Physical Sciences and Mathematics Commons^™

Biogeochemical Evolution Of Cryoconite Holes On Canada Glacier, Taylor Valley, Antarctica, Elizabeth A. Bagshaw, Martyn Tranter, Andrew G. Fountain, Kathleen A. Welch, Hassan J. Basagic, W. Berry Lyons

Geography Faculty Publications and Presentations

The cryoconite holes of the McMurdo Dry Valleys are simple, closed biogeochemical systems involving water, ice, mineral and organic debris, which serve as ecosystems for consortia of microorganisms. This study is the first to document the seasonal and annual chemical evolution of solutes in cryoconite holes. Samples of glacier ice, frozen cryoconite holes and those containing water were collected during the austral summer of 2005–2006. The isolation age was calculated from the excess Cl‾ in the holes, and varied from 0 to 5 years (a), consistent with the last hot summer when the cryoconite holes were open to the atmosphere. …

Goal-Oriented Job Scheduling For Parallel Computer Systems, Sangsuree Vasupongayya

Dissertations and Theses

System administrators for parallel computers face many difficulties when managing job scheduling systems. First, current production job schedulers use many parameters, which seem flexible but it is highly challenging to configure and tune these parameters. Second, fair share is an important scheduling goal, but it is not clear what kind of fair share can be expected under current schedulers and how fair share impacts scheduling performance. Third, several job runtime prediction methods were proposed to improve inaccurate user-estimated runtimes, but these methods could under-estimate runtimes by a large amount and it is not clear whether they are practical for use …

Templated Fabrication Of Large Area Subwavelength Antireflection Gratings On Silicon, Chih-Hung Sun, Wei-Lun Min, Nicholas C. Linn, Peng Jiang, Bin Jiang

Mathematics and Statistics Faculty Publications and Presentations

We report a cheap and scalable bottom-up technique for fabricating wafer-scale, subwavelength-structured antireflection coatings on single-crystalline silicon substrates. Spin-coated monolayer colloidal crystals are utilized as shadow masks to generate metallic nanohole arrays. Inverted pyramid arrays in silicon can then be templated against nanoholes by anisotropic wet etching. The resulting subwavelength gratings greatly suppress specular reflection at normal incidence. The reflection spectra for flat silicon and the templated gratings at long wavelengths agree well with the simulated results using a rigorous coupled wave analysis model. These subwavelength gratings are of great technological importance in crystalline silicon solar cells.

Report On Nutria Management And Research In The Pacific Northwest, Trevor Sheffels, Mark Sytsma

Center for Lakes and Reservoirs Publications and Presentations

The nutria (Myocastor coypus) is a large semi-aquatic mammal native to South America that has been introduced to numerous countries around the world, primarily for fur farming. Nutria were introduced in Oregon and Washington in the 1930s, and feral populations were documented in 1943. Populations are known to be expanding in both Oregon and Washington, and regional nutria damage and nuisance complaints have increased in recent years. Most of the extensive damage caused by nutria is a direct result of feeding and burrowing, but nutria are also capable of transporting parasites and pathogens transmittable to humans, livestock, and …

The Distribution And Reproductive Success Of The Western Snowy Plover Along The Oregon Coast - 2007, David J. Lauten, Kathleen J. Castelein, Raya Pruner, Marvin Friel, Eleanor P. Gaines

Institute for Natural Resources Publications

From 3 April – 21 September 2007, we monitored the distribution, abundance and productivity of the federally Threatened Western Snowy Plover (Charadrius alexandrinus nivosus) along the Oregon coast. From north to south, we surveyed and monitored plover activity at Sutton Beach, Siltcoos River estuary, the Dunes Overlook, North Tahkenitch Creek, Tenmile Creek, Coos Bay North Spit, Bandon Beach, and New River. Our objectives for the Oregon coastal population in 2007 were to: 1) estimate the size of the adult Snowy Plover population, 2) locate plover nests, 3) continue selected use of mini-exclosures (MEs) to protect nests from predators …

What Is Rcu, Fundamentally?, Paul E. Mckenney, Jonathan Walpole

Computer Science Faculty Publications and Presentations

Read-copy update (RCU) is a synchronization mechanism that was added to the Linux kernel in October of 2002. RCU achieves scalability improvements by allowing reads to occur concurrently with updates. In contrast with conventional locking primitives that ensure mutual exclusion among concurrent threads regardless of whether they be readers or updaters, or with reader-writer locks that allow concurrent reads but not in the presence of updates, RCU supports concurrency between a single updater and multiple readers. RCU ensures that reads are coherent by maintaining multiple versions of objects and ensuring that they are not freed up until all pre-existing read-side …

Global Conservation Of Biodiversity And Ecosystem Services, Will R. Turner, Katrina Brandon, Thomas M. Brooks, Robert Costanza

Institute for Sustainable Solutions Publications and Presentations

Habitat destruction has driven much of the current biodiversity extinction crisis, and it compromises the essential benefits, or ecosystem services, that humans derive from functioning ecosystems. Securing both species and ecosystem services might be accomplished with common solutions. Yet it is unknown whether these two major conservation objectives coincide broadly enough worldwide to enable global strategies for both goals to gain synergy. In this article, we assess the concordance between these two objectives, explore how the concordance varies across different regions, and examine the global potential for safeguarding biodiversity and ecosystem services simultaneously. We find that published global priority maps …

The Characterization Of Trna Modifying Enzymes S-Adenosylmethionine : Trna Ribosyltransferase-Isomerase (Quea) And A Novel Type I Gtp Cyclohydrolase, Shilah Amal Bonnett

Dissertations and Theses

Queuosine is a hypermodified nucleoside located in the wobble position of bacterial and eukaryotic tRNAs coding for Asp, Tyr, His and Asn. The biosynthesis involves the participation of S-adenosyl-methionine:tRNA ribosyltransferase-isomerase (QueA) and a GTP Cyclohydrolase-I. QueA catalyzes the transfer and isomerization of the ribosyl moiety from AdoMet to preQ1 modified tRNA. Substrate analogs of AdoMet were used to elucidate important substrate-enzyme interactions and to test key steps in the proposed chemical mechanism. Replacing AdoMet with SeAdoMet had little effect upon substrate binding but exhibited 30-fold reduction in kcat, consistent with deprotonation at C-5' as the first catalytic step. 7-deazaAdoMet failed …

Effects Of Human Choices On Characteristics Of Urban Ecosystems, Lawrence A. Baker, Anthony J. Brazel, Loren Bryne, Alex Felson, Morgan Grove, Kristina Hill, Kristen C. Nelson, Jason Walker, Vivek Shandas

Institute for Sustainable Solutions Publications and Presentations

Most urban ecology in cities remains an "ecology in cities" rather than an "ecology of cities." Accomplishing the latter requires the inclusion of humans within the concept of "ecosystem," both how humans alter the properties of urban ecosystems and how these alterations in turn influence human well-being. These influences are both direct (e.g., physiological and psychological influences on the human organism) and indirect, by influencing ecosystem sustainability. For the 2007 ESA meeting, Larry Baker, Loren Byrne, Jason Walker, and Alex Felson organized a symposium to address the relationships among human choices and urban ecosystems. In the introductory talk of this …

The Urban Heat Island Mitigation Impact Screening Tool (Mist), David J. Sailor, Nikolaas Dietsch

Mechanical and Materials Engineering Faculty Publications and Presentations

A web-based software tool has been developed to assist urban planners and air quality management officials in assessing the potential of urban heat island mitigation strategies to affect the urban climate, air quality, and energy consumption within their cities. The user of the tool can select from over 170 US cities for which to conduct the analysis, and can specify city-wide changes in surface reflectivity and/or vegetative cover. The Mitigation Impact Screening Tool (MIST) then extrapolates results from a suite of simulations for 20 cities to estimate air temperature changes associated with the specified changes in surface characteristics for the …

Pend Oreille River Model: Model Scenario Simulations, Robert Leslie Annear, Chris Berger, Scott A. Wells

Civil and Environmental Engineering Faculty Publications and Presentations

The Idaho Department of Environmental Quality is interested in developing a temperature and water quality Total Maximum Daily Load (TMDL) allocation for the Pend Oreille River between the Long Bridge near the historical Lake Pend Oreille outlet and Albeni Falls Dam (U.S. Army Corps of Engineer’s reservoir) as shown in Figure 1.

This management scenario report is an update of a prior report. The management scenarios had to be rerun because of a modeling error made with the outflows rate of Albeni Falls Dam. The new calibration error statistics were compared with the old statistics in Appendix B: Model Calibration …

Self-Assembled Biomimetic Antireflection Coatings, Nicholas C. Linn, Chih-Hung Sun, Peng Jiang, Bin Jiang

Mathematics and Statistics Faculty Publications and Presentations

The authors report a simple self-assembly technique for fabricating antireflection coatings that mimic antireflective moth eyes. Wafer-scale, nonclose-packed colloidal crystals with remarkable large hexagonal domains are created by a spin-coating technology. The resulting polymer-embedded colloidal crystals exhibit highly ordered surface modulation and can be used directly as templates to cast poly(dimethylsiloxane) (PDMS) molds. Moth-eye antireflection coatings with adjustable reflectivity can then be molded against the PDMS master. The specular reflection of replicated nipple arrays matches the theoretical prediction using a thin-film multilayer model. These biomimetic films may find important technological application in optical coatings and solar cells.

Environmental Controls On The Landscape-Scale Biogeography Of Stream Bacterial Communities, Noah Fierer, Jennifer L. Morse, Sean T. Berthrong, Emily S. Bernhardt, Robert B. Jackson

Environmental Science and Management Faculty Publications and Presentations

We determined the biogeographical distributions of stream bacteria and the biogeochemical factors that best explained heterogeneity for 23 locations within the Hubbard Brook watershed, a 3000-ha forested watershed in New Hampshire, USA. Our goal was to assess the factor, or set of factors, responsible for generating the biogeographical patterns exhibited by microorganisms at the landscape scale. We used DNA fingerprinting to characterize bacteria inhabiting fine benthic organic matter (FBOM) because of their important influence on stream nutrient dynamics. Across the watershed, streams of similar pH had similar FBOM bacterial communities. Streamwater pH was the single variable most strongly correlated with …

Interview With Anthony Boutard, Ayers Creek Farm, 2007 (Audio), Anthony Boutard

All Sustainability History Project Oral Histories

Interview of Anthony Boutard by Magda Gaytan at Ayers Creek Farm on August 10th, 2007.

The interview index is available for download.

Interview With Dan J. Wilson, Sudan Farms, 2007 (Audio), Dan J. Wilson

All Sustainability History Project Oral Histories

Interview of Dan J. Wilson by Jason Keaton at Canby, Oregon on August 10th, 2007.

The interview index is available for download.

Interview With Trevor Baird, Baird Family Orchard, 2007 (Audio), Trevor Baird

All Sustainability History Project Oral Histories

Interview of Trevor Baird by Adam Hopfe at Portland State University on August 7th, 2007.

The interview index is available for download.

Interview With Melissa & Rod Volbeda, Willamette Valley Cheese, 2007 (Audio), Melissa Volbeda, Rod Volbeda

All Sustainability History Project Oral Histories

Interview of Melissa and Rod Volbeda by Magda Gaytan on August 6th, 2007.

Willamette Valley Cheese Company tour photos available for download.

Chemomechanical Polymers As Sensors And Actuators For Biological And Medicinal Applications, Hans-Jörg Schneider, Kazuaki Kato, Robert M. Strongin

Chemistry Faculty Publications and Presentations

Changes in the chemical environment can trigger large motions in chemomechanical polymers. The unique feature of such intelligent materials, mostly in the form of hydrogels, is therefore, that they serve as sensors and actuators at the same time, and do not require any measuring devices, transducers or power supplies. Until recently the most often used of these materials responded to changes in pH. Chemists are now increasingly using supramolecular recognition sites in materials, which are covalently bound to the polymer backbone. This allows one to use a nearly unlimited variety of guest (or effector) compounds in the environment for a …

Interview With Dianne Stefani-Ruff, Portland Farmers Market, 2007 (Audio), Dianne Stefani-Ruff

All Sustainability History Project Oral Histories

Interview of Dianne Stefani-Ruff by Jennifer Bennett on July 31st, 2007.

The interview index is available for download.

Interview With Roger Allen Konka, Springwater Farm, 2007 (Audio), Roger Allen Konka

All Sustainability History Project Oral Histories

Interview of Roger Allen Konka by Michael Schott on July 29th, 2007.

The interview index is available for download.

Interview With Lyle N. Stanley, Gee Creek Farm, 2007 (Audio), Lyle N. Stanley

All Sustainability History Project Oral Histories

Interview of Lyle N. Stanley by Aaron Veal at Portland State University on July 28th, 2007.

The interview index is available for download.

Interview With Kathy & Matt Unger, Unger Farms, 2007 (Audio), Kathy Unger, Matt Unger

All Sustainability History Project Oral Histories

Interview of Kathy and Matt Unger by Alix Lefler at Cornelius, Oregon on July 25th, 2007.

The interview index is available for download.

Biosedimentology Of Thermal Features In The Uzon Caldera, Kamchatka, Russia : Implications For Biosignature Formation, Jessica Christine Goin

Dissertations and Theses

Modern hot springs serve as a habitat for microorganisms similar in metabolism, morphology, and cellular structure to the microbes that existed relatively early in Earth history. To maximize our ability to interpret evidence for these microorganisms and their communities in the rock record, we need to understand how their biosignatures form and become preserved.

This biosedimentological study of four thermal features in the Uzon Caldera (K4 Well, Ochki Pool, Thermophile Spring, and Zavarzin Pool) focused on identifying how chemical, physical and biological inputs contribute to the characteristics of sinter biofabrics. The biofabrics of K4 Well outflow channel were studied in …

Graduate Teaching Assistants' Statistical Knowledge For Teaching, Jennifer Ann Noll

Dissertations and Theses

This dissertation explores graduate teaching assistants’ (TAs’) statistical knowledge for teaching. Data collection methods that enabled the exploration of TA s’ statistical knowledge for teaching include: (a) a task-based web survey administered to 68 TAs from 18 universities across the United States; and, (b) a series of three taskbased interviews with a subset of five TAs from the larger survey population. Through and Strauss, 1967), I investigated the ways in which TAs reason about sampling tasks, and how they think about teaching and student learning in relation to sampling ideas. Building on past research in statistics education on K-12 and …

Hydrilla Verticillata - An Aquatic Invader!, Vanessa Howard

Center for Lakes and Reservoirs Publications and Presentations

Brochure on hydrilla

Green Crab Management: Reduction Of A Marine Invasive Population, Catherine E. De Rivera, Edwin D. Grosholz, Greg Ruiz, Amy A. Larson, Rebecca L. Kordas, Mark Sytsma

Environmental Science and Management Faculty Publications and Presentations

The overall goal of this study is to develop and demonstrate the capacity for local eradication of adult Carcinus maenas, European green crabs. This represents a conceptual shift in development of management options to address established invasions in marine systems, extending and exploring the application of terrestrial successes in this area. Specifically, this project tests the effects of removing green crabs from Bodega Harbor on the green crab population and on native shore crabs eaten by green crabs.

Pend Oreille River, Box Canyon Model: Model Scenario Simulations, Chris Berger, Robert Leslie Annear, Scott A. Wells

Civil and Environmental Engineering Faculty Publications and Presentations

The Washington Department of Ecology is interested in developing a temperature Total Maximum Daily Load (TMDL) allocation for the Pend Oreille River between the Albeni Falls Dam (U.S. Army Corps of Engineer’s reservoir) and Box Canyon Dam as shown in Figure 1. The Pend Oreille drainage basin is shown in Figure 2. An existing model of the Box Canyon reach was updated from CE-QUALW2 Version 3.0 to Version 3.5. This current research involves improving the calibration of the original model (1997 and 1998) and expanding the model using 2004 as an additional data set for calibration.

The use of field …

Potentiometric And Relaxometric Properties Of A Gadolinium-Based Mri Contrast Agent For Sensing Tissue Ph, Ferenc K. Kálmán, Mark Woods, Peter Caravan, Paul Jurek, Marga Spiller, Gyula Tircso, Róbert Király, Ernő Brücher, A. Dean Sherry

Chemistry Faculty Publications and Presentations

The pH-sensitive contrast agent, GdDOTA-4AmP (Gd1) has been successfully used to map tissue pH by MRI. Further studies now demonstrate that two distinct chemical forms of the complex can be prepared depending upon the pH at which Gd³⁺ is mixed with ligand 1. The desired pH-sensitive form of this complex, referred to here as a Type II complex, is obtained as the exclusive product only when the complexation reaction is performed above pH 8. At lower pH values, a second complex is formed that, by analogy with an intermediate formed during the preparation of GdDOTA, we tentatively assign …

Modeling Effects Of Channel Complexity And Hyporheic Flow On Stream Temperatures, Chris Berger, Scott A. Wells

Civil and Environmental Engineering Faculty Publications and Presentations

Stream temperatures are affected by multiple forcing functions, including surface heat exchange (including solar radiation, evaporation, conduction, and net long wave radiation) and hyporheic flows. Each of these forcing functions is directly influenced by the level of channel complexity in the stream channel and riparian shading. The interrelationship between channel complexity, hyporheic flow and stream temperature is highly complex, and efforts to manage for habitat diversity by managing channel complexity could result in unintended consequences on stream temperature. When planning modifications to stream channel complexity, consideration should be given to the effects such moderations could have on stream temperatures.

Urbanization …

Albumin-Binding Paracest Agents, M. Meser Ali, Mark Woods, Eul Hyun Suh, Zoltan Kovacs, Gyula Tircsó, Piyu Zhao, Vikram D. Kodibagkar, A. Dean Sherry

Chemistry Faculty Publications and Presentations

Lanthanide complexes (Eu³⁺, Gd³⁺ and Yb³⁺) of two different 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid tetraamide derivatives containing two (2) and four (3) O-benzyl-L-serine amide substituents were synthesized and their chemical exchange saturation transfer (CEST) and relaxometric properties were examined in the presence and absence of human serum albumin (HSA). Both Eu2 and Eu3 display a significant CEST effect from a single slowly exchanging Eu³⁺-bound water molecule, making these PARACEST complexes potentially useful as vascular MRI agents. Yb2 also showed a detectable CEST effect from both the Yb³⁺-bound water protons and the …