Comment on “A modified leapfrog scheme for shallow water equations” by Wen-Yih Sun and Oliver M.T. Sun

A recent paper published in this journal considers the numerical integration of the shallow-water equations using the leapfrog time-stepping scheme [Sun Wen-Yih, Sun Oliver MT. A modified leapfrog scheme for shallow water equations. Comput Fluids 2011;52:69–72]. The authors of that paper propose using the time-averaged height in the numerical calculation of the pressure-gradient force, instead of the instantaneous height at the middle time step. The authors show that this modification doubles the maximum Courant number (and hence the maximum time step) at which the integrations are stable, doubling the computational efficiency. Unfortunately, the pressure-averaging technique proposed by the authors is not original. It was devised and published by Shuman [5] and has been widely used in the atmosphere and ocean modelling community for over 40 years.

Effects of modified atmosphere packaging on quality of ‘Alphonso’ Mangoes

Postharvest quality of Alphonso mangoes (Mangifera indica L) is vital to ensure proper ripening and good quality. 500 g mature green mangoes, were subjected to three pre- packaging hot water dips (20, 30 & 40°C) for 40 min, two packaging films (OPP unperforated and perforated), using three levels of gas concentrations of 25,50 and 75% v/v CO2 treatments (balance N2) and stored at 10°C for 21 days. During the storage period headspace gas composition, weight loss, ascorbic acid, pulp firmness, external fruit colour and overall quality score were measured to determine optimum storage conditions. The most effective postharvest condition was found to be dipping in water maintained at 40°C for 40 min, followed by packaging under 50% CO2 in bags made of unperforated film when compared to mangoes packed under 25 and 75% CO2 which showed deteriorated quality including spoilage and mould. Good keeping quality of at least 21 days was achieved under these conditions, which was much superior to the control samples that showed deterioration after 12 days of storage.

A modified rapid enzymatic microtiter plate assay for the quantification of intracellular γ-aminobutyric acid and succinate semialdehyde in bacterial cells

The GABase assay is widely used to rapidly and accurately quantify levels of extracellular γ-aminobutyric acid (GABA). Here we demonstrate a modification of this assay that enables quantification of intracellular GABA in bacterial cells. Cells are lysed by boiling and ethanolamine-O-sulphate, a GABA transaminase inhibitor is used to distinguish between GABA and succinate semialdehyde.

Salts responsive nanovesicles through π-stacking induced self-assembly of backbone modified tripeptides

A set of backbone modified peptides of general formula Boc-Xx-m-ABA-Yy-OMe where m-ABA is meta-aminobenzoic acid and Xx and Yy are natural amino acids such as Phe, Gly, Pro, Leu, Ile, Tyr and Trp etc., are found to self-assemble into soft nanovesicular structures in methanol-water solution (9:1 by v/v). At higher concentration the peptides generate larger vesicles which are formed through fusion of smaller vesicles. The formation of vesicles has been facilitated through the participation of various noncovalent interactions such as aromatic pi-stacking, hydrogen bonding and hydrophobic interactions. Model study indicates that the pi-stacking induced self-assembly, mediated by m-ABA is essential for well structured vesicles formation. The presence of conformationally rigid m-ABA in the backbone of the peptides also helps to form vesicular structures by restricting the conformational entropy. The vesicular structures get disrupted in presence of various salts such as KCl, CaCl(2), N(n-Bu)(4)Br and (NH(4))(2)SO(4) in methanol-water solution. Fluorescence microscopy and UV studies reveal that the soft nanovesicles encapsulate organic dye molecules such as Rhodamine B and Acridine Orange which could be released through salts induced disruption of vesicles.

Changing European storm loss potentials under modified climate conditions according to ensemble simulations of the ECHAM5/MPI-OM1 GMC

A simple storm loss model is applied to an ensemble of ECHAM5/MPI-OM1 GCM simulations in order to estimate changes of insured loss potentials over Europe in the 21st century. Losses are computed based on the daily maximum wind speed for each grid point. The calibration of the loss model is performed using wind data from the ERA40-Reanalysis and German loss data. The obtained annual losses for the present climate conditions (20C, three realisations) reproduce the statistical features of the historical insurance loss data for Germany. The climate change experiments correspond to the SRES-Scenarios A1B and A2, and for each of them three realisations are considered. On average, insured loss potentials increase for all analysed European regions at the end of the 21st century. Changes are largest for Germany and France, and lowest for Portugal/Spain. Additionally, the spread between the single realisations is large, ranging e.g. for Germany from −4% to +43% in terms of mean annual loss. Moreover, almost all simulations show an increasing interannual variability of storm damage. This assessment is even more pronounced if no adaptation of building structure to climate change is considered. The increased loss potentials are linked with enhanced values for the high percentiles of surface wind maxima over Western and Central Europe, which in turn are associated with an enhanced number and increased intensity of extreme cyclones over the British Isles and the North Sea.

On Rossby waves modified by weak sinusoidal shear

The spatial structure of beta-plane Rossby waves in a sinusoidal basic zonal flow U 0cos(γ,y) is determined analytically in the (stable) asymptotic limit of weak shear, U 0γ2 0/β≈1. The propagating neutral normal modes are found to take their greatest amplitude in the region of maximum westerly flow, while their most rapid phase variation is achieved in the region of maximum easterly flow. These results are shown to be consistent with what is obtained by ray-tracing methods in the limit of small meridional disturbance wavelength.

Cortical thickness changes in the non-lesioned hemisphere associated with non-paretic arm immobilization in modified CI therapy

Recent evidence suggests that immobilization of the upper limb for 2–3 weeks induces changes in cortical thickness as well as motor performance. In constraint induced (CI) therapy, one of the most effective interventions for hemiplegia, the non-paretic arm is constrained to enforce the use of the paretic arm in the home setting. With the present study we aimed to explore whether non-paretic arm immobilization in CI therapy induces structural changes in the non-lesioned hemisphere, and how these changes are related to treatment benefit. 31 patients with chronic hemiparesis participated in CI therapy with (N = 14) and without (N = 17) constraint. Motor ability scores were acquired before and after treatment. Diffusion tensor imaging (DTI) data was obtained prior to treatment. Cortical thickness was measured with the Freesurfer software. In both groups cortical thickness in the contralesional primary somatosensory cortex increased and motor function improved with the intervention. However the cortical thickness change was not associated with the magnitude of motor function improvement. Moreover, the treatment effect and the cortical thickness change were not significantly different between the constraint and the non-constraint groups. There was no correlation between fractional anisotropy changes in the non-lesioned hemisphere and treatment outcome. CI therapy induced cortical thickness changes in contralesional sensorimotor regions, but this effect does not appear to be driven by the immobilization of the non-paretic arm, as indicated by the absence of differences between the constraint and the non-constraint groups. Our data does not suggest that the arm immobilization used in CI therapy is associated with noticeable cortical thinning.

Updated empirical model of genetically-modified maize grain production practices to achieve European Union labeling thresholds

An updated empirical approach is proposed for specifying coexistence requirements for genetically modified (GM) maize (Zea mays L.) production to ensure compliance with the 0.9% labeling threshold for food and feed in the European Union. The model improves on a previously published (Gustafson et al., 2006) empirical model by adding recent data sources to supplement the original database and including the following additional cases: (i) more than one GM maize source field adjacent to the conventional or organic field, (ii) the possibility of so-called “stacked” varieties with more than one GM trait, and (iii) lower pollen shed in the non-GM receptor field. These additional factors lead to the possibility for somewhat wider combinations of isolation distance and border rows than required in the original version of the empirical model. For instance, in the very conservative case of a 1-ha square non-GM maize field surrounded on all four sides by homozygous GM maize with 12 m isolation (the effective isolation distance for a single GM field), non-GM border rows of 12 m are required to be 95% confident of gene flow less than 0.9% in the non-GM field (with adventitious presence of 0.3%). Stacked traits of higher GM mass fraction and receptor fields of lower pollen shed would require a greater number of border rows to comply with the 0.9% threshold, and an updated extension to the model is provided to quantify these effects.

A modified PNN algorithm with optimal PD modeling using the orthogonal least squares method

In this paper a modified algorithm is suggested for developing polynomial neural network (PNN) models. Optimal partial description (PD) modeling is introduced at each layer of the PNN expansion, a task accomplished using the orthogonal least squares (OLS) method. Based on the initial PD models determined by the polynomial order and the number of PD inputs, OLS selects the most significant regressor terms reducing the output error variance. The method produces PNN models exhibiting a high level of accuracy and superior generalization capabilities. Additionally, parsimonious models are obtained comprising a considerably smaller number of parameters compared to the ones generated by means of the conventional PNN algorithm. Three benchmark examples are elaborated, including modeling of the gas furnace process as well as the iris and wine classification problems. Extensive simulation results and comparison with other methods in the literature, demonstrate the effectiveness of the suggested modeling approach.

Rescue of gene expression by modified REST decoy oligonucleotides in a cellular model of Huntington's disease

Transcriptional dysfunction is a prominent hallmark of Huntington's disease (HD). Several transcription factors have been implicated in the aetiology of HD progression and one of the most prominent is repressor element 1 (RE1) silencing transcription factor (REST). REST is a global repressor of neuronal gene expression and in the presence of mutant Huntingtin increased nuclear REST levels lead to elevated RE1 occupancy and a concomitant increase in target gene repression, including brain-derived neurotrophic factor. It is of great interest to devise strategies to reverse transcriptional dysregulation caused by increased nuclear REST and determine the consequences in HD. Thus far, such strategies have involved RNAi or mutant REST constructs. Decoys are double-stranded oligodeoxynucleotides corresponding to the DNA-binding element of a transcription factor and act to sequester it, thereby abrogating its transcriptional activity. Here, we report the use of a novel decoy strategy to rescue REST target gene expression in a cellular model of HD. We show that delivery of the decoy in cells expressing mutant Huntingtin leads to its specific interaction with REST, a reduction in REST occupancy of RE1s and rescue of target gene expression, including Bdnf. These data point to an alternative strategy for rebalancing the transcriptional dysregulation in HD.

Silica templating of a self-assembling peptide amphiphile that forms nanotapes

The peptide amphiphile C16-KTTKS templates silica polymerization, enabling the production of silica nanotape structures, imaged via electron microscopy (TEM and SEM). X-ray scattering shows that the nanotapes comprise stacked layers, as for the parent peptide amphiphile, but with a substantially increased layer spacing resulting from silica polymerization.

Computing Fresnel integrals via modified trapezium rules

In this paper we propose methods for computing Fresnel integrals based on truncated trapezium rule approximations to integrals on the real line, these trapezium rules modified to take into account poles of the integrand near the real axis. Our starting point is a method for computation of the error function of complex argument due to Matta and Reichel (J Math Phys 34:298–307, 1956) and Hunter and Regan (Math Comp 26:539–541, 1972). We construct approximations which we prove are exponentially convergent as a function of N , the number of quadrature points, obtaining explicit error bounds which show that accuracies of 10−15 uniformly on the real line are achieved with N=12 , this confirmed by computations. The approximations we obtain are attractive, additionally, in that they maintain small relative errors for small and large argument, are analytic on the real axis (echoing the analyticity of the Fresnel integrals), and are straightforward to implement.

Assessing and monitoring impacts of genetically modified plants on agro-ecosystems: the approach of AMIGA project

The environmental impacts of genetically modified crops is still a controversial issue in Europe. The overall risk assessment framework has recently been reinforced by the European Food Safety Authority(EFSA) and its implementation requires harmonized and efficient methodologies. The EU-funded research project AMIGA − Assessing and monitoring Impacts of Genetically modified plants on Agro-ecosystems − aims to address this issue, by providing a framework that establishes protection goals and baselines for European agro-ecosystems, improves knowledge on the potential long term environmental effects of genetically modified (GM) plants, tests the efficacy of the EFSA Guidance Document for the Environmental Risk Assessment, explores new strategies for post market monitoring, and provides a systematic analysis of economic aspects of Genetically Modified crops cultivation in the EU. Research focuses on ecological studies in different EU regions, the sustainability of GM crops is estimated by analysing the functional components of the agro-ecosystems and specific experimental protocols are being developed for this scope.

Neocuproine-functionalized silica-coated magnetic nanoparticles for extraction of copper(II) from aqueous solution

Neocuproine has been covalently bound to silica-coated maghemite(c-Fe2O3) magnetic nanoparticles (MNPs) by a phenyl ether linkage. The resulting MNPs are able to remove Cu(II) from 12 ppm aqueous solution with an extraction efficiency of up to 99% at pH 2.