Food waste (FW), brewery waste (BW), and fats, oils, and greases (FOG), are prevalent waste streams in municipalities across the country, particularly in the Pacific Northwest (PNW). Anaerobic digestion (AD), the microbial-mediated transformation of organic waste into methane-rich biogas, offers a sustainable, energy-generating, waste management solution for these wastes. Anaerobic...
Intraseasonal oscillations in the atmosphere-ocean system can affect weather patterns and regional ecosystems. In turn, these oscillations can be affected by climate variability, resulting in additive and/or non-linear responses of regional ecosystems to climate forcing. In the Northern California Current, a strong correlation was identified between the location of the...
Geospatial data analysis is a multifaceted discipline encompassing the collection, processing, and visualization of diverse datasets. It models and delineates the interactions of people, objects, and phenomena within geographical spaces and predicts patterns based on the relationships between different locations. Despite significant advancements in geospatial data engineering and analytics over...
This study examined water scarcity and vulnerability in Quintana Roo, along the northern Caribbean coast of Mexico where rapid growth of tourism in the past 40 years has limited the ability of rural and urban communities to obtain safe, reliable, and equitable access to water services and critical water infrastructure...
Cell signaling under external stimulation is a critical mechanism that governs many biological processes such as cell proliferation, cell migration, and cell apoptosis, etc. For multicellular organisms, the ability to synchronize heterogeneous individual cellular responses through intercellular communication is crucial to maintain normal functionality. However, even though the biological pathways...
Oregon's estuaries are important ecosystems for scientific study. Consequently, knowledge of what research has been conducted helps us identify benchmarks and plan new projects. A comprehensive bibliography of published research, technical reports, local documents, and data sets is one means of recording this knowledge. For these reasons, the Guin Library...
Oregon's estuaries are important ecosystems for scientific study. Consequently, knowledge of what research has been conducted helps us identify benchmarks and plan new projects. A comprehensive bibliography of published research, technical reports, local documents, and data sets is one means of recording this knowledge. For these reasons, the Guin Library...
Oregon's estuaries are important ecosystems for scientific study. Consequently, knowledge of what research has been conducted helps us identify benchmarks and plan new projects. A comprehensive bibliography of published research, technical reports, local documents, and data sets is one means of recording this knowledge. For these reasons, the Guin Library...
Oregon's estuaries are important ecosystems for scientific study. Consequently, knowledge of what research has been conducted helps us identify benchmarks and plan new projects. A comprehensive bibliography of published research, technical reports, local documents, and data sets is one means of recording this knowledge. For these reasons, the Guin Library...
Oregon's estuaries are important ecosystems for scientific study. Consequently, knowledge of what research has been conducted helps us identify benchmarks and plan new projects. A comprehensive bibliography of published research, technical reports, local documents, and data sets is one means of recording this knowledge. For these reasons, the Guin Library...
Harmful algal blooms (HABs) are a problem for coastal communities, the fishing industry, and coastal organisms. Pseudo-nitzschia spp. is a regularly occurring diatom in Oregon’s coastal waters. At times, Pseudo-nitzschia spp. can facultatively produce domoic acid, a neurotoxin that can bioaccumulate in the food chain. While regular shore-based sampling provides...
Emerging research shows that individual differences in how people use technology sometimes cluster by socioeconomic status (SES) and that when technology is not socioeconomically inclusive, low-SES individuals may abandon it. To understand how to improve technology’s SES-inclusivity, we present a multi-phase case study on SocioEconomicMag (SESMag), an emerging inspection method...
Over time, Open Source Software (OSS) has become indispensable in the creation and upkeep of software products, serving as the fundamental building block for widely used solutions in our daily lives, including applications that enable communication, entertainment, and productivity. A sustainable OSS ecosystem is one that attracts and retains a...
Propose a sampling plan to determine Hg contamination in the Nanay river basin.
The sampling plan is for a feasibility pilot, to investigate whether it is possible to safely collect samples for Hg analyses. Future studies will build on these initial results.
While digital inclusivity researchers and software practitioners have been trying to address exclusion biases in Windows, Icons, Menus, and Pointers (WIMP) user interfaces (UIs) for a long time, little has been done to investigate if and how inclusive software design and its methods that have been devised for WIMP UIs...
In the United States, children from underserved racial/ethnic backgrounds encounter greater environmental risk both in terms of the physical environment (e.g., housing quality, access to resources like health services and jobs, and exposure to environmental toxins) and the social environment (e.g., social support, neighborhood crime, racism, and discrimination), due to...
This thesis examines the impacts of the COVID-19 pandemic on farms in the Willamette Valley. Using semi-structured interviews, this study analyzes the economic and social challenges created by the pandemic and the adaptation strategies farmers employed to build resilience within the food system. This study found that the farmers experienced...
Concrete has been categorized as a key contributor of CO2 (carbon) emissions into the atmosphere. This is mostly associated with the production of ordinary portland cement (OPC). The concrete and cement industries are pursuing a path to reduce their carbon emissions generally in accordance with the climate change goals outlined...
During the first full school year of the Covid-19 pandemic, two central contexts for adolescent development—home and school—changed utterly. In Oregon, most middle- and high schoolers attended school entirely remotely from the beginning of the pandemic, in March, 2020, through the end of April, 2021, removing both the supports available...
Sensory stimulation from food-related cues elicits a number of rapid physiologic responses that prepare the gastrointestinal tract for efficient nutrient utilization and help minimize perturbations to metabolic homeostasis. Cephalic phase insulin release (CPIR) is one such response that specifically promotes glucose homeostasis by limiting the rise in blood sugar after...
Toxin production by cyanobacterial harmful algal blooms (cyanoHABs) in freshwater systems has lasting ecological and human impacts. Nutrients, light availability, hydrology, and microbial community composition impact the frequency and intensity of toxic cyanoHABs. Climate change will exacerbate toxic cyanoHABs, making real time and predictive monitoring a vital tool for managing...
The purpose of this study was to explore and describe how the orientations and knowledge of linguistically responsive teaching, as well as personal characteristics of school-based agriculture education (SBAE) teachers, influence the frequency of their implementation of linguistically responsive practices. Grounded in the Linguistically Responsive Teaching framework by Lucas and...
The objective of this dissertation is to enhance the monitoring of forest ecosystems through the utilization of remotely sensed data to address the exigencies posed by the Anthropocene. On a global scale, rising temperatures and fluctuating precipitation patterns have strained forests and produced shifts in natural disturbance regimes. Additionally, the...
Skeletal muscle mitochondria are highly plastic organelles, integral to whole-body health. High-fat diet (HFD) and exercise remodel the skeletal muscle mitochondria. Whereby, altered skeletal muscle mitochondrial function is linked to decreased skeletal muscle insulin sensitivity which can be reversed by exercise. However, the mechanisms that contribute to skeletal muscle remodeling...
The advancement of artificial intelligence (AI) has led to transformative developments across multiple sectors, fostering innovation and redefining our interactions with technology. As AI matures and becomes integrated into society, it offers numerous opportunities to address global challenges and revolutionize a wide array of human endeavors. These advances are driven...
This dissertation develops a framework for Curandera feminism, informed by familial healing practices, women of color feminisms, and institutional critique. My research centers my family’s generational Curandera practices. As I honor the call to be critical of the master’s tools, I seek possibilities for institutional change through Curandera feminism. Institutions...
Various natural language processing (NLP) tasks necessitate deep models that are fast, efficient, and small based on their ultimate application at the edge or elsewhere. While significant investigation has furthered the efficiency and reduced the size of these models, reducing their downstream latency without significant trade-offs remains a difficult task....
The body of work aims to contribute to the area of Quantitative analysis in Environmental Sciences, and is focused on the microbiome. The underlying theme for the dissertation is methods and workflow. The unique bioinformatics workflow used for the analysis of genomic data was used to answer distinct and pressing...
Coastal landslides and erosion are major natural hazards resulting in unstable slopes, constituting immense challenges to modern infrastructure. Developing, maintaining, and performing risk assessments of infrastructure on, or close to, these hazards require a detailed understanding of the geophysical processes destabilizing the slope. These efforts start with the collection of...
Bibliographia Bopyridarum is prepared and maintained by John Markham, Arch Cape, Oregon, USA. Any reports of errors or omissions are greatly appreciated. Please contact Dr. Markham with suggestions: jmarkham@seasurf.net This file is updated annually.
Agrivoltaic systems promote dual use of land by combining solar energy and agricultural production. Grazing sheep in these systems is popular but research on intentionally designed pastures to increase production is lacking. This study seeks to compare the herbage growth and lamb production in simple, diverse, and legume pasture mixes...
The European hazelnut (Corylus avellana L.) is a tree nut crop that is important in Oregon, which produces 99% of the United States’ hazelnuts but only 5% of the world’s supply. In order to maintain this market share, farmers in Oregon need cultivars that produce high quality nuts, mature early,...
In recent decades the habitat of North American beaver (Castor canadensis) has expanded from boreal forests into pan-Arctic tundra ecosystems. It is unknown how the advance of beavers into Arctic watersheds will impact microbial communities responsible for the mineralization of organic matter (OM), which has implications for carbon cycling. To...
Little scholarship exists on the contemporary trance dance movement known as Ecstatic Dance. This thesis investigates the myriad of pathways dancers in the Ecstatic Dance communities of Western Oregon experience movement-induced altered states of consciousness. A secondary aim was to provide a more visually and ethnographically accessible dance annotation system...
Multi-robot teams offer promising solutions for many long term deployments in remote and dangerous domains, such as extraterrestrial or underseas exploration. However, long term deployments present many problems preventing robot teams from operating effectively. Learning over long time scales is makes it difficult to assign credit to robots' actions, as...
The focus of this thesis is to design, characterize, and apply novel computational methods and molecular systems to interrogate heterogeneous human gut microbiome-related phenomena. In Chapter 2, I design, implement, and characterize a method for embedding co-occurrence patterns derived from massive 16s amplicon datasets. I use this method to 1....
Research relying on remotely sensed data on land use and deforestation has exploded in recent years. While satellite-based measures have clear advantages in terms of coverage, the presence of measurement error within these products is often overlooked. Here, we detail the econometric implications of these errors when analyzing the determinants...
Connectivity of fish populations is a crucial question for fisheries conservation and the development of spatial management plans. Both adult and larval movement define the extent and direction of ecological and evolutionary overlap between geographic regions and, therefore, how we define stocks for management purposes. Within that context, my work...
Today, there are six extant species of sea lion around the world, with the seventh (the Japanese sea lion) already having gone extinct due to a lack of proper conservation management. Because each of the surviving 6 sea lion species differ slightly in their anatomy, behavior, reproduction, and local habitats,...
Orthopaedic soft tissue degenerative diseases significantly affect the population, especially as it ages. Degeneration is characterized by a progressive loss of extracellular matrix (ECM) components necessary for the proper functioning of the tissues and joints, eventually leading to pain and dysfunction. In humans, the intervertebral disc (IVD) and tendon are...
Small-scale fisheries account for at least 40 percent of global fisheries catch, 90 percent of the people employed along capture fisheries value chains operate in small-scale fisheries, and 45 million women participate in small-scale fisheries globally. The past few years have brought warnings from policymakers and resource managers about risks...
Aroma is one of the major components that determines the quality of wine and consumer acceptability. Fruitiness is a highly desirable aroma quality in white wines and has been well accepted by consumers across the globe. Tropical fruit aroma has been substantially studied in Sauvignon Blanc wines due to its...
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DEDICATION
To the memory of my mother, Maria Jose de Castro Iobbi. Thank you for
Severe wildfires are increasing in the western United States, impacting vegetation structure, and in turn, forest regeneration conditions. These wildfires are also raising a substantial amount of scientific and management concern regarding the resilience of forested ecosystems, or the ability of the ecosystem to return to a pre-fire condition. This...
Hop (Humulus lupulus L. var. lupulus) is a diploid, dioecious plant with an extensive history of cultivation and use in brewing, as a textile, and for its therapeutic properties. Hop is prized for its ability to produce a variety of aromatic and flavor compounds, as well as compounds with anti-microbial...
Alzheimer’s Disease (AD) is a neurodegenerative pathology currently affecting nearly 44 million individuals worldwide, yet there are not currently any effective treatments or preventions for AD despite the rapid development in our understanding of the disease over the last four decades. The medical and sanitary innovations of the last century...
Back pain is the leading cause of disability worldwide, entailing a significant socioeconomic impact. A primary source of back pain can be attributed to intervertebral disc (IVD) degeneration allowing nerve ingrowth, facet joint arthritis, disc bulging, and osteophyte formations that press on nearby nerve roots or the spinal cord. While...
Pesticides benefit agriculture by increasing crop yield, quality, and security. However, pesticides may inadvertently harm bees, which are valuable as pollinators. Thus, candidate pesticides in development pipelines must be assessed for toxicity to bees.
Leveraging a data set of 382 molecules with toxicity labels from honey bee exposure experiments, we...
Systems biology is a powerful approach which considers and sheds light on all of the puzzle pieces which make up complex biological processes, and is an effective alternative to unraveling these processes using traditional molecular approaches alone. It is a natural companion approach for computational biology, which leverages the power...
Analysis of observations on sequential events over time is common in real life. Sequential measurements over time describing the behavior of systems are usually called time series data, which have been collected in a wide range of disciplines. Over the years there have been multiple research areas in studying stochastic...
Energetic resources transferred between distinct habitats or ecosystems, referred to as allochthonous resources, can greatly subsidize consumers in the recipient habitat, and thus influence food web structure and dynamics. Such subsidies may allow the growth of the consumer population to be decoupled from in situ productivity with effects on consumer...
Background: Mycobacterium abscessus (MAB) is a rapidly growing opportunistic pathogen that causes infections in immunocompromised patients. The highly impermeable cell wall and surface transport systems are major contributing factors to MAB intrinsic resistance, influencing the efficacy of bactericidal antibiotics. Phages are promising alternatives to antibiotics and have been used in...
Intrinsically disordered proteins (IDPs), protein regions (IDRs), and protein complexes continue to emerge at the forefront of protein science. Proteins and protein regions lacking specific structure are found in all organisms, and often have vital roles in numerous biological processes. Breaking the well-known structure-function paradigm, the understanding of disorder-based functionality...
Global environmental change is causing local extinctions of species. When species depend on one another, as in the mutualistic relationship between plants and pollinators, loss of one interaction partner may cause cascading effects within the community – such as additional extinctions and reduced pollination services. Network theory provides a way...
Climate change has pervasive impacts on Earth’s diverse ecosystems. Observed and projected effects that impact coastal environments pose unique challenges. Coastal regions provide numerous ecosystem services (e.g., fisheries, nursery habitats, erosion control, and water filtering and detoxification), house 40% of the US population, and contribute to 58% of the national...
Dysferlin is a ∼230 kDa terminally anchored membrane protein that is ubiquitously expressed, but is particularly enriched in skeletal and cardiac muscle tissue. Mutations covering the length of the protein have been linked to muscle wasting diseases including limb-girdle muscular dystrophy and Myoshi myopathy. Dysferlin has been shown to play...
Oceanic fronts mark the boundary between two water masses and are often sites of complex bio-physical processes and multi-trophic level interactions, making them particularly important features in marine ecosystems. As global climate change induces multi-scale shifts in the driving physical mechanisms of fronts, spatiotemporal tracking of frontal variability can aid...
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Maria T. Kavanaugh & Yvette H. Spitz
Oceanic fronts mark the boundary between two
Intensifications in seasonal temperature variation, attributed to increased greenhouse gas concentrations, are having an adverse effect on the forest composition of the northeastern United States. New York’s temperate broadleaf forests are undergoing alterations including a decline of the native sugar maple (Acer saccharum), as the species’ population begins to decrease...
This contribution aims to provide an economic assessment of the seabream and seabass industry in the Mediterranean, in order to describe the recent development and current situation of the economy and markets of this industry. It focuses on analyzing the economic and financial structure at different levels of aggregation (industry,...
In computer science, learning abstract fundamental programming concepts requiring students to understand memory management can be very difficult and lead to misunderstandings that carry on into advanced topics. This is especially true in data structures with abstract data types. Understanding how novice students think and reason about data structures is...
Oregon strawberries are known for their high quality, intense flavor, sweetness, and rich red color. With optimal weather conditions, including rainy and mild seasons, Oregon has one of the best strawberry farming environments. Amongst the factors for a suitable strawberry farming environment, soil significantly influences strawberry growth and quality. The...
The immune system is a complex network of cellular processes working in harmony to guard us against pathogenic attack. Of utmost importance is the ability of the immune system to discriminate between “self” and “non-self” and diseased versus healthy. Recognition of antigens complexed to major histocompatibility complex (MHC) molecules is...
Kelps are large brown algae in the order Laminariales and are foundation species that form the basis of kelp forests. Present across a quarter of the world’s coastlines, kelp forests provide diverse services to coastal communities, as habitat for commercially and culturally important species, as a food source for humans...
Given the many significant roles that bacteria play in modern food manufacturing, it is crucial that we have a fundamental understanding of how bacterial communities assemble and behave in the food manufacturing environment. The focus of this dissertation was to investigate both the spatial and temporal distributions of microbial communities...
Animals aggregate and interact in nonuniform and nonrandom patterns, which lead to group level characteristics that have important evolutionary and ecological consequences. Network analysis provides a useful conceptual framework for linking animal interactions at all scales from dyads to communities, to populations and ecosystems. Despite exciting theoretical and applied advances...
This study explores how multispecies social networks influence small farmers' perceptions of and responses to climate change across Oregon. Local food sovereignty and food system resilience depend on a robust local food system in which small farms play a critical role. To maintain their viability, small farmers must adapt to...
Counselors are tasked with being knowledgeable about assessing and treating a broad range of mental health issues. There has been an overall rise in mental health symptoms in individuals during the current COVID-19 pandemic, as well as the increased use of online internet forums as part of help-seeking behaviors. Obsessive-Compulsive...
The demand for the development of sustainable energy is an all time high as we burn through limited fossil fuel reserves and as environmental concerns rise every year. Renewable energy sources such as wind and solar power have limitations due to inconsistent power supply that cannot meet the regular needs...
Bangladesh is a developing country with burdens of environmental pollution and disparities in maternal and child health. Arsenic, manganese, and lead are pervasive environmental contaminants throughout Bangladesh with major exposures through drinking water and ambient pollution. Chronic exposures to arsenic, manganese, and lead in sensitive populations such as pregnant women,...
The climate of the Pacific Northwest is in flux, and existing forest ecosystems are stressed and poised to shift in fundamental ways, with or without human intervention. This dissertation probes the nature of forest responses to environmental change through investigations of morphology and genetics of three species of alder co-occurring...
Small-scale fisheries often suffer from weak, formal governance, and in response they organize in various ways. These self-organizational arrangements rely on the capacity of informal institutions, such as norms and communication, in generating social cohesion among actors in the supply chain and therefore improve the likelihood of generating commonly devised...
Coastal dunes provide a diverse set of ecosystem services including coastal protection against destructive surge and waves during storm events. Dunes are constantly evolving through various stages of response to storm events and post-storm recovery at rates that vary due to a range of drivers including pre-existing morphology, environmental forcing...
Wave energy has the potential to power large and small factions of economies around the world alike. Current methods for determining the amount of wave energy resource available to wave energy converter (WEC) devices entail capturing the look of the sea state at large by presenting characteristic wave heights, periods,...
Ph.D. candidate Qi Wei's thesis consists of two projects: Chemotherapy Project: a study based on the research paper "Predicting chemotherapy response of various cancer types using a variational auto-encoder approach" submitted to the bioRxiv preprint archive and accepted by the BMC bioinformatics; and Wound Monitor Project: implementing and assessing analytics...
Fluid-structure interaction (FSI) has been of significant research interest worldwide over the past several decades because of its variety of applications in both offshore and coastal engineering. Researchers analyzing FSI systems rely heavily on experimental tests in model scale in laboratories or large-scale sea trials. However, these tests are often...
Gamma Ray Bursts (GRBs) are the most energetic explosions in the Universe, producing up to $\sim10^{53}$ ergs of energy in the first few seconds of their emission -- the so-called prompt phase that is dominated by high energy X-ray and $\gamma$-ray photons. The very large luminosities released in these events...
Previous studies indicated that fertigating with nitrogen (N) was more effective than using granular N fertilizers in production of northern highbush blueberry (Vaccinium corymbosum L.). To build on these findings, four studies were conducted in western Oregon to determine whether fertigation was also an effective method for applying other nutrients,...
Local adaptation in plants may hold the key to understanding the level of resilience of an ecosystem and probability of persistence of a species in the face of rapid anthropogenic changes in climate and disturbance regime. Clonal species are especially important in wetlands, one of our most productive and vulnerable...
The pozzolanic reactivity test (PRT) is used to quantify the pozzolanic reactivity of supplementary cementitious materials (SCMs). The PRT computes reactivity by measuring heat release (Q) and calcium hydroxide (CH) consumption, as interpreted using thermodynamic modeling. The robustness of PRT is examined by experimentally varying CH-to-SCM ratio, solution-to-solid ratio, sulfate...
Specialized or secondary metabolism is a collection of pathways and small molecules that, while beneficial to an organism, are not strictly necessary for survival. Plants use secondary metabolites to, among other things, attract pollinators, defend against biotic and abiotic stressors, and form symbioses. Natural products from plants have seen an...
The persistent underrepresentation and marginalization of women of color in the disciplines of science, technology, engineering, and mathematics (STEM) are well-documented. However, much of the existing literature takes an “either/or” approach, focusing solely on the experiences of either “women” or “minorities” in STEM, without adequately examining the unique experiences of...