Characterising errors in airborne laser altimetry data to extract soil roughness

Airborne laser altimetry has the potential to make frequent detailed observations that are important for many aspects of studying land surface processes. However, the uncertainties inherent in airborne laser altimetry data have rarely been well measured. Uncertainty is often specified as generally as 20cm in elevation, and 40cm planimetric. To better constrain these uncertainties, we present an analysis of several datasets acquired specifically to study the temporal consistency of laser altimetry data, and thus assess its operational value. The error budget has three main components, each with a time regime. For measurements acquired less than 50ms apart, elevations have a local standard deviation in height of 3.5cm, enabling the local measurement of surface roughness of the order of 5cm. Points acquired seconds apart acquire an additional random error due to Differential Geographic Positioning System (DGPS) fluctuation. Measurements made up to an hour apart show an elevation drift of 7cm over a half hour. Over months, this drift gives rise to a random elevation offset between swathes, with an average of 6.4cm. The RMS planimetric error in point location was derived as 37.4cm. We conclude by considering the consequences of these uncertainties on the principle application of laser altimetry in the UK, intertidal zone monitoring.

Using scenarios to explore UK upland futures

Uplands around the world are facing significant social, economic and environmental changes, and decision-makers need to better understand what the future may hold if they are to adapt and maintain upland goods and services. This paper draws together all major research comprising eight studies that have used scenarios to describe possible futures for UK uplands. The paper evaluates which scenarios are perceived by stakeholders to be most likely and desirable, and assesses the benefits and drawbacks of the scenario methods used in UK uplands to date. Stakeholders agreed that the most desirable and likely scenario would be a continuation of hill farming (albeit at reduced levels) based on cross-compliance with environmental measures. The least desirable scenario is a withdrawal of government financial support for hill farming. Although this was deemed by stakeholders to be the least likely scenario, the loss of government support warrants close attention due to its potential implications for the local economy. Stakeholders noted that the environmental implications of this scenario are much less clear-cut. As such, there is an urgent need to understand the full implications of this scenario, so that upland stakeholders can adequately prepare, and policy-makers can better evaluate the likely implications of different policy options. The paper concludes that in future, upland scenario research needs to: (1) better integrate in-depth and representative participation from stakeholders during both scenario development and evaluation; and (2) make more effective use of visualisation techniques and simulation models. (C) 2009 Elsevier Ltd. All rights reserved.

Burkholderia Hep_Hag autotransporter (BuHA) proteins elicit a strong antibody response during experimental glanders but not human melioidosis

BACKGROUND: The bacterial biothreat agents Burkholderia mallei and Burkholderia pseudomallei are the cause of glanders and melioidosis, respectively. Genomic and epidemiological studies have shown that B. mallei is a recently emerged, host restricted clone of B. pseudomallei. RESULTS: Using bacteriophage-mediated immunoscreening we identified genes expressed in vivo during experimental equine glanders infection. A family of immunodominant antigens were identified that share protein domain architectures with hemagglutinins and invasins. These have been designated Burkholderia Hep_Hag autotransporter (BuHA) proteins. A total of 110/207 positive clones (53%) of a B. mallei expression library screened with sera from two infected horses belonged to this family. This contrasted with 6/189 positive clones (3%) of a B. pseudomallei expression library screened with serum from 21 patients with culture-proven melioidosis. CONCLUSION: Members of the BuHA proteins are found in other Gram-negative bacteria and have been shown to have important roles related to virulence. Compared with other bacterial species, the genomes of both B. mallei and B. pseudomallei contain a relative abundance of this family of proteins. The domain structures of these proteins suggest that they function as multimeric surface proteins that modulate interactions of the cell with the host and environment. Their effect on the cellular immune response to B. mallei and their potential as diagnostics for glanders requires further study.

Interpretation of recommended risk terms: differences between doctors and lay people

Objectives: To examine doctors' (Experiment 1) and doctors' and lay people's (Experiment 2) interpretations of two sets of recommended verbal labels for conveying information about side effects incidence rates. Method: Both studies used a controlled empirical methodology in which participants were presented with a hypothetical, but realistic, scenario involving a prescribed medication that was said to be associated with either mild or severe side effects. The probability of each side effect was described using one of the five descriptors advocated by the European Union (Experiment 1) or one of the six descriptors advocated in Calman's risk scale (Experiment 2), and study participants were required to estimate (numerically) the probability of each side effect occurring. Key findings: Experiment 1 showed that the doctors significantly overestimated the risk of side effects occurring when interpreting the five EU descriptors, compared with the assigned probability ranges. Experiment 2 showed that both groups significantly overestimated risk when given the six Calman descriptors, although the degree of overestimation was not as great for the doctors as for the lay people. Conclusion: On the basis of our findings, we argue that we are still a long way from achieving a standardised language of risk for use by both professionals and the general public, although there might be more potential for use of standardised terms among professionals. In the meantime, the EU and other regulatory bodies and health professionals should be very cautious about advocating the use of particular verbal labels for describing medication side effects.

Historical and idealized climate model experiments: an intercomparison of Earth system models of intermediate complexity

Both historical and idealized climate model experiments are performed with a variety of Earth system models of intermediate complexity (EMICs) as part of a community contribution to the Intergovernmental Panel on Climate Change Fifth Assessment Report. Historical simulations start at 850 CE and continue through to 2005. The standard simulations include changes in forcing from solar luminosity, Earth's orbital configuration, CO2, additional greenhouse gases, land use, and sulphate and volcanic aerosols. In spite of very different modelled pre-industrial global surface air temperatures, overall 20th century trends in surface air temperature and carbon uptake are reasonably well simulated when compared to observed trends. Land carbon fluxes show much more variation between models than ocean carbon fluxes, and recent land fluxes appear to be slightly underestimated. It is possible that recent modelled climate trends or climate–carbon feedbacks are overestimated resulting in too much land carbon loss or that carbon uptake due to CO2 and/or nitrogen fertilization is underestimated. Several one thousand year long, idealized, 2 × and 4 × CO2 experiments are used to quantify standard model characteristics, including transient and equilibrium climate sensitivities, and climate–carbon feedbacks. The values from EMICs generally fall within the range given by general circulation models. Seven additional historical simulations, each including a single specified forcing, are used to assess the contributions of different climate forcings to the overall climate and carbon cycle response. The response of surface air temperature is the linear sum of the individual forcings, while the carbon cycle response shows a non-linear interaction between land-use change and CO2 forcings for some models. Finally, the preindustrial portions of the last millennium simulations are used to assess historical model carbon-climate feedbacks. Given the specified forcing, there is a tendency for the EMICs to underestimate the drop in surface air temperature and CO2 between the Medieval Climate Anomaly and the Little Ice Age estimated from palaeoclimate reconstructions. This in turn could be a result of unforced variability within the climate system, uncertainty in the reconstructions of temperature and CO2, errors in the reconstructions of forcing used to drive the models, or the incomplete representation of certain processes within the models. Given the forcing datasets used in this study, the models calculate significant land-use emissions over the pre-industrial period. This implies that land-use emissions might need to be taken into account, when making estimates of climate–carbon feedbacks from palaeoclimate reconstructions.

Interhemispheric coupling, the West Antarctic Ice Sheet and warm Antarctic interglacials

Ice core evidence indicates that even though atmospheric CO2 concentrations did not exceed ~300 ppm at any point during the last 800 000 years, East Antarctica was at least ~3–4 °C warmer than preindustrial (CO2~280 ppm) in each of the last four interglacials. During the previous three interglacials, this anomalous warming was short lived (~3000 years) and apparently occurred before the completion of Northern Hemisphere deglaciation. Hereafter, we refer to these periods as "Warmer than Present Transients" (WPTs). We present a series of experiments to investigate the impact of deglacial meltwater on the Atlantic Meridional Overturning Circulation (AMOC) and Antarctic temperature. It is well known that a slowed AMOC would increase southern sea surface temperature (SST) through the bipolar seesaw and observational data suggests that the AMOC remained weak throughout the terminations preceding WPTs, strengthening rapidly at a time which coincides closely with peak Antarctic temperature. We present two 800 kyr transient simulations using the Intermediate Complexity model GENIE-1 which demonstrate that meltwater forcing generates transient southern warming that is consistent with the timing of WPTs, but is not sufficient (in this single parameterisation) to reproduce the magnitude of observed warmth. In order to investigate model and boundary condition uncertainty, we present three ensembles of transient GENIE-1 simulations across Termination II (135 000 to 124 000 BP) and three snapshot HadCM3 simulations at 130 000 BP. Only with consideration of the possible feedback of West Antarctic Ice Sheet (WAIS) retreat does it become possible to simulate the magnitude of observed warming.

The Mid-Brunhes Event and West Antarctic ice sheet stability

The complex cyclical nature of Pleistocene climate, driven by the evolving orbital configuration of the Earth, is well known but not well understood. A major climatic transition took place at the Mid-Brunhes Event (MBE), ca. 430 ka ago after which the amplitude of the ca.100 ka climate oscillations increased, with substantially warmer interglacials, including periods warmer than present. Recent modelling has indicated that while the timing of these warmer-than-present transient (WPT) events is consistent with southern warming due to a deglaciation-forced slowdown of the Atlantic Meridional Overturning Circulation, the magnitude of warming requires a local amplification, for which a candidate is the feedback of significant West Antarctic Ice Sheet (WAIS) retreat. We here extend this argument, based on the absence of WPTs in the early ice core record (450–800 ka ago), to hypothesize that the MBE could be a manifestation of decreased WAIS stability, triggered by ongoing subglacial erosion.

An optimized method for the extraction of bacterial mRNA from plant roots infected with Escherichia coli O157:H7

Analysis of microbial gene expression during host colonization provides valuable information on the nature of interaction, beneficial or pathogenic, and the adaptive processes involved. Isolation of bacterial mRNA for in planta analysis can be challenging where host nucleic acid may dominate the preparation, or inhibitory compounds affect downstream analysis, e.g., quantitative reverse transcriptase PCR (qPCR), microarray, or RNA-seq. The goal of this work was to optimize the isolation of bacterial mRNA of food-borne pathogens from living plants. Reported methods for recovery of phytopathogen-infected plant material, using hot phenol extraction and high concentration of bacterial inoculation or large amounts of infected tissues, were found to be inappropriate for plant roots inoculated with Escherichia coli O157:H7. The bacterial RNA yields were too low and increased plant material resulted in a dominance of plant RNA in the sample. To improve the yield of bacterial RNA and reduce the number of plants required, an optimized method was developed which combines bead beating with directed bacterial lysis using SDS and lysozyme. Inhibitory plant compounds, such as phenolics and polysaccharides, were counteracted with the addition of high-molecular-weight polyethylene glycol and hexadecyltrimethyl ammonium bromide. The new method increased the total yield of bacterial mRNA substantially and allowed assessment of gene expression by qPCR. This method can be applied to other bacterial species associated with plant roots, and also in the wider context of food safety.