Relaxing the Tropics to an ‘observed’ state: analysis using a simple baroclinic model

The technique of relaxation of the tropical atmosphere towards an analysis in a month-season forecast model has previously been successfully exploited in a number of contexts. Here it is shown that when tropical relaxation is used to investigate the possible origin of the observed anomalies in June–July 2007, a simple dynamical model is able to reproduce the observed component of the pattern of anomalies given by an ensemble of ECMWF forecast runs. Following this result, the simple model is used for a range of experiments on time-scales of relaxation, variables and regions relaxed based on a control model run with equatorial heating in a zonal flow. A theory based on scale analysis for the large-scale tropics is used to interpret the results. Typical relationships between scales are determined from the basic equations, and for a specified diabatic heating a chain of deductions for determining the dependent variables is derived. Different critical time-scales are found for tropical relaxation of different dependent variables to be effective. Vorticity has the longest critical time-scale, typically 1.2 days. For temperature and divergence, the time-scales are 10 hours and 3 hours, respectively. However not all the tropical fields, in particular the vertical motion, are reproduced correctly by the model unless divergence is heavily damped. To obtain the correct extra-tropical fields, it is crucial to have the correct rotational flow in the subtropics to initiate the Rossby wave propagation from there. It is sufficient to relax vorticity or temperature on a time-scale comparable or less than their critical time-scales to obtain this. However if the divergent advection of vorticity is important in the Rossby Wave Source then strong relaxation of divergence is required to accurately represent the tropical forcing of Rossby waves.

The water vapour continuum: brief history and recent developments

The water vapour continuum is characterised by absorption that varies smoothly with wavelength, from the visible to the microwave. It is present within the rotational and vibrational–rotational bands of water vapour, which consist of large numbers of narrow spectral lines, and in the many ‘windows’ between these bands. The continuum absorption in the window regions is of particular importance for the Earth’s radiation budget and for remote-sensing techniques that exploit these windows. Historically, most attention has focused on the 8–12 μm (mid-infrared) atmospheric window, where the continuum is relatively well-characterised, but there have been many fewer measurements within bands and in other window regions. In addition, the causes of the continuum remain a subject of controversy. This paper provides a brief historical overview of the development of understanding of the continuum and then reviews recent developments, with a focus on the near-infrared spectral region. Recent laboratory measurements in near-infrared windows, which reveal absorption typically an order of magnitude stronger than in widely used continuum models, are shown to have important consequences for remote-sensing techniques that use these windows for retrieving cloud properties.

Development and validation of a qPCR-based method for quantifying Shiga toxin-encoding and other lambdoid bacteriophages

P>To address whether seasonal variability exists among Shiga toxin-encoding bacteriophage (Stx phage) numbers on a cattle farm, conventional plaque assay was performed on water samples collected over a 17 month period. Distinct seasonal variation in bacteriophage numbers was evident, peaking between June and August. Removal of cattle from the pasture precipitated a reduction in bacteriophage numbers, and during the winter months, no bacteriophage infecting Escherichia coli were detected, a surprising occurrence considering that 1031 tailed-bacteriophages are estimated to populate the globe. To address this discrepancy a culture-independent method based on quantitative PCR was developed. Primers targeting the Q gene and stx genes were designed that accurately and discriminately quantified artificial mixed lambdoid bacteriophage populations. Application of these primer sets to water samples possessing no detectable phages by plaque assay, demonstrated that the number of lambdoid bacteriophage ranged from 4.7 x 104 to 6.5 x 106 ml-1, with one in 103 free lambdoid bacteriophages carrying a Shiga toxin operon (stx). Specific molecular biological tools and discriminatory gene targets have enabled virus populations in the natural environment to be enumerated and similar strategies could replace existing propagation-dependent techniques, which grossly underestimate the abundance of viral entities.

Effluent quality and ammonia emissions from out-wintering pads in England, Wales and Ireland

Out-wintering pads offer a reduced cost system for wintering cattle, minimising damage to pasture, providing animal welfare and production benefits, and generate, potentially, a more manageable effluent and lower ammonia emissions. The objectives of the present study were (i) to contribute to improved understanding of the factors impacting on effluent quality, ammonia emissions and animal welfare via observations on four farm-based out-wintering pads (ComOWPs) in England, Wales and Ireland and more detailed studies undertaken on four experimental OWPs (ExpOWPs) constructed at Rothamsted Research North Wyke, Devon, England and (ii) to corroborate the effluent quality data from both the ComOWPs and the ExpOWPs, with findings in the literature. Woodchip size, feeding management and area allowance were the treatment factors applied on the ExpOWPs. These three factors were randomised across the four ExpOWPs, over four 6–7 week periods. Effluent quality from the ExpOWPs was sampled frequently in a flow proportional way and analysed for total N (TN); total P (TP); total solids (TS); ammonium-N (NH4+-N); nitrate-N (NO3−-N). Beef cattle were periodically weighed for determination of live weight gain (LWG). An approximate nitrogen balance was calculated as a means of understanding its partitioning and fate during and after the ExpOWPs use. Effluent quality from the ComOWPs was sampled frequently, also in a flow-proportional way, and analysed for TN, TP, TS, NH4+-N, NO3−-N, total K and COD. Effluent quality data from the ExpOWPs showed no significant differences (P > 0.05) between treatments, with average concentrations of 1095 mg l−1, and 806 mg l−1, for TN and NH4+-N, respectively. Average effluent concentrations from the ComOWPs were 356 mg l−1 TN and 124 mg l−1 NH4+-N. Ammonia emissions from the ExpOWPs showed no significant differences (P > 0.05) between the treatments, with average mean emission rates of 2.5 g m−2 d−1 NH3-N, respectively. A positive correlation was established between NH3-N emission rate and wind speed. Emission rates from the ComOWPs ranged from 0.7 to 1.6 g m−2 d−1 NH3-N. Average daily LWG on the ExpOWPs was 1.33 kg steer−1 d−1. The effluent from both the ComOWPs and ExpOWPs were more similar with dirty water and of consistently lower strength than beef cattle slurry, as supported by findings in the literature, and therefore, it is suggested to be subject to the regulatory requirements of dirty water rather than slurry.

Inner plasma structure of the low-latitude reconnection layer

We report a clear transition through a reconnection layer at the low-latitude magnetopause which shows a complete traversal across all reconnected field lines during northwestward interplanetary magnetic field (IMF) conditions. The associated plasma populations confirm details of the electron and ion mixing and the time history and acceleration through the current layer. This case has low magnetic shear with a strong guide field and the reconnection layer contains a single density depletion layer on the magnetosheath side which we suggest results from nearly field-aligned magnetosheath flows. Within the reconnection boundary layer, there are two plasma boundaries, close to the inferred separatrices on the magnetosphere and magnetosheath sides (Ssp and Ssh) and two boundaries associated with the Alfvén waves (or Rotational Discontinuities, RDsp and RDsh). The data are consistent with these being launched from the reconnection site and the plasma distributions are well ordered and suggestive of the time elapsed since reconnection of the field lines observed. In each sub-layer between the boundaries the plasma distribution is different and is centered around the current sheet, responsible for magnetosheath acceleration. We show evidence for a velocity dispersion effect in the electron anisotropy that is consistent with the time elapsed since reconnection. In addition, new evidence is presented for the occurrence of partial reflection of magnetosheath electrons at the magnetopause current layer.

Coming to grips with 'abandoned arable' land in efforts to enhance communal grazing systems in the Eastern Cape province, South Africa

The communal lands of the Eastern Cape have been regarded as both tools and problems by policy-makers. In particular, communal lands are problematised as environmentally degraded, of suboptimum productivity and constraining economic development. The Eastern Cape Communal Lands Research Project was framed within this policy discourse with the aim of introducing legume-based pasture into ‘abandoned arable lands’. Initial results from community workshops show that the institutional arrangements for these arable lands vary widely and, with them, the capacity to utilise any new technology that may have application to them. Rather than simply draw on social capital, if a participatory research approach is to enhance the agency of the participating communites, it may need to contribute to social capital building and especially to create a dialogical space in which the matters being researched can be discussed meaningfully.

Investigation of sainfoin (Onobrychis viciifolia) cultivar differences on nitrogen balance and fecal egg count in artificially infected lambs

Research in ruminant nutrition and helminth control with forages, which contain condensed tannins (CT), suggests that varying responses may depend not only on CT concentration but also on CT composition. An experiment was designed to test this by feeding 2 dried sainfoin cultivars (Visnovsky and Perly), which differed in CT properties, to lambs that were artificially infected with the abomasal blood-sucking nematode Haemonchus contortus. Twenty-four infected lambs received one of these 2 cultivars; the feeds were either untreated or treated with the CT-binding polyethylene glycol over 4 wk (n = 6). The 2 cultivars were also fed to 2 × 6 uninfected lambs. Nutrient digestibility, N balance, ADG, plasma urea together with indicators of infection [fecal egg count (FEC), abomasal worm count, per capita female fecundity, erythrocytic indices, and serum protein] were determined. The specific effects of sainfoin cultivar, CT, and infection were evaluated by contrast analysis. Digestibility of both NDF and ADF were lower (P < 0.001) with Perly compared to Visnovsky. The apparent nutrient digestibility was reduced (P < 0.001) by CT. However, no clear cultivar effects were evident on N excretion and retention. Condensed tannins reduced (P = 0.05) body N retention and shifted (P < 0.001) N excretion from urine to feces. Unlike cultivar and CT, infection decreased (P = 0.002) ADG. Plasma urea concentration was lower (P = 0.007) in Perly- compared to Visnovsky-fed lambs and was decreased (P < 0.001) by CT. Plasma concentrations of essential and semi-essential AA were increased (P < 0.001) by CT. The groups of infected lambs did not clearly differ in abomasal worm counts and erythrocytic indicators. In the last 2 to 3 wk of the experiment, FEC was lower (P ≤ 0.01) when feeding CT. The lack of substantial cultivar effects suggests that the differences in CT properties may have been too small to result in nutritional and anthelmintic effects. The present results indicate that sainfoin CT had a mitigating effect on FEC and, consequently, pasture infectivity. However, the reduction was too low to expect any significant benefits in an Haemonchus-dominated system. Therefore, the use of sainfoin for controlling H. contortus should only be one component within an integrated worm control system.

One-port de-embedding technique for the quasi-optical characterization of integrated components

We describe a one-port de-embedding technique suitable for the quasi-optical characterization of terahertz integrated components at frequencies beyond the operational range of most vector network analyzers. This technique is also suitable when the manufacturing of precision terminations to sufficiently fine tolerances for the application of a TRL de-embedding technique is not possible. The technique is based on vector reflection measurements of a series of easily realizable test pieces. A theoretical analysis is presented for the precision of the technique when implemented using a quasi-optical null-balanced bridge reflectometer. The analysis takes into account quantization effects in the linear and angular encoders associated with the balancing procedure, as well as source power and detector noise equivalent power. The precision in measuring waveguide characteristic impedance and attenuation using this de-embedding technique is further analyzed after taking into account changes in the power coupled due to axial, rotational, and lateral alignment errors between the device under test and the instruments' test port. The analysis is based on the propagation of errors after assuming imperfect coupling of two fundamental Gaussian beams. The required precision in repositioning the samples at the instruments' test-port is discussed. Quasi-optical measurements using the de-embedding process for a WR-8 adjustable precision short at 125 GHz are presented. The de-embedding methodology may be extended to allow the determination of S-parameters of arbitrary two-port junctions. The measurement technique proposed should prove most useful above 325 GHz where there is a lack of measurement standards.

The troposphere-to-stratosphere transition in kinetic energy spectra and nonlinear spectral fluxes as seen in ECMWF analyses

Global horizontal wavenumber kinetic energy spectra and spectral fluxes of rotational kinetic energy and enstrophy are computed for a range of vertical levels using a T799 ECMWF operational analysis. Above 250 hPa, the kinetic energy spectra exhibit a distinct break between steep and shallow spectral ranges, reminiscent of dual power-law spectra seen in aircraft data and high-resolution general circulation models. The break separates a large-scale ‘‘balanced’’ regime in which rotational flow strongly dominates divergent flow and a mesoscale ‘‘unbalanced’’ regime where divergent energy is comparable to or larger than rotational energy. Between 230 and 100 hPa, the spectral break shifts to larger scales (from n 5 60 to n 5 20, where n is spherical harmonic index) as the balanced component of the flow preferentially decays. The location of the break remains fairly stable throughout the stratosphere. The spectral break in the analysis occurs at somewhat larger scales than the break seen in aircraft data. Nonlinear spectral fluxes defined for the rotational component of the flow maximize between about 300 and 200 hPa. Large-scale turbulence thus centers on the extratropical tropopause region, within which there are two distinct mechanisms of upscale energy transfer: eddy–eddy interactions sourcing the transient energy peak in synoptic scales, and zonal mean–eddy interactions forcing the zonal flow. A well-defined downscale enstrophy flux is clearly evident at these altitudes. In the stratosphere, the transient energy peak moves to planetary scales and zonal mean–eddy interactions become dominant.

Rigid body trajectories in different 6D spaces

The objective of this paper is to show that the group SE(3) with an imposed Lie-Poisson structure can be used to determine the trajectory in a spatial frame of a rigid body in Euclidean space. Identical results for the trajectory are obtained in spherical and hyperbolic space by scaling the linear displacements appropriately since the influence of the moments of inertia on the trajectories tends to zero as the scaling factor increases. The semidirect product of the linear and rotational motions gives the trajectory from a body frame perspective. It is shown that this cannot be used to determine the trajectory in the spatial frame. The body frame trajectory is thus independent of the velocity coupling. In addition, it is shown that the analysis can be greatly simplified by aligning the axes of the spatial frame with the axis of symmetry which is unchanging for a natural system with no forces and rotation about an axis of symmetry.

On Hamiltonian balanced dynamics and the slowest invariant manifold

The concept of a slowest invariant manifold is investigated for the five-component model of Lorenz under conservative dynamics. It is shown that Lorenz's model is a two-degree-of-freedom canonical Hamiltonian system, consisting of a nonlinear vorticity-triad oscillator coupled to a linear gravity wave oscillator, whose solutions consist of regular and chaotic orbits. When either the Rossby number or the rotational Froude number is small, there is a formal separation of timescales, and one can speak of fast and slow motion. In the same regime, the coupling is weak, and the Kolmogorov–Arnold-Moser theorem is shown to apply. The chaotic orbits are inherently unbalanced and are confined to regions sandwiched between invariant tori consisting of quasi-periodic regular orbits. The regular orbits generally contain free fast motion, but a slowest invariant manifold may be geometrically defined as the set of all slow cores of invariant tori (defined by zero fast action) that are smoothly related to such cores in the uncoupled system. This slowest invariant manifold is not global; in fact, its structure is fractal; but it is of nearly full measure in the limit of weak coupling. It is also nonlinearly stable. As the coupling increases, the slowest invariant manifold shrinks until it disappears altogether. The results clarify previous definitions of a slowest invariant manifold and highlight the ambiguity in the definition of “slowness.” An asymptotic procedure, analogous to standard initialization techniques, is found to yield nonzero free fast motion even when the core solutions contain none. A hierarchy of Hamiltonian balanced models preserving the symmetries in the original low-order model is formulated; these models are compared with classic balanced models, asymptotically initialized solutions of the full system and the slowest invariant manifold defined by the core solutions. The analysis suggests that for sufficiently small Rossby or rotational Froude numbers, a stable slowest invariant manifold can be defined for this system, which has zero free gravity wave activity, but it cannot be defined everywhere. The implications of the results for more complex systems are discussed.

Haptics in medicine and clinical skill acquisition

THE clinical skills of medical professionals rely strongly on the sense of touch, combined with anatomical and diagnostic knowledge. Haptic exploratory procedures allow the expert to detect anomalies via gross and fine palpation, squeezing, and contour following. Haptic feedback is also key to medical interventions, for example when an anaesthetist inserts an epidural needle, a surgeon makes an incision, a dental surgeon drills into a carious lesion, or a veterinarian sutures a wound. Yet, current trends in medical technology and training methods involve less haptic feedback to clinicians and trainees. For example, minimally invasive surgery removes the direct contact between the patient and clinician that gives rise to natural haptic feedback, and furthermore introduces scaling and rotational transforms that confuse the relationship between movements of the hand and the surgical site. Similarly, it is thought that computer-based medical simulation and training systems require high-resolution and realistic haptic feedback to the trainee for significant training transfer to occur. The science and technology of haptics thus has great potential to affect the performance of medical procedures and learning of clinical skills. This special section is about understanding

Inferring animal husbandry strategies in coastal zones through stable isotope analysis: new evidence from the Flemish coastal plain (Belgium, 1st-15th century AD)

In a proof-of-concept study, Britton et al. (2008) demonstrated that the isotopic composition of halophytic plants can be traced in the skeletal tissues of their animal consumers. Here we apply the method to domestic herbivore remains (n = 303) from nine archaeological sites in or near the Flemish coastal plain (Belgium), where, prior to embankments, salt-marshes offered extensive pasture grounds for domestic herbivores. The sites span a period of ∼1500 years (Roman to late medieval period), during which the coastal landscape was progressively transformed from little managed wetlands to a fully embanked polder area. The bulk collagen data show variations between sites and over time, which are consistent with this historical framework and are interpreted as reflecting environmental change and differences in animal management in the coastal plain throughout the late Holocene. The study demonstrates the immense value of faunal stable isotope analysis for characterising coastal husbandry strategies beyond the means of traditional zooarchaeological techniques.

Interpretation of ageostrophic winds and implications for jet stream maintenance

The use of ageostrophic flow to infer the presence of vertical circulations in the entrances and exits of the climatological jet streams is questioned. Problems of interpretation arise because of the use of different definitions of geostrophy in theoretical studies and in analyses of atmospheric data. The nature and role of the ageostrophic flow based on constant and variable Coriolis parameter definitions of geostrophy vary. In the latter the geostrophic divergence cannot be neglected, so the vertical motion is not associated solely with the ageostrophic flow. Evidence is presented suggesting that ageostrophic flow in the climatological jet streams is primarily determined by the kinematic requirements of wave retrogression rather than by a forcing process. These requirements are largely met by the rotational flow, with the divergent circulations present being geostrophically forced, and so playing a secondary, restoring role.

Experimentally driven atomistic model of 1,2 Polybutadiene

We present an efficient method of combining wide angle neutron scattering data with detailed atomistic models, allowing us to perform a quantitative and qualitative mapping of the organisation of the chain conformation in both glass and liquid phases. The structural refinement method presented in this work is based on the exploitation of the intrachain features of the diffraction pattern and its intimate linkage with atomistic models by the use of internal coordinates for bond lengths, valence angles and torsion rotations. Atomic connectivity is defined through these coordinates that are in turn assigned by pre-defined probability distributions, thus allowing for the models in question to be built stochastically. Incremental variation of these coordinates allows for the construction of models that minimise the differences between the observed and calculated structure factors. We present a series of neutron scattering data of 1,2 polybutadiene at the region 120-400K. Analysis of the experimental data yield bond lengths for C-C and C=C of 1.54Å and 1.35Å respectively. Valence angles of the backbone were found to be at 112° and the torsion distributions are characterised by five rotational states, a three-fold trans-skew± for the backbone and gauche± for the vinyl group. Rotational states of the vinyl group were found to be equally populated, indicating a largely atactic chan. The two backbone torsion angles exhibit different behaviour with respect to temperature of their trans population, with one of them adopting an almost all trans sequence. Consequently the resulting configuration leads to a rather persistent chain, something indicated by the value of the characteristic ratio extrapolated from the model. We compare our results with theoretical predictions, computer simulations, RIS models and previously reported experimental results.