QUAGMIRE v1.3: a quasi-geostrophic model for investigating rotating fluids experiments

QUAGMIRE is a quasi-geostrophic numerical model for performing fast, high-resolution simulations of multi-layer rotating annulus laboratory experiments on a desktop personal computer. The model uses a hybrid finite-difference/spectral approach to numerically integrate the coupled nonlinear partial differential equations of motion in cylindrical geometry in each layer. Version 1.3 implements the special case of two fluid layers of equal resting depths. The flow is forced either by a differentially rotating lid, or by relaxation to specified streamfunction or potential vorticity fields, or both. Dissipation is achieved through Ekman layer pumping and suction at the horizontal boundaries, including the internal interface. The effects of weak interfacial tension are included, as well as the linear topographic beta-effect and the quadratic centripetal beta-effect. Stochastic forcing may optionally be activated, to represent approximately the effects of random unresolved features. A leapfrog time stepping scheme is used, with a Robert filter. Flows simulated by the model agree well with those observed in the corresponding laboratory experiments.

Solute movement through intact columns of cryoturbated Upper Chalk

Cryoturbated Upper Chalk is a dichotomous porous medium wherein the intra-fragment porosity provides water storage and the inter-fragment porosity provides potential pathways for relatively rapid flow near saturation. Chloride tracer movement through 43 cm long and 45 cm diameter undisturbed chalk columns was studied at water application rates of 0.3, 1.0, and 1.5 cm h(-1). Microscale heterogeneity in effluent was recorded using a grid collection system consisting of 98 funnel-shaped cells each 3.5 cm in diameter. The total porosity of the columns was 0.47 +/- 0.02 m(3) m(-3), approximately 13% of pores were >15 mu m diameter, and the saturated hydraulic conductivity was 12.66 +/- 1.31 m day(-1). Although the column remained unsaturated during the leaching even at all application rates, proportionate flow through macropores increased as the application rate decreased. The number of dry cells (with 0 ml of effluent) increased as application rate decreased. Half of the leachate was collected from 15, 19 and 22 cells at 0.3, 1.0, 1.5 cm h(-1) application rates respectively. Similar breakthrough curves (BTCs) were obtained at all three application rates when plotted as a function of cumulative drainage, but they were distinctly different when plotted as a function of time. The BTCs indicate that the columns have similar drainage requirement irrespective of application rates, as the rise to the maxima (C/C-o) is almost similar. However, the time required to achieve that leaching requirement varies with application rates, and residence time was less in the case of a higher application rate. A two-region convection-dispersion model was used to describe the BTCs and fitted well (r(2) = 0.97-0-99). There was a linear relationship between dispersion coefficient and pore water velocity (correlation coefficient r = 0.95). The results demonstrate the microscale heterogeneity of hydrodynamic properties in the Upper Chalk. Copyright (C) 2007 John Wiley & Sons, Ltd.

The effect of soil phosphorus on particulate phosphorus in land runoff

Accumulation of surplus phosphorus (P) in the soil and the resulting increased transport of P in land runoff contribute to freshwater eutrophication. The effects of increasing soil P (19–194 mg Olsen-P (OP) kg−1) on the concentrations of particulate P (PP), and sorption properties (Qmax, k and EPCo) of suspended solids (SS) in overland flow from 15 unreplicated field plots established on a dispersive arable soil were measured over three monitoring periods under natural rainfall. Concentrations of PP in plot runoff increased linearly at a rate of 2.6 μg litre−1 per mg OP kg−1 of soil, but this rate was approximately 50% of the rate of increase in dissolved P (< 0.45 μm). Concentrations of SS in runoff were similar across all plots and contained a greater P sorption capacity (mean + 57%) than the soil because of enrichment with fine silt and clay (0.45–20 μm). As soil P increased, the P enrichment ratio of the SS declined exponentially, and the values of P saturation (Psat; 15–42%) and equilibrium P concentration (EPCo; 0.7–5.5 mg litre−1) in the SS fell within narrower ranges compared with the soils (6–74% and 0.1–10 mg litre−1, respectively). When OP was < 100 mg kg−1, Psat and EPCo values in the SS were smaller than those in the soil and vice-versa, suggesting that eroding particles from soils with both average and high P fertility would release P on entering the local (Rosemaund) stream. Increasing soil OP from average to high P fertility increased the P content of the SS by approximately 10%, but had no significant (P > 0.05) effect on the Psat, or EPCo, of the SS. Management options to reduce soil P status as a means of reducing P losses in land runoff and minimizing eutrophication risk may therefore have more limited effect than is currently assumed in catchment management.

Flux comparison of Eulerian and Lagrangian estimates of Agulhas leakage: A case study using a numerical model

Estimating the magnitude of Agulhas leakage, the volume flux of water from the Indian to the Atlantic Ocean, is difficult because of the presence of other circulation systems in the Agulhas region. Indian Ocean water in the Atlantic Ocean is vigorously mixed and diluted in the Cape Basin. Eulerian integration methods, where the velocity field perpendicular to a section is integrated to yield a flux, have to be calibrated so that only the flux by Agulhas leakage is sampled. Two Eulerian methods for estimating the magnitude of Agulhas leakage are tested within a high-resolution two-way nested model with the goal to devise a mooring-based measurement strategy. At the GoodHope line, a section halfway through the Cape Basin, the integrated velocity perpendicular to that line is compared to the magnitude of Agulhas leakage as determined from the transport carried by numerical Lagrangian floats. In the first method, integration is limited to the flux of water warmer and more saline than specific threshold values. These threshold values are determined by maximizing the correlation with the float-determined time series. By using the threshold values, approximately half of the leakage can directly be measured. The total amount of Agulhas leakage can be estimated using a linear regression, within a 90% confidence band of 12 Sv. In the second method, a subregion of the GoodHope line is sought so that integration over that subregion yields an Eulerian flux as close to the float-determined leakage as possible. It appears that when integration is limited within the model to the upper 300 m of the water column within 900 km of the African coast the time series have the smallest root-mean-square difference. This method yields a root-mean-square error of only 5.2 Sv but the 90% confidence band of the estimate is 20 Sv. It is concluded that the optimum thermohaline threshold method leads to more accurate estimates even though the directly measured transport is a factor of two lower than the actual magnitude of Agulhas leakage in this model.

The calculation of accurate normal coordinates I: general theory, and application to methane

The calculation of accurate and reliable vibrational potential functions and normal co-ordinates is discussed, for such simple polyatomic molecules as it may be possible. Such calculations should be corrected for the effects of anharmonicity and of resonance interactions between the vibrational states, and should be fitted to all the available information on all isotopic species: particularly the vibrational frequencies, Coriolis zeta constants and centrifugal distortion constants. The difficulties of making these corrections, and of making use of the observed data are reviewed. A programme for the Ferranti Mercury Computer is described by means of which harmonic vibration frequencies and normal co-ordinate vectors, zeta factors and centrifugal distortion constants can be calculated, from a given force field and from given G-matrix elements, etc. The programme has been used on up to 5 × 5 secular equations for which a single calculation and output of results takes approximately l min; it can readily be extended to larger determinants. The best methods of using such a programme and the possibility of reversing the direction of calculation are discussed. The methods are applied to calculating the best possible vibrational potential function for the methane molecule, making use of all the observed data.

Differential regulation of Krüppel-like factor family transcription factor expression in neonatal rat cardiac myocytes: effects of endothelin-1, oxidative stress and cytokines

Krüppel-like transcription factors (Klfs) modulate fundamental cell processes. Cardiac myocytes are terminally-differentiated, but hypertrophy in response to stimuli such as endothelin-1. H2O2 or cytokines promote myocyte apoptosis. Microarray studies of neonatal rat myocytes identified several Klfs as endothelin-1-responsive genes. We used quantitative PCR for further analysis of Klf expression in neonatal rat myocytes. In response to endothelin-1, Klf2 mRNA expression was rapidly increased ( approximately 9-fold; 15-30 min) with later increases in expression of Klf4 and Klf6 ( approximately 5-fold; 30-60 min). All were regulated as immediate early genes (cycloheximide did not inhibit the increases in expression). Klf5 expression was increased at 1-2 h ( approximately 13-fold) as a second phase response (cycloheximide inhibited the increase). These increases were transient and attenuated by U0126. H2O2 increased expression of Klf2, Klf4 and Klf6, but interleukin-1beta or tumor necrosis factor alpha downregulated Klf2 expression with no effect on Klf4 or Klf6. Of the Klfs which repress transcription, endothelin-1 rapidly downregulated expression of Klf3, Klf11 and Klf15. The dynamic regulation of expression of multiple Klf family members in cardiac myocytes suggests that, as a family, they are actively involved in regulating phenotypic responses (hypertrophy and apoptosis) to extracellular stimuli.

Temporal regulation of expression of immediate early and second phase transcripts by endothelin-1 in cardiomyocytes

Background: Endothelin-1 stimulates Gq protein-coupled receptors to promote proliferation in dividing cells or hypertrophy in terminally differentiated cardiomyocytes. In cardiomyocytes, endothelin-1 rapidly (within minutes) stimulates protein kinase signaling, including extracellular-signal regulated kinases 1/2 (ERK1/2; though not ERK5), with phenotypic/physiological changes developing from approximately 12 h. Hypertrophy is associated with changes in mRNA/protein expression, presumably consequent to protein kinase signaling, but the connections between early, transient signaling events and developed hypertrophy are unknown. Results: Using microarrays, we defined the early transcriptional responses of neonatal rat cardiomyocytes to endothelin-1 over 4 h, differentiating between immediate early gene (IEG) and second phase RNAs with cycloheximide. IEGs exhibited differential temporal and transient regulation, with expression of second phase RNAs within 1 h. Of transcripts upregulated at 30 minutes encoding established proteins, 28 were inhibited >50% by U0126 (which inhibits ERK1/2/5 signaling), with 9 inhibited 25-50%. Expression of only four transcripts was not inhibited. At 1 h, most RNAs (approximately 67%) were equally changed in total and polysomal RNA with approximately 17% of transcripts increased to a greater extent in polysomes. Thus, changes in expression of most protein-coding RNAs should be reflected in protein synthesis. However, approximately 16% of transcripts were essentially excluded from the polysomes, including some protein-coding mRNAs, presumably inefficiently translated. Conclusion: The phasic, temporal regulation of early transcriptional responses induced by endothelin-1 in cardiomyocytes indicates that, even in terminally differentiated cells, signals are propagated beyond the primary signaling pathways through transcriptional networks leading to phenotypic changes (that is, hypertrophy). Furthermore, ERK1/2 signaling plays a major role in this response.

Fast northward energy transfer in the Atlantic due to Agulhas rings

The adiabatic transit time of wave energy radiated by an Agulhas ring released in the South Atlantic Ocean to the North Atlantic Ocean is investigated in a two-layer ocean model. Of particular interest is the arrival time of baroclinic energy in the northern part of the Atlantic, because it is related to variations in the meridional overturning circulation. The influence of the Mid-Atlantic Ridge is also studied, because it allows for the conversion from barotropic to baroclinic wave energy and the generation of topographic waves. Barotropic energy from the ring is present in the northern part of the model basin within 10 days. From that time, the barotropic energy keeps rising to attain a maximum 500 days after initiation. This is independent of the presence or absence of a ridge in the model basin. Without a ridge in the model, the travel time of the baroclinic signal is 1300 days. This time is similar to the transit time of the ring from the eastern to the western coast of the model basin. In the presence of the ridge, the baroclinic signal arrives in the northern part of the model basin after approximately 10 days, which is the same time scale as that of the barotropic signal. It is apparent that the ridge can facilitate the energy conversion from barotropic to baroclinic waves and the slow baroclinic adjustment can be bypassed. The meridional overturning circulation, parameterized in two ways as either a purely barotropic or a purely baroclinic phenomenon, also responds after 1300 days. The ring temporarily increases the overturning strength. Th presence of the ridge does not alter the time scales.

Ensemble forecasts of a flood-producing storm: comparison of the influence of model-state perturbations and parameter modifications

High-resolution ensemble simulations (Δx = 1 km) are performed with the Met Office Unified Model for the Boscastle (Cornwall, UK) flash-flooding event of 16 August 2004. Forecast uncertainties arising from imperfections in the forecast model are analysed by comparing the simulation results produced by two types of perturbation strategy. Motivated by the meteorology of the event, one type of perturbation alters relevant physics choices or parameter settings in the model's parametrization schemes. The other type of perturbation is designed to account for representativity error in the boundary-layer parametrization. It makes direct changes to the model state and provides a lower bound against which to judge the spread produced by other uncertainties. The Boscastle has genuine skill at scales of approximately 60 km and an ensemble spread which can be estimated to within ∼ 10% with only eight members. Differences between the model-state perturbation and physics modification strategies are discussed, the former being more important for triggering and the latter for subsequent cell development, including the average internal structure of convective cells. Despite such differences, the spread in rainfall evaluated at skilful scales is shown to be only weakly sensitive to the perturbation strategy. This suggests that relatively simple strategies for treating model uncertainty may be sufficient for practical, convective-scale ensemble forecasting.

The proportionality of global warming to cumulative carbon emissions

The global temperature response to increasing atmospheric CO2 is often quantified by metrics such as equilibrium climate sensitivity and transient climate response1. These approaches, however, do not account for carbon cycle feedbacks and therefore do not fully represent the net response of the Earth system to anthropogenic CO2 emissions. Climate–carbon modelling experiments have shown that: (1) the warming per unit CO2 emitted does not depend on the background CO2 concentration2; (2) the total allowable emissions for climate stabilization do not depend on the timing of those emissions3, 4, 5; and (3) the temperature response to a pulse of CO2 is approximately constant on timescales of decades to centuries3, 6, 7, 8. Here we generalize these results and show that the carbon–climate response (CCR), defined as the ratio of temperature change to cumulative carbon emissions, is approximately independent of both the atmospheric CO2 concentration and its rate of change on these timescales. From observational constraints, we estimate CCR to be in the range 1.0–2.1 °C per trillion tonnes of carbon (Tt C) emitted (5th to 95th percentiles), consistent with twenty-first-century CCR values simulated by climate–carbon models. Uncertainty in land-use CO2 emissions and aerosol forcing, however, means that higher observationally constrained values cannot be excluded. The CCR, when evaluated from climate–carbon models under idealized conditions, represents a simple yet robust metric for comparing models, which aggregates both climate feedbacks and carbon cycle feedbacks. CCR is also likely to be a useful concept for climate change mitigation and policy; by combining the uncertainties associated with climate sensitivity, carbon sinks and climate–carbon feedbacks into a single quantity, the CCR allows CO2-induced global mean temperature change to be inferred directly from cumulative carbon emissions.

Is Energy Efficiency Priced in the Housing Market? Some Evidence from the United Kingdom.

This paper investigates whether energy performance ratings, as measured by mandatory Energy Performance Certificates (EPCs), are reflected in the sale prices of residential properties. This is the first large-scale empirical study of this topic in the UK involving approximately 400,000 dwellings in the period from 1995 to 2011. Applying hedonic regression and an augmented repeat sales regression, we find a positive relationship between the energy efficiency rating of a dwelling and the transaction price per square metre. The price effects of superior energy performance tend to be higher for terraced dwellings and flats compared to detached and semi-detached dwellings. The evidence is less clear-cut for house price growth rates but remains supportive of an overall positive association. Overall, the results of this study appear to support the hypothesis that energy efficiency levels are reflected in UK house prices, at least in recent years.

Predicting outcomes following cognitive behavior therapy in child anxiety disorders: the influence of genetic, demographic and clinical information

Background. Within a therapeutic gene by environment (GxE) framework, we recently demonstrated that variation in the Serotonin Transporter Promoter Polymorphism; 5HTTLPR and marker rs6330 in Nerve Growth Factor gene; NGF is associated with poorer outcomes following cognitive behaviour therapy (CBT) for child anxiety disorders. The aim of this study was to explore one potential means of extending the translational reach of G×E data in a way that may be clinically informative. We describe a ‘risk-index’ approach combining genetic, demographic and clinical data and test its ability to predict diagnostic outcome following CBT in anxious children. Method. DNA and clinical data were collected from 384 children with a primary anxiety disorder undergoing CBT. We tested our risk model in five cross-validation training sets. Results. In predicting treatment outcome, six variables had a minimum mean beta value of 0.5: 5HTTLPR, NGF rs6330, gender, primary anxiety severity, comorbid mood disorder and comorbid externalising disorder. A risk index (range 0-8) constructed from these variables had moderate predictive ability (AUC = .62-.69) in this study. Children scoring high on this index (5-8) were approximately three times as likely to retain their primary anxiety disorder at follow-up as compared to those children scoring 2 or less. Conclusion. Significant genetic, demographic and clinical predictors of outcome following CBT for anxiety-disordered children were identified. Combining these predictors within a risk-index could be used to identify which children are less likely to be diagnosis free following CBT alone or thus require longer or enhanced treatment. The ‘risk-index’ approach represents one means of harnessing the translational potential of G×E data.

Simulating the interannual variability of major dust storms on Mars using variable lifting thresholds

The redistribution of a finite amount of martian surface dust during global dust storms and in the intervening periods has been modelled in a dust lifting version of the UK Mars General Circulation Model. When using a constant, uniform threshold in the model’s wind stress lifting parameterisation and assuming an unlimited supply of surface dust, multiannual simulations displayed some variability in dust lifting activity from year to year, arising from internal variability manifested in surface wind stress, but dust storms were limited in size and formed within a relatively short seasonal window. Lifting thresholds were then allowed to vary at each model gridpoint, dependent on the rates of emission or deposition of dust. This enhanced interannual variability in dust storm magnitude and timing, such that model storms covered most of the observed ranges in size and initiation date within a single multiannual simulation. Peak storm magnitude in a given year was primarily determined by the availability of surface dust at a number of key sites in the southern hemisphere. The observed global dust storm (GDS) frequency of roughly one in every 3 years was approximately reproduced, but the model failed to generate these GDSs spontaneously in the southern hemisphere, where they have typically been observed to initiate. After several years of simulation, the surface threshold field—a proxy for net change in surface dust density—showed good qualitative agreement with the observed pattern of martian surface dust cover. The model produced a net northward cross-equatorial dust mass flux, which necessitated the addition of an artificial threshold decrease rate in order to allow the continued generation of dust storms over the course of a multiannual simulation. At standard model resolution, for the southward mass flux due to cross-equatorial flushing storms to offset the northward flux due to GDSs on a timescale of ∼3 years would require an increase in the former by a factor of 3–4. Results at higher model resolution and uncertainties in dust vertical profiles mean that quasi-periodic redistribution of dust on such a timescale nevertheless appears to be a plausible explanation for the observed GDS frequency.

RNA interference suppression of genes in glycosyl transferase families 43 and 47 in wheat starchy endosperm causes large decreases in arabinoxylan content

The cell walls of wheat (Triticum aestivum) starchy endosperm are dominated by arabinoxylan (AX), accounting for 65% to 70% of the polysaccharide content. Genes within two glycosyl transferase (GT) families, GT43 (IRREGULAR XYLEM9 [IRX9] and IRX14) and GT47 (IRX10), have previously been shown to be involved in the synthesis of the xylan backbone in Arabidopsis, and close homologs of these have been implicated in the synthesis of xylan in other species. Here, homologs of IRX10 TaGT47_2 and IRX9 TaGT43_2, which are highly expressed in wheat starchy endosperm cells, were suppressed by RNA interference (RNAi) constructs driven by a starchy endosperm-specific promoter. The total amount of AX was decreased by 40% to 50% and the degree of arabinosylation was increased by 25% to 30% in transgenic lines carrying either of the transgenes. The cell walls of starchy endosperm in sections of grain from TaGT43_2 and TaGT47_2 RNAi transgenics showed decreased immunolabeling for xylan and arabinoxylan epitopes and approximately 50% decreased cell wall thickness compared with controls. The proportion of AX that was water soluble was not significantly affected, but average AX polymer chain length was decreased in both TaGT43_2 and TaGT47_2 RNAi transgenics. However, the long AX chains seen in controls were absent in TaGT43_2 RNAi transgenics but still present in TaGT47_2 RNAi transgenics. The results support an emerging picture of IRX9-like and IRX10-like proteins acting as key components in the xylan synthesis machinery in both dicots and grasses. Since AX is the main component of dietary fiber in wheat foods, the TaGT43_2 and TaGT47_2 genes are of major importance to human nutrition.

Magnetic resonance imaging of a randomized controlled trial investigating predictors of recovery following psychological treatment in adolescents with moderate to severe unipolar depression: study protocol for Magnetic Resonance - Improving Mood with Psychoanalytic and Cognitive Therapies (MR-IMPACT)

Background Major depressive disorders (MDD) are a debilitating and pervasive group of mental illnesses afflicting many millions of people resulting in the loss of 110 million working days and more than 2,500 suicides per annum. Adolescent MDD patients attending NHS clinics show high rates of recurrence into adult life. A meta-analysis of recent research shows that psychological treatments are not as efficacious as previously thought. Modest treatment outcomes of approximately 65% of cases responding suggest that aetiological and clinical heterogeneity may hamper the better use of existing therapies and discovery of more effective treatments. Information with respect to optimal treatment choice for individuals is lacking, with no validated biomarkers to aid therapeutic decision-making. Methods/Design Magnetic resonance-Improving Mood with Psychoanalytic and Cognitive Therapies, the MR-IMPACT study, plans to identify brain regions implicated in the pathophysiology of depressions and examine whether there are specific behavioural or neural markers predicting remission and/or subsequent relapse in a subsample of depressed adolescents recruited to the IMPACT randomised controlled trial (Registration # ISRCTN83033550). Discussion MR-IMPACT is an investigative biomarker component of the IMPACT pragmatic effectiveness trial. The aim of this investigation is to identify neural markers and regional indicators of the pathophysiology of and treatment response for MDD in adolescents. We anticipate that these data may enable more targeted treatment delivery by identifying those patients who may be optimal candidates for therapeutic response.