Physical Sciences and Mathematics Commons^™

A Framework For The Statistical Analysis Of Mass Spectrometry Imaging Experiments, Kyle Bemis

Open Access Dissertations

Mass spectrometry (MS) imaging is a powerful investigation technique for a wide range of biological applications such as molecular histology of tissue, whole body sections, and bacterial films , and biomedical applications such as cancer diagnosis. MS imaging visualizes the spatial distribution of molecular ions in a sample by repeatedly collecting mass spectra across its surface, resulting in complex, high-dimensional imaging datasets. Two of the primary goals of statistical analysis of MS imaging experiments are classification (for supervised experiments), i.e. assigning pixels to pre-defined classes based on their spectral profiles, and segmentation (for unsupervised experiments), i.e. assigning pixels to newly …

Quantifying Terrestrial Ecosystem Carbon Dynamics With Mechanistically-Based Biogeochemistry Models And In Situ And Remotely Sensed Data, Shaoqing Liu

Open Access Dissertations

Terrestrial ecosystem plays a critical role in the global carbon cycle and climate system. Therefore, it is important to accurately quantify the carbon dynamics of terrestrial ecosystem under future climatic change condition. This dissertation evaluates the regional carbon dynamics by using upscaling approach, mechanistically-based biogeochemistry models and in situ and remotely sensed data.

The upscaling studies based on FLUXNET network has provided us the spatial and temporal pattern of the carbon fluxes but it fails to consider the atmospheric CO2 effect given its important physiological role in carbon assimilation. In the second chapter, we consider the effect of atmospheric CO2 …

Annual Forage Cropping-Systems For Midwestern Ruminant Livestock Production, John Ernest Mcmillan

Open Access Dissertations

Annual forage cropping systems are a vital aspect of livestock forage production. One area where this production system can be enhanced is the integration of novel annual forages into conventional cropping systems. Two separate projects were conducted to investigate alternative forage options in annual forage production. In the first discussed research trial, two sets of crops were sown following soft red winter wheat (Triticum aestivum L.) grain harvest, at two nitrogen application rates 56 and 112 kg ha-1 . The first set of crops were C4 summer annuals seeded within two weeks of wheat grain harvest and included, brown …

Characterizing The Effects Of Repetitive Head Trauma In Female Soccer Athletes For Prevention Of Mild Traumatic Brain Injury, Diana Otero Svaldi

Open Access Dissertations

As participation in women’s soccer continues to grow and the longevity of female athletes’ careers continues to increase, prevention of mTBI in women’s soccer has become a major concern for female athletes as the long-term risks associated with a history of mTBI are well documented. Among women’s sports, soccer exhibits the highest concussion rates, on par with those of men’s football at the collegiate level. Head impact monitoring technology has revealed that “concussive hits” occurring directly before symptomatic injury are not predictive of mTBI, suggesting that the cumulative effect of repetitive head impacts experienced by collision sport athletes should be …

Synthesis And Performance Of Novel Supramolecular Tools For Single-Particle Cryogenic Electron Microscopy And Drug And Gene Delivery, Kyle J. Wright

Open Access Dissertations

High-resolution biomacromolecular structure elucidation is fundamentally important to structure-based drug design and basic research into complex biochemical processes. Cryo-EM is an emerging alternative to XRD and NMR that is complementary in many ways relative to XRD and NMR. Materials approaches to cryo-EM are anticipated to greatly facilitate the cryo-EM process, allowing progress toward a more high-throughput application of cryo-EM to address challenges in structural biology. ^ Various affinity-based approaches inspired by approaches previously introduced for 2D crystallization were developed for facilitation of cryo-EM. A library of affinity lipopolymer constructs were synthesized consisting of lipopolymers of various PEG molecular weights conjugated …

Lower Food Web Dynamics In Lakes Michigan And Huron: Spatial And Temporal Responses To Recent Oligotrophication, Margaret Hutton Stadig

Open Access Theses

Nutrient abatement programs, originally enacted to counter eutrophication have successfully suppressed nutrient loads and relative primary production in marine and freshwater systems. Recently, the additive impacts of invasive filter feeders have further reduced offshore primary production in several aquatic systems throughout the world. It has been hypothesized that the biological activity of these invasive species may sequester nutrients within the nearshore benthic environment, creating steep gradients in primary production between nearshore and offshore habitats. In the Laurentian Great Lakes, past studies of oligotrophication have primarily focused on food web responses in offshore habitats. Organisms at higher trophic levels have been …

Mathematical Analysis Of Feedback Targets Of Bmp Signaling In Drosophila Embryonic Development, Yan Luo

Open Access Theses

Bone morphogenetic proteins (BMPs) drive a range of cellular processes especially in the early stages of embryonic development. This family of proteins acts as one of the most important extracellular signals in development pattern formation across the animal kingdom. Cells in embryos differentiate into different cell types in response to the concentration level of BMP. This complex process is regulated by multiple regulators that serve to tune the signal response.

Extensive experimental and computational research has been performed to analyze BMP regulation in Drosophila, a widely studied model organism, and has advanced our understanding of animal development. Because of …

Residual Effects Of Nitrogen Fertilization On Soil Nitrogen Pools And Corn Growth, Meghan E. Moser

Open Access Theses

Given the dynamic nature of soil nitrogen (N), inorganic N fertilization to corn (Zea mays L.) has potential to alter N pool balance by creating an accumulation or depletion of soil N. Current corn N recommendations in the common corn-soybean rotation of Indiana strive to find the best N rate that maximizes producer profit. Increasing our understanding of soil N will inform producers if they should adjust fertilizer rates for corn to influence maintenance of organic N and Carbon. Our objective was to determine residual N effects from fertilized corn in a corn-soybean rotation by measuring (1) soil N …

Gonadal Intersex In Teleosts: Mechanisms, Molecular Biomarkers And Diagnostic Assays, Ahmed M.E. Abdel-Moneim Mohamed

Open Access Dissertations

Natural and synthetic estrogenic and androgenic compounds are continuously released into aquatic ecosystems. Exposure of teleost fishes to these contaminants can negatively impact sex differentiation and reproductive output. Specifically, development of gonadal intersex in gonochoristic (fixed sex) fish species has been studied extensively in relation to exposure to this class of compounds. The main objectives of this dissertation were to: 1) conduct field and laboratory studies to investigate the molecular signaling pathways behind the development of gonadal intersex; and 2) establish molecular biomarkers and assays for testing the ability of environmental pollutants to develop this condition using a battery of …

A Study Of Short-Season Winter Cover Crops For Organic High Tunnel Production Systems, Luke Riley Freeman

Graduate Theses and Dissertations

This two-year study investigated short-season winter cover crops to improve soil quality and growth of subsequent vegetable crops in an organic high tunnel production system. Five winter cover crop treatments including a nontreated control, Austrian winter peas (Pisum arvense), bell beans (Vicia faba), mustard (Brassica juncea cv. Kodiak), and Daikon radish (Raphanus sativus var. longipinnatus) were grown in a high tunnel in a randomized complete block design from mid-November to mid-March, mowed and incorporated into the soil, and followed by a succession of vegetable crops including tomato (Lycopersicon lycopersicum, cv. ‘Plum Dandy’) and broccoli (Brassica oleracea var. italica, cv. ‘Bay …

Liming Characteristics Of A High-Calcium, Dry Flue Gas Desulfurization By-Product And Its Effects On Runoff Water Quality, Jason Richard Burgess-Conforti

Graduate Theses and Dissertations

In 2013, only 37% of the 32 million Mg of flue gas desulfurization (FGD) by-products generated in the United States were reused beneficially. If FGD by-products could be used as a beneficial soil amendment, millions of megagrams may be diverted away from surface impoundments and landfills. The purpose of this research was to identify the liming characteristics of a high-Ca dry FGD (DFGD) by-product in comparison to a Class-C fly ash (FA) and reagent-grade CaCO3, and to evaluate the effects of land application to a managed grassland on runoff, plant, and soil quality. Liming characteristics were determined by measuring the …

Soil And Plant Property Differences Among High-Yield Soybean Areas In Arkansas, Taylor Cass Adams

Graduate Theses and Dissertations

Continued achievement of soybean [Glycine max (L.) Merr.] yields greater than 6719 kg ha-1 (100 bu ac-1) will depend on decreasing the yield gap, which is contingent on gathering more information regarding the soil physical, chemical, and microbiological environment and the main plant factors contributing to high-yield soybean. Therefore, understanding the main factor differences between high- and average-yield areas may provide insight for making management decisions to increase yields. The objectives of this study were i) to evaluate the effects of region and soil depth on soil property differences between high- and average-soybean-yielding areas, ii) to determine which soil properties …

Cover Crop Establishment And Potential Benefits To Arkansas Farmers, Ashley Elizabeth Humphreys

Graduate Theses and Dissertations

Soybean farmers in Arkansas need best management practices (BMPs) that maximize the benefits of using cover crops including planting date and fertilization recommendations. An evaluation of cover crop species, planting dates, seeding rates, fertilizer rates, and N accumulation aids in providing these BMPs. The first objective of this research is to assess the effect of planting date on biomass production, as well as looking at the interaction of seeding rate or fertilizer rate for legumes or non-legumes, respectively, using Austrian winter pea (Pisum sativum), cereal rye (Secale cereale), black oats (Avena strigosa), wheat (Triticum aestivum), and tillage radish (Raphanus sativus). …

Intestinal Adaptation To Repeated Exposure Of Flavonoid-Rich Foods: In Vitro And Clinical Data, Bejamin W. Redan

Open Access Dissertations

Interest in application of flavonoids for chronic disease prevention has grown significantly, but the low oral bioavailability of these compounds from acute doses is commonly highlighted as a limitation when considering their biological significance. Still, the impact of broad dietary patterns such as repeated exposure on flavonoid’s absorption, metabolism, and eventual efficacy is critical to consider since evidence suggests that their bioavailability may be enhanced with repeated exposure. To fill this gap in knowledge, this dissertation will focus on three major areas including characterization of flavonoid metabolites, in addition to use of in vitro models and clinical work to test …

Evolutionary Potential Of A Dispersal-Restricted Species In Response To Climate Change, Lorena Torres Martinez

Open Access Dissertations

Habitat replacement and fragmentation associated with projected climate change pose a critical threat to global biodiversity. Edaphically limited plant species with restricted dispersal abilities will be especially handicapped to track their optimal climate spatially. Instead, the persistence of these species will depend on their capacity to adapt in situ to novel climate regimes. Here I evaluated the evolutionary potential of Lasthenia fremontii, an annual plant species restricted to ephemeral wetlands called vernal pools in California to adapt to the projected patterns of climate change. Across L. fremontii distribution there is a latitudinal gradient in precipitation which, combined with reduced …

Learning From Data: Plant Breeding Applications Of Machine Learning, Alencar Xavier

Open Access Dissertations

Increasingly, new sources of data are being incorporated into plant breeding pipelines. Enormous amounts of data from field phenomics and genotyping technologies places data mining and analysis into a completely different level that is challenging from practical and theoretical standpoints. Intelligent decision-making relies on our capability of extracting from data useful information that may help us to achieve our goals more efficiently. Many plant breeders, agronomists and geneticists perform analyses without knowing relevant underlying assumptions, strengths or pitfalls of the employed methods. The study endeavors to assess statistical learning properties and plant breeding applications of supervised and unsupervised machine learning …

Nutrient Runoff And Leachate After Land-Application Of Digestate In A Laboratory Study Using Rainfall Simulations, Min Xiao

Open Access Theses

There has been an increasing number of anaerobic digesters on livestock farms in the United States during the past two decades. Anaerobic digestion of manure allows production of renewable energy and generation of stabilized and nutrient-rich digestate that can be used as organic fertilizer. However, the majority of the existed studies using liquid digestate as fertilizer only focused on the effectiveness for crop yield, nutrient content and microorganism in soil. There is insufficient understanding in the environmental impact of digestate land-application. This laboratory study used six treatments including four different liquid digestate treatments, a chemical fertilizer treatment, and an unfertilized …

Investigation Of Cellular Microenvironments And Heterogeneity With Biodynamic Imaging, Daniel Alexander Merrill

Open Access Dissertations

Imaging of biological tissue in a relevant environment is critical to accurately assessing the effectiveness of chemotherapeutic agents in combatting cancer. Though many three-dimensional (3D) culture models exist, conventional in vitro assays continue to use two-dimensional (2D) cultures because of the difficulty in imaging through deep tissue. 3D tomographic imaging techniques exist and are being used in the development of 3D efficacy assays. However, most of these assays look at therapy endpoint (dead or living cancer cell count) and do not capture the dynamics of tissue response.

Biodynamic imaging (BDI) is a 3D tomographic imaging and assay technique that uses …

South Padre Island Beach Management: Assessment Of Dune Restoration, Shelby Rose Bessette

Theses and Dissertations

Dune restoration is a common method of increasing coastal resilience. A dune restoration program was initiated by the City of South Padre Island, TX in 2010 consisting primarily of plantings of Sea Oats, Uniola paniculata, and Bitter Panicum, Panicum amarum and has continued approximately annually thereafter. These restoration efforts were evaluated in this study by comparing dune ecological structure and function among reference sites and restoration plots ranging in age from 2 to 5 years. Plant and animal communities were examined using a combination of quadrat sampling, funnel traps, pit-falls and sweep nets. Soil organic content and soil electric …

The Impact Of Climate Change In Bangladesh On The Rice Market And Farm Households, Mst Ashrafun Nahar

Graduate Theses and Dissertations

Bangladesh is trying to achieve self-sufficiency in domestic rice production but climate change effects on agricultural production makes it challenging to attain the goal. The country is highly vulnerable to the effects of climate change since it is the major cause to rise in sea level, more warm summer, and happening food and cyclone in the country.

This study develops an Aggregate Farm Household Model to analyze the impact of potential land loss and yield reduction from climate change on production, consumption, prices, welfare, and the ability of government to achieve self-sufficiency in rice production. The model is calibrated to …

Stream Microbial Communities As Potential Indicators Of River And Landscape Disturbance In North-Central Arkansas, Wilson Howard Johnson

Graduate Theses and Dissertations

In the past decade, 29 shale basins have been actively developed across 20 states for extraction of natural gas (NG) via horizontal drilling/hydraulic fracturing (=fracking). This includes ~5000 wells within the Fayetteville shale of north-central Arkansas. Development often impacts both river- and landscapes, and management requires catchment-level evaluations over time, with organismal presence/absence as indicators. For this study next-generation sequencing was used to identify/characterize microbial communities within biofilm of eight Arkansas River tributaries, so as to gauge potential catchment influences. Streams spanned a gradient of landscape features and hydrological flows, with four serving as ‘potentially impacted catchment zones’ (PICZ) and …

Determination Of Optimum Fall And Spring Nitrogen Fertilizer Rate For Maximizing Grain Yield Of Soft Red Winter Wheat Sown At Variable Planting Dates, Lucas Vasconcelos Vieira

Graduate Theses and Dissertations

An optimum planting date is important for winter wheat nitrogen (N) management as it dramatically changes the growing environment including temperature and moisture, ultimately affecting fertilizer efficiency and grain yield (GY). In Arkansas, high precipitation in the fall often forces farmers to delay planting and current Arkansas recommendations include the application of fall N when soft red winter wheat (SRWW) is sown later than optimum, despite the lack of data supporting this practice. This study evaluated the effect of rate and timing of N application on GY of SRWW sown at variable planting dates in Arkansas. Granular urea was split …

Agro-Climatic Change, Crop Production And Mitigation Strategies-Case Studies In Arkansas, Usa And Kenya, John Westley Magugu

Graduate Theses and Dissertations

Although climate change impacts vary geographically and temporally, studies at local levels are not readily available for stakeholders to better understand how their local communities would be affected and what remedial measures could be more effective in their local contexts. This dissertation has examined climate change and its impacts in two different local contexts: eastern Arkansas in the USA and Nyando in Kenya. The first part of this dissertation develops agro-meteorological indicators and examines the relationship between agro-meteorological indicators and crop yields in eastern Arkansas between 1960 and 2014. Results reveal that temperature based indicators were more strongly correlated to …

Eucalyptus In Kenya; Impacts On Environment And Society, Brandy M. Garrett Kluthe

Graduate Theses and Dissertations

Eucalyptus trees were introduced to Kenya a little over a century ago. European colonization along with the development of a railway system increased the demand for a fast growing wood source. The expansion of the tree across the fertile lands in Kenya raises concerns about the environmental impact on ecosystems where it has been introduced. These concerns include degraded soils, loss of water resources, co-introduction of ectomycorrhizal species, and allelopathy. Economic benefits to local landowners were also explored as well as the potential for large Eucalyptus woodlots to maximize the sequestration of CO₂ from the atmosphere. This was examined through …

Design Of A Nutrient Reclamation System For The Cultivation Of Microalgae For Biofuel Production And Other Industrial Applications, Heather Sandefur

Graduate Theses and Dissertations

Microalgal biomass has been identified as a promising feedstock for a number of industrial applications, including the synthesis of new pharmaceutical and biofuel products. However, there are several economic limitations associated with the scale up of existing algal production processes. Critical economic studies of algae-based industrial processes highlight the high cost of supplying essential nutrients to microalgae cultures. With microalgae cells having relatively high nitrogen contents (4 to 8%), the N fertilizer cost in industrial-scale production is significant. In addition, the disposal of the large volumes of cell residuals that are generated during product extraction stages can pose other economic …

Geospatial Analysis Of Droughts, Rice And Wheat Production, And Agrarian Vulnerability: A District-Level Study Of The Self-Calibrated Palmer Drought Severity Index In India, Aaron Michael Shew

Graduate Theses and Dissertations

Droughts have affected more people than any other natural disaster in the last century, causing billions in economic damages and millions of deaths. As the Sea Surface Temperatures (SST) have heated in the Indian Ocean, drought patterns across South Asia have changed; the Indian monsoon has become more volatile and less predictable. In this study, monthly self-calibrated Palmer Drought Severity Index (sc-PDSI) data for the time period between 1950 and 2009 were interpolated to India’s districts; then the data were analyzed for changes in frequency and severity. The data were further evaluated using Anselin’s Local Moran’s I Statistic to elicit …

Dissemination And Persistence Of Plasmid Located, Integron Associated Antibiotic Resistant Genes In Wastewater Treatment Plant Effluent And Stream Water Bacteria, _ Suhartono

Graduate Theses and Dissertations

Transmissible plasmid-mediated integrons play important role in the persistence and dissemination of antibiotic resistance throughout the environment. Plasmids from 139 multi-antibiotic resistant Escherichia coli recovered from wastewater treatment plant effluent and upstream and downstream receiving stream water in Northwest Arkansas were extracted and profiled. Genes of class 1 and class 2 integrase (intI), mobilization (mob), sulfamethoxazole resistance (sul), and trimethoprim resistance (dfr) were detected using PCR and confirmed through DNA sequencing. Plasmids from almost half of the isolates (47%) were transmissible with mobF12 gene as the most frequently detected mobilization gene. Plasmid-borne class 1 with and without class 2 integrons …

Dietary Effects On The Stoichiometry Of Growth, Regulation, And Wastes Of Ozark Stream Insect Detritivores, Halvor Matthew Halvorson

Graduate Theses and Dissertations

A widespread stressor, anthropogenic nitrogen (N) and phosphorus (P) pollution can increase resource nutrient content and alter animal community composition in freshwater ecosystems. In this dissertation, I used ecological stoichiometry theory to examine effects of diet nutrient content and leaf litter type on growth, regulation, and wastes of aquatic invertebrate detritivores. I tested effects of leaf litter diet carbon:phosphorus (C:P) on growth and stoichiometric regulation of the detritivorous caddisfly Pycnopsyche lepida and used results to determine a threshold elemental ratio of oak litter C:P=1620 that confers peak growth of this species. This empirical, growth-based approach provided a more accurate estimate …

The Role Of Hydrologic Regimes In Driving Morphologic Divergence And The Trait Compositions Of Fish Assemblages, Lindsey A. Bruckerhoff

Graduate Theses and Dissertations

The hydrologic regime is an important determinant of the ecological integrity of a stream. Hydrologic regimes are defined by the magnitude, timing, frequency, rate of change, and duration of high and low flow events and capture long term patterns of variability and predictability of water movement in a stream. Flow regimes influence many aspects of the biophysical environment in lotic systems; therefore organisms have adapted to natural flow patterns. We investigated how fish have adapted to flow regimes at both a population and community level. In the first study presented in this thesis, we hypothesized fish exhibit phenotypic divergence to …

Identification Of Biomarkers For The Overall Survival Of Ovarian Cancer Patients, Kristi Mai

Graduate Theses and Dissertations

Rapid advance in sequencing technology has led to genome-wide analysis of genetic and epigenetic features simultaneously, making it possible to understand the biological mechanisms underlying cancer initiation and progression. However, how to identify important prognostic features poses a great challenge for both statistical modeling and computing. In this thesis, a network-based approach is applied to the Cancer Genome Atlas (TCGA) ovarian cancer data to identify important genes related to the overall survival of ovarian cancer patients. In the first step, a stepwise correlation-based selector is used to reduce the dimensionality of TCGA data, by filtering out a large number of …