Matrix-vector multiplication and triangular linear solver using GPGPU for symmetric positive definite matrices derived from elliptic equations

The modern GPUs are well suited for intensive computational tasks and massive parallel computation. Sparse matrix multiplication and linear triangular solver are the most important and heavily used kernels in scientific computation, and several challenges in developing a high performance kernel with the two modules is investigated. The main interest it to solve linear systems derived from the elliptic equations with triangular elements. The resulting linear system has a symmetric positive definite matrix. The sparse matrix is stored in the compressed sparse row (CSR) format. It is proposed a CUDA algorithm to execute the matrix vector multiplication using directly the CSR format. A dependence tree algorithm is used to determine which variables the linear triangular solver can determine in parallel. To increase the number of the parallel threads, a coloring graph algorithm is implemented to reorder the mesh numbering in a pre-processing phase. The proposed method is compared with parallel and serial available libraries. The results show that the proposed method improves the computation cost of the matrix vector multiplication. The pre-processing associated with the triangular solver needs to be executed just once in the proposed method. The conjugate gradient method was implemented and showed similar convergence rate for all the compared methods. The proposed method showed significant smaller execution time.

New Species of the Thorny Catfish Genus Leptodoras (Siluriformes: Doradidae) from Rio Fresco, Xingu Basin, Brazil

A new species of the thorny catfish genus Leptodoras (family Doradidae) is described. The new species shares three characters with its congeners, the modified oral hood with distinct upper labial extensions, the first gill arch with enlarged accessory lamellae extending well onto medial face of gill filaments, and the pelvic fin inserted in anterior half of body. The new species is distinguished from congeners by having a large dark submarginal blotch on distal half of dorsal-fin spine and anteriormost dorsal-fin branched rays, lower labial extension of modified oral hood extending more posteriorly than upper labial extension, relatively few midlateral scutes, gas bladder moderately sized (not reduced), paired bony capsules on anteriormost vertebrae reduced to paired cup-like laminar ossifications separated by a triangular septum, pair of small, swelling-like diverticula on each side of the anterior chamber of gas bladder, a well-developed anterior nuchal plate, and nuchal foramina present. The new species was discovered from a single specimen collected in the rio Fresco, a tributary of the rio Xingu, and is described based on this and on additional material recently collected in the same area. A discussion of its placement within Leptodoras is also presented.

Investigation of the relationship between the structure and function of Ts2, a neurotoxin from Tityus serrulatus venom

Scorpion toxins targeting voltage-gated sodium (NaV) channels are peptides that comprise 6076 amino acid residues cross-linked by four disulfide bridges. These toxins can be divided in two groups (a and beta toxins), according to their binding properties and mode of action. The scorpion a-toxin Ts2, previously described as a beta-toxin, was purified from the venom of Tityus serrulatus, the most dangerous Brazilian scorpion. In this study, seven mammalian NaV channel isoforms (rNaV1.2, rNaV1.3, rNaV1.4, hNaV1.5, mNaV1.6, rNaV1.7 and rNaV1.8) and one insect NaV channel isoform (DmNaV1) were used to investigate the subtype specificity and selectivity of Ts2. The electrophysiology assays showed that Ts2 inhibits rapid inactivation of NaV1.2, NaV1.3, NaV1.5, NaV1.6 and NaV1.7, but does not affect NaV1.4, NaV1.8 or DmNaV1. Interestingly, Ts2 significantly shifts the voltage dependence of activation of NaV1.3 channels. The 3D structure of this toxin was modeled based on the high sequence identity (72%) shared with Ts1, another T. serrulatus toxin. The overall fold of the Ts2 model consists of three beta-strands and one a-helix, and is arranged in a triangular shape forming a cysteine-stabilized a-helix/beta-sheet (CSa beta) motif.

An additional basal sauropodomorph specimen from the Upper Triassic Caturrita Formation, southern Brazil, with comments on the biogeography of plateosaurids

We describe an additional saurischian specimen from the Caturrita Formation (Norian) of the Parana Basin, southern Brazil. This material was collected in the 1950s and remained unstudied due to its fragmentary condition. Detailed comparisons with other saurischians worldwide reveal that some characters of the ilium, including the low ventral projection of the medial wall of the acetabulum and its concave ventral margin, together with the short triangular shape of the pre-acetabular process and its mound-like dorsocaudal edge, resemble those of sauropodomorphs such as Plateosaurus and Riojasaurus. This set of traits suggests that MN 1326-V has affinities with basal Sauropodomorpha, probably closer to plateosaurians than to Saturnalia-like taxa. Previous records of this clade in the Caturrita Formation include Unaysaurus, which has been related to Plateosaurus within Plateosauridae. Alternative schemes suggest that plateosaurids include Plateosaurus plus the Argentinean 'prosauropods' Coloradisaurus and Riojasaurus. Both hypotheses raise biogeographic questions, as a close relationship between faunas from South America and Europe excluding Africa and North America is not supported by geological and biostratigraphical evidence. Additionally, the absence of plateosaurids in other continents suggests that the geographical distribution of this taxon is inconsistent with the geological history of western Pangaea, and this demands further investigations of the phylogeny of sauropodomorphs or improved sampling.

Synthesis of Carbon Nanomaterials through Up-Cycling Agricultural and Municipal Solid Wastes

This work addresses the synthesis of carbon nanomaterials (CNMs) by up-cycling common solid wastes. These feedstocks could supersede the use of costly and often toxic or highly flammable chemicals, such as hydrocarbon gases, carbon monoxide, and hydrogen, which are commonly used as feedstocks in current nanomanufacturing processes for CNMs. Agricultural sugar cane bagasse and corn residues, scrap tire chips, and postconsumer polyethylene (PE) and polyethylene terephthalate (PET) bottle shreddings were either thermally treated by sole pyrolysis or by sequential pyrolysis and partial oxidation. The resulting gaseous carbon-bearing effluents were then channeled into a heated reactor. CNMs, including carbon nanotubes, were catalytically synthesized therein on stainless steel meshes. This work revealed that the structure of the resulting CNMs is determined by the feedstock type, through the disparate mixtures of carbon-bearing gases generated when different feedstocks are pyrolyzed. CNM characterization was conducted by scanning and transmission electron microscopy as well as by Raman spectroscopy and by thermogravimetric analysis. Gas chromatography was used to characterize the gases in the synthesis chamber. This work demonstrated an alternative method for efficient manufacturing of CNMs using both biodegradable and nonbiodegradable agricultural and municipal carbonaceous wastes.

Interactive quadrangulation with reeb atlases and connectivity textures

Creating high-quality quad meshes from triangulated surfaces is a highly nontrivial task that necessitates consideration of various application specific metrics of quality. In our work, we follow the premise that automatic reconstruction techniques may not generate outputs meeting all the subjective quality expectations of the user. Instead, we put the user at the center of the process by providing a flexible, interactive approach to quadrangulation design. By combining scalar field topology and combinatorial connectivity techniques, we present a new framework, following a coarse to fine design philosophy, which allows for explicit control of the subjective quality criteria on the output quad mesh, at interactive rates. Our quadrangulation framework uses the new notion of Reeb atlas editing, to define with a small amount of interactions a coarse quadrangulation of the model, capturing the main features of the shape, with user prescribed extraordinary vertices and alignment. Fine grain tuning is easily achieved with the notion of connectivity texturing, which allows for additional extraordinary vertices specification and explicit feature alignment, to capture the high-frequency geometries. Experiments demonstrate the interactivity and flexibility of our approach, as well as its ability to generate quad meshes of arbitrary resolution with high-quality statistics, while meeting the user's own subjective requirements.

Synthesis Methodology Applied to a Tunable Patch Filter With Independent Frequency and Bandwidth Control

A new methodology for the synthesis of tunable patch filters is presented. The methodology helps the designer to perform a theoretical analysis of the filter through a coupling matrix that includes the effect of the tuning elements used to tune the filter. This general methodology accounts for any tuning parameter desired and was applied to the design of a tunable dual-mode patch filter with independent control of center frequency and bandwidth (BW). The bandpass filter uses a single triangular resonator with two etched slots that split the fundamental degenerate modes and form the filter passband. Varactor diodes assembled across the slots are used to vary the frequency of each degenerate fundamental mode independently, which is feasible due to the nature of the coupling scheme of the filter. The varactor diode model used in simulations, their assembling, the dc bias configuration, and measured results are presented. The theory results are compared to the simulations and to measurements showing a very good agreement and validating the proposed methodology. The fabricated filter presents an elliptic response with 20% of center frequency tuning range around 3.2 GHz and a fractional BW variation from 4% to 12% with low insertion loss and high power handling with a 1-dB compression point higher than +14.5 dB.

Nitric oxide modulates metalloproteinase-2, collagen deposition and adhesion rate after polypropylene mesh implantation in the intra-abdominal wall

Prosthetic meshes are commonly used to correct abdominal wall defects. However, the inflammatory reaction induced by these devices in the peritoneum is not completely understood. We hypothesized that nitric oxide (NO), produced by nitric oxide synthase 2 (NOS2) may modulate the response induced by mesh implants in the abdominal wall and, consequently, affect the outcome of the surgical procedure. Polypropylene meshes were implanted in the peritoneal side of the abdominal wall in wild-type and NOS2-deficient (NOS2(-/-)) mice. After 15 days tissues around the mesh implant were collected, and inflammatory markers (the cytokine interleukin 1 beta (IL-1 beta) and NO) and tissue remodeling (collagen and metalloproteinases (MMP) 2 and 9) were analyzed. The lack of NOS2-derived NO induced a higher incidence of visceral adhesions at the mesh implantation site compared with wild-type mice that underwent the same procedure (P < 0.05). Additionally, higher levels of IL-1 beta were present in the mesh-implanted NOS2(-/-) animals compared with control and wild-type mice. Mesh implantation induced collagen I and III deposition, but in smaller amounts in NOS2(-/-) mice. MMP-9 activity after the surgical procedure was similarly increased in both groups. Conversely, MMP-2 activity was unchanged in mesh-implanted wild-type mice, but was significantly increased in NOS2(-/-) mice (P < 0.01), due to decreased S-nitrosylation of the enzyme in these animals. We conclude that NOS2-derived NO is crucial for an adequate response to and integration of polypropylene mesh implants in the peritoneum. NO deficiency results in a prolonged inflammatory reaction to the mesh implant, and reduced collagen deposition may contribute to an increased incidence of visceral adhesions. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Initial experience with Pomerantzeff's technique for reduction of the size of giant left atrium

Introduction: The most common indication for surgical correction of giant left atrium is associated with mitral valve insufficiency with or without atrial fibrillation. Several techniques for this purpose are already described with varying results. Objective: To present the initial experience with the tangential triangular resection technique (Pomerantzeff). Methods: From 2002 to 2010, four patients underwent mitral valve operation with reduction of left atrial volume by the technique of triangular resection tangential in our service. Three patients were female. The age ranged from 21 to 51 years old. The four patients presented with atrial fibrillation. Ejection fraction of left ventricle preoperatively ranged from 38% to 62%. The left atrial diameter ranged from 78mm to 140mm. After treatment of mitral dysfunction, the left atrium was reduced by resecting triangular tangential posterior wall between the pulmonary veins to avoid anatomic distortion of the mitral valve or pulmonary veins, reducing tension in the suture line. Results: Average hospital stay was 21.5 +/- 6.5 days. The mean cardiopulmonary bypass time was 130 +/- 30 minutes. There was no surgical bleeding or mortality in the postoperative period. All patients had sinus rhythm restored in the output of cardiopulmonary bypass, maintaining this rate postoperatively. The average diameter of the left atrium was reduced by 50.5% +/- 19.5%. The left ventricular ejection fraction improved in all patients. Conclusion: Initial results with this technique have shown effective reduction of the left atrium.

A generalized finite element method with global-local enrichment functions for confined plasticity problems

The main feature of partition of unity methods such as the generalized or extended finite element method is their ability of utilizing a priori knowledge about the solution of a problem in the form of enrichment functions. However, analytical derivation of enrichment functions with good approximation properties is mostly limited to two-dimensional linear problems. This paper presents a procedure to numerically generate proper enrichment functions for three-dimensional problems with confined plasticity where plastic evolution is gradual. This procedure involves the solution of boundary value problems around local regions exhibiting nonlinear behavior and the enrichment of the global solution space with the local solutions through the partition of unity method framework. This approach can produce accurate nonlinear solutions with a reduced computational cost compared to standard finite element methods since computationally intensive nonlinear iterations can be performed on coarse global meshes after the creation of enrichment functions properly describing localized nonlinear behavior. Several three-dimensional nonlinear problems based on the rate-independent J (2) plasticity theory with isotropic hardening are solved using the proposed procedure to demonstrate its robustness, accuracy and computational efficiency.

Catanduba, a new Theraphosinae spider genus from Central Brazil (Araneae, Theraphosidae)

A new genus, Catanduba, is proposed and supported on the cladistic analysis with the following synapomorphies: embolus tapering abruptly from half of the length, embolus tooth associated with PIK and a triangular basal nodule on male metatarsus I. Homoeomma simoni and Plesiopelma flavohirtum are transferred to Catanduba and five new species are described: C. tuskae, C. araguaia, C. piauiensis, C. canabrava and C. peruacu. The species occur mainly in central Brazil, in Cerrado areas, with some species also occurring in Atlantic forest (C. tuskae sp. n.) and Caatinga (C. piauiensis sp. n. and C. peruacu sp. n.).

Subdivision of Hysteresis Loss in Mn-Zn Ferrite Toroidal Cores

The hysteresis loss subdivision method proved to be a strong tool to help in the analysis of different energy dissipation mechanisms along the quasi-static hysteresis loop measured on electrical steels. This paper used the samemethod to discuss the mechanisms involving the energy loss dissipation in Mn-Zn ferrite toroidal cores. The samples, sintered under controlled atmosphere in industrial conditions, were measured under triangular waveform excitation at very low frequency (5 mHz) and peak flux densities varying from 0.05 T to 0.45 T. The results show a different behavior between the low inductions hysteresis loss (WLI) and the high induction hysteresis loss (WHI) which proves the existence of different energy dissipation mechanisms affecting these loss components.

STOCHASTIC MODEL FOR SIMULATING MAIZE YIELD

Maize is one of the most important crops in the world. The products generated from this crop are largely used in the starch industry, the animal and human nutrition sector, and biomass energy production and refineries. For these reasons, there is much interest in figuring the potential grain yield of maize genotypes in relation to the environment in which they will be grown, as the productivity directly affects agribusiness or farm profitability. Questions like these can be investigated with ecophysiological crop models, which can be organized according to different philosophies and structures. The main objective of this work is to conceptualize a stochastic model for predicting maize grain yield and productivity under different conditions of water supply while considering the uncertainties of daily climate data. Therefore, one focus is to explain the model construction in detail, and the other is to present some results in light of the philosophy adopted. A deterministic model was built as the basis for the stochastic model. The former performed well in terms of the curve shape of the above-ground dry matter over time as well as the grain yield under full and moderate water deficit conditions. Through the use of a triangular distribution for the harvest index and a bivariate normal distribution of the averaged daily solar radiation and air temperature, the stochastic model satisfactorily simulated grain productivity, i.e., it was found that 10,604 kg ha(-1) is the most likely grain productivity, very similar to the productivity simulated by the deterministic model and for the real conditions based on a field experiment.

GENERALIZED FINITE ELEMENT METHOD ON NONCONVENTIONAL HYBRID-MIXED FORMULATION

The generalized finite element method (GFEM) is applied to a nonconventional hybrid-mixed stress formulation (HMSF) for plane analysis. In the HMSF, three approximation fields are involved: stresses and displacements in the domain and displacement fields on the static boundary. The GFEM-HMSF shape functions are then generated by the product of a partition of unity associated to each field and the polynomials enrichment functions. In principle, the enrichment can be conducted independently over each of the HMSF approximation fields. However, stability and convergence features of the resulting numerical method can be affected mainly by spurious modes generated when enrichment is arbitrarily applied to the displacement fields. With the aim to efficiently explore the enrichment possibilities, an extension to GFEM-HMSF of the conventional Zienkiewicz-Patch-Test is proposed as a necessary condition to ensure numerical stability. Finally, once the extended Patch-Test is satisfied, some numerical analyses focusing on the selective enrichment over distorted meshes formed by bilinear quadrilateral finite elements are presented, thus showing the performance of the GFEM-HMSF combination.

BEM modeling of saturated porous media susceptible to damage

This paper deals with the numerical analysis of saturated porous media, taking into account the damage phenomena on the solid skeleton. The porous media is taken into poro-elastic framework, in full-saturated condition, based on Biot's Theory. A scalar damage model is assumed for this analysis. An implicit boundary element method (BEM) formulation, based on time-independent fundamental solutions, is developed and implemented to couple the fluid flow and two-dimensional elastostatic problems. The integration over boundary elements is evaluated using a numerical Gauss procedure. A semi-analytical scheme for the case of triangular domain cells is followed to carry out the relevant domain integrals. The non-linear problem is solved by a Newton-Raphson procedure. Numerical examples are presented, in order to validate the implemented formulation and to illustrate its efficacy. (C) 2011 Elsevier Ltd. All rights reserved.