Physical Sciences and Mathematics Commons^™

Exploring Student Perceptions Of Behavioral, Cognitive, And Emotional Engagement At The Activity Level In General Chemistry, Nicole Naibert, Elizabeth Vaughan, Kylee M. Brevick, Jack Barbera

Chemistry Faculty Publications and Presentations

Although active learning strategies are being incorporated into many higher-education STEM courses, not all students benefit from these activities to the same extent. As these types of activities are designed to engage students in their learning, differences in student engagement may explain some of the differences in learning outcomes. However, before student engagement in active learning activities can be meaningfully measured using a self-report survey, it is important to evaluate if students perceive engagement similarly to the literature definitions on which these measures are based. Therefore, this study sought to explore students’ perceptions of the behavioral, cognitive, and emotional dimensions …

A New Agent-Based Model Offers Insight Into Population-Wide Adoption Of Prosocial Common-Pool Behavior, Garry Sotnik, Thaddeus Shannon, Wayne Wakeland

Systems Science Faculty Publications and Presentations

New theoretical agent-based model of population-wide adoption of prosocial common-pool behavior with four parameters (initial percent of adopters, pressure to change behavior, synergy from behavior, and population density); dynamics in behavior, movement, freeriding, and group composition and size; and emergence of multilevel group selection. Theoretical analysis of model’s dynamics identified six regions in model’s parameter space, in which pressure-synergy combinations lead to different outcomes: extinction, persistence, and full adoption. Simulation results verified the theoretical analysis and demonstrated that increases in density reduce number of pressure-synergy combinations leading to population-wide adoption; initial percent of contributors affects underlying behavior and final outcomes, …

New Opportunities And Untapped Scientific Potential In The Abyssal Ocean, Jeffrey J. Marlowe, Rika E. Anderson, Anna-Louise Reysenbach, Jeffrey S. Seewald, Timothy M. Shank, Andreas P. Teske, V. Dorsey Wanless, S. Adam Soule

Biology Faculty Publications and Presentations

The abyssal ocean covers more than half of the Earth’s surface, yet remains understudied and underappreciated. In this Perspectives article, we mark the occasion of the Deep Submergence Vehicle Alvin’s increased depth range (from 4500 to 6500 m) to highlight the scientific potential of the abyssal seafloor. From a geologic perspective, ultra-slow spreading mid-ocean ridges, Petit Spot volcanism, transform faults, and subduction zones put the full life cycle of oceanic crust on display in the abyss, revealing constructive and destructive forces over wide ranges in time and space. Geochemically, the abyssal pressure regime influences the solubility of constituents such as …

An Automated Zoom Class Session Analysis Tool To Improve Education, Jack Arlo Cannon Ii

Dissertations and Theses

The recent shift towards remote education has presented new challenges for instructors with respect to teaching evaluation. Students in traditional classrooms send signals to instructors which provide feedback for the effectiveness of a given lecture. Virtual learning environments lack some of these communication channels and require new ways of collecting feedback. This work presents a suite of analysis tools for the virtual instructor. Given the transcript and video files for a Zoom meeting, this tool summarizes student sentiment and speaking characteristics. Sentiment scores are derived using state of the art Natural Language Processing (NLP) models. The video file is used …

Linear Nearest Neighbor Flocks With All Distinct Agents, Robert G. Lyons

Dissertations and Theses

This dissertation analyzes the global dynamics of 1-dimensional agent arrays with nearest neighbor linear couplings. The equations of motion are second order linear ODE's with constant coefficients. The novel part of this research is that the couplings are different for each agent. We allow the forces to depend on the relative position and relative velocity (damping terms) of the agents, and the coupling magnitudes differ for each agent. Further, we do not assume that the forces are "Newtonian'" (i.e., the force due to A on B equals minus the force of B on A) as this assumption does not apply …

Quadrature For Implicitly-Defined Finite Element Functions On Curvilinear Polygons, Jeffrey S. Ovall, Samuel E. Reynolds

Mathematics and Statistics Faculty Publications and Presentations

Abstract

H¹" role="presentation" style="box-sizing: border-box; margin: 0px; padding: 0px; display: inline-block; line-height: normal; font-size: 16.2px; word-spacing: normal; overflow-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; position: relative;">H1-conforming Galerkin methods on polygonal meshes such as VEM, BEM-FEM and Trefftz-FEM employ local finite element functions that are implicitly defined as solutions of Poisson problems having polynomial source and boundary data. Recently, such methods have been extended to allow for mesh cells that are curvilinear polygons. Such extensions present new challenges for determining suitable quadratures. We describe an approach …

Phosphorylation Of The Aggregate-Forming Protein Alpha-Synuclein On Serine-129 Inhibits Its Dna-Bending Properties, Sydney E. Dent, Dennisha P. King, Valerie R. Osterberg, Eleanor K. Adams, Marilyn R. Mackiewicz, Tamily A. Weissman, Vivek K. Unni

Chemistry Faculty Publications and Presentations

Alpha-synuclein (aSyn) is a vertebrate protein, normally found within the presynaptic nerve terminal and nucleus, which is known to form somatic and neuritic aggregates in certain neurodegenerative diseases. Disease-associated aggregates of aSyn are heavily phosphorylated at serine-129 (pSyn), while normal aSyn protein is not. Within the nucleus, aSyn can directly bind DNA, but the mechanism of binding and the potential modulatory roles of phosphorylation are poorly understood. Here we demonstrate using a combination of electrophoretic mobility shift assay and atomic force microscopy approaches that both aSyn and pSyn can bind DNA within the major groove, in a DNA length-dependent manner …

Adverse Reactions In A Phase 1 Trial Of The Anti-Malarial Dm1157: An Example Of Pharmacokinetic Modeling And Simulation Guiding Clinical Trial Decisions, Stephen J. Balevic, Shruti M. Raja, Rachel Randall, Gregory A. Deye, Thomas Conrad, Aya Nakamura, David H. Peyton, Sandra Shotwell, Katherine May Liebman, Multiple Additional Authors

Chemistry Faculty Publications and Presentations

Introduction: There is an urgent need to develop new drugs to treat malaria due to increasing resistance to first-line therapeutics targeting the causative organism, Plasmodium falciparum (P. falciparum). One drug candidate is DM1157, a small molecule that inhibits the formation of hemozoin, which protects P. falciparum from heme toxicity. We describe a first-in-human, phase 1 trial of DM1157 in healthy adult volunteers that was halted early because of significant toxicity.

Methods: Adverse events were summarized using descriptive statistics. We used pharmacokinetic modeling to quantitatively assess whether the DM1157 exposure needed for P. falciparum inhibition was achievable at safe doses.

Results: …

Rate Maximization In A Uav Based Full-Duplex Multi-User Communication Network Using Multi-Objective Optimization, Syed Muhammad Hashir, Sabyasachi Gupta, Gavin Megson, Ehsan Aryafar, Joseph Camp

Computer Science Faculty Publications and Presentations

In this paper, we study an unmanned-aerial-vehicle (UAV) based full-duplex (FD) multi-user communication network, where a UAV is deployed as a multiple-input–multiple-output (MIMO) FD base station (BS) to serve multiple FD users on the ground. We propose a multi-objective optimization framework which considers two desirable objective functions, namely sum uplink (UL) rate maximization and sum downlink (DL) rate maximization while providing quality-of-service to all the users in the communication network. A novel resource allocation multi-objective-optimization-problem (MOOP) is designed which optimizes the downlink beamformer, the beamwidth angle, and the 3D position of the UAV, and also the UL power of the …

A Biomimetic Model For Oxidative Metabolism Of Thiopurine Drugs, Oluyemi Oludare Alo

Dissertations and Theses

Type B hepatotoxicity has been reported for thiopurines, and this has limited their clinical uses. Although a lot of research has been done on thiopurines, the precise mechanism of their hepatotoxicity is still unclear. The results of the in vitro and in vivo experiments aimed at assessing the products of their CYP450-mediated bioactivation have been contradictory. Although it has been theorized that the hepatic toxicity of this class of drug is caused by their bioactivation to electrophilic reactive metabolite (RM) and concomitant protein binding to form immunogenic adducts, resulting in direct cellular dysfunction or an immune response via the formation …

Temperature And Predator Effects On Green Crabs (Carcinus Maenas) And Their Distribution In South Slough National Estuarine Research Reserve, Elissa Connolly-Randazzo

Dissertations and Theses

The invasive green crab (Carcinus maenas) has increased in abundance and distribution among Oregon's estuaries. Its global success in establishing in new environments and tolerance for abiotic stressors, such as temperature, raises concern for C. maenas to negatively influence native crab species, especially given global climate change. To improve in predicting invasion impacts, this work analyzed the results from a controlled tank experiment at Portland State University and the field data on a population of C. maenas in South Slough National Estuarine Research Reserve (SSNERR). The aquarium experiment documented predation pressure on C. maenas across a range of …

Spatial And Seasonal Variations Of Microplastic Concentrations In Portland's Freshwater Ecosystems, Rebecca Talbot

Dissertations and Theses

Microplastics are a pollutant of growing concern and are ubiquitous in a variety of environmental compartments. The majority of microplastics research to date has been conducted in marine waters, and less is known regarding the sources and delivery pathways of microplastics in urban rivers. The first chapter is comprised of a review of the scientific literature regarding the spatial and temporal factors affecting global freshwater microplastic distributions and abundances. Microplastic spatial distributions are heavily influenced by anthropogenic factors, with higher concentrations reported in regions characterized by urban land cover, high population density, and wastewater treatment plant effluent. Temporal variables of …

Effects Of Green Crab (Carcinus Maenas) Across Variable Densities Of Eelgrass (Zostera Marina), Kimberly Alexis Brown

Dissertations and Theses

Eelgrass (Zostera marina) plays a critical role in estuarine ecosystem function by sustaining a variety of marine and freshwater species, but it's increasingly threatened by the aggressive non-native green crab (Carcinus maenas). The abundance of C. maenas is on the rise within the coastal environment of Oregon and it is imperative to know how these populations will affect the long-term health of Z. marina. C. maenas have been linked to declines in Z. marina coverage and shellfish abundance, but there has been no research on to what extent the density of Z. marina affects its …

The New Shiny Penny? Regenerative Agriculture Beliefs And Practices Among Portland's Urban Agriculturalists, Melia Ann Chase

Dissertations and Theses

Regenerative agriculture (RA) is a set of farming and land management practices intended to support or enhance soil health and carbon sequestration potential of soils while producing food, fiber, or other agricultural products. It has received broad acclaim from scholars, corporations, and governmental bodies as a potential means of sequestering carbon and mitigating climate change impacts. It has also received critique and pushback for its vague definition, shifting metrics, and lack of acknowledgement of the Indigenous practices underlying the modern suite of regenerative practices. The purpose of this research is to investigate the beliefs Portland, Oregon urban agricultural practitioners hold …

Materials And Methodologies For Spectroscopic And Optical Analytical Applications In Cultural Heritage Conservation Science, Lyndsay Nichole Kissell

Dissertations and Theses

The field of conservation science falls in the intersection of science and art. The work of conservation scientists may include any single subdiscipline of chemistry, though it is most commonly a highly interdisciplinary field taking skills from analytical, organic, and inorganic chemistry, as well as surface and materials science. The aims of conservation scientists are to answer questions about the production and aging of material cultural heritage. Knowing the materials used by an artist can lead to insight about the intentions of the object and knowing how those materials degrade will enable the use of preventative measures to ensure the …

Inverse Modeling Of Atmospheric Ch4 And Δ13C-Ch4 Measurements From Surface Observation Sites To Understand Trends In Global Methane Emissions Over More Than Three Decades, Sayantani Karmakar

Dissertations and Theses

Methane (CH₄) is the second most important greenhouse gas with a radiative forcing of 0.97 W/m² including both direct and indirect effects and a global warming potential of 28 over a 100-year time horizon. Unlike CO₂ whose rate of growth in the atmosphere has remained positive and increased in recent decades, the behavior of atmospheric methane is considerably more complex and is much less understood on account of the spatiotemporal variability of its emissions which include biogenic (e.g., wetlands, ruminants, rice agriculture), thermogenic (fossil fuels), and pyrogenic (i.e., biomass burning) sources. After sustained growth during most …

Heat, Wildfire And Energy Demand: An Examination Of Residential Buildings And Community Equity, Chrissi Argyro Antonopoulos

Dissertations and Theses

Extreme heat and wildfire events are becoming more prolific and exacerbated by climate change, carrying significant implications for environmental and social systems. Residential buildings play a central role in protecting people from heat and pollutant exposure during extreme weather events, but the level of protection varies dramatically depending on building energy efficiency and technology availability. Low-income and communities of color have higher energy burdens compared to affluent populations, and underserved communities often do not have financial resources for, or access to, advanced building technologies. This dissertation explores the impacts of extreme heat and wildfire on residential buildings, focused specifically on …

More Than Words: Articulating The Multisensory Experiences Of Protected Area Visitors In Southern Nevada, Sara Nicole Temme

Dissertations and Theses

The complex sensory experiences of visitors to U.S. protected areas are not well understood. Previous research investigates visitor activities, motivations, and the ways place attachment cultivates support for conservation activities and other pro-environmental behavior. However, it is unclear how protected area visitor sensory experiences contribute to these behaviors. This study aims to articulate the multisensory experiences of visitors to the Desert National Wildlife Refuge Complex and the Spring Mountains National Recreation Area in southern Nevada, U.S.A. Specifically, it demonstrates the complexity of these experiences as present, intertwined, and embodied in all visit phases: before, during, and after. Utilizing a mixed-method …

Stakeholder Perceptions Of Microplastics Management In Oregon, Maya Hurst-Mayr

Environmental Science and Management Professional Master's Project Reports

There is currently no federal policy in the United States that specifically addresses microplastics (MPs) pollution. However, states are beginning to act on this issue; California's SB 1422 initiates measurement of MPs in drinking water resources and Senate Bill 1263 requires the state to adopt a strategy to reduce the ecological impact of MPs in marine ecosystems. Other West Coast states like Oregon and Washington are expected to follow California's example. It is important to know what the actors who are a part of shaping MPs policy in Oregon would see as barriers and opportunities to doing so. We conducted …

Identifying And Prioritizing Urban And Commercial Stormwater Concerns: City Of Grants Pass, Oregon, Amie Nicole Siedlecki

Environmental Science and Management Professional Master's Project Reports

For many communities, drinking water comes from surface water sources, or source water, such as rivers and creeks. Within the city of Grants Pass, Oregon, this is the case. The Rogue River, which spans 215 miles, beginning near Crater Lake and emptying into the ocean at Gold Beach, is Grants Pass' Rogue River, in relation to drinking water, is rarely an issue for the City of Grants Pass' Public Works Department, the potential contaminant sources (PCS) from the urban, commercial, and industrial geographical areas of Grants Pass is a concern. In order to deploy treatment processes that are capable of …

Data From: Inventory Of Glaciers And Perennial Snowfields Of The Conterminous Usa, Andrew G. Fountain, Bryce Glenn, Christopher Mcneil

Geology Faculty Datasets

This is an updated inventory of glaciers and perennial snowfields of the contiguous United States. All perennial snow and ice features greater than 0.01 km² are included. Outlines are mostly derived from aerial imagery provided by the National Agricultural Imagery Program, US Department of Agriculture with some satellite imagery in places where aerial imagery was not suitable. Imagery dates range from 2013 to 2020. Most (70%) of the outlines were acquired from 2015 imagery.

Reconstructability Analysis: Discrete Multivariate Modeling, Martin Zwick

Systems Science Faculty Publications and Presentations

An introduction to Reconstructability Analysis for the Discrete Multivariate Modeling course and for other purposes.

Estimating Transport Of Diesel Particulate Emissions In The Portland Metro Using Lagrangian-Based Dispersion Modeling, Andrew Mckinley Rogers

Environmental Science and Management Professional Master's Project Reports

Air pollution from diesel combustion is a well-known and serious problem which adversely impacts human and environmental health throughout the world. One of the primary pollutants of concern from diesel combustion are the solid particles formed as a byproduct of the incomplete combustion of the diesel, also known as diesel particulate matter. As a result of the ubiquitous use of diesel-fired engines in urban environments, understanding the transport of diesel particulate matter from the exhaust is paramount in assessing human exposure to this toxic pollutant. Air dispersion modeling is one method to study how diesel particulate matter is transported and …

Carli Creek Regional Water Quality Project: Assessing Water Quality Improvement At An Urban Stormwater Constructed Wetland, Christopher L. Desiderati

Environmental Science and Management Professional Master's Project Reports

Stormwater management is an ongoing challenge in the United States and the world at-large. As state and municipal agencies grapple with conflicting interests like encouraging land development, complying with permits to control stormwater discharges, “urban stream syndrome” effects, and charges to steward natural resources for the long-term, some agencies may turn to constructed wetlands (CWs) as aesthetically pleasing and functional natural analogs for attenuating pollution delivered by stormwater runoff to rivers and streams. Constructed wetlands retain pollutants via common physical, physicochemical, and biological principles such as settling, adsorption, or plant and algae uptake. The efficacy of constructed wetlands for pollutant …

Equivalence Of The Transition Heat Capacities Of Proteins And Dna, Matthew W. Eskew, Albert S. Benight

Chemistry Faculty Publications and Presentations

It has been reported for many globular proteins that the native heat capacity at 25°C, per gram, is the same. This has been interpreted to indicate that heat capacity is a fundamental property of native proteins that provides important information on molecular structure and stability. Heat capacities for both proteins and DNA has been suggested to be related to universal effects of hydration/solvation on native structures. Here we report on results from thermal denaturation analysis of two well-known proteins, human serum albumin and lysozyme, and a short DNA hairpin. The transition heat capacities at the Tm for the three molecules …

A One-Dimensional Field Dislocation Mechanics Model Using Discontinuous Galerkin Method, Ja'nya Breeden, Dow Drake, Jay Gopalakrishnan, Saurabh Puri

Mathematics and Statistics Faculty Publications and Presentations

A numerical solution strategy for a one-dimensional field dislocation mechanics (FDM) model using the Discontinuous Galerkin (DG) method is developed. The FDM model is capable of simulating the dynamics of discrete, nonsingular dislocations using a partial differential equation involving a conservation law for the Burgers vector content with constitutive input for nucleation and velocity. Modeling of individual dislocation lines with an equilibrium compact core structure in the context of this continuum elastoplastic framework requires a non-convex stored energy density. Permanent deformation and stress redistribution caused by the dissipative transport of dislocations is modeled using thermodynamics-based constitutive laws. A DG method …

Periodic Points Of Polynomials Over Finite Fields, Derek Garton

Mathematics and Statistics Faculty Publications and Presentations

Fix an odd prime p. If r is a positive integer and f is a polynomial with coefficients in Fpr, let Pp,r⁡(f) be the proportion of P1⁢(Fpr) that is periodic with respect to f. We show that as r increases, the expected value of Pp,r⁡(f), as f ranges over quadratic polynomials, is less than 22/(log⁡log⁡pr). This result follows from a uniformity theorem on specializations of dynamical systems of rational functions over residually finite Dedekind domains. The specialization theorem generalizes previous work by Juul et al. that holds for rings of integers of number fields. Moreover, under stronger hypotheses, we effectivize …

Patterns Of Interdisciplinary Collaboration Resemble Biogeochemical Relationships In The Mcmurdo Dry Valleys, Antarctica: A Historical Social Network Analysis Of Science, 1907–2016, Stephen M. Chignell, Adrian Howkins, Poppie Gullett, Andrew G. Fountain

Geology Faculty Publications and Presentations

Co-authorship networks can provide key insights into the production of scientific knowledge. This is particularly interesting in Antarctica, where most human activity relates to scientific research. Bibliometric studies of Antarctic science have provided a useful understanding of international and interdisciplinary collaboration, yet most research has focused on broad-scale analyses over recent time periods. Here, we take advantage of a ‘Goldilocks’ opportunity in the McMurdo Dry Valleys, an internationally important region of Antarctica and the largest ice-free region on the continent. The McMurdo Dry Valleys have attracted continuous and diverse scientific activity since 1958. It is a geographically confined region with …

Workflow Critical Path: A Data-Oriented Critical Path Metric For Holistic Hpc Workflows, Daniel D. Nguyen, Karen L. Karavanic

Computer Science Faculty Publications and Presentations

Current trends in HPC, such as the push to exascale, convergence with Big Data, and growing complexity of HPC applications, have created gaps that traditional performance tools do not cover. One example is Holistic HPC Workflows — HPC workflows comprising multiple codes, paradigms, or platforms that are not developed using a workflow management system. To diagnose the performance of these applications, we define a new metric called Workflow Critical Path (WCP), a data-oriented metric for Holistic HPC Workflows. WCP constructs graphs that span across the workflow codes and platforms, using data states as vertices and data mutations as edges. …

Distribution And Characterization Of Rhyolites Of The Strawberry Volcanics -- Evolution Of A Major Rhyolite Field Associated With Columbia River Basalt Magmatism, Eastern Oregon, Usa, Chanel Leigh Dvorak

Dissertations and Theses

The Strawberry Rhyolites constitute a significant rhyolite field among the largest in Oregon. Aerial coverage of approximately 386 km² and an overall estimated volume of ~67 km³ using a median thickness for each unit. On the other hand, the total volume could be greater than 100 km³ if greater thicknesses apply. The Strawberry Rhyolites, a largely unknown mid-Miocene silicic volcanic rocks, crop out amongst voluminous flood basalt flows of the Columbia River Basalt Group (CRBG) in eastern Oregon. The eruptive activity of the Strawberry Rhyolites is currently constrained to span a period of about 2 million years, …