The efficiency factorization multiplier for the Watson efficiency in partitioned linear models: some examples and a literature review

We consider partitioned linear models where the model matrix X = (X1 : X2) has full column rank, and concentrate on the special case whereX0 1X2 = 0 when we say that the model is orthogonally partitioned. We assume that the underlying covariance matrix is positive definite and introduce the efficiency factorization multiplier which relates the total Watson efficiency of ordinary least squares to the product of the two subset Watson efficiencies. We illustrate our findings with several examples and present a literature review

A new framework for large strain electromechanics based on convex multi-variable strain energies: Finite Element discretisation and computational implementation

In Gil and Ortigosa (2016), Gil and Ortigosa introduced a new convex multi-variable framework for the numerical simulation of Electro Active Polymers (EAPs) in the presence of extreme deformations and electric fields. This extends the concept of polyconvexity to strain energies which depend on non-strain based variables. The consideration of the new concept of multi-variable convexity guarantees the well posedness of generalised Gibbs’ energy density functionals and, hence, opens up the possibility of a new family of mixed variational principles. The aim of this paper is to present, as an example, the Finite Element implementation of two of these mixed variational principles. These types of enhanced methodologies are known to be necessary in scenarios in which the simpler displacement-potential based formulation yields non-physical results, such as volumetric locking, bending and shear locking, pressure oscillations and electro-mechanical locking, to name but a few. Crucially, the use of interpolation spaces in which some of the unknown fields are described as piecewise discontinuous across elements can be used in order to efficiently condense these fields out. This results in mixed formulations with a computational cost comparable to that of the displacement-potential based approach, yet far more accurate. Finally, a series of very challenging numerical examples are presented in order to demonstrate the accuracy, robustness and efficiency of the proposed methodology

A computational framework for large strain nearly and truly incompressible electromechanics based on convex multi-variable strain energies

The series of papers published by Gil and Ortigosa (Gil and Ortigosa, 2016; Ortigosa and Gil, 2016, 0000) introduced a new convex multi-variable variational and computational framework for the numerical simulation of Electro Active Polymers (EAPs) in scenarios characterised by extreme deformations and/or extreme electric fields. Building upon this body of work, five key novelties are incorporated in this paper. First, a generalisation of the concept of multi-variable convexity to energy functionals additively decomposed into isochoric and volumetric components. This decomposition is typical of nearly and truly incompressible materials, group which represents the majority of the most relevant EAPs. Second, convexification or regularisation strategies are applied to a priori non-convex multi-variable isochoric functionals to yield physically meaningful convex multi-variable functionals. Third, based on the mixed variational principles introduced in Gil and Ortigosa (2016) in the context of compressible electro-elasticity, a novel extended Hu–Washizu mixed variational principle for nearly and truly incompressible scenarios is presented. From the computational standpoint, a static condensation procedure is applied in order to condense out the element-wise extra fields, the resulting formulation having a comparable cost to the more standard three-field displacement-potential-pressure mixed formulation. Fourth, the computational framework for the three-field mixed variational principle in nearly and truly incompressible scenarios is also presented. In this case, the novelty resides in the consideration of convex multi-variable energy functionals. Ultimately, this leads to the definition of new tangent operators for the Helmholtz’s energy functional in the specific context of incompressible electro-elasticity. Fifth, a Petrov–Galerkin stabilisation technique is applied on the three-field formulation for the circumvention of the Ladyz˘enskaja–Babus˘ka–Brezzi (LBB) condition, enabling the use of linear tetrahedral finite elements for the interpolation of the unknowns of the problem. Finally, a series of challenging numerical examples is presented in order to provide an exhaustive comparison of the different variational formulations presented in this paper

Cationic polyamines inhibit anthrax lethal factor protease

BACKGROUND: Anthrax is a human disease that results from infection by the bacteria, Bacillus anthracis and has recently been used as a bioterrorist agent. Historically, this disease was associated with Bacillus spore exposure from wool or animal carcasses. While current vaccine approaches (targeted against the protective antigen) are effective for prophylaxis, multiple doses must be injected. Common antibiotics that block the germination process are effective but must be administered early in the infection cycle. In addition, new therapeutics are needed to specifically target the proteolytic activity of lethal factor (LF) associated with this bacterial infection. RESULTS: Using a fluorescence-based assay to identify and characterize inhibitors of anthrax lethal factor protease activity, we identified several chemically-distinct classes of inhibitory molecules including polyamines, aminoglycosides and cationic peptides. In these studies, spermine was demonstrated for the first time to inhibit anthrax LF with a K(i )value of 0.9 ± 0.09 μM (mean ± SEM; n = 3). Additional linear polyamines were also active as LF inhibitors with lower potencies. CONCLUSION: Based upon the studies reported herein, we chose linear polyamines related to spermine as potential lead optimization candidates and additional testing in cell-based models where cell penetration could be studied. During our screening process, we reproducibly demonstrated that the potencies of certain compounds, including neomycin but not neamine or spermine, were different depending upon the presence or absence of nucleic acids. Differential sensitivity to the presence/absence of nucleic acids may be an additional point to consider when comparing various classes of active compounds for lead optimization

Retinotopic Maps, Spatial Tuning, and Locations of Human Visual Areas in Surface Coordinates Characterized with Multifocal and Blocked fMRI Designs

The localization of visual areas in the human cortex is typically based on mapping the retinotopic organization with functional magnetic resonance imaging (fMRI). The most common approach is to encode the response phase for a slowly moving visual stimulus and to present the result on an individual's reconstructed cortical surface. The main aims of this study were to develop complementary general linear model (GLM)-based retinotopic mapping methods and to characterize the inter-individual variability of the visual area positions on the cortical surface. We studied 15 subjects with two methods: a 24-region multifocal checkerboard stimulus and a blocked presentation of object stimuli at different visual field locations. The retinotopic maps were based on weighted averaging of the GLM parameter estimates for the stimulus regions. In addition to localizing visual areas, both methods could be used to localize multiple retinotopic regions-of-interest. The two methods yielded consistent retinotopic maps in the visual areas V1, V2, V3, hV4, and V3AB. In the higher-level areas IPS0, VO1, LO1, LO2, TO1, and TO2, retinotopy could only be mapped with the blocked stimulus presentation. The gradual widening of spatial tuning and an increase in the responses to stimuli in the ipsilateral visual field along the hierarchy of visual areas likely reflected the increase in the average receptive field size. Finally, after registration to Freesurfer's surface-based atlas of the human cerebral cortex, we calculated the mean and variability of the visual area positions in the spherical surface-based coordinate system and generated probability maps of the visual areas on the average cortical surface. The inter-individual variability in the area locations decreased when the midpoints were calculated along the spherical cortical surface compared with volumetric coordinates. These results can facilitate both analysis of individual functional anatomy and comparisons of visual cortex topology across studies

Taxonomic and Environmental Variability in the Elemental Composition and Stoichiometry of Individual Dinoflagellate and Diatom Cells from the NW Mediterranean Sea

Here we present, for the first time, the elemental concentration, including C, N and O, of single phytoplankton cells collected from the sea. Plankton elemental concentration and stoichiometry are key variables in phytoplankton ecophysiology and ocean biogeochemistry, and are used to link cells and ecosystems. However, most field studies rely on bulk techniques that overestimate carbon and nitrogen because the samples include organic matter other than plankton organisms. Here we used X-ray microanalysis (XRMA), a technique that, unlike bulk analyses, gives simultaneous quotas of C, N, O, Mg, Si, P, and S, in single-cell organisms that can be collected directly from the sea. We analysed the elemental composition of dinoflagellates and diatoms (largely Chaetoceros spp.) collected from different sites of the Catalan coast (NW Mediterranean Sea). As expected, a lower C content is found in our cells compared to historical values of cultured cells. Our results indicate that, except for Si and O in diatoms, the mass of all elements is not a constant fraction of cell volume but rather decreases with increasing cell volume. Also, diatoms are significantly less dense in all the measured elements, except Si, compared to dinoflagellates. The N:P ratio of both groups is higher than the Redfield ratio, as it is the N:P nutrient ratio in deep NW Mediterranean Sea waters (N:P = 20–23). The results suggest that the P requirement is highest for bacterioplankton, followed by dinoflagellates, and lowest for diatoms, giving them a clear ecological advantage in P-limited environments like the Mediterranean Sea. Finally, the P concentration of cells of the same genera but growing under different nutrient conditions was the same, suggesting that the P quota of these cells is at a critical level. Our results indicate that XRMA is an accurate technique to determine single cell elemental quotas and derived conversion factors used to understand and model ocean biogeochemical cycles

Short-Lived Trace Gases in the Surface Ocean and the Atmosphere

The two-way exchange of trace gases between the ocean and the atmosphere is important for both the chemistry and physics of the atmosphere and the biogeochemistry of the oceans, including the global cycling of elements. Here we review these exchanges and their importance for a range of gases whose lifetimes are generally short compared to the main greenhouse gases and which are, in most cases, more reactive than them. Gases considered include sulphur and related compounds, organohalogens, non-methane hydrocarbons, ozone, ammonia and related compounds, hydrogen and carbon monoxide. Finally, we stress the interactivity of the system, the importance of process understanding for modeling, the need for more extensive field measurements and their better seasonal coverage, the importance of inter-calibration exercises and finally the need to show the importance of air-sea exchanges for global cycling and how the field fits into the broader context of Earth System Science