Isomap nonlinear dimensionality reduction and bimodality of Asian monsoon convection

It is known that the empirical orthogonal function method is unable to detect possible nonlinear structure in climate data. Here, isometric feature mapping (Isomap), as a tool for nonlinear dimensionality reduction, is applied to 1958–2001 ERA-40 sea-level pressure anomalies to study nonlinearity of the Asian summer monsoon intraseasonal variability. Using the leading two Isomap time series, the probability density function is shown to be bimodal. A two-dimensional bivariate Gaussian mixture model is then applied to identify the monsoon phases, the obtained regimes representing enhanced and suppressed phases, respectively. The relationship with the large-scale seasonal mean monsoon indicates that the frequency of monsoon regime occurrence is significantly perturbed in agreement with conceptual ideas, with preference for enhanced convection on intraseasonal time scales during large-scale strong monsoons. Trend analysis suggests a shift in concentration of monsoon convection, with less emphasis on South Asia and more on the East China Sea.

Large-scale surface mass balance of ice sheets from a comprehensive atmospheric model

The surface mass balance for Greenland and Antarctica has been calculated using model data from an AMIP-type experiment for the period 1979–2001 using the ECHAM5 spectral transform model at different triangular truncations. There is a significant reduction in the calculated ablation for the highest model resolution, T319 with an equivalent grid distance of ca 40 km. As a consequence the T319 model has a positive surface mass balance for both ice sheets during the period. For Greenland, the models at lower resolution, T106 and T63, on the other hand, have a much stronger ablation leading to a negative surface mass balance. Calculations have also been undertaken for a climate change experiment using the IPCC scenario A1B, with a T213 resolution (corresponding to a grid distance of some 60 km) and comparing two 30-year periods from the end of the twentieth century and the end of the twenty-first century, respectively. For Greenland there is change of 495 km3/year, going from a positive to a negative surface mass balance corresponding to a sea level rise of 1.4 mm/year. For Antarctica there is an increase in the positive surface mass balance of 285 km3/year corresponding to a sea level fall by 0.8 mm/year. The surface mass balance changes of the two ice sheets lead to a sea level rise of 7 cm at the end of this century compared to end of the twentieth century. Other possible mass losses such as due to changes in the calving of icebergs are not considered. It appears that such changes must increase significantly, and several times more than the surface mass balance changes, if the ice sheets are to make a major contribution to sea level rise this century. The model calculations indicate large inter-annual variations in all relevant parameters making it impossible to identify robust trends from the examined periods at the end of the twentieth century. The calculated inter-annual variations are similar in magnitude to observations. The 30-year trend in SMB at the end of the twenty-first century is significant. The increase in precipitation on the ice sheets follows closely the Clausius-Clapeyron relation and is the main reason for the increase in the surface mass balance of Antarctica. On Greenland precipitation in the form of snow is gradually starting to decrease and cannot compensate for the increase in ablation. Another factor is the proportionally higher temperature increase on Greenland leading to a larger ablation. It follows that a modest increase in temperature will not be sufficient to compensate for the increase in accumulation, but this will change when temperature increases go beyond any critical limit. Calculations show that such a limit for Greenland might well be passed during this century. For Antarctica this will take much longer and probably well into following centuries.

Molecular and phenotypic characterization of a mouse model of oculopharyngeal muscular dystrophy reveals severe muscular atrophy restricted to fast glycolytic fibres

Oculopharyngeal muscular dystrophy (OPMD) is an adult-onset disorder characterized by ptosis, dysphagia and proximal limb weakness. Autosomal-dominant OPMD is caused by a short (GCG)8–13 expansions within the first exon of the poly(A)-binding protein nuclear 1 gene (PABPN1), leading to an expanded polyalanine tract in the mutated protein. Expanded PABPN1 forms insoluble aggregates in the nuclei of skeletal muscle fibres. In order to gain insight into the different physiological processes affected in OPMD muscles, we have used a transgenic mouse model of OPMD (A17.1) and performed transcriptomic studies combined with a detailed phenotypic characterization of this model at three time points. The transcriptomic analysis revealed a massive gene deregulation in the A17.1 mice, among which we identified a significant deregulation of pathways associated with muscle atrophy. Using a mathematical model for progression, we have identified that one-third of the progressive genes were also associated with muscle atrophy. Functional and histological analysis of the skeletal muscle of this mouse model confirmed a severe and progressive muscular atrophy associated with a reduction in muscle strength. Moreover, muscle atrophy in the A17.1 mice was restricted to fast glycolytic fibres, containing a large number of intranuclear inclusions (INIs). The soleus muscle and, in particular, oxidative fibres were spared, even though they contained INIs albeit to a lesser degree. These results demonstrate a fibre-type specificity of muscle atrophy in this OPMD model. This study improves our understanding of the biological pathways modified in OPMD to identify potential biomarkers and new therapeutic targets.

Selected wheat seed defense proteins exhibit competitive binding to model microbial lipid interfaces

Puroindolines (Pins) and purothionins (Pths) are basic, amphiphilic, cysteine-rich wheat proteins that play a role in plant defense against microbial pathogens. We have examined the co-adsorption and sequential addition of Pins (Pin-a, Pin-b and a mutant form of Pin-b with Trp-44 to Arg-44 substitution) and β-purothionin (β-Pth) model anionic lipid layers, using a combination of surface pressure measurements, external reflection FTIR spectroscopy and neutron reflectometry. Results highlighted differences in the protein binding mechanisms, and in the competitive binding and penetration of lipid layers between respective Pins and β-Pth. Pin-a formed a blanket-like layer of protein below the lipid surface that resulted in the reduction or inhibition of β-Pth penetration of the lipid layer. Wild-type Pin-b participated in co-operative binding with β-Pth, whereas the mutant Pin-b did not bind to the lipid layer in the presence of β-Pth. The results provide further insight into the role of hydrophobic and cationic amino acid residues in antimicrobial activity.

Response of tropical cyclones to idealized climate change experiments in a global high resolution coupled general circulation model

We present an assessment of how tropical cyclone activity might change due to the influence of increased atmospheric carbon dioxide concentrations, using the UK’s High Resolution Global Environment Model (HiGEM) with N144 resolution (~90 km in the atmosphere and ~40 km in the ocean). Tropical cyclones are identified using a feature tracking algorithm applied to model output. Tropical cyclones from idealized 30-year 2×CO2 (2CO2) and 4×CO2 (4CO2) simulations are compared to those identified in a 150-year present-day simulation, which is separated into a 5-member ensemble of 30-year integrations. Tropical cyclones are shown to decrease in frequency globally by 9% in the 2CO2 and 26% in the 4CO2. Tropical cyclones only become more intese in the 4CO2, however uncoupled time slice experiments reveal an increase in intensity in the 2CO2. An investigation into the large-scale environmental conditions, known to influence tropical cyclone activity in the main development regions, is used to determine the response of tropical cyclone activity to increased atmospheric CO2. A weaker Walker circulation and a reduction in zonally averaged regions of updrafts lead to a shift in the location of tropical cyclones in the northern hemisphere. A decrease in mean ascent at 500 hPa contributes to the reduction of tropical cyclones in the 2CO2 in most basins. The larger reduction of tropical cyclones in the 4CO2 arises from further reduction of mean ascent at 500 hPa and a large enhancement of vertical wind shear, especially in the southern hemisphere, North Atlantic and North East Pacific.

Improved evaporative flux partitioning and carbon flux in the land surface model JULES: impact on the simulation of land surface processes in temperate Europe

The primary role of land surface models embedded in climate models is to partition surface available energy into upwards, radiative, sensible and latent heat fluxes. Partitioning of evapotranspiration, ET, is of fundamental importance: as a major component of the total surface latent heat flux, ET affects the simulated surface water balance, and related energy balance, and consequently the feedbacks with the atmosphere. In this context it is also crucial to credibly represent the CO2 exchange between ecosystems and their environment. In this study, JULES, the land surface model used in UK weather and climate models, has been evaluated for temperate Europe. Compared to eddy covariance flux measurements, the CO2 uptake by the ecosystem is underestimated and the ET overestimated. In addition, the contribution to ET from soil and intercepted water evaporation far outweighs the contribution of plant transpiration. To alleviate these biases, adaptations have been implemented in JULES, based on key literature references. These adaptations have improved the simulation of the spatio-temporal variability of the fluxes and the accuracy of the simulated GPP and ET, including its partitioning. This resulted in a shift of the seasonal soil moisture cycle. These adaptations are expected to increase the fidelity of climate simulations over Europe. Finally, the extreme summer of 2003 was used as evaluation benchmark for the use of the model in climate change studies. The improved model captures the impact of the 2003 drought on the carbon assimilation and the water use efficiency of the plants. It, however, underestimates the 2003 GPP anomalies. The simulations showed that a reduction of evaporation from the interception and soil reservoirs, albeit not of transpiration, largely explained the good correlation between the carbon and the water fluxes anomalies that was observed during 2003. This demonstrates the importance of being able to discriminate the response of individual component of the ET flux to environmental forcing.

Rescue of gene expression by modified REST decoy oligonucleotides in a cellular model of Huntington's disease

Transcriptional dysfunction is a prominent hallmark of Huntington's disease (HD). Several transcription factors have been implicated in the aetiology of HD progression and one of the most prominent is repressor element 1 (RE1) silencing transcription factor (REST). REST is a global repressor of neuronal gene expression and in the presence of mutant Huntingtin increased nuclear REST levels lead to elevated RE1 occupancy and a concomitant increase in target gene repression, including brain-derived neurotrophic factor. It is of great interest to devise strategies to reverse transcriptional dysregulation caused by increased nuclear REST and determine the consequences in HD. Thus far, such strategies have involved RNAi or mutant REST constructs. Decoys are double-stranded oligodeoxynucleotides corresponding to the DNA-binding element of a transcription factor and act to sequester it, thereby abrogating its transcriptional activity. Here, we report the use of a novel decoy strategy to rescue REST target gene expression in a cellular model of HD. We show that delivery of the decoy in cells expressing mutant Huntingtin leads to its specific interaction with REST, a reduction in REST occupancy of RE1s and rescue of target gene expression, including Bdnf. These data point to an alternative strategy for rebalancing the transcriptional dysregulation in HD.

The depression of tropical snow lines at the Last Glacial Maximum: what can we learn from climate and model experiments?

Analyses of simulations of the last glacial maximum (LGM) made with 17 atmospheric general circulation models (AGCMs) participating in the Paleoclimate Modelling Intercomparison Project, and a high-resolution (T106) version of one of the models (CCSR1), show that changes in the elevation of tropical snowlines (as estimated by the depression of the maximum altitude of the 0 °C isotherm) are primarily controlled by changes in sea-surface temperatures (SSTs). The correlation between the two variables, averaged for the tropics as a whole, is 95%, and remains >80% even at a regional scale. The reduction of tropical SSTs at the LGM results in a drier atmosphere and hence steeper lapse rates. Changes in atmospheric circulation patterns, particularly the weakening of the Asian monsoon system and related atmospheric humidity changes, amplify the reduction in snowline elevation in the northern tropics. Colder conditions over the tropical oceans combined with a weakened Asian monsoon could produce snowline lowering of up to 1000 m in certain regions, comparable to the changes shown by observations. Nevertheless, such large changes are not typical of all regions of the tropics. Analysis of the higher resolution CCSR1 simulation shows that differences between the free atmospheric and along-slope lapse rate can be large, and may provide an additional factor to explain regional variations in observed snowline changes.

An analysis of UK policies for domestic energy reduction using an agent based tool

This paper introduces a new agent-based model, which incorporates the actions of individual homeowners in a long-term domestic stock model, and details how it was applied in energy policy analysis. The results indicate that current policies are likely to fall significantly short of the 80% target and suggest that current subsidy levels need re-examining. In the model, current subsidy levels appear to offer too much support to some technologies, which in turn leads to the suppression of other technologies that have a greater energy saving potential. The model can be used by policy makers to develop further scenarios to find alternative, more effective, sets of policy measures. The model is currently limited to the owner-occupied stock in England, although it can be expanded, subject to the availability of data.

The real-time optimisation of DNO owned storage devices on the LV network for peak reduction

Energy storage is a potential alternative to conventional network reinforcementof the low voltage (LV) distribution network to ensure the grid’s infrastructure remainswithin its operating constraints. This paper presents a study on the control of such storagedevices, owned by distribution network operators. A deterministic model predictive control (MPC) controller and a stochastic receding horizon controller (SRHC) are presented, wherethe objective is to achieve the greatest peak reduction in demand, for a given storagedevice specification, taking into account the high level of uncertainty in the prediction of LV demand. The algorithms presented in this paper are compared to a standard set-pointcontroller and bench marked against a control algorithm with a perfect forecast. A specificcase study, using storage on the LV network, is presented, and the results of each algorithmare compared. A comprehensive analysis is then carried out simulating a large number of LV networks of varying numbers of households. The results show that the performance of each algorithm is dependent on the number of aggregated households. However, on a typical aggregation, the novel SRHC algorithm presented in this paper is shown to outperform each of the comparable storage control techniques.

A phosphoramidite-based [FeFe]H2ase functional mimic displaying fast electrocatalytic proton reduction

A phosphoramidite modified [FeFe]H2ase mimic is studied as a model for photodriven production of H2. On cathodic activation, the pyridyl–phosphoramidite complex exhibits a strongly enhanced rate of proton reduction over the previously reported pyridylphosphine model at the same overpotential. Analysis of the cyclic voltammograms shows an apparent H2 evolution rate strongly influenced by the presence of both side-bound pyridyl and phosphorous-bound dimethylamino moieties at the phosphoramidite ligands. This difference is ascribed to the basic amines acting as proton relays.

Key conclusions of the first international urban land surface model comparison project

he first international urban land surface model comparison was designed to identify three aspects of the urban surface-atmosphere interactions: (1) the dominant physical processes, (2) the level of complexity required to model these, and 3) the parameter requirements for such a model. Offline simulations from 32 land surface schemes, with varying complexity, contributed to the comparison. Model results were analysed within a framework of physical classifications and over four stages. The results show that the following are important urban processes; (i) multiple reflections of shortwave radiation within street canyons, (ii) reduction in the amount of visible sky from within the canyon, which impacts on the net long-wave radiation, iii) the contrast in surface temperatures between building roofs and street canyons, and (iv) evaporation from vegetation. Models that use an appropriate bulk albedo based on multiple solar reflections, represent building roof surfaces separately from street canyons and include a representation of vegetation demonstrate more skill, but require parameter information on the albedo, height of the buildings relative to the width of the streets (height to width ratio), the fraction of building roofs compared to street canyons from a plan view (plan area fraction) and the fraction of the surface that is vegetated. These results, whilst based on a single site and less than 18 months of data, have implications for the future design of urban land surface models, the data that need to be measured in urban observational campaigns, and what needs to be included in initiatives for regional and global parameter databases.

Incorporating toxicokinetics into an individual-based model for more realistic pesticide exposure estimates: A case study of the wood mouse

The potential risk of agricultural pesticides to mammals typically depends on internal concentrations within individuals, and these are determined by the amount ingested and by absorption, distribution, metabolism, and excretion (ADME). Pesticide residues ingested depend, amongst other things, on individual spatial choices which determine how much and when feeding sites and areas of pesticide application overlap, and can be calculated using individual-based models (IBMs). Internal concentrations can be calculated using toxicokinetic (TK) models, which are quantitative representations of ADME processes. Here we provide a population model for the wood mouse (Apodemus sylvaticus) in which TK submodels were incorporated into an IBM representation of individuals making choices about where to feed. This allows us to estimate the contribution of individual spatial choice and TK processes to risk. We compared the risk predicted by four IBMs: (i) “AllExposed-NonTK”: assuming no spatial choice so all mice have 100% exposure, no TK, (ii) “AllExposed-TK”: identical to (i) except that the TK processes are included where individuals vary because they have different temporal patterns of ingestion in the IBM, (iii) “Spatial-NonTK”: individual spatial choice, no TK, and (iv) “Spatial-TK”: individual spatial choice and with TK. The TK parameters for hypothetical pesticides used in this study were selected such that a conventional risk assessment would fail. Exposures were standardised using risk quotients (RQ; exposure divided by LD50 or LC50). We found that for the exposed sub-population including either spatial choice or TK reduced the RQ by 37–85%, and for the total population the reduction was 37–94%. However spatial choice and TK together had little further effect in reducing RQ. The reasons for this are that when the proportion of time spent in treated crop (PT) approaches 1, TK processes dominate and spatial choice has very little effect, and conversely if PT is small spatial choice dominates and TK makes little contribution to exposure reduction. The latter situation means that a short time spent in the pesticide-treated field mimics exposure from a small gavage dose, but TK only makes a substantial difference when the dose was consumed over a longer period. We concluded that a combined TK-IBM is most likely to bring added value to the risk assessment process when the temporal pattern of feeding, time spent in exposed area and TK parameters are at an intermediate level; for instance wood mice in foliar spray scenarios spending more time in crop fields because of better plant cover.

Measuring the impacts of distortions in the European Union cotton sector: a partial equilibrium analysis using the ATPSM model framework

The “cotton issue” has been a topic of several academic discussions for trade policy analysts. However the design of trade and agricultural policy in the EU and the USA has become a politically sensitive matter throughout the last five years. This study utilizing the Agricultural Trade Policy Simulation Model (ATPSM) aims to gain insights into the global cotton market, to explain why domestic support for cotton has become an issue, to quantify the impact of the new EU agricultural policy on the cotton sector, and to measure the effect of eliminating support policies on production and trade. Results indicate that full trade liberalization would lead the four West African countries to better terms of trade with the EU. If tariff reduction follows the so-called Swiss formula, world prices would increase by 3.5%.

Effects of high hydrostatic pressure and chemical reduction on the emulsification properties of gum arabic

Gum arabic is widely used in the food industry as an additive, both as a thickener and an emulsifier. This study has compared the emulsification properties of two types of gums, KLTA (Acacia senegal) and GCA (Acacia seyal), both in their native/untreated forms and after exposure to high pressure (800 MPa). Further studies were undertaken to chemically modify the disulphide linkages present and to investigate the effects of their reduction on the diffusion of the carbohydrate materials. The emulsification properties of the gum samples were examined by determining the droplet size distribution in a ‘‘model’’ oil-in-water system. Results showed that high pressure treatment and chemical reduction of gums changed the emulsification properties of both gums. The high molecular weight component in arabinogalactanproteins (AGP/GP), and more ‘‘branched’’ carbohydrates present in gum arabic, may be responsible for the emulsification properties of GCA gum, indicating that the emulsification mechanisms for KLTA and GCA were different.