Diagnostic tools for 3D unstructured oceanographic data

Most ocean models in current use are built upon structured meshes. It follows that most existing tools for extracting diagnostic quantities (volume and surface integrals, for example) from ocean model output are constructed using techniques and software tools which assume structured meshes. The greater complexity inherent in unstructured meshes (especially fully unstructured grids which are unstructured in the vertical as well as the horizontal direction) has left some oceanographers, accustomed to traditional methods, unclear on how to calculate diagnostics on these meshes. In this paper we show that tools for extracting diagnostic data from the new generation of unstructured ocean models can be constructed with relative ease using open source software. Higher level languages such as Python, in conjunction with packages such as NumPy, SciPy, VTK and MayaVi, provide many of the high-level primitives needed to perform 3D visualisation and evaluate diagnostic quantities, e.g. density fluxes. We demonstrate this in the particular case of calculating flux of vector fields through isosurfaces, using flow data obtained from the unstructured mesh finite element ocean code ICOM, however this tool can be applied to model output from any unstructured grid ocean code

Geostrophic balance preserving interpolation in mesh adaptive shallow-water ocean modelling

The accurate representation of geostrophic balance is an essential requirement for numerical modelling of geophysical flows. Significant effort is often put into the selection of accurate or optimal balance representation by the discretisation of the fundamental equations. The issue of accurate balance representation is particularly challenging when applying dynamic mesh adaptivity, where there is potential for additional imbalance injection when interpolating to new, optimised meshes. In the context of shallow-water modelling, we present a new method for preservation of geostrophic balance when applying dynamic mesh adaptivity. This approach is based upon interpolation of the Helmholtz decomposition of the Coriolis acceleration. We apply this in combination with a discretisation for which states in geostrophic balance are exactly steady solutions of the linearised equations on an f-plane; this method guarantees that a balanced and steady flow on a donor mesh remains balanced and steady after interpolation onto an arbitrary target mesh, to within machine precision. We further demonstrate the utility of this interpolant for states close to geostrophic balance, and show that it prevents pollution of the resulting solutions by imbalanced perturbations introduced by the interpolation

Numerical wave propagation for the triangular P1DGP1_{DG}-P2P2 finite element pair

Inertia-gravity mode and Rossby mode dispersion properties are examined for discretisations of the linearized rotating shallow-water equations using the $P1_{DG}$-$P2$ finite element pair on arbitrary triangulations in planar geometry. A discrete Helmholtz decomposition of the functions in the velocity space based on potentials taken from the pressure space is used to provide a complete description of the numerical wave propagation for the discretised equations. In the $f$-plane case, this decomposition is used to obtain decoupled equations for the geostrophic modes, the inertia-gravity modes, and the inertial oscillations. As has been noticed previously, the geostrophic modes are steady. The Helmholtz decomposition is used to show that the resulting inertia-gravity wave equation is third-order accurate in space. In general the \pdgp finite element pair is second-order accurate, so this leads to very accurate wave propagation. It is further shown that the only spurious modes supported by this discretisation are spurious inertial oscillations which have frequency $f$, and which do not propagate. The Helmholtz decomposition also allows a simple derivation of the quasi-geostrophic limit of the discretised $P1_{DG}$-$P2$ equations in the $\beta$-plane case, resulting in a Rossby wave equation which is also third-order accurate.Comment: Revised version prior to final journal submissio

Mixed finite elements for numerical weather prediction

We show how two-dimensional mixed finite element methods that satisfy the conditions of finite element exterior calculus can be used for the horizontal discretisation of dynamical cores for numerical weather prediction on pseudo-uniform grids. This family of mixed finite element methods can be thought of in the numerical weather prediction context as a generalisation of the popular polygonal C-grid finite difference methods. There are a few major advantages: the mixed finite element methods do not require an orthogonal grid, and they allow a degree of flexibility that can be exploited to ensure an appropriate ratio between the velocity and pressure degrees of freedom so as to avoid spurious mode branches in the numerical dispersion relation. These methods preserve several properties of the C-grid method when applied to linear barotropic wave propagation, namely: a) energy conservation, b) mass conservation, c) no spurious pressure modes, and d) steady geostrophic modes on the $f$-plane. We explain how these properties are preserved, and describe two examples that can be used on pseudo-uniform grids: the recently-developed modified RT0-Q0 element pair on quadrilaterals and the BDFM1-\pdg element pair on triangles. All of these mixed finite element methods have an exact 2:1 ratio of velocity degrees of freedom to pressure degrees of freedom. Finally we illustrate the properties with some numerical examples.Comment: Revision after referee comment

Supersonic Electroweak Baryogenesis: Achieving Baryogenesis for Fast Bubble Walls

Standard electroweak baryogenesis in the context of a first order phase transition is effective in generating the baryon asymmetry of the universe if the broken phase bubbles expand at subsonic speed, so that CP asymmetric currents can diffuse in front of the wall. Here we present a new mechanism for electroweak baryogenesis which operates for supersonic bubble walls. It relies on the formation of small bubbles of the symmetric phase behind the bubble wall, in the broken phase, due to the heating of the plasma as the wall passes by. We apply the mechanism to a model in which the Higgs field is coupled to several singlets, and find that enough baryon asymmetry is generated for reasonable values of the parameter space

Early diagnosis and follow-up of acute schistosomiasis in a cluster of infected Belgian travellers by detection of antibodies and circulating anodic antigen (CAA): a diagnostic evaluation study

Background: In order to evaluate the diagnostic value of schistosome circulating anodic antigen (CAA) detection, serum and urine CAA-levels were determined in a single cluster of 34 Belgian tourists at three timepoints within a period of 14 weeks following proven Schistosoma exposure in South Africa and compared with two in-house antibody assays. Methods: Samples were collected 4-5 and 7-8 weeks post-exposure and subsequently 5-6 weeks following praziquantel treatment. Schistosoma antibodies were detected by an adult worm antigen-immunofluorescence assay (AWA-IFA) and a soluble egg antigen-enzyme-linked immunosorbent assay (SEA-ELISA), while CAA concentrations were determined by the Up-Converting reporter Particle labelled Lateral Flow (UCP-LF) test. Results: Antibodies were detected in 25/34 (73%) travellers pre-treatment and in 27/34 (79%) post-treatment, with the AWA-IFA showing better performance than the SEA-ELISA. Pre-treatment, CAA was detected in 13/ 34 (38%) and 33/34 (97%) of the travellers in urine and serum, respectively. Post-treatment, all except one traveller became serum CAA negative. This in contrast to the detected antibodies, as well as the previously reported diagnostic results of this cluster. Conclusions: The UCP-LF CAA serum assay has been demonstrated as the most sensitive method for the diagnosis of early Schistosoma infections and post-treatment monitoring in travellers.Medical Microbiolog

Further studies on a hybrid cell-surface antigen associated with human chromosome 11 using a monoclonal antibody

A monoclonal antibody has been obtained that recognizes an antigen encoded by human chromosome 11. We present evidence that this monoclonal antibody recognizes the same or a similar antigenic activity as that previously called a 1 . Genetic information necessary for a 1 expression and recognition by the monoclonal antibody both map to 11p13 → 11pter. Mutants that have lost a 1 are no longer recognized by the monoclonal antibody. The macroglycolipid fraction of human erythrocyte membranes which contains the a 1 antigenic activity is able to convert antigen-negative Chinese hamster ovary cells into cells which are killed by the monoclonal antibody plus complement.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45556/1/11188_2005_Article_BF01543049.pd

Hyperemesis gravidarum severity, enteral tube feeding and cardiometabolic markers in offspring cord blood

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