Physical Sciences and Mathematics Commons^™

Assessing The Utility Of Breast Cancer Polygenic Risk Scores And Association With Clinical Factors In A Population Of Breast Cancer Patients, John L. Slunecka

Dissertations and Theses

INTRODUCTION: Breast cancer (BC) is the most common cancer among women and is classified as a complex disease. Advances in population genomics have led to the development of polygenic risk scores (PRSs) with the potential to enhance current risk models, but replication is often limited. OBJECTIVE: We sought to assess the predictive capabilities of two high-powered BC PRSs in a sample population selected for breast cancer. In addition, the capacity of the PRSs to predict clinical variables that could improve BC screening and treatments was explored. METHODS: Two published PRS algorithms (313 vs 3820) were used to score female subjects …

Using Biometrics, Behavioral Observations, And Multiple Molecular Techniques To Assess The Impacts Of Changes In Temperature And Salinity On The Common Bay Mussel (Mytilus Trossulus), Casey Martin

Dissertations and Theses

The intertidal zone is a place of rapid and frequent change that is home to a variety of creatures who are essential to the integrity of the habitat. Mussels are robust sessile bivalves that anchor to the rocks of the intertidal. The prominent species on the Oregon Coast, the Common Bay Mussel (Mytilus trossulus), plays an essential role as a coastal food source, water column filter, and barrier to prevent erosion due to wave action. Mytilus trossulus withstands daily shifts in temperature, salinity, and tide, as well as seasonal changes. Global climate change due to excess carbon emissions …

The Influence Of Polystyrene Microplastics On Juvenile Steelhead Trout (Oncorhynchus Mykiss), Kaitlyn Marie Baker

Dissertations and Theses

Mass production of plastic within the past decade has led to over 100 billion tons of plastics being added to the world’s oceans through rivers and effluent disposal and decomposition. For marine environments, the sudden and constant growth of microplastics (plastics 1 µm to 5 mm in diameter), is of particular concern to top-predatory fish such as steelhead trout (Oncorhynchus mykiss), who passively or actively uptake microplastics while consuming prey. Previous research has demonstrated clear detrimental impacts of microplastic accumulation in bivalves, seabirds, and zebrafish, including decreased diet, reproduction rates, and metabolism, as well as increased rates of …

Drivers And Dynamics Of Phytoplankton Communities And Harmful Algal Blooms In Mountain Lakes, Lara Stephanie Jansen

Dissertations and Theses

Harmful cyanobacterial blooms (cyanoHABs) are a complex and widespread disturbance in freshwater water bodies, impacting water quality for wildlife and human populations. While cyanobacteria often bloom in warm lakes impacted by human development like agriculture, blooms are increasingly reported in cooler waters with limited development in the surrounding watershed. As much of cyanoHAB research has focused on lakes in highly developed watersheds, the understanding of factors leading to cyanobacteria dominance and blooms in the absence of major development remains limited. Mountain lakes can serve as ideal systems to study bloom-forming cyanobacteria in watersheds with minimal development. In addition, mountain lakes …

Disentangling Groundwater Dynamics At Oregon's Mckenzie River Headwaters, Taylor Nicole Salazar

Dissertations and Theses

Widespread mountain snowpack declines have been occurring across the western United States over the last century, and are increasing in duration and severity, with several record-breaking low-snowpack years in the last decade. In the Pacific Northwest, summer streamflow is largely a result of melting snow and groundwater discharge, as summers are typically dry and warm in this Mediterranean bioclimate, thus making spring-fed rivers critical for regional water resources. However, current trends and predictions in hydroclimate modeling indicate spring-fed rivers will experience reduced summer discharge driven by the increasingly larger impact of anthropogenic climate change (warming) on (decreased) mountain snowpack. A …

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 …

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 …

Shallow Water Coral Distribution And Its Response To Climate Change, Amaury De Jesus

Dissertations and Theses

Shallow water corals are one of the main reef-building organisms that secrete carbonates as their skeletons, and therefore, are one of the major sinks of CO2 in the ocean. These reef builders are also very crucial to marine environments and human society. As the global energy demand continues rising, fossil fuel burning increases at a faster pace despite the increase in energy supply using clean and renewable energy. The increase of CO2 in the atmosphere has been shown to exacerbate global warming and may cause ocean acidification, threatening the habitat of shallow-water corals. Many recent observations show alarming signs of …

Fine Characterization Of Leafing Phenology In The Brazilian Atlantic Forest By Optical And Microwave Remote Sensing, James B. Bell

Dissertations and Theses

Tropical forests provide important ecosystem functions in the global biosphere, but they remain among the most poorly understood elements of land surface models, especially with regard to their seasonal dynamics. For instance, in seasonally dry forests, the pattern of the annual green-up in their canopies closely follows annual patterns of rainfall. The same, however, does not occur in wet forest canopies which are dominated by evergreen trees. In the latter, water is not scarce enough to limit leaf photosynthetic function. Canopy leafing phenology in these forests is therefore poorly characterized by optical remote sensing methods which are not sensitive to …

Machine Learning Approach To Predict Tdcs-Induced Electric Current In The Human Brain, Chikako Olsen

Dissertations and Theses

Background: Transcranial direct current stimulation (tDCS) is a promising non-invasive method for treating neurological and psychiatric disorders and enhancing cognitive function. However, the underlying mechanisms of tDCS are not fully understood, and there is no ground truth for determining, non-invasively, where in the brain tDCS electrical currents flow. At the same time, effective neuronal engagement from tDCS requires accurate localization of the induced currents to specific brain target regions. Machine Learning (ML) has the potential to significantly improve the accuracy and precision of tDCS current prediction. This study aims to develop a novel approach using ML to predict the location …

System Design For The Quantification Of Microbial Motility In Extreme Environments, Megan Marie Dubay

Dissertations and Theses

Motility of microorganisms is understudied but provides useful insights into their behavior. Organisms' ability to move autonomously changes how they interact with their environment--finding nutrients, interacting with other organisms, and avoiding unfavorable conditions. Understanding motility features can also be used to identify specific species, such as the identification of Vibrio cholerae in human samples. Motility might also be used as evidence of life existing in even the most extreme environments on Earth, and possibly beyond. Specialized microscopy systems can be required to examine the motility of microorganisms due to the nature of the environments to which the instruments are exposed. …

Post-Fire Erosional And Hydrological Processes Promoting Debris Flow Initiation In A Douglas Fir And Western Hemlock Forest In The Riverside Burn Area, Oregon, Morena Nicole Hammer

Dissertations and Theses

Post-fire debris flows initiated by overland flow in the Pacific Northwest (PNW) are largely undocumented. Instead, debris flows are typically initiated by shallow landslides that result in a mud slurry of water and sediments traveling downhill under the force of gravity. However, because of the Fall 2020 fires in Oregon, the typical initiation style and erosional patterns in burned catchments may have changed because of unusually high burn severity. Due to the intensity of these fires, we set out to determine how hydrologic processes and erosion occurred, when they occurred, and what process was primarily responsible for the erosion that …

Orthotrichum Lyellii As An Active Moss Biomonitor: Examining The Interplay Between Ambient Pm10, Bulk Deposition And Heavy Metals In An Urban Environment, Scott Bradley Kiel

Dissertations and Theses

The importance of monitoring and preventing pollution in the environment is a globally recognized issue. Of the criteria pollutants outlined by the United States Environmental Protection Agency, particulate matter is among these least understood in relation to toxicity and most wide-spread. Many governments have employed continuous air quality monitoring networks to track ambient levels of particulate matter, but are often too widespread to capture the heterogeneity of the urban environment, especially for heavy metal deposition. In Portland, OR, the epiphytic moss Orthotrichum lyellii was successfully used as a low-cost passive biomonitor to increase the spatial resolution of pollution around the …

Investigation Of The Association Of Exposures To Fire-Related Hazards With Pulmonary Function Of Firefighters, David G. Goldfarb

Dissertations and Theses

Background. Firefighters are habitually exposed to hazardous toxicants which place them at an elevated risk for numerous adverse health outcomes. An example of this is the associations observed in other works between inhalation of combustion byproducts from urban structural fires and both acute and chronic pulmonary dysfunction. To-date, the characterization of firefighters’ exposures to dangerous chemicals in smoke from non-wildfire incidents, both directly through personal monitoring and indirectly from work-related records is scarce. Prior works investigating the association between routine firefighting and pulmonary function have relied on crude metrics such as years of service and numbers of responses to …

Effects Of Pore-Forming Peptides (Melittin And Magainin 2) On The Phospholipid Bilayer Interior, Elmukhtar Ehmed Alhatmi

Dissertations and Theses

Antimicrobial peptides (AMPs) are one of the most promising solutions to drug-resistant bacteria. Melittin and magainin 2 are two of the most representative and extensively studied AMPs. In this research, I investigated the interaction of these two AMPs with three models of cell membranes: 80% POPC 20% POPG, 40%POPC 40% POPE and 20% POPG, and 80%POPC 20%POPG plus 30% mole fraction of cholesterol. Time-resolved fluorescence emission and fluorescence anisotropy decays of the fluorescent probe 1,6-diphenyl-1,3,5-hexatriene (DPH) were analyzed to determine the effects of AMPs on the bilayer headgroup packing and changes in the interior of the phospholipid bilayer during the …

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 …

Ecological Changes Of The Lower Niobrara River Valley And Lewis And Clark Lake Delta From Past To Present, Madalyn Christine Bollig

Dissertations and Theses

Over half of the world’s large river systems are impacted by dams. These may prevent sediment flow downstream, resulting in accumulation in the upstream reservoir. On the Missouri River, deltas and associated backwater-affected areas occur in nine locations across six reservoirs. One of these, the Lewis and Clark Lake delta-backwater, is influenced by sediment inputs from both the Missouri River and the Niobrara River. While the extension of the prograding delta into the reservoir has been well documented, there has been little research on upstream (backwater) effects of the delta on the lower Niobrara River. This study examined ecological changes …

Nonhematopoietic Erythropoietin: A Study Of Signaling, Structure, And Behavior, Nicholas John Pekas

Dissertations and Theses

Erythropoietin (EPO) is a cytokine hormone known for initiating red blood cell proliferation by binding to its homodimer receptor (EPOR)2 in the bone marrow. Recent progress in neurobiology has shown that EPO also exerts robust neurotrophic and neuroprotective activity in the CNS. It is widely thought that EPO’s neurotrophic activity is centrally involved in its antidepressant and cognitive enhancing effects. However, EPO’s potent erythropoietic effects prevent it from being used in the clinic to treat psychiatric disorders. A chemically engineered non-erythropoietic derivative of EPO, carbamoylated EPO (CEPO), produces psychoactive effects without activating hematopoiesis. However, CEPO is expensive to produce and …

Framework For The Evaluation Of Perturbations In The Systems Biology Landscape And Inter-Sample Similarity From Transcriptomic Datasets — A Digital Twin Perspective, Mariah Marie Hoffman

Dissertations and Theses

One approach to interrogating the complexities of human systems in their well-regulated and dysregulated states is through the use of digital twins. Digital twins are virtual representations of physical systems that are descriptive of an individual's state of health, an object fundamentally related to precision medicine. A key element for building a functional digital twin type for a disease or predicting the therapeutic efficacy of a potential treatment is harmonized, machine-parsable domain knowledge. Hypothesis-driven investigations are the gold standard for representing subsystems, but their results encompass a limited knowledge of the full biosystem. Multi-omics data is one rich source of …

Selenium Probes For The Detection Of Thioredoxin Reductase Activity, Tendai Joseph Mafireyi

Dissertations and Theses

The identification and quantification of proteins and enzymatic activity in living tissues frequently requires the use of invasive procedures such as biopsy. These techniques can inhibit measurements of protein levels in real-time, and the disruption of tissue can lead to the loss of important information concerning the spatial distribution and differential activities in various cell types. The use of small organic fluorescent probes that rely on activation or accumulation within a tissue embody robust methods of detection that address these issues. This dissertation describes the design, synthesis and evaluation of fluorescent probes that can detect the enzyme thioredoxin reductase (TrxR). …

Exploring Linkages Between Landscape Patterns And Freshwater And Estuarine Bivalves In The Coast Range Of Oregon, Kaegan Michael Scully-Engelmeyer

Dissertations and Theses

Spatial configurations of landscape variables (biotic, abiotic, and socio-ecological) affect and are affected by ecological processes and species in watersheds. This dissertation explores relationships among landscape patterns, ecosystem processes and bivalve species dynamics in coastal watersheds in Oregon, USA. I approached this broad topic through two primary avenues of research: investigating cross-ecosystem threats from pesticide use in forestland management to downstream aquatic environments, and the landscape ecology of an at-risk freshwater mussel species.

Terrestrial land use activities present cross-ecosystem threats to riverine and marine species and processes. Specifically, pesticide runoff can disrupt hormonal, reproductive, and developmental processes in aquatic organisms, …

Steady-State Transmembrane Water Exchange In Proliferating Cultures Of Saccharomyces Cerevisiae, Joseph O'Malley Armstrong

Dissertations and Theses

Cellular water exchange is often considered in terms of a change in volume, where a net flux of water moves across the cell membrane due to a change in osmotic pressure. Osmotic pressure can cause a cell to shrink or swell, however, rapid water exchange persists across the membrane even when the volume of the cell is constant. Steady-state transmembrane water exchange describes the exchange of water across the cell membranes which results in no net change in cell volume. This exchange is astonishingly rapid; the entire pool of intracellular water of a Saccharomyces cerevisiae cell may exchange 2-5 times …

Chemical Characterization Of Toxicologically Relevant Molecules In Cannabis Concentrates And Vaporizer Aerosols, Jiries Meehan-Atrash

Dissertations and Theses

Consumption of cannabis concentrates using the relatively novel non-combustion methods dabbing and vaping has steadily grown in popularity as cannabis legalization in North America has allowed increased access to sophisticated cannabis products and technology. In order to assess the safety of these products, it is necessary to gain a chemical understanding of the decomposition reactions that occur when the active ingredients are heated in the conditions seen when dabbing or vaping. This dissertation contains a manuscript that details efforts to structurally characterize a toxic cannabis concentrate adulterant, and three manuscripts that studied the chemical decomposition of the two primary cannabis …

Thermodynamics Of Ligand Binding And Global Structural Stability Of Human Serum Albumin, Matthew Walter Eskew

Dissertations and Theses

Protein structure is integral to its function. For the past 70 years differential scanning calorimetry has been used to measure protein structural stability. More recently it has been used to study macromolecular interactions. Interactions between proteins and ligands can manifest on differential scanning calorimetry melting curves or thermograms. Utilizing differential scanning calorimetry thermograms to detect or diagnose diseases has been a major goal in disease diagnostics. However, correlating specific ligand-protein interactions, as manifested in a thermogram, with a disease-specific plasma thermogram, has proven elusive.

Modified human serum albumin was utilized to develop a process to capture and retrieve ligands from …

Long Term Nutrient And Chlorophyll A Dynamics Across Long Island Sound And Impacts On Dissolved Oxygen Conditions Within The Western Sound (1991-2019), Sherry Perreira

Dissertations and Theses

Nitrogen overload, eutrophication, and hypoxia have been challenging and persistent water quality problems in Long Island Sound (LIS) over the past decades with major impacts on commercial industries, ecology, and recreational activities in the region. Recognizing these problems, the EPA enforced three phases of the Clean Water Act (CWA) to reduce nitrogen loads in an effort to improve this important estuary. This study examines how nitrogen (NH₃, NO_x & TDN), chlorophyll a (CHLA), and dissolved oxygen (DO) concentrations changed in LIS over the past 30 years, in response to water quality regulations as well as changes in …

A New Mathematical Theory For The Dynamics Of Large Tumor Populations, A Potential Mechanism For Cancer Dormancy & Recurrence And Experimental Observation Of Melanoma Progression In Zebrafish, Adeyinka A. Lesi

Dissertations and Theses

Cancer, a family of over a hundred disease varieties, results in 600,000 deaths in the U.S. alone. Yet, improvements in imaging technology to detect disease earlier, pharmaceutical developments to shrink or eliminate tumors, and modeling of biological interactions to guide treatment have prevented millions of deaths. Cancer patients with initially similar disease can experience vastly different outcomes, including sustained recovery, refractory disease or, remarkably, recurrence years after apparently successful treatment. The current understanding of such recurrences is that they depend on the random occurrence of critical mutations. Clearly, these biological changes appear to be sufficient for recurrence, but are they …

Pharmaceuticals And Personal Care Products In Pacific Northwest Coastal Ecosystems: Spatial Variation, Organism Effects, And Consumer Perspectives, Amy Lynne Ehrhart

Dissertations and Theses

Anthropogenic pollution poses a threat to marine organisms and ecosystems worldwide. Common chemical pollutants that enter the marine environment include legacy contaminants, which are well known and heavily regulated or banned pollutants, and emerging contaminants, which are more recently recognized as pollutants and often lack regulatory limits for their use and discharge. Wastewater treatment plant (WWTP) effluent is a major source of various contaminants of concern, particularly pharmaceutical and personal care products (PPCPs) that are not fully removed during treatment. PPCPs exist at low concentrations in the environment and may have unknown and subtle effects on marine life. Data gaps …

Investigating Dose-Dependent, Multi-Generational, And Strain-Specific Effects Of 17Α-Ethynylestradiol Exposure In Zebrafish (Danio Rerio), Decatur Mitochondria Foster

Dissertations and Theses

Endocrine disrupting chemicals (EDCs) pose a threat to biodiversity at the individual, population, and ecosystem level, as they can interfere with processes that are responsible for regulating metabolism, development, behavior, and reproduction in living organisms. 17α-ethynylestradiol (EE2) is a synthetic estrogen and EDC utilized in pharmaceutical and livestock industries, and contaminates waterways worldwide. This research explores the effects of dose-dependent and multi-generational exposure of EE2 in three strains of zebrafish. High dose (10-25 ng/L EE2) exposure led to complete reproductive failure, as well as significantly decreased survival and growth. A period in clean water (depuration) after exposure allowed for some …

Do Fungal Symbionts Of Salt Marsh Plants Affect Interspecies Competition?, Vanessa Robertson-Rojas

Dissertations and Theses

The effects of arbuscular mycorrhizal fungi (AMF) as salt marsh plant symbionts may have significant effects on landscape scale distribution patterns and plant-related ecosystem functions that are important to estuarine habitats. This work investigates the effects AMF have on Phalaris arundinacea, Deschampsia cespitosa, and Juncus balticus when grown in a common garden experiment. Plants were grown with and without AMF inoculation in both polyculture and monoculture communities and examined for a variety of response variables that represent different competition strategies. Factorial ANOVA analysis revealed a significant three-way interaction among fungal treatment type, community type, and species for …