Physical Sciences and Mathematics Commons^™

Synthesis And Structure−Activity Relationships Of Tambjamines And B‑Ring Functionalized Prodiginines As Potent Antimalarials, Papireddy Kancharla, Jane Xu Kelly, Kevin A. Reynolds

Chemistry Faculty Publications and Presentations

Synthesis and antimalarial activity of 94 novel bipyrrole tambjamines (TAs) and a library of B-ring functionalized tripyrrole prodiginines (PGs) against a panel of Plasmodium falciparum strains are described. The activity and structure–activity relationships demonstrate that the ring-C of PGs can be replaced by an alkylamine, providing for TAs with retained/enhanced potency. Furthermore, ring-B of PGs/TAs can be substituted with short alkyl substitutions at either 4-position (replacement of OMe) or 3- and 4-positions without impacting potency. Eight representative TAs and two PGs have been evaluated for antimalarial activity against multidrug-resistant P. yoelii in mice in the dose range of 5–100 mg/kg …

Rational Design Of Materials For The Protection Of Outdoor Metalworks, Natasja Alexandria Swartz

Dissertations and Theses

Protective coatings are commonly used to protect culturally significant works, such as outdoor sculptures and architectural elements. Given the valuable nature of such metalworks, there is a surprising lack of environmentally sustainable coatings available for their conservation. High performance clear coatings are not developed or thoroughly tested for compatibility and longevity on outdoor sculptures. This can make the implementation of both methods and materials, no matter how promising in a lab, a significant hurdle for the conservation science community. This dissertation work initially aims to replace high-VOC formulations such as acrylic lacquers and waxes currently used as protective coatings for …

Evaluation Of Data-Path Topologies For Self-Timed Conditional Statements, Navaneeth Prasannakumar Jamadagni

Dissertations and Theses

This research presents a methodology to evaluate data path topologies that implement a conditional statement for an average-case performance that is better than the worst-case performance. A conditional statement executes one of many alternatives depending on how Boolean conditions evaluate to true or false. Alternatives with simple computations take less time to execute. The self-timed designs can exploit the faster executing alternatives and provide an average-case behavior, where the average depends on the frequency of simple and complex computations, and the difference in the completion times of simple and complex computations. The frequency of simple and complex computations depends on …

The Design And Validation Of A Group Theory Concept Inventory, Kathleen Mary Melhuish

Dissertations and Theses

Within undergraduate mathematics education, there are few validated instruments designed for large-scale usage. The Group Concept Inventory (GCI) was created as an instrument to evaluate student conceptions related to introductory group theory topics. The inventory was created in three phases: domain analysis, question creation, and field-testing. The domain analysis phase included using an expert consensus protocol to arrive at the topics to be assessed, analyzing curriculum, and reviewing literature. From this analysis, items were created, evaluated, and field-tested. First, 383 students answered open-ended versions of the question set. The questions were converted to multiple-choice format from these responses and disseminated …

Tweakable Ciphers: Constructions And Applications, Robert Seth Terashima

Dissertations and Theses

Tweakable ciphers are a building block used to construct a variety of cryptographic algorithms. Typically, one proves (via a reduction) that a tweakable-cipher-based algorithm is about as secure as the underlying tweakable cipher. Hence improving the security or performance of tweakable ciphers immediately provides corresponding benefits to the wide array of cryptographic algorithms that employ them. We introduce new tweakable ciphers, some of which have better security and others of which have better performance than previous designs. Moreover, we demonstrate that tweakable ciphers can be used directly (as opposed to as a building block) to provide authenticated encryption with associated …

The Influence Of Surface Chemistry On The Photoelectrochemical Properties Of Fes(2) Photoanodes, Qi Tong

Dissertations and Theses

The recurring theme of this dissertation is the correlation between FeS₂ surface chemistry and key electrical and electronic properties of FeS₂. Efforts have been made to identify and characterize the FeS₂ surface, investigate the photoelectrochemistry of FeS₂ photoanodes under anhydrous and anoxic conditions, and investigate the influence of deliberate surface chemistry on FeS₂ photoelectrochemistry.

Infrared reflection-absorption spectroscopy (IRRAS) was used to investigate a thin adsorbate layer on pyrite. The results showed that the combination of angle-dependent studies and computational efforts are a powerful tool for characterizing the pyrite surface.

The photoelectrochemistry of FeS_{2 …}

Glacier Change On The Three Sisters Volcanoes, Oregon: 1900-2010, Justin George Ohlschlager

Dissertations and Theses

A glacier responds to changes in climate by subsequent retreat and advance as a result of changes in snow inputs and outputs. Understanding these changes is important because shrinking glaciers limit and diminish local water resources. They contribute to alpine runoff in the late-summer months by delaying the maximum runoff until late in the melt season. A comprehensive glacier and perennial snowfield inventory has not been completed for the Three Sisters in Central Oregon. Using aerial photography, Digital Elevation Models (DEMs), previous studies, and historical ground based photographs these glacier and perennial snowfields were defined and their surface area change …

Scalable Equivalence Checking For Behavioral Synthesis, Zhenkun Yang

Dissertations and Theses

Behavioral synthesis is the process of compiling an Electronic System Level (ESL) design to a register-transfer level (RTL) implementation. ESL specifications define the design functionality at a high level of abstraction (e.g., with C/C++ or SystemC), and thus provide a promising approach to address the exacting demands to develop feature-rich, optimized, and complex hardware systems within aggressive time-to-market schedules. Behavioral synthesis entails application of complex and error-prone transformations during the compilation process. Therefore, the adoption of behavioral synthesis highly depends on our ability to ensure that the synthesized RTL conforms to the ESL description. This dissertation provides an end-to-end scalable …

On The Coupling Of Dpg And Bem, Thomas Führer, Norbert Heuer, Michael Karkulik

Mathematics and Statistics Faculty Publications and Presentations

We develop and analyze strategies to couple the discontinuous Petrov-Galerkin method with optimal test functions to (i) least-squares boundary elements and (ii) various variants of standard Galerkin boundary elements. An essential feature of our method is that, despite the use of boundary integral equations, optimal test functions have to be computed only locally. We apply our findings to a standard transmission problem in full space and present numerical experiments to validate our theory.

On A Convex Set With Nondifferentiable Metric Projection, Shyan S. Akmal, Nguyen Mau Nam, J. J. P. Veerman

Mathematics and Statistics Faculty Publications and Presentations

A remarkable example of a nonempty closed convex set in the Euclidean plane for which the directional derivative of the metric projection mapping fails to exist was constructed by A. Shapiro. In this paper, we revisit and modify that construction to obtain a convex set with smooth boundary which possesses the same property.

Historical And Existing Vascular And Bryophyte Flora, Former Blue Heron Paper Mill, Willamette Falls, Oregon City, Oregon, John A. Christy, Philip Gaddis

Institute for Natural Resources Publications

Willamette Falls has long been a focus of botanical interest, but industrial development at the site has limited public access for over a century. The closure of the Blue Heron paper mill on the south bank of the river, and proposed redevelopment of the site, has given planners an opportunity to revisit this part of the falls and identify its current flora. As part of the preconstruction planning process for public access to the falls, Metro contracted John Christy to document the historical and existing vascular flora on the site, and Philip Gaddis joined us to document the bryophyte flora. …

Nmr-Based Structural Analysis Of Threonylcarbamoyl-Amp Synthase And Its Substrate Interactions, Kimberly A. Harris, Benjamin G. Bobay, Kathryn L. Sarachan, Alexis F. Sims, Yann Bilbille, Christopher Deutsch, Dirk Iwata-Reuyl, Paul F. Agris

Chemistry Faculty Publications and Presentations

The hypermodified nucleoside N(6)-threonylcarbamoyladenosine (t(6)A37) is present in many distinct tRNA species and has been found in organisms in all domains of life. This post-transcriptional modification enhances translation fidelity by stabilizing the anticodon/codon interaction in the ribosomal decoding site. The biosynthetic pathway of t(6)A37 is complex and not well understood. In bacteria, the following four proteins have been discovered to be both required and sufficient for t(6)A37 modification: TsaC, TsaD, TsaB, and TsaE. Of these, TsaC and TsaD are members of universally conserved protein families. Although TsaC has been shown to catalyze the formation of L-threonylcarbamoyl-AMP, a key intermediate in …

Portland’S Food Economy: Trends And Contributions, Jamaal Green, Greg Schrock, Jenny H. Liu

Institute for Sustainable Solutions Publications and Presentations

The primary goal of this report is to document the scope, growth, and contribution of the food economy to the city of Portland and the region. Specifically, this report addresses the following research questions:

• What is the "food economy," and how is it defined?
• What is the size of Portland’s food economy, and how has it changed in recent years?
• How is the food economy distributed spatially within the city and the region? How is this changing?
• What kind of employment opportunities does Portland’s food economy offer? How do they compare to the broader economy?
• Who works in Portland’s food …

A Scaffolded, Metamorphic Ctf For Reverse Engineering, Wu-Chang Feng

Computer Science Faculty Publications and Presentations

Hands-on Capture-the-Flag (CTF) challenges tap into and cultivate the intrinsic motivation within people to solve puzzles, much in the same way Sudoku and crossword puzzles do. While the format has been successful in security competitions, there have been a limited number of attempts to integrate them into a classroom environment. This paper describes MetaCTF, a metamorphic set of CTF challenges for teaching reverse code engineering. MetaCTF is 1) scaffolded in a way that allows students to make incremental progress, 2) integrated with the course material so that students can immediately apply knowledge gained in class, 3) polymorphic and metamorphic so …

Reinforced Imitative Graph Learning For Mobile User Profiling, Dongjie Wang, Pengyang Wang, Yanjie Fu, Kunpeng Liu, Hui Xiong, Charles Hughes

Computer Science Faculty Publications and Presentations

Mobile user profiling refers to the efforts of extracting users’ characteristics from mobile activities. In order to capture the dynamic varying of user characteristics for generating effective user profiling, we propose an imitation-based mobile user profiling framework. Considering the objective of teaching an autonomous agent to imitate user mobility based on the user’s profile, the user profile is the most accurate when the agent can perfectly mimic the user behavior patterns. The profiling framework is formulated into a reinforcement learning task, where an agent is a next-visit planner, an action is a POI that a user will visit next, and …

Deformation And Thermal Histories Of Ordinary Chondrites: Evidence For Postdeformation Annealing And Syn-Metamorphic Shock, Alexander M. Ruzicka, Richard Hugo, Melinda Hutson

Geology Faculty Publications and Presentations

We show that olivine microstructures in seven metamorphosed ordinary chondrites of different groups studied with optical and transmission electron microscopy can be used to evaluate the post-deformation cooling setting of the meteorites, and to discriminate between collisions affecting cold and warm parent bodies. The L6 chondrites Park (shock stage S1), Bruderheim (S4), Leedey (S4), and Morrow County (S5) were affected by variable shock deformation followed by relatively rapid cooling, and probably cooled as fragments liberated by impact in near-surface settings. In contrast, Kernouvé (H6 S1), Portales Valley (H6/7 S1), and MIL 99301 (LL6 S1) appear to have cooled slowly after …

Pseudocapacitors For Energy Storage, Anuradha Venkataraman

Dissertations and Theses

Fluctuation in the demand for electrical power and the intermittent nature of the supply of energy from renewable sources like solar and wind have made the need for energy storage a dire necessity. Current storage technologies like batteries and supercapacitors fall short either in terms of power output or in their ability to store sufficient energy. Pseudocapacitors combine features of both and offer an alternative to stabilize the power supply. They possess high rates of charge and discharge and are capable of storing much more energy in comparison to a supercapacitor. In the quest for solutions that are economical and …

Characterization, Dna Binding And Cleavage Activities Of New Prodigiosin And Tambjamine Analogues And Their Cu²⁺ And Zn²⁺ Complexes, Karen Chichetu

Dissertations and Theses

Prodigiosins and tambjamines are natural compounds from bacterial and marine sources belonging to a family containing a common 4-methoxy-2,2'-bipyrrole core. These compounds have received a lot of interest due to their promising biological activities. Studies have suggested DNA as a potential therapeutic target for the natural prodigiosin and tambjamine due to their ability to facilitate oxidative DNA cleavage in the presence of Cu²⁺. Based on this we sought to study the metal binding activity of new prodigiosin and tambjamine analogues. A new prodigiosin analogue was synthesized and complexed with Cu²⁺. This revealed 1:1 complex formation between …

Novel Cryptographic Primitives And Protocols For Censorship Resistance, Kevin Patrick Dyer

Dissertations and Theses

Internet users rely on the availability of websites and digital services to engage in political discussions, report on newsworthy events in real-time, watch videos, etc. However, sometimes those who control networks, such as governments, censor certain websites, block specific applications or throttle encrypted traffic. Understandably, when users are faced with egregious censorship, where certain websites or applications are banned, they seek reliable and efficient means to circumvent such blocks. This tension is evident in countries such as a Iran and China, where the Internet censorship infrastructure is pervasive and continues to increase in scope and effectiveness.

An arms race is …

Steps Towards Deciphering The Post-Polyketide Synthase Tailoring Steps In The Phoslactomycin Biosynthesis Pathway, Patience Marimo

Dissertations and Theses

Phoslactomycins (PLMs) are a group of natural products belonging to a polyketides class. These polyketides are synthesized by sequential reaction catalyzed by a collection of enzymes activities called polyketide synthases. A polyketide is a large class of diverse compounds that are characterized by more than two carbonyl groups connected by single intervening carbon atoms. In other words, a polyketide is a polymer whose monomer is a ketide. The PLMs are also known as phosphazomycins or phospholines. These compounds were isolated based on antifungal and antitumor activities. This array of promising biological activities has stimulated research into the field of PLMs …

A Multivariate Modeling Approach For Generating Ensemble Climatology Forcing For Hydrologic Applications, Sepideh Khajehei

Dissertations and Theses

Reliability and accuracy of the forcing data plays a vital role in the Hydrological Streamflow Prediction. Reliability of the forcing data leads to accurate predictions and ultimately reduction of uncertainty. Currently, Numerical Weather Prediction (NWP) models are developing ensemble forecasts for various temporal and spatial scales. However, it is proven that the raw products of the NWP models may be biased at the basin scale; unlike model grid scale, depending on the size of the catchment. Due to the large space-time variability of precipitation, bias-correcting the ensemble forecasts has proven to be a challenging task. In recent years, Ensemble Pre-Processing …

Evaluating Global Sensitivity Analysis Methods For Hydrologic Modeling Over The Columbia River Basin, Maysoun Ayad Hameed

Dissertations and Theses

Global Sensitivity Analysis (GSA) approach helps to identify the effectiveness of model parameters or inputs and thus provides essential information about the model performance. The effects of 14 parameters and one input (forcing data) of the Sacramento Soil Moisture Accounting (SAC-SMA) model are analyzed by using two GSA methods: Sobol' and Fourier Amplitude Sensitivity Test (FAST). The simulations are carried out over five sub-basins within the Columbia River Basin (CRB) for three different periods: one-year, four-year, and seven-year. The main parameter sensitivities (first-order) and the interactions sensitivities (second-order) are evaluated in this study. Our results show that some hydrological processes …

Dft Analysis Into The Intermediates Of Nickel Pyridenthiolate Catalysed Proton Reduction, Carolyn N. Virca, Theresa M. Mccormick

Chemistry Faculty Publications and Presentations

Nickel pyridine 2-thiolate (Ni(PyS)₃ −) has shown good stability and activity as a H₂ generation catalyst for use in solar energy storage. The experimentally proposed catalytic pathway is explored using DFT calculations. Free energy changes along the reaction coordinate, spin states, localization of charge and geometry of the intermediates were explored. Calculations were performed using Gaussian 09 with a B3P86/ 6-31+G(d) basis set and a CPCM water solvation model. Of particular interest were our findings that the first reduction occurs at the nickel rather than through non-innocent ligands and that water coordination is not favourable although protonation of …

Compiling Collapsing Rules In Certain Constructor Systems, Sergio Antoy, Andy Jost

Computer Science Faculty Publications and Presentations

The implementation of functional logic languages by means of graph rewriting requires a special handling of collapsing rules. Recent advances about the notion of a needed step in some constructor systems offer a new approach to this problem. We present two results: a transformation of a certain class of constructor-based rewrite systems that eliminates collapsing rules, and a rewrite-like relation that takes advantage of the absence of collapsing rules. We formally state and prove the correctness of these results. When used together, these results simplify without any loss of efficiency an implementation of graph rewriting and consequently of functional logic …

Naturally Occurring Background Levels Of Arsenic In The Soils Of Southwestern Oregon, Heather Ann Hurtado

Dissertations and Theses

This study examines the natural background concentrations of arsenic in the soils of southwest Oregon, using new samples in addition to data collected from previous theses (Khandoker, 1997 and Douglas, 1999). The original 213 samples were run by ICP-AES with a reporting limit of 20 ppm, and only three samples had detected values. The original samples were tested again (2013) at a lower reporting limit of 0.2 ppm by ICP-MS, as were 42 new samples (2013), to better ascertain the natural levels of arsenic in undisturbed soils. The aim is to add to the existing DEQ data set, which has …

Automatic Fault Injection For Driver Robustness Testing, Kai Cong, Li Lei, Zhenkun Yang, Fei Xie

Computer Science Faculty Publications and Presentations

Robustness testing is a crucial stage in the device driver development cycle. To accelerate driver robustness testing, effective fault scenarios need to be generated and injected without requiring much time and human effort. In this pa- per, we present a practical approach to automatic runtime generation and injection of fault scenarios for driver robust- ness testing. We identify target functions that can fail from runtime execution traces, generate effective fault scenarios on these target functions using a bounded trace-based it- erative strategy, and inject the generated fault scenarios at runtime to test driver robustness using a permutation-based injection mechanism. We …

Empirical Evidence For The Scale Dependence Of Biotic Interactions, Jonathan Belmaker, Phoebe Zarnetske, Sara Zonneveld, Sydne Record, Angela L. Strecker, Lydia Beaudrot

Environmental Science and Management Faculty Publications and Presentations

Aim: Although it is recognized that ecological patterns are scale dependent, the exact scales over which specific ecological processes operate are still a matter of controversy. In particular, understanding the scales over which biotic interactions operate is critical for predicting changes in species distributions in the face of the ongoing biodiversity crisis. It has been hypothesized that biotic interactions operate predominately at fine grains, yet this conjecture has received relatively little empirical scrutiny. We use US woodpeckers as a model system to assess the relative importance of biotic interactions, environmental suitability and geographic proximity to other intraspecific occurrence sites, …

A Posteriori Eigenvalue Error Estimation For The Schrödinger Operator With The Inverse Square Potential, Hengguang Li, Jeffrey S. Ovall

Mathematics and Statistics Faculty Publications and Presentations

We develop an a posteriori error estimate of hierarchical type for Dirichlet eigenvalue problems of the form (−∆ + (c/r) 2 )ψ = λψ on bounded domains Ω, where r is the distance to the origin, which is assumed to be in Ω. This error estimate is proven to be asymptotically identical to the eigenvalue approximation error on a family of geometrically-graded meshes. Numerical experiments demonstrate this asymptotic exactness in practice.

Rock Creek Restoration Macroinvertebrate Monitoring Report, Daniel Bedell

Environmental Science and Management Professional Master's Project Reports

Stream restoration is widely used to rebuild habitat for native fisheries, but it is not well understood how current habitat reconstruction practices affect biological diversity. Citizen Science programs have potential to provide supplemental macroinvertebrate data for effectiveness monitoring of reach-scale restoration projects but variability in training, experience and collection methods can make interpretation difficult. The Clackamas Water Environment Services Watershed Health Education Program (WHEP) is an example of a Citizen Science-based program actively collecting biological data from restored streams. The purpose of this project was to use WHEP student-collected data to detect benthic macroinvertebrate community responses to stream restoration practices. …

Hydrophobic Surfactant Proteins Strongly Induce Negative Curvature, Mariya Chavarha, Ryan W. Loney, Shankar B. Rananavare, Stephen B. Hall

Chemistry Faculty Publications and Presentations

The hydrophobic surfactant proteins SP-B and SP-C greatly accelerate the adsorption of vesicles containing the surfactant lipids to form a film that lowers the surface tension of the air/water interface in the lungs. Pulmonary surfactant enters the interface by a process analogous to the fusion of two vesicles. As with fusion, several factors affect adsorption according to how they alter the curvature of lipid leaflets, suggesting that adsorption proceeds via a rate-limiting structure with negative curvature, in which the hydrophilic face of the phospholipid leaflets is concave. In the studies reported here, we tested whether the surfactant proteins might promote …