Physical Sciences and Mathematics Commons^™

Data From: Drivers Of Zooplankton Community Composition In A Novel Ecosystem: Hawai’I Mangroves As A Case Study, Casey L. Lewis, Elise F. Granek

Environmental Science and Management Datasets

Management of established non-native plants is challenging because removal is expensive and can produce negative consequences, yet establishment can create novel ecosystems. Red mangrove propagules were introduced to Moloka'i, Hawai’i in 1902 to mitigate the effects of soil erosion and have since spread along the coast and to adjacent islands creating novel habitat. We compared zooplankton communities between novel mangrove and historical non-mangrove habitat both within fishponds and along open coastline to examine environmental factors, including mangrove presence, affecting zooplankton community composition.

Community composition patterns were driven by lunar cycle and site characteristics, including fishpond structure, mangrove and open coast …

Regional Characteristics And Variability Of Extreme Precipitation And Atmospheric Rivers In Past, Present, And Future Climates Over The Contiguous United States, Emily Anne Slinskey

Dissertations and Theses

This dissertation examines the regional and seasonal variability of extreme precipitation and atmospheric rivers (ARs) across the contiguous United States (CONUS) in past, present, and future climates. An extreme precipitation categorization scheme, designed to monitor and track the multi-scale variability of extreme precipitation, is applied to a range of precipitation measurement products as an assessment of observational uncertainty. To investigate the importance of ARs across the CONUS, an objective AR identification algorithm is applied to global reanalysis to identify and characterize AR characteristics regionally over the observational record. Projected change in AR day frequency, geometry, intensity, and associated precipitation is …

Climate Model Evaluation Of Atmospheric Rivers Over The Contiguous United States, Ilan González-Hirshfeld

Dissertations and Theses

Atmospheric rivers (ARs)--long corridors of intense atmospheric water vapor transport--significantly influence the hydrologic cycle and regional hydrometeorological extremes across the contiguous United States (CONUS). Ongoing and future climate change may alter AR characteristics and impacts, making confident climate model projections of future change, especially at regional scales, of critical importance. In order to better constrain uncertainty in such projections of future change, we perform a comprehensive climate model evaluation of AR climatology over the CONUS. Using an established AR detection algorithm, we evaluate the representation of ARs in historical simulations (1984-2013) from a suite of models participating in the sixth …

The Development And Application Of Instrumental Methods For The Identification Of Materials And Processes Used In The Manufacture Of Orotone, Hand-Colored Orotone, And Silvertone Photographs, Ivanny Jeannette Jácome-Valladares

Dissertations and Theses

Orotone photographs are positive photographic images on glass with a gold-colored metallic coating or backing. Although the materials and process used in the production of orotones have been previously documented, there is limited published scientific research on the subject. This study focused on expanding those published works by analyzing a greater number of photographs, including eleven orotones, four hand-colored orotones, two silvertones, and one uncoated orotone. The photographs, dating from the early to mid-20^th century, were from the University of Washington (UW) Libraries' collection, except for one orotone that was from the Portland Art Museum.

X-ray Fluorescence (XRF) spectroscopy, …

An Analysis Of Capillary Flow In Finite Length Interior Corners, Samuel Shaw Mohler

Dissertations and Theses

We analyze the mathematical robustness of slow massively parallel interior corner flows in low gravity environments. An interior corner provides a preferential orientation in low gravity environments. This is a luxury usually only found on earth. It also provides a passive pumping mechanism due to geometry of a conduit. The driving force for this flow is a pressure difference due to local surface curvature gradients. An alternative reasoning is that due to the geometrical constraints the interior corner surface energy is unbounded below. This results in the liquid wicking into corners indefinitely. Interior corner flow's main quantity of interest is …

Projections Of Large-Scale Atmospheric Circulation Patterns And Associated Temperature And Precipitation Over The Pacific Northwest Using Cmip6 Models, Graham Patrick Taylor

Dissertations and Theses

Projections of 500 hPa geopotential height (Z500) patterns over the Pacific Northwest of North America and their associated surface temperature, precipitation, and frequency of occurrence are assessed using models from the 6th phase of the Coupled Model Intercomparison Project (CMIP6). The self-organizing maps approach is applied to reanalysis data from the Modern-Era Retrospective Analysis for Research and Applications, version-2 (MERRA-2) to cluster daily Z500 anomalies into 12 representative patterns that span the range of historical circulation patterns. CMIP6 data for daily Z500 anomalies are mapped to each node for historical and end of century global warming experiments, and the resulting …

A Ground-Based Assessment Framework For Validating Diesel Particulate Emission Models And Applicability In Portland, Or, Kirsten Marie Sarle

Dissertations and Theses

Exposure to diesel emissions causes a range of health effects throughout the body, impairing; respiratory, cardiovascular, central nervous, renal, and cognitive systems. Diesel particulate matter (DPM) in Portland, Oregon is prevalent due to the layout of highly trafficked roadways, rail lines, and marine ports exposing a dense population to high levels of exhaust pollution. These high concentrations of ambient diesel emissions disproportionately impact minority and low-income populations.

Ground-based monitoring and modeling are two ways to assess ambient DPM. However, there are uncertainties in modeled DPM due to knowledge gaps in emissions inventories as well as lack of model validation against …

New Perspectives On Prolific And Voluminous Rhyolite Volcanism Of The Mahogany Mountain--Three Fingers Rhyolite Field, Eastern Oregon, Robert Andrew Jackson

Dissertations and Theses

Voluminous silicic volcanism of the Mahogany Mountain--Three Fingers rhyolite field (MM--TFrf) is spatially and temporally associated with mid-Miocene flood basalts of the Columbia River Basalt province. Early studies of the area advocated for a two-caldera model consisting of the Mahogany Mountain and the slightly younger Three Fingers caldera with pre- and post-caldera effusive rhyolite eruptions. Although close in time, the calderas were thought to be spatially offset producing the tuff of Leslie Gulch and the tuff of Spring Creek. Finding that the tuff of Spring Creek, that is exposed in Leslie Gulch, is an altered product of the tuff of …

Using Quantitative Stereology On High Resolution Sem Images To Estimate Diatom Percentages, Ariadna Covarrubias Ornelas

Dissertations and Theses

Diatoms are single-celled organisms of various shapes and sizes typically found in aquatic environments. When diatoms die, the organic material decomposes, and the outer skeletons (i.e., frustules) settle and accumulate as sedimentary deposits. These soils, called diatomaceous soils, exhibit nontraditional behavior since the diatom particles are typically hollow skeletons composed of amorphous silica with intricately patterned and abrasive surfaces. Recent studies have shown that diatomaceous soils are challenging geomaterials since even a small percentage of diatom particles will notably affect engineering behavior. Furthermore, laboratory studies on diatomaceous soil mixtures have demonstrated that many engineering soil properties depend on the percentage …

Field Trials And Long-Term Monitoring Of Microbially-Induced Desaturation For The Treatment Of Liquefiable Silty Soils, Kayla Rae Sorenson

Dissertations and Theses

Earthquake liquefaction hazards in silty soils are a critical problem in Portland, Oregon, and other areas around the world. This is a particular problem for existing facilities founded on liquefiable soils, for which there exists no cost-effective liquefaction mitigation solution at the present time. It is essential from both a seismic safety and a seismic resilience perspective to be able to mitigate potentially liquefiable soils underneath existing structures, and to do so in a cost-effective manner. Recent studies suggest that liquefaction mitigation using microbially-induced desaturation (MID) may provide this capability.

The objective of MID is to reduce earthquake-induced excess pore …

Modeling Cyanotoxin Production, Fate And Transport In Surface Waterbodies, Bernadel Rose Hintz Garstecki

Dissertations and Theses

Cyanobacteria exist throughout the world and are frequently associated with forming toxic blooms. The toxins produced by cyanobacteria, cyanotoxins, are harmful to both humans and animals. Rising temperatures due to global climate change, increased nutrient loading, and other anthropogenic impacts on waterbodies are expected to increase the prevalence of cyanobacteria. It is vital that we protect our drinking water supplies and natural water resources. Modeling the production and movement of these toxins is an important step in limiting exposure to them and evaluating management strategies to mitigate their impact. Cyanotoxins are diverse and the conditions under which they are formed …

Enrolling Reactive Oxygen Species In Photon-To-Chemical Energy Conversion: Fundamentals, Technological Advances, And Applications, Irving D. Rettig, Theresa M. Mccormick

Chemistry Faculty Publications and Presentations

In theory, oxygen (O2) is an ideal chemical reagent because of its high relative abundance and negligible environmental toxicity. In practice however, by the nature of its ground state electronic configuration, many chemical reactions involving O2 are spin forbidden which dramatically decreases its reactivity and thus its utility in applications. More reactive forms of O2 can be achieved by changing its electronic configuration through the use of photochemical and photophysical methods. This review highlights the roll of photon-to-chemical energy conversion in two of these reactive oxygen species (ROS): superoxide (O2−) and singlet oxygen (1O2), which can be accessed through a …

Simulation Of Light Propagation Captured By Photoemission Electron Microscopy (Peem), Nabila Islam

Dissertations and Theses

The Photoemission electron microscopes (PEEM) is a powerful tool capable of synchronously imaging wave nature of light manifested by interference patterns as well as its particle nature through the energy exchange between the incident photons and the photoemitted imaging electrons. PEEM offers a non-invasive high-resolution approach for studying light propagation and interaction phenomena within a nanophotonic waveguide [7,8]. The electric field intensity variation of the interference pattern yielded by the interaction between the incident light and the guided mode coupled into the waveguide produces varying photoemission yields creating contrast in PEEM image. The guided modes cannot be excited simply by …

Rowing Concerns: Collaborative Governance And Stakeholder Determination In The Central Oregon's Deschutes Basin, Noel Vineyard

Dissertations and Theses

In 2019, a coalition of irrigation districts in central Oregon's Deschutes Basin submitted the Deschutes Basin Habitat Conservation Plan to the US Department of Fish and Wildlife. This Habitat Conservation Plan purported to have been constructed through a collaborative governance structure between the irrigation districts and various community stakeholders who all had interests in basin management, however segments of the Basin's river recreation community began to raise concerns that their voices were not included. The purpose of this research was to investigate how stakeholder status in the Deschutes Basin is created through collaborative water governance processes like development of the …

Comparing Instruments For Measuring Runoff From Experimental Ecoroof Platforms: A Case Study On Test Plots At Portland State University, Chance F. Hodges

University Honors Theses

Stormwater management is a primary ecological benefit ecoroofs provide to ecosystems. Quantification of runoff from large scale ecoroofs is difficult to replicate, so researchers often utilize smaller experimental ecoroof platforms. This approach is becoming increasingly common, so it is useful to compare and contrast approaches for runoff measurement at the platform scale. This paper uses the four 17.86 m² ecoroof platforms located on the Science Research and Teaching Center (SRTC) at Portland State University (PSU) in Portland, OR as a case study. A unique condition of these platforms is that they are installed at grade on the roof with …

Cellular Remains In A ~3.42-Billion-Year-Old Subseafloor Hydrothermal Environment, Barbara Cavalazzi, Laurence Lamelle, Alexandre Simionovici, Sherry L. Cady, Michael J. Russell, Elena Bailo, Roberto Canteri, Emanuele Enrico, Alain Manceau, Multiple Additional Authors

Geology Faculty Publications and Presentations

Subsurface habitats on Earth host an extensive extant biosphere and likely provided one of Earth’s earliest microbial habitats. Although the site of life’s emergence continues to be debated, evidence of early life provides insights into its early evolution and metabolic affinity. Here, we present the discovery of exceptionally well-preserved, ~3.42-billion-year-old putative filamentous microfossils that inhabited a paleo-subseafloor hydrothermal vein system of the Barberton greenstone belt in South Africa. The filaments colonized the walls of conduits created by low-temperature hydrothermal fluid. Combined with their morphological and chemical characteristics as investigated over a range of scales, they can be considered the oldest …

Stemloop-Finder: A Tool For The Detection Of Dna Hairpins With Conserved Motifs., Alyssa A. Pratt, Ellis L. Torrance, George W. Kasun, Kenneth M. Stedman, Ignacio De La Higuera

Center for Life in Extreme Environments Publications

Nucleic acid secondary structures play important roles in regulating biological processes. StemLoop-Finder is a computational tool to recognize and annotate conserved structural motifs in large data sets. The program is optimized for the detection of stem-loop structures that may serve as origins of replication in circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses.

Application Of Topological Data Analysis To Multi-Resolution Matching Of Aerosol Optical Depth Maps, Dorcas Ofori-Boateng, Huikyo Lee, Krzysztof M. Gorski, Michael J. Garay, Yulia R. Gel

Mathematics and Statistics Faculty Publications and Presentations

Topological data analysis (TDA) combines concepts from algebraic topology, machine learning, statistics, and data science which allow us to study data in terms of their latent shape properties. Despite the use of TDA in a broad range of applications, from neuroscience to power systems to finance, the utility of TDA in Earth science applications is yet untapped. The current study aims to offer a new approach for analyzing multi-resolution Earth science datasets using the concept of data shape and associated intrinsic topological data characteristics. In particular, we develop a new topological approach to quantitatively compare two maps of geophysical variables …

Universal Biological Motions For Educational Robot Theatre And Games, Rajesh Venkatachalapathy, Martin Zwick, Adam Slowik, Kai Brooks, Mikhail Mayers, Roman Minko, Tyler Hull, Bliss Brass, Marek Perkowski

Systems Science Faculty Publications and Presentations

Paper presents a concept that is new to robotics education and social robotics. It is based on theatrical games, in motions for social robots and animatronic robots. Presented here motion model is based on Drift Differential Model from biology and Fokker-Planck equations. This model is used in various areas of science to describe many types of motion. The model was successfully verified on various simulated mobile robots and a motion game of three robots called "Mouse and Cheese."

Self-Contained Photon Coincidence Counting With Ni Myrio Ecosystem, Georges Oates Larsen, Andres H. La Rosa

University Honors Theses

Digital coincidence counting units (CCU) have made experimental verification of fundamental quantum mechanical principles financially accessible to undergraduate level teaching programs. However, recent implementations of these systems are not easily ported to National Instruments (NI) FPGAs, making them unsuitable for physics departments that have heavily invested in the NI ecosystem. Therefore, there is clear need for a detailed implementation based on an NI FPGA. We present a formal description of one such implementation, based on the NI myRIO (NI's lower-cost, student-oriented offering) which achieves 6.9 ns minimum guaranteed-distinguishable delay and 32.2 MHz peak coincidence counting rate with four input channels …

Case Study Of Scrum Methodology As Used By A Capstone Team, Lilly I. Yeaton

University Honors Theses

Scrum is widely used in the software industry to manage all kinds of projects. This case study examines the way in which a capstone team used the methodology and models the specific project management processes they used over the course of their project. These models and the process modifications therein are then compared to the team’s velocity at different points in the project. The results of this analysis suggest a correlation between asynchronous daily meetings and sprint reviews and improved velocity.

Functional Role Of The N-Terminal Domain In Connexin 46/50 By In Silico Mutagenesis And Molecular Dynamics Simulation, Umair Khan

University Honors Theses

Connexins form intercellular channels known as gap junctions that facilitate diverse physiological roles, from long-range electrical and chemical coupling to nutrient exchange. Recent structural studies on Cx46 and Cx50 have defined a novel and stable open state and implicated the amino-terminal (NT) domain as a major contributor to functional differences between connexin isoforms. This thesis presents two studies which use molecular dynamics simulations with these new structures to provide mechanistic insight into the function and behavior of the NTH in Cx46 and Cx50. In the first, residues in the NTH that differ between Cx46 and Cx50 are swapped between the …

Do Secondary Cyclones Increase The Category Scale Of Atmospheric Rivers?, Edgar Sanchez Fausto

University Honors Theses

Atmospheric rivers (ARs) play a crucial role in delivering precipitation worldwide. This makes them an important phenomenon for water resource specialists to study. One such interest is to understand what mechanisms make ARs produce significant rainfall and associated hazards such as flooding. One possible mechanism is that AR duration or intensity may increase when it interacts with a secondary cyclone, either of which can increase the AR category scale. The purpose of this study is to determine whether AR and secondary cyclone interactions increase the category scale ARs. Out of 52 AR events analyzed, 32 events contained at least one …

A Study Of Stable Isotopes In Snow On Mt. Hood, Oregon, Maya Felix

University Honors Theses

Over the 2020-2021 Winter, event-based and end-of-season snow samples were collected on Mt. Hood near Government Camp, OR and analyzed for their stable isotopic compositions of ¹⁸O and ²H. It was found that surficial snow collected through the winter had higher variation in isotopic values than samples from a snow pit collected in spring. This suggests homogenization occurred in the snowpack over the season from snow metamorphism, sublimation, and/or melting. Homogenization of the snowpack will likely become more pronounced as temperatures increase and rain falls more often than snow due to climate change. Research that utilizes the snowpack …

Literature Review: Pollutant Removal Efficacy Of Floating Treatment Wetlands Across Water Bodies, Sophie Johnson

University Honors Theses

Wetland numbers are declining worldwide and there is a need to replace the water filtration services they provide. One emerging option is floating treatment wetlands (FTW). FTW are a floating mat that serves as a habitat for aquatic plants whose roots are suspended in the water and that remove both organic and inorganic pollutants like nutrients (nitrogen and phosphorus), potentially toxic metals, and suspended solids. A literature search was performed to examine the efficacy of FTW pollutant removal. Specifically, I inspected 1) how effective FTW are at removing a range of nutrients; 2) what types of plants are most effective …

Automated Decision Making And Machine Learning: Regulatory Alternatives For Autonomous Settings, Alyssa Heminger

University Honors Theses

Given growing investment capital in research and development, accompanied by extensive literature on the subject by researchers in nearly every domain from civil engineering to legal studies, automated decision-support systems (ADM) are likely to see a place in the foreseeable future. Artificial intelligence (AI), as an automated system, can be defined as a broad range of computerized tasks designed to replicate human neural networks, store and organize large quantities of information, detect patterns, and make predictions with increasing accuracy and reliability. By itself, artificial intelligence is not quite science-fiction tropes (i.e. an uncontrollable existential threat to humanity) yet not without …

Soft Lithographic Replication Of High Length-Scale Micropillars From Laser-Ablated Fused-Silica Templates, Jason Pitts

University Honors Theses

Soft lithography is a well-established route to wafer-scale reproduction of micro- and nanoscale features in a wide variety of materials. Nevertheless, micron length scales have yet to be explored, despite the potential utility of such structures. Here, polymer micropillars of 6-12 μm length, approximately 0.5-1.5 μm wide at 10 μm spacing are reproduced from a polydimethylsiloxane (PDMS) mold made from patterned cellulose acetate (CA). The patterned CA was cast from a rigid fused silica template machined by a pulsed femtosecond laser. Pore topographic features were successfully reproduced in Norland Optical Adhesive (NOA), polycaprolactone (PCL), Nafion, acrylonitrile butadiene styrene (ABS), and …

Understanding Ransomware Trajectory To Create An Informed Prediction, J. D. Klusnick

University Honors Theses

Ransomware is a form of extortion in which digital files are rendered inaccessible until a ransom payment is made. Modern ransomware emerged in 2006 and its destructive influence has been expanding ever since. In recent years cybercriminals have evolved who they target, what computer systems they target, and how they infect those systems. Meanwhile, cybersecurity experts have modelled ransomware methods allowing them to innovate their defense techniques across three paradigms: recovery, detection, and prevention. Ultimately either ransomware attackers or ransomware defenders will dominate this ongoing conflict. A review of the literature indicates that the ransomware crime wave will likely be …

Total Synthesis And Antimalarial Activity Of 2-(-Hydroxybenzyl)-Prodigiosins, Isoheptylprodigiosin, And Geometric Isomers Of Tambjamine Myp1 Isolated From Marine Bacteria., Papireddy Kancharla, Yuexin Li, Monish Yeluguri, Rozalia A. Dodean, Kevin A. Reynolds, Jane X. Kelly

Chemistry Faculty Publications and Presentations

Highly efficient and straightforward synthetic routes toward the first total synthesis of 2-(-hydroxybenzyl)-prodigiosins (-), isoheptylprodigiosin (), and geometric isomers of tambjamine MYP1 ((/)-) have been developed. The crucial steps involved in these synthetic routes are the construction of methoxy-bipyrrole-carboxaldehydes (MBCs) and a 20-membered macrocyclic core and a regioselective demethylation of MBC analogues. These new synthetic routes enabled us to generate several natural prodiginines - in larger quantity. All of the synthesized natural products exhibited potent asexual blood-stage antiplasmodial activity at low nanomolar concentrations against a panel of parasites, with a great therapeutic index. Notably, prodiginines and - provided curative in …

Efficacy Of Ryr2 Inhibitor El20 In Induced Pluripotent Stem Cell-Derived Cardiomyocytes From A Patient With Catecholaminergic Polymorphic Ventricular Tachycardia., Tarah A. Word, Ann P. Quick, Christina Y. Miyake, Mayra K. Shak, Xiaolu Pan, Jean J. Kim, Hugh D. Allen, Martha Sibrian-Vazquez, Robert M. Strongin, Andrew P. Landstrom, Xander H T Wehrens

Chemistry Faculty Publications and Presentations

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an inherited cardiac arrhythmia syndrome that often leads to sudden cardiac death. The most common form of CPVT is caused by autosomal-dominant variants in the cardiac ryanodine receptor type-2 (RYR2) gene. Mutations in RYR2 promote calcium (Ca ) leak from the sarcoplasmic reticulum (SR), triggering lethal arrhythmias. Recently, it was demonstrated that tetracaine derivative EL20 specifically inhibits mutant RyR2, normalizes Ca handling and suppresses arrhythmias in a CPVT mouse model. The objective of this study was to determine whether EL20 normalizes SR Ca handling and arrhythmic events in induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) …