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Reassessment Of The Red Drum Stock In Mississippi Coastal Waters: The Role Of Ages 3-5 Year-Class Fish, Emily Satterfield 2017 The University of Southern Mississippi

Reassessment Of The Red Drum Stock In Mississippi Coastal Waters: The Role Of Ages 3-5 Year-Class Fish, Emily Satterfield

Master's Theses

Red Drum, Sciaenops ocellatus, are highly sought after by sport fishermen in Mississippi coastal waters. In 2016, Mississippi anglers made over 180,000 fishing trips targeting Red Drum, making it the second most targeted marine species. The current Fishery Management Plan of the Gulf of Mexico Fishery Management Council, prohibits harvest of Red Drum in federal waters. Monitoring of the stock in Mississippi state waters occurs at sites that are almost exclusively estuarine, using gear types selective for juvenile fish. Additional samples come from the for-hire-industry that typically targets larger Red Drum. This project’s goal was to target age ...


Adaptation Of The Genetic Risk Prediction Model Brcapro For Primary Care Settings, Philamer M. Atienza 2017 University of North Texas Health Science Center at Fort Worth

Adaptation Of The Genetic Risk Prediction Model Brcapro For Primary Care Settings, Philamer M. Atienza

Theses and Dissertations

Identifying women at high risks of carrying the breast cancer susceptibility genes is crucial for providing timely surveillance and necessary health management interventions. BRCAPRO is one of the most widely used statistical models for breast cancer risk prediction in genetic counseling. It provides carrier probabilities of BRCA1/2 mutations and calculates the risks of developing breast and ovarian cancers. This calculation requires extensive personal and family history information, which makes it difficult to use in primary care where a wider population could be reached. Thus, we developed a two-stage approach for the genetic risk prediction of BRCA1/2 mutation. In ...


A Statistical Method For The Conservative Adjustment Of False Discovery Rate (Q-Value), Yinglei Lai 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, Erin F E Pinkston 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, Colin P. Kirkmire 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, Karthik Devarajan, Guoli Wang 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, Amalia Magaret 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, Shivakumar Shivarudrappa 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 ...


An Evaluation Of Soil Test Information In Agricultural Decision Making, Bruce A. Babcock, Alicia L. Carriquiry, Hal S. Stern 2015 Iowa State University

An Evaluation Of Soil Test Information In Agricultural Decision Making, Bruce A. Babcock, Alicia L. Carriquiry, Hal S. Stern

Alicia L. Carriquiry

The value of soil-test information in planning fertilizer application levels is determined by using agricultural field-plot data to estimate the posterior distribution of mean soil-nitrate concentrations at a given location. Optimal decisions concerning fertilizer application levels are made with respect to this posterior distribution. Average reductions in fertilizer application rates range from 15 to 41 percent, depending on the form of prior information that is available.


Initiation And Early Development Of Fiber In Wild And Cultivated Cotton, Kara M. Butterworth, Dean C. Adams, Harry T. Horner, Jonathan F. Wendel 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, Elias Ayrey 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, Michael I. Premer 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, Sarah M. Nusser, Erwin E. Klaas 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 ...


Sampling Considerations For Disease Surveillance In Wildlife Populations, Sarah M. Nusser, William R. Clark, David L. Otis, Ling Huang 2014 Iowa State University

Sampling Considerations For Disease Surveillance In Wildlife Populations, Sarah M. Nusser, William R. Clark, David L. Otis, Ling Huang

Sarah M. Nusser

Disease surveillance in wildlife populations involves detecting the presence of a disease, characterizing its prevalence and spread, and subsequent monitoring. A probability sample of animals selected from the population and corresponding estimators of disease prevalence and detection provide estimates with quantifiable statistical properties, but this approach is rarely used. Although wildlife scientists often assume probability sampling and random disease distributions to calculate sample sizes, convenience samples (i.e., samples of readily available animals) are typically used, and disease distributions are rarely random. We demonstrate how landscape-based simulation can be used to explore properties of estimators from convenience samples in relation ...


Factors Influencing Wetland Use By Canada Geese, David E. Naugle, Jeffrey S. Gleason, Jonathan A. Jenks, Kenneth E. Higgins, Paul W. Mammenga, Sarah M. Nusser 2014 South Dakota State University

Factors Influencing Wetland Use By Canada Geese, David E. Naugle, Jeffrey S. Gleason, Jonathan A. Jenks, Kenneth E. Higgins, Paul W. Mammenga, Sarah M. Nusser

Sarah M. Nusser

Seasonal and semi-permanent wetlands in eastern South Dakota were surveyed in 1995 and 1996 to identify habitat characteristics influencing wetland use by Canada geese (Branta canadensis maxima). Position of a wetland within the landscape and its area were important landscape-scale features influencing wetland use by geese. Our delineation of potential Canada goose habitat using a wetland geographic information system indicated that distribution and area of semi-permanent wetlands likely limit Canada goose occurrence in regions outside the Prairie Coteau. Periodicity in hydrologic cycles within landscapes also may influence goose use of wetlands in eastern South Dakota.


Spectral Density Shrinkage For High-Dimensional Time Series, Mark Fiecas, Rainer von Sachs 2014 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 ...


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 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, Roderick J. Little, Sahar Zanganeh 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, 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 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, Dean C. Adams, F. James Rohlf, Dennis E. Slice 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 ...


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