Total body CD4+ T cell dynamics in treated and untreated SIV infection revealed by in vivo imaging

The peripheral blood represents only a small fraction of the total number of lymphocytes in the body. To develop a more thorough understanding of T cell dynamics, including the effects of SIV/SHIV/HIV infection on immune cell depletion and immune reconstitution following combination antiretroviral therapy (cART), one needs to utilize approaches that allow direct visualization of lymphoid tissues. In the present study, noninvasive in vivo imaging of the CD4+ T cell pool has revealed that the timing of the CD4+ T cell pool reconstitution following initiation of ART in SIV-infected nonhuman primates (NHPs) appears seemingly stochastic among clusters of lymph nodes within the same host. At 4 weeks following initiation or interruption of cART, the changes observed in peripheral blood (PB) are primarily related to changes in the whole-body CD4 pool rather than changes in lymphocyte trafficking. Lymph node CD4 pools in long-term antiretroviral-treated and plasma viral load-suppressed hosts appear suboptimally reconstituted compared with healthy controls, while splenic CD4 pools appear similar between the 2 groups

Substantial hysteresis in emergent temperature sensitivity of global wetland CH4 emissions

Wetland methane (CH4) emissions (FCH4) are important in global carbon budgets and climate change assessments. Currently, FCH4 projections rely on prescribed static temperature sensitivity that varies among biogeochemical models. Meta-analyses have proposed a consistent FCH4 temperature dependence across spatial scales for use in models; however, site-level studies demonstrate that FCH4 are often controlled by factors beyond temperature. Here, we evaluate the relationship between FCH4 and temperature using observations from the FLUXNET-CH4 database. Measurements collected across the globe show substantial seasonal hysteresis between FCH4 and temperature, suggesting larger FCH4 sensitivity to temperature later in the frost-free season (about 77% of site-years). Results derived from a machine-learning model and several regression models highlight the importance of representing the large spatial and temporal variability within site-years and ecosystem types. Mechanistic advancements in biogeochemical model parameterization and detailed measurements in factors modulating CH4 production are thus needed to improve global CH4 budget assessments. Wetland methane emissions contribute to global warming, and are oversimplified in climate models. Here the authors use eddy covariance measurements from 48 global sites to demonstrate seasonal hysteresis in methane-temperature relationships and suggest the importance of microbial processes.Peer reviewe

The design and evaluation of three "stream simulation" culverts in south central Oregon

Three culverts, judged to be fish barriers, were replaced with "stream simulation" culverts on the Fremont National Forest of south central Oregon. The culvert sites are located in the Fort Rock Basin in streams that are home to resident Great Basin redband trout (Oncorhynchus mykiss). Great Basin redband trout is the common name for the native trout in the Great Basin and is informally recognized as O.m. newberrii. The design process is discussed and documented for the three culvert replacements. The fish passage conditions in the new culverts were compared to the old culverts both quantitatively and qualitatively. One assumption with stream simulation culverts is that fish will be able to move through a culvert if the flow conditions are similar to that of the natural channel. Velocity measurements and channel characteristics were compared between the natural stream and the culvert. The comparisons were used to define whether similarity was achieved between the culvert and the natural stream. Velocity and channel characteristic measurements were taken during one discharge condition of spring snowmelt, the migration period for spawning redband trout. The comparisons were further examined to determine which would be appropriate metrics in the determination of success or failure of the installation. Channel stability was quantified at each culvert through three systems of channel stability measurements. Regional design guidelines were found to lack information regarding the invert elevation placement for designing a stream simulation culvert. Invert placement is likely to be critical in terms of permanence of placed streambed material in a culvert. There was a qualitative and quantitative improvement of flow conditions at the replacement culverts over the old culverts. All new culverts satisfied the regulatory criteria for fish passage. Two of the three culverts appeared to be similar to the natural stream when comparing similar habitat unit types. The comparisons at the third culvert site were statistically different from the natural stream. The differences may be attributed to the narrow low flow channel that existed through the culvert. Longitudinal thalweg velocity, cross-sectional velocity, and thalweg velocity distribution comparisons between the culvert and the natural stream appear to be appropriate metrics in the determination of success or failure of stream simulation culverts. Streambed material in the culverts exhibited limited evidence of movement after a minimal spring snowrnelt discharge. Stability of streambed material in the culverts at higher discharges was not tested

An assessment of measurements and modeling of turbulent fluxes over snow by eddy covariance at two complex mountain sites /by Michele L. Reba.

Snow is a major component of the annual water balance in many locations across the globe, including the mountainous regions of the interior western U.S. and Canada. As water is scarce and over-allocated in many parts of this region, it is of the utmost importance to accurately model the amount and timing of spring runoff. Most components of snow cover energy and mass balance models are validated through direct measurements such as snow water equivalent, density, temperature, and net radiation. However, validation data for turbulent fluxes are generally limited. Eddy covariance (EC) is the most direct method to measure turbulent fluxes. Findings from this research are based on EC and meteorological measurements from two mountain sites, a wind-exposed and a sheltered sub-canopy, during the 2004, 2005, and 2006 snow seasons.;EC systems have been used successfully over snow in mountain regions but detailed analysis of post-processing and data quality is lacking. The first component of this research focuses on the viability of EC technology over snow in mountainous terrain and makes a detailed analysis of data quality and the influence post-processing has on turbulent fluxes. Post-processing and data quality analysis of these data indicate that application of EC-technology at these sites was viable and data quality parameters were comparable to other reported eddy flux research.;As detailed analysis of site characteristics on EC measurements over snow is limited, this research then generalizes findings at two contrasting sites and highlights the challenges of measuring EC over snow. The exposed site yielded measured sensible and latent heat fluxes that were respectively five and two times the magnitude of those at the sheltered site. There was less inter-annual variability in EC-measured turbulent fluxes at the sheltered compared to the exposed site. Differences between sites are explored at seasonal, monthly and event based temporal scales. These findings highlight the importance of careful review of over-snow EC-measured fluxes and the meteorological conditions during which those measurements were conducted.;Improved modeling of the snow cover that is based on physical processes instead of on empirical relationships between climate and snowcover dynamics should better predict responses to climatic variability and trends. Measured turbulent fluxes are used to determine key model parameters and update the stability functions of an existing snow cover and energy balance model to improve simulated latent heat flux while retaining accuracy in simulating snow water equivalent. The adjustable parameters of roughness length and active layer depth influenced the accuracy with which the model simulated mass and latent heat flux. At the exposed site shorter roughness lengths and a thicker active layer was optimal, while longer roughness lengths and a thinner active layer was optimal at the sheltered site. These outcomes are related to the site characteristics and can be readily incorporated into a distributed snowmelt model.Thesis (Ph. D., Civil Engineering)--University of Idaho, December 2008

Residual herbicide concentrations in on-farm water storage–tailwater recovery systems: Preliminary assessment

On-farm water storage–tailwater recovery systems reduce groundwater usage and intercept agrochemical loads, but pesticide residue dynamics in these systems are not well understood. This study monitored concentrations of seven herbicides in seven northeast Arkansas tailwater recovery systems (April 2017–March 2018). Clomazone, glyphosate, metolachlor, and quinclorac were frequently detected, with minimal detections of 2,4-D, dicamba, and propanil. Concentrations peaked during the growing season (1 Apr.–15 Sept.), reflecting an interaction of application and precipitation. Clomazone, glyphosate, and quinclorac concentrations were greater in ditches (\u3c0.80–67, \u3c0.50–6.2, and \u3c0.40–62 μg L−1, respectively) than in the associated reservoir (\u3c0.80–6.0, \u3c0.50–4.1, and \u3c0.40–6.0 μg L−1, respectively), but metolachlor concentrations were not different between structure types (maximum 22–32 μg L−1). Off-season concentrations were mostly below detection, except for quinclorac. Cycling recovered tailwater through the system and irrigating from reservoirs may minimize risk of cross-crop contaminations with residual herbicides. Managed groundwater recharge should use reservoir water during winter to protect groundwater quality

Estimating surface sublimation losses from snowpacks in a mountain catchment using eddy covariance method and turbulent transfer calculations. Hydrological Processes

Abstract: Sublimation is a critical component of the snow cover mass balance. Although sublimation can be directly measured using eddy covariance (EC), such measurements are relatively uncommon in complex mountainous environments. The EC measurements of surface snowpack sublimation from three consecutive winter seasons (2004, 2005 and 2006) at a wind-exposed and wind-sheltered site were analysed to characterise sublimation in mountainous terrain. During the 2006 snow season, snow surface and near-surface air temperature, humidity and wind were also measured, permitting the calculation of sublimation rates and a comparison with EC measurements. This comparison showed that measured and simulated sublimation was very similar at the exposed site but less so at the sheltered site. Wind speeds at the exposed site were nearly four times than that at the sheltered site, and the exposed site yielded measured sublimation that was two times the magnitude of that at the sheltered site. The time variation of measured sublimation showed diurnal increases in the early afternoon and increased rates overall as the snow season progressed. Measured mean daily sublimation rates were 0.39 and 0.15 mm day À1 at the exposed and sheltered sites, respectively. At the exposed site, measured sublimation accounted for 16% and 41% of the maximum snow accumulation in 2006 and 2005, respectively. At the sheltered site, measured seasonal sublimation was approximately 4% in 2004 and 2006 and 8% in 2005 of the maximum snow water equivalent. Simulated sublimation was only available for 2006 and suggested smaller but comparable percentages to the sublimation estimated from observations. At the exposed site, a total of 42 mm sublimated for the snow season, which constituted 12% of the maximum accumulation. At the sheltered site, 17 mm (2.2% of maximum accumulation) was sublimated over the snow season

A new free-convection form to estimate sensible heat and latent heat fluxes for unstable cases

Free convection limit (FCL) approaches to estimate surface fluxes are of interest given the evidence that they may extend up to near neutral stability conditions. For measurements taken in the inertial sublayer, the formulation based on surface renewal theory and the analysis of small eddies (SRSE) to estimate the sensible heat flux (H) was extended to latent heat flux (LE) with the aim to derive their FCL approaches. For sensible heat flux (HFCL), the input requirements are traces of the fast-response (such as 10–20 Hz) air temperature and the zero-plane displacement. For latent heat flux (LEFCL), input requirements are fast response traces of water vapor density, mean temperature of the air, the available net surface energy (Rn-G, where Rn and G are the net radiation and soil heat flux, respectively) and the zero-plane displacement. Taking eddy covariance (EC) as a reference method, the performance of the FCL method was tested over a growing cotton field that involved three contrasting surfaces: partly mulched bare soil, a sparse canopy and a homogeneous canopy. Using traces at 10 Hz and 20 Hz, HFCL overestimated and underestimated the EC sensible heat flux (HEC), respectively. In general, LEFCL tended to slightly underestimate LEEC. The surface energy balance closure show that (HEC + LEEC) underestimated (Rn-G) in a range of 19% (homogeneous canopy) and 8% (sparse canopy). Given that, in general (HFCL + LEFCL) was closer to (Rn-G) than (HEC + LEEC), the FCL method may be recommended for field applications, especially when the wind speed is not available

Friction-Velocity Estimates Using the Trace of a Scalar and the Mean Wind Speed

A semi-empirical approach based on surface-renewal theory for estimating the friction velocity is tested for measurements taken in the inertial sublayer. For unstable cases, the input requirements are the mean wind speed and the high-frequency trace (10 or 20 Hz) of the air or sonic temperature. The method has been extended to traces of water vapour (H2O) and carbon dioxide (CO2) concentrations. For stable cases, the stability parameter must also be considered. The method’s performance, taking the direct friction velocity measured by sonic anemometry as a reference, was tested over a growing cotton field that included bare soil with some crop residues at the beginning of the season. In general, the proposed friction-velocity estimates are reliable. For unstable cases, the method shows the potential to outperform the wind logarithmic-law computation. Discarding cases with low wind speeds (e.g., \u3c 0.3 m s−1 and mean wind shear \u3c 1 Hz), the proposed approach may be recommended as an alternative method to estimating the friction velocity. There is the potential, based on the input requirements, that the proposed formulation may offer significant advantages in the estimation of the friction velocity in some marine environments

Automated mapping of rice fields using multi-year training sample normalization

Rice agriculture is of great ecological, environmental, and socioeconomic importance in the Lower Mississippi Alluvial Valley, as its distribution and size heavily impact food production and a number of ecosystem services. Long-term rice mapping is challenging as a result of insufficient training data – both in spatial amount and in temporal coverage, the high cost of powerful geospatial data processing platforms, and incomplete image coverage during the critical window to capture the unique rice signals. Here, we developed a simple yet effective method for rice field extraction without heavy reliance on the complete profiles of Landsat time series or repeated training data. The core is a multiple-year training sample normalization that extends the samples obtained in one year for classification in another year. Pseudo-invariant objects and a set of linear regressions were used to predict what the given vegetation index values of training samples would be if they had been acquired under the same conditions in a different mapping year. The generated pseudo training samples were further utilized to classify the mapping image. We experimented with four years’ Landsat Thematic Mapper and Operational Land Imager data and achieved comparable accuracies as the single-year classification. Because of its simplicity and low computational requirements, it can be efficiently implemented on cloud computing platforms, such as Google Earth Engine platform. This technique provides an affordable and effective solution to derive crop distribution information on a large-scale basis

Assessing the methane mitigation potential of innovative management in US rice production

Rice is an important global crop while also contributing significant anthropogenic methane (CH _4 ) emissions. To support the future of rice production, more information is needed on the impacts of sustainability-driven management used to grow rice with lower associated methane emissions. Recent support for the impacts of different growing practices in the US has prompted the application of a regional methodology (Tier 2) to estimate methane emissions in different rice growing regions. The methodology estimates rice methane emissions from the US Mid-South (MdS) and California (Cal) using region-specific scaling factors applied to a region-specific baseline flux. In our study, we leverage land cover data and soil clay content to estimate methane emissions using this approach, while also examining how changes in common production practices can affect overall emissions in the US. Our results indicated US rice cultivation produced between 0.32 and 0.45 Tg CH _4 annually, which were approximately 7% and 42% lower on average compared to Food and Agriculture Organization of the UN (FAO) and US Environmental Protection Agency (EPA) inventories, respectively. Our estimates were 63% greater on average compared to similar methods that lack regional context. Introducing aeration events into irrigation resulted in the greatest methane reductions across both regions. When accounting for differences between baseline and reduction scenarios, the US MdS typically had higher mitigation potential compared to Cal. The differences in cumulative mitigation potential across the 2008–2020 period were likely driven by lower production area clay content for the US MdS compared to Cal. The added spatial representation in the Tier 2 approach is useful in surveying how impactful methane-reducing practices might be within and across regions