Physical Sciences and Mathematics Commons^™

Long-Term Managed Flooding To Control Invasive Phalaris Arundinacea L. And Help Restore Native Vegetation In An Urban Palustrine Wetlands Ecosystem, Robert P. Lascheck

Environmental Science and Management Professional Master's Project Reports

We sought to determine the effects of 13 years of hydrologic management on the wetland plant community in Smith and Bybee Wetlands Natural Area (SBW), an 809 ha palustrine wetland complex in north Portland, Oregon. Previous management efforts resulted in an altered hydrologic regime; historically high water levels in spring and low water levels in fall were replaced by persistent water levels with minimal annual variations. A water control structure was installed in 2003 to better approximate historic seasonal hydrologic changes to reduce invasive Phalaris arundinacea (reed canarygrass) cover and promote native wetland vegetation growth. Vegetation monitoring has been carried …

Development Of An Effective Shade Model For Water Quality Management In Oregon, Erin Costello

Environmental Science and Management Professional Master's Project Reports

Warming stream temperatures degrade water quality by stressing cold-water species, promoting harmful algal blooms, lowering dissolved oxygen, and increasing the toxicity of some compounds. The influence of stream temperature on the survival of native salmon is of particular concern in the Pacific Northwest. Effective shade, the fraction of solar radiation blocked from reaching a stream, is directly related to in-stream temperature and can be manipulated by riparian management actions. Mechanistic models of effective shade are prohibitively data and cost intensive. The objective of this research was to develop an empirical model (Simple Shade) for evaluating effective shade across the state …

Structure And Mechanism Of A Bacterial T6a Biosynthesis System, Amit Luthra, William Swinehart, Susan Bayooz, Phuc Phan, Boguslaw Stec, Dirk Iwata-Reuyl, Manal A. Swairjo

Chemistry Faculty Publications and Presentations

The universal N(6)-threonylcarbamoyladenosine (t⁶A) modification at position 37 of ANN-decoding tRNAs is central to translational fidelity. In bacteria, t⁶A biosynthesis is catalyzed by the proteins TsaB, TsaC/TsaC2, TsaD and TsaE. Despite intense research, the molecular mechanisms underlying t⁶A biosynthesis are poorly understood. Here, we report biochemical and biophysical studies of the t⁶A biosynthesis system from Thermotoga maritima. Small angle X-ray scattering analysis reveals a symmetric 2:2 stoichiometric complex of TsaB and TsaD (TsaB₂D₂), as well as 2:2:2 complex (TsaB₂D₂E₂), in …

Evaluation Of The Influence Of Wording Changes And Course Type On Motivation Instrument Functioning In Chemistry, Regis Komperda, Kathryn N. Hosbein, Jack Barbera

Chemistry Faculty Publications and Presentations

Increased understanding of the importance of the affective domain in chemistry education research has led to the development and adaptation of instruments to measure chemistry-specific affective traits, including motivation. Many of these instruments are adapted from other fields by using the word ‘chemistry’ in place of other disciplines or more general ‘science’ wording. Psychometric evidence is then provided for the functioning of the new adapted instrument. When an instrument is adapted from general language to specific (e.g. replacing ‘science’ with ‘chemistry’), an opportunity exists to compare the functioning of the original instrument in the same context as the adapted instrument. …

Paracest Agents Encapsulated In Reverse Nano-Assembled Capsules (Racs): How Slow Molecular Tumbling Can Quench Cest Contrast, Annah Farashishiko, Jacqueline R. Slack, Mauro Botta, Mark Woods

Chemistry Faculty Publications and Presentations

Although paraCEST is a method with immense scope for generating image contrast in MRI, it suffers from the serious drawback of high detection limits. For a typical discrete paraCEST agent the detection limit is roughly an order of magnitude higher than that of a clinically used relaxation agent. One solution to this problem may be the incorporation of a large payload of paraCEST agents into a single macromolecular agent. Here we report a new synthetic method for accomplishing this goal: incorporating a large payload of the paraCEST agent DyDOTAM3+ into a Reverse Assembled nano-Capsule. An aggregate can be generated between …

Facile Synthesis Of Ligand-Free Iridium Nanoparticles And Their In Vitro Biocompatibility, Anna L. Brown, Hayden Winter, Andrea M. Goforth, Gaurav Sahay, Conroy Sun

Chemistry Faculty Publications and Presentations

High-density inorganic nanoparticles have shown promise in medical applications that utilize radiation including X-ray imaging and as radiation dose enhancers for radiotherapy. We have developed an aqueous synthetic method to produce small (~ 2 nm) iridium nanoparticles (IrNPs) by reduction of iridium(III) chloride using a borohydride reducing agent. Unlike other solution-based synthesis methods, uniform and monodispersed IrNPs are produced without the use of surfactants or other solubilizing ligands. These nanoparticles are highly crystalline as observed by X-ray diffraction and high-resolution transmission electron microscopy (TEM). In vitro metabolic toxicity assays using hepatocyte and macrophage cells demonstrate that both IrNPs and iridium(III) …

Bootcmatch: A Software Package For Bootstrap Amg Based On Graphweighted Matching, Pasqua D'Ambra, Salvatore Filipone, Panayot S. Vassilevski

Mathematics and Statistics Faculty Publications and Presentations

This article has two main objectives: one is to describe some extensions of an adaptive Algebraic Multigrid (AMG) method of the form previously proposed by the first and third authors, and a second one is to present a new software framework, named BootCMatch, which implements all the components needed to build and apply the described adaptive AMG both as a stand-alone solver and as a preconditioner in a Krylov method. The adaptive AMG presented is meant to handle general symmetric and positive definite (SPD) sparse linear systems, without assuming any a priori information of the problem and its origin; the …

Clustering And Multifacility Location With Constraints Via Distance Function Penalty Methods And Dc Programming, Mau Nam Nguyen, Thai An Nguyen, Sam Reynolds, Tuyen Tran

Mathematics and Statistics Faculty Publications and Presentations

This paper is a continuation of our effort in using mathematical optimization involving DC programming in clustering and multifacility location. We study a penalty method based on distance functions and apply it particularly to a number of problems in clustering and multifacility location in which the centers to be found must lie in some given set constraints. We also provide different numerical examples to test our method.

Intensity Inhomogeneity Correction Of Sd-Oct Data Using Macular Flatspace, Andrew Lang, Aaron Carass, Bruno M. Jedynak, Sharon D. Solomon, Peter A. Calabresi, Jerry L. Prince

Mathematics and Statistics Faculty Publications and Presentations

Images of the retina acquired using optical coherence tomography (OCT) often suffer from intensity inhomogeneity problems that degrade both the quality of the images and the performance of automated algorithms utilized to measure structural changes. This intensity variation has many causes, including off-axis acquisition, signal attenuation, multi-frame averaging, and vignetting, making it difficult to correct the data in a fundamental way. This paper presents a method for inhomogeneity correction by acting to reduce the variability of intensities within each layer. In particular, the N3 algorithm, which is popular in neuroimage analysis, is adapted to work for OCT data. N3 works …

On The Girth And Diameter Of Generalized Johnson Graphs, Louis Anthony Agong, Carmen Amarra, John Caughman, Ari J. Herman, Taiyo S. Terada

Mathematics and Statistics Faculty Publications and Presentations

Let v > k > i be non-negative integers. The generalized Johnson graph, J(v,k,i), is the graph whose vertices are the k-subsets of a v-set, where vertices A and B are adjacent whenever |A∩B|= i. In this article, we derive general formulas for the girth and diameter of J(v,k,i). Additionally, we provide a formula for the distance between any two vertices A and B in terms of the cardinality of their intersection.

Mapping Water Availability, Cost And Projected Consumptive Use In The Eastern United States With Comparisons To The West, Vincent C. Tidwell, Barbie D. Moreland, Calvin R. Shaneyfelt, Peter Kobos

Environmental Science and Management Faculty Publications and Presentations

The availability of freshwater supplies to meet future demand is a growing concern. Water availability metrics are needed to inform future water development decisions. Furthermore, with the help of water managers, water availability was mapped for over 1300 watersheds throughout the 31-contiguous states in the eastern U.S. complimenting a prior study of the west. The compiled set of water availability data is unique in that it considers multiple sources of water (fresh surface and groundwater, wastewater and brackish groundwater); accommodates institutional controls placed on water use; is accompanied by cost estimates to access, treat and convey each unique source of …

A Decision Tree Analysis Of Nonindigenous Species Risk From Ballast Water To The Lower Columbia River And Oregon Coast, Usa, Danielle Verna, Richard R. Rueb, Crysta Gantz, John Gala, Jeremiah Green, John A. Zalusky, Rian Vanden Hooff

Environmental Science and Management Faculty Publications and Presentations

Hazard characterization and risk assessment are commonly used to prioritize vectors of nonindigenous species (NIS) for inspection or other prevention opportunities. Commercial shipping vessels are a target of such vector-based management since ballast water has been known to transport NIS between aquatic ecosystems globally. Here we used a risk-based screening protocol to prioritize vessels discharging ballast water to the lower Columbia River and Oregon coast. We began by adapting established methods of assessing risk factors that influence the initial stages of the invasion process (arrival and survival). We created relative risk scales for each factor using data collected from vessels …

Exploratory Reconstructability Analysis Of Accident Tbi Data, Martin Zwick, Nancy Ann Carney, Rosemary Nettleton

Systems Science Faculty Publications and Presentations

This paper describes the use of reconstructability analysis to perform a secondary study of traumatic brain injury data from automobile accidents. Neutral searches were done and their results displayed with a hypergraph. Directed searches, using both variable-based and state-based models, were applied to predict performance on two cognitive tests and one neurological test. Very simple state-based models gave large uncertainty reductions for all three DVs and sizeable improvements in percent correct for the two cognitive test DVs which were equally sampled. Conditional probability distributions for these models are easily visualized with simple decision trees. Confounding variables and counter-intuitive findings are …

Connecting Chemistry To Community With Deliberative Democracy, Regis Komperda, Jack Barbera, Erin Shortlidge, Gwen Shusterman, Stem Education And Equity Institute, Portland State University

Biology Faculty Publications and Presentations

Science education communities have called for rethinking curricula to improve student understanding of the nature of science and the role of science in addressing controversial modern issues such as climate change, energy policy, and pollution levels. One approach to meeting this call is integrating these topics into class activities that require students to use discussion and scientific approaches to solve problems and deliberate potential policy solutions. Deliberative democracy (DD) is one such active learning approach in which students work in peer groups to reach a consensus on a scientific topic relevant to both real-world issues and course content. During DD …

A Bayesian Hierarchical Approach To Multivariate Nonstationary Hydrologic Frequency Analysis, C. Bracken, K. D. Holman, B. Rajagopalan, Hamid Moradkhani

Civil and Environmental Engineering Faculty Publications and Presentations

We present a general Bayesian hierarchical framework for conducting nonstationary frequency analysis of multiple hydrologic variables. In this, annual maxima from each variable are assumed to follow a generalized extreme value (GEV) distribution in which the location parameter is allowed to vary in time. A Gaussian elliptical copula is used to model the joint distribution of all variables. We demonstrate the utility of this framework with a joint frequency analysis model of annual peak snow water equivalent (SWE), annual peak flow, and annual peak reservoir elevation at Taylor Park dam in Colorado, USA. Indices of largescale climate drivers—El Ni~no Southern …

Glacier Recession And The Response Of Summer Streamflow In The Pacific Northwest United States, 1960–2099, Chris Frans, Erkan Istanbulluoglu, Dennis P. Lettenmaier, Andrew G. Fountain, Jon L. Riedel

Geology Faculty Publications and Presentations

The Pacific Northwest is the most highly glacierized region in the conterminous United States (858 glaciers; 466 km2). These glaciers have displayed ubiquitous patterns of retreat since the 1980s mostly in response to warming air temperatures. Glacier melt provides water for downstream uses including agricultural water supply, hydroelectric power generation, and for ecological systems adapted to cold reliable streamflow. While changes in glacier area have been studied within the region over an extended period of time, the hydrologic consequences of these changes are not well defined. We applied a high‐resolution glacio‐hydrological model to predict glacier mass balance, glacier area, and …

A Simplified, Object-Based Framework For Efficient Landslide Inventorying Using Lidar Digital Elevation Model Derivatives, Michael D. Bunn, Ben A. Leshcinsky, Michael J. Olsen, Adam M. Booth

Geology Faculty Publications and Presentations

Landslide inventory maps are critical to understand the factors governing landslide occurrence and estimate hazards or sediment delivery to channels. Numerous semi-automated approaches for landslide inventory mapping have been proposed to improve the efficiency and objectivity of the process, but these methods have not been widely adopted by practitioners because of the use of input parameters without physical meaning, a lack of transparency in machine-learning based mapping techniques, and limitations in resulting products, which are not ordinarily designed or tested on a large-scale or in diverse geologic units. To this end, this work presents a new semi-automated method, called the …

Winter Rain Versus Snow In Headwater Catchments: Responses Of An Unconfined Pumice Aquifer, South-Central Oregon, Usa, Michael L. Cummings, David A. Eibert

Geology Faculty Publications and Presentations

Winter precipitation in two headwaters catchments (elevation ~1600 m) in the rain shadow of the Cascades volcanic arc in south-central Oregon normally falls as snow. However, in water year 2015, winter precipitation fell mainly as rain. An eight year study of the unconfined pumice aquifer allowed inter-annual comparison of groundwater recharge during the freshet and discharge during the growing season. During these water years precipitation ranged from 67% (WY2014) to 132% (WY2017) of the 30 year average, and included the rain dominated winter of WY2015 when precipitation during the water year was 98% of the 30 year average. Change in …

A Shift From Drought To Extreme Rainfall Drives A Stable Landslide To Catastrophic Failure, Alexander L. Handwerger, Mong-Han Haung, Eric Jameson Fielding, Adam M. Booth, Roland Burgmann

Geology Faculty Publications and Presentations

The addition of water on or below the earth’s surface generates changes in stress that can trigger both stable and unstable sliding of landslides and faults. While these sliding behaviours are well-described by commonly used mechanical models developed from laboratory testing (e.g., critical-state soil mechanics and rate-and-state friction), less is known about the field-scale environmental conditions or kinematic behaviours that occur during the transition from stable to unstable sliding. Here we use radar interferometry (InSAR) and a simple 1D hydrological model to characterize 8 years of stable sliding of the Mud Creek landslide, California, USA, prior to its rapid acceleration …

The Littlefield Rhyolite And Associated Mafic Lavas: Bimodal Volcanism Of The Columbia River Magmatic Province, With Constraints On Age And Storage Sites Of Grande Ronde Basalt Magmas, Brian Mcculloch Webb, Martin J. Streck, William C. Mcintosh, Mark L. Ferns

Geology Faculty Publications and Presentations

We present data that distinguishes the long-known Littlefield Rhyolite of eastern Oregon (northwestern United States) into two distinct, voluminous, Snake River–type, high-temperature rhyolite lava packages that erupted in short sequence overk.y., with minimum volumes of 100 and 150 km3 respectively, contemporaneous with flood basalt volcanism of the Grande Ronde Basalt phase of the Columbia River Basalt Group. Contemporaneity of rhyolites with flood basalts is exceptionally demonstrated within the Malheur Gorge by intercalated mafic units belonging to the Grande Ronde Basalt that are stratigraphically constrained by underlying and overlying Littlefield Rhyolite flows, and the underlying Dinner Creek Tuff (unit 1). Our …

New Geologic Mapping Of The Northwestern Willamette Valley, Oregon, And Its American Viticultural Areas (Avas)— A Foundation For Understanding Their Terroir, Ray E. Wells, Ralph Haugerud, Alan Niem, Lina Ma, Ian Madin, Russell Evarts

Geology Faculty Publications and Presentations

A geologic map of the greater Portland, Oregon, metropolitan area is planned that will document the region’s complex geology (currently in review: “Geologic map of the greater Portland metropolitan area and surrounding region, Oregon and Washington,” by Wells, R.E., Haugerud, R.A., Niem, A., Niem, W., Ma, L., Evarts, R., Madin, I., and others). The map, which is planned to be published as a U.S. Geological Survey Scientific Investigations Map, will consist of 51 7.5′ quadrangles covering more than 2,500 square miles, and it will represent more than 100 person-years of geologic mapping and studies. The region was mapped at the …

The Effect Of Rare Variants In Trem2 And Pld3 On Longitudinal Cognitive Function In The Wisconsin Registry For Alzheimer's Prevention, Corinne D. Engelman, Burcu F. Darst, Murat Bilgel, Eva Vasiljevic, Rebecca L. Koscik, Bruno M. Jedynak, Sterling C. Johnson

Mathematics and Statistics Faculty Publications and Presentations

Recent studies have found an association between functional variants in TREM2 and PLD3 and Alzheimer's disease (AD), but their effect on cognitive function is unknown. We examined the effect of these variants on cognitive function in 1449 participants from the Wisconsin Registry for Alzheimer's Prevention, a longitudinal study of initially asymptomatic adults, aged 36–73 years at baseline, enriched for a parental history of AD. A comprehensive cognitive test battery was performed at up to 5 visits. A factor analysis resulted in 6 cognitive factors that were standardized into z scores (∼N [0, 1]); the mean of these z scores was …

Designing In-Headset Authoring Tools For Virtual Reality Video, Cuong Nguyen

Dissertations and Theses

Virtual Reality (VR) video is emerging as a new art form. Viewing VR video requires wearing the VR headset to fully experience the immersive surrounding of the content. However, the novel viewing experience of VR video creates new challenges and requirements for conventional video authoring tools, which were designed mainly for working with normal video on a desktop display. Designing effective authoring tools for VR video requires intuitive video interfaces specific to VR.

This dissertation develops new workflows and systems that enable filmmakers to create and improve VR video while fully immersed in a VR headset. We introduce a series …

Copper Nanowires Synthesis And Self-Assembly For Interconnect Applications, Srikar Rao Darmakkolla

Dissertations and Theses

One-dimensional (1D) nanomaterial self-assembly offers an excellent approach to the fabrication of highly complex nanodevices. Despite considerable effort and research, precisely controlling the orientation and positioning of nanowires (NWs) on a large-scale area and assembling into a functional device is still a state of the art problem. This thesis focuses on the dimensionally controlled copper nanowires (Cu NWs) synthesis, and magnetic field assisted self-assembly of cupronickel nanowires (Cu/Ni NWs) into interconnect structures on a carbon doped silicon dioxide (CDO) wafer.

CDO is a low dielectric constant (k) material used for copper interconnects in multilayered complex integrated circuits (ICs). …

Non-Native Mangroves (Rhizophora Mangle) Of Moloka'i, Hawai'i: A Socio-Ecological Analysis, Casey Lynette Lewis

Dissertations and Theses

The formation of novel ecosystems by non-native species poses management challenges that are both socially and ecologically complex. This complexity necessitates consideration of both ecological dynamics and social attitudes and perceptions. Red mangrove propagules were introduced to Moloka'i, Hawaii in 1902 to mitigate the effects of soil erosion and they have since spread along the coast and to adjacent islands creating novel habitat. Non-native mangroves in Hawai'i present a unique case study to examine diverse social attitudes and perceptions resulting from a long history of land cover transformations on the Hawaiian Islands, socio-cultural diversity of involved stakeholders, and the potential …

Investigation Of Aerosol Optical And Chemical Properties Using Humidity Controlled Cavity Ring-Down Spectroscopy, Xijing Zhu

Dissertations and Theses

Scientists have been observing a change in the climate since the beginning of the 20^th century that cannot be attributed to any of the natural influences of the past. Natural and anthropogenic substances and processes perturb the Earth's energy budget, contributing to climate change. In particular, aerosols (particles suspended in air) have long been recognized to be important in processes throughout the atmosphere that affect climate. They directly influence the radiative balance of the Earth's atmosphere, affect cloud formation and properties, and are also key air pollutants that contribute to a variety of respiratory and cardiovascular diseases. Despite their …

Managing Herbicide Resistance: Listening To The Perspectives Of The Practitioners, Jill Schroeder, David Shaw, Michael Barrett, Harold Coble, Amy Asmus, Raymond Jussaume, David E. Ervin

Economics Faculty Publications and Presentations

No abstract provided.

Confined Photonic Mode Propagation Observed In Photoemission Electron Microscopy, Theodore Stenmark, Robert Campbell Word, Rolf Konenkamp

Physics Faculty Publications and Presentations

Using photoemission electron microscopy (PEEM) we present a comparative analysis of the wavelength dependence of propagating fields in a simple optical slab waveguide and a thin film photonic crystal W1-type waveguide. We utilize an interferometric imaging approach for light in the near-ultraviolet regime where a 2-photon process is required to produce photoelectron emission. The typical spatial resolution in these experiments is < 30 nm. Electromagnetic theory and finite element simulations are shown to be in good agreement with the experimental observations. Our results indicate that multiphoton PEEM is a useful sub-wavelength characterization technique in thin film optics.

Variational Geometric Approach To Generalized Differential And Conjugate Calculi In Convex Analysis, Boris S. Mordukhovich, Nguyen Mau Nam, R. Blake Rector, T. Tran

Mathematics and Statistics Faculty Publications and Presentations

This paper develops a geometric approach of variational analysis for the case of convex objects considered in locally convex topological spaces and also in Banach space settings. Besides deriving in this way new results of convex calculus, we present an overview of some known achievements with their unified and simplified proofs based on the developed geometric variational schemes. Key words. Convex and variational analysis, Fenchel conjugates, normals and subgradients, coderivatives, convex calculus, optimal value functions.

Classification Of Minimal Separating Sets In Low Genus Surfaces, J. J. P. Veerman, William Maxwell, Victor Rielly, Austin K. Williams

Mathematics and Statistics Faculty Publications and Presentations

Consider a surface S and let M ⊂ S. If S \ M is not connected, then we say M separates S, and we refer to M as a separating set of S. If M separates S, and no proper subset of M separates S, then we say M is a minimal separating set of S. In this paper we use computational methods of combinatorial topology to classify the minimal separating sets of the orientable surfaces of genus g = 2 and g = 3. The classification for genus 0 and 1 was done …