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Articles 301 - 330 of 3436

Full-Text Articles in Physical Sciences and Mathematics

Navigating Molecular Complexity: A Multidimensional Approach Utilizing Computational Chemistry, Jacob Andrew Parkman Jun 2023

Navigating Molecular Complexity: A Multidimensional Approach Utilizing Computational Chemistry, Jacob Andrew Parkman

Theses and Dissertations

Preparing molecular coordinate files for molecular dynamics (MD) simulations can be a very time-consuming process. Herein we present the development of a user-friendly program that drastically reduces the time required to prepare these molecular coordinate files for MD software packages such as AmberTools. Our program, known as charge atomtype naming (CAN), creates and uses a library of structures such as amino acid monomers to update the charge, atom type, and name of atoms in any molecular structure (mol2) file. We demonstrate the utility of this new program by rapidly preparing structural files for MD simulations for polypeptides ranging from small …

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Design, Synthesis And Immunological Testing Of Minimal Oligosaccharide Epitopes For Glycoconjugate Vaccines Targeting Capsular Polysaccharides Of Serotypes 3, 4, 7f And 9v Of Streptococcus Pneumoniae, Seth A. Taylor Jun 2023

Design, Synthesis And Immunological Testing Of Minimal Oligosaccharide Epitopes For Glycoconjugate Vaccines Targeting Capsular Polysaccharides Of Serotypes 3, 4, 7f And 9v Of Streptococcus Pneumoniae, Seth A. Taylor

Theses and Dissertations

The rise in antibiotic resistant strains of bacteria has led to the need for new methods of combatting bacterial infection. Since the surfaces of bacteria are covered in uniquely patterned capsular polysaccharides, vaccines targeting these polysaccharides have become a popular field of research for protection against pathogenic bacteria. Though licensed polysaccharide vaccines are commercially available, they lack the efficiency to protect patients that are immunocompromised or at high risk because they elicit T cell independent immune responses, resulting in low-affinity antibodies. To elicit a T cell dependent response and thereby recruit B cells that produce high-affinity antibodies, a vaccine was …

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Investigating The Use Of Translational Methods To Characterize Therapeutic Interventions In Models Of Pulmonary Disease, Ashley Rae Chang Jun 2023

Investigating The Use Of Translational Methods To Characterize Therapeutic Interventions In Models Of Pulmonary Disease, Ashley Rae Chang

Theses and Dissertations

Idiopathic Pulmonary Fibrosis (IPF) is an interstitial lung disease with no known cause or cure. IPF has an incidence of 75/1,000,000 of the population, predominately in men over the age of 60. This relatively rare disease develops in a chronic and progressive way, ultimately leading to death within two to five years of diagnosis. Our use of translatable methodologies in the bleomycin mouse model of IPF led to the novel identification of the similarities between the average percent loss of lung function in previous human clinical trials to that of our mouse model data. There is no treatment for IPF …

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Soft Contact Lens Tear Film Proteomics For Clinical Diagnostic Biomarker Discovery, Robert Kimball Roden Jun 2023

Soft Contact Lens Tear Film Proteomics For Clinical Diagnostic Biomarker Discovery, Robert Kimball Roden

Theses and Dissertations

Human tear film is an accessible biospecimen rich with useful biological information. As tear protein biomarkers for both ocular and systemic diseases have been identified in tears, efforts are being made to create point-of-care tests useful for clinical diagnoses. However, there are significant obstacles to tear diagnostics, including inadequate sampling methods and biomarkers with insufficient sensitivity and specificity. Furthermore, tear film diagnostics are particularly challenging for dry eye disease (DED) patients, where low tear volume makes sampling more difficult and the multifactorial nature of DED makes identifying the exact pathological subtype very complex. As soft contact lenses (SCLs) are designed …

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Exploring Surface Silanization And Characterization Of Thin Films: From Surface Passivation To Microstructural Characterization Of Porous Silicon/Silica, And Exploratory Data Analysis Of X-Ray Photoelectron Spectroscopy Images, Behnam Moeini Jun 2023

Exploring Surface Silanization And Characterization Of Thin Films: From Surface Passivation To Microstructural Characterization Of Porous Silicon/Silica, And Exploratory Data Analysis Of X-Ray Photoelectron Spectroscopy Images, Behnam Moeini

Theses and Dissertations

Surface chemistry plays a key role in science and technology because materials interact with their environments through their surfaces. Understanding surface chemistry can help alter/improve the properties of materials. However, surface characterization and modification often require multiple characterization and synthesis techniques. Silicon/silica-based materials are technologically important, so studying their surface properties can enable future advancements. In this dissertation, I explore surface modification and characterization of different types of Si/SiO2 thin films, including silicon wafers, fused silica capillary columns, and oblique angle sputtered Si/SiO2 thin films. In Chapters 2-5, I first present a method to rapidly silanize silica surfaces using a …

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Raw Diffraction Data For 1tel-Aa-Vwa (Sumo), Wwpdb Id: 7n1o, Moriah H. Mathis, Braydan D. Bezzant, Diana T. Ramírez, Supeshala D. Nawarathnage, Tzanko I. Doukov, James Moody Jun 2023

Raw Diffraction Data For 1tel-Aa-Vwa (Sumo), Wwpdb Id: 7n1o, Moriah H. Mathis, Braydan D. Bezzant, Diana T. Ramírez, Supeshala D. Nawarathnage, Tzanko I. Doukov, James Moody

ScholarsArchive Data

This X-ray diffraction dataset was collected on October 21Oct2020 at SSRL Beamline BL9-2. The crystal was of Batch 1 1TEL-AA-vWa (SUMO) The solved structure used frames 1-999 and has been deposited in the wwPDB under the PDB ID 7N1O. This data can be readily processed using XDS, AutoProc, CCP4, HKL2000/3000, or other crystallographic X-ray diffraction data processing software. The files have a human-readable header but are otherwise binary.

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Raw Diffraction Data For 3tel-Hlx-Darpin (Sumo), Wwpdb Id: 7n2b, Supeshala D. Nawarathnage, Parag Laljibhai Gajjar, Derick R. Bunn, Cameron Stewart, Tzanko I. Doukov, James Moody Jun 2023

Raw Diffraction Data For 3tel-Hlx-Darpin (Sumo), Wwpdb Id: 7n2b, Supeshala D. Nawarathnage, Parag Laljibhai Gajjar, Derick R. Bunn, Cameron Stewart, Tzanko I. Doukov, James Moody

ScholarsArchive Data

This X-ray diffraction dataset was collected on October 21Oct2020 at SSRL Beamline BL9-2. The crystal was of 3TEL-hlx-DARPin (SUMO) The solved structure used frames 1-1799 and has been deposited in the wwPDB under the PDB ID 7N2B. This data can be readily processed using XDS, AutoProc, CCP4, HKL2000/3000, or other crystallographic X-ray diffraction data processing software. The files have a human-readable header but are otherwise binary.

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The Target Model For Genealogical Networks, Kolton Baldwin Jun 2023

The Target Model For Genealogical Networks, Kolton Baldwin

Theses and Dissertations

Several large-scale projects including FamilySearch, Ancestry, BALSAC (University of Quebec), and others have gathered incredible amounts of genealogical data ranging from millions to billions of individuals. To study the structure of this data, we propose a model that generates a genealogical network based on real-world genealogical data using two key features: (i) geodesic distance between couples prior to union and (ii) the number of children per couple. The distribution of the distance to a couples' nearest common ancestor in an observed community captures the global scale at which biological cycles form in the underlying genealogical network. Similarly, the number of …

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Conodont Sequence Biostratigraphy Of The Upper Honaker Trail Formation, Cheyenne Autumn Pratt Jun 2023

Conodont Sequence Biostratigraphy Of The Upper Honaker Trail Formation, Cheyenne Autumn Pratt

Theses and Dissertations

The Paradox Basin is a northwest-southeast trending intracratonic basin that formed in southwestern Colorado, southeastern Utah and adjacent parts of Arizona and New Mexico during the late Paleozoic Era. During rise of the adjacent Uncompahgre Uplift (Ancestral Rocky Mountains), the rapidly subsiding basin was filled with over 2000 m of Permo-Pennsylvanian sediments that reflect a complex interplay of changing tectonic, paleoecological, and climatic conditions that resulted in cyclic packages of mixed lowstand and non-marine siliciclastics and highstand shallow-platform carbonates. The 150 m-thick Honaker Trail formation straddles the transition from mostly marine carbonates to mostly non-marine siliciclastics on the southwest shelf …

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Optimal Ordering To Maximize Mev Arbitrage, Granton Michael White Jun 2023

Optimal Ordering To Maximize Mev Arbitrage, Granton Michael White

Theses and Dissertations

The rise of cryptocurrencies has brought with it new math problems with new sets of constraints. The MEV problem entails solving for the ordering of pending trades that maximizes a block creator's profit. In decentralized finance, time is a big constraint, so an exhaustive search of all possible orderings is impossible. I propose a solution to the MEV problem that gives a near optimal result that can be solved in a reasonable amount of time. I layout the method and the formulas required for my solution. Additionally, I test my solution on synthesized data to show that it works as …

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Hamiltonian Monte Carlo For Reconstructing Historical Earthquake-Induced Tsunamis, Jacob Paul Callahan Jun 2023

Hamiltonian Monte Carlo For Reconstructing Historical Earthquake-Induced Tsunamis, Jacob Paul Callahan

Theses and Dissertations

In many areas of the world, seismic hazards pose a great risk to both human and natural populations. In particular, earthquake-induced tsunamis are especially dangerous to many areas in the Pacific. The study and quantification of these seismic events can both help scientists better understand how these natural hazards occur and help at-risk populations make better preparations for these events. However, many events of interest occurred too long ago to be recorded by modern instruments, so data on these earthquakes are sparse and unreliable. To remedy this, a Bayesian method for reconstructing the source earthquakes for these historical tsunamis based …

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A Structural Analysis Of The Simpson Mountains, Hyrum A. Briscoe Jun 2023

A Structural Analysis Of The Simpson Mountains, Hyrum A. Briscoe

Theses and Dissertations

The Simpson Mountains have long been of economic interest and have renewed interest in their potential value. Field mapping of the project area redefined structural relationships between stratigraphic units. Geometric and kinematic analysis of structures in the Simpson Mountains show the range is deformed by the three most recent tectonic events: the Sevier Orogeny, the Laramide Orogeny, and Basin and Range Extension. Laramide structures define the range with a significant E-W normal fault and an E-W thrust fault, which are both likely related to Eocene-age igneous intrusions. Principal component analysis (PCA) of regional quartzite X-ray Fluorescence (XRF) data resulted in …

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Non-Tuberculous Mycobacterium Correlation With Geochemical Characteristics Of Soil And Basalt In Hawaii, Leeza Marie Wells Jun 2023

Non-Tuberculous Mycobacterium Correlation With Geochemical Characteristics Of Soil And Basalt In Hawaii, Leeza Marie Wells

Theses and Dissertations

Non-tuberculous mycobacteria (NTM) cause opportunistic lung disease though environmental exposure pathways. Among the United States, Hawaii has a significantly higher infection rate. Preliminary studies have shown certain environmental factors, such as phosphorus and other select soil geochemical characteristics, to be statistically significant to NTM occurrence. However, a model to predict NTM occurrence based on soil geochemistry had yet to be attempted. A selection of 40 NTM positive and 40 NTM negative soils from Oahu were selected for a geochemical analysis to search for possible correlations to mineralogy and elemental abundances that may promote, or inhibit, NTM growth in the environment. …

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Comparison Of The Unweighted Log-Rank And Weighted Prentice-Modified Wilcoxon Tests With Left-Truncated Data, Ellen Wight Jun 2023

Comparison Of The Unweighted Log-Rank And Weighted Prentice-Modified Wilcoxon Tests With Left-Truncated Data, Ellen Wight

Undergraduate Honors Theses

In survival analysis, there is a potential interaction between left-truncated data and rank test procedures for the difference between two groups that has not yet been investigated in depth. This study explores the effect of left truncation on the absolute and relative performance of the unweighted log-rank test and the weighted Prentice modification of the Gehan-Wilcoxon test. Resulting power from simulation study replications revealed that while left truncation does not affect which test performs better overall, it does affect the relative difference between the tests. It significantly worsens the individual performance of the Prentice-modified test, likely because of left truncation …

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"I Think They're Poisoning My Mind": Understanding The Motivations Of People Who Have Voluntarily Adopted Secure Email, Warda Usman May 2023

"I Think They're Poisoning My Mind": Understanding The Motivations Of People Who Have Voluntarily Adopted Secure Email, Warda Usman

Theses and Dissertations

Secure email systems that use end-to-end encryption are the best method we have for ensuring user privacy and security in email communication. However, the adoption of secure email remains low, with previous studies suggesting mainly that secure email is too complex or inconvenient to use. However, the perspectives of those who have, in fact, chosen to use an encrypted email system are largely overlooked. To understand these perspectives, we conducted a semi-structured interview study that aims to provide a comprehensive understanding of the mindsets underlying adoption and use of secure email services. Our participants come from a variety of countries …

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A Method Of Reconstructing Historical Destructive Landslides Using Bayesian Inference, Raelynn Wonnacott May 2023

A Method Of Reconstructing Historical Destructive Landslides Using Bayesian Inference, Raelynn Wonnacott

Theses and Dissertations

Along with being one of the most populated regions of the world, Indonesia has one of the highest natural disaster rates worldwide. One such natural disaster that Indonesia is particularly prone to are tsunamis. Tsunamis are primarily caused by earthquakes, volcanoes, landslides and debris flows. To effectively allocate resources and create emergency plans we need an understanding of the risk factors of the region. Understanding the source events of destructive tsunamis of the past are critical to understanding the these risk factors. We expand upon previous work focusing on earthquake-generated tsunamis to consider landslide-generated tsunamis. Using Bayesian inference and modern …

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Recommending Answers To Math Questions Using Kl-Divergence And The Approximate Xml Tree Matching Approach, Siqi Gao May 2023

Recommending Answers To Math Questions Using Kl-Divergence And The Approximate Xml Tree Matching Approach, Siqi Gao

Theses and Dissertations

Mathematics is the science and study of quality, structure, space, and change. It seeks out patterns, formulates new conjectures, and establishes the truth by rigorous deduction from appropriately chosen axioms and definitions. The study of mathematics makes a person better at solving problems. It gives someone skills that (s)he can use across other subjects and apply in many different job roles. In the modern world, builders use mathematics every day to do their work, since construction workers add, subtract, divide, multiply, and work with fractions. It is obvious that mathematics is a major contributor to many areas of study. For …

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Dd Slug Migration: Mathematical Model And Numerical Results, Joy Song May 2023

Dd Slug Migration: Mathematical Model And Numerical Results, Joy Song

Theses and Dissertations

Amoebae are commonly studied to understand embryogenesis, and the best-characterized amoebozoan species is Dictyostelium discoideum (Dd). Dd has a very simple life cycle with a range of developmental stages, among which we are most interested in the stage of a migrating slug. It has been observed that different sizes of Dd slugs maintain a proportional distribution of prestalk cells and prespore cells: prestalk cells occupy the anterior 20% of the slug, while prespore cells occupy the posterior 80%. However, it remains unknown how the migrating slug forms and preserves this anterior-posterior proportional pattern under so many different dynamics including cell …

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Selection-Based Convolution For Irregular Images And Graph Data, David Marvin Hart May 2023

Selection-Based Convolution For Irregular Images And Graph Data, David Marvin Hart

Theses and Dissertations

The field of Computer Vision continues to be revolutionized by advances in Convolutional Neural Networks. These networks are well suited for the regular grid structure of image data. However, there are many irregular image types that do not fit within such a framework, such as multi-view images, spherical images, superpixel representations, and texture maps for 3D meshes. These kinds of representations usually have specially designed networks that only operate and train on that unique form of data, thus requiring large datasets for each data domain. This dissertation aims to bridge the gap between standard convolutional networks and specialized ones. It …

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Algorithmic Fidelity And The Use Of Large Language Models In Social Science Research, Christopher Michael Rytting May 2023

Algorithmic Fidelity And The Use Of Large Language Models In Social Science Research, Christopher Michael Rytting

Theses and Dissertations

In this dissertation, we argue that large language models (LLMs) exhibit a considerable amount of \textit{algorithmic fidelity}, a property where they have modeled ideas, behaviors, and attitudes of the population who generated their training data. This has important implications for social science, as this fidelity theoretically allows for the use of LLMs as effective proxies for human beings in experiments and research. We demonstrate this empirically in various social science domains (political partisanship, demographic surveying, voting behavior, hot-button policy issues, news media, populism, congressional summaries), in various applications (replicating social science survey findings, assisting in coding of text datasets, inferring …

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Developing Genotypic And Phenotypic Systems For Early Analysis Of Drug-Resistant Bacteria, Yesman Akuoko May 2023

Developing Genotypic And Phenotypic Systems For Early Analysis Of Drug-Resistant Bacteria, Yesman Akuoko

Theses and Dissertations

Antimicrobial resistance in bacteria is a global health challenge with a projected fallout of 10 million deaths annually and cumulative costs of over 1 trillion dollars by 2050. The currently available tools exploited in the detection of bacteria or their DNA can be expensive, time inefficient, or lack multiplex capabilities among others. The research work highlighted in this dissertation advances techniques employed in the phenotypic or genotypic detection of bacteria and their DNA. In this dissertation, I present polymethyl methacrylate-pressure sensitive adhesive microfluidic platforms developed using a time-efficient, inexpensive fabrication technique. Microfluidic devices were then equipped with functionalized monoliths and …

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Popr: Probabilistic Offline Policy Ranking With Expert Data, Trevor F. Schwantes Apr 2023

Popr: Probabilistic Offline Policy Ranking With Expert Data, Trevor F. Schwantes

Theses and Dissertations

While existing off-policy evaluation (OPE) methods typically estimate the value of a policy, in real-world applications, OPE is often used to compare and rank policies before deploying them in the real world. This is also known as the offline policy ranking problem. While one can rank the policies based on point estimates from OPE, it is beneficial to estimate the full distribution of outcomes for policy ranking and selection. This paper introduces Probabilistic Offline Policy Ranking that works with expert trajectories. It introduces rigorous statistical inference capabilities to offline evaluation, which facilitates probabilistic comparisons of candidate policies before they are …

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Introducing Stochastic Time Delays In Gradient Optimization As A Method For Complex Loss Surface Navigation In High-Dimensional Settings, Eric Benson Manner Apr 2023

Introducing Stochastic Time Delays In Gradient Optimization As A Method For Complex Loss Surface Navigation In High-Dimensional Settings, Eric Benson Manner

Theses and Dissertations

Time delays are an inherent part of real-world systems. Besides the apparent slowing of the system, these time delays often cause destabilization in otherwise stable systems, and perhaps even more unexpectedly, can stabilize an unstable system. Here, we propose the Stochastic Time-Delayed Adaptation as a method for improving optimization on certain high-dimensional surfaces, which simply wraps a known optimizer --such as the Adam optimizer-- and is able to add a variety of time-delays. We begin by exploring time delays on certain gradient-based optimization methods and their affect on the optimizer's convergence properties. These optimizers include the standard gradient descent method …

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Zero And Few-Shot Concept Learning With Pre-Trained Embeddings, Jamison M. Moody Apr 2023

Zero And Few-Shot Concept Learning With Pre-Trained Embeddings, Jamison M. Moody

Theses and Dissertations

Neural networks typically struggle with reasoning tasks on out of domain data, something that humans can more easily adapt to. Humans come with prior knowledge of concepts and can segment their environment into building blocks (such as objects) that allow them to reason effectively in unfamiliar situations. Using this intuition, we train a network that utilizes fixed embeddings from the CLIP (Contrastive Language--Image Pre-training) model to do a simple task that the original CLIP model struggles with. The network learns concepts (such as "collide" and "avoid") in a supervised source domain in such a way that the network can adapt …

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A Game Theoretical Approach To Optimal Pitch Sequencing, William Melville Apr 2023

A Game Theoretical Approach To Optimal Pitch Sequencing, William Melville

Theses and Dissertations

This paper presents a game theoretical solution to the difficult challenge of optimal pitch sequencing. We model the batter/pitcher matchup as a zero-sum game and determine the equilibrium strategy for both the pitcher and batter. We conclude that the Stackelberg equilibrium and our newly defined decision point equilibrium serve as effective pitch sequencing strategies.

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Rigorous Computation Of The Evans Function, Devin Mcghie Apr 2023

Rigorous Computation Of The Evans Function, Devin Mcghie

Theses and Dissertations

We develop computer-assisted methods of proof for rigorous computation of the Evans function in order to prove stability of traveling waves. We use the parameterization method, series solutions, and the Newton-Kantorovich Theorem to obtain precise, rigorous error bounds for the numerical solution of the ODE used in the construction of the Evans function. We demonstrate these methods on a scalar reaction-diffusion model and on the Gray-Scott model.

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A Large-Scale Survey Of Brown Dwarf Atmospheres, Savanah Kay Turner Apr 2023

A Large-Scale Survey Of Brown Dwarf Atmospheres, Savanah Kay Turner

Theses and Dissertations

Brown dwarfs are substellar objects that fall in-between the smallest stars and largest planets in size and temperature. Due to their relatively cool temperatures, the atmospheres of these 'failed stars' have been shown to exhibit interesting properties such as iron, silicate, and salt clouds. Theoretical atmospheric models based on known physics and chemistry can be used as tools to interpret and understand our observations of brown dwarfs. I have fit archival and new infrared spectra of over 300 brown dwarfs with atmospheric models. Using the parameters of the best-fit models as estimates for the physical properties of the brown dwarfs …

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Comparative Gpr Analysis Of Carbonate Strandline Deposits, Sydney Adelaide Richards Apr 2023

Comparative Gpr Analysis Of Carbonate Strandline Deposits, Sydney Adelaide Richards

Theses and Dissertations

The Bahamas Island archipelago grows by the precipitation and secretion of calcium carbonate. A majority of this growth is by lateral accretion of shoreline sedimentary deposits. Previous research is not clear on whether the growth is largely due to eustasy, sediment input from catastrophic events, or a combination of both. The Bahamas is an ideal location for studying Holocene carbonate generation and deposition, but there is limited research on the analysis of strandlines in relation to lateral accretion. Carbonate strandline deposits are commonly classified as low-energy beach ridge deposits. Previous researchers have primarily focused on ooid shoals and subtidal regions. …

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Bézout Domains And Elementary Divisor Domains: Are They The Same?, Michael D. Walton Apr 2023

Bézout Domains And Elementary Divisor Domains: Are They The Same?, Michael D. Walton

Theses and Dissertations

This thesis examines the connections between Bézout domains and elementary divisor domains. I establish what both of these domains are, and I provide some clarifying examples of each. I state and prove some key results that have been established already in the literature. I describe a process by which I tried to show a distinction between Bézout domains and elementary divisor domains, and then provide an explicit example which shows that this process as formulated would not lead to an example of a Bézout domain which is not an elementary divisor domain. Throughout the thesis, I also state open questions …

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Use And Misuse Of X-Ray Photoelectron Spectroscopy (Xps): Reproducibility, Gross Errors, Data Reporting, And Peak Fitting, George Hobbs Major Apr 2023

Use And Misuse Of X-Ray Photoelectron Spectroscopy (Xps): Reproducibility, Gross Errors, Data Reporting, And Peak Fitting, George Hobbs Major

Theses and Dissertations

X-ray photoelectron spectroscopy (XPS) is the most widely used surface analysis technique for chemically probing surfaces. Its popularity stems from the large amount of information that can be gathered about the electronic states of the atoms it probes, including core shell information and valence electron information. Simple qualitative analysis (peak identification) can often be performed, but quantitative analysis is a much more complicated process. Although XPS usage has increased dramatically, so has the amount of erroneous analysis observed in the literature. In my thesis, I first present a perspective on how to improve the quality of surface and material data …

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