How well does the ECMWF Ensemble Prediction System predict blocking?

Forecasting atmospheric blocking is one of the main problems facing medium-range weather forecasters in the extratropics. The European Centre for Medium-Range Weather Forecasts (ECMWF) Ensemble Prediction System (EPS) provides an excellent basis for medium-range forecasting as it provides a number of different possible realizations of the meteorological future. This ensemble of forecasts attempts to account for uncertainties in both the initial conditions and the model formulation. Since 18 July 2000, routine output from the EPS has included the field of potential temperature on the potential vorticity (PV) D 2 PV units (PVU) surface, the dynamical tropopause. This has enabled the objective identification of blocking using an index based on the reversal of the meridional potential-temperature gradient. A year of EPS probability forecasts of Euro-Atlantic and Pacific blocking have been produced and are assessed in this paper, concentrating on the Euro-Atlantic sector. Standard verification techniques such as Brier scores, Relative Operating Characteristic (ROC) curves and reliability diagrams are used. It is shown that Euro-Atlantic sector-blocking forecasts are skilful relative to climatology out to 10 days, and are more skilful than the deterministic control forecast at all lead times. The EPS is also more skilful than a probabilistic version of this deterministic forecast, though the difference is smaller. In addition, it is shown that the onset of a sector-blocking episode is less well predicted than its decay. As the lead time increases, the probability forecasts tend towards a model climatology with slightly less blocking than is seen in the real atmosphere. This small under-forecasting bias in the blocking forecasts is possibly related to a westerly bias in the ECMWF model. Copyright © 2003 Royal Meteorological Society

North Atlantic Oscillation response to transient greenhouse gas forcing and the impact on European winter climate: a CMIP2 multi-model assessment

This study investigates the response of wintertime North Atlantic Oscillation (NAO) to increasing concentrations of atmospheric carbon dioxide (CO2) as simulated by 18 global coupled general circulation models that participated in phase 2 of the Coupled Model Intercomparison Project (CMIP2). NAO has been assessed in control and transient 80-year simulations produced by each model under constant forcing, and 1% per year increasing concentrations of CO2, respectively. Although generally able to simulate the main features of NAO, the majority of models overestimate the observed mean wintertime NAO index of 8 hPa by 5-10 hPa. Furthermore, none of the models, in either the control or perturbed simulations, are able to reproduce decadal trends as strong as that seen in the observed NAO index from 1970-1995. Of the 15 models able to simulate the NAO pressure dipole, 13 predict a positive increase in NAO with increasing CO2 concentrations. The magnitude of the response is generally small and highly model-dependent, which leads to large uncertainty in multi-model estimates such as the median estimate of 0.0061 +/- 0.0036 hPa per %CO2. Although an increase of 0.61 hPa in NAO for a doubling in CO2 represents only a relatively small shift of 0.18 standard deviations in the probability distribution of winter mean NAO, this can cause large relative increases in the probabilities of extreme values of NAO associated with damaging impacts. Despite the large differences in NAO responses, the models robustly predict similar statistically significant changes in winter mean temperature (warmer over most of Europe) and precipitation (an increase over Northern Europe). Although these changes present a pattern similar to that expected due to an increase in the NAO index, linear regression is used to show that the response is much greater than can be attributed to small increases in NAO. NAO trends are not the key contributor to model-predicted climate change in wintertime mean temperature and precipitation over Europe and the Mediterranean region. However, the models' inability to capture the observed decadal variability in NAO might also signify a major deficiency in their ability to simulate the NAO-related responses to climate change.

Using aircraft measurements to determine the refractive index of Saharan dust during the DODO Experiments

Much uncertainty in the value of the imaginary part of the refractive index of mineral dust contributes to uncertainty in the radiative effect of mineral dust in the atmosphere. A synthesis of optical, chemical and physical in-situ aircraft measurements from the DODO experiments during February and August 2006 are used to calculate the refractive index mineral dust encountered over West Africa. Radiative transfer modeling and measurements of broadband shortwave irradiance at a range of altitudes are used to test and validate these calculations for a specific dust event on 23 August 2006 over Mauritania. Two techniques are used to determine the refractive index: firstly a method combining measurements of scattering, absorption, size distributions and Mie code simulations, and secondly a method using composition measured on filter samples to apportion the content of internally mixed quartz, calcite and iron oxide-clay aggregates, where the iron oxide is represented by either hematite or goethite and clay by either illite or kaolinite. The imaginary part of the refractive index at 550 nm (ni550) is found to range between 0.0001 i to 0.0046 i, and where filter samples are available, agreement between methods is found depending on mineral combination assumed. The refractive indices are also found to agree well with AERONET data where comparisons are possible. ni550 is found to vary with dust source, which is investigated with the NAME model for each case. The relationship between both size distribution and ni550 on the accumulation mode single scattering albedo at 550 nm (ω0550) are examined and size distribution is found to have no correlation to ω0550, while ni550 shows a strong linear relationship with ω0550. Radiative transfer modeling was performed with different models (Mie-derived refractive indices, but also filter sampling composition assuming both internal and external mixing). Our calculations indicate that Mie-derived values of ni550 and the externally mixed dust where the iron oxide-clay aggregate corresponds to the goethite-kaolinite combination result in the best agreement with irradiance measurements. The radiative effect of the dust is found to be very sensitive to the mineral combination (and hence refractive index) assumed, and to whether the dust is assumed to be internally or externally mixed.

Calculating the exclusion probability and paternity index for X-chromosomal loci in the presence of substructure

There has been recent interest in the use of X-chromosomal loci for forensic and relatedness testing casework, with many authors developing new X-linked short tandem repeat (STR) loci suitable for forensic use. Here we present formulae for two key quantities in paternity testing, the average probability of exclusion and the paternity index, which are suitable for Xchromosomal loci in the presence of population substructure.

Revisiting youden’s index as a useful measure of the misclassification error in meta-analysis of diagnostic studies

The paper considers meta-analysis of diagnostic studies that use a continuous score for classification of study participants into healthy or diseased groups. Classification is often done on the basis of a threshold or cut-off value, which might vary between studies. Consequently, conventional meta-analysis methodology focusing solely on separate analysis of sensitivity and specificity might be confounded by a potentially unknown variation of the cut-off value. To cope with this phenomena it is suggested to use, instead, an overall estimate of the misclassification error previously suggested and used as Youden’s index and; furthermore, it is argued that this index is less prone to between-study variation of cut-off values. A simple Mantel–Haenszel estimator as a summary measure of the overall misclassification error is suggested, which adjusts for a potential study effect. The measure of the misclassification error based on Youden’s index is advantageous in that it easily allows an extension to a likelihood approach, which is then able to cope with unobserved heterogeneity via a nonparametric mixture model. All methods are illustrated at hand of an example on a diagnostic meta-analysis on duplex doppler ultrasound, with angiography as the standard for stroke prevention.

The binding site distance test score: a robust method for the assessment of predicted protein binding sites

We propose a novel method for scoring the accuracy of protein binding site predictions – the Binding-site Distance Test (BDT) score. Recently, the Matthews Correlation Coefficient (MCC) has been used to evaluate binding site predictions, both by developers of new methods and by the assessors for the community wide prediction experiment – CASP8. Whilst being a rigorous scoring method, the MCC does not take into account the actual 3D location of the predicted residues from the observed binding site. Thus, an incorrectly predicted site that is nevertheless close to the observed binding site will obtain an identical score to the same number of nonbinding residues predicted at random. The MCC is somewhat affected by the subjectivity of determining observed binding residues and the ambiguity of choosing distance cutoffs. By contrast the BDT method produces continuous scores ranging between 0 and 1, relating to the distance between the predicted and observed residues. Residues predicted close to the binding site will score higher than those more distant, providing a better reflection of the true accuracy of predictions. The CASP8 function predictions were evaluated using both the MCC and BDT methods and the scores were compared. The BDT was found to strongly correlate with the MCC scores whilst also being less susceptible to the subjectivity of defining binding residues. We therefore suggest that this new simple score is a potentially more robust method for future evaluations of protein-ligand binding site predictions.

Measuring productivity growth when technological change is biased - a new index and an application to UK agriculture

Productivity growth is conventionally measured by indices representing discreet approximations of the Divisia TFP index under the assumption that technological change is Hicks-neutral. When this assumption is violated, these indices are no longer meaningful because they conflate the effects of factor accumulation and technological change. We propose a way of adjusting the conventional TFP index that solves this problem. The method adopts a latent variable approach to the measurement of technical change biases that provides a simple means of correcting product and factor shares in the standard Tornqvist-Theil TFP index. An application to UK agriculture over the period 1953-2000 demonstrates that technical progress is strongly biased. The implications of that bias for productivity measurement are shown to be very large, with the conventional TFP index severely underestimating productivity growth. The result is explained primarily by the fact that technological change has favoured the rapidly accumulating factors against labour, the factor leaving the sector. (C) 2004 Elsevier B.V. All rights reserved.

Comparison of methane produced by straw fed sheep in open-circuit respiration with methane predicted by fermentation characteristics measured by an in vitro gas procedure

Reducing carbon conversion of ruminally degraded feed into methane increases feed efficiency and reduces emission of this potent greenhouse gas into the environment. Accurate, yet simple, predictions of methane production of ruminants on any feeding regime are important in the nutrition of ruminants, and in modeling methane produced by them. The current work investigated feed intake, digestibility and methane production by open-circuit respiration measurements in sheep fed 15 untreated, sodium hydroxide (NaOH) treated and anhydrous ammonia (NH3) treated wheat, barley and oat straws. In vitro fermentation characteristics of straws were obtained from incubations using the Hohenheim gas production system that measured gas production, true substrate degradability, short-chain fatty acid production and efficiency of microbial production from the ratio of truly degraded substrate to gas volume. In the 15 straws, organic matter (OM) intake and in vivo OM digestibility ranged from 563 to 1201 g and from 0.464 to 0.643, respectively. Total daily methane production ranged from 13.0 to 34.4 l, whereas methane produced/kg OM matter apparently digested in vivo varied from 35.0 to 61.8 l. The OM intake was positively related to total methane production (R2 = 0.81, P<0.0001), and in vivo OM digestibility was also positively associated with methane production (R2 = 0.67, P<0.001), but negatively associated with methane production/kg digestible OM intake (R2 = 0.61, P<0.001). In the in vitro incubations of the 15 straws, the ratio of acetate to propionate ranged from 2.3 to 2.8 (P<0.05) and efficiencies of microbial production ranged from 0.21 to 0.37 (P<0.05) at half asymptotic gas production. Total daily methane production, calculated from in vitro fermentation characteristics (i.e., true degradability, SCFA ratio and efficiency of microbial production) and OM intake, compared well with methane measured in the open-circuit respiration chamber (y = 2.5 + 0.86x, R2 = 0.89, P<0.0001, Sy.x = 2.3). Methane production from forage fed ruminants can be predicted accurately by simple in vitro incubations combining true substrate degradability and gas volume measurements, if feed intake is known.

A cross-taxonomic index for quantifying the health of farmland biodiversity

P>1. The development of sustainable, multi-functional agricultural systems involves reconciling the needs of agricultural production with the objectives for environmental protection, including biodiversity conservation. However, the definition of sustainability remains ambiguous and it has proven difficult to identify suitable indicators for monitoring progress towards, and the successful achievement of, sustainability. 2. In this study, we show that a trait-based approach can be used to assess the detrimental impacts of agricultural change to a broad range of taxonomic groupings and derive a standardised index of farmland biodiversity health, built around an objective of achieving stable or increasing populations in all species associated with agricultural landscapes. 3. To demonstrate its application, we assess the health of UK farmland biodiversity relative to this goal. Our results suggest that the populations of two-thirds of 333 plant and animal species assessed are unsustainable under current UK agricultural practices. 4. We then explore the potential benefits of an agri-environment scheme, Entry Level Stewardship (ELS), to farmland biodiversity in the UK under differing levels of risk mitigation delivery. We show that ELS has the potential to make a significant contribution to progress towards sustainability targets but that this potential is severely restricted by current patterns of scheme deployment. 5.Synthesis and applications: We have developed a cross-taxonomic sustainability index which can be used to assess both the current health of farmland biodiversity and the impacts of future agricultural changes relative to quantitative biodiversity targets. Although biodiversity conservation is just one of a number of factors that must be considered when defining sustainability, we believe our cross-taxonomic index has the potential to be a valuable tool for guiding the development of sustainable agricultural systems.

The agri-environmental Footprint Index

The Agri-Environmental Footprint project is developing a common methodology for assessing the environmental impact of European agri-environment schemes. The Agri-Environmental Footprint Index (AFI) has been constructed as a customisable approach. It is a farm-level index that aggregates the measurement of agri-environmental indicators. Farm-level impact scores can be aggregated at a regional level to track temporal change and/or to provide comparisons of the success (or otherwise) of an agri-environment scheme.

Conceptual development of a harmonised method for tracking change and evaluating policy in the agri-environment: The Agri-environmental Footprint Index

An aggregated farm-level index, the Agri-environmental Footprint Index (AFI), based on multiple criteria methods and representing a harmonised approach to evaluation of EU agri-environmental schemes is described. The index uses a common framework for the design and evaluation of policy that can be customised to locally relevant agri-environmental issues and circumstances. Evaluation can be strictly policy-focused, or broader and more holistic in that context-relevant assessment criteria that are not necessarily considered in the evaluated policy can nevertheless be incorporated. The Index structure is flexible, and can respond to diverse local needs. The process of Index construction is interactive, engaging farmers and other relevant stakeholders in a transparent decision-making process that can ensure acceptance of the outcome, help to forge an improved understanding of local agri-environmental priorities and potentially increase awareness of the critical role of farmers in environmental management. The structure of the AFI facilitates post-evaluation analysis of relative performance in different dimensions of the agri-environment, permitting identification of current strengths and weaknesses, and enabling future improvement in policy design. Quantification of the environmental impact of agriculture beyond the stated aims of policy using an 'unweighted' form of the AFI has potential as the basis of an ongoing system of environmental audit within a specified agricultural context. (C) 2009 Elsevier Ltd. All rights reserved.

The effects of triazole and strobilurin fungicide programmes on nitrogen uptake, partitioning, remobilization and grain N accumulation in winter wheat cultivars

Field experiments were conducted over 3 years to assess the effect of a triazole fungicide programme, and additions of strobilurin fungicides to it, on nitrogen uptake, accumulation and partitioning in a range of winter wheat cultivars. Commensurate with delayed senescence, fungicide programmes, particularly when including strobilurins, improved grain yield through improvements in both crop biomass and harvest index, although the relationship with green area duration of the flag leaf (GFLAD) depended on year and in some cases, cultivar. In all years fungicide treatments significantly increased the amount of nitrogen in the above-ground biomass, the amount of nitrogen in the grain and the nitrogen harvest index. All these effects could be linearly related to the fungicide effect on GFLAD. These relationships occasionally interacted with cultivar but there was no evidence that fungicide mode of action affected the relationship between GFLAD and yield of nitrogen in the grain. Fungicide treatments significantly reduced the amount of soil mineral N at harvest and when severe disease had been controlled, the net remobilization of N from the vegetation to the grain after anthesis. Fungicide maintained the filling of grain with both dry matter and nitrogen. The proportionate accumulation of nitrogen in the grain was later than that of dry matter and this difference was greater when fungicide had been applied. Effects of fungicide on grain protein concentration and its relationship with GFLAD were inconsistent over year and cultivar. There were several instances where grain protein concentration was unaffected despite large (1(.)5 t/ha) increases in grain yield following fungicide use. Dilution of grain protein concentration following fungicide use, when it did occur, was small compared with what would be predicted by adoption of other yield increasing techniques such as the selection of high yielding cultivars (based on currently available cultivars) or by growing wheat in favourable climates.

A longitudinal study of sero-conversion to tick-borne pathogens in smallholder dairy youngstock in Tanzania

A longitudinal study of sero-conversion of youngstock to the tick-borne pathogens Theileria parva, T mutans, Anaplasma marginale, Babesia bigemina and B. bovis was conducted over two years on smallholder dairy farms in Tanga region, Tanzania. There was evidence of maternal antibodies to all tick-borne pathogens in animals less than 18 weeks of age. Seroprevalence increased as expected with age in animals older than this but seroprevalence profiles underestimated the force of infection due to waning antibody levels between samplings. By the end of the 2-year study, less than 50% of study animals had seroconverted to each of the tick-borne pathogens investigated, consistent with the low levels of tick attachment observed on the study animals. Some associations between seroconversion to tick-borne pathogens, and counts of their known tick vectors on the animals, were identified as expected. However, some were not, suggesting that counts of some tick species may act as an index of rates of attachment of other vector species. Variation in acaricide treatment frequencies was not associated with variations in tick-borne pathogen seroprevalence suggesting that acaricides may be used more frequently than necessary on many farms. Most animals were zero-grazed, a management system associated with a significantly lower likelihood that animals seroconverted to any tick-borne pathogen exceptA. marginale. Seroprevalence varied locally with farm location (particularly for Babesia spp.) but was not well predicted by indices of ecological conditions. Our findings suggest that attempts to achieve a state of 'endemic stability' for tick-bome pathogens may be unreasonable on the smallholder dairy farms studied but reductions in the frequency of use of acaricides may be possible following prospective studies of effects on mortality and morbidity due to tick-bome pathogens. (c) 2005 Elsevier B.V. All rights reserved.