Digital Commons Network^™

Damage And Alteration Of Mangroves Inhabited By A Marine Wood-Borer, Timothy Mathias Davidson, Catherine E. De Rivera, Hwey-Lian Hsieh

Environmental Science and Management Faculty Publications and Presentations

Animals can exert a strong influence on the structure and function of foundation species such as mangroves. Because mangroves live at the interface of land and sea, both terrestrial and marine species affect them, including numerous herbivores and boring species. These organisms can affect the fecundity, performance, and morphology of mangroves. In a mangrove stand in southwestern Taiwan, we discovered that mangroves were extensively damaged by woodboring isopods Sphaeroma terebrans. We examined the relationships between burrowing damage from S. terebrans and metrics of mangrove fecundity, performance, and morphology. Individuals of Rhizophora stylosa that were more burrowed by isopods had significantly …

Spring Thaw Ionic Pulses Boost Nutrient Availability And Microbial Growth In Entombed Antarctic Dry Valley Cryoconite Holes, Jon Telling, Alexandre M. Anesio, Martyn Tranter, Andrew G. Fountain, Thomas H. Nylen, Jon Hawkings, Virendra B. Singh, Preeti Kaur, Michaela Musilova, Jemma L. Wadham

Geology Faculty Publications and Presentations

The seasonal melting of ice entombed cryoconite holes on McMurdo Dry Valley glaciers provides oases for life in the harsh environmental conditions of the polar desert where surface air temperatures only occasionally exceed 0°C during the Austral summer. Here we follow temporal changes in cryoconite hole biogeochemistry on Canada Glacier from fully frozen conditions through the initial stages of spring thaw toward fully melted holes. The cryoconite holes had a mean isolation age from the glacial drainage system of 3.4 years, with an increasing mass of aqueous nutrients (dissolved organic carbon, total nitrogen, total phosphorus) with longer isolation age. During …

Hydrogeology Of Pumice-Hosted Fens In The Winema-Fremont National Forest, Oregon, Usa, Michael L. Cummings, Jonathan Michael Weatherford, Leslie A. Mowbray

Geology Faculty Publications and Presentations

Subaerial fallout from the Holocene eruption of Mount Mazama in the Oregon Cascade Range was deposited upon relatively low permeability volcanic and volcaniclastic bedrock and regolith. In the Walker Rim study area, erosion by ephemeral streams shortly after the eruption disrupted the lateral continuity of the 270 to 300 cm-thick pumice deposit. Co-evolution of the surface- and ground-water systems in a low-relief, low-slope landscape allowed diffuse groundwater discharge from the banks of the evolving stream system. Accumulation of organic material from groundwater dependent ecosystems at these sites of discharge allowed peat deposits to form on gently sloping erosion surfaces cut …

Extended Necessary Condition For Local Operations And Classical Communication: Tight Bound For All Measurements, Scott M. Cohen

Physics Faculty Publications and Presentations

We give a necessary condition that a separable measurement can be implemented by local quantum operations and classical communication (LOCC) in any finite number of rounds of communication, generalizing and strengthening a result obtained previously. That earlier result involved a bound that is tight when the number of measurement operators defining the measurement is relatively small. The present results generalize that bound to one that is tight for any finite number of measurement operators, and we also provide an extension which holds when that number is infinite. We apply these results to the famous example on a 3 × 3 …

Spatial Thinking In Planning Practice: An Introduction To Gis, Yiping Fang, Vivek Shandas, Eugenio Arriaga Cordero

PDXOpen: Open Educational Resources

The goals of this textbook are to help students acquire the technical skills of using software and managing a database, and develop research skills of collecting data, analyzing information and presenting results. We emphasize that the need to investigate the potential and practicality of GIS technologies in a typical planning setting and evaluate its possible applications. GIS may not be necessary (or useful) for every planning application, and we anticipate these readings to provide the necessary foundation for discerning its appropriate use. Therefore, this textbook attempts to facilitate spatial thinking focusing more on open-ended planning questions, which require judgment and …

Sensitivity Of Columbia Basin Runoff To Long-Term Changes In Multi-Model Cmip5 Precipitation Simulations, Mehmet Demirel, Hamid Moradkhani

Civil and Environmental Engineering Faculty Publications and Presentations

In this study, we used precipitation elasticity index of streamflow, to reflect on the sensitivity of streamflow to changes in future precipitation. We estimated precipitation elasticity of streamflow from: (1) simulated streamflow by the VIC model using observed precipitation for the current climate (1963–2003); (2) simulated streamflow by the VIC model using simulated precipitation from 10 GCM - CMIP5 dataset for the future climate (2010–2099) including two different pathways (RCP4.5 and RCP8.5) and two different downscaled products (BCSD and MACA). The hydrological model was calibrated at 1/16 latitude-longitude resolution and the simulated streamflow was routed to the subbasin outlets of …

Selective Indicators For Optical Determination Of Disease Biomarkers, Lovemore Hakuna

Dissertations and Theses

The most abundant biological thiols, homocysteine (Hcy), cysteine (Cys) and glutathione (GSH) have been the subject of intense research due to their association with a wide range of diseases. They play a key role in maintaining the redox status of biological systems. Selective detection methods for these thiols are challenging due to their similar structures and properties. Current commercially available detection methods use separations, fragile and expensive enzymatic or immunogenic materials and complex instrumentation. This has led to a global effort towards developing simple and inexpensive optical probes and indicators selective for specific biological thiols.

Highly selective chemical probes and …

2014 Aquatic Weed Surveys In Timothy Lake, Lake Harriet, North Fork Reservoir, Faraday Lake, And Estacada Lake, Rich Miller, Mark D. Sytsma, Jeffrey Thomas Brittain

Center for Lakes and Reservoirs Publications and Presentations

The Clackamas River Hydroelectric Project No. 2195 (Project) is located on the Oak Grove Fork of the Clackamas River and the mainstem of the Clackamas River in Clackamas County, Oregon. Reservoirs included in the Project include Timothy Lake, Lake Harriet, North Fork Reservoir, Faraday Lake, and Estacada Lake. The operator of the Project, Portland General Electric (PGE), was issued a license on December 21, 2010 by the Federal Energy Regulatory Commission (FERC) for continued operations and maintenance. The Final Environmental Impact Statement (FEIS) for the license noted that regular surveys for invasive aquatic weed species would be conducted as part …

Human Whole-Blood (1)H2o Longitudinal Relaxation With Normal And High-Relaxivity Contrast Reagents: Influence Of Trans-Cell-Membrane Water Exchange, Gregory J. Wilson, Mark Woods, Charles S. Springer Jr., Sarah Bastawrous, Puneet Bhargava, Jeffrey H. Maki

Chemistry Faculty Publications and Presentations

PURPOSE: Accurate characterization of contrast reagent (CR) longitudinal relaxivity in whole blood is required to predict arterial signal intensity in contrast-enhanced MR angiography (CE-MRA). This study measured the longitudinal relaxation rate constants (R₁ ) over a concentration range for non-protein-binding and protein-binding CRs in ex vivo whole blood and plasma at 1.5 and 3.0 Tesla (T) under physiologic arterial conditions.

METHODS: Relaxivities of gadoteridol, gadobutrol, gadobenate, and gadofosveset were measured for [CR] from 0 to 18 mM [mmol(CR)/L(blood)]: the latter being the upper limit of what may be expected in CE-MRA.

RESULTS: In plasma, the ¹H2 O R …

The Distribution And Reproductive Success Of The Western Snowy Plover Along The Oregon Coast - 2014, David J. Lauten, Kathleen J. Castelein, J. Daniel Farrar, Adam A. Kotaich, Eleanor P. Gaines

Institute for Natural Resources Publications

We monitored the distribution, abundance and productivity of the federally threatened Western Snowy Plover (Charadrius nivosus nivosus) along the Oregon coast from 1 April – 15 September 2014. From north to south, we surveyed and monitored plover activity at Sutton Beach, Siltcoos River estuary, the Dunes Overlook, North and South Tahkenitch Creek, Tenmile Creek, Coos Bay North Spit, Bandon Snowy Plover Management Area, New River HRA and adjacent lands, and Floras Lake. Our objectives in 2014 were to: 1) estimate the size of the adult Snowy Plover population along the Oregon coast, 2) locate plover nests, 3) determine …

Empirical Demonstration Of Environmental Sensing In Catalytic Rna: Evolution Of Interpretive Behavior At The Origins Of Life, Niles Lehman, Tess Bernhard, Brian C. Larson, Andrew J.N. Robinson, Christopher C.B. Southgate

Chemistry Faculty Publications and Presentations

Background: The origins of life on the Earth required chemical entities to interact with their environments in ways that could respond to natural selection. The concept of interpretation, where biotic entities use signs in their environment as proxy for the existence of other items of selective value in their environment, has been proposed on theoretical grounds to be relevant to the origins and early evolution of life. However this concept has not been demonstrated empirically.

Results: Here, we present data that certain catalytic RNA sequences have properties that would enable interpretation of divalent cation levels in their environment. …

The Power Of Reflective Professional Development In Changing Elementary School Teachers' Instructional Practices, Carolina Christmann Cavedon

Dissertations and Theses

With the new goal of K-12 education being to prepare students to be college and career ready at the end of high school, education needs to start changing at the elementary school level. The literature suggests that teachers need reflective professional development (PD) to effectively teach to the new standards and to demonstrate change to their current instructional practices. This mixed-method multiple-case study investigated the impacts of a reflective professional development (PD) in changing elementary school teachers' instructional practices.

Teachers Instructional Portfolios (TIPs) were scored with a TIP rubric based on best practices in teaching mathematics problem-solving and science inquiry. …

Teachers Teaching Teachers: A Sustainable And Inexpensive Professional Development Program To Improve Instruction, Carol L. Campbell

Dissertations and Theses

School districts face tremendous budget challenges and, as a result, professional development has been "trimmed" from many school budgets. (Habegger & Hodanbosi, 2011). School administrators responsible for planning professional development face a daunting task and often focus on PowerPoints, district mandated training, one-shot presentations, and workshops that are delivered by expensive experts. These types of activities lack teacher collaboration, time for sharing of ideas and opportunity for reflection and analysis (Torff & Byrnes, 2011, Coggins, Zuckerman & Mckelvey, 2010).

The problem addressed in this study is that teacher professional development is usually planned by school administrators who are provided little …

Agricultural Classification Of Multi-Temporal Modis Imagery In Northwest Argentina Using Kansas Crop Phenologies, Jarrett Alexander Keifer

Dissertations and Theses

Subtropical deforestation in Latin America is thought to be driven by demand for agricultural land, particularly to grow soybeans. However, existing remote sensing methods that can differentiate crop types to verify this hypothesis require high spatial or spectral resolution data, or extensive ground truth information to develop training sites, none of which are freely available for much of the world. I developed a new method of crop classification based on the phenological signatures of crops extracted from multi-temporal MODIS vegetation indices. I tested and refined this method using the USDA Cropland Data Layer from Kansas, USA as a reference. I …

Confined Mesoscopic Fluid-Like Films Analyzed With Frequency Modulation And Acoustic Detection, Rodolfo Fernandez Rodriguez

Dissertations and Theses

Complete understanding of the physics underlying the changes in viscoelasticity, relaxation time, and phase transitions that mesoscopic fluid-like systems undergo at solid-liquid interfaces or under confinement remains one of the major challenges in condensed matter physics. Moreover, studies of confined mesoscopic fluid films are relevant to technological areas like adhesion, wetting processes and nanotribology.

This thesis addresses the interaction between two sliding solids interfaces separated by a nanometer sized gap, with emphasis on the role of the mesoscopic fluid film trapped between them. For this purpose we integrated two acoustic techniques, recently introduced by our group, into a sub-nanometer precision …

Using Art To Teach Students Science Outdoors: How Creative Science Instruction Influences Observation, Question Formation, And Involvement, Christina Schull Cone

Dissertations and Theses

Elementary education has become increasingly divided into subjects and focused on the demand for high math and reading scores. Consequently, teachers spend less time devoted to science and art instruction. However, teaching art and science is crucial to developing creative and rational thinking, especially for observation and questioning skills. In this study, third grade students attending an urban school in Portland, Oregon received instruction of an art strategy using observational and quantifying drawing techniques. This study examines, "Will an art strategy observing the local environment help students make observations and ask questions?" and "In what ways are student learning and …

Detection Of Variable Retention Time In Dram, Neraj Kumar

Dissertations and Theses

This thesis investigates a test method to detect the presence of Variable Retention Time (VRT) bits in manufactured DRAM. The VRT bits retention time is modeled as a 2-state random telegraph process that includes miscorrelation between test and use. The VRT defect is particularly sensitive to test and use conditions. A new test method is proposed to screen the VRT bits by simulating the use conditions during manufacturing test. Evaluation of the proposed test method required a bit-level VRT model to be parameterized as a function of temperature and voltage conditions. The complete 2-state VRT bit model combines models for …

Using Phylogenetically-Informed Annotation (Pia) To Search For Light-Interacting Genes In Transcriptomes From Non-Model Organisms, Daniel L. Speiser, Molly S. Pankey, Alexander K. Zaharoff, Barbara A. Battelle, Heather D. Bracken-Grissom, Jesse W. Breinholt, Seth M. Bybee, Thomas W. Cronin, Anders Garm, Annie R. Lindgren, Nipam H. Patel, Megan L. Porter, Meredith E. Protas, Ajna S. Rivera, Jeanne M. Serb, Kirk S. Zigler, Keith A. Crandall, Todd H. Oakley

Biology Faculty Publications and Presentations

Background: Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to …

Characterization And Modeling Of Nonlinear Dark Current In Digital Imagers, Justin Charles Dunlap

Dissertations and Theses

Dark current is an unwanted source of noise in images produced by digital imagers, the de facto standard of imaging. The two most common types of digital imager architectures, Charged-Coupled Devices (CCDs) and Complementary Metal-Oxide-Semiconductor (CMOS), are both prone to this noise source. To accurately reflect the information from light signals this noise must be removed. This practice is especially vital for scientific purposes such as in astronomical observations.

Presented in this dissertation are characterizations of dark current sources that present complications to the traditional methods of correction. In particular, it is observed that pixels in both CCDs and CMOS …

Modulation Of The Cardiac Calcium Release Channel By Homocysteine Thiolactone, Laura Jean Owen

Dissertations and Theses

Elevated levels in blood serum (≥10μmol/L) of the amino acid homocysteine is strongly correlated with the incidence of heart failure (HF). We present evidence that the cyclic thioester, homocysteine thiolactone (HTL), a metabolic product of homocysteine, irreversibly modifies proteins that regulate the contractile process in cardiac muscle. Two proteins found in the sarcoplasmic reticulum (SR), the Ca²⁺ pump (SERCA2), and the ryanodine receptor (RyR2), are responsible for controlling the cytosolic Ca²⁺ concentration and hence the contractile state of the heart. While both improper Ca²⁺ handling and elevated homocysteine levels have been considered bio-markers in HF, a direct …

The Journey To Becoming Constructivist, Presidential Award For Excellence In Mathematics And Science Teaching, Secondary Mathematics Teacher, Gerald E. Young

Dissertations and Theses

The purpose of this research study is to describe and analyze the self-reported experiences of exemplary high school mathematics teachers who underwent personal and professional transformations in order to develop and use a standards-based, constructivist (SBC) teaching paradigm in their classrooms. These teachers were all past recipients of the Presidential Award for Excellence in Mathematics and Science Teaching (PAEMST), an award that required them to demonstrate that their mathematics instruction was rigorous in the manner described by the NCTM standards.

The following research questions are addressed: (a) What are the paths SBC secondary mathematics teachers who received the PAEMST pursued …

Mimicking Metabolism Of A Reversed Chloroquine Antimalarial, Kelsie Lynn Kendrick

Dissertations and Theses

The aim of this study was to elucidate the oxidation products of a candidate antimalarial drug, PL69, using a porphyrin system and to determine the accuracy of the oxidation products produced, as compared to what is expected in metabolism. PL69 is a reversed chloroquine (RCQ) that is active against chloroquine resistant malaria. Porphyrin oxidation systems have been shown to mimic in vitro enzymatic metabolism reactions. PL69 and its known metabolite, PL16, were incubated with the porphyrin system, and then the oxidation products were collected and separated by HPLC. The oxidation products were characterized by NMR and mass spectrometry and compared …

Systems Theory And The Metaphysics Of Composition, Martin Zwick

Complex Systems Faculty Publications and Presentations

Ideas from systems theory - recursive unity and emergent attributes - are applied to the metaphysical and meta-metaphysical debates about the ontological status of composites. These ideas suggest the rejection of both extremes of universalism and nihilism, favoring instead the intermediate position that some composites exist in a nontrivial sense - those having unity and emergent novelty - while others do not. Systems theory is egalitarian: it posits that what exist are systems, equal in their ontological status. Some systems are fundamental, but what exists is not merely the fundamental, and the fundamental is not merely the foundational. The status …

Efficacy Of Plastic Mesh Tubes In Reducing Herbivory Damage By The Invasive Nutria (Myocastor Coypus) In An Urban Restoration Site, Trevor R. Sheffels, Mark D. Sytsma, Jacoby Carter, Jimmy D. Taylor

Environmental Science and Management Faculty Publications and Presentations

The restoration of stream corridors is becoming an increasingly important component of urban landscape planning, and the high cost of these projects necessitates the need to understand and address potential ecological obstacles to project success. The nutria (Myocastor coypus) is an invasive, semi-aquatic rodent native to South America that causes detrimental ecological impacts in riparian and wetland habitats throughout its introduced range, and techniques are needed to reduce nutria herbivory damage to urban stream restoration projects. We assessed the efficacy of standard Vexar® plastic mesh tubes in reducing nutria herbivory damage to newly established woody plants. The study was conducted …

Physical, Chemical And Biological Assessment Of Yoncalla Log Ponds, Rich Miller, Mark D. Sytsma, Angela L. Strecker

Center for Lakes and Reservoirs Publications and Presentations

The Yoncalla Log Ponds are a series of four ponds located in within the city limits of the town in Yoncalla in northern Douglas County, Oregon. The ponds were created in stages between the late 1930s and the 1950s and used for log storage through the 1970s (North Douglas Betterment 2014). North Douglas Betterment purchased the land surrounding the ponds and contracted with the Center for Lakes and Reservoirs at Portland State University to assess the current morphometry, vegetation and water quality status of the ponds and provide recommendations for management of the aquatic vegetation. The scope of this document …

Reducing The Effects Of Shot Noise Using Nanoparticles, Moshood K. Morakinyo, Shankar B. Rananavare

Chemistry Faculty Publications and Presentations

We present a hybrid nano-lithographic approach to minimizes the effects of line edge roughness and shot noise in nano-hole patterning by reflowing photoresist polymers around the nanoparticles deposited using self-assembly and simple etch chemistries. The method extends the transistor contact holes patterning limits to below 20 nm.

Nonsmooth Algorithms And Nesterov's Smoothing Technique For Generalized Fermat-Torricelli Problems, Nguyen Mau Nam, Nguyen Thai An, R. Blake Rector, Jie Sun

Mathematics and Statistics Faculty Publications and Presentations

We present algorithms for solving a number of new models of facility location which generalize the classical Fermat--Torricelli problem. Our first approach involves using Nesterov's smoothing technique and the minimization majorization principle to build smooth approximations that are convenient for applying smooth optimization schemes. Another approach uses subgradient-type algorithms to cope directly with the nondifferentiability of the cost functions. Convergence results of the algorithms are proved and numerical tests are presented to show the effectiveness of the proposed algorithms.

Bicyclists' Uptake Of Traffic-Related Air Pollution: Effects Of The Urban Transportation System, Alexander Y. Bigazzi

Dissertations and Theses

While bicyclists and other active travelers obtain health benefits from increased physical activity, they also risk uptake of traffic-related air pollution. But pollution uptake by urban bicyclists is not well understood due to a lack of direct measurements and insufficient analysis of the determinants of exposure and ventilation (breathing). This knowledge gap impedes pollution-conscious transportation planning, design, and health impact assessment.

The research presented in this dissertation generates new connections between transportation system characteristics and pollution uptake by bicyclists. The primary research questions are: 1) how do urban bicyclists' intake and uptake of air pollution vary with roadway and travel …

Development Of The Idaho Statewide Travel Demand Model Trip Matrices Using Cell Phone Od Data And Origin Destination Matrix Estimation, Ben Stabler

PSU Transportation Seminars

As part of the initial phase of development for the Idaho Statewide Travel Demand Model, Parsons Brinckerhoff developed a base year auto and truck trip matrix using AirSage cell phone OD data, a statewide network in Cube, traffic counts, and origin-destination matrix estimation (ODME) procedures. To begin, the 4000+ statewide zone system was aggregated into a 700 super zone system for collecting the cell phone OD data. Next, the cell phone data was collected for the month of September 2013 for the following market segments: Average weekday resident HBW, HBO, NHB, and visitor NHB trips. The cell phone trips were …

Inhalable Constituents Of Thirdhand Tobacco Smoke: Chemical Characterization And Health Impact Considerations, Mohamad Sleiman, Jennifer M. Logue, Wentai Luo, James F. Pankow, Lara A. Gundel, Hugo Destaillats

Chemistry Faculty Publications and Presentations

Tobacco smoke residues lingering in the indoor environment, also termed thirdhand smoke (THS), can be a source of long-term exposure to harmful pollutants. THS composition is affected by chemical transformations and by air–surface partitioning over time scales of minutes to months. This study identified and quantified airborne THS pollutants available for respiratory exposure, identified potential environmental tracers, and estimated health impacts to nonsmokers. In a ventilated 18 m3 laboratory chamber, six cigarettes were machine-smoked, and levels of particulate matter (PM2.5) and 58 volatile organic compounds (VOCs) were monitored during an aging period of 18 h. Results were compared with field …