An Overview of the Use of the SimSphere Soil Vegetation Atmosphere Transfer (SVAT) Model for the Study of Land-Atmosphere Interactions

Soil Vegetation Atmosphere Transfer (SVAT) models consist of deterministic mathematical representations of the physical processes involved between the land surface and the atmosphere and of their interactions, at time-steps acceptable for the study of land surface processes. The present article provides a comprehensive and systematic review of one such SVAT model suitable for use in mesoscale or boundary layer studies, originally developed by [1]. This model, which has evolved significantly both architecturally and functionally since its foundation, has been widely applied in over thirty interdisciplinary science investigations, and it is currently used as a learning resource for students in a number of educational institutes globally. The present review is also regarded as very timely, since a variation of a method using this specific SVAT model along with satellite observations is currently being considered in a scheme being developed for the operational retrieval of soil surface moisture by the US National Polar-orbiting Operational Environmental Satellite System (NPOESS), in a series of satellites that are due to be launched from 2016 onwards

New fire diurnal cycle characterizations to improve fire radiative energy assessments made from low-Earth orbit satellites sampling

Accurate near real time fire emissions estimates are required for air quality forecasts. To date, most approaches are based on satellite-derived estimates of fire radiative power (FRP), which can be converted to fire radiative energy (FRE) which is directly related to fire emissions. Uncertainties in these FRE estimations are often substantial. This is for a large part because the most often used low-Earth orbit satellite-based instruments like the MODerate-resolution Imaging Spectroradiometer (MODIS) have a relatively poor sampling of the usually pronounced fire diurnal cycle. In this paper we explore the spatial variation of this fire diurnal cycle and its drivers. Specifically, we assess how representing the fire diurnal cycle affects FRP and FRE estimations when using data collected at MODIS overpasses. Using data assimilation we explored three different methods to estimate hourly FRE, based on an incremental sophistication of parameterizing the fire diurnal cycle. We sampled data from the geostationary Meteosat Spinning Enhanced Visible and Infrared Imager (SEVIRI) at MODIS detection opportunities to drive the three approaches. The full SEVIRI time-series, providing full coverage of the diurnal cycle, were used to evaluate the results. Our study period comprised three years (2010–2012), and we focussed on Africa and the Mediterranean basin to avoid the use of potentially lower quality SEVIRI data obtained at very far off-nadir view angles. We found that the fire diurnal cycle varies substantially over the study region, and depends on both fuel and weather conditions. For example, more "intense" fires characterized by a fire diurnal cycle with high peak fire activity, long duration over the day, and with nighttime fire activity are most common in areas of large fire size (i.e., large burned area per fire event). These areas are most prevalent in relatively arid regions. Ignoring the fire diurnal cycle as done currently in some approaches caused structural errors, while generally overestimating FRE. Including information on the climatology of the fire diurnal cycle provided the most promising avenue to improve FRE estimations. This approach also improved the performance on relatively high spatiotemporal resolutions, although only when aggregating model results to coarser spatial and/or temporal scale good correlation was found with the full SEVIRI hourly reference dataset. In general model performance was best in areas of frequent fire and low errors of omission. We recommend the use of regionally varying fire diurnal cycle information within the Global Fire Assimilation System (GFAS) used in the Copernicus Atmosphere Monitoring Services, which will improve FRE estimates and may allow for further reconciliation of biomass burning emission estimates from different inventories

Quantifying pyroconvective injection heights using observations of fire energy: sensitivity of space-borne observations of carbon monoxide

We use observations of active fire area and fire radiative power (FRP) from the NASA Moderate Resolution Imaging Spectroradiometers (MODIS), together with a parameterized plume rise model, to estimate biomass burning injection heights during 2006. We use these injection heights in the GEOS-Chem (Goddard Earth Observing System Chemistry) atmospheric chemistry transport model to vertically distribute biomass burning emissions of carbon monoxide (CO) and to study the resulting atmospheric distribution. For 2006, we use over half a million FRP and fire area observations as input to the plume rise model. We find that convective heat fluxes and active fire area typically lie in the range of 1–100 kW m−2 and 0.001–100 ha, respectively, although in rare circumstances the convective heat flux can exceed 500 kW m−2. The resulting injection heights have a skewed probability distribution with approximately 80% of the injections remaining within the local boundary layer (BL), with occasional injection height exceeding 8 km. We do not find a strong correlation between the FRP-inferred surface convective heat flux and the resulting injection height, with environmental conditions often acting as a barrier to rapid vertical mixing even where the convective heat flux and active fire area are large. We also do not find a robust relationship between the underlying burnt vegetation type and the injection height. We find that CO columns calculated using the MODIS-inferred injection height (MODIS-INJ) are typically −9 to +6% different to the control calculation in which emissions are emitted into the BL, with differences typically largest over the point of emission. After applying MOPITT (Measurement of Pollution in the Troposphere) v5 scene-dependent averaging kernels we find that we are much less sensitive to our choice of injection height profile. The differences between the MOPITT and the model CO columns (max bias ~ 50%), due largely to uncertainties in emission inventories, are much larger than those introduced by the injection heights. We show that including a realistic diurnal variation in FRP (peaking in the afternoon) or accounting for subgrid-scale emission errors does not alter our main conclusions. Finally, we use a Bayesian maximum a posteriori approach constrained by MOPITT CO profiles to estimate the CO emissions but because of the inherent bias between model and MOPITT we find little impact on the resulting emission estimates. Studying the role of pyroconvection in the distribution of gases and particles in the atmosphere using global MOPITT CO observations (or any current spaceborne measurement of the atmosphere) is still associated with large errors, with the exception of a small subset of large fires and favourable environmental conditions, which will consequently lead to a bias in any analysis on a global scale

Mutations of the BRAF gene in human cancer

Cancers arise owing to the accumulation of mutations in critical genes that alter normal programmes of cell proliferation, differentiation and death. As the first stage of a systematic genome-wide screen for these genes, we have prioritized for analysis signalling pathways in which at least one gene is mutated in human cancer. The RAS RAF MEK ERK MAP kinase pathway mediates cellular responses to growth signals. RAS is mutated to an oncogenic form in about 15% of human cancer. The three RAF genes code for cytoplasmic serine/threonine kinases that are regulated by binding RAS. Here we report BRAF somatic missense mutations in 66% of malignant melanomas and at lower frequency in a wide range of human cancers. All mutations are within the kinase domain, with a single substitution (V599E) accounting for 80%. Mutated BRAF proteins have elevated kinase activity and are transforming in NIH3T3 cells. Furthermore, RAS function is not required for the growth of cancer cell lines with the V599E mutation. As BRAF is a serine/threonine kinase that is commonly activated by somatic point mutation in human cancer, it may provide new therapeutic opportunities in malignant melanoma

Fine sediment reduces vertical migrations of Gammarus pulex (Crustacea: Amphipoda) in response to surface water loss

Surface and subsurface sediments in river ecosystems are recognized as refuges that may promote invertebrate survival during disturbances such as floods and streambed drying. Refuge use is spatiotemporally variable, with environmental factors including substrate composition, in particular the proportion of fine sediment (FS), affecting the ability of organisms to move through interstitial spaces. We conducted a laboratory experiment to examine the effects of FS on the movement of Gammarus pulex Linnaeus (Crustacea: Amphipoda) into subsurface sediments in response to surface water loss. We hypothesized that increasing volumes of FS would impede and ultimately prevent individuals from migrating into the sediments. To test this hypothesis, the proportion of FS (1–2 mm diameter) present within an open gravel matrix (4–16 mm diameter) was varied from 10 to 20% by volume in 2.5% increments. Under control conditions (0% FS), 93% of individuals moved into subsurface sediments as the water level was reduced. The proportion of individuals moving into the subsurface decreased to 74% at 10% FS, and at 20% FS no individuals entered the sediments, supporting our hypothesis. These results demonstrate the importance of reducing FS inputs into river ecosystems and restoring FS-clogged riverbeds, to promote refuge use during increasingly common instream disturbances