Physical Sciences and Mathematics Commons^™

Analysis Of Large-Scale Population Genetic Data Using Efficient Algorithms And Data Structures, Ardalan Naseri

Electronic Theses and Dissertations

With the availability of genotyping data of very large samples, there is an increasing need for tools that can efficiently identify genetic relationships among all individuals in the sample. Modern biobanks cover genotypes up to 0.1%-1% of an entire large population. At this scale, genetic relatedness among samples is ubiquitous. However, current methods are not efficient for uncovering genetic relatedness at such a scale. We developed a new method, Random Projection for IBD Detection (RaPID), for detecting Identical-by-Descent (IBD) segments, a fundamental concept in genetics in large panels. RaPID detects all IBD segments over a certain length in time linear …

Characterizing Variable Flow Pathways And Geochemical History Of Seepage Under The Mississippi River Levee: 2011, 2015, And 2016 Floods, Kaitlin Marie Voll

Electronic Theses and Dissertations

Seepage beneath levees during flood stage becomes a concern when piping occurs, creating channels beneath the levee and forming sand boils where transported sediments discharge. Along the lower Mississippi River, pathways beneath the levee vary with surface geology, following deeper paths where the levee overlies channel fill deposits, and shallower paths where it overlies sand bar deposits. A preliminary investigation north of Vicksburg, MS, during the 2011 flood, demonstrated the potential for using aqueous geochemistry to differentiate sand boils forming at the end of deep and shallow flow pathways, though the study was limited to cation and trace metal analyses. …

Modeling Water Availability, Risk And Resilience In A Semi-Arid Basin In Southern Africa, Esther N. Mosase

Electronic Theses and Dissertations

Climate variability need to be incorporated into the management and planning of water resources, particularly in arid and semi-arid regions, where water availability is more sensitive to rainfall and air temperature. This study used modified Man-Kendall trend analysis test and ArcGIS to process data. Annual means of rainfall, minimum temperature and maximum temperature in the Limpopo River Basin (LRB) varied between 160 and 1109 mm, 8 °C to 20 °C and 23 °C to 32 °C respectively. The spatial pattern is generally increasing from west to east for rainfall and minimum temperature while maximum temperature increases from south to north …

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 …

Mapping And Risk Assessment Of Juniper Encroachment Into A Prairie Landscape, Kyle D. Kaskie

Electronic Theses and Dissertations

Juniper encroachment is a considerable threat to the prairie ecosystems of the Great Plains because it has the potential to alter native grasslands by changing soil characteristics, limiting herbaceous biomass, and hindering native community regeneration. Accurate maps of juniper cover and predictions of areas at risk for future expansion are needed to support proactive management measures. Therefore, our objectives are to: (1) Develop a practical workflow for large-scale juniper mapping using Landsat 8 Operational Land Imager (OLI) imagery and partial unmixing techniques, (2) Compare the classification accuracies from the resulting map based on different juniper density thresholds and different types …

Wi-Fi Finger-Printing Based Indoor Localization Using Nano-Scale Unmanned Aerial Vehicles, Appala Narasimha Raju Chekuri

Electronic Theses and Dissertations

Explosive growth in the number of mobile devices like smartphones, tablets, and smartwatches has escalated the demand for localization-based services, spurring development of numerous indoor localization techniques. Especially, widespread deployment of wireless LANs prompted ever increasing interests in WiFi-based indoor localization mechanisms. However, a critical shortcoming of such localization schemes is the intensive time and labor requirements for collecting and building the WiFi fingerprinting database, especially when the system needs to cover a large space. In this thesis, we propose to automate the WiFi fingerprint survey process using a group of nano-scale unmanned aerial vehicles (NAVs). The proposed system significantly …

Application Of Drainage Water Management And Saturated Buffers For Conservation Drainage In South Dakota, Abhinav Sharma

Electronic Theses and Dissertations

Edge of field practices such as drainage water management (DWM) and saturated buffers can reduce nutrient transport from croplands to surface waterbodies. DWM uses stackable weir boards in a control structure to manipulate the water table depth throughout the cropping season and reduce the amount of nutrient rich water draining out from the field. Saturated buffers, on the other hand, use a control structure to divert water draining out from the cropland to a vegetative strip via a subsurface tile installed parallel to a waterway. For the saturated buffer systems, a combination of natural denitrification, nitrogen mineralization, and plant uptake …

Land Use Change Sustainability And Carbon Turnover Rate In The Northern Great Plains Soil, Deepak Raj Joshi

Electronic Theses and Dissertations

Sustainable land management involves the management of land, water, biodiversity and other resources that meet human requirements while maintaining ecosystem services. In the northern Great Plains (NGP), the combined impacts of landuse and climate variability have placed many soils at the tipping point of sustainability. The objectives of this study were to: 1) calculate land-use changes from 2006 to 2012 and from 2012 to 2014 in South Dakota and Nebraska; 2) assess if land use changes had impacted on soil sustainability; 3) calculate variation in total carbon budget and turnover due to seasonal climate variability, biomass quality and soil properties; …

Walleye Fishery Ecology In Lake Oahe Of The Dakotas, Eli Felts

Electronic Theses and Dissertations

Walleye Sander vitreus is among the most popular sport fishes in North America and is the most sought-after fish in both South Dakota and North Dakota. Lake Oahe, a large main stem Missouri River reservoir, spans state boundaries and provides one of the most popular and productive Walleye fisheries in both Dakotas. The Walleye population of Lake Oahe has experienced wide fluctuations in abundance and size structure over the last 25 years which has caused high variability in angler use and satisfaction. Much of this variation is thought to be driven by Rainbow Smelt Osmserus mordax, which are the dominant …

Fast Isotope Ratio Mass Spectrometry (Firms): A Tandem Mass Spectrometry Technique For The Rapid And Semi-Comprehensive Evaluation Of Isotope Ratios, Fredrick Ochieng

Electronic Theses and Dissertations

Isotope ratios (IRs) are a measure of the variation in abundance of light isotopes versus heavy isotopes of an element, e.g. ¹H/²H,¹²C/¹³C, and ¹⁴N/¹⁵N. Because IRs change as a molecule undergoes certain chemical and physical processes, they represent unique fingerprints that can be used to trace the source of a chemical compound. Current techniques for determination of IRs each have major limitations, such as loss of structural information, vulnerability to contamination, high cost, large sample size requirements, low precision, limited applicability, and lengthy analysis. Fast Isotope Ratio Mass Spectrometry (FIRMS) …

Evaluating E. Coli Particle Attachment And The Impact On Transport During High Flows, Louis Amegbletor

Electronic Theses and Dissertations

Fecal indicator bacteria, including E. coli, are the leading cause of water quality impairments within assessed waters in the United States. The source of E. coli includes WWTP, leaking sewers, animal manure, wildlife, livestock, and stream bed sediment. Storm events contribute to bacteria loading within waters through wash-in of land sources of bacteria and resuspension of bacteria within sediments. Bacteria introduced into the water column are either attached to particles or are unattached (or free-living). The goal of this study was to examine the attachment of E. coli to different particle sizes, including their impact on contributing to water …

The Beam Dynamics And Beam Related Uncertainties In Fermilab Muon G-2 Experiment, Wanwei Wu

Electronic Theses and Dissertations

The anomaly of the muon magnetic moment, aμ ≡ (g-2)/2, has played an important role in constraining physics beyond the Standard Model for many years. Currently, the Standard Model prediction for aμ is accurate to 0.42 parts per million (ppm). The most recent muon g-2 experiment was done at Brookhaven National Laboratory (BNL) and determined aμ to 0.54 ppm, with a central value that differs from the Standard Model prediction by 3.3-3.6 standard deviations and provides a strong hint of new physics. The Fermilab Muon g-2 Experiment has a goal to measure aμ to unprecedented precision: 0.14 ppm, which could …

Geology Of The Northern Alto Relex Area, Big Bend National Park, Brewster County, Texas, Robert Schoen

Electronic Theses and Dissertations

Detailed, 1:12,000-scale geologic field mapping was conducted around Alto Relex in the northern Sierra Del Carmen Mountains in Big Bend National Park. Alto Relex is a prominent, near vertical, ~1000 foot-high fault-line scarp. Cretaceous rocks in the area were folded and faulted by Laramide compression, intruded by Tertiary sills and overprinted by high-angle normal faults from Basin and Range extension. During the Laramide Orogeny and Basin and Range extension, the underlying basement shear zone called, the Texas Lineament, was reactivated creating a transpressional and transtensional regimes. The general geology of this area was outlined by Moustafa (1988) working primarily from …

Structural Analysis Of The Northwest Wind Mountain Quadrangle, New Mexico: Proterozoic Shearing To Cenozoic Brittle Faulting In The Burro Mountains, Jensen Kohl Angelloz

Electronic Theses and Dissertations

Preliminary investigation of the Bullard Peak metamorphic series (BPMS) in the northwestern Wind Mountain quadrangle within the Burro Mountains of southwestern New Mexico suggests a possible previously unidentified shear zone, prompting detailed (1:12,000) geologic mapping and collection of structural data. The study area has a complex tectonic history, including 1) ~1.65 Ga metamorphism during accretion of the Mazatzal terrane to Laurentia’s southern margin; 2) ~1.4 Ga intrusion of Granite and Rhyolite Province granitoids; 3) significant uplift during the formation of the Ancestral Rockies (~300 Ma) and the Rocky Mountains (~70-50 Ma); and 4) inversion tectonics with reactivation of compressional faults …

Evaluating Potential For Water Quality Decline In Maine Lakes, Kaci N. Fitzgibbon

Electronic Theses and Dissertations

Understanding lake vulnerability with respect to eutrophication and loss of water quality is important for sustainability of aquatic ecosystems. This project aims at identifying and quantifying the effects of relevant physiochemical, climate, and watershed characteristics on lake vulnerability in order to develop management decision tools for the Maine Department of Environmental Protection (MEDEP). In a changing chemical and physical environment, using independent variables from each of these categories and then relating them to the summer lake epilimnetic phosphorus (P) concentrations allows for development of models to inform stakeholders of lake vulnerability to eutrophication problems.

We studied 24 lakes covering a …

Cellulose Nanofiber-Reinforced Impact Modified Polypropylene: Assessing Material Properties From Fused Layer Modeling And Injection Molding Processing, Jordan Elliott Sanders

Electronic Theses and Dissertations

The purpose of this research was to investigate the use of cellulose nanofibers (CNF) compounded into an impact modified polypropylene (IMPP) matrix. A IMPP was used because it shrinks less than a PP homopolymer during FLM processing. An assessment of material properties from fused layer modeling (FLM), an additive manufacturing (AM) method, and injection molding (IM) was conducted. Results showed that material property measurements in neat PP were statistically similar between IM and FLM for density, strain at yield and flexural stiffness. Additionally, PP plus the coupling agent maleic anhydride (MA) showed statistically similar results in comparison of IM and …

Geological Framework Of The Continental Shelf Of South Carolina Winyah Bay: Paleodrainage, Transgressions And Essential Fish Habitat, Amanda Roach

Electronic Theses and Dissertations

A regional geophysical survey of the inner continental shelf off central South Carolina was completed on a cooperative cruise between NOAA and Coastal Carolina University in July 2015. An integrated mapping suite comprised of subbottom echosounder, side scan, multibeam and split beam sonars was used to define the regional geologic framework, including paleodrainage patterns across the shelf and to identify potential fish habitat locations that will provide additional inputs to a thematic habitat mapping routine developed by NOAA. Results from the thematic mapper characterization suggest that large-scale framework elements such as paleochannel networks may play a role in determining benthic …

Only The Earth Remains: Exploring The Machine In Selected Lyric Poetry Of Robinson Jeffers, Mark Hutton

Electronic Theses and Dissertations

In The Machine in the Garden: Technology and the Pastoral Idea in America, Leo Marx “evaluates the uses of the pastoral ideal in the interpretation of American experience” (Marx 4). While Marx explores ways that pastoralism has been impacted by factors such as industrialism, it is the purpose of this project to explore Marx’s assertion regarding the presence of the figurative and literal machine within the poetry of Robinson Jeffers.

Jeffers’ poetry is generally located within the landscapes of California. His lyric poetry has a distinct connection to the land and is driven by inhumanism, which works to shift …

Study Of 2,5-Diaminoimidazolone, A Mutagenic Product Of Oxidation Of Guanine In Dna, Hannah Catherine J. Pollard

Electronic Theses and Dissertations

2,5-diaminoimidazolone (Iz) is an important product of a 4-electron oxidation of guanine. The present research focuses on the mechanisms of formation of Iz via pathways initiated by guanine oxidation by one-electron oxidants (OEOs) generated by X-ray radiolysis in aqueous solutions. The kinetics of formation and yields of Iz in reactions of native highly polymerized DNA with different OEOs have been compared using an HPLC-based quantitative analysis of low-molecular products generated from the reaction of DNA-bound Iz with primary amines. Mechanisms of Iz formation in DNA have been investigated including oxygen and superoxide dependence as well as the hypothesis that 8-oxo-G, …

Artificial Olfactory System For Multi-Component Analysis Of Gas Mixtures., Alexander Aleksandrovich Larin

Electronic Theses and Dissertations

Gas analysis is an important part of our world and gas sensing technology is becoming more essential for various aspects of our life. A novel approach for gas mixture analysis by using portable gas chromatography in combination with an array of highly integrated and selective metal oxide (MOX) sensors has been studied. We developed a system with small size (7 x 13 x 16 inches), low power consumption (~10 W) and absence of special carrier gases designed for portable field analysis (assuming apriori calibration). Low ppb and even sub-ppb level of detection for some VOCs was achieved during the analysis …

Transformation Of Nonlinear Waves In The Presence Of Wind, Current, And Vegetation, Haifei Chen

Electronic Theses and Dissertations

Accurate prediction of extreme wave events is crucial for the safe maritime activities and offshore operations. Improved knowledge of wave dissipation mechanisms due to breaking and vegetation leads to accurate wave forecast, protecting life and property along the coast. The scope of the thesis is to examine the wave transformations in the presence of wind, current, and vegetation, using a two-phase flow solver based on the open-source platform OpenFOAM. The Reynolds-Averaged Navier-Stokes (RANS) equations are coupled with a Volume of Fluid (VOF) surface capturing scheme and a turbulence closure model. This RANS-VOF model is adapted to develop a numerical wind-wave-current …

Geophysical Delineation Of Megaporosity And Fluid Migration Pathways For Geohazard Characterization Within The Delaware Basin, Culberson County, Texas, Jonathan David Woodard

Electronic Theses and Dissertations

ABSTRACT

Differential dissolution of gypsum karst within the Delaware Basin poses a significant threat to infrastructure that society depends on. The study area is located in Culberson County, Texas and traverses a distance of approximately 54 kilometers along RM 652 within the Gypsum Plain which is situated on the northern margin of the Chihuahua Desert and includes outcrops of Castile and Rustler strata that host karst geohazards. Regions of karst geohazard potential have been physically surveyed proximal to the study area in evaporites throughout the Castile Formation outcrop; minimal hazards, in comparison to the Castile Formation, have been documented in …

Water Chemistry Dynamics In Four Vernal Pools In Maine, Usa, Lydia H. Kifner

Electronic Theses and Dissertations

Vernal pools are small seasonal wetlands that are a common landscape feature that contribute to biodiversity in northeastern North American forests. However, even basic information about their biogeochemical functions, such as carbon cycling, is limited. Dissolved gas concentrations (CH₄, CO₂) and other water chemistry parameters were monitored weekly at the bottom and surface of four vernal pools in central and eastern Maine, USA, from April to August 2016. The vernal pools were supersaturated with respect to CH₄ and CO₂ at all sampling dates and locations. Concentrations of dissolved CH₄ and CO₂ ranged …

Evaluating Ligand Assisted Activation Of Small Molecules Through Proton Reduction And Alcohol Oxidation., Rahul Jain

Electronic Theses and Dissertations

Hydrogen is a potential alternate to the carbon fuels to meet the future demands for energy in an eco-friendly manner. Hydrogen produced by the electrolysis of water is stored in fuel cells which on demand can be converted into electrical energy upon the reaction with oxygen. In the quest for economically viable electrocatalysts for hydrogen evolution, the work in this dissertation describes evaluation of nickel based catalysts coordinated to redox active ligands, dialkyl/diarylphosphine benzenethiol and bis(thiosemicarbazone) for their ability to generate hydrogen with external acids as a proton source. A nickel complex with the benzenethiol ligand framework follows a traditional …

Authorship Identification Of Translation Algorithms., Keishin Nishiyama

Electronic Theses and Dissertations

Authorship analysis is a process of identifying a true writer of a given document and has been studied for decades. However, only a handful of studies of authorship analysis of translators are available despite the fact that online translations are widely available and also popularly employed in automatic translations of posts in social networking services. The identification of translation algorithms has potential to contribute to the investigation of cybercrimes, involving translation of scam messages by algorithmic translations to reach speakers of foreign languages. This study tested bag of words (BOW) approach in authorship attribution and the existing approaches to translator …

Greater London In The 21st Century : Assessing Coastal Flooding Mitigation Preparedness And Regional Population Risk In The Face Of Projected Sea-Level Rise., Nathan K Wright

Electronic Theses and Dissertations

Recent projections of +6-9m sea-level rise (SLR) over the next several decades present many social challenges for coastal regions during the 21^st century. These projections were applied to Greater London, UK as areal interpolated historical census data was overlaid on a 50m DEM alongside a polyline projection of the Thames Barrier. Population was projected to milestones of 2041, 2071, and 2101 using a capped, aggregated growth rate for each polygon while SLR was simulated for 1m, 5m, and 9m scenarios. The Thames Barrier maintained integrity for 1m and 5m scenarios but was breached at 9m. Population continued to increase …

Sample Size Calculations And Normalization Methods For Rna-Seq Data., Xiaohong Li

Electronic Theses and Dissertations

High-throughput RNA sequencing (RNA-seq) has become the preferred choice for transcriptomics and gene expression studies. With the rapid growth of RNA-seq applications, sample size calculation methods for RNA-seq experiment design and data normalization methods for DEG analysis are important issues to be explored and discussed. The underlying theme of this dissertation is to develop novel sample size calculation methods in RNA-seq experiment design using test statistics. I have also proposed two novel normalization methods for analysis of RNA-seq data. In chapter one, I present the test statistical methods including Wald’s test, log-transformed Wald’s test and likelihood ratio test statistics for …

Nonspreading Solutions In Integro-Difference Models With Allee And Overcompensation Effects., Garrett Luther Otto

Electronic Theses and Dissertations

Previous work in Integro-Difference models have generally considered Allee effects and over-compensation separately, and have either focused on bounded domain problems or asymptotic spreading results. Some recent results by Sullivan et al. (2017 PNAS 114(19), 5053-5058) combining Allee and over-compensation in an Integro-Difference framework have shown chaotic fluctuating spreading speeds. In this thesis, using a tractable parameterized growth function, we analytically demonstrate that when Allee and over-compensation are present solutions which persist but essentially remain in a compact domain exist. We investigate the stability of these solutions numerically. We also numerically demonstrate the existence of such solutions for more general …

Numerical Investigation Of Drop Impingement On Dry And Wet Surfaces., Yisen Guo

Electronic Theses and Dissertations

In-flight icing due to supercooled large droplets (SLDs) imposes great danger on aviation safety. Because of the large size, SLDs have different characteristics than typical cloud droplets that most icing encounters involve. As a result, SLDs more likely hit the wing surface and move into areas not protected by de-icing devices to form ice, which can lead to loss of lift, increase in drag, altered controllability, and eventually stall and loss of control of the aircraft. The phenomenon of droplet splashing is considered as the most important aspect of the SLD icing accretion problem. Although previous studies have established splashing …

Chemoselective Reagents For Derivatization Of Trace--Level Volatile Carbonyl Compounds Using A Microreactor Approach., Mumiye A. Ogunwale

Electronic Theses and Dissertations

Detection and analysis of trace level volatile aldehydes and ketones has become a significant research frontier because of the applicability for environmental monitoring and assessment, noninvasive diseases diagnosis, and in food safety assessment for the US Food and Drug Administration. The number of derivatization reagents for detection of aldehydes and ketones has increased considerably over the last decade. However, the majority of these derivatization reagents are not efficient in derivatizing unsaturated carbonyl compounds due to the presence of electron withdrawing groups adjacent to the reactive functional moieties making them insufficiently nucleophilic. The analysis of trace-level carbonyl compounds challenges existing analytical …