Porting and performance analysis of EC-Earth System on the BSC-MareNostrum Supercomputer

Earth System Models (ESM) have been successfuly developed over past few years, and are currently beeing used for simulating present day-climate, seasonal to interanual predictions of climate change. The supercomputer performance plays an important role in climate modeling since one of the challenging issues for climate modellers is to efficiently and accurately couple earth System components on present day computers architectures. At the Barcelona Supercomputing Center (BSC), we work with the EC- Earth System Model. The EC- Earth is an ESM, which currently consists of an atmosphere (IFS) and an ocean (NEMO) model that communicate with each other through the OASIS coupler. Additional modules (e.g. for chemistry and vegetation ) are under development. The EC-Earth ESM has been ported successfully over diferent high performance computin platforms (e.g, IBM P6 AIX, CRAY XT-5, Intelbased Linux Clusters, SGI Altix) at diferent sites in Europ (e.g., KNMI, ICHEC, ECMWF). The objective of the first phase of the project was to identify and document the issues related with the portability and performance of EC-Earth on the MareNostrum supercomputer, a System based on IBM PowerPC 970MP processors and run under a Linux Suse Distribution. EC-Earth was successfully ported to MareNostrum, and a compilation incompatibilty was solved by a two step compilation approach using XLF version 10.1 and 12.1 compilers. In addition, the EC-Earth performance was analyzed with respect to escalability and trace analysis with the Paravear software. This analysis showed that EC-Earth with a larger number of IFS CPUs (<128) is not feasible at the moment since some issues exists with the IFS-NEMO balance and MPI Communications.

Assessment of Tandem Mass Spectrometry and High Resolution Mass Spectrometry for the Analysis of Bupivacaine in Plasma

Triple quadrupole mass spectrometers coupled with high performance liquid chromatography are workhorses in quantitative bioanalyses. It provides substantial benefits including reproducibility, sensitivity and selectivity for trace analysis. Selected Reaction Monitoring allows targeted assay development but data sets generated contain very limited information. Data mining and analysis of non-targeted high-resolution mass spectrometry profiles of biological samples offer the opportunity to perform more exhaustive assessments, including quantitative and qualitative analysis. The objectives of this study was to test method precision and accuracy, statistically compare bupivacaine drug concentration in real study samples and verify if high resolution and accurate mass data collected in scan mode can actually permit retrospective data analysis, more specifically, extract metabolite related information. The precision and accuracy data presented using both instruments provided equivalent results. Overall, the accuracy was ranging from 106.2 to 113.2% and the precision observed was from 1.0 to 3.7%. Statistical comparisons using a linear regression between both methods reveal a coefficient of determination (R2) of 0.9996 and a slope of 1.02 demonstrating a very strong correlation between both methods. Individual sample comparison showed differences from -4.5% to 1.6% well within the accepted analytical error. Moreover, post acquisition extracted ion chromatograms at m/z 233.1648 ± 5 ppm (M-56) and m/z 305.2224 ± 5 ppm (M+16) revealed the presence of desbutyl-bupivacaine and three distinct hydroxylated bupivacaine metabolites. Post acquisition analysis allowed us to produce semiquantitative evaluations of the concentration-time profiles for bupicavaine metabolites.

Analysis of ⁸⁵Kr: a comparison at the 10-14 level using micro-liter samples

The isotopic abundance of 85Kr in the atmosphere, currently at the level of 10−11, has increased by orders of magnitude since the dawn of nuclear age. With a half-life of 10.76 years, 85Kr is of great interest as tracers for environmental samples such as air, groundwater and ice. Atom Trap Trace Analysis (ATTA) is an emerging method for the analysis of rare krypton isotopes at isotopic abundance levels as low as 10−14 using krypton gas samples of a few micro-liters. Both the reliability and reproducibility of the method are examined in the present study by an inter-comparison among different instruments. The 85Kr/Kr ratios of 12 samples, in the range of 10−13 to 10−10, are measured independently in three laboratories: a low-level counting laboratory in Bern, Switzerland, and two ATTA laboratories, one in Hefei, China, and another in Argonne, USA. The results are in agreement at the precision level of 5%.

Analysis of crystallographic slip and grain boundary sliding in a Ti-45Al-2Nb-2Mn (at%)-0.8 vol%TiB2 alloy by high temperature in situ mechanical testing

This work aims to contribute to a further understanding of the fundamentals of crystallographic slip and grain boundary sliding in the γ-TiAl Ti–45Al–2Nb–2Mn (at%)–0.8 vol%TiB2 intermetallic alloy, by means of in situ high-temperature tensile testing combined with electron backscatter diffraction (EBSD). Several microstructures, containing different fractions and sizes of lamellar colonies and equiaxed γ-grains, were fabricated by either centrifugal casting or powder metallurgy, followed by heat treatment at 1300 °C and furnace cooling. in situ tensile and tensile-creep experiments were performed in a scanning electron microscope (SEM) at temperatures ranging from 580 °C to 700 °C. EBSD was carried out in selected regions before and after straining. Our results suggest that, during constant strain rate tests, true twin γ/γ interfaces are the weakest barriers to dislocations and, thus, that the relevant length scale might be influenced by the distance between non-true twin boundaries. Under creep conditions both grain/colony boundary sliding (G/CBS) and crystallographic slip are observed to contribute to deformation. The incidence of boundary sliding is particularly high in γ grains of duplex microstructures. The slip activity during creep deformation in different microstructures was evaluated by trace analysis. Special emphasis was placed in distinguishing the compliance of different slip events with the Schmid law with respect to the applied stress.

The determination of trace residues on metal surfaces /

"U.S. Atomic Energy Commission Contract AT(29-1)-1106."

Partial microwave-assisted wet digestion of animal tissue using a baby-bottle sterilizer for analyte determination by inductively coupled plasma optical emission spectrometry

A procedure for partial digestion of bovine tissue is proposed using polytetrafluoroethylene (PTFE) microvessels inside a baby-bottle sterilizer under microwave radiation for multi-element determination by inductively coupled plasma optical emission spectrometry (ICP OES). Samples were directly weighed in laboratory-made polytetrafluoroethylene vessels. Nitric acid and hydrogen peroxide were added to the uncovered vessels, which were positioned inside the baby-bottle sterilizer, containing 500 mL of water. The hydrogen peroxide volume was fixed at 100 mu L The system was placed in a domestic microwave oven and partial digestion was carried out for the determination of Ca, Cu, Fe. Mg, Mn and Zn by inductively coupled plasma optical emission spectrometry. The single-vessel approach was used in the entire procedure, to minimize contamination in trace analysis. Better recoveries and lower residual carbon content (RCC) levels were obtained under the conditions established through a 2(4-1) fractional factorial design: 650 W microwave power, 7 min digestion time, 50 mu L nitric acid and 50 mg sample mass. The digestion efficiency was ascertained according to the residual carbon content determined by inductively coupled plasma optical emission spectrometry. The accuracy of the proposed procedure was checked against two certified reference materials. (C) 2009 Elsevier B.V. All rights reserved.

Quantification of endocrine disruptors and pesticides in water by gas chromatography–tandem mass spectrometry. Method validation using weighted linear regression schemes

Amulti-residue methodology based on a solid phase extraction followed by gas chromatography–tandem mass spectrometry was developed for trace analysis of 32 compounds in water matrices, including estrogens and several pesticides from different chemical families, some of them with endocrine disrupting properties. Matrix standard calibration solutions were prepared by adding known amounts of the analytes to a residue-free sample to compensate matrix-induced chromatographic response enhancement observed for certain pesticides. Validation was done mainly according to the International Conference on Harmonisation recommendations, as well as some European and American validation guidelines with specifications for pesticides analysis and/or GC–MS methodology. As the assumption of homoscedasticity was not met for analytical data, weighted least squares linear regression procedure was applied as a simple and effective way to counteract the greater influence of the greater concentrations on the fitted regression line, improving accuracy at the lower end of the calibration curve. The method was considered validated for 31 compounds after consistent evaluation of the key analytical parameters: specificity, linearity, limit of detection and quantification, range, precision, accuracy, extraction efficiency, stability and robustness.

Education and Training in Forensic Intelligence: a New Challenge

From recent calls for positioning forensic scientists within the criminal justice system, but also policing and intelligence missions, this paper emphasizes the need for the development of educational and training programs in the area of forensic intelligence, It is argued that an imbalance exists between perceived and actual understanding of forensic intelligence by police and forensic science managers, and that this imbalance can only be overcome through education. The challenge for forensic intelligence education and training is therefore to devise programs that increase forensic intelligence awareness, firstly for managers to help prevent poor decisions on how to develop information processing. Two recent European courses are presented as examples of education offerings, along with lessons learned and suggested paths forward. It is concluded that the new focus on forensic intelligence could restore a pro-active approach to forensic science, better quantify its efficiency and let it get more involved in investigative and managerial decisions. A new educational challenge is opened to forensic science university programs around the world: to refocus criminal trace analysis on a more holistic security problem solving approach.

O problema da contaminação na determinação de traços de alumínio

The most common difficulties which occur in trace analysis are those which involve contamination, mainly when the measurement is at very low concentration of ubiquitous elements as aluminium. The worst situation is when a separation step is necessary, because it requires extra-manipulations of the sample. This article describes the degree of contamination and its control for the aluminium trace analysis in dialysis solutions, when aluminium content of about 15 µg/l must be determinated.

Análise potenciométrica de redissolução com ultramicroeletrodos: fundamentos e aplicações na determinação de metais traços

The Potentiometric Stripping Analysis (PSA) is described with emphasis on ultramicroelectrode applications with a laboratory developed computer based instrumentation. The technique potentialities as compared with the voltammetric approach are pointed out based on the current literature. Some results of trace metals analysis including zinc, cadmium, lead and copper in vinegar and canned food samples are presented. The mainly advantage found in our laboratory was the technique capability to analyse natural samples with minimum matrix interference and the low level of noise found in our determinations.

Determinação de elementos-traço: relatório de dois exercícios interlaboratoriais

Results of two intercomparison exercises are reported. In the first one, the participants were asked to determine Cd, Cu, Pb and Zn, at the sub mg mL-1 level, in an acidified aqueous solution. In the second one, the participants were asked to determine mercury (total) in two homogeneous biological samples, hair and fish. The exercises were considered satisfactory and few reported results were discharged (3s criteria).

Amostragem de suspensões: Emprego da técnica na análise direta de amostras

This review presents some characteristics related to slurry sampling in trace analysis in terms of its advantages, limitations and applications, as well as the latest advance in this area, such as mechanization, chemical modifiers, stabilization agents and others. The reviewed applications include foods, biological and geological materials.

Extração e pré-concentração de compostos orgânicos voláteis por permeação em membrana para análise cromatográfica

This work discusses sample preparation processes for gas chromatography (GC) based on the technique of extraction through membrane permeation (MPE). The MPE technique may be easily coupled to GC via a relatively simple device, which is a module that holds the membrane and is directly connected to the GC column. The possibility of operational errors due to sample handling is substantially reduced in an MPE-GC system because the sample preparation and the chemical analysis are accomplished as a one-step process. The MPE technique is of relatively wide application as it can be used for aqueous samples, solid samples and gaseous samples. Depending on the type of sample the extraction is performed with the membrane in direct contact with the sample or in contact with its headspace. The MPE-GC technique is very useful in trace analysis, due to the time-dependent enrichment of the analyte. A typical application of MPE-GC is the analysis of VOCs present in water that may be accomplished with detection limits at the low ppb (mugL-1) level.

Métodos de amostragem e análise para compostos reduzidos de enxofre atmosférico

This work presents a review of sampling and analytical methods that can be applied to atmospheric traces of reduced sulphur compounds (RSC) in the atmosphere. Sampling methodology involving discontinuous methods with preconcentration is mostly used. For the most part, adsorption on solids and cryogenic capture are applied as a procedure. The analysis of these compounds has been done mainly by gas chromatography with FPD, fluorescence and spectrophotometry. Advantages and disadvantages of the methodologies are also mentioned in this paper, aiming to guide the reader towards the most appropriate choice of a sampling and analytical method for RSCs.

Développement de techniques analytiques pour la détermination des agents anti-infectieux dans les eaux environnementales

Les agents anti-infectieux sont utilisés pour traiter ou prévenir les infections chez les humains, les animaux, les insectes et les plantes. L’apparition de traces de ces substances dans les eaux usées, les eaux naturelles et même l’eau potable dans plusieurs pays du monde soulève l’inquiétude de la communauté scientifique surtout à cause de leur activité biologique. Le but de ces travaux de recherche a été d’étudier la présence d’anti-infectieux dans les eaux environnementales contaminées (c.-à-d. eaux usées, eaux naturelles et eau potable) ainsi que de développer de nouvelles méthodes analytiques capables de quantifier et confirmer leur présence dans ces matrices. Une méta-analyse sur l’occurrence des anti-infectieux dans les eaux environnementales contaminées a démontré qu’au moins 68 composés et 10 de leurs produits de transformation ont été quantifiés à ce jour. Les concentrations environnementales varient entre 0.1 ng/L et 1 mg/L, selon le composé, la matrice et la source de contamination. D’après cette étude, les effets nuisibles des anti-infectieux sur le biote aquatique sont possibles et ces substances peuvent aussi avoir un effet indirect sur la santé humaine à cause de sa possible contribution à la dissémination de la résistance aux anti-infecteiux chez les bactéries. Les premiers tests préliminaires de développement d’une méthode de détermination des anti-infectieux dans les eaux usées ont montré les difficultés à surmonter lors de l’extraction sur phase solide (SPE) ainsi que l’importance de la sélectivité du détecteur. On a décrit une nouvelle méthode de quantification des anti-infectieux utilisant la SPE en tandem dans le mode manuel et la chromatographie liquide couplée à la spectrométrie de masse en tandem (LC-MS/MS). Les six anti-infectieux ciblés (sulfaméthoxazole, triméthoprime, ciprofloxacin, levofloxacin, clarithromycin et azithromycin) ont été quantifiés à des concentrations entre 39 et 276 ng/L dans les échantillons d’affluent et d’effluent provenant d’une station d’épuration appliquant un traitement primaire et physico- chimique. Les concentrations retrouvées dans les effluents indiquent que la masse moyenne totale de ces substances, déversées hebdomadairement dans le fleuve St. Laurent, était de ~ 2 kg. En vue de réduire le temps total d’analyse et simplifier les manipulations, on a travaillé sur une nouvelle méthode de SPE couplée-LC-MS/MS. Cette méthode a utilisé une technique de permutation de colonnes pour préconcentrer 1.00 mL d’échantillon dans une colonne de SPE couplée. La performance analytique de la méthode a permis la quantification des six anti-infectieux dans les eaux usées municipales et les limites de détection étaient du même ordre de grandeur (13-60 ng/L) que les méthodes basées sur la SPE manuelle. Ensuite, l’application des colonnes de SPE couplée de chromatographie à débit turbulent pour la préconcentration de six anti-infectieux dans les eaux usées a été explorée pour diminuer les effets de matrice. Les résultats obtenus ont indiqué que ces colonnes sont une solution de réchange intéressante aux colonnes de SPE couplée traditionnelles. Finalement, en vue de permettre l’analyse des anti-infectieux dans les eaux de surface et l’eau potable, une méthode SPE couplée-LC-MS/MS utilisant des injections de grand volume (10 mL) a été développée. Le volume de fuite de plusieurs colonnes de SPE couplée a été estimé et la colonne ayant la meilleure rétention a été choisie. Les limites de détection et de confirmation de la méthode ont été entre 1 à 6 ng/L. L’analyse des échantillons réels a démontré que la concentration des trois anti-infectieux ciblés (sulfaméthoxazole, triméthoprime et clarithromycine) était au dessous de la limite de détection de la méthode. La mesure des masses exactes par spectrométrie de masse à temps d’envol et les spectres des ions produits utilisant une pente d’énergie de collision inverse dans un spectromètre de masse à triple quadripôle ont été explorés comme des méthodes de confirmation possibles.