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 …

Detangling The Interrelationships Between Self-Regulation And Ill-Structured Problem Solving In Problem-Based Learning, Xun Ge, Victor Law, Kun Huang

Interdisciplinary Journal of Problem-Based Learning

One of the goals for problem-based learning (PBL) is to promote self-regulation. Although self-regulation has been studied extensively, its interrelationships with ill-structured problem solving have been unclear. In order to clarify the interrelationships, this article proposes a conceptual framework illustrating the iterative processes among problem-solving stages (i.e., problem representation and solution generation) and self-regulation phases (i.e., planning, execution, and reflection). The dynamics of the interrelationships are further illustrated with three ill-structured problem-solving examples in different domains (i.e., information problem solving, historical inquiry, and science inquiry). The proposed framework contributes to research and practice by providing a new lens to examine …

Persistence Of Trace Organic Contaminants From A Commercial Biosolids-Based Fertilizer In Aerobic Soils, Travis A. Banet, Jihyun R. Kim, Michael L. Mashtare

The Summer Undergraduate Research Fellowship (SURF) Symposium

Municipal biosolids are recycled as agricultural fertilizers. Recent studies have raised concerns due to the presence of emerging contaminants in municipal biosolids. Previous research suggests that these contaminants have the potential to reside in biosolids-based fertilizers that are commercially distributed. Use of these products in urban/suburban areas may provide a pathway for these contaminants to enter ecosystems and impact human and environmental health. Soils from Purdue University’s community garden and MiracleGro Potting Mix were chosen to represent commonly used urban/suburban growth media. Triclosan, triclocarban, and methyl parabens were selected as compounds of interest for this study. A heat treated commercial …

Ifly: Code Development For An App To Support Automating Entomological Data Collection, Michael P. Cosentino, Trevor Stamper

The Summer Undergraduate Research Fellowship (SURF) Symposium

We are developing a prototype entomological data-collection application called "iFly," which runs on a field-capable iPad device. In this phase, we tackled refining screens and introducing a database manager to streamline operations as info is entered, stored, retrieved and delivered. We used SQLite3 database in Apple's Xcode Integrated Development Environment (IDE). Xcode gives mixed programming results. Apple's iOS environment ensures functional and fairly error-free apps can be built. But the sophisticated Xcode IDE requires specialist developers and valuable project time is spent as new programmers learn key techniques. The iFly prototype was advanced with improved database integration; however, more work …

Assembly Of Nucleic Acid-Based Nanoparticles By Gas-Liquid Segmented Flow Microfluidics, Matthew L. Capek, Ross Verheul, David H. Thompson

The Summer Undergraduate Research Fellowship (SURF) Symposium

The development of novel and efficient mixing methods is important for optimizing the efficiency of many biological and chemical processes. Tuning the physical and performance properties of nucleic acid-based nanoparticles is one such example known to be strongly affected by mixing efficiency. The characteristics of DNA nanoparticles (such as size, polydispersity, ζ-potential, and gel shift) are important to ensure their therapeutic potency, and new methods to optimize these characteristics are of significant importance to achieve the highest efficacy. In the present study, a simple segmented flow microfluidics system has been developed to augment mixing of pDNA/bPEI nanoparticles. This DNA and …

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 …

Manufacturer Perspectives On Content Transparency And Material Health In The Us Building Products Industry, Alexandra A. Muller

Open Access Theses

Flawed U.S. federal regulation of chemicals has resulted in a materials market that undervalues human and environmental health in favor of the more traditional attributes of price, performance and aesthetics. In the building products industry, global, dynamic supply chains and proprietary information concerns further complicate the task of assessing the material health of products.

Voluntary material health programs in the green building industry are intended to incentivize the manufacture and selection of safer products by getting companies to gather and assess ingredient, hazard and risk information from their supply chain. Building product manufacturers considered early adopters of the main material …

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 …

Enhancing Silymarin Fractionation Via Molecular Modeling Using The Conductor-Like Screening Model For Real Solvents, Emma C. Brace

Open Access Theses

The market for bio-based products from plant sources is on the rise. There is a global challenge to implement environmentally clean practices for the production of fuels and pharmaceuticals from sustainable resources. A significant hurdle for discovery of comparable plant-derived products is the extensive volume of trial-and-error experimentation required. To alleviate the experimental burden, a quantum mechanics based molecular modeling approach known as the COnductor-like Screening Model for Real Solvents (COSMO-RS) was used to predict the best biphasic solvent system to purify silymarins from an aqueous mixture. Silymarins are a class of flavonolignans present in milk thistle ( Silybum marianum …

Failure Of Surface Color Cues Under Natural Changes In Lighting, David H. Foster, Iván Marín-Franch

MODVIS Workshop

Color allows us to effortlessly discriminate and identify surfaces and objects by their reflected light. Although the reflected spectrum changes with the illumination spectrum, cone photoreceptor signals can be transformed to give useful cues for surface color. But what happens when both the spectrum and the geometry of the illumination change, as with lighting from the sun and sky? Is it possible, as a matter of principle, to obtain reliable cues by processing cone signals alone? This question was addressed here by estimating the information provided by cone signals from time-lapse hyperspectral radiance images of five outdoor scenes under natural …

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 …

Behavioral Responses And Policy Evaluation: Revisiting Water And Fuel Policies, Shanxia Sun

Open Access Dissertations

In my dissertation, I examine how policies regulating agricultural production and clean technology impact the environment. I focus on policies affecting water depletion, water pollution, and fuel consumption. I assess their cost-effectiveness by modeling and quantifying the behavioral responses of farmers and households.

My first essay focuses on decreasing groundwater depletion through increasing irrigation efficiency in Mexico. I quantify the impacts of different sources of inefficiency on groundwater extraction, and I evaluate the effectiveness of alternative policies that aim to reduce the over-extraction of groundwater. I find that mechanisms of electricity cost-sharing implemented in many wells have a sizable impact …

Economic And Environmental Impacts Of A Hypothetical Global Gmo Ban, Harrison H. Mahaffey

Open Access Theses

The objective of this research is to assess the global economic and greenhouse gas emission impacts of GMO crops. This is done by modeling two counterfactual scenarios and evaluating them apart and in combination. The first scenario models the impact of a global GMO ban. The second scenario models the impact of increased GMO penetration. The focus is on the price and welfare impacts, and land use change greenhouse gas (GHG) emissions associated with GMO technologies. Much of the prior work on the economic impacts of GMO technology has relied on a combination of partial equilibrium analysis and econometric techniques. …

Investigating U.S. Resident Perceptions Of Corporate Social Responsibility In Food And Agriculture, Carissa Jae Morgan

Open Access Theses

Corporations are prioritizing corporate social responsibility (CSR) activities by investing in and actively promoting their social practices. In the U.S. of the modern food supply chain creates a unique challenge for corporations to address concerns about social issues of consumers and non-consumers alike. This study is motivated by the need to better understand individuals’ perceptions of CSR as it pertains to the food supply chain. In April 2015 an online survey collected information from 1,201 U.S. residents with the objective of investigating individuals’ perceptions of relative importance of eight prominent CSR areas relevant to food and agriculture. Demographic, household consumption, …

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 …

Developing Probability Maps For Locating And Scouting Unprotected Areas Of Gravel Hill Prairies On Rodman Soils Along The Wabash River Valley Near Lafayette, Indiana, Ryan W.R. Schroeder

Engagement & Service-Learning Summit

No abstract provided.

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, …

Missing Gene Identification Using Functional Coherence Scores, Meghana Chitale, Ishita K. Khan, Daisuke Kihara

Department of Biological Sciences Faculty Publications

Reconstructing metabolic and signaling pathways is an effective way of interpreting a genome sequence. A challenge in a pathway reconstruction is that often genes in a pathway cannot be easily found, reflecting current imperfect information of the target organism. In this work, we developed a new method for finding missing genes, which integrates multiple features, including gene expression, phylogenetic profile, and function association scores. Particularly, for considering function association between candidate genes and neighboring proteins to the target missing gene in the network, we used Co-occurrence Association Score (CAS) and PubMed Association Score (PAS), which are designed for capturing functional …