Physical Sciences and Mathematics Commons^™

A Framework For Superimposed Applications : Techniques To Represent, Access, Transform, And Interchange Bi-Level Information, Sudarshan Srivivasa Murthy

Dissertations and Theses

Superimposed applications (SAs) superimpose (that is, overlay) new information and structures (such as annotations) on parts (such as sub-documents) of existing base information (BI). In this setting, SA developers and users work with bi-level information, a combination of the superimposed information and the referenced BI parts.

We have designed a framework to assist SAs in the following bi-level-information-management activities: representation, access, transformation, and interchange. This framework defines the abstraction context agent to activate any BI part and to retrieve information from the context of the part. It includes means to represent and access bi-level information in a conceptual model (the …

Interview With Lynne Nelson, Oregon Mortuary & Cemetery Board, 2009 (Audio), Lynne Nelson

All Sustainability History Project Oral Histories

Interview of Lynne Nelson by Daniel Donovan in Portland, Oregon on March 9th, 2009.

The interview index is available for download.

Interview With Daniel Hilton, Mt. Hood Community College, 2009 (Audio), Daniel Hilton

All Sustainability History Project Oral Histories

Interview of Daniel Hilton by Cory Minick at Mt. Hood Community College on March 5th, 2009.

The interview index is available for download.

Interview With Patricia Swenney, Spiral Of Life, 2009 (Audio), Patricia Swenney

All Sustainability History Project Oral Histories

Interview of Patricia Swenney by Hanna Flagg on March 5th, 2009.

The interview index is available for download.

Interview With Bruce Polone, Vancouver Granite Works, 2009 (Audio), Bruce Polone

All Sustainability History Project Oral Histories

Interview of Bruce Polone by Dylan Bless in Portland, Oregon on March 5th, 2009.

The interview index is available for download.

Interview With Michael Imlah, Congregation Shaarie Torah, 2009 (Audio), Michael Imlah

All Sustainability History Project Oral Histories

Interview of Michael Imlah by Dennis LaPrade at Congregation Shaarie Torah, Portland, Oregon on March 4th, 2009.

The interview index is available for download.

Improving Travel Information Products Via Robust Estimation Techniques, David Maier, Kristin A. Tufte, Rafael J. Fernández Moctezuma

TREC Final Reports

Traffic-monitoring systems, such as those using loop detectors, are prone to coverage gaps, arising from sensor noise, processing errors and transmission problems. Such gaps adversely affect the accuracy of Advanced Traveler Information Systems. This project will explore models based on historical data that can provide estimates to fill such gaps. We build on an initial study by Mr. Rafael J. Fernandez-Moctezuma, using both a linear model and an artificial neural network (ANN) trained on historical data to estimate values for reporting gaps. These initial models were 80% and 89% accurate, respectively, in estimating the correct speed range, and misclassifications were …

Synthesis And Evaluation Of Lanthanide Ion Dota-Tetraamide Complexes Bearing Peripheral Hydroxyl Groups, Azhar Pasha, Mai Lin, Gyula Tircso, Cynthia L. Rostollan, Mark Woods, Garry Kiefer, A. Dean Sherry, Xiankai Sun

Chemistry Faculty Publications and Presentations

The use of lanthanide-based contrast agents for magnetic resonance imaging has become an integral component of this important diagnostic modality. These inert chelates typically possess high thermodynamic stability constants that serve as a predictor for in vivo stability and low toxicity. Recently, a new class of contrast agents was reported having a significantly lower degree of thermodynamic stability while exhibiting biodistribution profiles indicative of high stability under biological conditions. These observations are suggestive that the nature of contrast agent stability is also dependent upon the kinetics of complex dissociation, a feature of potential importance when contemplating the design of new …

Data Assimilation, Adaptive Observations And Applications, Humberto Carlos Godinez Vasquez

Dissertations and Theses

Sensitivity analysis, data assimilation and targeting observation strategies are methods that are applied to various complex mathematical models of fluid dynamics. In this research we investigate new directions to improve on the current strategies used to deploy additional observational resources (targeting strategies) for data assimilation in dynamical systems of fluid mechanics.

Targeting strategies aim to determine optimal locations where additional observations will improve the solution of the data assimilation process by identifying regions where state errors in the model have a high potential to grow.

Properly accounting for nonlinear error growth is an unresolved issue in targeted observations for numerical …

Vegetation, Environmental Characteristics, And Their Relationships: Variation Within The Annually Flooded Riparian Zones Of The John Day River Basin, Oregon, Samuel J. Hartsfield

Dissertations and Theses

I hypothesized that vegetation and physical environmental characteristics would differ between the upper and lower extents of the annually flooded riparian zone on the John Day River, and that relationships between species and environmental variables would display differences between these two zones. Vegetation, environmental variables, and relationships between them were assessed for the entire annually flooded riparian zone, and for the proposed upper and lower zones. Data were collected from 60 one-square-meter quadrats: 30 in each the upper and lower zones. Sites were randomly selected and located so that flood duration was roughly equal at all sites within each zone. …

Characterization Of Putative Self-Resistance Genes In The Biosynthetic Gene Cluster Of Hygromycin A From Streptomyces Hygroscopicus Nrrl 2388, Vidya Dhote

Dissertations and Theses

Streptomyces hygroscopicus NRRL 2388 produces an aminocyclitol antibiotic called hygromycin A (HA), which targets bacterial protein synthesis by inhibiting the peptidyl transferase reaction. The hyg6, hygl9, hyg21, hyg28, and hyg29 genes in the biosynthetic gene cluster of HA are predicted to confer self-resistance to the producer strain by different mechanisms. Targeted gene disruptions and in vitro characterization of recombinant proteins were carried out to elucidate the functions of these genes. The hyg21 gene encodes an O-phosphotransferase with a proposed role in HA inactivation by phosphorylation. Disruption of hyg21 led to a significant decrease in HA production but did not …

Synthesis Of Aptamer-Porphyrin Conjugate For Photodynamic Therapy & Synthesis And Stability Of Mixed Thiol/Lipid Coated Gold Nanoparticles, Sarita Sitaula

Dissertations and Theses

An underlying problem in Photodynamic Therapy (PDT) is low selectivity of photosensitizers currently being used for the treatment of tumors. This thesis is focused on developing new PDT drugs and is divided into two parts. The first chapter describes a method for selective delivery of the photosensitizers to the tumor site by conjugating porphyrins to an aptamer for the targeted PDT. To achieve this, a novel synthesis of 2'-porphyrin-modified uridine was developed. The 3'-H-phosphonate derivatives of both 2'-porphyrin and 2'-dithiaporphyrin modified uridine were also synthesized. The 3'41-phosphonate derivative of 2'-porphyrin-modified uridine was conjugated to a 19-mer DNA and to a …

Global Methane Emissions From Wetlands, Rice Paddies, And Lakes, Qianlai Zhuang, John M. Melack, Sergey Zimov, Katey Marion Walter, Christopher Lee Butenhoff, M. A. K. Khalil

Physics Faculty Publications and Presentations

The current concentration of atmospheric methane is 1774±1.8 parts per billion, and it accounts for 18% of total greenhouse gas radiative forcing [Forster et al., 2007]. Atmospheric methane is 22 times more effective, on a per-unit-mass basis, than carbon dioxide in absorbing long-wave radiation on a 100-year time horizon, and it plays an important role in atmospheric ozone chemistry (e.g., in the presence of nitrous oxides, tropospheric methane oxidation will lead to the formation of ozone). Wetlands are a large source of atmospheric methane, Arctic lakes have recently been recognized as a major source [e.g., Walter et al., 2006], and …

Spokane River In Idaho And Washington Tmdl Water Quality And Hydrodynamic Modeling Quality Assurance Project Plan -- Draft, Scott A. Wells, Chris Berger

Civil and Environmental Engineering Faculty Publications and Presentations

The focus of this present study is to perform the following tasks:

• Converting the Upper Spokane River CE‐QUAL‐W2 models (Washington and Idaho) to version 3.6

• Combining the Washington and Idaho models

• Reviewing and updating model boundary conditions

• Check model calibration

• Meet with stakeholders

• Develop and Run Modeling Scenarios

• Create reports on calibration and scenario runs

Measuring The Effects Of Food Carbon Footprint Training On Consumer Knowledge, Transfer Intentions, And Environmental Self-Efficacy, Wayne Wakeland, Lindsay Sears, Kumar Venkat

Systems Science Faculty Publications and Presentations

The supply chains through which foods are produced, processed, and transported can have a significant impact on the environment in terms of the carbon dioxide (CO2) that is emitted during each of these phases; however, little research has incorporated information about environmental impact into supply chain scenarios. Moreover, many consumers are unaware of how their food choices may impact the environment in this way. To fill these gaps, a tool called CarbonScope was developed to show consumers the CO2 emissions associated with different food types and food transportation scenarios. A short training was designed that walks participants through various food …

Enhancing Science Teachers' Understanding Of Ecosystem Interactions With Qualitative Conceptual Models, Marion Dresner, Monica Elser

Environmental Science and Management Faculty Publications and Presentations

The project described in this article explores how a series of conceptual ecological models can be used to portray the improvement in ecological understanding over the span of a short course. The course involved high school teachers working collaboratively on ecological research projects. Teachers were asked to construct qualitative conceptual models (a diagram of important ecosystem components and the linkages between these components) and write explanatory essays at three points during their research experience. The progression in development of teachers’ models spanned initial intuitive explanation, with misconceptions, to the post-test elaboration of a more complex and accurate understanding of ecological …

Is Parallel Programming Hard, And If So, Why?, Paul E. Mckenney, Maged M. Michael, Manish Gupta, Philip William Howard, Josh Triplett, Jonathan Walpole

Computer Science Faculty Publications and Presentations

Of the 200+ parallel-programming languages and environments created in the 1990s, almost all are now defunct. Given that parallel systems are now well within the budget of the typical hobbyist or graduate student, it is not unreasonable to expect a new cohort in excess of several thousand parallel languages and environments to appear in the 2010s. If this expected new cohort is to have more practical impact than did its 1990s counterpart, a robust and widely applicable framework will be required that encompasses exactly what, if anything, is hard about parallel programming. This paper revisits the fundamental precepts of concurrent …

Programmer Friendly Refactoring Tools, Emerson Murphy-Hill

Dissertations and Theses

Tools that perform semi-automated refactoring are currently under-utilized by programmers. If more programmers adopted refactoring tools, software projects could make enormous productivity gains. However, as more advanced refactoring tools are designed, a great chasm widens between how the tools must be used and how programmers want to use them. This dissertation begins to bridge this chasm by exposing usability guidelines to direct the design of the next generation of programmer-friendly refactoring tools, so that refactoring tools fit the way programmers behave, not vice-versa.

One Rna Plays Three Roles To Provide Catalytic Activity To A Group I Intron Lacking An Endogenous Internal Guide Sequence, Nilesh Vaidya, Niles Lehman

Chemistry Faculty Publications and Presentations

Catalytic RNA molecules possess simultaneously a genotype and a phenotype. However, a single RNA genotype has the potential to adopt two or perhaps more distinct phenotypes as a result of differential folding and/or catalytic activity. Such multifunctionality would be particularly significant if the phenotypes were functionally inter-related in a common biochemical pathway. Here, this phenomenon is demonstrated by the ability of the Azoarcus group I ribozyme to function when its canonical internal guide sequence (GUG) has been removed from the 5? end of the molecule, and added back exogenously in trans. The presence of GUG triplets in noncovalent fragments of …

The Role Of Water And Other Resources In The Invasion Of Rubus Armeniacus In Pacific Northwest Ecosystems, Joshua Sundance Caplan

Dissertations and Theses

The factors influencing the invasive success of Rubus armeniacus (Himalayan blackberry) in the Pacific Northwest of North America are only partly understood, but have important implications for its management and for our understanding of the processes driving invasive plant proliferation in regions with seasonally fluctuating resources. I identified patterns of R. armeniacus occurrence and growth under widely ranging soil and light conditions in western Oregon. I found that light availability was a primary determinant of R. armeniacus occurrence and growth. I also found that R. armeniacus was tolerant of a wide range of soil conditions, notably coarse texture, and could …

Studies Of Dna Hybridization Reactions And Applications In Genetic Assays, Fidelis Manyanga

Dissertations and Theses

The intent of this study was to investigate two fundamental aspects of short DNA duplex stability and how that stability differs for duplex molecules consisting of either all perfect match Watson/Crick base pairs or a mixture of perfect match Watson/Crick base pairs and mismatch base pairs. Theoretical and experimental investigations of the origins of the nucleation term in the free energy of DNA duplex formation were revisited. Thermodynamic parameters (ΔG, ΔH, Δ S and Tm) of short DNA/DNA duplexes ranging in length from 6 to 35 base pairs were systematically evaluated by Differential Scanning Calorimetry …

Nanometrology Device Standards For Scanning Probe Mmicroscopes And Processes For Their Fabrication And Use, Peter Moeck

Physics Faculty Publications and Presentations

Nanometrology device standards and methods for fabricating and using such devices in conjunction With scanning probe microscopes are described. The fabrication methods comprise: (1) epitaxial growth that produces nanometer sized islands of knoWn morphology, structural, morphological and chemical stability in typical nanometrology environments, and large height-to-width nano-island aspect ratios, and (2) marking suitable crystallographic directions on the device for alignment With a scanning direction.

Winter Precipitation Intensity And Enso/Pdo Variability In The Willamette Valley Of Oregon, Sarah Praskievicz, Heejun Chang

Geography Faculty Publications and Presentations

There is growing concern about the effects of inter-annual climatic variability, such as the El-Niño Southern Oscillation (ENSO) and the Pacific Decadal Oscillation (PDO), on regional hydrology and water resources. We analyzed patterns of wintertime precipitation intensity, using both simple intensity and number of heavy precipitation days per year, for eight stations in northwestern Oregon’s Willamette Valley for the period 1972–2006, and examined the separate and combined influence of ENSO and PDO on precipitation intensity. The analysis was accomplished using Kendall’s tau and analysis of variance (ANOVA) to determine differences in precipitation intensity among combinations of positive and negative ENSO …

Non-Linearity In Ecosystem Services: Temporal And Spatial Variability In Coastal Protection, Evamaria W. Koch, Edward Barbier, Brian R. Silliman, Denise J. Reed, Gerardo M. E. Perillo, Sally D. Hacker, Elise F. Granek, Jurgenne H. Primavera, Nyawira Muthiga, Stephen Polasky, Benjamin S. Halpern, Christopher J. Kennedy, Carrie V. Kappel, Eric Wolanski

Institute for Sustainable Solutions Publications and Presentations

Natural processes tend to vary over time and space, as well as between species. The ecosystem services these natural processes provide are therefore also highly variable. It is often assumed that ecosystem services are provided linearly (unvaryingly, at a steady rate), but natural processes are characterized by thresholds and limiting functions. In this paper, we describe the variability observed in wave attenuation provided by marshes, mangroves, seagrasses, and coral reefs and therefore also in coastal protection. We calculate the economic consequences of assuming coastal protection to be linear. We suggest that, in order to refine ecosystem-based management practices, it is …

Toward A New Sustainable Economy, Robert Costanza

Institute for Sustainable Solutions Publications and Presentations

The current financial meltdown is the result of under-regulated markets built on an ideology of free market capitalism and unlimited economic growth. The fundamental problem is that the underlying assumptions of this ideology are not consistent with what we now know about the real state of the world. The financial world is, in essence, a set of markers for goods, services, and risks in the real world and when those markers are allowed to deviate too far from reality, ?adjustments? must ultimately follow and crisis and panic can ensue. To solve this and future financial crisis requires that we reconnect …

Introduction To Common Native And Potential Invasive Freshwater Plants In Alaska, Vanessa Howard Morgan, Mark Sytsma

Center for Lakes and Reservoirs Publications and Presentations

Freshwater aquatic plants are found in most lakes and rivers in Alaska. They range from tiny floating plants that can form mats on a lake surface to emergent plants growing two meters above the water. Aquatic plants are an important part of freshwater environments. They provide food and shelter for a wide variety of insects, fish, mammals, and birds; stabilize shorelines; and form an important link in nutrient cycles. To date, Alaska has had relatively few problems with invasive, non-native aquatic plants. However, invasive aquatic plants pose an increasing threat to human safety and the integrity of native aquatic communities. …

Beyond Gdp: The Need For New Measures Of Progress, Robert Costanza, Maureen Hart, John Talberth, Stephen Posner

Institute for Sustainable Solutions Publications and Presentations

This paper is a call for better indicators of human well-being in nations around the world. We critique the inappropriate use of Gross Domestic Product (GDP) as a measure of national well-being, something for which it was never designed. We also question the idea that economic growth is always synonymous with improved well-being. Useful measures of progress and well-being must be measures of the degree to which society?s goals (i.e., to sustainably provide basic human needs for food, shelter, freedom, participation, etc.) are met, rather than measures of the mere volume of marketed economic activity, which is only one means …

The Mckee Preserve Management Options At Bandon Dunes Golf Resort, Ashley Marie Edwards

Environmental Science and Management Professional Master's Project Reports

The McKee Preserve is a new conservation area at Bandon Dunes Golf Resort, located on the southern Oregon coast. The Preserve is 250 acres in size and is made up of 13 different natural resource communities. One important resource is silvery phacelia (Phacelia argentea), which is a state threatened plant species and is a species of concern federally. The goal of this project was to perform plant inventories for silvery phacelia and kinnikinnick that will be used to establish a functional management plan for the Preserve. Other resources of interest to the Preserve have been included in the …

The Potential Contribution Of Organic Salts To New Particle Growth, Kelley Barsanti, Peter H. Mcmurry, J. N. Smith

Civil and Environmental Engineering Faculty Publications and Presentations

Field and lab measurements suggest that low-molecular weight (MW) organic acids and bases exist in accumulation and nucleation mode particles, despite their relatively high pure-liquid vapor pressures. The mechanism(s) by which such compounds contribute to the mass growth of existing aerosol particles and newly formed particles has not been thoroughly explored. One mechanism by which low- MW compounds may contribute to new particle growth is through the formation of organic salts. In this paper we use thermodynamic modeling to explore the potential for organic salt formation by atmospherically relevant organic acids and bases for two system types: one in which …

State Of The River Report For Toxics, Bradley Carter

Environmental Science and Management Professional Master's Project Reports

The United States Environmental Protection Agency (EPA) strives to prevent pollution, protect water quality and improve ecosystems in order to reduce risks to human health and the environment. As outlined in the Agency’s Strategic Plan, the Columbia River Basin was identified as a "National Priority" and designated as one of our nation’s seven "Large Aquatic Ecosystems". This designation grants legislative status equal to the Chesapeake Bay, Great Lakes, Gulf of Mexico, South Florida Ecosystem, Long Island Sound and Puget Sound. The Strategic Plan is the Agency’s road map of future work efforts, and targets specific goals that are expected to …