Statistical Models Commons^™

Paper Structure Formation Simulation, Tyler R. Seekins

Electronic Theses and Dissertations

On the surface, paper appears simple, but closer inspection yields a rich collection of chaotic dynamics and random variables. Predictive simulation of paper product properties is desirable for screening candidate experiments and optimizing recipes but existing models are inadequate for practical use. We present a novel structure simulation and generation system designed to narrow the gap between mathematical model and practical prediction. Realistic inputs to the system are preserved as randomly distributed variables. Rapid fiber placement (~1 second/fiber) is achieved with probabilistic approximation of chaotic fluid dynamics and minimization of potential energy to determine flexible fiber conformations. Resulting digital packed …

Population Viability And Connectivity Of The Federally Threatened Eastern Indigo Snake In Central Peninsular Florida, Javan Bauder

Doctoral Dissertations

Understanding the factors influencing the likelihood of persistence of real-world populations requires both an accurate understanding of the traits and behaviors of individuals within those populations (e.g., movement, habitat selection, survival, fecundity, dispersal) but also an understanding of how those traits and behaviors are influenced by landscape features. The federally threatened eastern indigo snake (EIS, Drymarchon couperi) has declined throughout its range primarily due to anthropogenically-induced habitat loss and fragmentation making spatially-explicit assessments of population viability and connectivity essential for understanding its current status and directing future conservation efforts. The primary goal of my dissertation was to understand how …

Automatic 13C Chemical Shift Reference Correction Of Protein Nmr Spectral Data Using Data Mining And Bayesian Statistical Modeling, Xi Chen

Theses and Dissertations--Molecular and Cellular Biochemistry

Nuclear magnetic resonance (NMR) is a highly versatile analytical technique for studying molecular configuration, conformation, and dynamics, especially of biomacromolecules such as proteins. However, due to the intrinsic properties of NMR experiments, results from the NMR instruments require a refencing step before the down-the-line analysis. Poor chemical shift referencing, especially for ¹³C in protein Nuclear Magnetic Resonance (NMR) experiments, fundamentally limits and even prevents effective study of biomacromolecules via NMR. There is no available method that can rereference carbon chemical shifts from protein NMR without secondary experimental information such as structure or resonance assignment.

To solve this problem, we …

Adult Atlantic Sturgeon Population Dynamics In The York River, Virginia, Jason E. Kahn

Graduate Theses, Dissertations, and Problem Reports

Sturgeon first appear in the fossil record in the Triassic Period just over 200 million years ago and are among the most primitive of the bony fishes. Despite their large size and historic presence along the East Coast, Atlantic sturgeon were not targeted for their meat and caviar as a commercial fishery until 1880. By 1905 they had declined to less than one percent of their pre-fishing abundance but the fishery continued. Prior to 1980, there had been very little research on Atlantic sturgeon, primarily limited to documenting landing location and poundage, maximum longevity, or weight of eggs per fish. …

Methods For Estimating Mountain Goat Occupancy And Abundance, Molly Mcdevitt

Graduate Student Theses, Dissertations, & Professional Papers

Abundance and occupancy are two parameters of central interest to the field of ecology. Furthermore, accurate (both precise and unbiased) estimates are key pieces to the puzzle of effective wildlife management decision-making. While there exist a variety of sampling techniques and statistical models for effectively estimating population parameters for frequently encountered and large mammals, methods for sampling unmarked and rare species are few and far between. The first step to acquiring usable parameter estimates is through the use of sampling theory and incorporation of probabilistic sampling designs to collect count-data and occurrence-data. Often, it is assumed that probabilistic sampling designs …

Real-Time Dengue Forecasting In Thailand: A Comparison Of Penalized Regression Approaches Using Internet Search Data, Caroline Kusiak

Masters Theses

Dengue fever affects over 390 million people annually worldwide and is of particu- lar concern in Southeast Asia where it is one of the leading causes of hospitalization. Modeling trends in dengue occurrence can provide valuable information to Public Health officials, however many challenges arise depending on the data available. In Thailand, reporting of dengue cases is often delayed by more than 6 weeks, and a small fraction of cases may not be reported until over 11 months after they occurred. This study shows that incorporating data on Google Search trends can improve dis- ease predictions in settings with severely …

Habitat Preferences Of Blue Marlin (Makaira Nigricans) And Black Marlin (Istiompax Indica) In The Eastern Pacific Ocean, Nima Farchadi, Michael G. Hinton, Andrew R. Thompson, Zhi-Yong Yin

Theses

Overexploitation and climate change can reduce the abundance and shift the spatial distribution of marine species. Determining the habitat suitability of a mobile pelagic species, such as Makaira nigricans (BUM) and Istiompax indica (BLM), can help describe their spatiotemporal distribution patterns over a broad spatial scale, which is a crucial need for fisheries management. Using 14 years (1997-2010) of Inter-American Tropical Tuna Commission (IATTC) catch data from purse-seine vessels in the eastern Pacific Ocean (EPO), we modeled the dynamic habitat suitability of BUM and BLM in response to environmental variables within the EPO using a species distribution model (MaxEnt) with …

Coastal Wetland Dynamics Under Sea-Level Rise And Wetland Restoration In The Northern Gulf Of Mexico Using Bayesian Multilevel Models And A Web Tool, Tyler Hardy

Master's Theses

There is currently a lack of modeling framework to predict how relative sea-level rise (SLR), combined with restoration activities, affects landscapes of coastal wetlands with uncertainties accounted for at the entire northern Gulf of Mexico (NGOM). I developed such a modeling framework – Bayesian multi-level models to study the spatial pattern of wetland loss in the NGOM, driven by relative RSLR, vegetation productivity, tidal range, coastal slope, and wave height – all interacting with river-borne sediment availability, indicated by hydrological regimes. These interactions have not been comprehensively investigated before. I further modified this model to assess the efficacy of restoration …

An Empirical Analysis Of Climatic, Geographic, And Cultural Determinants Of International Tourism, Ethan Straus

Honors Theses

Each year, billions of people visit different countries all around the world. For many of those countries, tourism is their primary industry, leading to millions of jobs and dollars in revenue. It is expected that by 2020 total International Tourism Receipts will reach 2 trillion US dollars annually. Currently, tourism employs an estimated 200 million people around the world. With the continued progression of climate change, the tourism industry is facing a newfound threat. Global temperatures and the seal level are both expected to rise significantly by the end of the century. Additionally, the Intergovernmental Panel on Climate Change has …

Spatio-Temporal Dynamics Of Atlantic Cod Bycatch In The Maine Lobster Fishery And Its Impacts On Stock Assessment, Robert E. Boenish

Electronic Theses and Dissertations

Of the most iconic fish species in the world, the Atlantic cod (Gadus morhua, hereafter, cod) has been a mainstay in the North Atlantic for centuries. While many global fish stocks have received increased pressure with the advent of new, more efficient fishing technology in the mid-20^th century, exceptional pressure has been placed on this prized gadoid. Bycatch, or the unintended catch of organisms, is one of the biggest global fisheries issues. Directly resulting from the failed recovery of cod in the GoM, attention has been placed as to possible sources of unaccounted catch. Among the most …

Life-History Characteristics And Fishery Dynamics Of Red Drum (Sciaenops Ocellatus), In The North-Central Gulf Of Mexico, Corbin Bennetts

Master's Theses

Red Drum (Sciaenops ocellatus) are highly targeted recreationally in the Gulf of Mexico, and support a small commercial fishery in Mississippi. Despite their popularity, the stock is assessed using data limited approaches that necessitate accurate life history information. I estimated the year-specific and year-aggregated escapement rates for the Mississippi stock (years 2004 to 2015), which were sensitive to mortality estimation methods; year-aggregated estimates were 6.9 to 28.2 % depending on the method, but temporal patterns were consistent. I then addressed concerns with previously estimated life-history characteristics by describing the sex-specific growth and reproductive dynamics. The three-parameter von Bertalanffy …

Longitudinal Tracking Of Physiological State With Electromyographic Signals., Robert Warren Stallard

Electronic Theses and Dissertations

Electrophysiological measurements have been used in recent history to classify instantaneous physiological configurations, e.g., hand gestures. This work investigates the feasibility of working with changes in physiological configurations over time (i.e., longitudinally) using a variety of algorithms from the machine learning domain. We demonstrate a high degree of classification accuracy for a binary classification problem derived from electromyography measurements before and after a 35-day bedrest. The problem difficulty is increased with a more dynamic experiment testing for changes in astronaut sensorimotor performance by taking electromyography and force plate measurements before, during, and after a jump from a small platform. A …

Spatial Modelling And Wildlife Health Surveillance: A Case Study Of White Nose Syndrome In Ontario, Lauren Yee

Theses and Dissertations (Comprehensive)

Wildlife data is often limited by survey effort, small sample sizes, and spatial biases associated with collection and missing data. These factors can create unique challenges from a surveillance perspective when trying to extract spatial patterns of habitat suitability and disease distributions for conservation and management purposes. This thesis examined data quality from a wildlife health database in the context of spatial analysis of wildlife disease. Spatial analysis of the data to predict habitat suitability of bats and white nose syndrome afflicted bats was examined by using the MaxEnt modelling method. Methods to reduce spatial bias were examined and specific …

Seasonal Resource Selection And Habitat Treatment Use By A Fringe Population Of Greater Sage-Grouse, Rhett Boswell

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

Movement and habitat selection by Greater Sage-grouse (Centrocercus uropasianus) is of great interest to wildlife managers tasked with applying conservation measures for this iconic western species. Current technology has created small and lightweight GPS (Global Positioning Systems) transmitters that can be attached to sage-grouse. Using GIS software and statistical programs such as Program R, land managers can analyze GPS location data to assess how sage-grouse are geospatially interacting with their habitats. Within the Panguitch Sage-Grouse Management Area (SGMA) thousands of acres of land have been restored or manipulated to enhance sage-grouse habitat; this usually involves removal of pinyon pine …

Modelling Bird Migration With Motus Data And Bayesian State-Space Models, Justin Baldwin

Masters Theses

Bird migration is a poorly-known yet important phenomenon, as understanding movement patterns of birds can inform conservation strategies and public health policy for animal-borne diseases. Recent advances in wildlife tracking technology, in particular the Motus system, have allowed researchers to track even small flying birds and insects with radio transmitters that weigh fractions of a gram. This system relies on a community-based distributed sensor network that detects tagged animals as they move through the detection nodes on journeys that range from small local movements to intercontinental migrations. The quantity of data generated by the Motus system is unprecedented, is on …

Statistical Methods For High Dimensional Data Arising From Large Epidemiological Studies, Hui Xu

Doctoral Dissertations

In this thesis, we propose statistical models for addressing commonly encountered data types and study designs in large epidemiologic investigations aimed at understanding the molecular basis of complex disorders. The motivating applications come from diverse disease areas in Women's Health, including the study of type II diabetes in the Women's Health Initiative (WHI), invasive breast cancer in the Nurses' Health Study and the study of the metabolomic underpinnings of cardiovascular disease in the WHI. We have also put significant effort into making the implementation of the proposed methods accessible through freely available, user-friendly software packages in R. The first chapter …

Statistical Methods For Two Problems In Cancer Research: Analysis Of Rna-Seq Data From Archival Samples And Characterization Of Onset Of Multiple Primary Cancers, Jialu Li

Dissertations & Theses (Open Access)

My dissertation is focused on quantitative methodology development and application for two important topics in translational and clinical cancer research.

The first topic was motivated by the challenge of applying transcriptome sequencing (RNA-seq) to formalin-fixation and paraffin-embedding (FFPE) tumor samples for reliable diagnostic development. We designed a biospecimen study to directly compare gene expression results from different protocols to prepare libraries for RNA-seq from human breast cancer tissues, with randomization to fresh-frozen (FF) or FFPE conditions. To comprehensively evaluate the FFPE RNA-seq data quality for expression profiling, we developed multiple computational methods for assessment, such as the uniformity and continuity …

Network Exploration Of Correlated Multivariate Protein Data For Alzheimer's Disease Association, Matthew J. Lane

Theses

Alzheimer Disease (AD) is difficult to diagnose by using genetic testing or other traditional methods. Unlike diseases with simple genetic risk components, there exists no single marker determining as to whether someone will develop AD. Furthermore, AD is highly heterogeneous and different subgroups of individuals develop the disease due to differing factors. Traditional diagnostic methods using perceivable cognitive deficiencies are often too little too late due to the brain having suffered damage from decades of disease progression. In order to observe AD at early stages prior to the observation of cognitive deficiencies, biomarkers with greater accuracy are required. By using …

Towards Deeper Understanding In Neuroimaging, Rex Devon Hjelm

Computer Science ETDs

Neuroimaging is a growing domain of research, with advances in machine learning having tremendous potential to expand understanding in neuroscience and improve public health. Deep neural networks have recently and rapidly achieved historic success in numerous domains, and as a consequence have completely redefined the landscape of automated learners, giving promise of significant advances in numerous domains of research. Despite recent advances and advantages over traditional machine learning methods, deep neural networks have yet to have permeated significantly into neuroscience studies, particularly as a tool for discovery. This dissertation presents well-established and novel tools for unsupervised learning which aid in …

Resolving Gnetum Evolutionary History, Angela Mcfadden

All Master's Theses

Gnetum are non-flowering seed plants of the tropics, indigenous to South America, Africa, and Asia. This group of about 40 species is fascinating to botanists because it shares distinctive morphological characteristics with flowering plants, such as broad leaves, woody stems, and flower-like strobili. There are still questions surrounding the relationships within the genus of Gnetum. With that in mind, I focused my work on generating phylogenetic hypotheses, using two molecular data sets: a concatenation of over 60 different chloroplast genes (66,815 base pairs), and the whole chloroplast genome (128,772 base pairs). This allowed me to compare the two phylogenies …

Estimation Problems In Complex Field Studies With Deep Interactions: Time-To-Event And Local Regression Models For Environmental Effects On Vital Rates, Krzysztof M. Sakrejda

Doctoral Dissertations

Field studies that measure vital rates in context over extended time periods are a cornerstone of our understanding of population processes. These studies inform us about the relationship between biological process and environmental noise in an irreplaceable way. These data sets bring ``big data'' and ``big model'' challenges, which limit the application of standard software (e.g., \textbf{BUGS}). The environmental sensitivity of vital rates is also expected to exhibit interactions and non-linearity, which typically result in difficult model selection questions in large data sets. Finally, long-term ecological data sets often contain complex temporal structure. In commonly applied discrete-time models complex temporal …

Computational Modeling Of Rna-Small Molecule And Rna-Protein Interactions, Lu Chen

Dissertations & Theses (Open Access)

The past decade has witnessed an era of RNA biology; despite the considerable discoveries nowadays, challenges still remain when one aims to screen RNA-interacting small molecule or RNA-interacting protein. These challenges imply an immediate need for cost-efficient while predictive computational tools capable of generating insightful hypotheses to discover novel RNA-interacting small molecule or RNA-interacting protein. Thus, we implemented novel computational models in this dissertation to predict RNA-ligand interactions (Chapter 1) and RNA-protein interactions (Chapter 2).

Targeting RNA has not garnered comparable interest as protein, and is restricted by lack of computational tools for structure-based drug design. To test the potential …

Using Capture-Mark-Recapture Techniques To Estimate Detection Probabilities & Fidelity Of Expression For The Critically Endangered James Spinymussel (Pleurobema Collina)., Alaina C. Esposito

Masters Theses, 2010-2019

The critically endangered James Spinymussel (Pleurobema collina) is a species of freshwater mussel endemic to Virginia’s James and Dan River basins. In the last 20 years, P. collina has experienced a substantial decline in numbers and currently occupies approximately 10% of its original habitat; however, little information is known about this species to assist in conservation. A 230-meter reach of transitional habitat in Swift Run was selected for repeat observations to estimate detection probabilities using a Capture-Mark-Recapture framework. In June 2014, visual scouting began to locate and tag P. collina (including other mussels in the community) with PIT …

A Model For Determining Drivers Of Phenology In Western United States Rangelands, Joseph R. St. Peter

Graduate Student Theses, Dissertations, & Professional Papers

Plant phenology has long been used as an indicator of climate. Recent changes in plant phenology are evidence of the influence of climate change. Modeling plant phenology has become an effective tool to understand the impacts of climate change. Using machine learning techniques I developed a modeling process for accurately predicting phenology across a diverse landscape. This model uses individual site data to set site specific climate thresholds for plant phenology. This model also identifies the limiting factors to vegetation phenology for rangelands in the western United States. NDVI remotely sensed data was used to quantify land surface phenology and …

Identifying The Spatial Distribution Of Three Plethodontid Salamanders In Great Smoky Mountains National Park Using Two Habitat Modeling Methods, Matthew Stephen Kookogey

Masters Theses

The main objective was to create habitat models of three plethodontid salamander species (Desmognathus conanti, D. ocoee, and Plethodon jordani) in GSMNP. To investigate the relationships between salamanders and their habitats, I used three models—logistic regression with use-availability sampling, logistic regression with case-control sampling, and Mahalanobis distance (D²)—for each species to gain a robust view of the relationships. The secondary objective was to compare the different modeling methods within and across the three species. Elevation was the dominant variable for all three species.

D² for D. conanti predicted low elevations, close proximity …

A Geospatial Based Decision Framework For Extending Marssim Regulatory Principles Into The Subsurface, Robert Nathan Stewart

Doctoral Dissertations

The Multi-Agency Radiological Site Survey Investigation Manual (MARSSIM) is a regulatory guidance document regarding compliance evaluation of radiologically contaminated soils and buildings (USNRC, 2000). Compliance is determined by comparing radiological measurements to established limits using a combination of hypothesis testing and scanning measurements. Scanning allows investigators to identify localized pockets of contamination missed during sampling and allows investigators to assess radiological exposure at different spatial scales. Scale is important in radiological dose assessment as regulatory limits can vary with the size of the contaminated area and sites are often evaluated at more than one scale (USNRC, 2000). Unfortunately, scanning is …

Survival Prediction For Brain Tumor Patients Using Gene Expression Data, Vinicius Bonato

Dissertations & Theses (Open Access)

Brain tumor is one of the most aggressive types of cancer in humans, with an estimated median survival time of 12 months and only 4% of the patients surviving more than 5 years after disease diagnosis. Until recently, brain tumor prognosis has been based only on clinical information such as tumor grade and patient age, but there are reports indicating that molecular profiling of gliomas can reveal subgroups of patients with distinct survival rates. We hypothesize that coupling molecular profiling of brain tumors with clinical information might improve predictions of patient survival time and, consequently, better guide future treatment decisions. …

The Extent Of Interaction Between The Scallop And Prawn Fleets In The Shark Bay Scallop Managed Fishery, John Dickson

Theses : Honours

The Shark Bay Managed Scallop Fishery is Western Australia's most important scallop fishery with an annual value of between $2 and $58 million. In addition to this the fishery is an important source of regional employment with approximately 160 skippers and crew employed during the 2005 season. Two separate fleets are permitted to fish for scallops in this fishery, the first consisting of dedicated scallop fishing vessels (Class A licences) and the second of prawn fishing vessels (Class B licences) that are allowed to take scallops under a catch sharing arrangement. Concerns exist over the interactions between these two fleets …

Mark-Recapture Creel Survey And Survival Models, Shampa Saha

Mathematics & Statistics Theses & Dissertations

In this dissertation, we consider a model based approach to the estimation of exploitation rate of a fish population by combining mark-recapture procedures with a creel survey. We also consider the analysis of a proportional hazards survival model for randomly censored observations, known as the Koziol-Green model. The model assumes that the lifetime survivor function is a power of the censored time survivor function.

In Chapter 2, we introduce the model based approach to the estimation of the exploitation rate of a fish population by combining mark-recapture procedures with a creel survey. We assume that in the beginning of a …

A Statistical Approach To The Study Of The Ecosystems Of Seven Ponds In East-Central Illinois, Gregory Lee Orr

Masters Theses

Gross primary productivity, heterotrophic bacterial numbers, and net phytoplankton densities of seven ponds in Coles County, Illinois, were studied in relation to physical, chemical, and biological habitat variables (light intensity and duration, turbidity, water temperature, pH, dissolved oxygen, sulfur, nitrogen, phosphorus, production, bacteria, and phytoplankton). Ten observations were made for each pond (except where otherwise noted) from 17 June through 25 August 1974. Stepwise multiple linear regression analyses of the data were used in order to determine those environmental factors which were important in predicting (i.e., significantly correlated with) bacterial and phytoplankton densities, and production. A multiple linear regression equation …