Digital Commons Network^™

Large-Scale Assembly Of Periodic Nanostructures With Metastable Square Lattices, Chih-Hung Sun, Wei-Lun Min, Nicholas C. Linn, Peng Jiang, Bin Jiang

Mathematics and Statistics Faculty Publications and Presentations

This article reports a simple and scalable spin-coating technique for assembling non-close-packed colloidal crystals with metastable square lattices over wafer-scale areas. The authors observe the alternate formation of hexagonal and square diffraction patterns when the thickness of the colloidal crystals is gradually reduced during spin coating. No prepatterned templates are needed to induce the formation of the resulting metastable crystals with square arrangement. This bottom-up technology also enables the large-scale production of a variety of squarely ordered nanostructures that are consistent with the industry-standard rectilinear coordinate system for simplified addressing and circuit interconnection. Broadband moth-eye antireflection gratings with square lattices …

Mangrove-Exported Nutrient Incorporation By Sessile Coral Reef Invertebrates, Elise F. Granek, Jana E. Compton, Donald L. Phillips

Environmental Science and Management Faculty Publications and Presentations

Coastal mangrove forests were historically considered as a source of organic matter (OM) for adjacent marine systems due to high net primary production; yet recent research suggesting little uptake through the food web because of low nutritional quality, challenges the concept of trophic linkage between mangrove forests and coral reefs. To examine the importance of mangrove forests to coral reef nutrient availability, we examined sessile reef-forming invertebrate consumers including hard corals, sponges, a bivalve mollusc, polychaete annelid and tunicate, and potential sources of OM (decaying mangrove leaves, microalgae, macroalgae, and seagrass) in Bocas del Toro, Panama. Using stable isotope analyses …

Gravity Effects On Capillary Flows In Sharp Corners, Enrique Ramé, Mark M. Weislogel

Mechanical and Materials Engineering Faculty Publications and Presentations

We analyze the effect of gravity on capillary flows in sharp corners. We consider gravity perpendicular and parallel to the channel axis. We analyze both steady and unsteady flows. In the steady analysis the main result is a closed form expression for the flow rate as a function of the two gravity components. Good agreement with steady experiments is offered as support of the model. The unsteady analysis is restricted to “small” values of the two gravity parameters and is accomplished using a similarity formulation. The similarity coefficients of the gravity corrections are fully determined by the coefficients of the …

Practical Approximations To Quantify The Impact Of Time Windows And Delivery Sizes On Vmt Multi-Stop Tours, Miguel A. Figliozzi

Civil and Environmental Engineering Faculty Publications and Presentations

This paper studies approximations to the average length of Vehicle Routing Problems (VRP). The approximations are valuable for strategic and planning analysis of transportation and logistics problems. The research focus is on VRP with varying number of customers, demands, and locations. This modeling environment can be used in transport and logistics models that deal with a distribution center serving an area with daily variations in the demand. The routes are calculated daily based on what freight is available. New approximations and experimental settings are introduced. Average distance travelled is estimated as a function of the number of customers served and …

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 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 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.

Reconstructability Analysis In Biomedical Research, Martin Zwick

Complex Systems Faculty Publications and Presentations

This talk explains reconstructability analysis (RA), a graphical modeling methodology based in information theory & graph theory which overlaps more familiar machine learning & statistical methods such as log-linear models & Bayesian networks. The talk reports on the use of RA in a recent bioinformatics study of human gene (SNP) - disease (diabetes) association & epistasis & in some other biomedical applications of RA.

Keywords: Reconstructability Analysis, biomedical research, bioinformatics, categorical data, multivariate statistics, exploratory modeling, confirmatory modeling

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 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.

Faculty Senate Monthly Packet March 2009, Portland State University Faculty Senate

Faculty Senate Monthly Packets

Faculty Senate minutes from meeting held March 2, 2009. This item contains the agenda, minutes, and attachments for the Faculty Senate meeting on this date. Some issues accompanied by reports from officers of administration and faculty committees.

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 …

Raps Sheet, March 2009, Retirement Association Of Portland State

RAPS Sheet: Monthly Newsletter

No abstract provided.

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 …

Assessing The Prediction Potential Of An In Silico Computer Model Of Intracranial Pressure Dynamics, Wayne Wakeland, Rachel Agbeko, Kevin Vinecore, Mark Peters, Brahm Goldstein

Complex Systems Faculty Publications and Presentations

Objective: Traumatic brain injury (TBI) frequently results in poor outcome, suggesting that new approaches are needed. We hypothesized that a patient-specific in silico computer model of intracranial pressure (ICP) dynamics may predict the ICP response to therapy.

Design: In silico model analysis of prospectively collected data.

Setting: Twenty-three and 16-bed pediatric intensive care units in two tertiary care academic hospitals.

Patients: Nine subjects with severe TBI undergoing ICP monitoring (7 M/2 F, age range 3-17 years).

Interventions: Random changes in head-of-bed (HOB) (0[degrees], 10[degrees], 20[degrees], 30[degrees], 40[degrees]) elevation and respiratory rate (to achieve a [DELTA]ETco2 = +/-3-4 mm Hg) were …

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 …

An Inverse Method For Predicting Tissue-Level Mechanics From Cellular Mechanical Input, Wangdo Kim, Derek C. Tretheway, Sean S. Kohles

Mechanical and Materials Engineering Faculty Publications and Presentations

Extracellular matrix (ECM) provides a dynamic three-dimensional structure which translates mechanical stimuli to cells. This local mechanical stimulation may direct biological function including tissue development. Theories describing the role of mechanical regulators hypothesize the cellular response to variations in the external mechanical forces on the ECM. The exact ECM mechanical stimulation required to generate a specific pattern of localized cellular displacement is still unknown. The cell to tissue inverse problem offers an alternative approach to clarify this relationship. Developed for structural dynamics, the inverse dynamics problem translates measurements of local state variables (at the cell level) into an unknown or …

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 …

Faculty Senate Monthly Packet February 2009, Portland State University Faculty Senate

Faculty Senate Monthly Packets

The February 2009 Monthly packet includes the February agenda and appendices and the Faculty Senate minutes and attachments from the meeting held February 2009.

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.

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 …

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

Complex Systems 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 …

U.S. Current Account Debate With Japan Then, With China Now, Hiro Ito

Economics Faculty Publications and Presentations

This paper examines two U.S. current account deficit episodes, one in the 1980s and the other in the current 2000s, in which Japan and China, respectively, are the current account surplus countries that are criticized for contributing to the deficits. In both periods, U.S. policy makers pointed out the underdeveloped and closed financial markets of the current account surplus countries and advocated for these countries to fix the deficiencies, a position akin to the current “saving glut” argument. In both episodes, the current account surplus countries have criticized the United States for its low saving, especially public saving (the “Twin …

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 …

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 …