Digital Commons Network^™

Antibacterial Targets In Fatty Acid Biosynthesis, H. Tonie Wright, Kevin A. Reynolds

Chemistry Faculty Publications and Presentations

The fatty acid biosynthesis pathway is an attractive but still largely unexploited target for development of new anti-bacterial agents. The extended use of the anti-tuberculosis drug isoniazid and the antiseptic triclosan, which are inhibitors of fatty acid biosynthesis, validates this pathway as a target for anti-bacterial development. Differences in subcellular organization of the bacterial and eukaryotic multi-enzyme fatty acid synthase systems offer the prospect of inhibitors with host vs. target specificity. Platensimycin, platencin, and phomallenic acids, newly discovered natural product inhibitors of the condensation steps in fatty acid biosynthesis, represent new classes of compounds with antibiotic potential. An almost complete …

Probing Reactivity And Substrate Specificity Of Both Subunits Of The Dimeric Mycobacterium Tuberculosis Fabh Using Alkyl-Coa Disulfide Inhibitors And Acyl-Coa Substrates, Sarbjot Sachdeva, Faik Musayev, Mamoun M. Alhamadsheh, J. Neel Scarsdale, H. Tonie Wright, Kevin A. Reynolds

Chemistry Faculty Publications and Presentations

The dimeric Mycobacterium tuberculosis FabH (mtFabH) catalyses a Claisen-type condensation between an acyl-CoA and malonyl-acyl carrier protein (ACP) to initiate the Type II fatty acid synthase cycle. To analyze the initial covalent acylation of mtFabH with acyl-CoA, we challenged it with mixture of C6-C20 acyl-CoAs and the ESI-MS analysis showed reaction at both subunits and a strict specificity for C12 acyl CoA. Crystallographic and ESI-MS studies of mtFabH with a decyl-CoA disulfide inhibitor revealed a decyl chain bound in acyl-binding channels of both subunits through disulfide linkage to the active site cysteine. These data provide the first unequivocal evidence that …

Using Building Energy Simulation And Geospatial Modeling Techniques In Determine High Resolution Building Sector Energy Consumption Profiles, Shem C. Heiple

Dissertations and Theses

A technique is presented for estimating hourly and seasonal energy consumption profiles in the building sector at spatial scales down to the individual taxlot or parcel. The method combines annual building energy simulations for cityspecific prototypical buildings and commonly available geospatial data in a Geographical Information System (GIS) framework. Hourly results can be extracted for any day and exported as a raster output at spatial scales as fine as an individual parcel (

Directflow: A Domain-Specific Language For Information-Flow Systems, Andrew P. Black, Chuan-Kai Lin

Computer Science Faculty Publications and Presentations

Programs that process streams of information are commonly built by assembling reusable information-flow components. In some systems the components must be chosen from a pre-defined set of primitives; in others the programmer can create new custom components using a general-purpose programming language. Neither approach is ideal: restricting programmers to a set of primitive components limits the expressivity of the system, while allowing programmers to define new components in a general-purpose language makes it difficult or impossible to reason about the composite system. We advocate defining information-flow components in a domain-specific language (DSL) that enables us to infer the properties of …

Why Don’T People Use Refactoring Tools?, Andrew P. Black, Emerson Murphy-Hill

Computer Science Faculty Publications and Presentations

Tools that perform refactoring are currently under-utilized by programmers. 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. In this position paper, we characterize the dominant process of refactoring, demonstrate that many research tools do not support this process, and initiate a call to action for designers of future refactoring tools.

North America. Climate Change 2007: Impacts, Adaptation And Vulnerability, Christopher B. Fields, Linda D. Mortsch, Michael Brklacich, Donald L. Forbes, Paul Kovacs, Jonathan A. Patz, Steven W. Running, Michael J. Scott, Jean Andrey, Dan Cayan, Mike Demuth, Alan Hamlet, Gregory Jones, Evan Mills, Scott Mills, Charles K. Minns, David J. Sailor, Mark Saunders, Daniel Scott, William Solecki

Mechanical and Materials Engineering Faculty Publications and Presentations

The United States (U.S.) and Canada will experience climate changes through direct effects of local changes (e.g., temperature, precipitation and extreme weather events), as well as through indirect effects, transmitted among regions by interconnected economies and migrations of humans and other species. Variations in wealth and geography, however, lead to an uneven distribution of likely impacts, vulnerabilities and capacities to adapt. This chapter reviews and synthesises the state of knowledge on direct and indirect impacts, vulnerability and adaptations for North America (comprising Canada and the U.S). Hawaii and other U.S. protectorates are discussed in Chapter 16 on Small Islands, and …

Observation Of Microslip Dynamics At High-Speed Microcontacts, Brian Borovsky, Adam M. Booth, Erin Manlove

Geology Faculty Publications and Presentations

The high-speed tribological properties of microscale contacts are studied using an indenter probe and quartz crystal microbalance. Elastic and dissipative shear forces are monitored as a function of contact radius for sapphire/gold interfaces with an adsorbed octadecanethiol monolayer. We observe shear force transitions understood as taking the interface from slipping to stuck conditions. We relate this behavior to the presence of interfacial microslip. Dynamic modeling shows that our observations are consistent with an interface that, when sliding, experiences full slip during half of each cycle. We discuss the implications for this technique as a sensitive probe of sliding friction.

Cache Coherence Protocol Verification Using Ωmega, Ki Yung Ahn

Computer Science Faculty Publications and Presentations

We verify some correctness properties of the DASH cache coherence protocol using Ωmega. Ωmega is a language with a rich type system featuring GADTs, type functions, and user-guided type checking rules. Cache coherence protocols have both safety properties and liveness properties. We show how to describe some of the safety properties of DASH cache coherence protocol in mega. Since liveness properties are not easily expressed by types, we investigate invariants sufficient to imply some of the liveness properties of concern, and assert those invariants as well in the type system of Ωmega. Using Ωmega, we can have both a working …

Protecting The Internet With Public Work, Ed Kaiser, Wu-Chang Feng

Computer Science Faculty Publications and Presentations

Distributed denial-of-service attacks represent a growing problem for networked systems. To tackle this problem, this paper explores the addition of a public work function to the service advertisement mechanisms used by such systems. When under attack, services advertise this function along with their location information and clients must attach a solution to the function with subsequent requests. The function, which can be made specific to the source of traffic, is publicly verifiable, allowing arbitrary network devices at the edges of the network to quickly verify that subsequent communication from the source will be accepted by the destination. We describe a …

The Portland Spectator, December 2006, Portland State University. Student Publications Board

Portland Spectator

Editor: Crystal Joele Rea

Articles in this issue include: Investigating why "Christmas" has becomes politically incorrect; The REAL reason that we celebrate Christmas; Curriculum and the Student Bill of Right; The reason why feminism is stupid; An examination of what caused the power shift from Republican to Democrat; Solutions to holiday shopping; and Another look at illegal immigration.

Interview With Ron Hays, Eagle Creek Natural Building, 2006 (Audio), Ron Hays

All Sustainability History Project Oral Histories

Interview of Ron Hays by Joe Arbow at SE Portland, Oregon on December 8th, 2006.

The interview index is available for download.

Interview With Dan Lajoie, Departure: Architecture Planning, 2006 (Audio), Dan Lajoie

All Sustainability History Project Oral Histories

Interview of Dan Lajoie by Tirsa Firncrook in SE Portland, Oregon on December 4th, 2006.

The interview index is available for download.

Interview With Steven Edward Koch, Koch Landscape Architecture, 2006, Steven Edward Koch

All Sustainability History Project Oral Histories

Interview of Steven Edward Koch by Robyn Russnogle on December 4th, 2006.

The interview index is available for download.

Statistical Thermodynamics And Kinetics Of Dna Multiplex Hybridization Reactions, Albert S. Benight, M. T. Horne, D. J. Fish

Chemistry Faculty Publications and Presentations

A general analytical description of the equilibrium and reaction kinetics of DNA multiplex hybridization has been developed. In this approach, multiplex hybridization is considered to be a competitive multichannel reaction process: a system wherein many species can react both specifically and nonspecifically with one another. General equations are presented that can consider equilibrium and kinetic models of multiplex hybridization systems comprised, in principle, of any number of targets and probes. Numerical solutions to these systems for both equilibrium and kinetic behaviors are provided. Practical examples demonstrate clear differences between results obtained from more common simplex methods, in which individual hybridization …

The Distribution And Reproductive Success Of The Western Snowy Plover Along The Oregon Coast - 2006, David J. Lauten, Kathleen J. Castelein, Susan Weston, Krista Eucken, Eleanor P. Gaines

Institute for Natural Resources Publications

Part of the Oregon Bidiversity Information Center Report

Interview With Yianni Doulis, Yianni Doulis Architecture, 2006 (Audio), Yianni Doulis

All Sustainability History Project Oral Histories

Interview of Yianni Doulis by Daniel Woodward in NW Portland, Oregon on December 1st, 2006.

The interview index is available for download.

Interview With Carol Mayer-Reed, Mayer/Reed, 2006 (Audio), Carol Mayer-Reed

All Sustainability History Project Oral Histories

Interview of Carol Mayer-Reed by Robyn Russnogle at on December 1st, 2006.

The interview index is available for download.

Interview With Greg Sawyer, Providence Builders, 2006 (Audio), Greg Sawyer

All Sustainability History Project Oral Histories

Interview of Greg Sawyer by Amy Evangelista in NE Portland, Oregon on December 1st, 2006.

The interview index is available for download.

Gridfields: Model-Driven Data Transformation In The Physical Sciences, Bill Howe

Dissertations and Theses

Scientists' ability to generate and store simulation results is outpacing their ability to analyze them via ad hoc programs. We observe that these programs exhibit an algebraic structure that can be used to facilitate reasoning and improve performance. In this dissertation, we present a formal data model that exposes this algebraic structure, then implement the model, evaluate it, and use it to express, optimize, and reason about data transformations in a variety of scientific domains.

Simulation results are defined over a logical grid structure that allows a continuous domain to be represented discretely in the computer. Existing approaches for manipulating …

Interview With Alisa Kane, Office Of Sustainable Development, 2006 (Audio), Alisa Kane

All Sustainability History Project Oral Histories

Interview of Alisa Kane by Daniel Woodward at City of Portland Office of Sustainable Development, Oregon on November 30th, 2006.

The interview index is available for download.

Interview With Jessica Green, Macdonald Environmental Planning, 2006 (Audio), Jessica Green

All Sustainability History Project Oral Histories

Interview of Jessica Green by Cory Angell in SW Portland, Oregon on November 29th, 2006.

The interview index is available for download.

Interview With Laurel Macdonald-Bonnell, Macdonald Environmental, 2006 (Audio), Laurel Macdonald-Bonnell

All Sustainability History Project Oral Histories

Interview of Laurel McDonald by Chloe Collins at MacDonald Environmental Planning on November 29th, 2006.

The interview index is available for download.

Interview With Michael Zilis, Walker Macy, 2006 (Audio), Michael Zilis

All Sustainability History Project Oral Histories

Interview of Michael Zilis by Gerald Bones at Portland, Oregon on November 29th, 2006.

The interview index is available for download.

Interview With Christopher Weaver, Plm, 2006 (Audio), Christopher Weaver

All Sustainability History Project Oral Histories

Interview of Christopher Weaver by Gerald Bones at Hillsboro, Oregon on November 29th, 2006.

The interview index is available for download.

Interview With Brian Croak, Croak Creations, 2006 (Audio), Brian Croak

All Sustainability History Project Oral Histories

Interview of Brian Croak by Chloe Collins on November 28th, 2006.

The interview index is available for download.

Interview With Dell M. Turner, Green Roofing Contractor, 2006 (Audio), Dell M. Turner

All Sustainability History Project Oral Histories

Interview of Dell M. Turner by Padraic Keene at Portland State University on November 28th, 2006.

The interview index is available for download.

Interview With Chelsea Cochran, Walker Macy, 2006 (Audio), Chelsea Cochran

All Sustainability History Project Oral Histories

Interview of Chelsea Cochran by Cory Angell at Walker Macy, Portland Oregon on November 27th, 2006.

The interview index is available for download.

Interview With Jason Desanto, Our United Villages, 2006 (Audio), Jason Desanto

All Sustainability History Project Oral Histories

Interview of Jason DeSanto by Joe Arbow in Portland, Oregon on November 16th, 2006.

The interview index is available for download.

Adolescent Mothers: Youth In Need Of Developmentally Appropriate Services, Patricia Arlyne Zimmerman

Dissertations and Theses

This research examines the childhood abuse and maltreatment experiences of adolescent mothers (age 14 to 17) to investigate if these experiences have hindered their socioemotional development and consequently, their parenting behaviors and attitudes. Data were gathered using four standardized self-report instruments: the Child Trauma Questionnaire (CTQ), the Trauma Symptom Checklist for Children (TSCC), the BarOn Emotional Quotient Inventory-Youth Version (EQi-YV), and the Adult Adolescent Parenting Inventory (AAPI-2). Two additional questionnaires were developed to gather demographic and social service information to add to the knowledge base of the field, and to examine what (if any) developmentally focused services young mothers may …

A New Vision For New Orleans And The Mississippi Delta: Applying Ecological Economics And Ecological Engineering, Robert Costanza, John W. Day, William J. Mitsch

Institute for Sustainable Solutions Publications and Presentations

The restoration of New Orleans and the rest of the Mississippi delta after Hurricane Katrina can become another disaster waiting to happen, or it can become a model of sustainable development. Sea level is rising, precipitation patterns are changing, hurricane intensity is increasing, energy costs are predicted to soar, and the city is continuing to sink. Most of New Orleans is currently from 0.6 to 5 m (2?15 feet) below sea level. The conventional approach of simply rebuilding the levees and the city behind them will only delay the inevitable. If New Orleans, and the delta in which it is …