Digital Commons Network^™

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.

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 …

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 …

Evaluating Parameter Uncertainty In Transportation Demand Models, Natalie Mae Gray

Theses and Dissertations

The inherent uncertainty in travel forecasting models -- arising from errors in input data, parameter estimation, or model formulation -- is receiving increasing attention from the scholarly and practicing community. In this research, we investigate the variance in forecasted traffic volumes resulting from varying the mode and destination choice parameters in an advanced trip-based travel demand model. Using Latin hypercube sampling to construct several hundred combinations of parameters across the plausible parameter space, we introduce substantial changes to mode and destination choice logsums and probabilities. However, the aggregate effects of of these changes on forecasted traffic volumes is small, with …

Evaluating Effects Of Urban Growth Within The Greater Salt Lake Area On Local Meteorological Conditions Using Urban Canopy Modeling, Corey L. Smithson

Theses and Dissertations

The increasing urbanization of the greater Salt Lake City area (GSLA) has contributed to the development of an urban canopy over this area. This canopy refers to the effects of building profiles, varying land surface properties and anthropogenic heating on local meteorological conditions including temperature, humidity, and wind velocity. Urban Canopy Models (UCMs) can be used to represent these characteristics on a mesoscale without needing to develop models accounting for effects of individual buildings. One method used to classify urban areas are Local Climate Zones (LCZs), which assign different properties to different types of urban areas. A baseline model that …

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 …

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 …

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 …

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. …

Validating A Predictive Early Kindergarten Dynamic Assessment Of Word Level Reading And Language, Taylor Jordan Cena

Theses and Dissertations

The purpose of this study was to examine the preliminary psychometrics to revisions to the decoding subtest of the Predictive Early Assessment of Reading and Language (PEARL) dynamic assessment and to further examine the predictive validity of the language subtest of the PEARL. Specific aims were to (a) determine if kindergarten students made gains on the PEARL decoding subtest from pretest to a delayed standard posttest and to a delayed novel posttest, indicating that floor effects were mitigated, (b) to examine if there was variance in the delayed standard posttest and novel posttest scores, (c) to determine if there was …

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 …

Examining The Validity Of The Cubed Narrative Language Measures Listening And Reading Subtests, Trevor David Read

Theses and Dissertations

Purpose: The purpose of this study was to examine the concurrent and predictive validity of the CUBED Narrative Language Measures Listening and Reading subtests to evaluate their psychometric properties as defined by Deno (2003). Method: Evidence of concurrent validity for the NLM Listening and Reading subtests was examined using data from 1,146 preschool through third grade students. The NLM subtests were compared to similar subtests from other assessments administered at approximately the same time. Evidence of predictive validity was examined using data from these same NLM subtests from 1,512 kindergarten through third grade students, including 71 third grade students for …

Nonsolvent-Induced Phase Separation Inside Liquid Droplets, Rami Alhasan, Tanner A. Wilcoxson, Dakota S. Banks, Sion Jung, Douglas R. Tree

Faculty Publications

Nonsolvent-induced phase separation (NIPS) is a popular method for creating polymeric particles with internal microstructure, but many fundamental questions remain surrounding the kinetics of the complex coupled mass transfer and phase separation processes. In this work, we use simulations of a phase-field model to examine how (i) finite domain boundaries of a polymer droplet and (ii) solvent/nonsolvent miscibility affect the NIPS process. To isolate the effects of phase separation kinetics and solvent/nonsolvent mass transfer on the NIPS process, we study two different cases. First, we investigate droplet concentrations that originate inside the two-phase region, where phase separation kinetics alone governs …

Vortex Particle Method For Electric Ducted Fan In Non-Axisymmetric Flow, Eduardo Alvarez, Cibin Joseph, Andrew Ning

Faculty Publications

The vortex particle method has been reformulated in recent work as a large eddy simulation (LES) in a scheme that is both meshless and numerically stable, solving long-standing issues of numerical stability. In this study, we build upon this meshless LES scheme to create a simulation framework for electric ducted fans. This poses the challenge of introducing solid boundaries in the vorticity form of the Navier-Stokes equations without a mesh. Rotor blades are introduced in our computational domain through an actuator line model (ALM) following well-established practices for LES. A novel, vorticity-based, actuator surface model (ASM) is developed for the …

"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 …

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 …

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 …

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 …

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 …

Methods For Designing Compact And Deployable Origami-Inspired Flat-Foldable Spacecraft Antennas And Other Systems, Collin Ryan Ynchausti

Theses and Dissertations

There are times when it is desirable for devices to be stowed compactly, ``transported'' to the location of their desired use, and then deployed to another stable shape or configuration to perform their designed function. Origami-based mechanisms are beneficial in these cases due to their compact, folded nature and large deployments. Unlike traditional mechanical design, compliant mechanism and origami-based design approaches inherently have coupled characteristics, creating complex design problems. The research presented here discusses metrics, methods, and designs to aid in the design of origami-adapted and compliant mechanisms, focusing on the design case of deployable space systems. First, the hexagonal …

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 …

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 …

Coaching Elementary Teachers In Literacy: Does Feedback Type Matter To Low And High Implementers?, Elizabeth Cutrer, Erica Ellsworth Miller, Erjola Gjini, Melia Fonoimoana Garrett

Faculty Publications

For literacy coaches and teachers, feedback is an integral component of effective coaching. Yet, little is understood

about the interaction between feedback and high/low implementing teachers within coaching sessions. This multiple

case study explored the types of feedback literacy coaches provided both high and low implementing teachers over a

two-year period. In the first year, the literacy coaches provided at least twice as much instructional feedback as

emotional feedback to low-implementing teachers. Those teachers not only received more feedback in general, but the

feedback they received was primarily what they needed to do to improve. In contrast, during the same …

Caveat Emptor: Scan Quality Of Elsevier’S Digital Backfile Pdf Collection, Gregory M. Nelson, Paul Kj Robbins, Dennis L. Eggett

Faculty Publications

Scans of journal articles originally published in print, otherwise known as digital journal backfiles, benefit library patrons by providing near instantaneous access to important older information and full-text searchability. Digital backfiles can serve as a reliable surrogate for their corresponding print journals which could be removed from the library, freeing up space for other patron services. Both benefits are realized when the scanned articles are of sufficient clarity to replace the print versions. Several studies have analyzed small and subject-narrow sections of Elsevier’s digital backfile. This article contains a scan-quality analysis from 1578 journals that contain nearly four million articles …

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 …

The Effect Of Musical Training On Second Language Grammar Acquisition, Deven Joseph Hunsaker

Theses and Dissertations

Music's effect on non-musical domains has been an area of intense research. Musical training has been shown to positively affect the processing of phonology, lexical tone, and syntax. While music also has positive effects in second language phonology acquisition, its effect on grammar acquisition is contested. This thesis aimed to study the under-researched topic of music and second language grammar acquisition using electroencephalography (EEG), thereby studying the electrical responses of the brain. Beginning level Spanish students were trained on a new grammatical principle prior to performing a grammaticality judgment task, and their behavioral and neural results were analyzed. Those students …

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 …

A Statistical Approach For Analyzing Expectations Alignment Between Design Teams And Their Project Stakeholders, Matthew Christian Goodson

Theses and Dissertations

Successful project management requires continuous communication aligning the expectations between project stakeholders and the project team. Expectations include both product expectations (how the product will look, feel, and perform) and programmatic expectations (timelines, deliverables, expenditure of project resources). In order to make the most effective use of project resources throughout the life of the project, a process or tool for quickly aligning expectations as closely as possible should be employed early on in the project. Project management literature is lacking in tools for aligning expectations, and solutions and best practices need to be determined since the current best option is …

Gradient-Based Optimization Of Highly Flexible Aeroelastic Structures, Taylor G. Mcdonnell

Theses and Dissertations

Design optimization is a method that can be used to automate the design process to obtain better results. When applied to aeroelastic structures, design optimization often leads to the creation of highly flexible aeroelastic structures. There are, however, a number of conventional design procedures that must be modified when dealing with highly flexible aeroelastic structures. First, the deformed geometry must be the baseline for weight, structural, and stability analyses. Second, potential couplings between aeroelasticity and rigid-body dynamics must be considered. Third, dynamic analyses must be modified to handle large nonlinear displacements. These modifications to the conventional design process significantly increase …

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 …