Aspectos técnicos envolvidos na construção de um "cluster beowulf"

Beowulf cluster is perhaps the cheapest way to construct a high performance computers. The strategy of reaching a high power computing isn't so difficult, but buying and configurating should be done carefully. Technical aspects of hardware components and message-passing libraries are considered, with some results given as examples.

The role of fast atom bombardment mass spectroscopy (FABMS) in cluster characterization

Fast atom bombardment mass spectroscopy has been used to study a large number of cationic phosphine-containing transition-metal-gold clusters, which ranged in mass from 1000 to 4000. Many of these clusters have been previously characterized and were examined in order to test the usefulness of the FABMS technique. Results showed that FABMS is excellent in giving the correct molecular formula and when combined with NMR, IR, and microanalysis gave a reliable characterization for cationic clusters¹. Recently FABMS has become one of the techniques employed as routine in cluster characterization2,3 and also is an effective tool for the structure analysis of large biomolecules4. Some results in the present work reinforce the importance of these data in the characterization of clusters in the absence of crystals with quality for X-ray analysis.

Electrocatalytic oxidation of methanol by the [Ru3O(OAc)6(py)2(CH3OH)]3+cluster: improving the metal-ligand electron transfer by accessing the higher oxidation states of a multicentered system

The [Ru3O(Ac)6(py)2(CH3OH)]+ cluster provides an effective electrocatalytic species for the oxidation of methanol under mild conditions. This complex exhibits characteristic electrochemical waves at -1.02, 0.15 and 1.18 V, associated with the Ru3III,II,II/Ru3III,III,II/Ru 3III,III,III /Ru3IV,III,III successive redox couples, respectively. Above 1.7 V, formation of two RuIV centers enhances the 2-electron oxidation of the methanol ligand yielding formaldehyde, in agreement with the theoretical evolution of the HOMO levels as a function of the oxidation states. This work illustrates an important strategy to improve the efficiency of the oxidation catalysis, by using a multicentered redox catalyst and accessing its multiple higher oxidation states.

Use of data mining and spectral profiles to differentiate condition after harvest of coffee plants

This study aimed at identifying different conditions of coffee plants after harvesting period, using data mining and spectral behavior profiles from Hyperion/EO1 sensor. The Hyperion image, with spatial resolution of 30 m, was acquired in August 28th, 2008, at the end of the coffee harvest season in the studied area. For pre-processing imaging, atmospheric and signal/noise effect corrections were carried out using Flaash and MNF (Minimum Noise Fraction Transform) algorithms, respectively. Spectral behavior profiles (38) of different coffee varieties were generated from 150 Hyperion bands. The spectral behavior profiles were analyzed by Expectation-Maximization (EM) algorithm considering 2; 3; 4 and 5 clusters. T-test with 5% of significance was used to verify the similarity among the wavelength cluster means. The results demonstrated that it is possible to separate five different clusters, which were comprised by different coffee crop conditions making possible to improve future intervention actions.

Software for calculation of reservoir active capacity with the sequent-peak algorithm

It is presented a software developed with Delphi programming language to compute the reservoir's annual regulated active storage, based on the sequent-peak algorithm. Mathematical models used for that purpose generally require extended hydrological series. Usually, the analysis of those series is performed with spreadsheets or graphical representations. Based on that, it was developed a software for calculation of reservoir active capacity. An example calculation is shown by 30-years (from 1977 to 2009) monthly mean flow historical data, from Corrente River, located at São Francisco River Basin, Brazil. As an additional tool, an interface was developed to manage water resources, helping to manipulate data and to point out information that it would be of interest to the user. Moreover, with that interface irrigation districts where water consumption is higher can be analyzed as a function of specific seasonal water demands situations. From a practical application, it is possible to conclude that the program provides the calculation originally proposed. It was designed to keep information organized and retrievable at any time, and to show simulation on seasonal water demands throughout the year, contributing with the elements of study concerning reservoir projects. This program, with its functionality, is an important tool for decision making in the water resources management.

Adaptation of "Niagara Rosada" grape must to winemaking by partial cluster dehydration

This study aimed to verify the influence of partial dehydration of "Niagara Rosada" grape clusters in physicochemical quality of the pre- fermentation must. In Brazil, during the winemaking process it is common to need to adjust the grape must when the physicochemical characteristics of the raw material are insufficient to produce wines in accordance with the Brazilian legislation for classification of beverages, which establishes the minimum alcohol content of 8.6 % for the beverage to be considered wine. Therefore, given that the reduction in the water content of grape berries allows the concentration of chemical compounds present in its composition, especially the concentration of total soluble solids, we proceeded with the treatments that were formed by the combination of two temperatures (T1-37.1ºC and T2-22.9 ºC) two air speeds (S1: 1.79 m s-1 and S2: 3.21 m s-1) and a control (T0) that has not gone through the dehydration treatment. Analysis of pH, Total Titratable Acidity (TTA) were performed in mEq L-1, Total Soluble Solids (TSS) in ºBrix, water content on a dry basis and Concentration of Phenolic Compounds (CPC) in mg of gallic acid per 100g of must. The average comparison test identified statistically significant modifications for the adaptation of must for winemaking purposes, having the treatment with 22.9 ºC and air speed of 1.79 m s-1 shown the largest increase in the concentration of total soluble solids, followed by the second best result for concentration of phenolic compounds.

Análise de detecção de cluster na caracterização espaço-temporal da tuberculose bovina no estado da Bahia

A tuberculose bovina (BTB) é uma enfermidade causada pela infecção pelo Mycobacterium bovis que acomete o homem e diversas espécies de mamíferos. A BTB tem grande importância por causar prejuízos econômicos nas regiões infectadas e por seu impacto na saúde pública. Foi realizado inquérito epidemiológico no Estado da Bahia, entre 2008 e 2010, com o objetivo de estimar a prevalência e conhecer a distribuição espaço temporal da enfermidade. O Estado foi estratificado em quatro regiões, cada uma com características epidemiológicas e demográficas homogêneas representativas de formas de produção pecuária. Um total de 18.810 cabeças com idade superior a 2 anos foi amostrado em 1350 propriedades. O teste cervical comparativo foi aplicado em cada animal selecionado, sendo considerados positivos os animais reagentes positivos ou duas vezes inconclusivos. Latitude e Longitude foram tomadas para cada propriedade amostrada com o auxilio do aparelho de Global Positioning System (GPS). O teste de Cuzick-and-Edwards e a análise de rastreio espacial (spatial scan statistic) foram utilizados para identificar qualquer agrupamento espacial de BTB. A prevalência de rebanho na Bahia, indicando a proporção de propriedades foco, foi de 1,6% (IC 95%: 1,0% - 2,69% por região). Nenhuma evidência significativa (P<0.05) de aglomeração espacial ou clustering foi detectada, possivelmente devido à baixa prevalência da doença. Estes resultados sugerem que a BTB tem baixa prevalência no estado da Bahia e que, nestas condições epidemiológicas, os focos encontrados não podem ser explicados por fatores espacialmente estruturados.

Algorithm to determine the intersection curves between bezier surfaces by the solution of multivariable polynomial system and the differential marching method

The determination of the intersection curve between Bézier Surfaces may be seen as the composition of two separated problems: determining initial points and tracing the intersection curve from these points. The Bézier Surface is represented by a parametric function (polynomial with two variables) that maps a point in the tridimensional space from the bidimensional parametric space. In this article, it is proposed an algorithm to determine the initial points of the intersection curve of Bézier Surfaces, based on the solution of polynomial systems with the Projected Polyhedral Method, followed by a method for tracing the intersection curves (Marching Method with differential equations). In order to allow the use of the Projected Polyhedral Method, the equations of the system must be represented in terms of the Bernstein basis, and towards this goal it is proposed a robust and reliable algorithm to exactly transform a multivariable polynomial in terms of power basis to a polynomial written in terms of Bernstein basis .

Numerical Simulation of the Cavitation in the Hydrodynamic Lubrication of Journal Bearings: a Parallel Algorithm

In this paper we present an algorithm for the numerical simulation of the cavitation in the hydrodynamic lubrication of journal bearings. Despite the fact that this physical process is usually modelled as a free boundary problem, we adopted the equivalent variational inequality formulation. We propose a two-level iterative algorithm, where the outer iteration is associated to the penalty method, used to transform the variational inequality into a variational equation, and the inner iteration is associated to the conjugate gradient method, used to solve the linear system generated by applying the finite element method to the variational equation. This inner part was implemented using the element by element strategy, which is easily parallelized. We analyse the behavior of two physical parameters and discuss some numerical results. Also, we analyse some results related to the performance of a parallel implementation of the algorithm.

A 37-kb restriction map of the human immunoglobulin lambda variable locus, VB cluster, harboring four functional genes and two non-coding Vl sequences

The human immunoglobulin lambda variable locus (IGLV) is mapped at chromosome 22 band q11.1-q11.2. The 30 functional germline v-lambda genes sequenced untill now have been subgrouped into 10 families (Vl1 to Vl10). The number of Vl genes has been estimated at approximately 70. This locus is formed by three gene clusters (VA, VB and VC) that encompass the variable coding genes (V) responsible for the synthesis of lambda-type Ig light chains, and the Jl-Cl cluster with the joining segments and the constant genes. Recently the entire variable lambda gene locus was mapped by contig methodology and its one- megabase DNA totally sequenced. All the known functional V-lambda genes and pseudogenes were located. We screened a human genomic DNA cosmid library and isolated a clone with an insert of 37 kb (cosmid 8.3) encompassing four functional genes (IGLV7S1, IGLV1S1, IGLV1S2 and IGLV5a), a pseudogene (VlA) and a vestigial sequence (vg1) to study in detail the positions of the restriction sites surrounding the Vl genes. We generated a high resolution restriction map, locating 31 restriction sites in 37 kb of the VB cluster, a region rich in functional Vl genes. This mapping information opens the perspective for further RFLP studies and sequencing

Comparison of the efficacy of biodegradable and non-biodegradable scintillation liquids on the counting of tritium- and [14C]-labeled compounds

The widespread use of ³H and 14C in research has generated a large volume of waste mixed with scintillation liquid, requiring an effective control and appropriate storage of liquid radioactive waste. In the present study, we compared the efficacy of three commercially available scintillation liquids, Optiphase HiSafe 3, Ultima-Gold™ AB (biodegradable) and Insta-Gel-XF (non-biodegradable), in terms of [14C]-glucose and [³H]-thymidine counting efficiency. We also analyzed the effect of the relative amount of water (1.6 to 50%), radioisotope concentration (0.1 to 100 nCi/ml), pH (2 to 10) and color of the solutions (samples containing 0.1 to 1.0 mg/ml of Trypan blue) on the counting efficiency in the presence of these scintillation liquids. There were few significant differences in the efficiency of 14C and ³H counting obtained with biodegradable or non-biodegradable scintillation liquids. However, there was an 83 and 94% reduction in the efficiency of 14C and ³H counting, respectively, in samples colored with 1 mg/ml Trypan blue, but not with 0.1 mg/ml, independent of the scintillation liquid used. Considering the low cost of biodegradable scintillation cocktails and their efficacy, these results show that traditional hazardous scintillation fluids may be replaced with the new safe biodegradable fluids without impairment of ³H and 14C counting efficiency. The use of biodegradable scintillation cocktails minimizes both human and environmental exposure to hazardous solvents. In addition, some biodegradable scintillation liquids can be 40% less expensive than the traditional hazardous cocktails.

Enterococcus gallinarum carrying the vanA gene cluster: first report in Brazil

In 2000, Enterococcus faecalis resistant to vancomycin was first reported at a tertiary hospital in Porto Alegre, southern Brazil. The resistance spread to other hospitals and surveillance programs were established by hospital infection committees to prevent the spread of vancomycin-resistant enterococci. In February 2002, an isolate initially identified at the genus level as Enterococcus was obtained by surveillance culture (rectal swab) from a patient admitted to a hospital for treatment of septic arthritis in the shoulder. The isolate proved to be resistant to vancomycin by the disc diffusion method and confirmed by an E-test resulting in a minimal inhibitory concentration of > or = 256 µg/ml. This isolate was sent to a reference laboratory (Laboratório Especial de Bacteriologia e Epidemiologia Molecular, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, USP) for further study and proved to be an E. gallinarum by the polymerase chain reaction (PCR) using specific primers for the species. Due to the phenotype of unusually high vancomycin resistance, the isolate presumably had the resistance genes (vanA and vanB) and this was confirmed by PCR, which indicated the presence of the vanA gene. A 10.8-kb Tn1546-related transposon was also identified by long-PCR. Interspecies transfer of the vancomycin-resistance gene from the donor E. gallinarum was performed in a successful conjugation experiment in vitro, using E. faecium GE-1 and E. faecalis JH22 as receptors. This is the first report of the detection of a vanA determinant naturally acquired by E. gallinarum in Brazil, indicating the importance of characterizing VRE by both phenotype and genotype methods.

APOA1/C3/A4 gene cluster variability and lipid levels in Brazilian children

Genetic studies have suggested that polymorphisms of genes coding for apolipoproteins are significant determinants of serum lipoprotein and lipid levels in adults. However, only a few studies have investigated the association of these polymorphisms in children. Therefore, in the present investigation we studied the distribution of APOA1 -75 G>A, +83 C>T, APOC3 -482 C>T, -455 T>C and 3238 C>G, and APOA4 Q360H and T347S polymorphisms and their influence on plasma lipoprotein levels in children from a Brazilian northeastern admixed population. The seven polymorphic sites were genotyped in 414 children aged 5 to 15 years (mean 8.9 ± 2.9). The genotypes of the seven polymorphic sites were assessed by PCR-RFLP methods. The frequencies of the less common alleles were, in general, intermediate among parental populations, as expected. Strong linkage disequilibrium was detected between polymorphisms at the APOA1, APOC3 and APOA4 loci in this admixed population sample. Overall the genotype effects seen in adults were weaker or absent in children. The APOC3/-455 and APOA4 T347S variants showed significant effects on HDL cholesterol in girls (P = 0.033 and P = 0.016, respectively). Significantly higher plasma total (P = 0.003) and LDL cholesterol (P = 0.004) levels were observed in boys who were carriers of the 3238G allele at the APOC3/3238 C>G site. These results disclosed an overall absence of associations between these polymorphisms and lipids in children. This finding is not unexpected because expression of the effect of these polymorphisms might depend on the interaction with environmental variables both internal and external to the individual.

The miR-17-92 cluster regulates FOG-2 expression and inhibits proliferation of mouse embryonic cardiomyocytes

MicroRNAs (miRNAs) have gradually been recognized as regulators of embryonic development; however, relatively few miRNAs have been identified that regulate cardiac development. A series of recent papers have established an essential role for the miRNA-17-92 (miR-17-92) cluster of miRNAs in the development of the heart. Previous research has shown that the Friend of Gata-2 (FOG-2) is critical for cardiac development. To investigate the possibility that the miR-17-92 cluster regulates FOG-2 expression and inhibits proliferation in mouse embryonic cardiomyocytes we initially used bioinformatics to analyze 3’ untranslated regions (3’UTR) of FOG-2 to predict the potential of miR-17-92 to target it. We used luciferase assays to demonstrate that miR-17-5p and miR-20a of miR-17-92 interact with the predicted target sites in the 3’UTR of FOG-2. Furthermore, RT-PCR and Western blot were used to demonstrate the post-transcriptional regulation of FOG-2 by miR-17-92 in embryonic cardiomyocytes from E12.5-day pregnant C57BL/6J mice. Finally, EdU cell assays together with the FOG-2 rescue strategy were employed to evaluate the effect of proliferation on embryonic cardiomyocytes. We first found that the miR-17-5p and miR-20a of miR-17-92 directly target the 3’UTR of FOG-2 and post-transcriptionally repress the expression of FOG-2. Moreover, our findings demonstrated that over-expression of miR-17-92 may inhibit cell proliferation via post-transcriptional repression of FOG-2 in embryonic cardiomyocytes. These results indicate that the miR-17-92 cluster regulates the expression of FOG-2 protein and suggest that the miR-17-92 cluster might play an important role in heart development.

Performance assessment of the single photon emission microscope: high spatial resolution SPECT imaging of small animal organs

The single photon emission microscope (SPEM) is an instrument developed to obtain high spatial resolution single photon emission computed tomography (SPECT) images of small structures inside the mouse brain. SPEM consists of two independent imaging devices, which combine a multipinhole collimator, a high-resolution, thallium-doped cesium iodide [CsI(Tl)] columnar scintillator, a demagnifying/intensifier tube, and an electron-multiplying charge-coupling device (CCD). Collimators have 300- and 450-µm diameter pinholes on tungsten slabs, in hexagonal arrays of 19 and 7 holes. Projection data are acquired in a photon-counting strategy, where CCD frames are stored at 50 frames per second, with a radius of rotation of 35 mm and magnification factor of one. The image reconstruction software tool is based on the maximum likelihood algorithm. Our aim was to evaluate the spatial resolution and sensitivity attainable with the seven-pinhole imaging device, together with the linearity for quantification on the tomographic images, and to test the instrument in obtaining tomographic images of different mouse organs. A spatial resolution better than 500 µm and a sensitivity of 21.6 counts·s-1·MBq-1 were reached, as well as a correlation coefficient between activity and intensity better than 0.99, when imaging 99mTc sources. Images of the thyroid, heart, lungs, and bones of mice were registered using 99mTc-labeled radiopharmaceuticals in times appropriate for routine preclinical experimentation of <1 h per projection data set. Detailed experimental protocols and images of the aforementioned organs are shown. We plan to extend the instrument's field of view to fix larger animals and to combine data from both detectors to reduce the acquisition time or applied activity.