Physical Sciences and Mathematics Commons^™

Creating Regression Model For Non-Markov Transition Probability Using Pseudo-Observations, Michael Gray

Dissertations and Theses

A multi-state model is a graphical tool widely used to illustrate a transitional relationship between states in many applications. We will study the transition probabilities of an illness-death model, which is an example of a multi-state model. We will investigate transition probabilities using a counting process approach. Aalen-Johansen estimator is the gold-standard in estimating a transition probability. However, Aalen-Johansen estimator may be biased when the Markov assumption is violated. Therefore, Aalen-Johansen estimator is an unreliable estimator when the Markov assumption is violated. Several papers have published non-parametric estimators that accommodate for non-Markov models using a counting process approach.

Furthermore, there …

Survival Times And Investment Analysis With Dynamic Learning, Zhenzhen Li

Dissertations and Theses

The central statistical problem of survival analysis is to determine and characterize the conditional distribution of a survival time given a history of some observed health markers.

This dissertation contributes to the modeling of such conditional distributions in a setup where the health markers evolve randomly over time in a manner that can be represented by an Ito stochastic process, that is, a stochastic process that can be written as a sum of a time integral of some stochastic process and an Ito integral of some stochastic process, with both integrands subject to certain restrictions.

The random survival time is …

Uhv-Shear-Force Acoustic Near-Field Microscopy And Its Implementation In The Study Of Confined Mesoscopic Fluids, Theodore Alex Brockman

Dissertations and Theses

The design, construction, and implementation of Shear-force Acoustic Near-Field Microscopy (SANM), operational from ultrahigh vacuum (UHV) to ambient conditions--offering a pristine environment for more reliable characterization the hydrophobic/hydrophilic wetting properties of surfaces--is presented. SANM capitalizes on its sensitivity to the evanescent near-field acoustic emissions from a mesoscopic fluid (confined between the apex of a laterally oscillating tapered nanosized probe and a flat substrate) when subjected to shear motion. This distinct capability provides direct access to the fluid’s viscoelastic response when subjected to shear interactions, in contrast to indirect measurements performed by other standard probe proximity scanning techniques. The entire …

The Role Of The Armed Forces Of The Philippines (Afp) In Disaster Response And Adaptation Strategies To Climatic Disasters In Manila, Edmundo Nicolas Jr.

Geography Masters Research Papers

This study described the roles of the Armed Forces of the Philippines (AFP) in Disaster Risk Reduction Management (DRRM) in Metro Manila and how climate-induced hazards impact the role of the military. It used a qualitative approach, which involved semi- structured interviews among AFP officers and barangay leaders with expertise and experience in DRRM and an analysis of selected policy documents and military doctrine. These methods revealed that: (1) the military acts as a political first-aid, since they are the first responders – thus, the face of the local government – in climactic disasters during peacetime; (2) the military is …

End-To-End Gpu Acceleration Of Low-Order-Refined Preconditioning For High-Order Finite Element Discretizations, Will Pazner, Tzanio Kolev, Jean-Sylvain Camier

Mathematics and Statistics Faculty Publications and Presentations

In this article, we present algorithms and implementations for the end-to-end GPU acceleration of matrix-free low-order-refined preconditioning of high-order finite element problems. The methods described here allow for the construction of effective preconditioners for high-order problems with optimal memory usage and computational complexity. The preconditioners are based on the construction of a spectrally equivalent low-order discretization on a refined mesh, which is then amenable to, for example, algebraic multigrid preconditioning. The constants of equivalence are independent of mesh size and polynomial degree. For vector finite element problems in H(curl) and H(div) (e.g., for electromagnetic or radiation diffusion problems), …

Stability Of Retinol In Liposomes As Measured By Fluorescence Lifetime Spectroscopy And Flim, Louis Sumrall, L. Smith, Elmukhtar Ehmed Alhatmi, Yekaterina G. Chmykh, D. Mitchell, Jay Nadeau

Physics Faculty Publications and Presentations

Retinol shows complex photophysical properties that make it potentially useful as an exogenous or endogenous probe of membrane microenvironment, but it has not been fully explored. In this study, we use bulk fluorescence lifetime measurements and fluorescence lifetime imaging microscopy (FLIM) to examine the stability of retinol in phosphatidylcholine (PC) multilamellar and unilamellar vesicles with and without cholesterol. We find that both light and exposure to ambient temperature and oxygen contribute to retinol degradation, with the addition of an antioxidant such as butylated hydroxytoluene (BHT) essential to provide stability, especially in the absence of cholesterol. With exposure to ultraviolet light …

Flash-Rt: Using High-Dose Radiation For Clinical Radiation Therapy, Deja Stubbs

University Honors Theses

This paper is a literature review on the possible mechanisms behind the FLASH effect and why such research can advance the world of radiology treatment by modifying current clinical linear accelerators to produce ultra-high doses of radiation. Radiation Therapy, also known as external Beam Radiation Therapy, is a common type of cancer treatment. Globally, cancer is the second-leading cause of death, but has seen an increase in survival rates over the past couple of years. Cancer can develop in almost any part of the body since cancer is defined as uncontrolled cell growth. The FLASH Effect is seen when treating …

Indigenous Water Justice: Theory, Gaps, And Opportunities For Application, Ruby Howard

University Honors Theses

Indigenous people are particularly at risk of water scarcity in the U.S. and abroad, and face high rates of nonexistent or failing water infrastructure, water pollution, pipeline proposals that threaten water resources, and water-related climate change impacts. They also are often unequipped, politically and economically, to react and adapt to these impacts, resulting in devastating health impacts. Due to this widespread insecurity, many scholars are calling for the application of a theory and set of principles known as water justice. However, Indigenous people have pointed out that water justice literature does not focus enough on Indigenous issues, often neglecting the …

Pfas In News Media: A Quantitative And Qualitative Analysis, Madison Haley

University Honors Theses

News media analysis allows for a greater understanding of mainstream public concerns throughout time. The history of US news articles covering per- and polyfluoroalkyl substances (PFAS), a class of chemicals posing increasing threats to public health and the environment, demonstrates Americans' awareness and perceptions of these chemicals over time. Based on the quantitative and qualitative analyses of PFAS-related national news articles in 2012-2022, this study discusses media representations and public perceptions of PFAS during the stated period. Results indicate an over 5700% increase in PFAS-related news articles over the 10-year timespan. Further, thematic analysis reveals that PFAS-related news articles are …

What Is The Mathematics In Mathematics Education?, Eva Thanheiser

Mathematics and Statistics Faculty Publications and Presentations

In this paper I tackle the question What is the mathematics in mathematics education? By providing three different frames for the word mathematics.

1.

Frame 1: Mathematics as an abstract body of knowledge/ideas, the organization of that into systems and structures, and a set of methods for reaching conclusions.

2.

Frame 2: Mathematics as contextual, ever present, as a lens or language to make sense of the world.

3.

Frame 3: Mathematics as a verb (not a noun), a human activity, part of one’s identity.

After introducing the frames and examining their distinction and their overlap, I discuss their implication …

Willow Abundance And Condition Mapping In Rocky Mountain National Park, Eric M. Nielsen

Institute for Natural Resources Publications

Riparian and wetland willow species have undergone serious declines in Rocky Mountain National Park as a consequence of a variety of environmental changes and, most recently, damage resulting from moose overpopulation. To address concerns about the long-term status of willows in the park, we developed remote sensing-based raster maps of riparian and wetland willow species presence, canopy cover percentage, canopy height, and leaf area index. All outputs were produced at 3-meter resolution, and represent willows as they existed in 2021. The mapping was performed via random forests classification and regression models trained on several hundred vegetation plots from a variety …

Implementing A Functional Logic Programming Language Via The Fair Scheme, Andrew Michael Jost

Dissertations and Theses

This document presents a new compiler for the Functional Logic programming language Curry based on a novel pull-tabbing evaluation strategy called the Fair Scheme. A simple version of the Fair Scheme is proven sound, complete, and optimal. An elaborated version is also developed, which supports narrowing computations and other features of Curry, such as constraint programming, equational constraints, and set functions.

The Fair Scheme is used to develop a new Curry system called Sprite, a high-quality, performant implementation whose aims are to promote practical uses of Curry and to serve as a laboratory for further research. An important aspect of …

A Gridded Co2 Emissions Inventory For Portland, Or, James Eckhardt Powell

Dissertations and Theses

Here we develop a new high resolution inventory of CO₂ emissions for the three Oregon counties which comprise the bulk of the City of Portland, Oregon, USA. Locally curated and long-running data collection efforts for on-road traffic activity and emission rates are used to model on-road emissions, and a new survey of the area's natural gas network informs the building energy model. The inventory estimates total emissions of CO₂ for each hour of the year 2018 in the on-road, residential, and commercial building sectors at 1 km² resolution. The onroad inventory compares to within 3% with an …

Phytoplankton Community As An Indicator Of Cyanobacteria Harmful Algal Blooms In High Mountain Lakes, Victoria Elizabeth Avalos

Dissertations and Theses

Cyanobacteria blooms are a growing issue worldwide and can be harmful to both aquatic life and human health. Warm temperatures, nutrient loading, stable water columns, and selective grazing of zooplankton and phytoplankton can contribute to cyanobacteria bloom formation. In this study, I characterized the algal communities and water quality differences in two physiographically similar lakes with relatively little human influences, Odell and Crescent Lakes, Oregon, to better understand potential contributing factors to cyanobacteria harmful algal bloom formation (cyanobacteria bloom) in Odell Lake.

There are three hypotheses in this study:

1. If there was a cyanobacteria bloom in Odell Lake, but not …

Evapotranspiration Of Residential Lawns Across The United States, Noortje H. Grijseels, Elizaveta Litvak, Meghan Avolio, Anika R. Bratt, Jeannine Cavender-Bares, Peter M. Groffman, Sarah E. Hobbie, Susannah B. Lerman, Jennifer L. Morse, Multiple Additional Authors

Environmental Science and Management Faculty Publications and Presentations

Despite interest in the contribution of evapotranspiration (ET) of residential turfgrass lawns to household and municipal water budgets across the United States, the spatial and temporal variability of residential lawn ET across large scales is highly uncertain. We measured instantaneous ET (ET_inst) of lawns in 79 residential yards in six metropolitan areas: Baltimore, Boston, Miami, Minneapolis-St. Paul (mesic climates), Los Angeles and Phoenix (arid climates). Each yard had one of four landscape types and management practices: traditional lawn-dominated yards with high or low fertilizer input, yards with water-conserving features, and yards with wildlife-friendly features. We measured ET_{inst …}

Caspi: Collaborative Photon Processing For Active Single-Photon Imaging, Jongho Lee, Atul Ingle, Jenu V. Chacko, Kevin W. Eliceiri, Mohit Gupta

Computer Science Faculty Publications and Presentations

Image sensors capable of capturing individual photons have made tremendous progress in recent years. However, this technology faces a major limitation. Because they capture scene information at the individual photon level, the raw data is sparse and noisy. Here we propose CASPI: Collaborative Photon Processing for Active Single-Photon Imaging, a technology-agnostic, application-agnostic, and training-free photon processing pipeline for emerging high-resolution single-photon cameras. By collaboratively exploiting both local and non-local correlations in the spatio-temporal photon data cubes, CASPI estimates scene properties reliably even under very challenging lighting conditions. We demonstrate the versatility of CASPI with two applications: LiDAR imaging over a …

Divergence-Conforming Velocity And Vorticity Approximations For Incompressible Fluids Obtained With Minimal Facet Coupling, Jay Gopalakrishnan, Lukas Kogler, Philip L. Lederer, Joachim Schöberl

Mathematics and Statistics Faculty Publications and Presentations

We introduce two new lowest order methods, a mixed method, and a hybrid discontinuous Galerkin method, for the approximation of incompressible flows. Both methods use divergence-conforming linear Brezzi–Douglas–Marini space for approximating the velocity and the lowest order Raviart–Thomas space for approximating the vorticity. Our methods are based on the physically correct viscous stress tensor of the fluid, involving the symmetric gradient of velocity (rather than the gradient), provide exactly divergence-free discrete velocity solutions, and optimal error estimates that are also pressure robust. We explain how the methods are constructed using the minimal number of coupling degrees of freedom per facet. …

Quantum Multi-Solution Bernoulli Search With Applications To Bitcoin’S Post-Quantum Security, Alexandru Cojocaru, Juan Garay, Fang Song, Petros Wallden

Computer Science Faculty Publications and Presentations

A proof of work (PoW) is an important cryptographic construct which enables a party to convince other parties that they have invested some effort in solving a computational task. Arguably, its main impact has been in the setting of cryptocurrencies such as Bitcoin and its underlying blockchain protocol, which have received significant attention in recent years due to its potential for various applications as well as for solving fundamental distributed computing questions in novel threat models. PoWs enable the linking of blocks in the blockchain data structure, and thus the problem of interest is the feasibility of obtaining a sequence …

Glacialwater: A Dynamic Microbial Medium, Gilda Varliero, Pedro H. Lebre, Andrew G. Fountain, Beat Frey, Alexandre M. Anesio, Don A. Cowan

Geology Faculty Publications and Presentations

Microbial communities and nutrient dynamics in glaciers and ice sheets continuously change as the hydrological conditions within and on the ice change. Glaciers and ice sheets can be considered bioreactors as microbiomes transform nutrients that enter these icy systems and alter the meltwater chemistry. Global warming is increasing meltwater discharge, affecting nutrient and cell export, and altering proglacial systems. In this review, we integrate the current understanding of glacial hydrology, microbial activity, and nutrient and carbon dynamics to highlight their interdependence and variability on daily and seasonal time scales, as well as their impact on proglacial environments.

Impacts Of Floodplain Restoration On Water Temperature And Macroinvertebrates In Whychus Creek, Oregon, Wesley Nathan Noone

Dissertations and Theses

Stream restoration is a proposed climate adaptation tool, however, outcomes of floodplain restoration on stream temperature have been debated. Despite a growing number of studies that investigated water temperature in restored streams, few have quantified thermal heterogeneity in new habitat types created by restored hydrogeomorphic processes and the impact of thermal diversity on the aquatic macroinvertebrate community. In this study, I evaluated three hypotheses: 1) restoration increases habitat diversity, 2) habitat diversity increases water temperature heterogeneity, and 3) restored reaches have more diverse macroinvertebrate communities. I collected a total of 40 macroinvertebrate samples and characterized environmental conditions in three reaches …

Cyclic Behavior Of Transitional Fine-Grained Soils In Northern Willamette Valley, Frank Jarman

Civil and Environmental Engineering Master's Project Reports

As discussed within studies from Idriss and Boulanger (2008) and Bray and Sancio (2006), the undrained cyclic shear behavior of low-plasticity fine-grained soils will transition between liquefaction (sand-like behavior) to cyclic softening (clay-like behavior) over a narrow range of plasticity index (PI). Despite not being sufficiently understood, the cyclic behavior of low plasticity silts has become an increasingly important field of study due to the significant impact it has on ground deformations and infrastructure failure in areas that are seismically active. Laboratory tests were performed on soils by third party consultants on a site located in the northern Willamette Valley, …

Ce-Qual-W2 Performance Assessment Modeling 1979 Grh Flume Study, Logan Negherbon

Civil and Environmental Engineering Master's Project Reports

In an early review of numerical reservoir hydrodynamic models, the US Army Corps of Engineers developed a physical model at the US Army Waterways Experiment Station to assess the performance of modeling cold water underflow with numerous 2-dimensional and 3-dimensional numerical hydrodynamic models. Within this effort, the precursor for CE-QUAL-W2, the Laterally Averaged Reservoir Model, was defined and applied with limited success in representing the vertical velocity profile and outflow temperatures series collected from the physical model in the General Reservoir Hydrodynamics flume. CE-QUAL-W2 has since been modified from this early form in numerous ways including incorporation of higher order …

An Examination Of The Current Knowledge Of Contaminants In Mangroves: Hawaii And Globally, Geoffrey Szafranski

Environmental Science and Management Professional Master's Project Reports

The geographic range of mangrove forests is shifting quickly as they expand poleward in response to climate change while simultaneously being removed from their native extent to clear space for anthropogenic land-uses. Mangrove forests are also known to be sinks for anthropogenic contamination. Yet contamination research is under-researched in mangrove ecosystems, specifically the environmental fate, effect on biodiversity, and risk to human populations from contamination in the context of these changing conditions requires further research. The goal of this thesis is to address this data gap through analysis of contamination in the literature and through an investigational survey of mangrove …

Management Plan For The Western Painted Turtle At The Sandy River Delta In Troutdale, Oregon, Emma Scott

Environmental Science and Management Professional Master's Project Reports

This management plan has been prepared for the Lower Columbia Estuary Partnership and is intended to provide guidance for the improvement and protection of western painted turtle (Chrysemys picta bellii) habitat at the Sandy River Delta in Troutdale, Oregon. The Sandy River Delta is a 1500-acre natural area situated where the Columbia and Sandy Rivers meet. Its dynamic floodplain habitat supports a diverse assemblage of species, including the western painted turtle, an Oregon Conservation Strategy Species. A small, unknown number of western painted turtles utilize the wetland habitats of the Sandy River Delta, and the frequency in observations …

Longitudinal Changes In Alzheimer’S-Related Plasma Biomarkers And Brain Amyloid, Murat Bilgel, Abhay Moghekar, Henrik Zetterberg, Bruno Jedynak, Multiple Additional Authors

Mathematics and Statistics Faculty Publications and Presentations

Introduction Understanding longitudinal plasma biomarker trajectories relative to brain amyloid changes can help devise Alzheimer’s progression assessment strategies.

Methods We examined the temporal order of changes in plasma amyloid-β ratio (Aβ42/Aβ40), glial fibrillary acidic protein (GFAP), neurofilament light chain (NfL), and phosphorylated tau ratios (p-tau181/Aβ42, p-tau231/Aβ42) relative to 11C-Pittsburgh compound B (PiB) positron emission tomography (PET) cortical amyloid burden (PiB−/+). Participants (n = 199) were cognitively normal at index visit with a median 6.1-year follow-up.

Results PiB groups exhibited different rates of longitudinal change in Aβ42/Aβ40 (β = 5.41 × 10-4, SE = 1.95 × 10-4, p = 0.0073). …

Studies On Bonding, Syntheses, And Applications Of Diarylhalonium Compounds, Shubhendu Karandikar

Dissertations and Theses

Organic compounds containing functionalized benzenoid rings have found tremendous applications in pharmaceuticals, agrochemicals, commodity chemicals, and beyond. As a result, development of methods for the synthesis of functionalized benzenoid rings has gained much attention from the synthetic community. Although many transition-metal mediated methods to functionalize benzenoid rings are known, there has been an upsurge of activity in developing protocols for decoration of benzenoid cores promoted by p-block elements. This excitement stems from the sustainability of earth-abundant elements and unique reactivity patterns observed within the p-block. Among these, transformations promoted by hypervalent halogen compounds, and especially, the diarylhalonium salts are very …

7-Deazaguanines In Dna: Functional And Structural Elucidation Of A Dna Modification System, Samanthi Herath Gedara, Andrew Gustafson, Dirk Iwata-Reuyl, Multiple Additional Authors

Chemistry Faculty Publications and Presentations

The modified nucleosides 2′-deoxy-7-cyano- and 2′-deoxy-7-amido-7-deazaguanosine (dPreQ₀ and dADG, respectively) recently discovered in DNA are the products of the bacterial queuosine tRNA modification pathway and the dpd gene cluster, the latter of which encodes proteins that comprise the elaborate Dpd restriction–modification system present in diverse bacteria. Recent genetic studies implicated the dpdA, dpdB and dpdC genes as encoding proteins necessary for DNA modification, with dpdD–dpdK contributing to the restriction phenotype. Here we report the in vitro reconstitution of the Dpd modification machinery from Salmonella enterica serovar Montevideo, the elucidation of the roles of each protein and the X-ray …

Toward Efficient Rendering: A Neural Network Approach, Qiqi Hou

Dissertations and Theses

Physically-based image synthesis has attracted considerable attention due to its wide applications in visual effects, video games, design visualization, and simulation. However, obtaining visually satisfactory renderings with ray tracing algorithms often requires casting a large number of rays and thus takes a vast amount of computation. The extensive computational and memory requirements of ray tracing methods pose a challenge, especially when running these rendering algorithms on resource-constrained platforms, and impede their applications that require high resolutions and refresh rates. This thesis presents three methods to address the challenge of efficient rendering.

First, we present a hybrid rendering method to speed …

Tools For Quantifying Bacterial Motility Using Digital Holographic Microscopy As Applied To Studying The Simulated Microgravity Environment, Jacqueline Marie Acres

Dissertations and Theses

Digital holographic microcopy (DHM) is a label-free technique that has gained attention in recent years as a tool for volumetric imaging. One application of DHM is for the study of microbial motility with the advantage being that organisms may freely move within their environment. Images created from DHM are in the form of holograms. Holograms are time recordings showing XY information with the Z information contained within. Z information can be retrieved from the holograms directly through a variety of numerical techniques or through reconstruction. Datasets generated from DHM are large and processing remains a challenging task. Here, we show …

Microbial Motility At The Bottom Of North America: Digital Holographic Microscopy And Genomic Motility Signatures In Badwater Spring, Death Valley National Park, Carl Snyder, Jakob P. Centlvre, Shrikant Bhute, Jay Nadeau, Multiple Additional Authors

Physics Faculty Publications and Presentations

Motility is widely distributed across the tree of life and can be recognized by microscopy regardless of phylogenetic affiliation, biochemical composition, or mechanism. Microscopy has thus been proposed as a potential tool for detection of biosignatures for extraterrestrial life; however, traditional light microscopy is poorly suited for this purpose, as it requires sample preparation, involves fragile moving parts, and has a limited volume of view. In this study, we deployed a field-portable digital holographic microscope (DHM) to explore microbial motility in Badwater Spring, a saline spring in Death Valley National Park, and complemented DHM imaging with 16S rRNA gene amplicon …