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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 …

Authentic Science In Education: Studies In Course-Based Research At The United States Military Academy, Anthony M. Chase

Open Access Dissertations

This dissertation consists of two studies at the United States Military Academy. Both studies involve the use of Course-based Undergraduate Research Experiences (CUREs). These experiences give students the ability to engage in undergraduate research at an early point in their academic career by replacing traditional laboratory activities with semester-long research projects. Both studies show an implementation of this type of instruction from the Center for Authentic Science Practice in Education (CASPiE). Study 1 shows the specific method of implementation at the military academy and explores learning-based outcomes. Primarily the outcome of critical thinking is demonstrated. Critical thinking is a construct …

Exploring The Potential Impacts Of Climate Change On North America's Laurentian Great Lakes Tourism Sector, Natalie Chin

Open Access Dissertations

Climate change is one of the major challenges facing the global hospitality and tourism sector in the coming century and, given the important role that weather and climate play in all aspects of the tourism experience, tourism businesses owners need to start thinking about and enacting climate change adaptation strategies now. This work has utilized a combination of social science and physical science methods to (1) understand how the Great Lakes tourism sector could be impacted by climate change and (2) provide some insights into how researchers can help business owners prepare for these potential impacts. Overall, the results of …

The Role Of African Leafy Vegetables In Food Security, Marcia M. Croft

Open Access Dissertations

African leafy vegetables (ALVs) are a diverse set of crops grown across sub-Saharan Africa. They have been a staple of traditional diets and contain many critical micronutrients but their importance has been largely ignored by researchers and policymakers at the expense of imported crops. Availability, accessibility, and utilization of ALVs are limited by factors across the supply chain. This research investigated seed systems, drought tolerance, hydroponic production, market barriers, consumer preference, and the impact of gender as related to ALVs. We found that ALVs play an important role in food security and that critical differences exist between formal and informal …

Physiological Aspects Of Relative Changes In Nitrogen And Plant Density Stress Tolerances Over A 38-Year Period Of Us Maize Hybrid Introductions, Keru Chen

Open Access Dissertations

Incremental gains in grain yield of maize hybrids over the decades are the consequence of genotype, environment and management interactions. Historically, genetic improvements in newer hybrids have included longer active grain filling periods (achieved by advancing silking and extending functional stay green in maize leaves); stronger source and sink during grain filling; enhanced tolerance to higher density; and canopy architecture changes. Newer hybrids were known to accumulate more dry matter and nitrogen in the post-silking period, but achieving a more comprehensive knowledge of pre-silking and post-silking dynamics required further understanding of dry matter and nitrogen partitioning in individual organs, as …

Nanoparticle Toxicity And Molecular Mechanisms In Fish: A Case Study With Silver Nanoparticles, Jiejun Gao

Open Access Dissertations

Nanoparticles (NPs) are widely used in a myriad of commercial and industrial products making their entry to the environment a likely event. NPs have unique physical-chemical properties that result from their small size and high surface area to volume ratio, making them highly reactive and potentially toxic. In Chapter 1, we summarize the effects and mechanisms of metal-based NPs on the vascular system. In vitro studies have shown that NPs are anti-angiogenic because they cause inflammation, oxidative stress, and apoptosis of endothelial cells resulting in increased permeability and decreased proliferation and migration. Whole animal studies examining the effects of NPs …

Syk Promotes Tgf-Beta-Induced P-Body Clearance In Breast Cancer Cells Through The Enhancement Of Autophagy, Shana D. Hardy

Open Access Dissertations

SYK is a protein tyrosine kinase that plays an essential role in the development and activation of immune cells. Its expression, however, is not limited to immune cells. SYK is expressed in a variety of epithelial cell types and epithelial-derived tumors. Reports regarding the role of SYK expression in these diverse cell types and tumors have been opposing. In breast cancer, SYK expression has been overwhelmingly associated with tumor suppression. The loss of Syk expression is observed in invasive breast carcinoma tissue and cell lines and the reintroduction of Syk into metastatic breast cancer cells suppresses tumor growth and metastasis. …

Low Rank Methods For Optimizing Clustering, Yangyang Hou

Open Access Dissertations

Complex optimization models and problems in machine learning often have the majority of information in a low rank subspace. By careful exploitation of these low rank structures in clustering problems, we find new optimization approaches that reduce the memory and computational cost.

We discuss two cases where this arises. First, we consider the NEO-K-Means (Non-Exhaustive, Overlapping K-Means) objective as a way to address overlapping and outliers in an integrated fashion. Optimizing this discrete objective is NP-hard, and even though there is a convex relaxation of the objective, straightforward convex optimization approaches are too expensive for large datasets. We utilize low …

Concurrent Detection And Isolation Of Cellular And Molecular Biomarkers, Wanfeng Huang

Open Access Dissertations

Detection of cancer markers such as protein biomolecules and cancer cells in bodily fluids is of great importance in early diagnosis, prognosis as well as evaluation of therapy efficacy. Numerous devices have been developed for detecting either cellular or molecular targets, however there has not yet been a system that can simultaneously detect both cellular and molecular targets effectively. Molecule and cell-based assays are important because each type of target can tell a different story about the state of the disease and the two types of information can potentially be combined and/or compared for more accurate biological or clinical assessments. …

Modeling For Thermal Resistance Of Non-O157 Shiga Toxin Producing Escherichia Coli In Ground Beef, Jagpinder S. Brar

Open Access Dissertations

Predictive models in microbiology are used for estimating the growth or survival of microorganism in a set of environmental conditions. A validated predictive model provides an alternative to extensive survival and shelf life studies. In this study, a predictive inactivation model for non-O157 shiga toxin producing Escherichia coli (STEC) in ground beef was developed. Six strains of non-O157 STEC; E. coli O26:H1, E. coli O45:H2, E. coli O103:H2, E. coli O111:H8, E. coli O121:H9, and E. coli O145: nonmotile, has similar pathogenicity as E. coli O157:H7 and can cause serious food borne illnesses. These pathogens are considered as an adulterant …

Exploring The Cause Of Injury Or Death In Grain Entrapment, Engulfment And Extrication, Salah F. Issa

Open Access Dissertations

Grain entrapments and engulfments are one of most common hazards associated with grain storage facilities. Since the 1970’s over 1,880 incidents have been documented in agricultural confined spaces of which 65% of all recorded incidents were grain entrapments and engulfments. There have been several studies conducted on the contributing factors behind these incidents; however, there have been very few attempts to understand the environmental, physiological or psychological factors the victims experience while entrapped, engulfed, or extricated. This includes understanding how secondary injuries are caused by grain or during extrication by first responders. The research effort was divided into three segments. …

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 …

Ambient Ionization - Mass Spectrometry: Advances Toward Intrasurgical Cancer Detection, Alan Keith Jarmusch

Open Access Dissertations

My dissertation research has focused on the development of ambient ionization – mass spectrometry (MS) for clinical measurements, specifically intrasurgical cancer detection. The molecular differences between normal and cancerous tissue were detected via direct tissue analysis in vitro by touch spray ionization (TS) or by analyzing sectioned or smeared tissue using desorption electrospray ionization (DESI). The physical form of the tissue, e.g. in vitro sampling, sectioned, or smeared, was inconsequential in differentiating normal from cancerous tissue; however, the spectra acquired by TS and DESI differed due to differences in ionization processes. We envision that TS-MS and DESI-MS could impact diagnostic …

Functional And Structural Characterization Of The Mevalonate Diphosphate Decarboxylase And The Isopentenyl Diphosphate Isomerase From Enterococcus Faecalis, Chun-Liang Chen

Open Access Dissertations

Enterococcus faecalis causes a diverse range of nosocomial infections (in wounds, the gastrointestinal tract, the blood stream and the endocardium), and multidrug-resistant strains have become a serious issue across countries. Vancomycin, a FDA-approved drug for the disruption of the bacterial cell wall biosynthesis, has been utilized to treat infectious diseases caused by Enterococci; however, the prevalence of vancomycin-resistant enterococci (VRE) threatens communities all over the world. We aim at developing novel therapeutic strategies to control bacterial growth of Enterococci, and we focus on targeting two essential enzymes involved in poly-isoprenoid biosynthesis in Enterococcus faecalis; one is the mevalonate diphosphate decarboxylase …

Redox-Active Ligand Uranium Complexes For Approaches To Multi-Electron Chemistry, John J. Kiernicki

Open Access Dissertations

While transition metal complexes are known to participate in multi-electron redox chemistry to facilitate important organometallic transformations, actinides, due to their low redox potentials, have a propensity to perform single electron chemistry. Because of its highly reducing nature, the ability to control the electronics of low-valent uranium is highly sought after as this may lead to unprecedented reactivity. Our lab has specifically been interested in mediating multi-electron transformations at uranium by employing redox-active ligands. Redox-active ligands can be used to facilitate multi-electron processes such as oxidative addition and reductive elimination at single metal centers. Using primarily 2,6-((Mes)N=CMe)2C5H3N) ( MesPDIMe) as …

Optimal Design Of Sound Absorbing Systems With Microperforated Panels, Nicholas Nakjoo Kim

Open Access Dissertations

As the development of technology makes economic prosperity and life more convenient, people now desire a higher quality of life. This quality of life is based not only on the convenience in their life but also on clean and eco-friendly environments. To meet that requirement, much research is being performed in many areas of eco-friendly technology, such as renewable energy, biodegradable content, and batteries for electronic vehicles.

This tendency is also obvious in the acoustics area, where there are continuing attempts to replace fiber-glass sound absorbers with fiber-free materials. The combination of microperfoated panels (MPP) (one of the fiber-free sound …

Device Design Factors For Enhancing The Functionality Of Chronic Intracortical Microelectrodes, Heui Chang Lee

Open Access Dissertations

Intracortical microelectrodes are devices used in brain-computer interfaces (BCI) to help regain lost motor, sensory, and cognitive functions of individuals with neurological disorders. However, the long-term performance of microelectrode arrays is hampered by a series of inflammatory tissue responses. The consequence of the inflammatory response is the formation of a dense astroglial sheath around the vicinity of the electrode, impeding the electrical conduction between the electrode and neurons. Furthermore, due to the cascade of neuroinflammatory events, the number of neurons is significantly reduced near the electrode, manifested by decrease in signal-to-noise ratio (SNR) and the yield of electrodes. Over time, …

The Development Of Preclinical Strategies For Facilitation Of Lead Candidate Selection, Christopher Dale Kulczar

Open Access Dissertations

Chapter 1 details a background of techniques used for modeling the blood-brain barrier (BBB). The BBB represents a diffusive barrier to both paracellular and transcellular movement of many compounds in and out of the brain. The main rate- limiting barriers of the BBB include exclusive tight junctions that prevent the movement of hydrophilic molecules through intercellular gaps, and efflux proteins in the membrane which pump many hydrophobic molecules back into the blood. In addition, the BBB contains metabolizing enzymes, including Cytochrome P450s. This barrier acts to protect the vulnerable tissues of the brain from harmful xenobiotics, but also can serve …

Functional Diversity Enhances Detection Of Ecosystem Stability And Resolution Of Predator-Prey Interactions Within A Multitrophic Community, Ashley Lorraine Kissick

Open Access Dissertations

Habitat fragmentation and loss are principal factors that contribute to the decline of biodiversity which in turn has a negative impact on ecosystem function. There has been growing interest in understanding diversity’s role in the mechanisms behind ecosystem resilience with much attention focusing on how functional diversity, or the range of species’ ecological roles in a community, impacts ecosystem function. Under the functional insurance hypothesis, stability in ecosystems is maintained by species that perform similar functions but have asynchronous responses to disturbance. There are three proposed stability mechanisms that operate through species’ asynchronous responses: cross-scale resilience, response diversity, and density …

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 …

College Students' Suicidal Ideation: Testing The Predictions Of The Existential - Constructivist Theory Of Suicide, Jennifer Danielle Lockman

Open Access Dissertations

Suicide is the second leading cause of death in the college student population (Schwartz, 2006), and empirically supported theories for understanding suicide among college students are lacking (Lester, 1989; Prinstein, 2008; Rogers & Benson, 2013). Although not yet examined empirically, Rogers (2001) proposed an Existential - Constructivist Theory of Suicide (ECTS), in which existential distress and the inability to reconstruct meaning from adverse life events contribute to suicidal ideation. ECTS includes both interpersonal and intrapersonal drivers of suicidal ideation, and for this reason, may better explain suicidal ideation in college students than existing theoretical models. Existing research focuses on Joiner’s …

Hydrodynamics Of Swimming Microorganisms In Complex Fluids, Gaojin Li

Open Access Dissertations

Swimming motion of microorganisms, such as spermatozoa, plankton, algae and bacteria, etc., ubiquitously occurs in nature. It affects many biological processes, including reproduction, infection and the marine life ecosystem. The hydrodynamic effects are important in microorganism swimming, their nutrient uptake, fertilization, collective motions and formation of colonies. In nature, microorganisms have evolved to use various fascinating ways for locomotion and transport. Different designs are also developed for the locomotion of artificial nano- and microswimmers. In this study, we use several different computational models to investigate the behavior of microswimmers.

Microorganisms typically swim in the low Reynolds number regime, where inertia …

Managing Bacterial Wilt, Caused By Erwinia Tracheiphila, On Muskmelon With Early Control Of Striped Cucumber Beetle ( Acalymma Vittatum (F)), And Through Varietal Selection, Ahmad Shah Mohammadi

Open Access Dissertations

Muskmelon (Cucumis melo L), is an important vegetable crop in the United States. It is grown throughout the US, and Indiana ranked 4th in production after California, Arizona and Georgia with 12.4 thousand metric tons and market value of $7.6 million in 2015. Bacterial wilt of cucurbits, which is caused by Erwinia tracheiphila (E. F. Smith), and vectored by striped cucumber beetle (Acalymma vittatum (F)), is one of the most serious diseases of muskmelon that influences muskmelon quality and yield. Many cultivars of muskmelon are grown around the United States, especially in the Midwest. Muskmelon cultivars differ in …

Bayesian Causal Inference Of Cell Signal Transduction From Proteomics Experiments, Robert D. O. Ness

Open Access Dissertations

Cell signal transduction describes how a cell senses and processes signals from the environment using networks of interacting proteins. In computational systems biology, investigators apply machine learning methods for causal inference to develop causal Bayesian network models of signal transduction from experimental data. Directed edges in the network represent causal regulatory relationships, and the model can be used to predict the effects of interventions to signal transduction. Causal inference approaches applied to proteomics experiments use statistical associations between observed signaling protein concentrations to infer a causal Bayesian network model, but there is no experimental and analysis framework for applying these …

Poetry Matters: Radical Politics In Postmodern American Poetry, Christopher J. Padgett

Open Access Dissertations

Directly or indirectly, poetry produced in the postmodern era is implicated in the politics of the time. Postmodern American poetry, then, is not reducible to a single poetic mode or to a specific set of stylistic features. In other words, a more comprehensive understanding of postmodern American poetry can be made by employing a flexible version of Raymond Williams’ notion of uneven development, a theory that insists on the synchronic existence of dominant, residual, and emergent cultural elements. As the stylistically and politically diverse work of the six poets—Susan Howe, Robert Grenier, Gary Snyder, A.R. Ammons, Sherman Alexie, and Kenneth …

Laser-Processed Parchment Paper For Fabrication Of Chronic Wound Dressings With Selective Oxygenation, Manuel Ochoa

Open Access Dissertations

Chronic non-healing wounds (e.g., diabetic foot ulcers and bed sores) impact over 6.5 million Americans per year, costs in excess of $25 billion to treat on an annual basis, and are on the rise due to increasing levels of obesity and diabetes compounded by an aging population. A major inhibitor of healing is suboptimal oxygenation of the wound bed. Unlike acute injuries that receive sufficient oxygen via a functional blood vessel network, chronic wounds often suffer from the lack of a proper vascular network; thus being incapable of providing sufficient oxygen for tissue growth. Typical medical treatment of hypoxic chronic …

Towards Building A Prototype Spin-Logic Device, Ashish Verma Penumatcha

Open Access Dissertations

Since the late 1980s, several key discoveries, such as Giant and Tunneling Magne- toresistance, and advances in magnetic materials have paved the way for exponentially higher bit-densities in magnetic storage. In particular, the discovery of Spin-Transfer Torque (STT) has allowed information to be written to individual magnets using spin-currents. This has replaced the more traditional Oersted-field control used in field-MRAMs and allowed further scaling of magnetic-memories. A less obvious con- sequence of STT is that it has made possible a logic-technology based on magnets controlled by spin-polarized currents. Charge-coupled Spin Logic (CSL) is one such device proposal that couples a …

Experimentally Validated 3d Md Model For Afm-Based Tip-Based Nanomanufacturing, Rapeepan Promyoo

Open Access Dissertations

In order to control AFM-based TBN to produce precise nano-geometry efficiently, there is a need to conduct a more focused study of the effects of different parameters, such as feed, speed, and depth of cut on the process performance and outcome. This is achieved by experimentally validating a MD simulation model of nanomachining, and using it to conduct parametric studies to guide AFM-based TBN. A 3D MD model with a larger domain size was developed and used to gain a unique insight into the nanoindentation and nanoscratching processes such as the effect of tip speed (e.g. effect of tip speed …

Graphlet Based Network Analysis, Mahmudur Rahman

Open Access Dissertations

The majority of the existing works on network analysis, study properties that are related to the global topology of a network. Examples of such properties include diameter, power-law exponent, and spectra of graph Laplacians. Such works enhance our understanding of real-life networks, or enable us to generate synthetic graphs with real-life graph properties. However, many of the existing problems on networks require the study of local topological structures of a network.

Graphlets which are induced small subgraphs capture the local topological structure of a network effectively. They are becoming increasingly popular for characterizing large networks in recent years. Graphlet based …

Investigating The Effects Of Ph On Alphaviral E3-E2 Glycoprotein Association, Organization, And Cellular Tropism, Jason Michael Sequra

Open Access Dissertations

In alphaviruses the role of E3 is required in protecting the fusion peptide region of E1 during intracellular transport. Throughout viral processing, the association of E2 and E3 is required for the successful trafficking and incorporation of E1 into the mature virion. This E3-E2 association has been observed to extend to mature virions in the solved structure for the envelope of Semliki Forest virus (SFV) and supported by the solved structure for the entire Venezuelan equine encephalitis virion (VEEV) with exclusive contacts being made between E3-E2. Immunization with monoclonal antibodies against VEEV E3 provided protection for mice challenged by lethal …