Physical Sciences and Mathematics Commons^™

The Grace Programming Language Draft Specification Version 0.3.53, Andrew P. Black, Kim B. Bruce, James Noble

Computer Science Faculty Publications and Presentations

This is a specification of the Grace Programming Language. This specification is notably incomplete and everything is subject to change. In particular, this version does not address the library, nested static type system, module system, metadata, immutable data and pure methods, and other areas. For discussion and rationale, see http://gracelang.org.

It is designed for use by university students learning programming in CS1 and CS2 classes that are based on object-oriented programming, faculty and teaching assistants developing materials for 1st and 2nd year programming classes, programming researchers needing an object-oriented programming language as a research vehicle, and programming designers in search …

Substituent Effects On Reactivity And Allergenicity Of Benzoquinone, Wilbes Mbiya

Dissertations and Theses

Benzoquinone (BQ) is an extremely potent electrophilic contact allergen that haptenates endogenous proteins through Michael addition (MA). It is also hypothesized that BQ may haptenate proteins via free radical formation. The objective of this study was to assess the inductive effects (activating and deactivating) of substituents on BQ reactivity and the mechanistic pathway of covalent binding to nucleophilic thiols. The BQ binding by Cys34 on human serum albumin was studied, and for reactivity studies, nitrobenzenethiol (NBT) was used as a surrogate for protein binding of the BQ and benzoquinone derivatives (BQD). Stopped flow techniques were used to determine pseudo-first order …

Elementary Teacher Candidates' Images Of Mathematics, Diverse Students, And Teaching: An Exploratory Study With Implications For Culturally Responsive Mathematics Education, Bernd Richard Ferner

Dissertations and Theses

Children from many culturally diverse backgrounds do not achieve in mathematics at the same rates as their counterparts from the dominant White, European-American culture (Gay, 2010). This so-called achievement gap is an artifact of an educational system that continues to fail to provide equal learning opportunities to culturally diverse children (Ladson-Billings, 2006; Nieto & Bode, 2011). Teachers who employ culturally responsive teaching (Gay, 2010) may help to close this opportunity gap and hence, the achievement gap. This study investigated, "How do elementary teacher candidates perceive teaching mathematics in a multicultural environment"; Using a critical constructivism research paradigm, this qualitative instrumental …

Ccaat/Enhancer-Binding Protein Delta (C/Ebp-Delta) Expression In Antarctic Fishes: Implications For Cell Cycle And Apoptosis, Isaac Martin Sleadd

Dissertations and Theses

Chapter 1: Antarctic fishes are extremely cold adapted. Despite their inability to upregulate heat shock proteins, recent studies have demonstrated a capacity for heat response in these animals. A cDNA microarray study looked at the Notothenioid fish Trematomus bernacchii and revealed heat sensitivities for hundreds of genes, two of which code for members of the CCAAT/Enhancer-binding protein (C/EBP) family of transcription factors. These molecular switches are best known for their roles in apoptosis, inflammation and cell cycle arrest. This dissertation further elucidates the role of C/EBP-delta in the Antarctic fishes T. bernacchii and Pagothenia borchgrevinki.

Chapter 2: C/EBP-delta is constitutively …

A Novel Approach To Flow Estimation In Tidal Rivers, Hamed Moftakhari Rostamkhani, David A. Jay, Stefan A. Talke, Tobias Kukulka, Peter D. Bromirski

Civil and Environmental Engineering Faculty Publications and Presentations

Reliable estimation of river discharge to the ocean from large tidal rivers is vital for water resources management and climate analyses. Due to the difficulties inherent in measuring tidal-river discharge, flow records are often limited in length and/or quality and tidal records often predate discharge records. Tidal theory indicates that tides and river discharge interact through quadratic bed friction, which diminishes and distorts the tidal wave as discharge increases. We use this phenomenon to develop a method of estimating river discharge for time periods with tidal data but no flow record. Employing sequential 32 day harmonic analyses of tidal properties, …

The Role Of Wood Microsites At Timberline-Alpine Meadow Borders For Conifer Regeneration, Adelaide Chapman Johnson

Dissertations and Theses

This research aimed to determine whether wood microsites ("nurse logs"), which are regeneration sites in Pacific Northwest (PNW) subalpine forests, supported regeneration at timberline-alpine meadow borders. Upward advance of forests and conifer invasion into alpine meadows, which may be occurring in conjunction with climate warming, have gained worldwide attention. Successful alpine meadow seedling regeneration depends on suitable substrate availability, or microsites, for seedling establishment. To better understand factors associated with wood microsite occurrence, mechanisms of wood input were determined and four specific hypotheses were posed to assess: (1) seedling density and seedling survival; (2) growing season length, summer mean growing …

Contesting Sustainability: Bikes, Race, And Politics In Portlandia, Amy Lubitow, Thaddeus R. Miller

Urban Studies and Planning Faculty Publications and Presentations

Despite decade old calls for a "just sustainability," urban sustainability policy and practice remains oriented toward environmental outcomes and eco-lifestyle projects. Notions of equity, justice, and inclusion continue to be marginalized in favor of technological solutions, such as green buildings, that are visible, easy to implement, and help to promote economic development. By examining a controversy over a bikeway development project in a rapidly gentrifying neighborhood in Northeast Portland, Oregon, this article explores how despite apolitical appeals to broadly shared values or visions of what a sustainable city ought to look like, sustainability projects can be—and perhaps should be—hotly contested. …

Landslide Velocity, Thickness, And Rheology From Remote Sensing; La Clapiere Landslide, France, Adam M. Booth, Michael P. Lamb, Jean-Philippe Avouac, Christophe Delacourt

Geology Faculty Publications and Presentations

Quantifying the velocity, volume, and rheology of deep, slow-moving landslides is essential for hazard prediction and understanding landscape evolution, but existing field-based methods are difficult or impossible to implement at remote sites. Here we present a novel and widely applicable method for constraining landslide 3-D deformation and thickness by inverting surface change data from repeat stereo imagery. Our analysis of La Clapiere, an approximately 1 km (super 2) bedrock landslide, reveals a concave-up failure surface with considerable roughness over length scales of tens of meters. Calibrating the thickness model with independent, local thickness measurements, we find a maximum thickness of …

Classifying Reanalysis Surface Temperature Probability Density Functions (Pdfs) Over North America With Cluster Analysis, Paul C. Loikith, Benjamin R. Lintner, Jinwon Kim, Huikyo Lee

Geography Faculty Publications and Presentations

An important step in projecting future climate change impacts on extremes involves quantifying the underlying probability distribution functions (PDFs) of climate variables. However, doing so can prove challenging when multiple models and large domains are considered. Here an approach to PDF quantification using k-means clustering is considered. A standard clustering algorithm (with k = 5 clusters) is applied to 33 years of daily January surface temperature from two state-of-the-art reanalysis products, the North American Regional Reanalysis and the Modern Era Retrospective Analysis for Research and Applications. The resulting cluster assignments yield spatially coherent patterns that can be broadly related to …

Social-Ecological Dynamics Of Coral Reef Resource Use And Management, Sarah J. Freed

Dissertations and Theses

This dissertation investigates social and ecological factors that facilitate effective management of coral reefs as social-ecological systems. Meta-analytical and field-based methods were employed to examine current management challenges and identify strategies that improve management effectiveness and coral reef health. A meta-analysis was used to evaluate biological indicators of reef health in relation to the types of fishing regulations in place (no-take areas, gear restriction areas, and periodic closures) and the actor groups (community-based, co-management, state, private) involved in management efforts for coral reef fisheries throughout the world. Other than enhancement of fish biomass within no-take areas that was significantly greater …

Natural Area Stewardship Volunteers: Motivations, Attitudes, Behaviors, Corinne Handelman

Dissertations and Theses

To better understand the value of those who engage in environmental stewardship of natural areas, we studied volunteer steward's motivation to participate, their sustainable behaviors and attitudes toward stewardship-related constructs. Specifically, we designed and conducted a survey of volunteers who work as stewards in urban natural areas in Portland, Oregon. We hypothesize that as volunteer frequency increases: participants will be more motivated to participate for environmental reasons, volunteers will be more likely to feel a strong connection to the stewardship site, participants will be more likely to engage in public pro-environmental behaviors, and their level of environmental literacy will increase. …

Accelerated Thermokarst Formation In The Mcmurdo Dry Valleys, Antarctica, Joseph S. Levy, Andrew G. Fountain, James L. Dickson, James W. Head, Marianne Okal, David R. Marchant, Jaclyn Watters

Geology Faculty Publications and Presentations

Thermokarst is a land surface lowered and disrupted by melting ground ice. Thermokarst is a major driver of landscape change in the Arctic, but has been considered to be a minor process in Antarctica. Here, we use ground-based and airborne LiDAR coupled with timelapse imaging and meteorological data to show that 1) thermokarst formation has accelerated in Garwood Valley, Antarctica; 2) the rate of thermokarst erosion is presently,10 times the average Holocene rate; and 3) the increased rate of thermokarst formation is driven most strongly by increasing insolation and sediment/albedo feedbacks. This suggests that sediment enhancement of insolation-driven melting may …

Pinhole Neutral Atom Microscopy, Philip James Witham

Dissertations and Theses

This work presents a new form of microscopy, the instrument constructed to demonstrate it, the images produced and the image contrast mechanisms seen for the first time. Some of its future scientific potential is described and finally, recent work towards advancing the method is discussed.

Many forms of microscopy exist, each with unique advantages. Of several broad categories that they could be grouped into, those that use particle beams have proven very generally useful for micro and nano-scale imaging, including Scanning Electron, Transmission Electron, and Ion Beam microscopes. These have the disadvantage, however, of implanting electric charges into the sample, …

Characterization Of The Shallow Subsurface Geohydrology Of The Ni-Les'tun Unit On The Bandon Marsh National Wildlife Refuge, Christopher Madison Beard

Dissertations and Theses

The Bandon Marsh is a large marsh restoration project located in southwest Oregon. The land has been previously used for dairy farms and much of the marsh was used for cattle grazing. The goal of the restoration is to recreate a natural habitat for shorebirds and fish. The purpose of this thesis is to gather and analyze data on the geology of the marsh and both ground and surface water quality to evaluate its ability to support biology.

The US Fish and Wildlife Service began restoration on the Bandon marsh in 2005. Research on the Ni-les'tun Unit began in that …

Grounding Zone Processes: Ice Mechanics And Margin Lakes, Kamb Ice Stream And Whillans Ice Stream, West Antarctica, Mason Joseph Fried

Dissertations and Theses

The lateral "corners" where Kamb and Whillans Ice Streams (KIS and WIS) discharge into the Ross Ice Shelf share common geometries and ice mechanical settings. At both corners of the now-stagnant KIS outlet, shear margins of apparently different ages confine regions with a relatively flat, smooth surface expression. These features are called the "Duckfoot" on the northern, right-lateral side and the "Goosefoot" on the other. It has been suggested, on evidence found in ice internal layers, that the flat ice terrains on KIS were afloat in the recent past, at a time when the ice stream grounding line was upstream …

Arsenic Mobility And Compositional Variability In High-Silica Ash Flow Tuffs, Courtney Beth Young Savoie

Dissertations and Theses

Volcanic rocks typically have only low to moderate arsenic concentrations, none-the-less, elevated levels of arsenic in ground waters have been associated with pyroclastic and volcaniclastic rocks and sediments in many parts of the world. The potential for arsenic leaching from these deposits is particularly problematic as they often comprise important water-bearing units in volcanic terrains. However, the role that chemical and mineralogical variations play in controlling the occurrence and mobility of arsenic from pyroclastic rocks is largely unexplored.

This study uses chemical and X-ray diffraction data to characterize and classify 49 samples of ash-flow tuffs, and 11 samples of tuffaceous …

Developing Thyronamine Analog Pharmaceuticals Targeting Taar1 To Treat Methamphetamine Addiction, Troy Andrew Wahl

Dissertations and Theses

As a part of the overall program in the Grandy laboratory at Oregon Health & Science University (OHSU), studying the underlying chemical biology of methamphetamine (Meth) addiction, this dissertation reports on the development of six new thyronamine analogs which were synthesized and assayed against trace amine associated receptor 1 (TAAR1), giving preliminary results consistent with the analogs being inverse agonists. Due to highly variable TAAR1 expression levels in the assays, based on inter-assay response to control Meth stimulation as well as other possible factors, kinetic models were developed to qualitatively explain the assay results. The models set approximate limits on …

Direct Imaging Of Optical Diffraction In Photoemission Electron Microscopy, Robert Campbell Word, Joseph Fitzgerald, Rolf Kӧnenkamp

Physics Faculty Publications and Presentations

We report the visualization of optical diffraction at the boundaries of semiconductor and metal nanostructures in non-linear photoemission electron microscopy. We observe light diffracting into photonic and plasmonic modes of planar samples, and into photonic vacuum modes above sample surfaces. In either case, the electron photoemission rate from the sample material is spatially modulated resulting in photoemission images with information on the electric field distribution at the sample/vacuum interface. The resolution in these images is typically ∼30 nm, i.e., significantly below the wavelengths of the exciting light. Optical phase shifts and absorption losses for the diffracted modes can be determined.

Water Track Modification Of Soil Ecosystems In The Lake Hoare Basin, Taylor Valley, Antarctica, Joseph S. Levy, Andrew G. Fountain, Michael N. Gooseff, John E. Barrett, Robert Vantreese, Kathleen A. Welch, W. Berry Lyons, Uffe N. Nielsen, Diana H. Wall

Geology Faculty Publications and Presentations

Water tracks are zones of high soil moisture that route shallow groundwater down-slope, through the active layer and above the ice table. A water track in Taylor Valley, McMurdo Dry Valleys, was analysed for surface hydrogeological, geochemical, and biological characteristics in order to test the hypothesis that water tracks provide spatial structure to Antarctic soil ecosystems by changing the physical conditions in the soil environment within the water tracks from those outside the water tracks. The presence of the water track significantly affected the distribution of biotic and abiotic ecosystem parameters: increasing soil moisture, soil salinity, and soil organic matter …

A Parabolic Equation Analysis Of The Underwater Noise Radiated By Impact Pile Driving, Nathan Laws

Dissertations and Theses

Impact pile driving can produce extremely high underwater sound levels, which are of increasing environmental concern due to their deleterious effects on marine wildlife. Prediction of underwater sound levels is important to the assessment and mitigation of the environmental impacts caused by pile driving. Current prediction methods are limited and do not account for the dynamic pile driving source, inhomogeneities in bathymetry and sediment, or physics-based sound wave propagation.

In this thesis, a computational model is presented that analyzes and predicts the underwater noise radiated by pile driving and is suitable for shallow, inhomogeneous environments and long propagation ranges. The …

Hydrogeologic Characterization Of Dutch Canyon, Scappoose, Oregon, Derrick Lee Wagner

Dissertations and Theses

Dutch Canyon is located directly west of the City of Scappoose in Columbia County Oregon. This area is proximate to Highway 30, a major access corridor to downtown Portland, and is experiencing a population increase, which is expected to continue and likely accelerate. As a result, there is growing pressure on water resources. Individual and community efforts to utilize groundwater resources have been hampered by generally poor groundwater yields and water quality concerns outside of the Columbia River corridor and a lack of published hydrogeologic information for the region.

The intent of this study is to identify the water-bearing units …

Crystallographic Image Processing With Unambiguous 2d Bravais Lattice Identification On The Basis Of A Geometric Akaike Information Criterion, Taylor Thomas Bilyeu

Dissertations and Theses

Crystallographic image processing (CIP) is a technique first used to aid in the structure determination of periodic organic complexes imaged with a high-resolution transmission electron microscope (TEM). The technique has subsequently been utilized for TEM images of inorganic crystals, scanning TEM images, and even scanning probe microscope (SPM) images of two-dimensional periodic arrays. We have written software specialized for use on such SPM images. A key step in the CIP process requires that an experimental image be classified as one of only 17 possible mathematical plane symmetry groups. The current methods used for making this symmetry determination are not entirely …

Integrating Economics And System Dynamics Approaches For Modeling An Ecological-Economic System, Takuro Uehara, Yoko Nagase, Wayne W. Wakeland

Wayne W. Wakeland

This article describes collaboration between system dynamicists and economists to model a multi-sector, ecological-economic model of population and resource dynamics that is firmly based on economic theory and leverages the strengths of both fields. This model illuminates how an SD approach allows model complexity to be extended in order to effectively model interactions between an economic system and an ecological system. Specifically, the simulation exercise demonstrates how SD model analysis can help explain the counterintuitive model behaviors due to increases in the natural resource carrying capacity or regeneration rate. The simulation results also reveal that allowing for out-of-equilibrium states (adaptation) …

The Wicked Problem Of Chemicals Policy: Opportunities For Innovation, Jennifer H. Allen

Institute for Sustainable Solutions Publications and Presentations

Many environmental challenges facing society today, such as climate change and integrated water management, have been described as “wicked problems” due to their biological, physical, and social complexity. Wicked problems extend across media such as air, land, and water; across political jurisdictions and landscape boundaries; and across traditional policy arenas. Traditional policy approaches that are media-specific, rely on single agencies for implementation, and that do not effectively engage stakeholders and partners outside of government are generally ineffective in addressing these issues. The management of toxic chemicals is a classic “wicked problem.” Existing toxics policies often exacerbate the “wicked” nature of …

Coupling Fast Water Exchange To Slow Molecular Tumbling In Gd3+ Chelates: Why Faster Is Not Always Better, Stefano Avedano, Mauro Botta, Julian Saunders Haigh, Dario L. Lango, Mark Woods

Chemistry Faculty Publications and Presentations

The influence of dynamics on solution state structure is a widely overlooked consideration in chemistry. Variations in Gd³⁺ chelate hydration with changing coordination geometry and dissociative water exchange kinetics substantially impact the effectiveness (or relaxivity) of monohydrated Gd³⁺ chelates as T1-shortening contrast agents for MRI. Theory shows that relaxivity is highly dependent upon the Gd³⁺–water proton distance (rGdH), and yet this distance is almost never considered as a variable in assessing the relaxivity of a Gd³⁺ chelate as a potential contrast agent. The consequence of this omission can be seen when considering …

Economics Of Redd+ And Community Forestry, Randall Bluffstone

Economics Faculty Publications and Presentations

Reducing Emission from Deforestation and Forest Degradation (REDD+) is a payment for ecosystem services (PES) system created under the Framework Convention on Climate Change (FCCC) that tries to reduce deforestation and degradation in countries not subject to requirements under the convention (non-Annex 1 countries) and, therefore, release less and sequester more carbon. Other cobenefits have been added, such as biodiversity protection, poverty reduction and afforestation, which make up the '+' in REDD+. The '+', therefore, attempts to address potentially negative, unintended effects on non-carbon ecosystem services and take account of effects on those who currently have claims to forests. Many …

Integrating Economics And System Dynamics Approaches For Modeling An Ecological-Economic System, Takuro Uehara, Yoko Nagase, Wayne Wakeland

Systems Science Faculty Publications and Presentations

This article describes collaboration between system dynamicists and economists to model a multi-sector, ecological-economic model of population and resource dynamics that is firmly based on economic theory and leverages the strengths of both fields. This model illuminates how an SD approach allows model complexity to be extended in order to effectively model interactions between an economic system and an ecological system. Specifically, the simulation exercise demonstrates how SD model analysis can help explain the counterintuitive model behaviors due to increases in the natural resource carrying capacity or regeneration rate. The simulation results also reveal that allowing for out-of-equilibrium states (adaptation) …

Microbial Biogeochemistry Of Boiling Springs Lake: A Physically Dynamic, Oligotrophic, Low-P H Geothermal Ecosystem, Patricia Lynne Siering, Gordon V. Wolfe, Mark S. Wilson, A. N. Yip, Cynthia M. Carey, Colin D. Wardman, Russell Scott Shapiro, Kenneth M. Stedman, Jennifer E. Kyle, Tong Yuan, Joy D. Van Nostrand, Zhili He, Jizhong Zhou

Biology Faculty Publications and Presentations

Boiling Springs Lake (BSL) in Lassen Volcanic National Park, California, is North America's largest hot spring, but little is known about the physical, chemical, and biological features of the system. Using a remotely operated vessel, we characterized the bathymetry and near-surface temperatures at sub-meter resolution. The majority of the 1.2 ha, pH 2.2 lake is 10 m deep and 50-52 [degrees]C, but temperatures reach 93 [degrees]C locally. We extracted DNA from water and sediments collected from warm (52 [degrees]C) and hot (73-83 [degrees]C) sites separated by 180 m. Gene clone libraries and functional gene microarray (GeoChip 3.0) were used to …

Interspecific Variation In Leaf-Level Biogenic Emissions Of The Bambuseae, Andrea Natalie Melnychenko

Dissertations and Theses

Plants emit a diverse range of biogenic volatile organic compounds (BVOCs) into the atmosphere, of which isoprene is the most abundantly emitted. Isoprene significantly affects biological and atmospheric processes, but the range of isoprene and BVOCs present in bamboos has not been well characterized. In this thesis I explore the range of isoprene emission found in bamboos and relate it to plant morphological and physiological characteristics. In addition, I measure and relate the entire suite of BVOCs present in the bamboos to their fundamental isoprene emission rate.

Interspecific variation in isoprene emission documented in a comprehensive survey of bamboos. Two …

Preserving Nature Through Film: Wilderness Alps Of Stehekin And The North Cascades, 1956-1968, Nicolas Timothy Bergmann

Dissertations and Theses

On March 22, 1958 David Brower's film Wilderness Alps of Stehekin premiered to an audience of conservationists in Seattle, Washington. Almost two years in the making, the thirty-one minute film advocated the preservation of nature in Washington's North Cascades through the creation of a national park. Over the next decade, Wilderness Alps of Stehekin became the most influential publicity tool in the struggle to preserve the North Cascades. Because of the region's geographic isolation, the film was the first time many people throughout the nation were exposed to the scenic grandeur of the area. Images of craggy peaks and colorful …