The Classification Of Basket Neural Cells In The Mammalian Neocortex, 2021 University of South Carolina
The Classification Of Basket Neural Cells In The Mammalian Neocortex, Sreya Pudi
Basket neuronal cells of the mammalian neocortex have been classically categorized into two or more groups. Originally, it was thought that the large and small types are the naturally occurring groups that emerge from reasons that relate to neurobiological function and anatomical position. Later, a study based on anatomical and physiological features of these neurons introduced a third type, the net basket cell which is intermediate in size as compared to the large and small types. In this study, multivariate analysis was used to test the hypothesis that the large and small types are morphologically distinct groups. The results of ...
Splitting Up A Complex Mess: The Effectiveness Of Statistical Analysis On Delimiting Species Complexes, Sara N. Schoen
Masters Theses, 2020-current
Recent studies have highlighted a need for more refined tools in species delimitation. This is especially true when considering diversity within species complexes, where members are morphologically similar and traditional tools have thus far failed to provide clearly defined boundaries between species. This project seeks to refine our traditional tools of species delimitation and apply new tools to the challenges created by species complexes. The focus organisms of this study are the anurans of the Limnonectes kuhlii complex. This species complex comprises more than 25 species of stream frogs from Southeast Asia. Traditionally, morphometrics (particularly linear measures) has been the ...
Biological And Practical Implications Of Genome-Wide Association Study Of Schizophrenia Using Bayesian Variable Selection, 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, 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
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
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 ...
Compound-Specific Isotope Analysis Of Amino Acids In Biological Tissues: Applications In Forensic Entomology, Food Authentication And Soft-Biometrics In Humans, Mayara Patricia Viana De Matos
Graduate Theses, Dissertations, and Problem Reports
In this work we demonstrate the power of compound-specific isotope analysis (CSIA) to analyze proteinaceous biological materials in three distinct forensic applications, including: 1) linking necrophagous blow flies in different life stages to their primary carrion diet; 2) identifying the harvesting area of oysters for food authentication purposes; and 3) the ability to predict biometric traits about humans from their hair.
In the first application, we measured the amino-acid-level fractionation that occurs at each major life stage of Calliphora vicina (Robineau-Desvoidy) (Diptera: Calliphoridae) blow flies. Adult blow flies oviposited on raw pork muscle, beef muscle, or chicken liver. Larvae, pupae ...
Statistical Algorithms And Bioinformatics Tools Development For Computational Analysis Of High-Throughput Transcriptomic Data, 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, 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
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), 2017 George Washington University
A Statistical Method For The Conservative Adjustment Of False Discovery Rate (Q-Value), Yinglei Lai
Epidemiology Faculty Publications
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.
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
Cal Poly Humboldt 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 ...
Application Of Non-Rated Line Officer Attrition Levels And Career Field Stability, 2016 Air Force Institute of Technology
Application Of Non-Rated Line Officer Attrition Levels And Career Field Stability, Christine L. Zens
Theses and Dissertations
The Air Force monitors the strength of its active duty officer force and attempts to achieve the difficult challenge of employing a diversity of talent among career specialties and experience levels. This study completes two objectives, predicting future manning levels for 23 career fields, and providing a statistical framework to assess the stability of these fields. The first part of the study applies regression and survival analysis to subpopulations within the active duty Air Force officer corps, and then aggregates them by year to forecast future personnel levels. Four career fields are considered, including Acquisitions (ACQ), Logistics (LOG), Support (SPT ...
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 University of Southern Mississippi
Macrobenthic Communities In The Northern Gulf Of Mexico Hypoxic Zone: Testing The Pearson-Rosenberg Model, Shivakumar Shivarudrappa
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, 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 ...
Mixtures Of Self-Modelling Regressions, 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, 2013 University of California - San Diego