variables (presence or absence), group testing is efficient when the prevalence is low, so that estimation, detection, and sample size methods have been developed under the binomial model. However, when the event is rare (low prevalence

Methodology/Principal Findings: This research proposes three sample size procedures (two computational and one analytic) for estimating prevalence using group testing under inverse (negative) binomial sampling. These methods provide the required number of positive pools (r_m) …

Muscle Organization In Individuals With And Without Pain And Joint Dysfunction, J. C. Nickel, Y. M. Gonzalez, W. D. Mccall, R. Ohrbach, D. B. Marx, H. Liu, L. R. Iwasaki

Department of Statistics: Faculty Publications

Central nervous system organization of masticatory muscles determines the magnitude of joint and muscle forces. Validated computer-assisted models of neuromuscular organization during biting were used to determine organization in individuals with and without temporomandibular disorders (TMD). Ninety-one individuals (47 women, 44 men) were assigned to one of four diagnostic groups based on the presence (+) or absence (-) of pain (P) and bilateral temporomandibular joint disc displacement (DD). Electromyography and bite-forces were measured during right and left incisor and molar biting. Two three-dimensional models employing neuromuscular objectives of minimization of joint loads (MJL) or muscle effort (MME) simulated biting tasks. …

Learning Interdisciplinary Pedagogies, Alison J. Friedow, Erin E. Blankenship, Jennifer L. Green, Walter Stroup

Department of Statistics: Faculty Publications

Advocates of interdisciplinary teaching and learning in higher education suggest that interdisciplinary courses “promise a wide range of desirable educational outcomes for students” (Newell 1994: 35). These outcomes include enhanced affective and cognitive abilities, increased understanding of multiple perspectives, greater appreciation for ambiguity, and superior capacities for creative thinking, among others (35). Despite claims about the possibilities interdisciplinary learning offers, we have few examples of how faculty from different disciplines work together to create interdisciplinary classroom environments where such outcomes can occur. In short, more examples of how faculty from different disciplines actually develop, engage, and revise interdisciplinary pedagogies with …

Drosophila Melanogaster Selection For Survival Of Bacillus Cereus Infection: Life History Trait Indirect Responses, Junjie Ma, Andrew K. Benson, Stephen D. Kachman, Zhen Hu, Lawrence G. Harshman

Department of Statistics: Faculty Publications

To study evolved resistance/tolerance in an insect model, we carried out an experimental evolution study using D. melanogaster and the opportunistic pathogen B. cereus as the agent of selection. The selected lines evolved a 3.0- to 3.3-log increase in the concentration of spores required for 50% mortality after 18–24 generations of selection. In the absence of any treatment, selected lines evolved an increase in egg production and delayed development time. The latter response could be interpreted as a cost of evolution. Alternatively, delayed development might have been a target of selection resulting in increased adult fat body function including production …

Prediction In Several Conventional Contexts, Bertrand Clarke, Jennifer Clarke

Department of Statistics: Faculty Publications

We review predictive techniques from several traditional branches of statistics. Starting with prediction based on the normal model and on the empirical distribution function, we proceed to techniques for various forms of regression and classification. Then, we turn to time series, longitudinal data, and survival analysis. Our focus throughout is on the mechanics of prediction more than on the properties of predictors.

Comment On Article By Sancetta, Bertrand Clarke

Department of Statistics: Faculty Publications

This paper makes a landmark contribution in three senses.

First, it provides many results that are fundamentally important in their own right. I refer specifically to Theorems 3 and 8. Theorem 3 treats arbitrary loss functions by breaking the integral into two terms, one It, where a difference of losses is bounded and another, IIt, where a bound on the moments of a difference of losses must be used. (All notation here is the same as the author's unless noted otherwise.) The treatment of these two terms reveals the role of the relative entropy and how the tails of the …

Water Quality Models For Stormwater Runoff In Two Lincoln, Nebraska Urban Watersheds, Jake Fisher

Department of Civil and Environmental Engineering: Dissertations, Theses, and Student Research

Water quality monitoring was conducted in two urban watersheds (Colonial Hills and Taylor Park) located in southeast Lincoln, NE over a three year period spanning from October 2008 through September 2011. In-line probes continuously measured for turbidity, conductivity, dissolved oxygen, and water temperature while other water quality constituents were analyzed for discrete water samples collected using grab and automatic sampling techniques. The water quality data was used to calculate event mean concentrations (EMCs) for sixteen storm events sampled over the duration of the project period. Three types of stormwater quality multiple linear regression models were developed for the estimation of …

Studying The Handling Of Heat Stressed Cattle Using The Additive Bi-Logistic Model To Fit Body Temperature, Fan Yang

Department of Statistics: Dissertations, Theses, and Student Research

Daily activities consume the energy of heifers, subsequently causing an elevation of body temperature, depending on the ambient conditions. A better understanding of the dynamics of body temperature (Tb) would be helpful when deciding how to process and handle heifers. It would also lead to specific recommendations on moving heifers under different ambient conditions, especially during the summer. In this study, a bi-logistic mixed model is used to describe the dynamics of Tb during the moving event. Data were taken from heifers in pens located at different distances from the heifer work station on four separate summer days under hot …

Habitat Use And Abundance Patterns Of Sandhill Cranes In The Central Platte River Valley, Nebraska, 2003–2010, Todd Joseph Buckley

School of Natural Resources: Dissertations, Theses, and Student Research

The Central Platte River Valley (CPRV) in Nebraska is an important spring stopover area for the midcontinent population of sandhill cranes. Alterations to crop rotation and loss habitat in the CPRV pose a risk to the population. Personnel drove designated routes in the CPRV from 2003–2010 to record the presence of cranes in agricultural fields and estimate abundance. I developed and evaluated models to predict habitat use and flock sizes. Alfalfa was predicted to receive the highest use followed by corn, soybeans, winter wheat, grassland, and shrubland. Use of all habitats and flock size increased as field area increased. Flock …

Effects Of Animal Diet, Manure Application Rate, And Tillage On Transport Of Microorganisms From Manure-Amended Fields, Lisa M. Durso, John Gilley, David B. Marx, Bryan Woodbury

Department of Statistics: Faculty Publications

Manure from cattle fed distillers’ grain or corn diets was applied to fields, and the fields were subjected to rainfall simulation tests. Manure was added at three rates on till and no-till plots. Correlations between microbial transport and runoff characteristics were identified. Results indicate that diet affects phage but not bacterial transport from manure-amended fields.

A Study On Facility Planning Using Discrete Event Simulation: Case Study Of A Grain Delivery Terminal, Sarah M. Asio

Department of Industrial and Management Systems Engineering: Dissertations, Theses, and Student Research

The application of traditional approaches to the design of efficient facilities can be tedious and time consuming when uncertainty and a number of constraints exist. Queuing models and mathematical programming techniques are not able to capture the complex interaction between resources, the environment and space constraints for dynamic stochastic processes. In the following study discrete event simulation is applied to the facility planning process for a grain delivery terminal. The discrete event simulation approach has been applied to studies such as capacity planning and facility layout for a gasoline station and evaluating the resource requirements for a manufacturing facility. To …

A Comparison Of Spatial Prediction Techniques Using Both Hard And Soft Data, Megan L. Liedtke Tesar

Department of Statistics: Dissertations, Theses, and Student Research

The overall goal of this research, which is common to most spatial studies, is to predict a value of interest at an unsampled location based on measured values at nearby sampled locations.  To accomplish this goal, ordinary kriging can be used to obtain the best linear unbiased predictor.  However, there is often a large amount of variability surrounding the measurements of environmental variables, and traditional prediction methods, such as ordinary kriging, do not account for an attribute with more than one level of uncertainty.  This dissertation addresses this limitation by introducing a new methodology called weighted kriging.  This prediction technique …

Variation In Sclerotinia Sclerotiorum Bean Isolates From Multisite Resistance Screening Locations, Lindsey Otto-Hanson, James R, Steadman, Rebecca Higgins, Kent M. Eskridge

Department of Statistics: Faculty Publications

There is no complete resistance to Sclerotinia sclerotiorum, cause of white mold in dry bean (Phaseolus vulgaris). Variable resistance expression is one problem in screening for improved white mold resistance. With no previous information in the literature, pathogen variation in multisite screening nurseries was evaluated as one cause of diverse resistance expression. In all, 10 isolates of S. sclerotiorum used in greenhouse screening and 146 isolates collected from nine white mold field screening nurseries in major bean production areas in the United States were compared using mycelial compatibility groupings (MCGs) and an aggressiveness test. These 10 greenhouse …

Development Of An Internet Based System For Modeling Biotin Metabolism Using Bayesian Networks, Jinglei Zhou, Dong Wang, Vicki L. Schlegel, Janos Zempleni

Department of Statistics: Faculty Publications

Biotin is an essential water-soluble vitamin crucial for maintaining normal body functions. The importance of biotin for human health has been under-appreciated but there is plenty of opportunity for future research with great importance for human health. Currently, carrying out predictions of biotin metabolism involves tedious manual manipulations. In this paper, we report the development of BiotinNet, an internet based program that uses Bayesian networks to integrate published data on various aspects of biotin metabolism. Users can provide a combination of values on the levels of biotin related metabolites to obtain the predictions on other metabolites that are not specified. …

Reference Priors For Exponential Families With Increasing Dimension, Bertrand Clarke, Subhashis Ghosal

Department of Statistics: Faculty Publications

In this article, we establish the asymptotic normality of the posterior distribution for the natural parameter in an exponential family based on independent and identically distributed data. The mode of convergence is expected Kullback-Leibler distance and the number of parameters p is increasing with the sample size n. Using this, we give an asymptotic expansion of the Shannon mutual information valid when p = pm increases at a sufficiently slow rate. The second term in the asymptotic expansion is the largest term that depends on the prior and can be optimized to give Jeffrey's prior as the reference prior in …

Weakly Positioned Nucleosomes Enhance The Transcriptional Competency Of Chromatin, Yaakov Belch, Jingyi Yang, Yang Liu, Sridhar A. Malkaram, Rong Liu, Jean-Jack M. Riethoven, Istvan Ladunga

Department of Statistics: Faculty Publications

Background: Transcription is affected by nucleosomal resistance against polymerase passage. In turn, nucleosomal resistance is determined by DNA sequence, histone chaperones and remodeling enzymes. The contributions of these factors are widely debated: one recent title claims ‘‘… DNA-encoded nucleosome organization…’’ while another title states that ‘‘histone-DNA interactions are not the major determinant of nucleosome positions.’’ These opposing conclusions were drawn from similar experiments analyzed by idealized methods. We attempt to resolve this controversy to reveal nucleosomal competency for transcription.

Methodology/Principal Findings: To this end, we analyzed 26 in vivo, nonlinked, and in vitro genome-wide nucleosome maps/replicates by new, rigorous …

Estimating Teacher Effects Using Value-Added Models, Jennifer L. Green

Department of Statistics: Dissertations, Theses, and Student Research

Value-added modeling is an alternative approach to test-based accountability systems based on the proportions of students scoring at or above pre-determined proficiency levels. Value-added modeling techniques provide opportunities to estimate an individual teacher’s effect on student learning, while allowing for the possibility to control for the effect of non-educational factors beyond a school system’s control, such as socioeconomic status. However, numerous considerations exist when using value-added models to estimate teacher effects and defining what the teacher effects really describe. Chapter 2 provides an introduction to value-added methodology by describing several value-added models available for estimating teacher effects and their respective …

The Textural Discontinuity Hypothesis And Its Relation To Nomadism, Migration, Decline, And Competition, Aaron L. Alai

School of Natural Resources: Dissertations, Theses, and Student Research

The causes of nomadism, migration, and decline in vertebrates are debated issues in the ecological sciences. Literature suggests nomadism may arise in species that specialize in granivory, nectivory, or the utilization of rodent outbreaks. Migration is thought to arise as a result of the exploitation of certain scarce or variable food resources. Species decline is hypothesized to be the result of many different factors as well; large species, island species and specialists may be more prone to decline.

A fresh perspective regarding the causes for species nomadism, migration, and decline is being investigated utilizing the ideas within the Textural Discontinuity …

Principal Component Analysis And Biochemical Characterization Of Protein And Starch Reveal Primary Targets For Improving Sorghum Grain, Joshua H. Wong, D. B. Marx, Jeff D. Wilson, Bob B. Buchanan, Peggy G. Lemaux, Jeffrey F. Pedersen

Department of Statistics: Faculty Publications

Limited progress has been made on genetic improvement of the digestibility of sorghum grain because of variability among different varieties. In this study, we applied multiple techniques to assess digestibility of grain from 18 sorghum lines to identify major components responsible for variability. We also identified storage proteins and enzymes as potential targets for genetic modification to improve digestibility. Results from principal component analysis revealed that content of amylose and total starch, together with protein digestibility (PD), accounted for 94% of variation in digestibility. Control of amylose content is understood and manageable. Up-regulation of genes associated with starch accumulation is …

Reference Priors For Exponential Families With Increasing Dimension, Bertrand S. Clarke, Subhashis Ghosal

Department of Statistics: Faculty Publications

In this article, we establish the asymptotic normality of the posterior distribution for the natural parameter in an exponential family based on independent and identically distributed data. The mode of convergence is expected Kullback-Leibler distance and the number of parameters p is increasing with the sample size n. Using this, we give an asymptotic expansion of the Shannon mutual information valid when p = pn increases at a sufficiently slow rate. The second term in the asymptotic expansion is the largest term that depends on the prior and can be optimized to give Jeffreys’ prior as the reference prior in …

Desiderata For A Predictive Theory Of Statistics, Bertrand Clarke

Department of Statistics: Faculty Publications

In many contexts the predictive validation of models or their associated prediction strategies is of greater importance than model identification which may be practically impossible. This is particularly so in fields involving complex or high dimensional data where model selection, or more generally predictor selection is the main focus of effort. This paper suggests a unified treatment for predictive analyses based on six 'desiderata'. These desiderata are an effort to clarify what criteria a good predictive theory of statistics should satisfy.

Fully Exponential Laplace Approximation Em Algorithm For Nonlinear Mixed Effects Models, Meijian Zhou

Department of Statistics: Dissertations, Theses, and Student Research

Nonlinear mixed effects models provide a flexible and powerful platform for the analysis of clustered data that arise in numerous fields, such as pharmacology, biology, agriculture, forestry, and economics. This dissertation focuses on fitting parametric nonlinear mixed effects models with single- and multi-level random effects. A new, efficient, and accurate method that gives an error of order O(1/n²), fully exponential Laplace approximation EM algorithm (FELA-EM), for obtaining restricted maximum likelihood (REML) estimates in nonlinear mixed effects models is developed. Sample codes for implementing FELA-EM algorithm in R are given. Simulation studies have been conducted to evaluate …

Sequence Comparison And Stochastic Model Based On Multi-Order Markov Models, Xiang Fang

Department of Statistics: Dissertations, Theses, and Student Research

This dissertation presents two statistical methodologies developed on multi-order Markov models. First, we introduce an alignment-free sequence comparison method, which represents a sequence using a multi-order transition matrix (MTM). The MTM contains information of multi-order dependencies and provides a comprehensive representation of the heterogeneous composition within a sequence. Based on the MTM, a distance measure is developed for pair-wise comparison of sequences. The new method is compared with the traditional maximum likelihood (ML) method, the complete composition vector (CCV) method and the improved version of the complete composition vector (ICCV) method using simulated sequences. We further illustrate the application of …

The Em Algorithm For Group Testing Regression Models Under Matrix Pooling, Christopher R. Bilder, Boan Zhang

Department of Statistics: Faculty Publications

No abstract provided.

Temporomandibular Joint Loads In Subjects With And Without Disc Displacement, Laura R. Iwasaki, Michael J. Crosby, Yoly Gonzalez, Willard D. Mccall, David B. Marx, Richard Ohrbach, Jeffrey C. Nickel

Department of Statistics: Faculty Publications

The likelihood of development of degenerative joint disease (DJD) of the temporomandibular joint (TMJ) is related to the integrity of the TMJ disc. Predilection for mechanical failure of the TMJ disc may reflect inter-individual differences in TMJ loads. Nine females and eight males in each of normal TMJ disc position and bilateral disc displacement diagnostic groups consented to participate in our study. Disc position was determined by bilateral magnetic resonance images of the joints. Three-dimensional (3D) anatomical geometry of each subject was used in a validated computer-assisted numerical model to calculate ipsilateral and contralateral TMJ loads for a range of …

Temporomandibular Joint Loads In Subjects With And Without Disc Displacement, Laura R. Iwasaki, Michael J. Crosby, Yoly Gonzalez, Willard D. Mccall, David B. Marx, Richard Ohrbach, Jeffrey C. Nickel

Department of Statistics: Faculty Publications

The likelihood of development of degenerative joint disease (DJD) of the temporomandibular joint (TMJ) is related to the integrity of the TMJ disc. Predilection for mechanical failure of the TMJ disc may reflect inter-individual differences in TMJ loads. Nine females and eight males in each of normal TMJ disc position and bilateral disc displacement diagnostic groups consented to participate in our study. Disc position was determined by bilateral magnetic resonance images of the joints. Three-dimensional (3D) anatomical geometry of each subject was used in a validated computer-assisted numerical model to calculate ipsilateral and contralateral TMJ loads for a range of …

Spatial Clustering Using The Likelihood Function, April Kerby

Department of Statistics: Dissertations, Theses, and Student Research

Researchers have been using clustering algorithms for many years to group similar observations based on a set of recorded characteristics. The majority of these algorithms maximize the similarity of the observations within a cluster, while at the same time maximize the dissimilarity with observations in other clusters. However, nearly all of the current clustering algorithms do not take into account the actual geographic location of the observation during the clustering process. This dissertation consists of three papers which propose a method to incorporate the geographical location of an observation into the clustering algorithm, known as spatial clustering. The first paper …

Detecting Differentially Expressed Genes While Controlling The False Discovery Rate For Microarray Data, Shuo Jiao

Department of Statistics: Dissertations, Theses, and Student Research

Microarray is an important technology which enables people to investigate the expression levels of thousands of genes at the same time. One common goal of microarray data analysis is to detect differentially expressed genes while controlling the false discovery rate. This dissertation consists with four papers written to address this goal. The dissertation is organized as follows: In Chapter 1, a brief introduction of the Affymetrix GeneChip microarray technology is provided. The concept of differentially expressed genes and the definition of the false discovery rate are also introduced. In Chapter 2, a literature review of the related works on this …

An Improved String Composition Method For Sequence Comparison, Guoqing Lu, Shunpu Zhang, Xiang Fang

Department of Statistics: Faculty Publications

Background: Historically, two categories of computational algorithms (alignment-based and alignment-free) have been applied to sequence comparison–one of the most fundamental issues in bioinformatics. Multiple sequence alignment, although dominantly used by biologists, possesses both fundamental as well as computational limitations. Consequently, alignment-free methods have been explored as important alternatives in estimating sequence similarity. Of the alignment-free methods, the string composition vector (CV) methods, which use the frequencies of nucleotide or amino acid strings to represent sequence information, show promising results in genome sequence comparison of prokaryotes. The existing CV-based methods, however, suffer certain statistical problems, thereby underestimating the amount of evolutionary …