A model of the hemodynamic response and oxygen delivery to brain

A recent nonlinear system by Friston et al. (2000. NeuroImage 12: 466–477) links the changes in BOLD response to changes in neural activity. The system consists of five subsystems, linking: (1) neural activity to flow changes; (2) flow changes to oxygen delivery to tissue; (3) flow changes to changes in blood volume and venous outflow; (4) changes in flow, volume, and oxygen extraction fraction to deoxyhemoglobin changes; and finally (5) volume and deoxyhemoglobin changes to the BOLD response. Friston et al. exploit, in subsystem 2, a model by Buxton and Frank coupling flow changes to changes in oxygen metabolism which assumes tissue oxygen concentration to be close to zero. We describe below a model of the coupling between flow and oxygen delivery which takes into account the modulatory effect of changes in tissue oxygen concentration. The major development has been to extend the original Buxton and Frank model for oxygen transport to a full dynamic capillary model making the model applicable to both transient and steady state conditions. Furthermore our modification enables us to determine the time series of CMRO2 changes under different conditions, including CO2 challenges. We compare the differences in the performance of the “Friston system” using the original model of Buxton and Frank and that of our model. We also compare the data predicted by our model (with appropriate parameters) to data from a series of OIS studies. The qualitative differences in the behaviour of the models are exposed by different experimental simulations and by comparison with the results of OIS data from brief and extended stimulation protocols and from experiments using hypercapnia.

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.

General circulation model estimates of aerosol transport and radiative forcing during the Indian Ocean Experiment

Aerosol sources, transport, and sinks are simulated, and aerosol direct radiative effects are assessed over the Indian Ocean for the Indian Ocean Experiment (INDOEX) Intensive Field Phase during January to March 1999 using the Laboratoire de Me´te´orologie Dynamique (LMDZT) general circulation model. The model reproduces the latitudinal gradient in aerosol mass concentration and optical depth (AOD). The model-predicted aerosol concentrations and AODs agree reasonably well with measurements but are systematically underestimated during high-pollution episodes, especially in the month of March. The largest aerosol loads are found over southwestern China, the Bay of Bengal, and the Indian subcontinent. Aerosol emissions from the Indian subcontinent are transported into the Indian Ocean through either the west coast or the east coast of India. Over the INDOEX region, carbonaceous aerosols are the largest contributor to the estimated AOD, followed by sulfate, dust, sea salt, and fly ash. During the northeast winter monsoon, natural and anthropogenic aerosols reduce the solar flux reaching the surface by 25 W m�2, leading to 10–15% less insolation at the surface. A doubling of black carbon (BC) emissions from Asia results in an aerosol single-scattering albedo that is much smaller than in situ measurements, reflecting the fact that BC emissions are not underestimated in proportion to other (mostly scattering) aerosol types. South Asia is the dominant contributor to sulfate aerosols over the INDOEX region and accounts for 60–70% of the AOD by sulfate. It is also an important but not the dominant contributor to carbonaceous aerosols over the INDOEX region with a contribution of less than 40% to the AOD by this aerosol species. The presence of elevated plumes brings significant quantities of aerosols to the Indian Ocean that are generated over Africa and Southeast and east Asia.

Linguistic and cognitive motivations for the typological primacy model of third language (L3) transfer: considering the role of timing of acquisition and proficiency in the previous languages

This article elucidates the Typological Primacy Model (TPM; Rothman, 2010, 2011, 2013) for the initial stages of adult third language (L3) morphosyntactic transfer, addressing questions that stem from the model and its application. The TPM maintains that structural proximity between the L3 and the L1 and/or the L2 determines L3 transfer. In addition to demonstrating empirical support for the TPM, this article articulates a proposal for how the mind unconsciously determines typological (structural) proximity based on linguistic cues from the L3 input stream used by the parser early on to determine holistic transfer of one previous (the L1 or the L2) system. This articulated version of the TPM is motivated by argumentation appealing to cognitive and linguistic factors. Finally, in line with the general tenets of the TPM, I ponder if and why L3 transfer might obtain differently depending on the type of bilingual (e.g. early vs. late) and proficiency level of bilingualism involved in the L3 process.

Evaluating adjusted forcing and model spread for historical and future scenarios in the CMIP5 generation of climate models

We utilize energy budget diagnostics from the Coupled Model Intercomparison Project phase 5 (CMIP5) to evaluate the models' climate forcing since preindustrial times employing an established regression technique. The climate forcing evaluated this way, termed the adjusted forcing (AF), includes a rapid adjustment term associated with cloud changes and other tropospheric and land-surface changes. We estimate a 2010 total anthropogenic and natural AF from CMIP5 models of 1.9 ± 0.9 W m−2 (5–95% range). The projected AF of the Representative Concentration Pathway simulations are lower than their expected radiative forcing (RF) in 2095 but agree well with efficacy weighted forcings from integrated assessment models. The smaller AF, compared to RF, is likely due to cloud adjustment. Multimodel time series of temperature change and AF from 1850 to 2100 have large intermodel spreads throughout the period. The intermodel spread of temperature change is principally driven by forcing differences in the present day and climate feedback differences in 2095, although forcing differences are still important for model spread at 2095. We find no significant relationship between the equilibrium climate sensitivity (ECS) of a model and its 2003 AF, in contrast to that found in older models where higher ECS models generally had less forcing. Given the large present-day model spread, there is no indication of any tendency by modelling groups to adjust their aerosol forcing in order to produce observed trends. Instead, some CMIP5 models have a relatively large positive forcing and overestimate the observed temperature change.

An isotope dilution model for partitioning phenylalanine and tyrosine uptake by the mammary gland of lactating dairy cows

An isotope dilution model for partitioning phenylalanine and tyrosine uptake by the mammary gland of the lactating dairy cow is constructed and solved in the steady state. The model contains four intracellular and four extracellular pools and conservation of mass principles are applied to generate the fundamental equations describing the behaviour of the system. The experimental measurements required for model solution are milk secretion and plasma flow rate across the gland in combination with phenylalanine and tyrosine concentrations and plateau isotopic enrichments in arterial and venous plasma and free and protein bound milk during a constant infusion of [1-(13)C]phenylalanine and [2,3,5,6-(2)H]tyrosine tracer. If assumptions are made, model solution enables determination of steady state flows for phenylalanine and tyrosine inflow to the gland, outflow from it and bypass, and flows representing the synthesis and degradation of constitutive protein and hydroxylation. The model is effective in providing information about the fates of phenylalanine and tyrosine in the mammary gland and could be used as part of a more complex system describing amino acid metabolism in the whole ruminant.

Unrestricted Skyrme-tensor time-dependent Hartree-Fock model and its application to the nuclear response from spherical to triaxial nuclei

The nuclear time-dependent Hartree-Fock model formulated in three-dimensional space, based on the full standard Skyrme energy density functional complemented with the tensor force, is presented. Full self-consistency is achieved by the model. The application to the isovector giant dipole resonance is discussed in the linear limit, ranging from spherical nuclei (16O and 120Sn) to systems displaying axial or triaxial deformation (24Mg, 28Si, 178Os, 190W and 238U). Particular attention is paid to the spin-dependent terms from the central sector of the functional, recently included together with the tensor. They turn out to be capable of producing a qualitative change on the strength distribution in this channel. The effect on the deformation properties is also discussed. The quantitative effects on the linear response are small and, overall, the giant dipole energy remains unaffected. Calculations are compared to predictions from the (quasi)-particle random-phase approximation and experimental data where available, finding good agreement

Vertical structure and physical processes of the Madden-Julian oscillation: exploring key model physics in climate simulations

Aimed at reducing deficiencies in representing the Madden-Julian oscillation (MJO) in general circulation models (GCMs), a global model evaluation project on vertical structure and physical processes of the MJO was coordinated. In this paper, results from the climate simulation component of this project are reported. It is shown that the MJO remains a great challenge in these latest generation GCMs. The systematic eastward propagation of the MJO is only well simulated in about one-fourth of the total participating models. The observed vertical westward tilt with altitude of the MJO is well simulated in good MJO models, but not in the poor ones. Damped Kelvin wave responses to the east of convection in the lower troposphere could be responsible for the missing MJO preconditioning process in these poor MJO models. Several process-oriented diagnostics were conducted to discriminate key processes for realistic MJO simulations. While large-scale rainfall partition and low-level mean zonal winds over the Indo-Pacific in a model are not found to be closely associated with its MJO skill, two metrics, including the low-level relative humidity difference between high and low rain events and seasonal mean gross moist stability, exhibit statistically significant correlations with the MJO performance. It is further indicated that increased cloud-radiative feedback tends to be associated with reduced amplitude of intraseasonal variability, which is incompatible with the radiative instability theory previously proposed for the MJO. Results in this study confirm that inclusion of air-sea interaction can lead to significant improvement in simulating the MJO.

A coupled cloud physics–radiation parameterization of the bulk optical properties of cirrus and its impact on the Met Office unified model global atmosphere 5.0 configuration

A new coupled cloud physics–radiation parameterization of the bulk optical properties of ice clouds is presented. The parameterization is consistent with assumptions in the cloud physics scheme regarding particle size distributions (PSDs) and mass–dimensional relationships. The parameterization is based on a weighted ice crystal habit mixture model, and its bulk optical properties are parameterized as simple functions of wavelength and ice water content (IWC). This approach directly couples IWC to the bulk optical properties, negating the need for diagnosed variables, such as the ice crystal effective dimension. The parameterization is implemented into the Met Office Unified Model Global Atmosphere 5.0 (GA5) configuration. The GA5 configuration is used to simulate the annual 20-yr shortwave (SW) and longwave (LW) fluxes at the top of the atmosphere (TOA), as well as the temperature structure of the atmosphere, under various microphysical assumptions. The coupled parameterization is directly compared against the current operational radiation parameterization, while maintaining the same cloud physics assumptions. In this experiment, the impacts of the two parameterizations on the SW and LW radiative effects at TOA are also investigated and compared against observations. The 20-yr simulations are compared against the latest observations of the atmospheric temperature and radiative fluxes at TOA. The comparisons demonstrate that the choice of PSD and the assumed ice crystal shape distribution are as important as each other. Moreover, the consistent radiation parameterization removes a long-standing tropical troposphere cold temperature bias but slightly warms the southern midlatitudes by about 0.5 K.

Linguistic and cognitive motivations for the typological primacy model of third language (L3) transfer: timing of acquisition and proficiency considered

This article elucidates the Typological Primacy Model (TPM; Rothman, 2010, 2011, 2013) for the initial stages of adult third language (L3) morphosyntactic transfer, addressing questions that stem from the model and its application. The TPM maintains that structural proximity between the L3 and the L1 and/or the L2 determines L3 transfer. In addition to demonstrating empirical support for the TPM, this article articulates a proposal for how the mind unconsciously determines typological (structural) proximity based on linguistic cues from the L3 input stream used by the parser early on to determine holistic transfer of one previous (the L1 or the L2) system. This articulated version of the TPM is motivated by argumentation appealing to cognitive and linguistic factors. Finally, in line with the general tenets of the TPM, I ponder if and why L3 transfer might obtain differently depending on the type of bilingual (e.g. early vs. late) and proficiency level of bilingualism involved in the L3 process.

Current model capabilities for simulating black carbon and sulfate concentrations in the Arctic atmosphere: a multi-model evaluation using a comprehensive measurement data set

The concentrations of sulfate, black carbon (BC) and other aerosols in the Arctic are characterized by high values in late winter and spring (so-called Arctic Haze) and low values in summer. Models have long been struggling to capture this seasonality and especially the high concentrations associated with Arctic Haze. In this study, we evaluate sulfate and BC concentrations from eleven different models driven with the same emission inventory against a comprehensive pan-Arctic measurement data set over a time period of 2 years (2008–2009). The set of models consisted of one Lagrangian particle dispersion model, four chemistry transport models (CTMs), one atmospheric chemistry-weather forecast model and five chemistry climate models (CCMs), of which two were nudged to meteorological analyses and three were running freely. The measurement data set consisted of surface measurements of equivalent BC (eBC) from five stations (Alert, Barrow, Pallas, Tiksi and Zeppelin), elemental carbon (EC) from Station Nord and Alert and aircraft measurements of refractory BC (rBC) from six different campaigns. We find that the models generally captured the measured eBC or rBC and sulfate concentrations quite well, compared to previous comparisons. However, the aerosol seasonality at the surface is still too weak in most models. Concentrations of eBC and sulfate averaged over three surface sites are underestimated in winter/spring in all but one model (model means for January–March underestimated by 59 and 37 % for BC and sulfate, respectively), whereas concentrations in summer are overestimated in the model mean (by 88 and 44 % for July–September), but with overestimates as well as underestimates present in individual models. The most pronounced eBC underestimates, not included in the above multi-site average, are found for the station Tiksi in Siberia where the measured annual mean eBC concentration is 3 times higher than the average annual mean for all other stations. This suggests an underestimate of BC sources in Russia in the emission inventory used. Based on the campaign data, biomass burning was identified as another cause of the modeling problems. For sulfate, very large differences were found in the model ensemble, with an apparent anti-correlation between modeled surface concentrations and total atmospheric columns. There is a strong correlation between observed sulfate and eBC concentrations with consistent sulfate/eBC slopes found for all Arctic stations, indicating that the sources contributing to sulfate and BC are similar throughout the Arctic and that the aerosols are internally mixed and undergo similar removal. However, only three models reproduced this finding, whereas sulfate and BC are weakly correlated in the other models. Overall, no class of models (e.g., CTMs, CCMs) performed better than the others and differences are independent of model resolution.

The role of CO2 and dynamic vegetation on the impact of temperate land use change in the HadCM3 coupled climate model

Human induced land-use change (LUC) alters the biogeophysical characteristics of the land surface influencing the surface energy balance. The level of atmospheric CO2 is expected to increase in the coming century and beyond, modifying temperature and precipitation patterns and altering the distribution and physiology of natural vegetation. It is important to constrain how CO2-induced climate and vegetation change may influence the regional extent to which LUC alters climate. This sensitivity study uses the HadCM3 coupled climate model under a range of equilibrium forcings to show that the impact of LUC declines under increasing atmospheric CO2, specifically in temperate and boreal regions. A surface energy balance analysis is used to diagnose how these changes occur. In Northern Hemisphere winter this pattern is attributed in part to the decline in winter snow cover and in the summer due to a reduction in latent cooling with higher levels of CO2. The CO2-induced change in natural vegetation distribution is also shown to play a significant role. Simulations run at elevated CO2 yet present day vegetation show a significantly increased sensitivity to LUC, driven in part by an increase in latent cooling. This study shows that modelling the impact of LUC needs to accurately simulate CO2 driven changes in precipitation and snowfall, and incorporate accurate, dynamic vegetation distribution.

A high-order arbitrarily unstructured finite-volume model of the global atmosphere: tests solving the shallow-water equations

Simulations of the global atmosphere for weather and climate forecasting require fast and accurate solutions and so operational models use high-order finite differences on regular structured grids. This precludes the use of local refinement; techniques allowing local refinement are either expensive (eg. high-order finite element techniques) or have reduced accuracy at changes in resolution (eg. unstructured finite-volume with linear differencing). We present solutions of the shallow-water equations for westerly flow over a mid-latitude mountain from a finite-volume model written using OpenFOAM. A second/third-order accurate differencing scheme is applied on arbitrarily unstructured meshes made up of various shapes and refinement patterns. The results are as accurate as equivalent resolution spectral methods. Using lower order differencing reduces accuracy at a refinement pattern which allows errors from refinement of the mountain to accumulate and reduces the global accuracy over a 15 day simulation. We have therefore introduced a scheme which fits a 2D cubic polynomial approximately on a stencil around each cell. Using this scheme means that refinement of the mountain improves the accuracy after a 15 day simulation. This is a more severe test of local mesh refinement for global simulations than has been presented but a realistic test if these techniques are to be used operationally. These efficient, high-order schemes may make it possible for local mesh refinement to be used by weather and climate forecast models.

Simulating metals and mine discharges in river basins using a new integrated catchment model for metals: pollution impacts and restoration strategies in the Aries-Mures river system in Transylvania, Romania

The INtegrated CAtchment (INCA) model has been developed to simulate the impact of mine discharges on river systems. The model accounts for the key kinetic chemical processes operating as well as the dilution, mixing and redistribution of pollutants in rivers downstream of mine discharges or acid rock drainage sites. The model is dynamic and simulates the day-to-day behaviour of hydrology and eight metals (cadmium, mercury, copper, zinc, lead, arsenic, manganese and chromium) as well as cyanide and ammonia. The model is semi-distributed and can simulate catchments, sub-catchment and in-stream river behaviour. The model has been applied to the Roia Montan Mine in Transylvania, Romania, and used to assess the impacts of old mine adits on the local catchments as well as on the downstream Aries and Mures river system. The question of mine restoration is investigated and a set of clean-up scenarios investigated. It is shown that the planned restoration will generate a much improved water quality from the mine and also alleviate the metal pollution of the river system.