Improvements in the score matrix calculation method using parallel score estimating algorithm

The increasing amount of sequences stored in genomic databases has become unfeasible to the sequential analysis. Then, the parallel computing brought its power to the Bioinformatics through parallel algorithms to align and analyze the sequences, providing improvements mainly in the running time of these algorithms. In many situations, the parallel strategy contributes to reducing the computational complexity of the big problems. This work shows some results obtained by an implementation of a parallel score estimating technique for the score matrix calculation stage, which is the first stage of a progressive multiple sequence alignment. The performance and quality of the parallel score estimating are compared with the results of a dynamic programming approach also implemented in parallel. This comparison shows a significant reduction of running time. Moreover, the quality of the final alignment, using the new strategy, is analyzed and compared with the quality of the approach with dynamic programming.

Bit-parallel coprocessor for standard ECC-GF(2m) on FPGA

This paper presents the design of a high-speed coprocessor for Elliptic Curve Cryptography over binary Galois Field (ECC- GF(2m)). The purpose of our coprocessor is to accelerate the scalar multiplication performed over elliptic curve points represented by affine coordinates in polynomial basis. Our method consists of using elliptic curve parameters over GF(2163) in accordance with international security requirements to implement a bit-parallel coprocessor on field-programmable gate-array (FPGA). Our coprocessor performs modular inversion by using a process based on the Stein's algorithm. Results are presented and compared to results of other related works. We conclude that our coprocessor is suitable for comparing with any other ECC-hardware proposal, since its speed is comparable to projective coordinate designs.

Using Threads to Overcome Synchronization Delays in Parallel Multiple Progressive Alignment Algorithms

Sao Paulo State Research Foundation-FAPESP

Comparison of compressive strength between three different plates for mandibular angle fractures fixation

The present study aims to compare three types of internal fixation for fractures of the mandibular angle. Mechanical testing was performed on replicas of polyurethane hemimandibles sectioned at the angle region to simulate a fracture and fixed with three different hardwares. Fixation devices enrolled on this survey included the grid plates with and without an intermediate bar and the method described by Champy and colleagues in 1978 and the sample consisted of 10 hemimandibles for each group. Vertical loadings were applied on each hemimandible and recorded after a vertical displacement of 3 and 5 mm. Statistical analysis was made by means of the variance analysis (ANOVA) and the Duncan test with a significance level of 5%. The Champy technique showed a statistically significant increased resistance when compared to the grid plates after vertical displacements of 3 and 5 mm. The results of this survey suggest that the Champy technique, when compared to the grid plate positioned at the middle of the mandibular bone (placement site selected for this study), is more resistant than the grid plate and that the inclusion or not of an intermediate bar to the grid plates does not improve its resistance after linear vertical loadings.

Seasonal variation of biotic and abiotic parameters in parallel neotropical fishponds

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Recovery Tests of an Hybrid Current Limiter Composed of a SFCL in Parallel to an Air-Core Power Reactor

The resistive-type superconducting fault current limiters (RSFCL) prototypes using YBCO-coated conductors have shown current limitation for medium voltage class applications for acting time up to 80 ms. By connecting an air-core reactor in parallel with the RSFCL, thus making an hybrid current limiter, one can extend the acting time for up to 1 s. In this work, we report the performance of a hybrid current limiter subjected to an AC peak fault current of 2 kA during 1 s for which within the first 80 ms the SFCL limits the current concurrently with the air-core reactor, and for the remaining 920 ms, only the air-core reactor limits the current. In order to evaluate the actual conditions for subsequent reconnection of RSFCL to the power grid, the hybrid fault current limiter was tested varying the time interval for recovery from 900 ms and 1.2 s, followed again by the concurrent operation of the hybrid limiter during 1 s (SFCL during 80 ms). From this evaluation test, the recovery time can be measured and compared using the voltage peak generated in superconducting module from the first and second fault test. The recovery time was also determined through the pulsed current method (PCM) on short-length sample test. The results showed that the fault current was limited from 1.9 kA down to 514 A after 1 cycle of 60 Hz frequency, with recovery time lower than 1.2 s for two subsequent fault current tests.

Analysis of residual stress and hardness in regions of pre-manufactured and manual bends in fixation plates for maxillary advancement

The aim of this study was to analyze, through Vickers hardness test and photoelasticity analysis, pre-bent areas, manually bent areas, and areas without bends of 10-mm advancement pre-bent titanium plates (Leibinger system). The work was divided into three groups: group I-region without bend, group II-region of 90° manual bend, and group III-region of 90° pre-fabricated bends. All the materials were evaluated through hardness analysis by the Vickers hardness test, stress analysis by residual images obtained in a polariscope, and photoelastic analysis by reflection during the manual bending. The data obtained from the hardness tests were statistically analyzed using ANOVA and Tukey's tests at a significance level of 5 %. The pre-bent plate (group III) showed hardness means statistically significantly higher (P < 0.05) than those of the other groups (I-region without bends, II-90° manually bent region). Through the study of photoelastic reflection, it was possible to identify that the stress gradually increased, reaching a pink color (1.81 δ / λ), as the bending was performed. A general analysis of the results showed that the bent plate region of pre-bent titanium presented the best results.

Development and validation of a stability-indicative agar diffusion assay to determine the potency of flucloxacillin sodium in capsules

Flucloxacillin sodium (FLU) is a semi-synthetic penicillin active against many gram-positive bacteria such as streptococci and penicilinase-producing staphylococci, including methicillin-susceptible S. aureus. This study describes the development and validation of a microbiological assay, applying the diffusion agar method for the determination of FLU, as well as the evaluation of the ability of the method in determining the stability of FLU in capsules against acidic and basic hydrolysis, photolytic and oxidative degradations, using S. aureus ATCC 25923 as micro-organism test and 3 x 3 parallel line assay design (three doses of the standard and three doses of the sample in each plate), with six plates for each assay, according to the Brazilian Pharmacopoeia. The validation method showed good results including linearity, precision, accuracy, robustness and selectivity. The assay is based on the inhibitory effect of FLU using Staphylococcus aureus ATCC 25923. The results of the assay were treated by analysis of variance (ANOVA) and were found to be linear (r = 0.9997) in the range from 1.5 to 6.0 μg/mL, precise (repeatability: R.S.D. = 1.63 and intermediate precision: R.S.D. = 1.64) and accurate (98.96%). FLU solution (from the capsules) exposed to direct UVC light (254 nm), alkaline and acid hydrolysis and hydrogen peroxide causing oxidation were used to evaluate the specificity of the bioassay. Comparison of bioassay and liquid chromatography by ANOVA showed no difference between methodologies. The results demonstrated the validity of the proposed bioassay, which is a simple and useful alternative methodology for FLU determination in routine quality control.

Hybrid methods for lot sizing on parallel machines

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Qualidade da madeira de árvores de guapuruvu (schizolobium parahyba (vell.) blake) com 15 anos provenientes de área de recuperação florestal

Pós-graduação em Ciência Florestal - FCA

A Randomized, Naturalistic, Parallel-Group Study for the Long-Term Treatment of Panic Disorder With Clonazepam or Paroxetine

This long-term extension of an 8-week randomized, naturalistic study in patients with panic disorder with or without agoraphobia compared the efficacy and safety of clonazepam (n = 47) and paroxetine (n = 37) over a 3-year total treatment duration. Target doses for all patients were 2 mg/d clonazepam and 40 mg/d paroxetine (both taken at bedtime). This study reports data from the long-term period (34 months), following the initial 8-week treatment phase. Thus, total treatment duration was 36 months. Patients with a good primary outcome during acute treatment continued monotherapy with clonazepam or paroxetine, but patients with partial primary treatment success were switched to the combination therapy. At initiation of the long-term study, the mean doses of clonazepam and paroxetine were 1.9 (SD, 0.30) and 38.4 (SD, 3.74) mg/d, respectively. These doses were maintained until month 36 (clonazepam 1.9 [ SD, 0.29] mg/d and paroxetine 38.2 [SD, 3.87] mg/d). Long-term treatment with clonazepam led to a small but significantly better Clinical Global Impression (CGI)-Improvement rating than treatment with paroxetine (mean difference: CGI-Severity scale -3.48 vs -3.24, respectively, P = 0.02; CGI-Improvement scale 1.06 vs 1.11, respectively, P = 0.04). Both treatments similarly reduced the number of panic attacks and severity of anxiety. Patients treated with clonazepam had significantly fewer adverse events than those treated with paroxetine (28.9% vs 70.6%, P < 0.001). The efficacy of clonazepam and paroxetine for the treatment of panic disorder was maintained over the long-term course. There was a significant advantage with clonazepam over paroxetine with respect to the frequency and nature of adverse events.

Two extensions for the ALWABP: Parallel stations and collaborative approach

In this article, we introduce two new variants of the Assembly Line Worker Assignment and Balancing Problem (ALWABP) that allow parallelization of and collaboration between heterogeneous workers. These new approaches suppose an additional level of complexity in the Line Design and Assignment process, but also higher flexibility; which may be particularly useful in practical situations where the aim is to progressively integrate slow or limited workers in conventional assembly lines. We present linear models and heuristic procedures for these two new problems. Computational results show the efficiency of the proposed approaches and the efficacy of the studied layouts in different situations. (C) 2012 Elsevier B.V. All rights reserved.

Detecting an abnormality in a recovery boiler using dynamic multivariate data analysis with parallel coordinate plots

Data visualization techniques are powerful in the handling and analysis of multivariate systems. One such technique known as parallel coordinates was used to support the diagnosis of an event, detected by a neural network-based monitoring system, in a boiler at a Brazilian Kraft pulp mill. Its attractiveness is the possibility of the visualization of several variables simultaneously. The diagnostic procedure was carried out step-by-step going through exploratory, explanatory, confirmatory, and communicative goals. This tool allowed the visualization of the boiler dynamics in an easier way, compared to commonly used univariate trend plots. In addition it facilitated analysis of other aspects, namely relationships among process variables, distinct modes of operation and discrepant data. The whole analysis revealed firstly that the period involving the detected event was associated with a transition between two distinct normal modes of operation, and secondly the presence of unusual changes in process variables at this time.

Evaluation of perforated steel plates as connection in glulam-concrete composite structures

This paper shows the results of an experimental investigation carried out on a connection element of glulam and concrete composite structures, through double-sided push-out shear tests. The connection system was composed of perforated steel plates glued with epoxy adhesive. Five specimens were made and tested under shear forces. This innovative connection system showed an average initial slip modulus equivalent to 339.4 kN/mm. In addition, the connection system was evaluated by means of numerical simulations and the software ANSYS was used for this purpose. The numerical simulations demonstrated good agreement with the experimental data, especially in the regime of elastic-linear behavior of materials. (C) 2011 Elsevier Ltd. All rights reserved.

Maximum Series-Parallel Subgraph

Consider the NP-hard problem of, given a simple graph G, to find a series-parallel subgraph of G with the maximum number of edges. The algorithm that, given a connected graph G, outputs a spanning tree of G, is a 1/2-approximation. Indeed, if n is the number of vertices in G, any spanning tree in G has n-1 edges and any series-parallel graph on n vertices has at most 2n-3 edges. We present a 7/12 -approximation for this problem and results showing the limits of our approach.