Impacts of seawater acidification on mantle gene expression patterns of the Baltic Sea blue mussel: implications for shell formation and energy metabolism, link to supplementary material

Marine organisms have to cope with increasing CO2 partial pressures and decreasing pH in the oceans. We elucidated the impacts of an 8-week acclimation period to four seawater pCO2 treatments (39, 113, 243 and 405 Pa/385, 1,120, 2,400 and 4,000 µatm) on mantle gene expression patterns in the blue mussel Mytilus edulis from the Baltic Sea. Based on the M. edulis mantle tissue transcriptome, the expression of several genes involved in metabolism, calcification and stress responses was assessed in the outer (marginal and pallial zone) and the inner mantle tissues (central zone) using quantitative real-time PCR. The expression of genes involved in energy and protein metabolism (F-ATPase, hexokinase and elongation factor alpha) was strongly affected by acclimation to moderately elevated CO2 partial pressures. Expression of a chitinase, potentially important for the calcification process, was strongly depressed (maximum ninefold), correlating with a linear decrease in shell growth observed in the experimental animals. Interestingly, shell matrix protein candidate genes were less affected by CO2 in both tissues. A compensatory process toward enhanced shell protection is indicated by a massive increase in the expression of tyrosinase, a gene involved in periostracum formation (maximum 220-fold). Using correlation matrices and a force-directed layout network graph, we were able to uncover possible underlying regulatory networks and the connections between different pathways, thereby providing a molecular basis of observed changes in animal physiology in response to ocean acidification.

Towards convection-resolving, global atmospheric simulations with the Model for Prediction Across Scales (MPAS) v3.1: an extreme scaling experiment, links to sourcecode of model and grides

The Model for Prediction Across Scales (MPAS) is a novel set of Earth system simulation components and consists of an atmospheric model, an ocean model and a land-ice model. Its distinct features are the use of unstructured Voronoi meshes and C-grid discretisation to address shortcomings of global models on regular grids and the use of limited area models nested in a forcing data set, with respect to parallel scalability, numerical accuracy and physical consistency. This concept allows one to include the feedback of regional land use information on weather and climate at local and global scales in a consistent way, which is impossible to achieve with traditional limited area modelling approaches. Here, we present an in-depth evaluation of MPAS with regards to technical aspects of performing model runs and scalability for three medium-size meshes on four different high-performance computing (HPC) sites with different architectures and compilers. We uncover model limitations and identify new aspects for the model optimisation that are introduced by the use of unstructured Voronoi meshes. We further demonstrate the model performance of MPAS in terms of its capability to reproduce the dynamics of the West African monsoon (WAM) and its associated precipitation in a pilot study. Constrained by available computational resources, we compare 11-month runs for two meshes with observations and a reference simulation from the Weather Research and Forecasting (WRF) model. We show that MPAS can reproduce the atmospheric dynamics on global and local scales in this experiment, but identify a precipitation excess for the West African region. Finally, we conduct extreme scaling tests on a global 3?km mesh with more than 65 million horizontal grid cells on up to half a million cores. We discuss necessary modifications of the model code to improve its parallel performance in general and specific to the HPC environment. We confirm good scaling (70?% parallel efficiency or better) of the MPAS model and provide numbers on the computational requirements for experiments with the 3?km mesh. In doing so, we show that global, convection-resolving atmospheric simulations with MPAS are within reach of current and next generations of high-end computing facilities.

Combined Conduction-Convection-Radiation Heat Transfer of Slip Flow inside a Micro-channel Filled with a Cellular Porous Material

Combined conduction–convection–radiation heat transfer is investigated numerically in a micro-channel filled with a saturated cellular porous medium, with the channel walls held at a constant heat flux. Invoking the velocity slip and temperature jump, the thermal behaviour of the porous–fluid system are studied by considering hydrodynamically fully developed flow and applying the Darcy–Brinkman flow model. One energy equation model based on the local thermal equilibrium condition is adopted to evaluate the temperature field within the porous medium. Combined conduction and radiation heat transfer is treated as an effective conduction process with a temperature-dependent effective thermal conductivity. Results are reported in terms of the average Nusselt number and dimensionless temperature distribution, as a function of velocity slip coefficient, temperature jump coefficient, porous medium shape parameter and radiation parameters. Results show that increasing the radiation parameter (Tr)(Tr) and the temperature jump coefficient flattens the dimensionless temperature profile. The Nusselt numbers are more sensitive to the variation in the temperature jump coefficient rather than to the velocity slip coefficient. Such that for high porous medium shape parameter, the Nusselt number is found to be independent of velocity slip. Furthermore, it is found that as the temperature jump coefficient increases, the Nusselt number decrease. In addition, for high temperature jump coefficients, the Nusselt number is found to be insensitive to the radiation parameters and porous medium shape parameter. It is also concluded that compared with the conventional macro-channels, wherein using a porous material enhances the rate of heat transfer (up to about 40 % compared to the clear channel), insertion of a porous material inside a micro-channel in slip regime does not effectively enhance the rate of heat transfer that is about 2 %.

Convection-diffusion in MHD: Comparison of primitive variable and vector potential solutions of the magnetic induction equation

Abstract not available

Toward assessing the effects of aerosols on deep convection: a numerical study using the WRF-Chemistry model

As the formative agents of cloud droplets, aerosols play an undeniably important role in the development of clouds and precipitation. Few meteorological models have been developed or adapted to simulate aerosols and their contribution to cloud and precipitation processes. The Weather Research and Forecasting model (WRF) has recently been coupled with an atmospheric chemistry suite and is jointly referred to as WRF-Chem, allowing atmospheric chemistry and meteorology to influence each other’s evolution within a mesoscale modeling framework. Provided that the model physics are robust, this framework allows the feedbacks between aerosol chemistry, cloud physics, and dynamics to be investigated. This study focuses on the effects of aerosols on meteorology, specifically, the interaction of aerosol chemical species with microphysical processes represented within the framework of the WRF-Chem. Aerosols are represented by eight size bins using the Model for Simulating Aerosol Interactions and Chemistry (MOSAIC) sectional parameterization, which is linked to the Purdue Lin bulk microphysics scheme. The aim of this study is to examine the sensitivity of deep convective precipitation modeled by the 2D WRF-Chem to varying aerosol number concentration and aerosol type. A systematic study has been performed regarding the effects of aerosols on parameters such as total precipitation, updraft/downdraft speed, distribution of hydrometeor species, and organizational features, within idealized maritime and continental thermodynamic environments. Initial results were obtained using WRFv3.0.1, and a second series of tests were run using WRFv3.2 after several changes to the activation, autoconversion, and Lin et al. microphysics schemes added by the WRF community, as well as the implementation of prescribed vertical levels by the author. The results of WRFv3.2 runs contrasted starkly with WRFv3.0.1 runs. The WRFv3.0.1 runs produced a propagating system resembling a developing squall line, whereas the WRFv3.2 runs did not. The response of total precipitation, updraft/downdraft speeds, and system organization to increasing aerosol concentrations were opposite between runs with different versions of WRF. Results of the WRFv3.2 runs, however, were in better agreement in timing and magnitude of vertical velocity and hydrometeor content with a WRFv3.0.1 run using single-moment Lin et al. microphysics, than WRFv3.0.1 runs with chemistry. One result consistent throughout all simulations was an inhibition in warm-rain processes due to enhanced aerosol concentrations, which resulted in a delay of precipitation onset that ranged from 2-3 minutes in WRFv3.2 runs, and up to 15 minutes in WRFv.3.0.1 runs. This result was not observed in a previous study by Ntelekos et al. (2009) using the WRF-Chem, perhaps due to their use of coarser horizontal and vertical resolution within their experiment. The changes to microphysical processes such as activation and autoconversion from WRFv3.0.1 to WRFv3.2, along with changes in the packing of vertical levels, had more impact than the varying aerosol concentrations even though the range of aerosol tested was greater than that observed in field studies. In order to take full advantage of the input of aerosols now offered by the chemistry module in WRF, the author recommends that a fully double-moment microphysics scheme be linked, rather than the limited double-moment Lin et al. scheme that currently exists. With this modification, the WRF-Chem will be a powerful tool for studying aerosol-cloud interactions and allow comparison of results with other studies using more modern and complex microphysical parameterizations.

Seismic waveform inversion for core-mantle boundary topography

International audience

Savani: A variable resolution whole-mantle model of anisotropic shear velocity variations based on multiple data sets

International audience

Large Rayleigh number thermal convection: heat flux predictions and strongly nonlinear solutions

We investigate the structure of strongly nonlinear Rayleigh–Bénard convection cells in the asymptotic limit of large Rayleigh number and fixed, moderate Prandtl number. Unlike the flows analyzed in prior theoretical studies of infinite Prandtl number convection, our cellular solutions exhibit dynamically inviscid constant-vorticity cores. By solving an integral equation for the cell-edge temperature distribution, we are able to predict, as a function of cell aspect ratio, the value of the core vorticity, details of the flow within the thin boundary layers and rising/falling plumes adjacent to the edges of the convection cell, and, in particular, the bulk heat flux through the layer. The results of our asymptotic analysis are corroborated using full pseudospectral numerical simulations and confirm that the heat flux is maximized for convection cells that are roughly square in cross section.

Experimental and modeling studies of forced convection storage and drying systems for sweet potatoes

Sweet potato is an important strategic agricultural crop grown in many countries around the world. The roots and aerial vine components of the crop are used for both human consumption and, to some extent as a cheap source of animal feed. In spite of its economic value and growing contribution to health and nutrition, harvested sweet potato roots and aerial vine components has limited shelf-life and is easily susceptible to post-harvest losses. Although post-harvest losses of both sweet potato roots and aerial vine components is significant, there is no information available that will support the design and development of appropriate storage and preservation systems. In this context, the present study was initiated to improve scientific knowledge about sweet potato post-harvest handling. Additionally, the study also seeks to develop a PV ventilated mud storehouse for storage of sweet potato roots under tropical conditions. In study one, airflow resistance of sweet potato aerial vine components was investigated. The influence of different operating parameters such as airflow rate, moisture content and bulk depth at different levels on airflow resistance was analyzed. All the operating parameters were observed to have significant (P < 0.01) effect on airflow resistance. Prediction models were developed and were found to adequately describe the experimental pressure drop data. In study two, the resistance of airflow through unwashed and clean sweet potato roots was investigated. The effect of sweet potato roots shape factor, surface roughness, orientation to airflow, and presence of soil fraction on airflow resistance was also assessed. The pressure drop through unwashed and clean sweet potato roots was observed to increase with higher airflow, bed depth, root grade composition, and presence of soil fraction. The physical properties of the roots were incorporated into a modified Ergun model and compared with a modified Shedd’s model. The modified Ergun model provided the best fit to the experimental data when compared with the modified Shedd’s model. In study three, the effect of sweet potato root size (medium and large), different air velocity and temperature on the cooling/or heating rate and time of individual sweet potato roots were investigated. Also, a simulation model which is based on the fundamental solution of the transient equations was proposed for estimating the cooling and heating time at the centre of sweet potato roots. The results showed that increasing air velocity during cooling and heating significantly (P < 0.05) affects the cooling and heating times. Furthermore, the cooling and heating times were significantly different (P < 0.05) among medium and large size sweet potato roots. Comparison of the simulation results with experimental data confirmed that the transient simulation model can be used to accurately estimate the cooling and heating times of whole sweet potato roots under forced convection conditions. In study four, the performance of charcoal evaporative cooling pad configurations for integration into sweet potato roots storage systems was investigated. The experiments were carried out at different levels of air velocity, water flow rates, and three pad configurations: single layer pad (SLP), double layers pad (DLP) and triple layers pad (TLP) made out of small and large size charcoal particles. The results showed that higher air velocity has tremendous effect on pressure drop. Increasing the water flow rate above the range tested had no practical benefits in terms of cooling. It was observed that DLP and TLD configurations with larger wet surface area for both types of pads provided high cooling efficiencies. In study five, CFD technique in the ANSYS Fluent software was used to simulate airflow distribution in a low-cost mud storehouse. By theoretically investigating different geometries of air inlet, plenum chamber, and outlet as well as its placement using ANSYS Fluent software, an acceptable geometry with uniform air distribution was selected and constructed. Experimental measurements validated the selected design. In study six, the performance of the developed PV ventilated system was investigated. Field measurements showed satisfactory results of the directly coupled PV ventilated system. Furthermore, the option of integrating a low-cost evaporative cooling system into the mud storage structure was also investigated. The results showed a reduction of ambient temperature inside the mud storehouse while relative humidity was enhanced. The ability of the developed storage system to provide and maintain airflow, temperature and relative humidity which are the key parameters for shelf-life extension of sweet potato roots highlight its ability to reduce post-harvest losses at the farmer level, particularly under tropical climate conditions.

Uncover the mantle: rediscovering Gregório Lopes palette and technique with a study on the painting “Mater Misericordiae”

Grego´rio Lopes (c. 1490–1550) was one of the most prominent painters of the renaissance and Mannerism in Portugal. The painting “Mater Misericordiae” made for the Sesimbra Holy House of Mercy, circa 1535–1538, is one of the most significant works of the artist, and his only painting on this theme, being also one of the most significant Portuguese paintings of sixteenth century. The recent restoration provided the possibility to study materially the painting for the first time, with a multianalytical methodology incorporating portable energy-dispersive X-ray fluorescence spectroscopy, scanning electron microscopy–energy-dispersive spectroscopy, micro-X-ray diffraction, micro-Raman spectroscopy and high-performance liquid chromatography coupled to diode array and mass spectrometry detectors. The analytical study was complemented by infrared reflectography, allowing the study of the underdrawing technique and also by dendrochronology to confirm the date of the wooden panels (1535–1538). The results of this study were compared with previous ones on the painter’s workshop, and significant differences and similitudes were found in the materials and techniques used

SPHERA, a new Italian convection-permitting regional reanalysis: improving heavy-rainfall representation and describing hail-prone environments

Extreme weather events related to deep convection are high-impact critical phenomena whose reliable numerical simulation is still challenging. High-resolution (convection-permitting) modeling setups allow to switch off physical parameterizations accountable for substantial errors in convection representation. A new convection-permitting reanalysis over Italy (SPHERA) has been produced at ARPAE to enhance the representation and understanding of extreme weather situations. SPHERA is obtained through a dynamical downscaling of the global reanalysis ERA5 using the non-hydrostatic model COSMO at 2.2 km grid spacing over 1995-2020. This thesis aims to verify the expectations placed on SPHERA by analyzing two weather phenomena that are particularly challenging to simulate: heavy rainfall and hail. A quantitative statistical analysis over Italy during 2003-2017 for daily and hourly precipitation is presented to compare the performance of SPHERA with its driver ERA5 considering the national network of rain gauges as reference. Furthermore, two extreme precipitation events are deeply investigated. SPHERA shows a quantitative added skill over ERA5 for moderate to severe and rapid accumulations in terms of adherence to the observations, higher detailing of the spatial fields, and more precise temporal matching. These results prompted the use of SPHERA for the investigation of hailstorms, for which the combination of multiple information is crucial to reduce the substantial uncertainties permeating their understanding. A proxy for hail is developed by combining hail-favoring environmental numerical predictors with observations of ESWD hail reports and satellite overshooting top detections. The procedure is applied to the extended summer season (April-October) of 2016-2018 over the whole SPHERA spatial domain. The results indicate maximum hail likelihood over pre-Alpine regions and the northern Adriatic sea around 15 UTC in June-July, in agreement with recent European hail climatologies. The method demonstrates enhanced performance in case of severe hail occurrences and the ability to separate between ambient signatures depending on hail severity.

Multimodal Mri-based Study In Patients With Spg4 Mutations.

Mutations in the SPG4 gene (SPG4-HSP) are the most frequent cause of hereditary spastic paraplegia, but the extent of the neurodegeneration related to the disease is not yet known. Therefore, our objective is to identify regions of the central nervous system damaged in patients with SPG4-HSP using a multi-modal neuroimaging approach. In addition, we aimed to identify possible clinical correlates of such damage. Eleven patients (mean age 46.0 ± 15.0 years, 8 men) with molecular confirmation of hereditary spastic paraplegia, and 23 matched healthy controls (mean age 51.4 ± 14.1years, 17 men) underwent MRI scans in a 3T scanner. We used 3D T1 images to perform volumetric measurements of the brain and spinal cord. We then performed tract-based spatial statistics and tractography analyses of diffusion tensor images to assess microstructural integrity of white matter tracts. Disease severity was quantified with the Spastic Paraplegia Rating Scale. Correlations were then carried out between MRI metrics and clinical data. Volumetric analyses did not identify macroscopic abnormalities in the brain of hereditary spastic paraplegia patients. In contrast, we found extensive fractional anisotropy reduction in the corticospinal tracts, cingulate gyri and splenium of the corpus callosum. Spinal cord morphometry identified atrophy without flattening in the group of patients with hereditary spastic paraplegia. Fractional anisotropy of the corpus callosum and pyramidal tracts did correlate with disease severity. Hereditary spastic paraplegia is characterized by relative sparing of the cortical mantle and remarkable damage to the distal portions of the corticospinal tracts, extending into the spinal cord.