Multiple biological sequence alignment in heterogeneous multicore clusters with user-selectable task allocation policies

Multiple Sequence Alignment (MSA) is an important problem in Bioinformatics that aims to align more than two sequences in order to emphasize similarity regions. This problem is known to be NP-Hard, so heuristic methods are used to solve it. DIALIGN-TX is an iterative heuristic method for MSA that generates alignments by concatenating ungapped regions with high similarity. Usually, the first phase of MSA algorithms is parallelized by distributing several independent tasks among the nodes. Even though heterogeneous multicore clusters are becoming very common nowadays, very few task allocation policies were proposed for this type of architecture. This paper proposes an MPI/OpenMP master/slave parallel strategy to run DIALIGN-TX in heterogeneous multicore clusters, with several allocation policies. We show that an appropriate choice of the master node has great impact on the overall system performance. Also, the results obtained in a heterogeneous multicore cluster composed of 4 nodes (30 cores), with real sequence sets show that the execution time can be drastically reduced when the appropriate allocation policy is used.     

Pile burning of cutting debris in stands of hazel (Corylus avellana): An experimental study of smouldering combustion towards the validation of a burning protocol

Smouldering combustion in burning piles was experimentally investigated by studying temperature changes in six piles of 2 m of diameter of cutting debris of hazel (Corylus avellana) for three days after extinction. The piles were monitored using an IR camera and K-type thermocouples. The experiment was designed in order to study how the maximum temperature of the charcoal might be influenced by the individual and interaction effects of both the quality of extinction and the elapsed time until the start of extinction of the piles. The piles that were properly extinguished (i.e. using a high-pressure, homogeneously distributed water flow of 50 l/min for 4 min) had a uniform temperature profile and did not have significant hot spots. The temperature reached equilibrium with the environment in less than 10 h after extinction. In contrast, a smouldering front moved throughout the poorly extinguished piles, which had a wide temperature distribution and hot spots of up to 700 °C. A simulation of windy conditions after three days of experiments on a poorly extinguished pile showed that the reactivation of charcoal combustion was possible. It gave a high-risk scenario to cause a wildfire, with hot smouldering embers being transported by wind flow. The results are of interest to improve pile burning protocols so that the number of wildfires caused by such practices may be reduced.     

Water Resources Assessment at Piracicaba,Capivari and Jundiaí River Basins: A Dynamic Systems Approach

The Piracicaba, Capivari, and Jundiaí River Basins (RB-PCJ) are mainly located in the State of São Paulo, Brazil. Using a dynamics systems simulation model (WRM-PCJ) to assess water resources sustainability, five 50-year simulations were run. WRM-PCJ was developed as a tool to aid decision and policy makers on the RB-PCJ Watershed Committee. The model has 254 variables. The model was calibrated and validated using available information from the 80s. Falkenmark Water Stress Index went from 1,403 m³ person^???1 year^???1 in 2004 to 734 m³ P^???1 year^???1 in 2054, and Xu Sustainability Index from 0.44 to 0.20. In 2004, the Keller River Basin Development Phase was Conservation, and by 2054 was Augmentation. The three criteria used to evaluate water resources showed that the watershed is at crucial water resources management turning point. The WRM-PCJ performed well, and it proved to be an excellent tool for decision and policy makers at RB-PCJ.     

A matching-to-sample feedback technique for training self-control of tinnitus.

Treated 30 individuals (aged 24–82 yrs) with subjective tinnitus aurium with a matching-to-sample feedback procedure. Ss' tinnitus sounds were reproduced audiometrically on all characteristics and were presented to them in the noninvolved ear or in both ears when the tinnitus was binaural. This experimental sound was then reduced in 5-db steps within sessions, and Ss had the task of concentrating on reducing the loudness of their tinnitus until a match was achieved between it and the experimental sound at each new db level. Results show a significant difference in db levels from baseline to final training session. Nearly all Ss demonstrated a marked reduction in tinnitus loudness, with several eliminating it completely. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Multi-Objective Optimization using Grid Computing

This paper analyzes some technical and practical issues concerning the use of parallel systems to solve multi-objective optimization problems using enumerative search. This technique constitutes a conceptually simple search strategy, and it is based on evaluating each possible solution from a given finite search space. The results obtained by enumeration are impractical for most computer platforms and researchers, but they exhibit a great interest because they can be used to be compared against the values obtained by stochastic techniques. We analyze here the use of a grid computing system to cope with the limits of enumerative search. After evaluating the performance of the sequential algorithm, we present, first, a parallel algorithm targeted to multiprocessor systems. Then, we design a distributed version prepared to be executed on a federation of geographically distributed computers known as a computational grid. Our conclusion is that this kind of systems can provide to the community with a large and precise set of Pareto fronts that would be otherwise unknown.     

Extracting Low-Frequency Spatio-Temporal Patterns in Ambient Power System Data Using Blind Source Separation

Wide-area techniques provide a powerful tool to extract spatio-temporal patterns from high-dimensional datasets and can be used for event detection and visualization, data fusion, stability assessment, and coherency analysis. In this paper, a novel blind source separation-based approach for extracting low-frequency spatio-temporal patterns from measured ambient power system data is proposed and a spatio-temporal visualization index is also suggested. This methodology combines a nonlinear hierarchical neural network with a Blind Source Separation (BSS) technique. The neural network allows reducing noise and removing the nonlinear relations among data (preserve dynamic features of interest), while the BSS technique permits extracting spatial and temporal patterns. In addition, the proposed approach takes advantage of the latest techniques in nonlinear estimation of non-stationary time series. Finally, application examples of the proposed framework on real test cases recorded from an actual power system by Phasor Measurement Units (PMUs) are presented. The obtained results show that the temporal patterns can be used for extracting and identifying the low-frequency oscillation modes and the spatial patterns can be used for identifying modes with the most contribution in original data. Compared to other BSS approaches, the proposed method has shown to be better for the analysis of real ambient data.     

pH-responsive drug delivery system based on hollow silicon dioxide micropillars coated with polyelectrolyte multilayers

We report on the fabrication of polyelectrolyte multilayer-coated hollow silicon dioxide micropillars as pH-responsive drug delivery systems. Silicon dioxide micropillars are based on macroporous silicon formed by electrochemical etching. Due to their hollow core capable of being loaded with chemically active agents, silicon dioxide micropillars provide additional function such as drug delivery system. The polyelectrolyte multilayer was assembled by the layer-by-layer technique based on the alternative deposition of cationic and anionic polyelectrolytes. The polyelectrolyte pair poly(allylamine hydrochloride) and sodium poly(styrene sulfonate) exhibited pH-responsive properties for the loading and release of a positively charged drug doxorubicin. The drug release rate was observed to be higher at pH 5.2 compared to that at pH 7.4. Furthermore, we assessed the effect of the number of polyelectrolyte bilayers on the drug release loading and release rate. Thus, this hybrid composite could be potentially applicable as a pH-controlled system for localized drug release.     

Identification of Phenylpyrazolone Dimers as a New Class of Anti-Trypanosoma cruzi Agents

Chagas disease is becoming a worldwide problem; it is currently estimated that over six million people are infected. The two drugs in current use, benznidazole and nifurtimox, require long treatment regimens, show limited efficacy in the chronic phase of infection, and are known to cause adverse effects. Phenotypic screening of an in-house library led to the identification of 2,2′-methylenebis(5-(4-bromophenyl)-4,4-dimethyl-2,4-dihydro-3H-pyrazol-3-one), a phenyldihydropyrazolone dimer, which shows an in vitro pIC₅₀ value of 5.4 against Trypanosoma cruzi. Initial optimization was done by varying substituents of the phenyl ring, after which attempts were made to replace the phenyl ring. Finally, the linker between the dimer units was varied, ultimately leading to 2,2′-methylenebis(5-(3-bromo-4-methoxyphenyl)-4,4-dimethyl-2,4-dihydro-3H-pyrazol-3-one (NPD-0228) as the most potent analogue. NPD-0228 has an in vitro pIC₅₀ value of 6.4 against intracellular amastigotes of T. cruzi and no apparent toxicity against the human MRC-5 cell line and murine cardiac cells.     

Mechanical resistance properties of gravel used in subsurface flow constructed wetlands: implications for clogging

Gravel constitutes the filter medium in subsurface flow constructed wetlands (SSF CWs) and its porosity and hydraulic conductivity decrease over time (clogging), limiting the lifespan of the systems. Using gravel of poor quality accelerates clogging in wetlands. In this study, gravel samples from six different wetland systems were compared with regards to their mineral composition and mechanical resistance properties. Results showed that both mineralogy and texture are related to mechanical resistance. Accordingly, gravel with high content of quartz (> 80%) showed a lower percentage of broken particles (0.18-1.03%) than those with lower content of quartz (2.42-4.56% media broken). Although granite is formed by high durability minerals, its non-uniform texture results in a lower resistance to abrasion (ca. 10% less resistance than calcareous gravel). Therefore, it is recommended to use gravels composed mainly of quartz or, when it is not available, limestone gravels (rounded and uniform) are recommended instead. The resistance to abrasion (LAA test) seems to be a good indicator to determine the mechanical properties of gravels used in CWs. It is recommended to use gravels with LAA below 30% in order to avoid a rapid clogging due to gravel crumbling and subsequent mineral solids accumulation.