Rodrigo M. S. de Oliveira

Whole-Genome Sequence of Corynebacterium pseudotuberculosis PAT10 Strain Isolated from Sheep in Patagonia, Argentina

In this work, we report the complete genome sequence of a Corynebacterium pseudotuberculosis PAT10 isolate, collected from a lung abscess in an Argentine sheep in Patagonia, whose pathogen also required an investigation of its pathogenesis. Thus, the analysis of the genome sequence offers a means to better understanding of the molecular and genetic basis of virulence of this bacterium.

Whole genome sequencing of environmental Vibrio cholerae O1 from 10 nanograms of DNA using short reads.

Multiple Displacement Amplification (MDA) of DNA using φ29 (phi29) DNA polymerase amplifies DNA several billion-fold, which has proved to be potentially very useful for evaluating genome information in a culture-independent manner. Whole genome sequencing using DNA from a single prokaryotic genome copy amplified by MDA has not yet been achieved due to the formation of chimeras and skewed amplification of genomic regions during the MDA step, which then precludes genome assembly. We have hereby addressed the issue by using 10 ng of genomic Vibrio cholerae DNA extracted within an agarose plug to ensure circularity as a starting point for MDA and then sequencing the amplified yield using the SOLiD platform. We successfully managed to assemble the entire genome of V. cholerae strain LMA3984-4 (environmental O1 strain isolated in urban Amazonia) using a hybrid de novo assembly strategy. Using our method, only 178 out of 16,713 (1%) of contigs were not able to be inserted into either chromosome scaffold, and out of these 178, only 3 appeared to be chimeras. The other contigs seem to be the result of template-independent non-specific amplification during MDA, yielding spurious reads. Extraction of genomic DNA within an agarose plug in order to ensure circularity of the extracted genome might be key to minimizing amplification bias by MDA for WGS.

FDTD Formulation for Graphene Modeling Based on Piecewise Linear Recursive Convolution and Thin Material Sheets Techniques

A finite-difference time-domain formulation based on piecewise linear recursive convolution method and on thin material sheets technique is developed for modeling terahertz graphene antennas and some other photonic components. The graphene sheets are modeled by specific recursive equations obtained for tangential electric field components, allowing one to easily apply voltage or current sources between the sheets. The effective conductivity of graphene sheets in Yees three-dimensional lattice is calculated and used in simulations. A bow-tie-like geometry is investigated, aiming at resonance tuning. The developed numerical formulation is validated by comparison of results to data published in literature.

An automatic methodology for obtaining optimum shape factors for the radial point interpolation method

In this letter, a methodology is proposed for automatically (and locally) obtaining the shape factor c for the Gaussian basis functions, for each support domain, in order to increase numerical precision and mainly to avoid matrix inversion impossibilities. The concept of calibration function is introduced, which is used for obtaining c. The methodology developed was applied for a 2-D numerical experiment, which results are compared to analytical solution. This comparison revels that the results associated to the developed methodology are very close to the analytical solution for the entire bandwidth of the excitation pulse. The proposed methodology is called in this work Local Shape Factor Calibration Method (LSFCM).

UPML FORMULATION FOR TRUNCATING CONDUCTIVE MEDIA IN CURVILINEAR COORDINATES

This work presents a formulation based on UPML for truncating conductive media by using a local and non-orthogonal coordinate system to solve Maxwell’s equations by the FDTD method. The detailed procedure for obtaining the UPML equations for this case is shown and the complete equation set is provided.

Novel technique for locating an intruder in 3D environments by using a cooperative system of multistatic radars

the aim of this work is to present a new methodology, based on vector and geometrical techniques, for determining the position of an intruder in a residence (3D problem). Initially, modifications in the electromagnetic responses of the environment, caused by movements of the trespasser, are detected. It is worth mentioning that slight movements are detected by high frequency components of the used pulse. The differences between the signals (before and after any movement) are used to define a sphere and ellipsoids, which are used for estimating the position of the invader. In this work, multiple radars are used in a cooperative manner. The multiple estimates obtained are used to determine a mean position and its standard deviation, introducing the concept of sphere of estimates. The electromagnetic simulations were performed by using the FDTD method. Results were obtained for single and double floor residences.

Particle Swarm Optimization Applied for Locating an Intruder by an Ultra-Wideband Radar Network

As it was shown by the authors in a previous work, the Finite-Difference Time-Domain (FDTD) method is adequate to solve numerically Maxwells Equations for simulating the propagation of Ultra-Wideband (UWB) pulses in complex environments. These pulses are important in practice in high-resolution radar and GPS systems and in high performance (wideband) wireless communication links, because they are immune to selective frequency fading related to complex environments, such as residences, offices, laboratories among others. In this case, it is necessary to use spread spectrum techniques for transmission, in order to avoid interferences to other wireless systems, such as cell phone networks, GPS, Bluetooth and IEEE802.11. It is worth to mention that by combining these techniques to UWB pulses; it is possible to obtain a signal with power spectrum density under noise threshold, what is a very interesting characteristic for this application. The proposed simulated environment is a building consisting of several rooms (laboratories) separated by masonry. Internal and external walls are characterized by specific widths and electrical parameters. Wood doors were included in the analysis domain. The analysis region is then limited by U-PML (Uniaxial Perfectly Matched Layers) technique and the system is excited by omni-directional antennas. In order to make the simulations more real, Additive White Gaussian Noise was considered. Aiming at verifying the robustness of the radar network, objects are included in the domain in a semi-random spatial distribution, increasing the contribution of the wave scattering phenomena. Omni-directional antennas were used to register transient electric field in specific points of the scenery, which are adequate for the propose of this work. From those transient responses, it is possible to determine the time intervals the electromagnetic signal requires to travel through the paths transceiver-intruder-transceiver and transceiver-intruder-receivers, forming, this way, a non-linear system of equations (involving circle and ellipses equations, respectively). In order to estimate the intruder position, the PSO method is used and a new methodology was conceived. The main idea is to apply PSO to determine the equidistant point to the circle and to the two ellipses generated by using the data extracted from received transient signals (those three curves usually does not have a single interception point for highly

Parallel-FDTD and experimental results of SAR for flat and head phantoms @ 900 MHz

In this work, computational simulations were performed in order to characterize the way electromagnetic radiation interacts with the human head. Average of realistic parameters of bio-materials, such as bones and head liquids, as well as near field radiation parameters of a half-wave dipole are beeing considered in order to achieve results. This way, a software was developed in which Maxwells equations are numerically solved by using a Beowulf cluster. The solver is based on the finite-difference time-domain method, associated to domain truncation by the uniaxial perfectly mactched layers technique and full-wave solutions have been obtained from the simulation. All averaged SAR values and electric field distributions inside modeled analysed structures have been compared to experimental results obtained in a full setup laboratory with all equipments necessary to perform dosimetric validations of telecomunication devices as shown in IEEE 1528.

A Meshless Discretization Methodology Based on Lennard-Jones Forces

A meshless discretization methodology based on the Lennard-Jones force is presented. The new methodology, named Lennard-Jones discretization method (LJDM), can be seen as an enhancement of Coulombs Law discretization method (CLDM). Because CLDM is based on the repulsive Coulombs forces, it can produce conformal discretization node sets with soft transitions in the space surrounding geometrically different objects. However, in CLDM, reference nodal arrangement (RNA) can be drastically modified, making it difficult to deterministically define a stop criterion and convergence using an invariable set of values for free parameters. This problem is solved in this letter by employing an adapted version of the Lennard-Jones vector force, which is a composition of repulsive and attractive contributions. The main role of attractive forces is preserving RNA, while repulsive forces produce conformal discretization. Analysis of simulation error as function of LJDM and CLDM iterations shows that the inclusion of attractive forces makes LJDM superior to CLDM because convergence and stability are found to be assured for constant sets of free parameters over the discretization iterations.

Soil ionization in different types of grounding grids simulated by FDTD method

The main goal of this work is to analyze the soil ionization effects in different types of grounding grids. The analysis was performed by implementing a software based on the FDTD method, for modeling the non-linear behavior of the ground due the application of high intensity lightning currents. Step voltages on the soil surface were calculated from the border of the grounding grid to a point 1 m away from it. The ionization influence is determined by comparing the results to data obtained by modeling linear ground. The obtained results are physically consistent.