Notes on spiking neural P systems and finite automata

Spiking neural P systems (in short, SN P systems) are membrane computing models inspired by the pulse coding of information in biological neurons. SN P systems with standard rules have neurons that emit at most one spike (the pulse) each step, and have either an input or output neuron connected to the environment. A variant known as SN P modules generalize SN P systems by using extended rules (more than one spike can be emitted each step) and a set of input and output neurons. In this work we continue relating SN P modules and finite automata. In particular, we amend and improve previous constructions for the simulatons of deterministic finite automata and state transducers. Our improvements reduce the number of neurons from three down to one, so our results are optimal. We also simulate finite automata with output, and we use these simulations to generate automatic sequences.     

A Review of Element-Based Galerkin Methods for Numerical Weather Prediction: Finite Elements,Spectral Elements,and Discontinuous Galerkin

Numerical weather prediction (NWP) is in a period of transition. As resolutions increase, global models are moving towards fully nonhydrostatic dynamical cores, with the local and global models using the same governing equations; therefore we have reached a point where it will be necessary to use a single model for both applications. The new dynamical cores at the heart of these unified models are designed to scale efficiently on clusters with hundreds of thousands or even millions of CPU cores and GPUs. Operational and research NWP codes currently use a wide range of numerical methods: finite differences, spectral transform, finite volumes and, increasingly, finite/spectral elements and discontinuous Galerkin, which constitute element-based Galerkin (EBG) methods. Due to their important role in this transition, will EBGs be the dominant power behind NWP in the next 10 years, or will they just be one of many methods to choose from? One decade after the review of numerical methods for atmospheric modeling by Steppeler et al. (Meteorol Atmos Phys 82:287–301, 2003), this review discusses EBG methods as a viable numerical approach for the next-generation NWP models. One well-known weakness of EBG methods is the generation of unphysical oscillations in advection-dominated flows; special attention is hence devoted to dissipation-based stabilization methods. Since EBGs are geometrically flexible and allow both conforming and non-conforming meshes, as well as grid adaptivity, this review is concluded with a short overview of how mesh generation and dynamic mesh refinement are becoming as important for atmospheric modeling as they have been for engineering applications for many years.     

A grid middleware for distributed Java computing with MPI binding and process migration supports

“Grid” computing has emerged as an important new research field. With years of efforts, grid researchers have successfully developed grid technologies including security solutions,resource management protocols, information query protocols, and data management services. How-ever, as the ultimate goal of grid computing is to design an infrastructure which supports dynarnic,cross-organizational resource sharing, there is a need of solutions for efficient and transparent task re-scheduling in the grid. In this research, a new grid middleware is proposed, called G-JavaMPI. This middleware adds the parallel computing capability of Java to the grid with the support of a Grid-enabled message passing interface (MPI) for inter-process communication between Java processes executed at dif-ferent grid points. A special feature of the proposed G-JavaMPI is the support of Java process migration with post-migration message redirection. With these supports, it is possible to migrate executing Java process from site to site for continuous computation, if some site is scheduled to be turned down for system reconfiguration. Moreover, the proposed G-JavaMPI middleware is very portable since it requires no modification of underlying OS, Java virtual machine, and MPI package. Preliminary performance tests have been conducted. The proposed mechanisms have shown good migration efficiency in a simulated grid environment.     

A dielectrophoretic chip packaged at wafer level

The paper presents a dielectrophoretic chip, fully enclosed, with bulk silicon electrodes fabricated using wafer-to-wafer bonding techniques and packaged at the wafer level. The silicon electrodes, which are bonded to two glass dies, define in the same time the walls of the microfluidic channel. The device is fabricated from a silicon wafer that is bonded (at wafer level) anodically and using SU8 photoresist between two glass wafers. The first glass die includes drilled holes for inlet/outlet connections while the second glass die assure the electrical connections, through via holes and a metallization layer, between the silicon electrodes and a printing circuit board.     

Multi-rate model predictive control of particle size distribution in a semibatch emulsion copolymerization reactor

A multi-rate model predictive controller algorithm is presented for the in-batch closed-loop control of the full particle size distribution (PSD) in a semibatch emulsion copolymerization system. The lack of frequent measurements of the PSD and the measurement delay of these measurements are addressed through the use of frequent density measurements from which the current conditions of the system are estimated. The high dimensionality of the discretized full PSD is reduced by the use of model order reduction based on principal component analysis. This method effectively reduces the size of the problem while preserving the main characteristics of the population balance system. Disturbances that perturb the surfactant and monomer amounts inside the semibatch vinyl acetate–butyl acrylate reactor are considered to demonstrate the performance of the proposed control algorithm.     

In situ validation of MERIS marine reflectance off the southwest Iberian Peninsula: assessment of vicarious adjustment and corrections for near-land adjacency

Water-leaving reflectance (ρ_w) data from the European Space Agency ocean colour sensor Medium Resolution Imaging Spectrometer (MERIS) was validated with in situ ρ_w between October 2008 and November 2011, off Sagres on the southwest coast of the Iberian Peninsula. The study area is exceptional, since Stations A, B, and C at 2, 10, and 18 km offshore are in optically deep waters at approximately 40, 100, and 160 m, respectively. These stations showed consistently similar bio-optical properties, characteristic of Case 1 waters, enabling the evaluation of adjacency effects independent of the usual co-varying inputs of coastal waters. Using the third reprocessing of MERIS with the standard MEGS 8.1 processor, four different combinations of procedures were tested to improve the calibration between MERIS products and in situ data. These combinations included no vicarious adjustment (NoVIC), vicarious adjustment (VIC), and, for mitigating the effects of land adjacency on MERIS ρ_w, the improved contrast between ocean and land (ICOL) processor (version 2.7.4) and VIC + ICOL. Out of approximately 130 potential matchups for each station, 38–77%, 74–86%, and 88–90% were achieved at Stations A, B, and C, respectively, depending on which of the four combinations were used. Analyses of ρ_w comparing these various procedures, including statistics, scatter plots, histograms, and MERIS full-resolution images, showed that the VIC procedure compared with NoVIC produced minimal changes to the calibration. For example, at the oceanic Station C, the regression slope was closer to unity at all wavelengths with NoVIC compared to VIC, whereas, with the exception of wavelengths 412 and 443 nm, the intercept, mean ratio (MR), absolute percentage difference (APD), and relative percentage difference (RPD) were better with NoVIC. The differences for MR and APD indicate that there was marginal improvement for these two bands with VIC, and an over-adjustment with RPD. ICOL also showed inconsistent results for improving the retrieval of the near-shore conditions, but under some conditions, such as ρ_w at wavelength 560 nm, the improvement was striking. VIC + ICOL showed results intermediate between those of VIC and ICOL implemented separately. In relation to other validation sites, the offshore Station C at Sagres had much in common with the Mediterranean deep water, BOUSSOLE buoy, although the matchup statistics between MERIS ρ_w and in situ ρ_w were much better for Sagres than for BOUSSOLE. Strikingly, the matchup statistics for ρ_w at Sagres were very similar to those for the Acqua Alta Oceanographic Tower (AAOT), where the AAOT showed more scatter at 412 nm, probably because of the atmospheric correction where the aerosol optical thickness is higher at the AAOT. Conversely, Sagres showed much greater scatter at 665 nm in the red as the values were generally close to the limits of detection owing to the clearer waters at Sagres compared to the more turbid waters at the AAOT.     

Data Distribution in a Peer to Peer Storage System

This article presents distributions for data storage in a P2P system. In peer to peer storage system we have to face a continuous stream of peer failures. So to insure data durability data are usually disseminated using a dispersal redundant scheme and a dynamic data reconstruction process is used to rebuild lost data. There is an important communication traffic to maintain data integrity. So, it is important to reduce the impact of this reconstruction process on peer. To minimize end user traffic according to the reconstruction process, distribution must take into account a new measure: The maximum disturbance cost of a peer. To begin with, we define a static distribution scheme which minimizes this reconstruction cost based on prime numbers theory. We compare this distribution with the random distribution, the most used in data distribution.This Project () is supported by the ACI GRID CGP2P and the ACI MD GDX.     

Proteomic Helicobacter pylori biomarkers discriminative of low-grade gastric MALT lymphoma and duodenal ulcer

To date no reliable diagnostic method exists to predict, among the very large and clinically heterogeneous group of Helicobacter pylori‐infected patients, the extremely small group at risk for developing low‐grade gastric MALT lymphoma (LG‐MALT). Search of proteomic biomarkers holds promise for the classification of the H. pylori strains with regard to this severe clinical outcome. In the present study 69 H. pylori strains isolated from patients with two different H. pylori‐associated diseases, duodenal ulcer (DU, n=29) and LG‐MALT (n=40) were used. Protein expression patterns of the strains were analyzed by using the high‐throughput methodology SELDI. Selected proteins were purified by means of chromatographic and electrophoretic methods in view of further sequencing by LC‐MS/MS. Univariate analysis (Mann–Whitney test) of the protein expression patterns generated nine significant biomarkers that can discriminate between H. pylori strains from patients with DU and LG‐MALT. These biomarkers are of low molecular weight, ranging from 6 to 26.6 kDa. Among them, two are overexpressed in LG‐MALT strains and seven – in DU strains. Two biomarker proteins, one overexpressed in LG‐MALT strains (13.2 kDa) and another one – overexpressed in DU strains (26.6 kDa), were purified to homogeneity and identified by using LC‐MS/MS as a 50S ribosomal protein L7/L12 and a urease subunit, respectively. These biomarkers can be included in novel protein arrays for the differential diagnosis of H. pylori‐associated clinical outcomes.