Generation of candidate human influenza vaccine strains in cell culture: rehearsing the European response to an H7N1 pandemic threat

Background: Although H5N1 avian influenza viruses pose the most obvious imminent pandemic threat, there have been several recent zoonotic incidents involving transmission of H7 viruses to humans. Vaccines are the primary public health defense against pandemics, but reliance on embryonated chickens eggs to propagate vaccine and logistic problems posed by the use of new technology may slow our ability to respond rapidly in a pandemic situation. Objectives: We sought to generate an H7 candidate vaccine virus suitable for administration to humans whose generation and amplification avoided the use of eggs. Methods: We generated a suitable H7 vaccine virus by reverse genetics. This virus, known as RD3, comprises the internal genes of A/Puerto Rico/8/34 with surface antigens of the highly pathogenic avian strain A/Chicken/Italy/13474/99 (H7N1). The multi-basic amino acid site in the HA gene, associated with high pathogenicity in chickens, was removed. Results: The HA modification did not alter the antigenicity of the virus and the resultant single basic motif was stably retained following several passages in Vero and PER. C6 cells. RD3 was attenuated for growth in embryonated eggs, chickens, and ferrets. RD3 induced an antibody response in infected animals reactive against both the homologous virus and other H7 influenza viruses associated with recent infection by H7 viruses in humans. Conclusions: This is the first report of a candidate H7 vaccine virus for use in humans generated by reverse genetics and propagated entirely in mammalian tissue culture. The vaccine has potential use against a wide range of H7 strains.

The equatorial response to higher latitude forcing

The classic view, following Charney and Webster and Holton, is that significant midlatitude forcing of the Tropics can be expected only in regions with westerly winds in the upper troposphere because it is only in these regions that stationary Rossby waves will be able to propagate toward the equator. Here it is shown that higherlatitude forcing can project directly onto equatorial waves and give a significant tropical response in both easterly and westerly tropical flow. The equatorial response to higher-latitude forcing is considered in the context of a dry atmosphere and a localized higher-latitude forcing with eastward or westward phase speed. Previous ideas of the Doppler shifting of equatorial waves by zonal flows are extended to include consideration of a forcing involving a range of zonal wavenumbers. A Gill-type model suggests that there can be significant forcing of equatorial waves by either vorticity forcing or heating in higher latitudes. In agreement with the theory, the Kelvin wave response to eastward forcing is peaked at high frequencies/short periods but reduces only slowly with decreasing frequency. Primitive-equation experiments confirm the strong equatorial response associated with a deep Kelvin wave for forcing in midlatitudes. The response is strongest in the Eastern Hemisphere with its equatorial, upper-tropospheric easterlies. The possible importance of this equatorial response in the organization of large-scale, deep tropical convection and the initiation of the Madden–Julian oscillation is discussed. The ability of westward forcing in higher latitudes to trigger Rossby–gravity and Rossby waves is found in the primitive-equation model to be significant but rather less robust. These wave signatures are clearest in the lower troposphere. For shorter periods the Rossby–gravity wave dominates, and for upper-tropospheric forcing, downward and eastward wave activity propagation is seen. Upper-tropospheric westerlies are found to enhance the response.

Coordinated Cluster and ground-based instrument observations of transient changes in the magnetopause boundary layer during an interval of predominantly northward IMF: relation to reconnection pulses and FTE signatures

We study a series of transient entries into the low-latitude boundary layer (LLBL) of all four Cluster spacecraft during an outbound pass through the mid-afternoon magnetopause ([X(GSM), Y(GSM), Z(GSM)] approximate to [2, 7, 9] R(E)). The events take place during an interval of northward IMF, as seen in the data from the ACE satellite and lagged by a propagation delay of 75 min that is well-defined by two separate studies: (1) the magnetospheric variations prior to the northward turning (Lockwood et al., 2001, this issue) and (2) the field clock angle seen by Cluster after it had emerged into the magnetosheath (Opgenoorth et al., 2001, this issue). With an additional lag of 16.5 min, the transient LLBL events cor-relate well with swings of the IMF clock angle (in GSM) to near 90degrees. Most of this additional lag is explained by ground-based observations, which reveal signatures of transient reconnection in the pre-noon sector that then take 10-15 min to propagate eastward to 15 MLT, where they are observed by Cluster. The eastward phase speed of these signatures agrees very well with the motion deduced by the cross-correlation of the signatures seen on the four Cluster spacecraft. The evidence that these events are reconnection pulses includes: transient erosion of the noon 630 nm (cusp/cleft) aurora to lower latitudes; transient and travelling enhancements of the flow into the polar cap, imaged by the AMIE technique; and poleward-moving events moving into the polar cap, seen by the EISCAT Svalbard Radar (ESR). A pass of the DMSP-F15 satellite reveals that the open field lines near noon have been opened for some time: the more recently opened field lines were found closer to dusk where the flow transient and the poleward-moving event intersected the satellite pass. The events at Cluster have ion and electron characteristics predicted and observed by Lockwood and Hapgood (1998) for a Flux Transfer Event (FTE), with allowance for magnetospheric ion reflection at Alfvenic disturbances in the magnetopause reconnection layer. Like FTEs, the events are about 1 R(E) in their direction of motion and show a rise in the magnetic field strength, but unlike FTEs, in general, they show no pressure excess in their core and hence, no characteristic bipolar signature in the boundary-normal component. However, most of the events were observed when the magnetic field was southward, i.e. on the edge of the interior magnetic cusp, or when the field was parallel to the magnetic equatorial plane. Only when the satellite begins to emerge from the exterior boundary (when the field was northward), do the events start to show a pressure excess in their core and the consequent bipolar signature. We identify the events as the first observations of FTEs at middle altitudes.

A multispacecraft analysis of a small-scale transient entrained by solar wind streams

The images taken by the Heliospheric Imagers (HIs), part of the SECCHI imaging package onboard the pair of STEREO spacecraft, provide information on the radial and latitudinal evolution of the plasma compressed inside corotating interaction regions (CIRs). A plasma density wave imaged by the HI instrument onboard STEREO-B was found to propagate towards STEREO-A, enabling a comparison between simultaneous remotesensing and in situ observations of its structure to be performed. In situ measurements made by STEREO-A show that the plasma density wave is associated with the passage of a CIR. The magnetic field compressed after the CIR stream interface (SI) is found to have a planar distribution. Minimum variance analysis of the magnetic field vectors shows that the SI is inclined at 54° to the orbital plane of the STEREO-A spacecraft. This inclination of the CIR SI is comparable to the inclination of the associated plasma density wave observed by HI. A small-scale magnetic cloud with a flux rope topology and radial extent of 0.08 AU is also embedded prior to the SI. The pitch-angle distribution of suprathermal electrons measured by the STEREO-A SWEA instrument shows that an open magnetic field topology in the cloud replaced the heliospheric current sheet locally. These observations confirm that HI observes CIRs in difference images when a small-scale transient is caught up in the compression region.

Tolerance traits and the stability of mutualism

Identifying factors which allow the evolution and persistence of cooperative interactions between species is a fundamental issue in evolutionary ecology. Various hypotheses have been suggested which generally focus on mechanisms that allow cooperative genotypes in different species to maintain interactions over space and time. Here, we emphasise the fact that even within mutualisms (interactions with net positive fitness effects for both partners), there may still be inherent costs, such as the occasional predation by ants upon aphids. Individuals engaged in mutualisms benefit from minimising these costs as long as it is not at the expense of breaking the interspecific interaction, which offers a net positive benefit. The most common and obvious defence traits to minimise interspecific interaction costs are resistance traits, which act to reduce encounter rate between two organisms. Tolerance traits, in contrast, minimise fitness costs to the actor, but without reducing encounter rate. Given that, by definition, it is beneficial to remain in mutualistic interactions, the only viable traits to minimise costs are tolerance-based 'defence' strategies. Thus, we propose that tolerance traits are an important factor promoting stability in mutualisms. Furthermore, because resistance traits tend to propagate coevolutionary arms races between antagonists, whilst tolerance traits do not, we also suggest that tolerance-based defence strategies may be important in facilitating the transition from antagonistic interactions into mutualisms. For example, the mutualism between ants and aphids has been suggested to have evolved from parasitism. We describe how phenotypic plasticity in honeydew production may be a tolerance trait that has prevented escalation into an antagonistic arms race and instead led to mutualistic coevolution.

Equatorial waves in opposite QBO phases

A methodology for identifying equatorial waves is used to analyze the multilevel 40-yr ECMWF Re-Analysis (ERA-40) data for two different years (1992 and 1993) to investigate the behavior of the equatorial waves under opposite phases of the quasi-biennial oscillation (QBO). A comprehensive view of 3D structures and of zonal and vertical propagation of equatorial Kelvin, westward-moving mixed Rossby–gravity (WMRG), and n = 1 Rossby (R1) waves in different QBO phases is presented. Consistent with expectation based on theory, upward-propagating Kelvin waves occur more frequently during the easterly QBO phase than during the westerly QBO phase. However, the westward-moving WMRG and R1 waves show the opposite behavior. The presence of vertically propagating equatorial waves in the stratosphere also depends on the upper tropospheric winds and tropospheric forcing. Typical propagation parameters such as the zonal wavenumber, zonal phase speed, period, vertical wavelength, and vertical group velocity are found. In general, waves in the lower stratosphere have a smaller zonal wavenumber, shorter period, faster phase speed, and shorter vertical wavelength than those in the upper troposphere. All of the waves in the lower stratosphere show an upward group velocity and downward phase speed. When the phase of the QBO is not favorable for waves to propagate, their phase speed in the lower stratosphere is larger and their period is shorter than in the favorable phase, suggesting Doppler shifting by the ambient flow and a filtering of the slow waves. Tropospheric WMRG and R1 waves in the Western Hemisphere also show upward phase speed and downward group velocity, with an indication of their forcing from middle latitudes. Although the waves observed in the lower stratosphere are dominated by “free” waves, there is evidence of some connection with previous tropical convection in the favorable year for the Kelvin waves in the warm water hemisphere and WMRG and R1 waves in the Western Hemisphere, which is suggestive of the importance of convective forcing for the existence of propagating coupled Kelvin waves and midlatitude forcing for the existence of coupled WMRG and R1 waves.

The influence of the QBO on the propagation of equatorial waves into the stratosphere

The variation of stratospheric equatorial wave characteristics with the phase of the quasi-biennial oscillation (QBO) is investigated using ECMWF Re-Analysis and NOAA outgoing longwave radiation (OLR) data. The impact of the QBO phases on the upward propagation of equatorial waves is found to be consistent and significant. In the easterly phase, there is larger Kelvin wave amplitude but smaller westward-moving mixed Rossby–gravity (WMRG) and n = 1 Rossby (R1) wave amplitude due to reduced propagation from the upper troposphere into the lower stratosphere, compared with the westerly phase. Differences in the wave amplitude exist in a deeper layer in summer than in winter, consistent with the seasonality of ambient zonal winds. There is a strong evidence of Kelvin wave amplitude peaking just below the descending westerly phase, suggesting that Kelvin waves act to bring the westerly phase downward. However, the corresponding evidence for WMRG and R1 waves is less clear. In the lower stratosphere there is zonal variation in equatorial waves. This reflects the zonal asymmetry of wave amplitudes in the upper troposphere, the source for the lower-stratospheric waves. In easterly winters the upper-tropospheric WMRG and R1 waves over the eastern Pacific region appear to be somewhat stronger compared to climatology, perhaps because of the accumulation of waves that are unable to propagate upward into the lower stratosphere. Vertical propagation features of these waves are generally consistent with theory and suggest a mixture of Doppler shifting by ambient flows and filtering. Some lower-stratosphere equatorial waves have a connection with preceding tropical convection, especially for Kelvin and R1 waves in winter.

ENSO impact on Kelvin waves and associated tropical convection

The impact of El Nino–Southern Oscillation (ENSO) on atmospheric Kelvin waves and associated tropical convection is investigated using the ECMWF Re-Analysis, NOAA outgoing longwave radiation (OLR), and the analysis technique introduced in a previous study. It is found that the phase of ENSO has a substantial impact on Kelvin waves and associated convection over the equatorial central-eastern Pacific. El Nino (La Nina) events enhance (suppress) variability of the upper-tropospheric Kelvin wave and the associated convection there, both in extended boreal winter and summer. The mechanism of the impact is through changes in the ENSO-related thermal conditions and the ambient flow. In El Nino years, because of SST increase in the equatorial central-eastern Pacific, variability of eastward-moving convection, which is mainly associated with Kelvin waves, intensifies in the region. In addition, owing to the weakening of the equatorial eastern Pacific westerly duct in the upper troposphere in El Nino years, Kelvin waves amplify there. In La Nina years, the opposite occurs. However, the stronger westerly duct in La Nina winters allows more NH extratropical Rossby wave activity to propagate equatorward and force Kelvin waves around 200 hPa, partially offsetting the in situ weakening effect of the stronger westerlies on the waves. In general, in El Nino years Kelvin waves are more convectively and vertically coupled and propagate more upward into the lower stratosphere over the central-eastern Pacific. The ENSO impact in other regions is not clear, although in winter over the eastern Indian and western Pacific Oceans Kelvin waves and their associated convection are slightly weaker in El Nino than in La Nina years.

Regional and monthly and clear-sky aerosol direct radiative effect (and forcing) derived from the GlobAEROSOL-AATSR satellite aerosol product

Using the GlobAEROSOL-AATSR dataset, estimates of the instantaneous, clear-sky, direct aerosol radiative effect and radiative forcing have been produced for the year 2006. Aerosol Robotic Network sun-photometer measurements have been used to characterise the random and systematic error in the GlobAEROSOL product for 22 regions covering the globe. Representative aerosol properties for each region were derived from the results of a wide range of literature sources and, along with the de-biased GlobAEROSOL AODs, were used to drive an offline version of the Met Office unified model radiation scheme. In addition to the mean AOD, best-estimate run of the radiation scheme, a range of additional calculations were done to propagate uncertainty estimates in the AOD, optical properties, surface albedo and errors due to the temporal and spatial averaging of the AOD fields. This analysis produced monthly, regional estimates of the clear-sky aerosol radiative effect and its uncertainty, which were combined to produce annual, global mean values of (−6.7±3.9)Wm−2 at the top of atmosphere (TOA) and (−12±6)Wm−2 at the surface. These results were then used to give estimates of regional, clear-sky aerosol direct radiative forcing, using modelled pre-industrial AOD fields for the year 1750 calculated for the AEROCOM PRE experiment. However, as it was not possible to quantify the uncertainty in the pre-industrial aerosol loading, these figures can only be taken as indicative and their uncertainties as lower bounds on the likely errors. Although the uncertainty on aerosol radiative effect presented here is considerably larger than most previous estimates, the explicit inclusion of the major sources of error in the calculations suggest that they are closer to the true constraint on this figure from similar methodologies, and point to the need for more, improved estimates of both global aerosol loading and aerosol optical properties.

Rossby wave propagation on potential vorticity fronts with finite width

The horizontal gradient of potential vorticity (PV) across the tropopause typically declines with lead time in global numerical weather forecasts and tends towards a steady value dependent on model resolution. This paper examines how spreading the tropopause PV contrast over a broader frontal zone affects the propagation of Rossby waves. The approach taken is to analyse Rossby waves on a PV front of finite width in a simple single-layer model. The dispersion relation for linear Rossby waves on a PV front of infinitesimal width is well known; here an approximate correction is derived for the case of a finite width front, valid in the limit that the front is narrow compared to the zonal wavelength. Broadening the front causes a decrease in both the jet speed and the ability of waves to propagate upstream. The contribution of these changes to Rossby wave phase speeds cancel at leading order. At second order the decrease in jet speed dominates, meaning phase speeds are slower on broader PV fronts. This asymptotic phase speed result is shown to hold for a wide class of single-layer dynamics with a varying range of PV inversion operators. The phase speed dependence on frontal width is verified by numerical simulations and also shown to be robust at finite wave amplitude, and estimates are made for the error in Rossby wave propagation speeds due to the PV gradient error present in numerical weather forecast models.

Eddies and variability in the Mozambique Channel

Between 1995 and 2000, on average 4 eddies per year are observed from satellite altimetry to propagate southward through the Mozambique Channel, into the upstream Agulhas region. Further south, these eddies have been found to control the timing and frequenc yof Agulhas ring shedding. Within the Mozambique Channel, anomalous SSH amplitudes rise to 30 cm ; in agreement with in situ measured velocities. Comparison of an observed velocit ysection with GCM model results shows that the Mozambique Channel eddies in these models are too surface intensified. Also, the number of eddies formed in the models is in disagreement with our observational analysis. Moored current meter measurements observing the passage of three eddies in 2000 are extended to a 5-year time series b yreferencing the anomalous surface currents estimated from altimeter data to a s ynoptic LADCP velocit y measurement. The results show intermittent edd ypassage at the mooring location. A statistical analysis of SSH observations in different parts of the Mozambique Channel shows a southward decrease of the dominant frequency of the variability, going from 7 per year in the extension of the South Equatorial Current north of Madagascar to 4 per year south of Madagascar. The observations suggest that frequency reduction is related to the Rossb ywaves coming in from the east

Bayesian analysis of uncertainty in the GlobCover 2009 land cover product at climate model grid scale

Land cover data derived from satellites are commonly used to prescribe inputs to models of the land surface. Since such data inevitably contains errors, quantifying how uncertainties in the data affect a model’s output is important. To do so, a spatial distribution of possible land cover values is required to propagate through the model’s simulation. However, at large scales, such as those required for climate models, such spatial modelling can be difficult. Also, computer models often require land cover proportions at sites larger than the original map scale as inputs, and it is the uncertainty in these proportions that this article discusses. This paper describes a Monte Carlo sampling scheme that generates realisations of land cover proportions from the posterior distribution as implied by a Bayesian analysis that combines spatial information in the land cover map and its associated confusion matrix. The technique is computationally simple and has been applied previously to the Land Cover Map 2000 for the region of England and Wales. This article demonstrates the ability of the technique to scale up to large (global) satellite derived land cover maps and reports its application to the GlobCover 2009 data product. The results show that, in general, the GlobCover data possesses only small biases, with the largest belonging to non–vegetated surfaces. In vegetated surfaces, the most prominent area of uncertainty is Southern Africa, which represents a complex heterogeneous landscape. It is also clear from this study that greater resources need to be devoted to the construction of comprehensive confusion matrices.

The modelling of electrical current NDT methods and its application to weld testing

Discussion of the numerical modeling of NDT methods based on the potential drop and the disruption of power lines to describe the nature, importance and application of modeling. La 1ère partie est consacrée aux applications aux contrôles par courants de Foucault. The first part is devoted to applications for inspection by eddy currents.

Transgenic approaches to crop improvement

Transgenic crops are now grown commercially on several million hectares, principally in North America. To date, the predominant crops are maize (corn), soybean, cotton, and potatoes. In addition, there have been field trials of transgenics from at least 52 species including all the major field crops, vegetables, and several herbaceous and woody species. This review summarizes recent data relating to such trials, particularly in terms of the trends away from simple, single gene traits such as herbicide and insect resistance towards more complex agronomic traits such as growth rate and increased photosynthetic efficiency. Much of the recent information is derived from inspection of patent databases, a useful source of information on commercial priorities. The review also discusses the time scale for the introduction of these transgenes into breeding populations and their eventual release as new varieties.

Use of thermography and fibre optics microscopy for the evaluation of railway structures in the Athens Metro in Greece (Invited Paper)

Rolling Contact Fatigue (RCF) is one of the main issues that concern, at least initially, the head of the railway; progressively they can be of very high importance as they can propagate inside the material with the risk of damaging the railway. In this work, two different non-destructive techniques, infrared thermography (IRT) and fibre optics microscopy (FOM), were used in the inspection of railways for the tracing of defects and deterioration signs. In the first instance, two different approaches (dynamic and pulsed thermography) were used, whilst in the case of FOM, microscopic characterisation of the railway heads and classification of the deterioration -- damage on the railways according to the UIC (International Union of Railways) code, took place. Results from both techniques are presented and discussed.