Physical Sciences and Mathematics Commons^™

Coarse-Grained Simulation Of Pegylated And Tethered Protein Devices At All Experimentally Accessible Surface Residues On Β-Lactamase For Stability Analysis And Comparison, Addison K. Smith, Mehran Sultani, Joshua Wilkerson, Brandon Timmerman, Emily Long Zhao, Bradley C. Bundy, Thomas A. Knotts

Faculty Publications

PEGylated and surface-tethered proteins are used in a variety of biotechnological applications, but traditional methods offer little control over the placement of the functionalization sites on the protein. Fortunately, recent experimental methods functionalize the protein at any location on the amino acid sequence, so the question becomes one of selecting the site that will result in the best protein function. This work shows how molecular simulation can be used to screen potential attachment sites for surface tethering or PEGylation. Previous simulation work has shown promise in this regard for a model protein, but these studies are limited to screening only …

Mean Square Displacement For A Discrete Centroid Model Of Cell Motion And A Mathematical Analysis Of Focal Adhesion Lifetimes And Their Effect On Cell Motility, Mary Ellen Furner Rosen

Theses and Dissertations

One of the characteristics that distinguishes living things from non-living things is motility. On the cellular level, the motility or non-motility of different types of cells can be life building, life-saving or life-threatening. A thorough study of cell motion is needed to help understand the underlying mechanisms that enhance or prohibit cell motion. We introduce a discrete centroid model of cell motion in the context of a generalized random walk. We find an approximation for the theoretical mean square displacement (MSD) that uses a subset of the state space to estimate the MSD for the entire space. We give some …

Sp2 Bonded Carbon For Soft X-Ray Detector Windows, Joseph T. Rowley

Theses and Dissertations

Energy Dispersive X-Ray Spectroscopy (EDS) is a technique used to analyze materials to determine their elemental makeup. This technique is used extensively in the semiconductor industry, metallurgical industry, biology, chemistry, materials science, and other fields. EDS detectors are often attached to scanning electron microscopes (SEM) or transmission electron microscopes (TEM) and are actively cooled by liquid nitrogen or Peltier devices. A thin membrane, or window, is fitted to the front of the detector which allows for an airtight seal as well as transmission of x-rays. The challenge for these windows is maximizing the transmission of x-rays while maintaining mechanical integrity. …

The "What"-"Where" Network: A Tool For One-Shot Image Recognition And Localization, Daniel Hurlburt

Theses and Dissertations

One common shortcoming of modern computer vision is the inability of most models to generalize to new classes—one/few shot image recognition. We propose a new problem formulation for this task and present a network architecture and training methodology to solve this task. Further, we provide insights into how careful focus on how not just the data, but the way data presented to the model can have significant impact on performance. Using these method, we achieve high accuracy in few-shot image recognition tasks.

The Nabataean Façade Monuments Of Petra, Jordan: An Assessment Of The Façade Monuments And Their Geological Environment., Josie M. Newbold

Theses and Dissertations

The Nabataean people controlled the Petra region of modern-day Jordan from sometime before 300 BCE until the Roman Annexation of the Nabataean kingdom in 106 CE. The Nabataeans are known for the monumental façades carved into the sandstone cliffs surrounding their capital city. The first survey of the façade monuments was undertaken by Brünnow and Domaszewski in 1904. They created a typology that has only been slightly modified by subsequent authors including Judith McKenzie (1990). This typology does not account for all of the variations in façade types in Petra, thus creating a need for a new typology proposed in …

Modeling Continental-Scale Outdoor Environmental Sound Levels With Limited Data, Katrina Lynn Pedersen

Theses and Dissertations

Modeling outdoor acoustic environments is a challenging problem because outdoor acoustic environments are the combination of diverse sources and propagation effects, including barriers to propagation such as buildings or vegetation. Outdoor acoustic environments are most commonly modeled on small geographic scales (e.g., within a single city). Extending modeling efforts to continental scales is particularly challenging due to an increase in the variety of geographic environments. Furthermore, acoustic data on which to train and validate models are expensive to collect and therefore relatively limited. It is unclear how models trained on this limited acoustic data will perform across continental-scales, which likely …

Sources Of Formaldehyde In Bountiful Ut Data, Nitish Bhardwaj, Ariel Kelsch, Delbert Eatough, Ryan Thalman, Nancy Daher, Kerry Kelly, Isabel Cristina Jaramillo, Jaron Hansen

ScholarsArchive Data

Source of Formaldehyde in Bountiful, UT Data

This file contains the X and U matrix used in the positive matrix factorization analysis done on the data collected in Bountiful, UT. The X matrix contains the concentration of species measured and the U matrix is the calculated uncertainty in each measured value. This data is stored in the Excel format.

Included in this file is the two-hour averaged concentrations of formaldehyde and ozone, wind direction, time of day, and date that the data was collected at the Bountiful, UT air sampling site located at the Bountiful Utah High School. This data …

In Vitro Screening Of Tp5801 Against Kinases For Nature Communications Publication, Joshua Andersen

ScholarsArchive Data

Data from screen of TP-5801 against in vitro kinases

Improvement In 14-3-3 Binding Site Prediction, Katherine K. Mccormack

ScholarsArchive Data

The 14-3-3 family of phospho-binding proteins regulate a variety of major cellular processes through interaction with a network of dynamic proteins. Deregulation of the 14-3-3 interaction network contributes to a variety of degenerative disorders and cancers. Our lab focuses on identifying novel 14-3-3 interactions and understanding how 14-3-3 binding regulates protein function. A major gap in this process is that identifying the phospho-site where 14-3-3 docks on a given protein is time- and resource-consuming. Prediction algorithms have been developed to predict canonical 14-3-3 binding sites, however, there are many non-canonical sites that existing software is unable to predict. To fill …

Kinase Screen Data For Nature Communications Publication, Joshua Andersen

ScholarsArchive Data

A TNK1 peptide encompassing S502 was screened against 245 Ser/Thr kinases. This file contains kinase activity values (against S502) from an n=1 experiment. These data support a manuscript to be published in Nature Communications (Chan and Egbert et al.)

Leveraging The Inductive Bias Of Large Language Models For Abstract Textual Reasoning, Christopher Michael Rytting

Theses and Dissertations

Large natural language models (such as GPT-2 or T5) demonstrate impressive abilities across a range of general NLP tasks. Here, we show that the knowledge embedded in such models provides a useful inductive bias, not just on traditional NLP tasks, but also in the nontraditional task of training a symbolic reasoning engine. We observe that these engines learn quickly and generalize in a natural way that reflects human intuition. For example, training such a system to model block-stacking might naturally generalize to stacking other types of objects because of structure in the real world that has been partially captured by …

A Water Budget And Solute Flux Budget For Waimea River Watershed, Kauai, Hi, U.S.A., Joseph Harold Tolworthy

Theses and Dissertations

Waimea Canyon is a deep V-shaped canyon on the island of Kauai, Hawaii in which the Waimea River and its tributaries flow. The shape and size of the canyon are noteworthy and unusual compared to its contemporary canyons on the Hawaiian Islands which are usually U-shaped or flat bottomed. This could be because there is significantly more physical erosion in Waimea Canyon compared to others. A water budget was created using ArcGIS Pro and data from the University of Hawaii’s rainfall and evapotranspiration atlases, as well as from the United States Geological Survey’s stream gage data. A mass flux was …

Nature And Origin Of The East Traverse Mountains Mega-Landslide, Northern Utah (Usa), Rodney Ryan Chadburn

Theses and Dissertations

The East Traverse Mountains are an E-W trending mountain range dividing Utah and Salt Lake valleys in northern Utah. Geologically perplexing, the nature of the East Traverse Mountains has been under investigation for 140 years. Previously, the mountain range was proposed to be a dismembered but still coherent down-faulted block that experienced 4 km of post-thrusting extension within the Charleston-Nebo thrust sheet. However, new insight on the origin of the East Traverse Mountains indicate that it is a mega landslide, roughly ~100 km3 in size, which catastrophically slid from the upper reaches of the Little-Cottonwood stock to its present-day location. …

Instrumentation And Application Of Image-Charge Detection Of Electrospray-Charged Microparticles And Microdroplets, Jiuzhi Gao

Theses and Dissertations

Image-charge detection is emerging as an important tool to analyze heavy and heterogeneous samples because of its unique advantages in measuring highly charged microparticles. Conventional image-charge detection instruments include at least three fundamental components: an ionization source, an aerodynamic particle delivery system, and an image-charge detector. Here I report research efforts that investigated the mechanisms of image-charge detection and proposed some instrumental developments of these components to suit specific research purposes. In Chapter 2, I report an investigation of the electrospray ionization (ESI) mechanism based on an observation that a certain portion of charged particles generated with an ESI source …

Methods For Generative Adversarial Output Enhancement, Michael B. Brodie

Theses and Dissertations

Generative Adversarial Networks (GAN) learn to synthesize novel samples for a given data distribution. While GANs can train on diverse data of various modalities, the most successful use cases to date apply GANs to computer vision tasks. Despite significant advances in training algorithms and network architectures, GANs still struggle to consistently generate high-quality outputs after training. We present a series of papers that improve GAN output inference qualitatively and quantitatively. The first chapter, Alpha Model Domination, addresses a related subfield of Multiple Choice Learning, which -- like GANs -- aims to generate diverse sets of outputs. The next chapter, CoachGAN, …

Structures And Characteristics Of Macromolecular Interactions In Gas Phase Using Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry, Jiewen Shen

Theses and Dissertations

This dissertation investigates non-covalent macromolecular chemistry using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) based techniques. The included studies reveal the impact of molecular structure on conformation and binding energetics. Supramolecules that might be too heavy to be dissociated in single collision-induced dissociation (CID) were dissociated using sustained off-resonance collision induced dissociation (SORI-CID) techniques. Relative binding energies and thresholds were evaluated for various macromolecular host-guest systems. Besides the non-covalent binding energies, conformation characterization was undertaken by a novel method to determine collision cross sectional areas using FTICR (CRAFTI, and multi-CRAFTI), initially developed by the Dearden lab. The systems chosen …

Novel Αvβ6 Inhibitor Reduces Fibrotic Progression In Idiopathic Pulmonary Fibrosis Murine Model, Rebecca C. Viazzo Winegar

Theses and Dissertations

Idiopathic pulmonary fibrosis (IPF) is one of the most aggressive and severe interstitial lung diseases (ILDs) for which there is no cure. IPF is characterized by an excessive accumulation of fibroblasts which secrete an abundance of extracellular proteins such as collagen. These processes lead to repetitive tissue scarring and fibrosis in the lung parenchyma. As a result, lungs become rigid limiting oxygen intake and gas exchange. Once diagnosed, IPF is fatal within 2-3 years. There is no known cause or proven treatment that significantly improves outcomes. Although the cause is unknown, the current model of IPF suggests that an overactive …

Metalearning By Exploiting Granular Machine Learning Pipeline Metadata, Brandon J. Schoenfeld

Theses and Dissertations

Automatic machine learning (AutoML) systems have been shown to perform better when they use metamodels trained offline. Existing offline metalearning approaches treat ML models as black boxes. However, modern ML models often compose multiple ML algorithms into ML pipelines. We expand previous metalearning work on estimating the performance and ranking of ML models by exploiting the metadata about which ML algorithms are used in a given pipeline. We propose a dynamically assembled neural network with the potential to model arbitrary DAG structures. We compare our proposed metamodel against reasonable baselines that exploit varying amounts of pipeline metadata, including metamodels used …

Galectin-1 Improves Sarcolemma Repair And Decreases The Inflammatory Response In Lgmd2b Models, Matthew F. Rathgeber

Theses and Dissertations

Limb-girdle muscular dystrophy type 2B (LGMD2B) is caused by mutations in the dysferlin gene, resulting in non-functional dysferlin, a key protein found in muscle membrane. Treatment options available for patients are chiefly palliative in nature and focus on maintaining ambulation. Our hypothesis is that galectin-1 (Gal-1), a soluble carbohydrate binding protein, increases membrane repair capacity, myogenic potential, M2 macrophage polarization and decreases NF-κB inflammation in dysferlin-deficient models. To test this hypothesis, we used recombinant human galectin-1 (rHsGal-1) to treat dysferlin-deficient models. We show that rHsGal-1 treatments of 48 h-72 h promotes myogenic maturation as indicated through improvements in size, myotube …

Eigenvalues Of Differential Operators And Nontrivial Zeros Of L-Functions, Dongsheng Wu

Theses and Dissertations

The Hilbert-P\'olya conjecture asserts that the non-trivial zeros of the Riemann zeta function $\zeta(s)$ correspond (in a certain canonical way) to the eigenvalues of some positive operator. R. Meyer constructed a differential operator $D_-$ acting on a function space $\H$ and showed that the eigenvalues of the adjoint of $D_-$ are exactly the nontrivial zeros of $\zeta(s)$ with multiplicity correspondence. We follow Meyer's construction with a slight modification. Specifically, we define two function spaces $\H_\cap$ and $\H_-$ on $(0,\infty)$ and characterize them via the Mellin transform. This allows us to show that $Z\H_\cap\subseteq\H_-$ where $Zf(x)=\sum_{n=1}^\infty f(nx)$. Also, the differential operator …

Varying The Aspect Ratio Of Toroidal Ion Traps: Implications For Design, Performance, And Miniaturization, Praneeth Madushan Hettikankanange

Theses and Dissertations

A large aspect ratio leads to higher ion capacity in miniaturized ion trap mass spectrometers. The aspect ratio (AR) of an ion trap represents the ratio between an extended trapping dimension and the characteristic trapping dimension. In contrast to linear and rectilinear traps, changing the AR of a toroidal ion trap (TorIT) results in changes to the degree of curvature and shape of the trapping potential, and hence, on performance as a mass analyzer. SIMION simulations show that higher-order terms in the trapping potential vary strongly for small and moderate AR values (below ~10), with the effects asymptotically flattening for …

Segment And Intersection Crash Analysis Methodologies For Utah Highways, Camille Cherie Lunt

Theses and Dissertations

This research focuses on the Crash Analysis Methodology for Segments (CAMS) which provides a way for engineers at the Utah Department of Transportation (UDOT) to prioritize safety improvements on state-owned roadways. Unlike the Utah crash analysis methodologies that come before it, the CAMS focuses exclusively on segment-related crashes. The benefits of such an analysis can be found in identifying locations that have safety concerns unbiased from intersections and their related crashes. The CAMS uses UDOT data to create a spreadsheet of roadway segments and their associated crashes. Each segment is homogeneous with respect to five variables: Annual Average Daily Traffic …

Building A Predictive Model For Stratigraphic Transitions And Lateral Facies Changes In The Cretaceous Almond Formation, Wyoming, Joseph E. Phillips

Theses and Dissertations

The Cretaceous Almond Formation, located in the Greater Green River Basin, records deposition of coastal plain fluvial sandstones and shallow marginal-marine sandstones in a net-transgressive sequence along the western margin of the Cretaceous Interior Seaway (CIS) from the late Campanian to early Maastrichtian. The Almond Formation is an important hydrocarbon reservoir, with development mainly along the Wamsutter Arch and the northeast margins of the Washakie Basin. Previous studies have primarily focused on outcrops along the eastern flank of the Rock Springs Uplift and subsurface data targeting the Wamsutter Arch. Further development of the Almond petroleum system requires extending our understanding …

The Impact Of Experiential Virtual Dinosaur Excavation Assignments On Exam Preparation And Performance Inâ An Introductory, University-Level Geology Course, Nicole Elizabeth Ortiz

Theses and Dissertations

Advocates assert that experiential/applicational learning facilitates deep understanding but there is a dearth of empirical research testing the effectiveness of experiential learning in university geology courses. Domack (1999) and Moecher (2004) document applicational assignments within geology courses. These evaluations, however, are based solely on instructor opinion and informal student comments. To evaluate the effectiveness of experiential assignments this study utilizes empirical data from control and test groups in each of two semesters of Geology 100, a general education course on dinosaurs. Control groups completed traditional research papers which were replaced by experiential assignments in the test groups. The first semester …

Trace: A Differentiable Approach To Line-Level Stroke Recovery For Offline Handwritten Text, Taylor Neil Archibald

Theses and Dissertations

Stroke order and velocity are helpful features in the fields of signature verification, handwriting recognition, and handwriting synthesis. Recovering these features from offline handwritten text is a challenging and well-studied problem. We propose a new model called TRACE (Trajectory Recovery by an Adaptively-trained Convolutional Encoder). TRACE is a differentiable approach using a convolutional recurrent neural network (CRNN) to infer temporal stroke information from long lines of offline handwritten text with many characters. TRACE is perhaps the first system to be trained end-to-end on entire lines of text of arbitrary width and does not require the use of dynamic exemplars. Moreover, …

Lithofacies, Sequence Stratigraphy, And Sedimentology Of Desert Creek Platform, Slope, And Basin Carbonates, Southern Margin Of The Aneth Complex, Middle Pennsylvanian, Paradox Basin, Utah, Christopher M. Perfili

Theses and Dissertations

The Aneth Field in the Paradox Basin (SE Utah) has produced nearly 500 MMbbls of oil from phylloid-algal and oolitic carbonate reservoirs of the lower and upper Desert Creek (Paradox Formation, Middle Pennsylvanian) sequences, respectively. The oil resides in a 150 to 200 foot-thick isolated carbonate platform located in a distal ramp setting on the southwest margin of the Paradox Basin. The horseshoe-shaped platform is roughly 12 miles in diameter with an aerial extent of approximately 144 square miles. Evaluation of the platform-to-basin transition on the leeward (southern) margin of the Aneth Platform, the focus of this study, was made …

An Ulk1-Independent Mechanism Of Atg9a Regulation In Basal Autophagy, Ashari Rashmi Kannangara

Theses and Dissertations

Macroautophagy (hereafter referred to as autophagy) is the bulk degradation and recycling of cytoplasmic materials by forming a double membrane vesicle called the autophagosome. Autophagosome formation is regulated by the coordinated action of a set of proteins. ATG9A is the only multispanning transmembrane protein that plays an essential role in autophagosome formation, yet its function is largely elusive. Previous studies have shown that the C-terminus of ATG9A plays an important role in regulating its trafficking and proper function in autophagy. In line with that idea, we previously identified an AMPK- and ULK1- mediated phosphorylation on the C terminus of ATG9A …

Formulating A Crowd State Prediction Problem For Application To Crowd Control, Brooks A. Butler

Theses and Dissertations

This project considers a new application of crowd control, namely, keeping the public safe during large scale demonstrations. This problem is difficult for a variety of reasons, including limited access to informative sensing and effective actuation mechanisms, as well as limited understanding of crowd psychology and dynamics. This project takes a first step towards solving this problem by formulating a crowd state prediction problem in consideration of recent work involving crowd behavior identification, crowd movement modeling, and crowd psychology modeling. We build a non-linear crowd behavior model incorporating components of personality modeling, human emotion modeling, group opinion dynamics, and group …

Predicting Plans And Actions In Two-Player Repeated Games, Najma Mathema

Theses and Dissertations

Artificial intelligence (AI) agents will need to interact with both other AI agents and humans. One way to enable effective interaction is to create models of associates to help to predict the modeled agents' actions, plans, and intentions. If AI agents are able to predict what other agents in their environment will be doing in the future and can understand the intentions of these other agents, the AI agents can use these predictions in their planning, decision-making and assessing their own potential. Prior work [13, 14] introduced the S# algorithm, which is designed as a robust algorithm for many two-player …

Semantic-Driven Unsupervised Image-To-Image Translation For Distinct Image Domains, Wesley Ackerman

Theses and Dissertations

We expand the scope of image-to-image translation to include more distinct image domains, where the image sets have analogous structures, but may not share object types between them. Semantic-Driven Unsupervised Image-to-Image Translation for Distinct Image Domains (SUNIT) is built to more successfully translate images in this setting, where content from one domain is not found in the other. Our method trains an image translation model by learning encodings for semantic segmentations of images. These segmentations are translated between image domains to learn meaningful mappings between the structures in the two domains. The translated segmentations are then used as the basis …