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Biological And Practical Implications Of Genome-Wide Association Study Of Schizophrenia Using Bayesian Variable Selection, Benazir Rowe, Xiangning Chen, Zuoheng Wang, Jingchun Chen, Amei Amei 2019 University of Nevada, Las Vegas

Biological And Practical Implications Of Genome-Wide Association Study Of Schizophrenia Using Bayesian Variable Selection, Benazir Rowe, Xiangning Chen, Zuoheng Wang, Jingchun Chen, Amei Amei

School of Medicine Faculty Publications

Genome-wide association studies (GWAS) have identified over 100 loci associated with schizophrenia. Most of these studies test genetic variants for association one at a time. In this study, we performed GWAS of the molecular genetics of schizophrenia (MGS) dataset with 5334 subjects using multivariate Bayesian variable selection (BVS) method Posterior Inference via Model Averaging and Subset Selection (piMASS) and compared our results with the previous univariate analysis of the MGS dataset. We showed that piMASS can improve the power of detecting schizophrenia-associated SNPs, potentially leading to new discoveries from existing data without increasing the sample size. We tested SNPs in ...


Population Health Management, Data And Technology, Helena Ladd, Cody Hepp, Anna McCloud, Hannah Granger, Mary Ellen Hethcox, Samuel Calabrese 2019 Ohio Northern University

Population Health Management, Data And Technology, Helena Ladd, Cody Hepp, Anna Mccloud, Hannah Granger, Mary Ellen Hethcox, Samuel Calabrese

Pharmacy and Wellness Review

No abstract provided.


Mu Transposon Insertion Sites And Meiotic Recombination Events Co-Localize With Epigenetic Marks For Open Chromatin Across The Maize Genome, Sanzhen Liu, Cheng-Ting Yeh, Tieming Ji, Kai Ying, Haiyan Wu, Ho Man Tang, Yan Fu, Daniel S. Nettleton, Patrick S. Schnable 2019 Iowa State University

Mu Transposon Insertion Sites And Meiotic Recombination Events Co-Localize With Epigenetic Marks For Open Chromatin Across The Maize Genome, Sanzhen Liu, Cheng-Ting Yeh, Tieming Ji, Kai Ying, Haiyan Wu, Ho Man Tang, Yan Fu, Daniel S. Nettleton, Patrick S. Schnable

Dan Nettleton

The Mu transposon system of maize is highly active, with each of the ∼50–100 copies transposing on average once each generation. The approximately one dozen distinct Mutransposons contain highly similar ∼215 bp terminal inverted repeats (TIRs) and generate 9-bp target site duplications (TSDs) upon insertion. Using a novel genome walking strategy that uses these conserved TIRs as primer binding sites, Mu insertion sites were amplified from Mu stocks and sequenced via 454 technology. 94% of ∼965,000 reads carried Mu TIRs, demonstrating the specificity of this strategy. Among these TIRs, 21 novel Mu TIRs were discovered, revealing additional ...


Unified Methods For Feature Selection In Large-Scale Genomic Studies With Censored Survival Outcomes, Lauren Spirko-Burns, Karthik Devarajan 2019 Temple University

Unified Methods For Feature Selection In Large-Scale Genomic Studies With Censored Survival Outcomes, Lauren Spirko-Burns, Karthik Devarajan

COBRA Preprint Series

One of the major goals in large-scale genomic studies is to identify genes with a prognostic impact on time-to-event outcomes which provide insight into the disease's process. With rapid developments in high-throughput genomic technologies in the past two decades, the scientific community is able to monitor the expression levels of tens of thousands of genes and proteins resulting in enormous data sets where the number of genomic features is far greater than the number of subjects. Methods based on univariate Cox regression are often used to select genomic features related to survival outcome; however, the Cox model assumes proportional ...


Mixtures Of Self-Modelling Regressions, Rhonda D. Szczesniak, Kert Viele, Robin L. Cooper 2019 Cincinnati Children's Hospital Medical Center

Mixtures Of Self-Modelling Regressions, Rhonda D. Szczesniak, Kert Viele, Robin L. Cooper

Robin L. Cooper

A shape invariant model for functions f1,...,fn specifies that each individual function fi can be related to a common shape function g through the relation fi(x) = aig(cix + di) + bi. We consider a flexible mixture model that allows multiple shape functions g1,...,gK, where each fi is a shape invariant transformation of one of those gK. We derive an MCMC algorithm for fitting the model using Bayesian Adaptive Regression Splines (BARS), propose a strategy to improve its mixing properties and utilize existing model selection ...


Statistical Algorithms And Bioinformatics Tools Development For Computational Analysis Of High-Throughput Transcriptomic Data, Adam McDermaid 2018 South Dakota State University

Statistical Algorithms And Bioinformatics Tools Development For Computational Analysis Of High-Throughput Transcriptomic Data, Adam Mcdermaid

Electronic Theses and Dissertations

Next-Generation Sequencing technologies allow for a substantial increase in the amount of data available for various biological studies. In order to effectively and efficiently analyze this data, computational approaches combining mathematics, statistics, computer science, and biology are implemented. Even with the substantial efforts devoted to development of these approaches, numerous issues and pitfalls remain. One of these issues is mapping uncertainty, in which read alignment results are biased due to the inherent difficulties associated with accurately aligning RNA-Sequencing reads. GeneQC is an alignment quality control tool that provides insight into the severity of mapping uncertainty in each annotated gene from ...


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


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 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 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 ...


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 ...


Mixtures Of Self-Modelling Regressions, Rhonda D. Szczesniak, Kert Viele, Robin L. Cooper 2014 Cincinnati Children's Hospital Medical Center

Mixtures Of Self-Modelling Regressions, Rhonda D. Szczesniak, Kert Viele, Robin L. Cooper

Statistics Faculty Publications

A shape invariant model for functions f1,...,fn specifies that each individual function fi can be related to a common shape function g through the relation fi(x) = aig(cix + di) + bi. We consider a flexible mixture model that allows multiple shape functions g1,...,gK, where each fi is a shape invariant transformation of one of those gK. We derive an MCMC algorithm for fitting the model using Bayesian Adaptive Regression Splines (BARS), propose a strategy to improve its mixing properties and utilize existing model selection ...


Spectral Density Shrinkage For High-Dimensional Time Series, Mark Fiecas, Rainer von Sachs 2013 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 ...


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