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 …

An Examination Of Geographic Patterns Of Soil Climate And Its Classification In The U.S. System Of Soil Taxonomy, Hans Edwin Winzeler

Open Access Dissertations

Soil climate, the record of temporal patterns of soil moisture and temperature, is an important component of the structure of U.S. Soil Taxonomy. The U.S. Soil Survey has used the Newhall Simulation Model (NSM) for estimating soil climate from atmospheric climate records at weather stations since the 1970s. The current soil climate map of the U.S. was published in 1994 by using NSM runs from selected weather stations along with knowledge-based hand-drawn mapping procedures. We developed a revised soil climate mapping methodology using the NSM and digital soil mapping techniques.

The new methodology is called Grid Element Newhall Simulation Model …

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 …

Is Metabolism Goal-Directed? Investigating The Validity Of Modeling Biological Systems With Cybernetic Control Via Omic Data, Frank T. Devilbiss

Open Access Dissertations

Cybernetic models are uniquely juxtaposed to other metabolic modeling frameworks in that they describe the time-dependent regulation of cellular reactions in terms of dynamic "metabolic goals." This approach contrasts starkly with purely mechanistic descriptions of metabolic regulation which seek to explain metabolic processes in high resolution — a clearly daunting undertaking. Over a span of three decades, cybernetic models have been used to predict metabolic phenomena ranging from resource consumption in mixed-substrate environments to intracellular reaction fluxes of intricate metabolic networks. While the cybernetic approach has been validated in its utility for the prediction of metabolic phenomena, its central feature, …

Crop Modeling For Assessing And Mitigating The Impacts Of Extreme Climatic Events On The Us Agriculture System, Zhenong Jin

Open Access Dissertations

The US agriculture system is the world’s largest producer of maize and soybean, and typically supplies more than one-third of their global trading. Nearly 90% of the US maize and soybean production is rainfed, thus is susceptible to climate change stressors such as heat waves and droughts. Process-based crop and cropping system models are important tools for climate change impact assessments and risk management. As data- science is becoming a new frontier for agriculture growth, the incoming decade calls for operational platforms that use hyper-local growth monitoring, high-resolution real-time weather and satellite data assimilation and cropping system modeling to help …

Advances In Solid Phase Microextraction For The Analysis Of Volatile Compounds In Explosives, Tire Treatments, And Entomological Specimens, William D. Kranz

Open Access Dissertations

Solid phase microextraction is a powerful and versatile technique, well-suited to the analysis of numerous samples of forensic interest. The exceptional sensitivity of the SPME platform, combined with its adaptability to traditional GC-MS systems and its ability to extract samples with minimal work-up, make it appropriate to applications in forensic laboratories.

In a series of research projects, solid phase microextraction was employed for the analysis of explosives, commercial tire treatments, and entomological specimens. In the first project, the volatile organic compounds emanating from two brands of pseudo-explosive training aids for use in detector dog imprinting were determined by SPME-GC-MS, and …

Hydrologic And Water Quality Impacts From Perennial Crop Production On Marginal Lands, Qingyu Feng

Open Access Dissertations

Marginal lands are proposed as a viable option for producing biofeedstocks as these lands are not heavily engaged in agricultural production or may not be suitable for intensive row-crop food/feed production. However, meeting biofeedstock production goals will require large amount of marginal lands and the unintended consequences of producing biofeedstocks on marginal lands are not fully clear. The overall goal of this study was to evaluate the productivity of biofeedstocks on marginal lands and the potential impacts on hydrologic and water quality processes from the land use conversion.

This study was conducted in the Upper Mississippi River Basin (UMRB). First, …

New Strategies To Reveal Protein Candidates In Protein-Protein Interactome Study, Meng-Chieh Chen

Open Access Theses

Comprehensive protein-protein interaction network analysis can help reveal protein functions in a system-wide manner. A reliable knowledgebase of interaction networks is not only important for selecting the candidates for drug therapies, but also for evaluating the disease risk. In current interaction databases, 322579 interactions comprised of 56460 proteins have been reported (statistical analysis from APID: Agile Protein Interaction DataAnalyzer; http://bioinfow.dep.usal.es/apid/index.htm). The huge datasets are contributed mainly by yeast -two -hybrid (Y2H) screening and affinity-purification followed by mass spectrometry (AP-MS). High false positive rates and failing to cover certain interaction categories are the limitations of these two methods. Here, we developed …

Liquid Swine Manure Application Timing And Instincttm Impacts On Net Soil Nitrogen Mineralization And Corn Yield, Min Xu

Open Access Theses

Nitrogen (N) is one of the most expensive variable input costs for corn production. Optimized manure management is essential to ensure maximum crop N utilization and to reduce the risk of N loss. A field study was conducted in central Indiana from 2011-2013 to assess liquid swine ( Sus scrofa L.) manure N availability when applied at different times or co-applied with InstinctTM , a microencapsulated form of nitrapyrin. Soil inorganic N contents, soil N mineralization, corn yield, grain N content, whole plant N concentrations of corn at the V6 growth stage, and ear leaf N concentrations of corn at …

Assessing Positional Accuracy And Correcting Point Data For Digital Soil Mapping At Varying Scales, Minerva J. Dorantes

Open Access Theses

Accuracy, timeliness, and the effect of scale of soil maps are rarely assessed. The recent increase in the use of GIS technologies and modelling software in natural resources and land management, has increased the demand for soil information at a finer resolution worldwide. Most of the world's developing countries rely on soils information at a scale that is too coarse for practical planning, and have obstacles impeding collection of new data, such as civil war and a lack of collection resources. The United States has an exhaustive collection of soils data at a fine scale. However, its location information is …

Vegetation And Soil Characteristics Of Pine Plantations And Naturally Regenerated Hardwood Forests On The Hoosier National Forest, Patrick James Duffy

Open Access Theses

During the 1930s there was widespread erosion on farmland and subsequent land abandonment. As a result, Pinus strobus L. (white pine), P. resinosa Aiton (red pine), and P. echinata Mill. (shortleaf pine) were planted in the Midwest to prevent erosion and rehabilitate sites. These species were selected due to their wide availability at the time. Currently, it is the goal of the U.S. Forest Service to provide a more natural and sustainable landscape, in part by removing these non-native Pinus stands and by replacing them with native hardwood species. The ultimate success of hardwood restoration depends, in part, on the …

Cosmogenic Beryllium Cycling In A Natural Forest Setting, Grace Conyers

Open Access Theses

10 Bemet , or cosmogenic beryllium, has a long half-life of 1.4 million years and quick adsorption on soil particles, which may make it ideal for dating soil erosion in historical context. However, there are questions on about the fundamental assumptions of the retentivity of 10 Bemet . This manuscript explores these assumptions and the context of nutrient cycling in a natural forest setting.

To see if 10 Bemet was being cycled through the trees, and at what rate, we looked at the[10 Bemet ] in the soil, 4 species of trees, and their leaves. The isotopic ratio 10 Be/9 …

Deforestation Of Cloud Forest In The Central Highlands Of Guatemala: Soil Erosion And Sustainability Implications For Q'Eqchi' Maya Communities, Ian Christopher Pope

Open Access Theses

Understanding the nexus between deforestation, food production, land degradation, and culture contributes knowledge that is useful for development practitioners working to enhance conservation and food security. Documenting deforestation and soil erosion in the Sierra Yalijux and Sierra Sacranix in the Central Highlands of Guatemala adds new knowledge about the rates and dynamics of deforestation and land degradation in areas with unique and sensitive cloud forest ecosystems. It also suggests possible areas of emphasis for efforts targeted at combining cloud forest conservation with sustainability for indigenous Q'eqchi' communities. In addition, this work contributes to a small but growing body of literature …

Oxidative Stress In Algae: Method Development And Effects Of Temperature On Antioxidant Nuclear Signaling Compounds, Md Noman Siddiqui

Open Access Theses

Non-enzymatic antioxidants neutralize the oxidative stress through scavenging reactive oxygen species. The structural complexity of non-enzymatic nuclear signaling antioxidants poses are more challenges for traditional quantitative analysis as these compounds have multiple forms and structurally diverse than proteins and therefore, challenge traditional analytical techniques. Current analytical methods cannot distinguish the carotenoids, and vitamin A and D metabolites within a single sample. To find an appropriate method to measure all the nuclear signaling compounds in algae, Isochrysis sp. , under thermal stress, HPLC/ESI-MS and HPLC /APPI-MS was used. Standards of those compounds were run by QQQ HPLC/ ESI-MS and HPLC /APPI-MS …

Study Of The Sustainbility Issues Of Food Production Using Vertical Farm Methods In An Urban Environment Within The State Of Indiana, Victor Mendez Perez

Open Access Theses

There are several problems around the globe related to water scarcity, energy shortages, deforestation and loss of fertile land, and food security. Climate change is making environmental and social issues arise. Issues such as, changes in the agricultural landscape, increasing population (9 billion is the expected population for 2040), rising food borne illnesses, scarcity of drinking water, and more crop failure due to plant pathogens and insect pests, among other factors make this study specially significant. Vertical farming could be a potencial solution to some of these problems.

Due to these problems the present thesis analyzed vertical farming as a …

Pharmaceuticals And Personal Care Products: Emerging Contaminants In Aquatic Ecosystems, Jenny E. Zenobio

Open Access Theses

In recent years, the presence of pharmaceuticals and personal care products (PPCPs) in aquatic systems has led to research on their fate and effects. PPCPs have been found in mixture in wastewater effluents, surface, ground, and drinking water at low concentrations from areas of intense urbanization. Although adverse effects to human health from the current environmental concentrations are unlikely, the impacts to ecological receptors are not clear. We performed field and laboratory studies to quantify and evaluate effects of PPCPs on fish. First, a field study was conducted at the Baca National Wildlife Refuge, Colorado (2010-2012) because a portion of …

Estimation Of Variation For High-Throughput Molecular Biological Experiments With Small Sample Size, Danni Yu

Open Access Dissertations

Motivation: In the quantification of molecular components, a large variation can affect and even potentially mislead the biological conclusions. Meanwhile, the high-throughput experiments often involve a small number of samples due to the limitation of cost and time. In such cases, the stochastic information may dominate the outcome of an experiment because there may not be enough samples to present the true biological information. It is challenging to distinguish the changes in phenotype from the stochastic variation.

Methods: Since the biological molecules have been quantified with different technologies, different statistical methods are required. Focusing on three types of important high-throughput …

Nitrogen And Potassium Dynamics Of Selected Indiana Soils, Chun Zhao

Open Access Dissertations

Nitrogen (N) is the most limiting essential nutrient for crop growth. Numerous studies have been performed to improve N fertilizer recommendations. Accurate prediction of soil N supply has been found to be one of the most important factors that determine optimum fertilizer N rates. Seven soils collected from various locations across Indiana at four different depths were tested for N mineralization potential. Results showed that laboratory mineralizable N in the top layer (0-15 cm) of the seven soils ranged from 50 to 68 mg N kg-1 soil. In addition, more than 50% of the total mineralizable N was contributed from …