Physical Sciences and Mathematics Commons^™

Spatial Factor Models For High-Dimensional And Large Spatial Data: An Application In Forest Variable Mapping, Daniel Taylor-Rodríguez, Andrew O. Finley, Abhirup Datta, Chad Babcock, Hans-Erik Andersen, Bruce D. Cook, Douglas C. Morton, Sudipto Banerjee

Mathematics and Statistics Faculty Publications and Presentations

Gathering information about forest variables is an expensive and arduous activity. As such, directly collecting the data required to produce high-resolution maps over large spatial domains is infeasible. Next generation collection initiatives of remotely sensed Light Detection and Ranging (LiDAR) data are specifically aimed at producing complete-coverage maps over large spatial domains. Given that LiDAR data and forest characteristics are often strongly correlated, it is possible to make use of the former to model, predict, and map forest variables over regions of interest. This entails dealing with the high-dimensional (∼10² ) spatially dependent LiDAR outcomes over a large number …

Patterns And Drivers Of Recent Disturbances Across The Temperate Forest Biome, Andreas Sommerfeld, Cornelius Senf, Brian Buma, Anthony W. D'Amato, Tiphaine Despres, Ignacio Díaz-Hormazábal, Shawn Fraver, Lee E. Frelich, Alvaro G. Gutiérrez, Sarah J. Hart, Brian J. Harvey, Hong S. He, Tomáš Hlásny, Andrés Holz, Multiple Additional Authors

Geography Faculty Publications and Presentations

Increasing evidence indicates that forest disturbances are changing in response to global change, yet local variability in disturbance remains high. We quantified this considerable variability and analyzed whether recent disturbance episodes around the globe were consistently driven by climate, and if human influence modulates patterns of forest disturbance. We combined remote sensing data on recent (2001–2014) disturbances with in-depth local information for 50 protected landscapes and their surroundings across the temperate biome. Disturbance patterns are highly variable, and shaped by variation in disturbance agents and traits of prevailing tree species. However, high disturbance activity is consistently linked to warmer and …

Water Flow And Biofilm Cover Influence Environmental Dna Detection In Recirculating Streams, Arial Shogren, Jennifer L. Tank, Scott P. Egan, Olivia August, Emma J. Rosi, Brittany R. Hanrahan, Mark A. Renshaw, Crysta A. Gantz, Diogo Bolster

Environmental Science and Management Faculty Publications and Presentations

The increasing use of environmental DNA (eDNA) for determination of species presence in aquatic ecosystems is an invaluable technique for both ecology as a field and for the management of aquatic ecosystems. We examined the degradation dynamics of fish eDNA using an experimental array of recirculating streams, also using a “nested” primer assay to estimate degradation among eDNA fragment sizes. We introduced eDNA into streams with a range of water velocities (0.1–0.8 m s–1) and substrate biofilm coverage (0–100%) and monitored eDNA concentrations over time (∼10 d) to assess how biophysical conditions influence eDNA persistence. We found that the presence …

Using Transboundary Wildfire Exposure Assessments To Improve Fire Management Programs: A Case Study In Greece, Palaiologos Palaiologou, Alan A. Ager, Max Nielsen-Pincus, Cody Evers, Kostas Kalabokidis

Environmental Science and Management Faculty Publications and Presentations

Numerous catastrophic wildfires in Greece have demonstrated that relying on fire suppression as the primary risk-management strategy is inadequate and that existing wildfire-risk governance needs to be re-examined. In this research, we used simulation modelling to assess the spatial scale of wildfire exposure to communities and cultural monuments in Chalkidiki, Greece. The study area typifies many areas in Greece in terms of fire regimes, ownership patterns and fire-risk mitigation. Fire-transmission networks were built to quantify connectivity among land tenures and populated places. We found that agricultural and unmanaged wildlands are key land categories that transmit fire exposure to other land …

The Economic Contribution Of Stewardship Contracting: Two Case Studies From The Mount Hood National Forest, Jean M. Daniels, Max Nielsen-Pincus, Mike Paruszkiewicz, Nathan Poage

Environmental Science and Management Faculty Publications and Presentations

We conducted an economic analysis of two case study stewardship contracts on the Mount Hood National Forest in western Oregon. Stewardship contracting has been embraced by some federal managers to achieve restoration goals while providing economic benefits to local communities. Little is known about economic contributions from stewardship contracts, including how they compare against Secure Rural Schools funding or the century-old payments to counties revenue sharing system. Using expenditure data from sale purchasers, contractors, and fiscal agents, we developed methodology to track spending and used IMPLAN software to estimate economic contributions and multipliers. Results showed that (1) commercial thinning, service …

Multivalency Regulates Activity In An Intrinsically Disordered Transcription Factor, Sarah Clark, Janette B. Myers, Ashleigh King, Radovan Fiala, Jiri Novacek, Grant Pearce, Steve L. Reichow, Elisar J. Barbar

Chemistry Faculty Publications and Presentations

The transcription factor ASCIZ (ATMIN, ZNF822) has an unusually high number of recognition motifs for the product of its main target gene, the hub protein LC8 (DYNLL1). Using a combination of biophysical methods, structural analysis by NMR and electron microscopy, and cellular transcription assays, we developed a model that proposes a concerted role of intrinsic disorder and multiple LC8 binding events in regulating LC8 transcription. We demonstrate that the long intrinsically disordered C-terminal domain of ASCIZ binds LC8 to form a dynamic ensemble of complexes with a gradient of transcriptional activity that is inversely proportional to LC8 occupancy. The preference …

Assessing Transboundary Wildfire Exposure In The Southwestern United States, Alan A. Ager, Palaiologos Palaiologou, Cody Evers, Michelle A. Day, Ana M.G. Barros

Environmental Science and Management Faculty Publications and Presentations

We assessed transboundary wildfire exposure among federal, state, and private lands and 447 communities in the state of Arizona, southwestern United States. The study quantified the relative magnitude of transboundary (incoming, outgoing) versus nontransboundary (i.e., self-burning) wildfire exposure based on land tenure or community of the simulated ignition and the resulting fire perimeter. We developed and described several new metrics to quantify and map transboundary exposure. We found that incoming transboundary fire accounted for 37% of the total area burned on large parcels of federal and state lands, whereas 63% of the area burned was burned by ignitions within the …

Connecting Chemistry To Community With Deliberative Democracy, Regis Komperda, Jack Barbera, Erin Shortlidge, Gwen Shusterman, Stem Education And Equity Institute, Portland State University

Biology Faculty Publications and Presentations

Science education communities have called for rethinking curricula to improve student understanding of the nature of science and the role of science in addressing controversial modern issues such as climate change, energy policy, and pollution levels. One approach to meeting this call is integrating these topics into class activities that require students to use discussion and scientific approaches to solve problems and deliberate potential policy solutions. Deliberative democracy (DD) is one such active learning approach in which students work in peer groups to reach a consensus on a scientific topic relevant to both real-world issues and course content. During DD …

Bioassessment Of A Drinking Water Reservoir Using Plankton: High Throughput Sequencing Vs. Traditional Morphological Method, Wanli Gao, Zhaojin Chen, Yuying Li, Yangdong Pan, Jingya Zhu, Shijun Guo, Lanqun Hu, Jin Huang

Environmental Science and Management Faculty Publications and Presentations

Drinking water safety is increasingly perceived as one of the top global environmental issues. Plankton has been commonly used as a bioindicator for water quality in lakes and reservoirs. Recently, DNA sequencing technology has been applied to bioassessment. In this study, we compared the effectiveness of the 16S and 18S rRNA high throughput sequencing method (HTS) and the traditional optical microscopy method (TOM) in the bioassessment of drinking water quality. Five stations reflecting different habitats and hydrological conditions in Danjiangkou Reservoir, one of the largest drinking water reservoirs in Asia, were sampled May 2016. Non-metric multi-dimensional scaling (NMDS) analysis showed …

Northwest Forest Plan The First 20 Years (1994-2013): Watershed Condition Status And Trend, Stephanie A. Miller, Sean N. Gordon, Peter Eldred, Ronald M. Beloin, Steve Wilcox, Mark Raggon, Heidi Andersen, Ariel Muldoon

Institute for Sustainable Solutions Publications and Presentations

We used two data sets to evaluate stream and upslope/riparian condition for sixth-field watersheds in each aquatic province within the Northwest Forest Plan (NWFP) area. The stream evaluation was based on stream sampling data collected from 2002 to the 2013 (214 watersheds) as part of an eight year repeating (rotating) sample design. We are currently halfway through our second rotation of stream sampling, and have repeated 110 watersheds since the second rotation began in 2009. The analysis presented in this report uses roughly half the number of watersheds as was originally intended by the sample design since re-visitation will not …

Prozac In The Water: Chronic Fluoxetine Exposure And Predation Risk Interact To Shape Behaviors In An Estuarine Crab, Joseph R. Peters, Elise F. Granek, Catherine E. De Rivera, Matthew Rollins

Environmental Science and Management Faculty Publications and Presentations

Predators exert considerable top-down pressure on ecosystems by directly consuming prey or indirectly influencing their foraging behaviors and habitat use. Prey is, therefore, forced to balance predation risk with resource reward. A growing list of anthropogenic stressors such as rising temperatures and ocean acidification has been shown to influence prey risk behaviors and subsequently alter important ecosystem processes. Yet, limited attention has been paid to the effects of chronic pharmaceutical exposure on risk behavior or as an ecological stressor, despite widespread detection and persistence of these contaminants in aquatic environments. In the laboratory, we simulated estuarine conditions of the shore …

Life’S Late Digital Revolution And Why It Matters For The Study Of The Origins Of Life, David A. Baum, Niles Lehman

Chemistry Faculty Publications and Presentations

The information contained in life exists in two forms, analog and digital. Analog information is manifest mainly in the differing concentrations of chemicals that get passed from generation to generation and can vary from cell to cell. Digital information is encoded in linear polymers such as DNA and RNA, whose side chains come in discrete chemical forms. Here, we argue that the analog form of information preceded the digital. Acceptance of this dichotomy, and this progression, can help direct future studies on how life originated and initially complexified on the primordial Earth, as well as expected trajectories for other, independent …

Assessing The Potential Of Land Use Modification To Mitigate Ambient No2 And Its Consequences For Respiratory Health, Meenakshi Rao, Linda A. George, Vivek Shandas, Todd N. Rosenstiel

Urban Studies and Planning Faculty Publications and Presentations

Understanding how local land use and land cover (LULC) shapes intra-urban concentrations of atmospheric pollutants—and thus human health—is a key component in designing healthier cities. Here, NO₂ is modeled based on spatially dense summer and winter NO₂ observations in Portland-Hillsboro-Vancouver (USA), and the spatial variation of NO₂ with LULC investigated using random forest, an ensemble data learning technique. The NO₂ random forest model, together with BenMAP, is further used to develop a better understanding of the relationship among LULC, ambient NO₂ and respiratory health. The impact of land use modifications on ambient NO₂, …

Effectiveness Of Indoor Plants For Passive Removal Of Indoor Ozone, Omed A. Abbass, David J. Sailor, Elliott T. Gall

Mechanical and Materials Engineering Faculty Publications and Presentations

Indoor vegetation is often proposed as a passive approach for improving indoor air quality. While studies of outdoor environments indicate that vegetation can be an important sink of outdoor ozone, there is scant data in the literature concerning the dynamics of ozone uptake by indoor plants. This study determined ozone deposition velocities (v_d) for five common indoor plants (Peace Lily, Ficus, Calathia, Dieffenbachia, Golden Pothos). The transient v_d was calculated, using measured leaf areas for each plant, for exposures mimicking three diurnal cycles where ozone concentrations in chamber tests were elevated for 8 h followed by …

Columbia River Basin Salmon And Steelhead Long-Term Recovery Situation Assessment, Oregon Solutions, William D. Ruckelshaus Center

National Policy Consensus Center Publications and Reports

In the fall of 2012, after consulting with a wide range of salmon recovery partners, NOAA Fisheries asked Oregon Consensus and the William D. Ruckelshaus Center (university-based, neutral, third-party institutions devoted to promoting collaborative governance and consensusbased public policy) to conduct an independent, impartial situation assessment to explore regional views about how best to approach comprehensive, long-term salmon and steelhead recovery in the Basin. The centers assembled an Assessment Team comprised of practitioners and academics from Washington, Oregon and Idaho.

The Assessment Team conducted 206 semi-structured interviews with individuals selected for their knowledge of, engagement in, and/or concern for salmon …

Simplified Reversed Chloroquines To Overcome Malaria Resistance To Quinoline-Based Drugs, Bornface Gunsaru, Steven J. Burgess, Westin Morrill, Jane X. Kelly, Shawheen Shomloo, Martin J. Smilkstein, Katherine May Liebman, David H. Peyton

Chemistry Faculty Publications and Presentations

Building on our earlier work of attaching a chemosensitizer (reversal agent) to a known drug pharmacophore, we have now expanded the structure-activity relationship study to include simplified versions of the chemosensitizer. The change from two aromatic rings in this head group to a single ring does not appear to detrimentally affect the antimalarial activity of the compounds. Data from in vitro heme binding and beta-hematin inhibition assays suggest that the single aromatic RCQ compounds retain activities against Plasmodium falciparum similar to those of CQ, although other mechanisms of action may be relevant to their activities.

Topological And Thermodynamic Factors That Influence The Evolution Of Small Networks Of Catalytic Rna Species, Jessica Anne Mellor Yeates, Philippe Nghe, Niles Lehman

Chemistry Faculty Publications and Presentations

An RNA-directed recombination reaction can result in a network of interacting RNA species. It is now becoming increasingly apparent that such networks could have been an important feature of the RNA world during the nascent evolution of life on the Earth. However, the means by which such small RNA networks assimilate other available genotypes in the environment to grow and evolve into the more complex networks that are thought to have existed in the prebiotic milieu are not known. Here, we used the ability of fragments of the Azoarcus group I intron ribozyme to covalently self-assemble via genotype-selfish and genotype-cooperative …

Divergent Trends In Ecosystem Services Under Different Climate-Management Futures In A Fire-Prone Forest Landscape, Joshua S. Halofsky, Jessica E. Halofsky, Miles A. Hemstrom, Anita T. Morzillo, Xiaoping Zhou, Daniel C. Donato

Institute for Natural Resources Publications

While ecosystem services and climate change are often examined independently, quantitative assessments integrating these fields are needed to inform future land management decisions. Using climate-informed state-and-transition simulations, we examined projected trends and trade-offs for a suite of ecosystem services under four climate change scenarios and two management scenarios (active management emphasizing fuel treatments and no management other than fire suppression) in a fire-prone landscape of dry and moist mixed-conifer forests in central Oregon, USA. Focal ecosystem services included fire potential (regulating service), timber volume (provisioning service), and potential wildlife habitat (supporting service). Projections without climate change suggested active management in …

Factors Affecting Snowy Plover Chick Survival In A Managed Population, Stephen J. Dinsmore, Eleanor P. Gaines, Scott F. Pearson, David J. Lauten, Kathleen J. Castelein

Institute for Natural Resources Publications

Understanding survival of precocial chicks in the period immediately following hatching has important conservation implications because population growth is often sensitive to post-hatching survival. We studied federally threatened Western Snowy Plover (Charadrius nivosus nivosus) broods at the northern limit of their range in coastal Oregon (n ¼ 1,157) and Washington (n ¼ 84) from 1991 to 2011 in an attempt to understand seasonal, annual, and spatial patterns of chick survival. In Oregon, plover chick survival increased with age, varied between sites, and was greater at sites with predator management. The mean probability of surviving from hatch to fledging at 28 …

The T6a Modification Acts As A Positive Determinant For The Anticodon Nuclease Prrc, And Is Distinctively Nonessential In Streptococcus Mutans, Jo Marie Bacusmo, Silvia S. Orsini, Jennifer Hu, Michael Demott, Patrick C. Thiaville, Ameer Elfarash, Mellie June Paulines, Diego Rojas-Benítez, Birthe Meineke, Christopher Deutsch, Dirk Iwata-Reuyl, Patrick A. Limbach, Peter C. Dedon, Kelly C. Rice, Stewart Shuman, Valérie De Crécy-Lagard

Chemistry Faculty Publications and Presentations

Endoribonuclease toxins (ribotoxins) are produced by bacteria and fungi to respond to stress, eliminate non-self competitor species, or interdict virus infection. PrrC is a bacterial ribotoxin that targets and cleaves tRNALys UUU in the anticodon loop. In vitro studies suggested that the post-transcriptional modification threonylcarbamoyl adenosine (t⁶A) is required for PrrC activity but this prediction had never been validated in vivo. Here, by using t⁶A-deficient yeast derivatives, it is shown that t⁶A is a positive determinant for PrrC proteins from various bacterial species. Streptococcus mutans is one of the few bacteria where the t …

Reduced Snow Cover Alters Root-Microbe Interactions And Decreases Nitrification Rates In A Northern Hardwood Forest, Patrick O. Sorensen, Pamela H. Templer, Lynn M. Christenson, Jorge Durán, Timothy J. Fahey, Melany C. Fisk, Peter M. Groffman, Jennifer L. Morse, Adrien C. Finzi

Environmental Science and Management Faculty Publications and Presentations

Snow cover is projected to decline during the next century in many ecosystems that currently experience a seasonal snowpack. Because snow insulates soils from frigid winter air temperatures, soils are expected to become colder and experience more winter soil freeze-thaw cycles as snow cover continues to decline. Tree roots are adversely affected by snowpack reduction, but whether loss of snow will affect root-microbe interactions remains largely unknown. The objective of this study was to distinguish and attribute direct (e.g., winter snow-and/ or soil frost-mediated) vs. indirect (e.g., root-mediated) effects of winter climate change on microbial biomass, the potential activity of …

Reproductive Output Of Mosses Under Experimental Warming On Fildes Peninsula, King George Island, Maritime Antarctica, Angélica Casanova-Katny, G. A. Torres-Mellado, Sarah M. Eppley

Biology Faculty Publications and Presentations

Background: Mosses dominate much of the vegetation in the Antarctic, but the effect of climatic change on moss growth and sexual reproduction has scarcely been studied. In Antarctica, mosses infrequently produce sporophytes; whether this is due to physiological limitation or an adaptive response is unknown. We studied the effect of experimental warming (with Open Top Chambers, OTCs) on sporophyte production on Fildes Peninsula, King George Island for four moss species (Bartramia patens, Hennediella antarctica, Polytrichastrum alpinum, and Sanionia georgicouncinata). To determine whether reducing cold stress increases sexual reproduction as would be predicted if sex is …

Genomics-Informed Isolation And Characterization Of A Symbiotic Nanoarchaeota System From A Terrestrial Geothermal Environment, Louie Wurch, Richard J. Giannone, Bernard S. Belisle, Carolyn Swift, Sagar Utturkar, Robert L. Hettich, Anna-Louise Reysenbach, Mircea Podar

Biology Faculty Publications and Presentations

Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured. However, cultivation is important for characterizing an organism’s physiology and testing its genome-encoded potential. Here we use single-cell genomics to infer cultivation conditions for the isolation of an ectosymbiotic Nanoarchaeota (‘Nanopusillus acidilobi’) and its host (Acidilobus, a crenarchaeote) from a terrestrial geothermal environment. The cells of ‘Nanopusillus’ are among the smallest known cellular organisms (100–300 nm). They appear to have a complete genetic information processing machinery, but lack almost all primary biosynthetic functions as well as respiration and …

Scientifically Defensible Fish Conservation And Recovery Plans: Addressing Diffuse Threats And Developing Rigorous Adaptive Management Plans, Kathleen G. Maas-Hebner, Carl B. Schreck, Robert M. Hughes, J. Alan Yeakley, Nancy Molina

Environmental Science and Management Faculty Publications and Presentations

We discuss the importance of addressing diffuse threats to long-term species and habitat viability in fish conservation and recovery planning. In the Pacific Northwest, USA, salmonid management plans have typically focused on degraded freshwater habitat, dams, fish passage, harvest rates, and hatchery releases. However, such plans inadequately address threats related to human population and economic growth, intra- and interspecific competition, and changes in climate, ocean, and estuarine conditions. Based on reviews conducted on eight conservation and/or recovery plans, we found that though threats resulting from such changes are difficult to model and/or predict, they are especially important for wide-ranging diadromous …

The Value Of Long-Term Stream Invertebrate Data Collected By Citizen Scientists, Patrick M. Edwards

Environmental Science and Management Faculty Publications and Presentations

The purpose of this investigation was to systematically examine the variability associated with temporally-oriented invertebrate data collected by citizen scientists and consider the value of such data for use in stream management. Variability in invertebrate data was estimated for three sources of variation: sampling, within-reach spatial and long-term temporal. Long-term temporal data were also evaluated using ordinations and an Index of Biotic Integrity (IBI). Through two separate investigations over an 11-year study period, participants collected more than 400 within-reach samples during 44 sampling events at three streams in the western United States. Within-reach invertebrate abundance coefficient of variation (CV) ranged …

Bridge Over Troubled Waters: A Synthesis Session To Connect Scientific And Decision Making Sectors, Kaitlin Goldsmith, Elise F. Granek, Amy Lubitow, Michael Papenfus

Environmental Science and Management Faculty Publications and Presentations

Lack of access to relevant scientific data has limited decision makers from incorporating scientific information into their management and policy schemes. Yet, there is increasing interest among decision makers and scientists to integrate coastal and marine science into the policy and management process. Strategies designed to build communication between decision makers and scientists can be an effective means to disseminate and/or generate policy relevant scientific information. Here researchers develop, test, and present a workshop model designed to bridge the gap between coastal and marine decision makers and scientists. Researchers identify successful components of such a workshop as well as areas …

Ecosystem Services In Managing Residential Landscapes: Priorities, Value Dimensions, And Cross-Regional Patterns, Kelli L. Larson, Jennifer L. Morse, Peter M. Groffman, Neil D. Bettez, Tara Trammell

Environmental Science and Management Faculty Publications and Presentations

Although ecosystem services have been intensively examined in certain domains (e.g., forests and wetlands), little research has assessed ecosystem services for the most dominant landscape type in urban ecosystems—namely, residential yards. In this paper, we report findings of a cross-site survey of homeowners in six U.S. cities to 1) examine how residents subjectively value various ecosystem services, 2) explore distinctive dimensions of those values, and 3) test the urban homogenization hypothesis. This hypothesis posits that urbanization leads to similarities in the social-ecological dynamics across cities in diverse biomes. By extension, the thesis suggests that residents’ ecosystem service priorities for residential …

Assessing The Impacts Of Federal Forest Planning On Wildfire Risk Mitigation In The Pacific Northwest, Usa, Alan A. Ager, Michelle A. Day, Karen C. Short, Cody R. Evers

Environmental Science and Management Faculty Publications and Presentations

We analyzed the impact of amenity and biodiversity protection as mandated in national forest plans on the implementation of hazardous fuel reduction treatments aimed at protecting the wildland urban interface (WUI) and restoring fire resilient forests. We used simulation modeling to delineate areas on national forests that can potentially transmit fires to adjacent WUI. We then intersected these areas with national forest planning maps to determine where mechanical treatments are allowed for restoration and fire protection, versus areas where they are prohibited. We found that a large proportion of the national forest lands (79%) can spawn fires that burn adjacent …

Mechanisms Of Methane Transport Through Populus Trichocarpa, Ellynne Marie Kutschera, M. A. K. Khalil, Andrew Rice, Todd Rosenstiel

Physics Faculty Publications and Presentations

Although the dynamics of methane (CH4) emission from croplands and wetlands have been fairly well investigated, the contribution of trees to global CH4 emission and the mechanisms of tree transport are relatively unknown. CH4 emissions from the common wetland tree species Populus trichocarpa (black cottonwood) native to the Pacific Northwest were measured under hydroponic conditions in order to separate plant transport mechanisms from the influence of soil processes. Roots were exposed to CH4 enriched water and canopy emissions of CH4 were measured. The average flux for 34 trials (at temperatures ranging from 17 to 25 °C) was 2.8 ± 2.2 …

Three Simple Experiments To Examine The Effect Of Sediment Pollution On Algae-Based Food Webs In Streams, Patrick M. Edwards, Rodney Shroufe

Environmental Science and Management Faculty Publications and Presentations

Streams and stream macroinvertebrates are ideal natural systems for ecological inquiry. We present three simple experiments that students can use to conduct field-based investigations which illustrate the importance of algae-based food webs in streams and measure the effects of sediment pollution (scour and deposition) on stream ecological processes. Over the past 5 years, we have conducted these experiments 19 times with our students. We report on the results and reliability of these experiments and make suggestions for other educators who may want to conduct them.