Parallel Mesh Partitioning in Alya

The Alya System is the BSC simulation code for multi-physics problems [1]. It is based on a Variational Multiscale Finite Element Method for unstructured meshes. Work distribution is achieved by partitioning the original mesh into subdomains (submeshes). This pre-partition step has until now been done in serial by only one process, using the metis library [2]. This is a huge bottleneck when larger meshes with millions of elements have to be partitioned. This is due to the data not fitting in the memory of a single computing node and in the cases where the data does fit; Alya takes too long in the partitioning step. In this document we explain the tasks done to design, implement and test a new parallel partitioning algorithm for Alya. In this algorithm a subset of the workers, is in charge of partition the mesh in parallel, using the parmetis library [3]. Partitioning workers, load consecutive parts of the main mesh, with a parallel space partitioning bin structure [4], capable of obtaining the adjacent boundary elements of their respective submeshes. With this local mesh, each of the partitioning workers is able to create its local element adjacency graph and to partition the mesh. We have validated our new algorithm using a Navier-Stokes problem on a small cube mesh of 1000 elements. Then we performed a scalability test on a 30M element mesh to check if the time to partition the mesh is reduced proportionally with the number of partitioning workers. We have also done a comparison between metis and parmetis, the balancing of the element distribution among the domains, to test how the use of many partitioning workers to partition the mesh affects the scalability of Alya. We have noticed in these tests that it’s better to use fewer partitioning workers to partition the mesh. Finally we have two sections explaining the results and the future work that has to be done in order to finalise and improve the parallel partition algorithm

A New Multi-Resource cumulatives Constraint with Negative Heights

This paper presents a new cumulatives constraint which generalizes the original cumulative constraint in different ways. The two most important aspects consist in permitting multiple cumulative resources as well as negative heights for the resource consumption of the tasks. This allows modeling in an easy way new scheduling and planning problems. The introduction of negative heights has forced us to come up with new propagation algorithms and to revisit existing ones. The first propagation algorithm is derived from an idea called sweep which is extensively used in computational geometry; the second algorithm is based on a combination of sweep and constructive disjunction, while the last is a generalization of task intervals to this new context. A real-life timetabling problem originally motivated this constraint which was implemented within the SICStus finite domain solver and evaluated against different problem patterns

Factores de riesgo asociados a pacientes tuberculosos con microscopía del esputo positiva

ResumenObjetivoEl factor determinante para la producción de casos de tuberculosis por transmisión exógena es la existencia de pacientes con baciloscopias positivas. El objetivo de este estudio fue determinar los factores de riesgo asociados a pacientes con microscopía positiva en secreciones respiratorias.MétodosSe estudiaron los casos incidentes de tuberculosis del período 1992–1998 en la provincia de Lleida. Las variables del estudio fueron: edad, sexo, infección por el VIH, uso de drogas por vía parenteral (UDVP), consumo de alcohol, existencia de cavernas y resultado de la microcopia del esputo. Se calculó la tasa de incidencia por 100.000 personas-año. La asociación de la variable dependiente –caso de tuberculosis con baciloscopia positiva– con el resto de variables independientes se determinó con la odds ratio (ORc, cruda, y ORa, ajustada mediante regresión logística no condicional) con su intervalo de confianza (IC) del 95%.ResultadosSe detectaron 905 casos nuevos de tuberculosis. La tasa de incidencia del período 1992–1998 decreció desde 38,8 a 30,8. El 44,9% de los casos (n = 406) presentó una baciloscopia positiva. El riesgo de ser bacilífero se asoció positivamente con la presencia de cavernas en la radiografía de tórax (ORa = 6,8; IC del 95%, 4,8-9,5), el género masculino (ORa = 1,8; IC del 95%, 1,3-2,6) y el consumo de alcohol (ORa = 1,6; IC del 95%, 1,1–2,3) y fue inferior en los menores de 15 años (ORa = 0,2; IC del 95%, 0,1-0,5) y coinfectados por el VIH (ORa = 0,5; IC del 95%, 0,3-0,9).ConclusionesLa infección por el VIH implica un reducido impacto en la endemia tuberculosa. El estudio de contactos y la implantación de tratamientos directamente observados se deben considerar no sólo para los coinfectados por el VIH y UDVP, sino para adultos varones, con consumo excesivo de alcohol, especialmente si presentan lesiones cavernosas.SummaryObjectiveThe main factor responsible for producing new cases of tuberculosis by exogen transmission is the existence of Mycobacterium tuberculosis in the sputum of tuberculosis patients. The objective of this study was to determine the risk factors associated to positive smear tuberculosis cases in Lleida (Spain).MethodsWe studied new cases of tuberculosis over the period 1992-1998. The variables considered were: age, gender, coinfection with HIV, injection drug use (IDU), consumption of alcohol, existence of caverns in thorax X-ray, and laboratory results of direct smear examination. We calculated the incidence rates for 100,000 persons-year. The association between the dependent variable –case of tuberculosis with positive Mycobacterium tuberculosis smear– and the remaining independent variables were assessed obtaining odds ratios (OR) and 95% confidence intervals (CI) (crude –cOR– and adjusted –aOR– by non conditional logistic regression).ResultsWe detected 905 new cases of tuberculosis. The rates in the period 1992–1998 decreased from 38.8 to 30.8. 44.9% of cases (n = 406) presented a positive direct smear. There was a positive association between the risk of being a positive smear patient and having caverns in thorax x-ray (aOR = 6.8; 95% CI, 4.8-95), being male (aOR = 1.8; 95% CI, 1.3-2.6) and consuming alcohol (aOR = 1.6; 95% CI, 1.1-2.3) and this risk was significant lower in those under 15 years old (aOR = 0.2; 95% CI, 0.1-0.5), and coinfection with HIV (aOR = 0.5; 95% CI, 0.3-0.9).ConclusionsHIV infection implies a reduced impact in endemecity of tuberculosis. Study of contacts and the implementation of directly observed treatment must be considered not only for coinfected HIV cases and IDU but also for adult males, especially those who consume alcohol, particularly when they have caverns

Ressenyes bibliogràfiques

Abstract not availabl

Models and Strategies for Variants of the Job Shop Scheduling Problem

Recently, a variety of constraint programming and Boolean satisfiability approaches to scheduling problems have been introduced. They have in common the use of relatively simple propagation mechanisms and an adaptive way to focus on the most constrained part of the problem. In some cases, these methods compare favorably to more classical constraint programming methods relying on propagation algorithms for global unary or cumulative resource constraints and dedicated search heuristics. In particular, we described an approach that combines restarting, with a generic adaptive heuristic and solution guided branching on a simple model based on a decomposition of disjunctive constraints. In this paper, we introduce an adaptation of this technique for an important subclass of job shop scheduling problems (JSPs), where the objective function involves minimization of earliness/tardiness costs. We further show that our technique can be improved by adding domain specific information for one variant of the JSP (involving time lag constraints). In particular we introduce a dedicated greedy heuristic, and an improved model for the case where the maximal time lag is 0 (also referred to as no-wait JSPs).Comment: Principles and Practice of Constraint Programming - CP 2011, Perugia : Italy (2011

The Proteome of Biologically Active Membrane Vesicles from Piscirickettsia salmonis LF-89 Type Strain Identifies Plasmid-Encoded Putative Toxins

Indexación: Scopus.Piscirickettsia salmonis is the predominant bacterial pathogen affecting the Chilean salmonid industry. This bacterium is the etiological agent of piscirickettsiosis, a significant fish disease. Membrane vesicles (MVs) released by P. salmonis deliver several virulence factors to host cells. To improve on existing knowledge for the pathogenicity-associated functions of P. salmonis MVs, we studied the proteome of purified MVs from the P. salmonis LF-89 type strain using multidimensional protein identification technology. Initially, the cytotoxicity of different MV concentration purified from P. salmonis LF-89 was confirmed in an in vivo adult zebrafish infection model. The cumulative mortality of zebrafish injected with MVs showed a dose-dependent pattern. Analyses identified 452 proteins of different subcellular origins; most of them were associated with the cytoplasmic compartment and were mainly related to key functions for pathogen survival. Interestingly, previously unidentified putative virulence-related proteins were identified in P. salmonis MVs, such as outer membrane porin F and hemolysin. Additionally, five amino acid sequences corresponding to the Bordetella pertussis toxin subunit 1 and two amino acid sequences corresponding to the heat-labile enterotoxin alpha chain of Escherichia coli were located in the P. salmonis MV proteome. Curiously, these putative toxins were located in a plasmid region of P. salmonis LF-89. Based on the identified proteins, we propose that the protein composition of P. salmonis LF-89 MVs could reflect total protein characteristics of this P. salmonis type strain. © 2017 Oliver, Hernández, Tandberg, Valenzuela, Lagos, Haro, Sánchez, Ruiz, Sanhueza-Oyarzún, Cortés, Villar, Artigues, Winther-Larsen, Avendaño-Herrera and Yáñez.https://www.frontiersin.org/articles/10.3389/fcimb.2017.00420/ful

Transmission of ‘Candidatus Phytoplasma pyri’ by naturally infected Cacopsylla pyri to peach, an approach to the epidemiology of peach yellow leaf roll (PYLR) in Spain

Peach orchards in the northeast of Spain were severely affected in 2012 by a previously unreported disease in this area. The symptoms included early reddening, leaf curling, decline, abnormal fruits, and in some cases death of the peach trees. All the infected peach samples were positive for ‘Candidatus Phytoplasma pyri’, but none were infected by the ‘Ca. Phytoplasma prunorum’. In this work, potential vectors able to transmit ‘Ca. Phytoplasma pyri’ from pear to peach and between peach trees were studied and their infective potential was analysed at different times of the year. Transmission trials of the phytoplasma with potential vectors to an artificial feeding medium for insects and to healthy peach trees were conducted. Additionally, isolated phytoplasmas were genetically characterized to determine which isolates were able to infect peach trees. Results showed that the only insect species captured inside peach plots that was a carrier of the ‘Ca. Phytoplasma pyri’ phytoplasma was Cacopsylla pyri. Other insect species captured and known to be phytoplasma transmitters were present in very low numbers, and were not infected with ‘Ca. Phytoplasma pyri’ phytoplasma. A total of 1928 individuals of C. pyri were captured in the peach orchards, of which around 49% were phytoplasma carriers. All the peach trees exposed to C. pyri in 2014, and 65% in 2015, were infected by ‘Ca. Phytoplasma pyri’ 1 year after exposure, showing that this species is able to transmit the phytoplasma to peach. Molecular characterization showed that some genotypes are preferentially determined in peach.info:eu-repo/semantics/acceptedVersio

A capacity management tool for a portfolio of industrialization projects

The management of a project portfolio is a complex decision process because it encompasses the achievement of multiple objectives. A critical point that increases the complexity in the decision-making process of a portfolio manager is the allocation of human resources to manage the projects of the portfolio, project managers, which is crucial to the organization’s performance. In this case, the project manager can manage more than one project simultaneously and it is necessary to assign project managers to the projects, considering that project activities have an amount of work to be accomplished. The main objective of this work was to provide support for this capacity management problem, which aims to provide an easier decision-making process for the capacity management of an industrialization project portfolio. Therefore, it was developed: a hybrid model that creates a schedule respecting the resource constraints and the established due dates; a recommendation system that considers project managers’ allocation and projects requirements; and, an automatic status report that allows identifying the project portfolio capacity usage.This work is supported by: European Structural and Investment Funds in the FEDER component, through the Operational Competitiveness and Internationalization Programme (COMPETE 2020) [Project nº 39479; Funding Reference: POCI-01-0247-FEDER-39479]

Mitochondrial translocation of oxidized cofilin induces caspase-independent necrotic-like programmed cell death of T cells

Oxidative stress leads to T-cell hyporesponsiveness or death. The actin-binding protein cofilin is oxidized during oxidative stress, which provokes a stiff actin cytoskeleton and T-cell hyporesponsiveness. Here, we show that long-term oxidative stress leads to translocation of cofilin into the mitochondria and necrotic-like programmed cell death (PCD) in human T cells. Notably, cofilin mutants that functionally mimic oxidation by a single mutation at oxidation-sensitive cysteins (Cys-39 or Cys-80) predominately localize within the mitochondria. The expression of these mutants alone ultimately leads to necrotic-like PCD in T cells. Accordingly, cofilin knockdown partially protects T cells from the fatal effects of long-term oxidative stress. Thus, we introduce the oxidation and mitochondrial localization of cofilin as the checkpoint for necrotic-like PCD upon oxidative stress as it occurs, for example, in tumor environments

The design of the wide field monitor for LOFT

LOFT (Large Observatory For x-ray Timing) is one of the ESA M3 missions selected within the Cosmic Vision program in 2011 to carry out an assessment phase study and compete for a launch opportunity in 2022-2024. The phase-A studies of all M3 missions were completed at the end of 2013. LOFT is designed to carry on-board two instruments with sensitivity in the 2-50 keV range: a 10 m 2 class Large Area Detector (LAD) with a <1{\deg} collimated FoV and a wide field monitor (WFM) making use of coded masks and providing an instantaneous coverage of more than 1/3 of the sky. The prime goal of the WFM will be to detect transient sources to be observed by the LAD. However, thanks to its unique combination of a wide field of view (FoV) and energy resolution (better than 500 eV), the WFM will be also an excellent monitoring instrument to study the long term variability of many classes of X-ray sources. The WFM consists of 10 independent and identical coded mask cameras arranged in 5 pairs to provide the desired sky coverage. We provide here an overview of the instrument design, configuration, and capabilities of the LOFT WFM. The compact and modular design of the WFM could easily make the instrument concept adaptable for other missions.Comment: Proc. SPIE 9144, Space Telescopes and Instrumentation 2014: Ultraviolet to Gamma Ray, 91442