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  1. Abstract

    Hyperspectral imaging allows for rapid, non-destructive and objective assessments of crop health. Narrowband-hyperspectral data was used to select wavelength regions that can be exploited to identify wheat infected with soil-borne mosaic virus. First, leaf samples were scanned in the lab to investigate spectral differences between healthy and diseased leaves, including non-symptomatic and symptomatic areas within a diseased leaf. The potential of 84 commonly used vegetation indices to find infection was explored. A machine-learning approach was used to create a classification model to automatically separate pixels into symptomatic, non-symptomatic and healthy classes. The success rate of the model was 69.7% using the full spectrum. It was very encouraging that by using a subset of only four broad bands, sampled to simulate a data set from a much simpler and less costly multispectral camera, accuracy increased to 71.3%. Next, the classification models were validated on field data. Infection in the field was successfully identified using classifiers trained on the entire spectrum of the hyperspectral data acquired in a lab setting, with the best accuracy being 64.9%. Using a subset of wavelengths, simulating multispectral data, the accuracy dropped by only 3 percentage points to 61.9%. This research shows the potential of using lab scans to train classifiers to be successfully applied in the field, even when simultaneously reducing the hyperspectral data to multispectral data.

     
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  2. Abstract

    Streams are complex where biology, hydrology, and atmospheric processes are all important. Because quantifying and modeling of these systems can be challenging, many teams go directly to prescribed restoration treatments and principles. Restoration on the Middle Fork of the John Day River in Oregon, USA, shows how a project that was designed according to widely accepted restoration principles may lead to outcomes contrary to one of the project's stated goals: reducing peak temperatures for endangered salmonids on the site. This study employed the most sophisticated equipment available for stream temperature monitoring, including approximately 1 million independent hourly measurements in the 2‐week period considered. These data were collected along the river channel with fiber optic–distributed temperature sensing and were used to quantify thermal dynamics. These observations were paired with a physically based stream temperature model which was then employed to predict temperature change from design alternatives. Restored‐reach impact on peak temperature was directly correlated with the air–water interfacial area and the percentage of effective shade (R2 > 0.99). The increase in air–water area of the proposed design was predicted to increase daytime stream temperature by as much as 0.5°C upon completion of the work. Shade from riparian vegetation was found to potentially mitigate stream temperature increases, though only after decades of growth. A moderately dense canopy of 5 m tall trees blocking 17% of daily shortwave solar radiation is predicted to mitigate predicted temperature increases over the 1,800 m reach but also increases nighttime temperatures due to blocking of long‐wave radiation. These outcomes may not be intuitive to restoration practitioners and show how quantitative analysis can benefit the design of a project. This is significant in an area where riparian vegetation has been difficult to reestablish. Without quantitative analysis, restoration efforts can lead to outcomes opposite to stated goals and may be costly and disruptive interventions to fragile stream systems.

     
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  3. Abstract

    Beaver dam analogs (BDAs) are a stream restoration technique that is rapidly gaining popularity in the western United States. These low‐cost, stream‐spanning structures, designed after natural beaver dams, are being installed to confer the ecologic, hydrologic, and geomorphic benefits of beaver dams in streams that are often too degraded to provide suitable beaver habitat. BDAs are intended to slow streamflow, reduce the erosive power of the stream, and promote aggradation, making them attractive restoration tools in incised channels. Despite increasing adoption of BDAs, few studies to date have monitored the impacts of BDAs on channel form. Here, we examine the geomorphic changes that occurred within the first year of restoration efforts in Wyoming using high‐resolution visible light orthomosaics and elevation data collected with unoccupied aerial vehicles (UAVs). By leveraging the advantages of rapidly acquired images from UAV surveys with recent advancements in structure‐from‐motion photogrammetry, we constructed centimeter‐scale digital elevation models (DEMs) of the restoration reach and an upstream control reach. Through DEM differencing, we identified areas of enhanced erosion and deposition near the BDAs, suggesting BDA installation initiated a unique geomorphic response in the channel. Both reaches were characterized by net erosion during the first year of restoration efforts. While erosion around the BDAs may seem counter to the long‐term goal of BDA‐induced aggradation, short‐term net erosion is consistent with high precipitation during the study and with theoretical channel evolution models of beaver‐related stream restoration that predict initial channel widening and erosion before net deposition. To better understand the impacts of BDAs on channel morphology and restoration efforts in the western United States, it is imperative that we consistently assess the effects of beaver‐inspired restoration projects across a range of hydrologic and geomorphic settings and that we continue this monitoring in the future.

     
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  4. Abstract

    The design and construction of a waste rock pile influences water infiltration and may promote the production of contaminated mine drainage. The objective of this project is to evaluate the use of an active fiber optic distributed temperature sensing (aFO‐DTS) protocol to measure infiltration and soil moisture within a flow control layer capping an experimental waste rock pile. Five hundred meters of fiber optic cable were installed in a waste rock pile that is 70 m long, 10 m wide, and was covered with 0.60 m of fine compacted sand and 0.25 m of non‐reactive crushed waste rock. Volumetric water content was assessed by heating the fiber optic cable with 15‐min heat pulses at 15 W/m every 30 min. To test the aFO‐DTS system 14 mm of recharge was applied to the top surface of the waste rock pile over 4 h, simulating a major rain event. The average volumetric water content in the FCL increased from 0.10 to 0.24 over the duration of the test. The volumetric water content measured with aFO‐DTS in the FCL and waste rock was within ±0.06 and ±0.03, respectively, compared with values measured using 96 dielectric soil moisture probes over the same time period. Additional results illustrate how water can be confined within the FCL and monitored through an aFO‐DTS protocol serving as a practical means to measure soil moisture at an industrial capacity.

     
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  5. Abstract

    Stratification can cause turbulence spectra to deviate from Kolmogorov's isotropicpower law scaling in the universal equilibrium range at high Reynolds numbers. However, a consensus has not been reached with regard to the exact shape of the spectra. Here we propose a shape of the turbulent kinetic energy and temperature spectra in horizontal wavenumber for the equilibrium range that consists of three regimes at small Froude number: the buoyancy subrange, a transition region, and the isotropic inertial subrange through dimensional analysis and substantial revision of previous theoretical approximation. These spectral regimes are confirmed by various observations in the atmospheric boundary layer. The representation of the transition region in direct numerical simulations will require large‐scale separation between the Dougherty‐Ozmidov scale and the Kolmogorov scale for strongly stratified turbulence at high Reynolds numbers, which is still challenging computationally. In addition, we suggest that the failure of Monin‐Obukhov similarity theory in the very stable atmospheric boundary layer is due to the fact that it does not consider the buoyancy scale that characterizes the transition region.

     
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  6. Abstract

    Rivers are dynamic, complex integrators of their environment, which makes verification of the beneficial outcomes of restoration challenging. Thermal regime is central to habitat suitability and is often a focus in planning and evaluating the impact of restoration and climate resilience. Among these concerns, high summer stream temperature has frequently been identified as a limiting factor for salmon, steelhead, and trout. Our objective was to demonstrate the utility of combining high resolution thermal observation and modelling to evaluate restoration designed to mitigate stream thermal processes. This was demonstrated on the Middle Fork of the John Day River which is a critically impacted salmonid fishery in northeast Oregon, USA. We employed distributed temperature sensing and energy‐balance modelling to define the thermal regime. Restoration was predicted to result in a 0.7°C reduction of peak daily stream temperatures while increasing night temperatures by 0.9°C. This combined modelling and monitoring approach suggests that the 2012 restoration offered relief for native fish species stressed by excessive stream temperatures. This powerful combination of technology can be used in many projects to make optimal use of restoration investments to achieve durable and quantifiable improvements in habitat.

     
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  7. Abstract

    Internal waves strongly influence the physical and chemical environment of coastal ecosystems worldwide. We report novel observations from a distributed temperature sensing (DTS) system that tracked the transformation of internal waves from the shelf break to the surf zone over a narrow shelf slope region in the South China Sea. The spatially continuous view of temperature fields provides a perspective of physical processes commonly available only in laboratory settings or numerical models, including internal wave reflection off a natural slope, shoreward transport of dense fluid within trapped cores, and observations of internal rundown (near‐bed, offshore‐directed jets of water preceding a breaking internal wave). Analysis shows that the fate of internal waves on this shelf—whether transmitted into shallow waters or reflected back offshore—is mediated by local water column density structure and background currents set by the previous shoaling internal waves, highlighting the importance of wave‐wave interactions in nearshore internal wave dynamics.

     
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  8. Abstract

    Circulation patterns over the inner continental shelf can be spatially complex and highly variable in time. However, few studies have examined alongshore variability over short scales of kilometers or less. To observe inner‐shelf bottom temperatures with high (5‐m) horizontal resolution, a fiber‐optic distributed temperature sensing system was deployed along a 5‐km‐long portion of the 15‐m isobath within a larger‐scale mooring array south of Martha's Vineyard, MA. Over the span of 4 months, variability at a range of scales was observed along the cable over time periods of less than a day. Notably, rapid cooling events propagated down the cable away from a tidal mixing front, showing that propagating fronts on the inner shelf can be generated locally near shallow bathymetric features in addition to remote offshore locations. Propagation velocities of observed fronts were influenced by background tidal currents in the alongshore component and show a weak correlation with theoretical gravity current speeds in the cross‐shore component. These events provide a source of cold, dense water into the inner shelf. However, differences in the magnitude and frequency of cooling events at sites separated by a few kilometers in the alongshore direction suggest that the characteristics of small‐scale variability can vary dramatically and can result in differential fluxes of water, heat, and other tracers. Thus, under stratified conditions, prolonged subsurface observations with high spatial and temporal resolution are needed to characterize the implications of three‐dimensional circulation patterns on exchange, especially in regions where the coastline and isobaths are not straight.

     
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  9. Abstract

    Ploidy level in plants may influence ecological functioning, demography and response to climate change. However, measuring ploidy level typically requires intensive cell or molecular methods.

    We map ploidy level variation in quaking aspen, a dominant North American tree species that can be diploid or triploid and that grows in spatially extensive clones. We identify the predictors and spatial scale of ploidy level variation using a combination of genetic and ground‐based and airborne remote sensing methods.

    We show that ground‐based leaf spectra and airborne canopy spectra can both classify aspen by ploidy level with a precision‐recall harmonic mean of 0.75–0.95 and Cohen's kappa ofc.0.6–0.9. Ground‐based bark spectra cannot classify ploidy level better than chance. We also found that diploids are more common on higher elevation and steeper sites in a network of forest plots in Colorado, and that ploidy level distribution varies at subkilometer spatial scales.

    Synthesis. Our proof‐of‐concept study shows that remote sensing of ploidy level could become feasible in this tree species. Mapping ploidy level across landscapes could provide insights into the genetic basis of species' responses to climate change.

     
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  10. Abstract Stable boundary layers are still a relatively problematic component of atmospheric modeling, despite their frequent occurrence. While general agreement exists that Monin-Obukhov similarity is not applicable in the stable boundary layer (SBL) due to the non-homogeneous, non-stationary flow, no universal organizing theory for the surface SBL has been presented. The SAVANT (Stable Atmospheric Variability ANd Transport) field campaign took place in the fall of 2018 to explore under what conditions shallow drainage flow is generated. The campaign took place in an agricultural setting and covered the period of both pre- and post-harvest, allowing for not only a basic exploration of the boundary layer but a robust data set for applied agricultural understanding of aerosol dispersion, and impacts of changes in surface cover on drainage flows. This article provides a description of the field campaign. Examples of publicly available data products are presented, as well as examples of shallow drainage flow and corresponding lidar measurements of dispersion. Additionally, the field campaign was used to provide educational opportunities for students from several disciplines and the outcomes of these joint educational ventures are discussed as models for future collaborations. 
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