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This data is derived from sampling poplar trees at the GWAS common garden in Clatskanie, Oregon. This is intermediate level data from LCMS experiments that were done at ORNL from root tissue and soluble root exudates collected from 24 trees in the common garden in October of 2022.
These data are from the manuscript “Application of Genomic Prediction in a Populus trichocarpa Breeding Program”, by Brian J. Stanton, David Macaya-Sanz, Chanaka Roshan Abeyratne, David Kainer, Kathy Haiby, Austin Himes, Carlos Gantz, Gerald A. Tuskan, and Stephen P. DiFazio. The data are based on genome resequencing to approximately 10X depth on two collections of Populus trichocarpa trees from Oregon, Washington, California, and British Columbia. The first collection consists of 293 genets collected by Poplar Innovations LLC for a breeding program. The second collection consists of 961 trees collected for the purpose of genome-wide association studies. These genets were sequenced using short, paired-end Illumina sequence reads (Chhetri et al. 2019). Reads were aligned to the P. trichocarpa ′Stettler-14′ reference (Hofmeister et al. 2020), with minor modifications to correct mis-assemblies (Zhou et al. 2020), and variants were called as per methods described in (Abeyratne et al. 2023). Identified variants were filtered using GATK’s VariantFiltration tool (DePristo et al. 2011), with filter expression flag set to “AF < 0.01 || AF > 0.99 || QD < 10.0 || ExcessHet > 20.0 || FS > 10.0 || MQ < 58.0”. SNPs with severe departures from Hardy−Weinberg expectations (exact-test p< 0.01) were also removed using vcftools --hwe flag (Danecek et al. 2011), resulting in 15,627,211 bi-allelic SNPs. The data included here consist of 141,903 high quality bi-allelic genome-wide SNPs obtained by further filtering the original SNP dataset using vcftools with flags --maf 0.05, --max-maf 0.95, --max-missing 0.95, --min-meanDP 10.75, --max-meanDP 43.00, --thin 2000. Collectively, these filtering parameters removed SNPs with 1) a minor allele frequency ≤ 0.05; 2) proportion of missing data for individual loci exceeding 5%; 3) sequencing depth more than 2X mean-depth or less than 0.5X mean-depth; or 4) a distance of
Background: Older adults spend a considerable amount of time inside their residences; however, most research investigates out-of-home mobility and its health correlates. We measured indoor mobility using room-to-room transitions, tested their psychometric properties, and correlated indoor mobility with cognitive and functional status. Materials and Methods: Community-dwelling older adults living alone ( n = 139; age = 78.1 ± 8.6 years) from the Oregon Center for Aging & Technology (ORCATECH) and Minority Aging Research Study (MARS) were included in the study. Two indoor mobility features were developed using non-parametric parameters (frequency; stability): Indoor mobility frequency (room-to-room transitions/day) was detected using passive infrared (PIR) motion sensors fixed on the walls in four geographic locations (bathroom; bedroom; kitchen; living room) and using door contact sensors attached to the egress door in the entrance. Indoor mobility stability was estimated by variances of number of room-to-room transitions over a week. Test-retest reliability (Intra-class coefficient, ICC) and the minimal clinically important difference (MCID) defined as the standard error of measurement (SEM) were generated. Generalized estimating equations models related mobility features with mild cognitive impairment (MCI) and functional status (gait speed). Results: An average of 206 days (±127) of sensor data were analyzed per individual. Indoor mobility frequency and stability showed good to excellent test-retest reliability (ICCs = 0.91[0.88–0.94]; 0.59[0.48–0.70]). The MCIDs of mobility frequency and mobility stability were 18 and 0.09, respectively. On average, a higher indoor mobility frequency was associated with faster gait speed (β = 0.53, p = 0.04), suggesting an increase of 5.3 room-to-room transitions per day was associated with an increase of 10 cm/s gait speed. A decrease in mobility stability was associated with MCI (β = −0.04, p = 0.03). Discussion: Mobility frequency and stability in the home are clinically meaningful and reliable features. Pervasive-sensing systems deployed in homes can objectively reveal cognitive and functional status in older adults who live alone.
Large-diameter trees store disproportionally massive amounts of carbon and are a major driver of carbon cycle dynamics in forests worldwide. In the temperate forests of the western United States, proposed changes to Forest Plans would significantly weaken protections for a large portion of trees greater than 53 cm (21 inches) in diameter (herein referred to as “large-diameter trees”) across 11.5 million acres (~4.7 million ha) of National Forest lands. This study is among the first to report how carbon storage in large trees and forest ecosystems would be affected by a proposed policy. We examined the proportion of large-diameter trees on National Forest lands east of the Cascade Mountains crest in Oregon and Washington, their contribution to overall aboveground carbon (AGC) storage, and the potential reduction in carbon stocks resulting from widespread harvest. We analyzed forest inventory data collected on 3,335 plots and found that large trees play a major role in the accumulated carbon stock of these forests. Tree AGC (kg) increases sharply with tree diameter at breast height (DBH; cm) among five dominant tree species. Large trees accounted for 2.0 to 3.7% of all stems (DBH ≥ 1” or 2.54 cm) among five tree species; but held 33 to 46% of the total AGC stored by each species. Pooled across the five dominant species, large trees accounted for 3% of the 636,520 trees occurring on the inventory plots but stored 42% of the total AGC. A recently proposed large-scale vegetation management project that involved widespread harvest of large trees, mostly grand fir, would have removed ~44% of the AGC stored in these large-diameter trees, and released a large amount of carbon dioxide to the atmosphere. Given the urgency of keeping additional carbon out of the atmosphere and continuing carbon accumulation from the atmosphere to protect the climate system, it would be prudent to continue protecting ecosystems with large trees for their carbon stores, and also for their co-benefits of habitat for biodiversity, resilience to drought and fire, and microclimate buffering under future climate extremes.
Introduction: In temperate regions, one of the most critical determinants of present range-wide genetic diversity was the Pleistocene climate oscillations, the most recent one created by the last glacial maximum (LGM). This study aimed to describe N. luetkeana genetic structure across its entire range (Alaska to California) and test different models of population connectivity within the Salish Sea. This region was colonized after the LGM and has been under increased disturbance in recent decades. Methods: We utilized microsatellite markers to study N. luetkeana genetic diversity at 53 sites across its range. Using higher sampling density in the Salish Sea, we employed a seascape genetics approach and tested isolation by hydrodynamic transport and environment models. Results: At the species distribution scale, we found four main groups of genetic co-ancestry, Alaska; Washington with Vancouver Island’s outer coast and Juan de Fuca Strait; Washington’s inner Salish Sea; and Oregon with California. The highest allelic richness (AR) levels were found in California, near the trailing range edge, although AR was also high in Alaska. The inner Salish Sea region had the poorest diversity across the species distribution. Nevertheless, a pattern of isolation by hydrodynamic transport and environment was supported in this region. Discussion: The levels of allelic, private allele richness and genetic differentiation suggest that during the LGM, bull kelp had both northern and southern glacial refugia in the Prince of Wales Island-Haida Gwaii region and Central California, respectively. Genetic diversity in Northern California sites seems resilient to recent disturbances, whereas the low levels of genetic diversity in the inner Salish Sea are concerning.
Plants are colonized by numerous microorganisms serving important symbiotic functions that are vital to plant growth and success. Understanding and harnessing these interactions will be useful in both managed and natural ecosystems faced with global change, but it is still unclear how variation in environmental conditions and soils influence the trajectory of these interactions. In this study, we examine how nitrogen addition alters plant-fungal interactions within two species of Populus - Populus deltoides and P. trichocarpa. In this experiment, we manipulated plant host, starting soil (native vs. away for each tree species), and nitrogen addition in a fully factorial replicated design. After ~10 weeks of growth, we destructively harvested the plants and characterized plant growth factors and the soil and root endosphere fungal communities using targeted amplicon sequencing of the ITS2 gene region. Overall, we found nitrogen addition altered plant growth factors, e.g., plant height, chlorophyll density, and plant N content. Interestingly, nitrogen addition resulted in a lower fungal alpha diversity in soils but not plant roots. Further, there was an interactive effect of tree species, soil origin, and nitrogen addition on soil fungal community composition. Starting soils collected from Oregon and West Virginia were dominated by the ectomycorrhizal fungi Inocybe (55.8% relative abundance), but interestingly when P. deltoides was grown in its native West Virginia soil, the roots selected for a high abundance of the arbuscular mycorrhizal fungi, Rhizophagus. These results highlight the importance of soil origin and plant species on establishing plant-fungal interactions.
Stepping On is a community-based intervention that has been shown in a randomized controlled trial to reduce fall risk. The Wisconsin Institute for Healthy Aging adapted Stepping On for use in the United States and developed a training infrastructure to enable dissemination. The purpose of this study is to: (1) describe the personal characteristics of Stepping On participants; (2) quantify participants’ functional and self-reported health status at enrollment, and (3) measure changes in participants’ functional and self-reported health status after completing the program. Both survey and observed functional status [timed up and go (TUG) test] data were collected between September 2011 and December 2013 for 366 participants enrolled in 32 Stepping On programs delivered in Colorado, New York, and Oregon. Paired t-tests and general estimating equations models adjusted for socio-demographic factors were performed to assess changes over the program period. Among the 266 participants with pre–post survey data, the average participant age was 78.7 (SD ± 8.0) years. Most participants were female (83.4%), white (96.9%), and in good health (49.4%). The TUG test scores decreased significantly (p < 0.001) for all 254 participants with pre–post data. The change was most noticeable among high risk participants where TUG time decreased from 17.6 to 14.4 s. The adjusted odds ratio of feeling confident about keeping from falling was more than three times greater after completing Stepping On. Further, the adjusted odds ratios of reporting “no difficulty” for getting out of a straight back chair increased by 89%. Intended for older adults who have fallen in the past or are afraid of falling, Stepping On has the potential to reduce the frequency and burden of older adult falls.
Tai Chi: Moving for Better Balance (TCMBB) is an evidence-based fall prevention exercise program being disseminated in selected communities through state injury prevention programs. This study: (1) describes the personal characteristics of TCMBB participants; (2) quantifies participants’ functional and self-reported health status at enrollment; and (3) measures changes in participants’ functional and self-reported health status post-intervention. There were 421 participants enrolled in 36 TCMBB programs delivered in Colorado, New York, and Oregon. Of the 209 participants who completed both baseline enrollment and post-intervention surveys, the average age of participants was 75.3 (SD ± 8.2) years. Most participants were female (81.3%), non-Hispanic (96.1%), White (94.1%), and described themselves as in excellent or very good health (52.2%). Paired t-test and general estimating equation models assessed changes over the 3-month program period. Pre- and post-assessment self-reported surveys and objective functional data [Timed Up and Go (TUG) test] were collected. On average, TUG test scores decreased (p < 0.001) for all participants; however, the decrease was most noticeable among high-risk participants (mean decreased from 18.5 to 15.7 s). The adjusted odds ratio of reporting feeling confident that a participant could keep themselves from falling was five times greater after completing the program. TCMBB, which addresses gait and balance problems, can be an effective way to reduce falls among the older adult population. By helping older adults maintain their functional abilities, TCMBB can help community-dwelling older adults continue to live independently.
Offshore synthetic fuel production and marine carbon dioxide removal can be enabled by direct ocean capture, which extracts carbon dioxide from the ocean that then can be used as a feedstock for fuel production or sequestered underground. To maximize carbon capture, plants require a variety of low-carbon energy sources to operate, such as variable renewable energy. However, the impacts of variable power on direct ocean capture have not yet been thoroughly investigated. To facilitate future deployments, a generalizable model for electrodialysis-based direct ocean capture plants is created to evaluate plant performance and electricity costs under intermittent power availability. This open-source Python-based model captures key aspects of the electrochemistry, ocean chemistry, post-processing, and operation scenarios under various conditions. To incorporate realistic energy supply dynamics and cost estimates, the model is coupled with the National Renewable Energy Laboratory’s H2Integrate tool, which simulates hybrid energy system performance profiles and costs. This integrated framework is designed to provide system-level insights while maintaining computational efficiency and flexibility for scenario exploration. Initial evaluations show similar results to those predicted by the industry, and demonstrate how a given plant could function with variable power in different deployment locations, such as with wind energy off the coast of Texas and with wind and wave energy off the coast of Oregon. The results suggest that electrochemical systems with greater tolerances for power variability and low minimum power requirements may offer operational advantages in variable-energy contexts. However, further research is needed to quantify these benefits and evaluate their implications across different deployment scenarios.
This paper presents a modeling study conducted on the central Oregon coast for wave resource characterization using the unstructured-grid SWAN model coupled with a nested-grid WWIII model. The flexibility of models of various spatial resolutions and the effects of open- boundary conditions simulated by a nested-grid WWIII model with different physics packages were evaluated. The model results demonstrate the advantage of the unstructured-grid modeling approach for flexible model resolution and good model skills in simulating the six wave resource parameters recommended by the International Electrotechnical Commission in comparison to the observed data in Year 2009 at National Data Buoy Center Buoy 46050. Notably, spectral analysis indicates that the ST4 physics package improves upon the model skill of the ST2 physics package for predicting wave power density for large waves, which is important for wave resource assessment, device load calculation, and risk management. In addition, bivariate distributions show the simulated sea state of maximum occurrence with the ST4 physics package matched the observed data better than that with the ST2 physics package. This study demonstrated that the unstructured-grid wave modeling approach, driven by the nested-grid regional WWIII outputs with the ST4 physics package, can efficiently provide accurate wave hindcasts to support wave resource characterization. Our study also suggests that wind effects need to be considered if the dimension of the model domain is greater than approximately 100 km, or O (10^2 km).
Wave energy converter (WEC) arrays deployed in coastal regions may create physical disturbances, potentially resulting in environmental stresses. Presently, limited information is available on the nature of these physical disturbance or the resultant effects. A quantitative Spatial Environmental Assessment Tool (SEAT) for evaluating the potential effects of wave energy converter (WEC) arrays on nearshore hydrodynamics and sediment transport is presented for the central Oregon coast (USA) through coupled numerical model simulations of an array of WECs. Derived climatological wave conditions were used as inputs to the model to allow for the calculation of risk metrics associated with various hydrodynamic and sediment transport variables such as maximum shear stress, bottom velocity, and change in bed elevation. The risk maps provided simple, quantitative, and spatially-resolved means of evaluating physical changes in the vicinity of a hypothetical WEC array in response to varying wave conditions. The near-field risk of sediment mobility was determined to be moderate in the lee of the densely spaced array, where the potential for increased sediment deposition could result in benthic habitat alteration. Modifications to the nearshore sediment deposition and erosion patterns were observed near headlands and topographic features, which could have implications for littoral sediment transport. The results illustrate the benefits of a risk evaluation tool for facilitating coastal resource management at early market marine renewable energy sites.
Industry-specific tools for analyzing and optimizing the design of wave energy converters (WECs) and associated power systems are essential to advancing marine renewable energy. This study aims to quantify the influence of phase information on the device power output of a virtual WEC array. We run the phase-resolving wave model FUNWAVE-TVD (Total Variation Diminishing) to generate directional waves at the PacWave South site offshore from Newport, Oregon, where future WECs are expected to be installed for testing. The two broad cases presented correspond to mean wave climates during warm months (March–August) and cold months (September–February). FUNWAVE-TVD time series of sea-surface elevation are then used in WEC-Sim, a time domain numerical model, to simulate the hydrodynamic response of each device in the array and estimate their power output. For comparison, WEC-Sim is also run with wave energy spectra calculated from the FUNWAVE-TVD simulations, which do not retain phase information, and with wave spectra computed using the phase-averaged model Simulating WAves Nearshore (SWAN). The use of spectral data in WEC-Sim requires a conversion from frequency to time domain by means of random superposition of wave components, which are not necessarily consistent because of the linear assumption implicit in this method. Thus, power response is characterized by multiple realizations of the wave climates.
The development of the Modular High-Temperature Gas-Cooled Reactor is a significant milestone in advanced nuclear reactor technology. One of the concerns for the reactor’s safe operation is the effects of a loss-of-flow accident (LOFA) where the coolant circulators are tripped, and forced coolant flow through the core is lost. Depending on the steam generator placement, loop or intracore natural circulation develops to help transfer heat from the core to the reactor cavity, cooling system. This paper investigates the fundamental physical phenomena associated with intracore coolant natural circulation flow in a one-sixth Computational Fluid Dynamics (CFD) model of the Oregon State University High Temperature Test Facility (OSU HTTF) following a loss-of-flow accident transient. This study employs conjugate heat transfer and steady-state flow along with an SST k-ω turbulence model to characterize the phenomenon of core channel-to-channel natural convection. Previous studies have revealed the importance of complex flow distribution in the inlet and outlet plenums with the potential to generate hot coolant jets. For this reason, complete upper and lower plenum volumes are included in the analyzed computational domain. CFD results also include parametric studies performed for a mesh sensitivity analysis, generated using the STAR-CCM+ software. The resulting channel axial velocities and flow directions support the test facility scaling analysis and similarity group distortions calculation.
Thermal heterogeneity of rivers is essential to support freshwater biodiversity. Salmon behaviorally thermoregulate by moving from patches of warm water to cold water. When implementing river restoration projects, it is essential to monitor changes in temperature and thermal heterogeneity through time to assess the impacts to a river’s thermal regime. Lightweight sensors that record both thermal infrared (TIR) and multispectral data carried via unoccupied aircraft systems (UASs) present an opportunity to monitor temperature variations at high spatial (<0.5 m) and temporal resolution, facilitating the detection of the small patches of varying temperatures salmon require. Here, we present methods to classify and filter visible wetted area, including a novel procedure to measure canopy cover, and extract and correct radiant surface water temperature to evaluate changes in the variability of stream temperature pre- and post-restoration followed by a high-intensity fire in a section of the river corridor of the South Fork McKenzie River, Oregon. We used a simple linear model to correct the TIR data by imaging a water bath where the temperature increased from 9.5 to 33.4 °C. The resulting model reduced the mean absolute error from 1.62 to 0.35 °C. We applied this correction to TIR-measured temperatures of wetted cells classified using NDWI imagery acquired in the field. We found warmer conditions (+2.6 °C) after restoration (p < 0.001) and median absolute deviation for pre-restoration (0.30) to be less than both that of post-restoration (0.85) and post-fire (0.79) orthomosaics. In addition, there was statistically significant evidence to support the hypothesis of shifts in temperature distributions pre- and post-restoration (KS test 2009 vs. 2019, p < 0.001, D = 0.99; KS test 2019 vs. 2021, p < 0.001, D = 0.10). Moreover, we used a Generalized Additive Model (GAM) that included spatial and environmental predictors (i.e., canopy cover calculated from multispectral NDVI and photogrammetrically derived digital elevation model) to model TIR temperature from a transect along the main river channel. This model explained 89% of the deviance, and the predictor variables showed statistical significance. Collectively, our study underscored the potential of a multispectral/TIR sensor to assess thermal heterogeneity in large and complex river systems.
Sleep disturbances are common in older adults and may contribute to disease progression in certain populations (e.g., Alzheimer’s disease). Light therapy is a simple and cost-effective intervention to improve sleep. Primary barriers to light therapy are: (1) poor acceptability of the use of devices, and (2) inflexibility of current devices to deliver beyond a fixed light spectrum and throughout the entirety of the day. However, dynamic, tunable lighting integrated into the native home lighting system can potentially overcome these limitations. Herein, we describe our protocol to implement a whole-home tunable lighting system installed throughout the homes of healthy older adults already enrolled in an existing study with embedded home assessment platforms (Oregon Center for Aging & Technology—ORCATECH). Within ORCATECH, continuous data on room location, activity, sleep, and general health parameters are collected at a minute-to-minute resolution over years of participation. This single-arm longitudinal protocol collected participants’ light usage in addition to ORCATECH outcome measures over a several month period before and after light installation. The protocol was implemented with four subjects living in three ORCATECH homes. Technical/usability challenges and feasibility/acceptability outcomes were explored. The successful implementation of our protocol supports the feasibility of implementing and integrating tunable whole-home lighting systems into an automated home-based assessment platform for continuous data collection of outcome variables, including long-term sleep measures. Challenges and iterative approaches are discussed. This protocol will inform the implementation of future clinical intervention trials using light therapy in patients at risk for developing Alzheimer’s disease and related conditions.
As the wave energy sector grows and looks to the Blue Economy for commercialization opportunities, there is a distinct and pressing need to clearly understand and quantify the coupled impacts of wave energy converter (WEC) size and wave resource characteristics on the annual energy production, spatial variability and temporal variability. Utilizing generic frequency domain representations of the Oscilla Power Triton WEC and spectral wave conditions at PacWave (Oregon), Los Angeles (California) and WETS (Hawaii), a series of interesting results emerge. Firstly, the ‘optimal’ WEC size, from an energy standpoint, is fundamentally dependent on the frequency distribution of the incoming wave variance density spectrum. Secondly, and from a seasonality perspective, the seasonal WEC energy generation doesn’t necessarily follow the seasonal distribution of gross wave power. Finally, from an hourly power variability perspective, a reduction in WEC size generally decreases variability. However, for each of the locations investigated, there appears to be a WEC size threshold; a threshold where further reducing WEC size results in increased power variability.
Premise of the study: We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome) accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. Methods and Results: More than 350 million sequence reads from the mRNA libraries prepared from three B. sylvaticum genotypes were assembled into 120,091 (Corvallis), 104,950 (Spain), and 177,682 (Greece) transcript contigs. In comparison with the B. distachyon Bd21 reference genome and GenBank protein sequences, we estimate >90% exome coverage for B. sylvaticum . The transcripts were assigned Gene Ontology and InterPro annotations. Brachypodium sylvaticum sequence reads aligned against the Bd21 genome revealed 394,654 single-nucleotide polymorphisms (SNPs) and >20,000 simple sequence repeat (SSR) DNA sites. Conclusions: To our knowledge, this is the first report of transcriptome sequencing of invasive plant species with a closely related sequenced reference genome. The sequences and identified SNP variant and SSR sites will provide tools for developing novel genetic markers for use in genotyping and characterization of invasive behavior of B. sylvaticum.
Objectives/Scope: The goal of this work was to develop a consistent and semi-automated seafloor survey method for generating high-resolution, benthic habitat maps for environmental assessments and monitoring of marine renewable energy sites. Sediment profile and plan view imaging (SPI/PV) technology was combined with multibeam bathymetry and acoustic backscatter methods to demonstrate a rapid, cost-effective benthic mapping protocol. A key technical innovation of this project was the development of an image processing platform that automatically measures key features from the images. Methods: Multibeam echosounder (MBES) acoustic and SPI/PV surveys were conducted at three coastal areas off the U.S. west coast, including the PacWave South energy test site off of Newport, Oregon. Point data on physical and biological sediment conditions obtained from the SPI/PV imagery were used to efficiently ground-truth the high-resolution MBES bathymetry and backscatter mosaics. The SPI camera is an optical corer that obtains an undisturbed 21 by 15 cm, high-resolution, cross-sectional image of the sediment–water interface and upper sediment column. The plan view camera attached to the SPI camera frame captures a downward looking view of the seabed immediately before the SPI image is obtained. As part of this project, we developed a computer vision image processing platform (iSPI) that uses deep convolutional neural networks and other approaches to automatically identify and measure key features in the images, such as grain size and surface relief. Results: Detailed benthic habitat maps were generated using this mapping approach for three different marine settings. The sites mapped included a silt-dominated embayment; a sloping, nearshore, transitional very fine to coarse sand bottom; and a medium, sand-dominated continental shelf marine energy test site. In each case, acoustic and imaging surveys were completed in less than week, and detailed benthic habitat maps were generated within 60 days. The results were placed within the Coastal and Marine Ecological Classification Standard (CMECS) habitat mapping framework, and various combinations of the bathymetry, backscatter, and SPI and PV data were used to generate CMECS component maps. Novel Information: This project developed and demonstrated a repeatable and cost-effective approach for efficiently mapping benthic habitat conditions over broad areas of the seafloor by combining state-of-the-art acoustic and imaging techniques. The primary survey tools used in this project have been used previously in both the offshore renewable (wind) and oil and gas sectors to map and monitor benthic environments. This project’s innovations include 1) the focused use of high-resolution SPI/PV imagery to ground-truth acoustic mosaics, and 2) the development of a computer automated image analysis processing tool that both streamlines and standardizes the generation of data from the imagery and makes the data extraction process more cost-effective and repeatable.