A Statistical Method For The Conservative Adjustment Of False Discovery Rate (Q-Value), 2017 George Washington University

#### A Statistical Method For The Conservative Adjustment Of False Discovery Rate (Q-Value), Yinglei Lai

*Epidemiology and Biostatistics Faculty Publications*

### Background

*q*-value is a widely used statistical method for estimating false discovery rate (FDR), which is a conventional significance measure in the analysis of genome-wide expression data. *q*-value is a random variable and it may underestimate FDR in practice. An underestimated FDR can lead to unexpected false discoveries in the follow-up validation experiments. This issue has not been well addressed in literature, especially in the situation when the permutation procedure is necessary for *p*-value calculation.

### Results

We proposed a statistical method for the conservative adjustment of *q*-value. In practice, it is usually necessary to calculate *p ...*

Juvenile Remains: Predicting Body Mass And Stature In Modern American Populations, 2017 Humboldt State University

#### Juvenile Remains: Predicting Body Mass And Stature In Modern American Populations, Erin F E Pinkston

*Theses and projects*

There are increasing numbers of unidentified persons in the U.S. and abroad. To generate positive identifications, forensic anthropologists and others working in the medicolegal field employ a variety of methods to produce biological profiles to match to case files and missing persons databases. Body mass, and stature are two important components of a biological profile, and both can be estimated using regression formulae derived from skeletal metrics. In cases of unidentified juvenile remains, these are particularly important metrics, as it is difficult or impossible to determine sex in prepubescent remains, and the quality of ancestry estimation is currently under ...

Estimating The Effects Of Overstory Retention, Vegetative Competition, And Site Quality On The Height Growth Of Small Ponderosa Pine Trees Using Regression Quantiles, 2017 University of Montana, Missoula

#### Estimating The Effects Of Overstory Retention, Vegetative Competition, And Site Quality On The Height Growth Of Small Ponderosa Pine Trees Using Regression Quantiles, Colin P. Kirkmire

*Graduate Student Theses, Dissertations, & Professional Papers*

Ponderosa pine (*Pinus ponderosa* C. Lawson) forests in the Inland Northwestern region of the US are increasingly managed under multi-aged silvicultural systems that provide stand structure for wildlife habitat, timber production, enhanced aesthetic, or restoration of presettlement conditions (O'Hara 2005). Partial retention harvest, where an element of the previous stand's overstory structure is retained, is commonly used to achieve a multi-aged stand structure. However, little is known about how ponderosa pine trees in the understory respond to overstory and understory competitive factors following partial retention harvest. The height growth of small trees was hypothesized to be influenced by ...

Hpcnmf: A High-Performance Toolbox For Non-Negative Matrix Factorization, 2016 Fox Chase Cancer Center

#### Hpcnmf: A High-Performance Toolbox For Non-Negative Matrix Factorization, Karthik Devarajan, Guoli Wang

*COBRA Preprint Series*

Non-negative matrix factorization (NMF) is a widely used machine learning algorithm for dimension reduction of large-scale data. It has found successful applications in a variety of fields such as computational biology, neuroscience, natural language processing, information retrieval, image processing and speech recognition. In bioinformatics, for example, it has been used to extract patterns and profiles from genomic and text-mining data as well as in protein sequence and structure analysis. While the scientific performance of NMF is very promising in dealing with high dimensional data sets and complex data structures, its computational cost is high and sometimes could be critical for ...

Models For Hsv Shedding Must Account For Two Levels Of Overdispersion, 2016 University of Washington - Seattle Campus

#### Models For Hsv Shedding Must Account For Two Levels Of Overdispersion, Amalia Magaret

*UW Biostatistics Working Paper Series*

We have frequently implemented crossover studies to evaluate new therapeutic interventions for genital herpes simplex virus infection. The outcome measured to assess the efficacy of interventions on herpes disease severity is the viral shedding rate, defined as the frequency of detection of HSV on the genital skin and mucosa. We performed a simulation study to ascertain whether our standard model, which we have used previously, was appropriately considering all the necessary features of the shedding data to provide correct inference. We simulated shedding data under our standard, validated assumptions and assessed the ability of 5 different models to reproduce the ...

Macrobenthic Communities In The Northern Gulf Of Mexico Hypoxic Zone: Testing The Pearson-Rosenberg Model, 2015 The University of Southern Mississippi

#### Macrobenthic Communities In The Northern Gulf Of Mexico Hypoxic Zone: Testing The Pearson-Rosenberg Model, Shivakumar Shivarudrappa

*Dissertations*

The Pearson and Rosenberg (P-R) conceptual model of macrobenthic succession was used to assess the impact of hypoxia (dissolved oxygen [DO] ≤ 2 mg/L) on the macrobenthic community on the continental shelf of northern Gulf of Mexico for the first time. The model uses a stress-response relationship between environmental parameters and the macrobenthic community to determine the ecological condition of the benthic habitat. The ecological significance of dissolved oxygen in a benthic habitat is well understood. In addition, the annual recurrence of bottom-water hypoxia on the Louisiana/Texas shelf during summer months is well documented.

The P-R model illustrates the ...

Initiation And Early Development Of Fiber In Wild And Cultivated Cotton, 2015 Iowa State University

#### Initiation And Early Development Of Fiber In Wild And Cultivated Cotton, Kara M. Butterworth, Dean C. Adams, Harry T. Horner, Jonathan F. Wendel

*Jonathan F. Wendel*

Cultivated cotton fiber has undergone transformation from short, coarse fibers found in progenitor wild species to economically important, long, fine fibers grown globally. Morphological transformation requires understanding of development of wild fiber and developmental differences between wild and cultivated fiber.We examined early development of fibers, including abundance and placement on seed surface, nucleus position, presence of vacuoles, and fiber size and shape. Four species were studied using microscopic, morphometric, and statistical methods: Gossypium raimondii (wild D genome), Gossypium herbaceum (cultivated A genome), Gossypium hirsutum (wild tetraploid), and Gossypium hirsutum (cultivated tetraploid). Early fiber development is highly asynchronous in G ...

Individual Tree Measurements From Three-Dimensional Point Clouds, 2015 University of Maine - Main

#### Individual Tree Measurements From Three-Dimensional Point Clouds, Elias Ayrey

*Electronic Theses and Dissertations*

This study develops and tests novel methodologies for measuring the attributes of individual trees from three-dimensional point clouds generated from an aerial platform. Recently, advancements in technology have allowed for the acquisition of very high resolution three-dimensional point clouds that can be used to map the forest in a virtual environment. These point clouds can be interpreted to produce valuable forest attributes across entire landscapes with minimal field labor, which can then aid forest managers in their planning and decision making.

Biometrics derived from point clouds are often generated on a plot level, with estimates spanning many meters (rather than ...

Evaluating The Long-Term Effects Of Logging Residue Removals In Great Lakes Aspen Forests, 2015 Michigan Technological University

#### Evaluating The Long-Term Effects Of Logging Residue Removals In Great Lakes Aspen Forests, Michael I. Premer

*Dissertations, Master's Theses and Master's Reports*

Commercial aspen (*Populus* spp.) forests of the Great Lakes region are primarily managed for timber products such as pulp fiber and panel board, but logging residues (topwood and non-merchantable bolewood) are potentially important for utilization in the bioenergy market. In some regions, pulp and paper mills already utilize residues as fuel in combustion for heat and electricity, and progressive energy policies will likely cause an increase in biomass feedstock demand. The effects of removing residues, which have a comparatively high concentration of macronutrients, is poorly understood when evaluating long-term site productivity, future timber yields, plant diversity, stand dynamics, and consequently ...

Survey Methods For Assessing Land Cover Map Accuracy, 2014 Iowa State University

#### Survey Methods For Assessing Land Cover Map Accuracy, Sarah M. Nusser, Erwin E. Klaas

*Sarah M. Nusser*

The increasing availability of digital photographic materials has fueled efforts by agencies and organizations to generate land cover maps for states, regions, and the United States as a whole. Regardless of the information sources and classification methods used, land cover maps are subject to numerous sources of error. In order to understand the quality of the information contained in these maps, it is desirable to generate statistically valid estimates of accuracy rates describing misclassification errors. We explored a full sample survey framework for creating accuracy assessment study designs that balance statistical and operational considerations in relation to study objectives for ...

Adaptive Mechanisms Of Campylobacter Jejuni To Erythromycin Treatment, 2013 Iowa State University

#### Adaptive Mechanisms Of Campylobacter Jejuni To Erythromycin Treatment, Qingqing Xia, Wayne T. Muraoka, Zhangqi Shen, Orhan Sahin, Hongning Wang, Zuowei Wu, Peng Liu, Qijing Zhang

*Veterinary Microbiology and Preventive Medicine Publications*

**Background**

Macrolide is the drug of choice to treat human campylobacteriosis, but Campylobacter resistance to this antibiotic is rising. The mechanisms employed by Campylobacter jejuni to adapt to erythromycin treatment remain unknown and are examined in this study. The transcriptomic response of C. jejuni NCTC 11168 to erythromycin (Ery) treatment was determined by competitive microarray hybridizations. Representative genes identified to be differentially expressed were further characterized by constructing mutants and assessing their involvement in antimicrobial susceptibility, oxidative stress tolerance, and chicken colonization.

**Results**

Following the treatment with an inhibitory dose of Ery, 139 genes were up-regulated and 119 were down-regulated ...

Missing At Random And Ignorability For Inferences About Subsets Of Parameters With Missing Data, 2013 University of Michigan

#### Missing At Random And Ignorability For Inferences About Subsets Of Parameters With Missing Data, Roderick J. Little, Sahar Zanganeh

*The University of Michigan Department of Biostatistics Working Paper Series*

For likelihood-based inferences from data with missing values, Rubin (1976) showed that the missing data mechanism can be ignored when (a) the missing data are missing at random (MAR), in the sense that missingness does not depend on the missing values after conditioning on the observed data, and (b) the parameters of the data model and the missing-data mechanism are distinct; that is, there are no a priori ties, via parameter space restrictions or prior distributions, between the parameters of the data model and the parameters of the model for the mechanism. Rubin described (a) and (b) as the "weakest ...

Global Quantitative Assessment Of The Colorectal Polyp Burden In Familial Adenomatous Polyposis Using A Web-Based Tool, 2013 The University of Texas M.D. Anderson Cancer Center

#### Global Quantitative Assessment Of The Colorectal Polyp Burden In Familial Adenomatous Polyposis Using A Web-Based Tool, Patrick M. Lynch, Jeffrey S. Morris, William A. Ross, Miguel A. Rodriguez-Bigas, Juan Posadas, Rossa Khalaf, Diane M. Weber, Valerie O. Sepeda, Bernard Levin, Imad Shureiqi

*Jeffrey S. Morris*

Background: Accurate measures of the total polyp burden in familial adenomatous polyposis (FAP) are lacking. Current assessment tools include polyp quantitation in limited-field photographs and qualitative total colorectal polyp burden by video.

Objective: To develop global quantitative tools of the FAP colorectal adenoma burden.

Design: A single-arm, phase II trial.

Patients: Twenty-seven patients with FAP.

Intervention: Treatment with celecoxib for 6 months, with before-treatment and after-treatment videos posted to an intranet with an interactive site for scoring.

Main Outcome Measurements: Global adenoma counts and sizes (grouped into categories: less than 2 mm, 2-4 mm, and greater than 4 mm) were ...

A Field Comes Of Age: Geometric Morphometrics In The 21st Century, 2013 Iowa State University

#### A Field Comes Of Age: Geometric Morphometrics In The 21st Century, Dean C. Adams, F. James Rohlf, Dennis E. Slice

*Ecology, Evolution and Organismal Biology Publications*

Twenty years ago, Rohlf and Marcus proclaimed that a "revolution in morphometrics" was underway, where classic analyses based on sets of linear distances were being supplanted by geometric approaches making use of the coordinates of anatomical landmarks. Since that time the field of geometric morphometrics has matured into a rich and cohesive discipline for the study of shape variation and covariation. The development of the field is identified with the Procrustes paradigm, a methodological approach to shape analysis arising from the intersection of the statistical shape theory and analytical procedures for obtaining shape variables from landmark data. In this review ...

A Non-Iterative Implementation Of Tango's Score Confidence Interval For A Paired Difference Of Proportions, 2012 Quintiles Inc

#### A Non-Iterative Implementation Of Tango's Score Confidence Interval For A Paired Difference Of Proportions, Zhao Yang

*Zhao (Tony) Yang, Ph.D.*

For matched-pair binary data, a variety of approaches have been proposed for the construction of a confidence interval (CI) for the difference of marginal probabilities between two procedures. The score-based approximate CI has been shown to outperform other asymptotic CIs. Tango's method provides a score CI by inverting a score test statistic using an iterative procedure. In this paper, we propose an efficient non-iterative method with closed-form expression to calculate Tango's CIs. Examples illustrate the practical application of the new approach.

Spectral Density Shrinkage For High-Dimensional Time Series, 2012 University of California - San Diego

#### Spectral Density Shrinkage For High-Dimensional Time Series, Mark Fiecas, Rainer Von Sachs

*Mark Fiecas*

Time series data obtained from neurophysiological signals is often high-dimensional and the length of the time series is often short relative to the number of dimensions. Thus, it is difficult or sometimes impossible to compute statistics that are based on the spectral density matrix because these matrices are numerically unstable. In this work, we discuss the importance of regularization for spectral analysis of high-dimensional time series and propose shrinkage estimation for estimating high-dimensional spectral density matrices. The shrinkage estimator is derived from a penalized log-likelihood, and the optimal penalty parameter has a closed-form solution, which can be estimated using the ...

Confidence Intervals For The Difference Of Marginal Probabilities In Clustered Matched-Pair Binary Data, 2012 Quintiles Inc

#### Confidence Intervals For The Difference Of Marginal Probabilities In Clustered Matched-Pair Binary Data, Zhao Yang

*Zhao (Tony) Yang, Ph.D.*

Although there are several available test statistics to assess the difference of marginal probabilities in clustered matched-pair binary data, associated confidence intervals (CIs) are not readily available. Herein, the construction of corresponding CIs is proposed, and the performance of each CI is investigated. The results from Monte Carlo simulation study indicate that the proposed CIs perform well in maintaining the nominal coverage probability: for small to medium numbers of clusters, the intra-cluster correlation coefficient-adjusted McNemar statistic and its associated Wald or Score CIs are preferred; however, this statistic becomes conservative when the number of clusters is larger so that alternative ...

Testing Marginal Homogeneity In Matched-Pair Polytomous Data, 2012 Quintiles Inc

#### Testing Marginal Homogeneity In Matched-Pair Polytomous Data, Zhao Yang

*Zhao (Tony) Yang, Ph.D.*

Statistical tests for assessing marginal homogeneity of matched-pair polytomous data can be classified as a score-type test or a Wald-type test; the Wald-type Bhapkar test is a more powerful alternative to the score-type Stuart–Maxwell test, and the Bhapkar test tends to be liberal. Extending the authors’ earlier work, an additional test of each classification is proposed for testing marginal homogeneity, and the relationships among the available test statistics are established. The results from some limited simulation study suggest that the new proposals are very competitive alternatives to the extant methods. These results are the basis of the authors’ recommendations ...

Testing Ratio Of Marginal Probabilities In Clustered Matched-Pair Binary Data, 2012 Quintiles Inc

#### Testing Ratio Of Marginal Probabilities In Clustered Matched-Pair Binary Data, Zhao Yang

*Zhao (Tony) Yang, Ph.D.*

In diagnostic methods evaluation, analysts commonly focus on the relative size of the treatment difference (ratio of marginal probabilities) between a new and an existing procedures. To assess non-inferiority (a new procedure is, to a pre-specified amount, no worse than an existing procedure) via a ratio of marginal probabilities between two procedures using clustered matched-pair binary data, four ICC-adjusted test statistics are investigated. The calculation of corresponding confidence intervals is also proposed. None of the tests considered require structural within-cluster correlation or distributional assumptions. Results of an extensive Monte Carlo simulation study illustrate that the new approaches effectively maintain the ...

Testing Non-Inferiority For Clustered Matched-Pair Binary Data In Diagnostic Medicine, 2012 Quintiles Inc

#### Testing Non-Inferiority For Clustered Matched-Pair Binary Data In Diagnostic Medicine, Zhao Yang

*Zhao (Tony) Yang, Ph.D.*

Testing non-inferiority in active-controlled clinical trials examines whether a new procedure is, to a pre-specified amount, no worse than an existing procedure. To assess non-inferiority between two procedures using clustered matched-pair binary data, two new statistical tests are systematically compared to existing tests. The calculation of corresponding confidence interval is also proposed. None of the tests considered requires structural within-cluster correlation or distributional assumptions. The results of an extensive Monte Carlo simulation study illustrate that the performance of the statistics depends on several factors including the number of clusters, cluster size, probability of success in the test procedure, the homogeneity ...