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.

2D hexagonal mesoporous platinum films exhibiting biaxial, in-plane pore alignment

The synthesis of 2D hexagonal mesoporous platinum films with biaxial, in-plane pore alignment is demonstrated by electrodeposition through an aligned lyotropic liquid crystal templating phase. Shear force is used to align a hexagonal lyotropic liquid crystalline templating phase of an inexpensive and a commercially available surfactant, C16EO10, at the surface of an electrode. Electrodeposition and subsequent characterisation of the films produced shows that the orientation and alignment of the phase is transferred to the deposited material. Transmission electron microscopy confirms the expected nanostructure of the films, whilst transmission and grazing incidence small angle X-ray scattering analysis confirms biaxial, in plane alignment of the pore structure. In addition further electrochemical studies in dilute sulfuric acid and methanol show that the pores are accessible to electrolyte solution as indicated by a large current flow; the modified electrode therefore has a high surface area, that catalyses methanol oxidation, and the pores have a very large aspect ratio (of theoretical maximum 2 × 105). Films with such aligned mesoporosity will advance the field of nanotechnology where the control of pore structure is paramount. The method reported is sufficiently generic to be used to control the structure and order of many materials, thus increasing the potential for the development of a wide range of novel electronic and optical devices.

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.

Endogenous cholinergic tone modulates spontaneous network level neuronal activity in primary cortical cultures grown on multi-electrode arrays

Background Cortical cultures grown long-term on multi-electrode arrays (MEAs) are frequently and extensively used as models of cortical networks in studies of neuronal firing activity, neuropharmacology, toxicology and mechanisms underlying synaptic plasticity. However, in contrast to the predominantly asynchronous neuronal firing activity exhibited by intact cortex, electrophysiological activity of mature cortical cultures is dominated by spontaneous epileptiform-like global burst events which hinders their effective use in network-level studies, particularly for neurally-controlled animat (‘artificial animal’) applications. Thus, the identification of culture features that can be exploited to produce neuronal activity more representative of that seen in vivo could increase the utility and relevance of studies that employ these preparations. Acetylcholine has a recognised neuromodulatory role affecting excitability, rhythmicity, plasticity and information flow in vivo although its endogenous production by cortical cultures and subsequent functional influence upon neuronal excitability remains unknown. Results Consequently, using MEA electrophysiological recording supported by immunohistochemical and RT-qPCR methods, we demonstrate for the first time, the presence of intrinsic cholinergic neurons and significant, endogenous cholinergic tone in cortical cultures with a characterisation of the muscarinic and nicotinic components that underlie modulation of spontaneous neuronal activity. We found that tonic muscarinic ACh receptor (mAChR) activation affects global excitability and burst event regularity in a culture age-dependent manner whilst, in contrast, tonic nicotinic ACh receptor (nAChR) activation can modulate burst duration and the proportion of spikes occurring within bursts in a spatio-temporal fashion. Conclusions We suggest that the presence of significant endogenous cholinergic tone in cortical cultures and the comparability of its modulatory effects to those seen in intact brain tissues support emerging, exploitable commonalities between in vivo and in vitro preparations. We conclude that experimental manipulation of endogenous cholinergic tone could offer a novel opportunity to improve the use of cortical cultures for studies of network-level mechanisms in a manner that remains largely consistent with its functional role.

Classification of cortical microcircuits based on micro-electrode-array data from slices of rat barrel cortex

The bewildering complexity of cortical microcircuits at the single cell level gives rise to surprisingly robust emergent activity patterns at the level of laminar and columnar local field potentials (LFPs) in response to targeted local stimuli. Here we report the results of our multivariate data-analytic approach based on simultaneous multi-site recordings using micro-electrode-array chips for investigation of the microcircuitary of rat somatosensory (barrel) cortex. We find high repeatability of stimulus-induced responses, and typical spatial distributions of LFP responses to stimuli in supragranular, granular, and infragranular layers, where the last form a particularly distinct class. Population spikes appear to travel with about 33 cm/s from granular to infragranular layers. Responses within barrel related columns have different profiles than those in neighbouring columns to the left or interchangeably to the right. Variations between slices occur, but can be minimized by strictly obeying controlled experimental protocols. Cluster analysis on normalized recordings indicates specific spatial distributions of time series reflecting the location of sources and sinks independent of the stimulus layer. Although the precise correspondences between single cell activity and LFPs are still far from clear, a sophisticated neuroinformatics approach in combination with multi-site LFP recordings in the standardized slice preparation is suitable for comparing normal conditions to genetically or pharmacologically altered situations based on real cortical microcircuitry.

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.

Concurrent recordings of bladder afferents from multiple nerves using a microfabricated PDMS microchannel electrode array

In this paper we present a compliant neural interface designed to record bladder afferent activity. We developed the implant's microfabrication process using multiple layers of silicone rubber and thin metal so that a gold microelectrode array is embedded within four parallel polydimethylsiloxane (PDMS) microchannels (5 mm long, 100 μm wide, 100 μm deep). Electrode impedance at 1 kHz was optimized using a reactive ion etching (RIE) step, which increased the porosity of the electrode surface. The electrodes did not deteriorate after a 3 month immersion in phosphate buffered saline (PBS) at 37 °C. Due to the unique microscopic topography of the metal film on PDMS, the electrodes are extremely compliant and can withstand handling during implantation (twisting and bending) without electrical failure. The device was transplanted acutely to anaesthetized rats, and strands of the dorsal branch of roots L6 and S1 were surgically teased and inserted in three microchannels under saline immersion to allow for simultaneous in vivo recordings in an acute setting. We utilized a tripole electrode configuration to maintain background noise low and improve the signal to noise ratio. The device could distinguish two types of afferent nerve activity related to increasing bladder filling and contraction. To our knowledge, this is the first report of multichannel recordings of bladder afferent activity.

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.

Microchannel electrode interfaces to assess bladder afferent activity

By placing axons into polymeric micro-channels hosting embedded electrodes the extracellular amplitude of action potentials is greatly increased, allowing for robust recording and noise suppression. We are developing such an electrode interface to record electrical activity from bladder afferents to restore bladder control in patients suffering from spinal cord injury. Here we describe our microchannel electrode interface in terms of design, microfabrication and electrode characteristics and report on in vivo bladder function after implantation of teased dorsal rootlets within microchannels.

Compliant Multi-electrode Micro-channel Array for Recording Afferent Nerve Activity

We have fabricated a compliant neural interface to record afferent nerve activity. Stretchable gold electrodes were evaporated on a polydimethylsiloxane (PDMS) substrate and were encapsulated using photo-patternable PDMS. The built-in microstructure of the gold film on PDMS allows the electrodes to twist and flex repeatedly, without loss of electrical conductivity. PDMS microchannels (5mm long, 100μm wide, 100μm deep) were then plasma bonded irreversibly on top of the electrode array to define five parallel-conduit implants. The soft gold microelectrodes have a low impedance of ~200kΩ at the 1kHz frequency range. Teased nerves from the L6 dorsal root of an anaesthetized Sprague Dawley rat were threaded through the microchannels. Acute tripolar recordings of cutaneous activity are demonstrated, from multiple nerve rootlets simultaneously. Confinement of the axons within narrow microchannels allows for reliable recordings of low amplitude afferents. This electrode technology promises exciting applications in neuroprosthetic devices including bladder fullness monitors and peripheral nervous system implants.