Comment on ``Piecewise potential vorticity inversion: Elementary tests''

Egger (2008) constructs some idealised experiments to test the usefulness of piecewise potential vorticity inversion (PPVI) in the diagnosis of Rossby wave dynamics and baroclinic development. He concludes that, ``PPVI does not help us to understand the dynamics of linear Rossby waves. It provides local tendencies of the streamfunction which are unrelated to the true ones. The same way, the motion of baroclinic waves in shear flow cannot be understood by using PPVI. Moreover, the effect of boundary temperatures as determined by PPVI is unrelated to the flow evolution.'' He goes further in arguing that we should not consider velocities as ``induced'' by PV anomalies defined by carving up the global domain. However, these conclusions partly reflect the limitations of his idealised experiments and the manner in which the PV components were partitioned from one another.

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.

The influence of different artificial soil types on the acute toxicity of carbendazim to the earthworm Eisenia fetida in laboratory toxicity tests

Field populations of earthworms have shown a varied response in mortality to the fungicide carbendazim, the toxic reference substance used in agrochemical field trials. The aim of this study was to determine the influence of soil conditions as a potential cause of this variation. Laboratory acute toxicity tests were conducted using a range of artificial soils with varying soil components (organic matter, clay, pH and moisture). Batch adsorption/desorption studies were run to determine the influence of the soil properties on carbendazim behaviour. Adsorption was shown to be correlated with organic matter content and pH and this in turn could be linked to Eisenia fetida mortality, with lower mortality occurring with increased adsorption. Overall while E.fetida mortality did vary significantly between several of the soils the calculated LC50 values in the different soils did not cover a wide range (6.04-16.00 mg kg(-1)), showing that under these laboratory conditions soil components did not greatly influence carbendazim toxicity to E.fietida. (c) 2007 Elsevier Masson SAS. All rights reserved.

A capture–recapture approach for screening using two diagnostic tests with availability of disease status for the test positives only

The article considers screening human populations with two screening tests. If any of the two tests is positive, then full evaluation of the disease status is undertaken; however, if both diagnostic tests are negative, then disease status remains unknown. This procedure leads to a data constellation in which, for each disease status, the 2 × 2 table associated with the two diagnostic tests used in screening has exactly one empty, unknown cell. To estimate the unobserved cell counts, previous approaches assume independence of the two diagnostic tests and use specific models, including the special mixture model of Walter or unconstrained capture–recapture estimates. Often, as is also demonstrated in this article by means of a simple test, the independence of the two screening tests is not supported by the data. Two new estimators are suggested that allow associations of the screening test, although the form of association must be assumed to be homogeneous over disease status. These estimators are modifications of the simple capture–recapture estimator and easy to construct. The estimators are investigated for several screening studies with fully evaluated disease status in which the superior behavior of the new estimators compared to the previous conventional ones can be shown. Finally, the performance of the new estimators is compared with maximum likelihood estimators, which are more difficult to obtain in these models. The results indicate the loss of efficiency as minor.

Effect of growth time on the surface and adhesion properties of Lactobacillus rhamnosus GG

Aims: To investigate the changes in the surface properties of Lactobacillus rhamnosus GG during growth, and relate them with the ability of the Lactobacillus cells to adhere to Caco-2 cells. Methods and Results: Lactobacillus rhamnosus GG was grown in complex medium, and cell samples taken at four time points and freeze dried. Untreated and trypsin treated freeze dried samples were analysed for their composition using SDS-PAGE analysis and Fourier transform infrared spectroscopy (FTIR), hydrophobicity and zeta potential, and for their ability to adhere to Caco-2 cells. The results suggested that in the case of early exponential phase samples (4 and 8 h), the net surface properties, i.e. hydrophobicity and charge, were determined to a large extent by anionic hydrophilic components, whereas in the case of stationary phase samples (13 and 26 h), hydrophobic proteins seemed to play the biggest role. Considerable differences were also observed between the ability of the different samples to adhere to Caco-2 cells; maximum adhesion was observed for the early stationary phase sample (13 h). The results suggested that the adhesion to Caco-2 cells was influenced by both proteins and non-proteinaceous compounds present on the surface of the Lactobacillus cells. Conclusion: The surface properties of Lact. rhamnosus GG changed during growth, which in return affected the ability of the Lactobacillus cells to adhere to Caco-2 cells. Significance and Impact of the Study: The levels of adhesion of Lactobacillus cells to Caco-2 cells were influenced by the growth time and reflected changes on the bacterial surface. This study provides critical information on the physicochemical factors that influence bacterial adhesion to intestinal cells.

The effect of consumption volume on profile and liking of oral nutritional supplements of varied sweetness: sequential profiling and boredom tests

Oral nutrition supplements (ONS) are routinely prescribed to those with, or at risk of, malnutrition. Previous research identified poor compliance due to taste and sweetness. This paper investigates taste and hedonic liking of ONS, of varying sweetness and metallic levels, over consumption volume; an important consideration as patients are prescribed large volumes of ONS daily. A sequential descriptive profile was developed to determine the perception of sensory attributes over repeat consumption of ONS. Changes in liking of ONS following repeat consumption were characterised by a boredom test. Certain flavour (metallic taste, soya milk flavour) and mouthfeel (mouthdrying, mouthcoating) attributes built up over increased consumption volume (p 0.002). Hedonic liking data from two cohorts, healthy older volunteers (n = 32, median age 73) and patients (n = 28, median age 85), suggested such build-up was disliked. Efforts made to improve the palatability of ONS must take account of the build up of taste and mouthfeel characteristics over increased consumption volume.

Phyto-activity of biocides used to manipulate herbivory: tests of three pesticides on fourteen plant species

1. We tested three pesticides used for field manipulations of herbivory for direct phytoactive effects on the germination and growth of 14 herbaceous plant species selected to provide a range of life-history strategies and functional groups. 2. We report three companion experiments: (A) Two insecticides, chlorpyrifos (granular soil insecticide) and dimethoate (foliar spray), were applied in fully-factorial combination to pot-germinated individuals of 12 species. (B) The same fully-factorial design was used to test for direct effects on the germination of four herbaceous legumes. (C) The molluscicide, metaldehyde, was tested for direct effects on the germination and growth of six plant species. 3. The insecticides had few significant effects on growth and germination. Dimethoate acted only on growth stimulating Anisantha sterilis, Sonchus asper and Stellaria graminea. In contrast, chlorpyrifos acted on germination increasing the germination of Trifolium dubium and Trifolium pratense. There was also a significant interactive effect of chlorpyrifos and dimethoate on the germination of T pratense. However, all. effects were relatively small in magnitude and explanatory power. The molluscicide had no significant effect on plant germination or growth. 4. The small number and size of direct effects of the pesticides on plant performance is encouraging for the use of these pesticides in manipulative experiments on herbivory, especially for the molluscicide. However, a smatt number of direct (positive) effects of the insecticides on some plant species need to be taken into account when interpreting field manipulations of herbivory with these compounds, and emphasises the importance of conducting tests for direct phyto-active effects. (C) 2004 Elsevier GmbH. All rights reserved.

Iron-regulated surface determinant protein a mediates adhesion of staphylococcus aureus to human corneocyte envelope proteins

The ability of Staphylococcus aureus to colonize the human nares is a crucial prerequisite for disease. IsdA is a major S. aureus surface protein that is expressed during human infection and required for nasal colonization and survival on human skin. In this work, we show that IsdA binds to involucrin, loricrin, and cytokeratin K10, proteins that are present in the cornified envelope of human desquamated epithelial cells. To measure the forces and dynamics of the interaction between IsdA and loricrin (the most abundant protein of the cornified envelope), single-molecule force spectroscopy was used, demonstrating high-specificity binding. IsdA acts as a cellular adhesin to the human ligands, promoting whole-cell binding to immobilized proteins, even in the absence of other S. aureus components (as shown by heterologous expression in Lactococcus lactis). Inhibition experiments revealed the binding of the human ligands to the same IsdA region. This region was mapped to the NEAT domain of IsdA. The NEAT domain also was found to be required for S. aureus whole-cell binding to the ligands as well as to human nasal cells. Thus, IsdA is an important adhesin to human ligands, which predominate in its primary ecological niche.

A capture-recapture approach for screening using two diagnostic tests with availability of disease status for the test positives only

The article considers screening human populations with two screening tests. If any of the two tests is positive, then full evaluation of the disease status is undertaken; however, if both diagnostic tests are negative, then disease status remains unknown. This procedure leads to a data constellation in which, for each disease status, the 2 x 2 table associated with the two diagnostic tests used in screening has exactly one empty, unknown cell. To estimate the unobserved cell counts, previous approaches assume independence of the two diagnostic tests and use specific models, including the special mixture model of Walter or unconstrained capture-recapture estimates. Often, as is also demonstrated in this article by means of a simple test, the independence of the two screening tests is not supported by the data. Two new estimators are suggested that allow associations of the screening test, although the form of association must be assumed to be homogeneous over disease status. These estimators are modifications of the simple capture-recapture estimator and easy to construct. The estimators are investigated for several screening studies with fully evaluated disease status in which the superior behavior of the new estimators compared to the previous conventional ones can be shown. Finally, the performance of the new estimators is compared with maximum likelihood estimators, which are more difficult to obtain in these models. The results indicate the loss of efficiency as minor.

Heat shock protein 27 is the major differentially phosphorylated protein involved in renal epithelial cellular stress response and controls focal adhesion organization and apoptosis

We used two-dimensional difference gel electrophoresis to determine early changes in the stress-response pathways that precede focal adhesion disorganization linked to the onset of apoptosis of renal epithelial cells. Treatment of LLC-PK1 cells with the model nephrotoxicant 1,2-(dichlorovinyl)-L-cysteine (DCVC) resulted in a >1.5-fold up- and down-regulation of 14 and 9 proteins, respectively, preceding the onset of apoptosis. Proteins included those involved in metabolism, i.e. aconitase and pyruvate dehydrogenase, and those related to stress responses and cytoskeletal reorganization, i.e. cofilin, Hsp27, and alpha-b-crystallin. The most prominent changes were found for Hsp27, which was related to a pI shift in association with an altered phosphorylation status of serine residue 82. Although both p38 and JNK were activated by DCVC, only inhibition of p38 with SB203580 reduced Hsp27 phosphorylation, which was associated with accelerated reorganization of focal adhesions, cell detachment, and apoptosis. In contrast, inhibition of JNK with SP600125 maintained cell adhesion as well as protection against apoptosis. Active JNK co-localized at focal adhesions after DCVC treatment in a FAK-dependent manner. Inhibition of active JNK localization at focal adhesions did not prevent DCVC-induced phosphorylation of Hsp27. Overexpression of a phosphorylation-defective mutant Hsp27 acted as a dominant negative and accelerated the DCVC-induced changes in the focal adhesions as well as the onset of apoptosis. Our data fit a model whereby early p38 activation results in a rapid phosphorylation of Hsp27, a requirement for proper maintenance of cell adhesion, thus suppressing renal epithelial cell apoptosis.