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...
At a time when environmental conditions are rapidly changing, understanding how thermal extremes impact wildlife is imperative to fully understanding the consequences of climate change in natural ecosystems. While many organisms are currently impacted by rapidly warming and more erratic environmental conditions, identifying and investigating model species whose life histories...
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....
Climate model simulations and paleoclimate proxies are two tools that enable an understanding of the climate history of the Earth. When utilized together, they form a powerful paradigm for understanding past changes. Proxies are the only physical link to the past conditions on Earth, and models “fill in the gaps”...
The South Pole ice core (SPC14), drilled in the field seasons of 2014/2015 and 2015/2016, is an intermediate length, 1,751-m ice core which preserves a 54,000-year record of past climate and atmospheric composition. The SPC14 ice core adds to the spatial grid of ice cores in Antarctica extending into the...
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...
Forest composition in Paraguay has been in a state of change for the past half century due to land management practices, forest fragmentation, and deforestation for agriculture. How these factors affect dendrological diversity and wood anatomy in Paraguay is not well understood. This thesis documents Paraguayan forest composition on the...
Species declines and extinctions have been recorded across taxa as evidence of an ongoing global biodiversity crisis. Amphibians are at the forefront of these declines with nearly one third of amphibian species estimated to be at risk of extinction. While many factors contribute to population declines and extinctions, the role...
Plant-parasitic nematodes cause more than US $100 billion in annual agriculture loss worldwide. Thorough knowledge of their genetic diversity, and interactions with endosymbionts and environment have the potential to provide valuable insights into the basic biology of these animals, and assist future efforts aimed at management of these plant parasites....
Understanding structural evolution in solids as composition changes is essential to materials properties prediction. Such structure-properties relationships are the theme of solid state chemistry. Materials scientists and chemists have utilized an abundance of simple crystal structures to enhance understanding of chemical and structural origins of properties in materials for decades....
In the event of a mid-flight flameout of a gas turbine engine, reignition is paramount to occupant safety. Ignition at high altitude can be challenging, due in part to the potentially lower ambient pressures. An understanding of the effects of sub-atmospheric pressures on the temperature evolution of spark kernels is...
Dearomatization reactions exist broadly in biosynthesis and chemical synthesis. The highly functionalized atoms of arenes can be masked by it aromaticity, and upon dearomatization, those reactive atoms can be readily applied to bond formation and further manipulation. The total synthesis of (–)-cephalotaxine and (–)- homoharringtonine is described via an oxidative...
Reconstructing the sensitivity of past climate to forcings, and of ancient glaciers and ice sheets to this climate, can allow us to better understand the range of climate and cryosphere behavior we may see in the coming centuries. The Arctic is a region of particular importance due to its well-documented...
The objective of this dissertation was to understand the physical mechanisms affecting inversion events in a complex forested mountain landscape. This work was motivated by the long-term studies of climate at the Andrews Forest, short-term studies of vertical temperature, light, wind, and moisture gradient in old-growth trees, and interest in...
Vibrio coralliilyticus (Vcor) is a bacterial pathogen that is well adapted to shellfish hatcheries and is very pathogenic to the larvae of the Pacific oyster Crassostrea gigas. Vcor has been associated with several large scale larval mortality events in the Pacific Northwest that interrupt the supply of seed oysters available...
Global biodiversity decline is primarily driven by habitat loss. Deforestation, the primary driver of terrestrial habitat loss, is increasing worldwide, with the most significant impact in the world biodiversity hotspots. Sadly, specific knowledge of such impacts in biodiversity-rich but data-poor countries are still unknown, and many national and regional narratives...
This dissertation examines the impact of the German naturalist and literary figure Johann Wolfgang von Goethe’s ideas on twentieth century Anglophone plant morphology and biology. Goethe interpreted the organ forms of flowering plants as metamorphoses of each other. His literary, historical, and philosophical writings suggest themes of alienation from and...
Characiform fishes form one of the most diverse freshwater fish clades in the world. Comprising more than 2000 species and distributed primarily in South America and Africa, characiforms vary dramatically in their ecomorphology. However, the evolutionary processes responsible for the immense ecomorphological diversity remains unknown. Recently, a study postulated that...
A sewer geyser is a series of ejecting air-water mixture eruptions through vertical shafts of drainage systems. In field observed geyser incidents, manhole covers were blown into the air and they were followed by ejecting air-water mixture eruptions that lasted for several seconds at a time. Trapped air in sewer...
Methane is a product of biogeochemical processes which respond to changes in climate. The history of atmospheric methane is recorded by ice cores providing insight into past changes in these biogeochemical processes. This dissertation is comprised of three studies which focus on centennial- and millenial-scale variability of methane from ice...
Markov chains have long been used to sample from probability distributions and simulate dynamical systems. In both cases we would like to know how long it takes for the chain's distribution to converge to within varepsilon of the stationary distribution in total variation distance; the answer to this is, called...
One of the biggest hurdles for a juvenile salmonid (Oncorhynchus mykiss) is migrating downstream from freshwater spawning grounds to the ocean. Juveniles from wild broodstock were reared from the South Santiam River for more than 1 year at the Oregon Hatchery Research Center (OHRC) in Alsea, OR. The fish were...
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David L.G. Noakes
One of the biggest hurdles for a juvenile salmonid (Oncorhynchus mykiss) is
In this project, I explore the use of monomania as a literary and rhetorical device that pathologizes deviance from certain norms—in this case, sexual and political norms— and allows for contradiction, dissonance, and reform. Using Nathaniel Hawthorne’s short story “The Birthmark” and Edmund Clarence Stedman’s poem “How Old Brown Took...
Designation of areas as marine wilderness has been proposed as a strategy for managing the increasing threats facing the world’s oceans. Although social factors influence marine protected area success, the human dimensions of marine wilderness remain minimally explored. This thesis examines views of marine wilderness expressed by a representative sample...
The goal of dissertation research was to use geochemical, statistical and geological methods to constrain and understand climate variability over several different time scales. Specifically, I have addressed three questions regarding past climate change: (1) how does the record of Irish cirque glaciers constrain the dimensions of the Irish Ice...
Two-photon, planar laser-induced fluorescence (PLIF) of carbon-monoxide (CO) and two-dimensional thermometry employing two-color, hydroxyl radical (OH) PLIF are used to characterize atmospheric-pressure inverse diffusion flames. These flames are important tools to aid the understanding of secondary reaction zones that may form in gas turbine engines when film-cooling air reacts with...
Increasingly, objectives for forests with moderate- or mixed-severity fire regimes are to restore successionally diverse landscapes that are resistant and resilient to current and future stressors. Maintaining native species and characteristic processes requires this successional diversity, but methods to achieve it are poorly explained in the literature. In the Inland...
Operating autonomous underwater vehicles (AUVs) near shore is challenging—heavy shipping traffic and other hazards threaten AUV safety at the surface, and strong ocean currents impede navigation when underwater. Predictive models of ocean currents have been shown to improve navigation accuracy, but these forecasts are typically noisy, making it challenging to...
The authors investigate atmospheric internal gravity waves (IGWs): their generation and induction of global intermittent turbulence in the nocturnal stable atmospheric boundary layer based on the new concept of turbulence generation discussed in a prior paper by Sun et al. The IGWs are generated by air lifted by convergence forced...
Although surfers have high incidental exposure to marine waters, no studies have investigated if surfer risk behaviors (such as surfing during advisories, near an outfall, during a rain event, or use of personal protective equipment) increase or decrease the risk of acquiring waterborne illnesses. We used a web-based survey to...
Vibrio tubiashii is reported to be a bacterial pathogen of larval Eastern oysters (Crassostrea virginica) and Pacific oysters (Crassostrea
gigas) and has been associated with major hatchery crashes, causing shortages in seed oysters for commercial shellfish
producers. Another bacterium, Vibrio coralliilyticus, a well-known coral pathogen, has recently been shown to...
Lead zirconate titanate (PZT) is the dominant ferroelectric material in the market due to its excellent piezoelectric properties, relatively high Curie transition temperature (T[subscript C]), low cost, etc. However, because of emerging applications with requirements for high temperature (T[subscript C] > 400 °C) ferroelectrics, researchers are increasingly looking at alternative...
The results presented in this dissertation address a number of questions regarding late Pleistocene and Holocene ice-sheet and climate interactions, spanning disciplines involving paleoclimatology and atmospheric science. These studies use various techniques in geochemistry, climate modeling, and ice-sheet modeling to address ice- sheet response to climate and the attendant interactions...
This article examines resident proximity and attachment to a new system of marine reserves in Oregon (USA), and the extent that these factors are related to both self-assessed and factual knowledge about these reserves. Data were from a survey of residents along the Oregon coast (n = 596). Residents reported...
This thesis presents an interactive software tool for tracking a moving object in a video. In particular, we focus on the problem of tracking a player in American football videos. Object tracking is one of the fundamental problems in computer vision. It is one of the most important components in...
Nearly all soils are comprised of mixtures of coarse and fine particles. Behavior under mechanical and thermal loading of soil is strongly influenced (and in some cases, governed) by the ratio of coarse to fine particles. A better understanding of the fundamental behavior of soil mixtures will provide insight to...
The information in this report is for the purpose of informing cooperators in industry, colleagues at other universities, and others of the results of research in field crops. Reference to products and companies in this publication is for specific information only and does not endorse or recommend that product or...
Protected area creation, including creation of marine reserves (MRs), is increasingly molded by ecosystem based management (EBM) that integrates biological and social information in the pre and post establishment phases. Collecting social data from large and representative samples of the public (as opposed to other stakeholder groups) before establishing a...
The Rusty Blackbird (Euphagus carolinus) has suffered significant population declines across its entire geographic range and the mechanisms associated with this decline are poorly understood. Although much of the Rusty Blackbird breeding habitat in Alaska has remained relatively unaltered by anthropogenic activities, this species continues to decline by an estimated...
Turbulence measurements for very stable conditions near the surface are contrasted
among three sites: a high altitude basin during winter with grass or snow-covered
grass, a broad valley with complex agricultural land use, and a more narrow valley that is
influenced by a valley cold pool and cold air drainage....
We present a new hypothesis to explain the millennial-scale temperature variability recorded in ice cores known as Dansgaard-Oeschger (DO) cycles. We propose that an ice shelf acted in concert with sea ice to set the slow and fast timescales of the DO cycle, respectively. The abrupt warming at the onset...
Ice cores are considered the gold standard for recording past climate and biogeochemical changes. However, gas records derived from ice core analysis have until now been largely limited to centennial and longer timescales because sufficient temporal resolution and analytical precision have been lacking, except during rare times when atmospheric concentrations...
During rapid variations of the atmospheric mixing ratio of a trace gas, diffusive transport in the porous firn layer atop ice sheets and glaciers alters the isotopic composition of that gas relative to the overlying atmosphere. Records of past atmospheric trace gas isotopic composition from ice cores and firn need...
The Mars Science Laboratory mission aims to land a car-sized rover on Mars’ surface and operate it for at least one Mars year in order to assess whether its field area was ever capable of supporting microbial life. Here we describe the approach used to identify, characterize, and assess environmental...
Along the Pacific coast of North America, from Alaska to Mexico, harmful algal blooms (HABs) have caused losses to natural resources and coastal economies, and have resulted in human sicknesses and deaths for decades. Recent reports indicate a possible increase in their prevalence and impacts of these events on living...
The optical response of metallic structures is dominated by the dynamics of their free electron plasma. Plasmonics, the area of optics specializing in the electromagnetic behavior of heterogeneous structures with metallic inclusions, is undergoing rapid development, fueled in part by recent progress in experimental fabrication techniques and novel
theoretical approaches....