Computational Modeling and Sub-Grid Scale Stabilization of Incompressibility and Convection in the Numerical Simulation of Friction Stir Welding Processes

This paper deals with the computational modeling and sub-grid scale stabilization of incompressibility and convection in the numerical simulation of the material flow around the probe tool in a friction stir welding (FSW) process. Within the paradigmatic framework of the multiscale stabilization methods, suitable pressure and convective derivative of the temperature sub-grid scale stabilized coupled thermomechanical formulations have been developed using an Eulerian description. Norton-Hoff and Sheppard-Wright thermo-rigid-viscoplastic constitutive material models have been considered. Constitutive equations for the sub-grid scale models have been proposed and an approximation of the sub-grid scale variables has been given. In particular, algebraic sub-grid scale (ASGS) and orthogonal sub-grid scale (OSGS) methods for mixed velocity, pressure and temperature P1/P1/P1 linear elements have been considered. Furthermore, it has been shown that well known classical stabilized formulations, such as the Galerkin least-squares (GLS) for incompressible (or quasi-incompressible) problems or the Streamline Upwind/Petrov-Galerkin (SUPG) method for convection dominant problems, can be recovered as particular cases of the multiscale stabilization framework considered. Using a product formula algorithm for the solution of the coupled thermomechanical problem, the resulting algebraic system of equations has been solved using a staggered procedure in which a mechanical problem, defined by the linear momentum balance equation, under quasi-static conditions, and the incompressibility equation, is solved first at constant temperature. Then a thermal problem, defined by the energy balance equation, is solved keeping constant the mechanical variables, i.e. velocity and pressure. The computational model has been implemented in an enhanced version of the finite element software COMET, developed by the authors at the International Center for Numerical Methods in Engineering (CIMNE). Two numerical examples have been considered. The first one deals with the numerical simulation of a coupled thermomechanical flow in a 2D rectangular domain. Steady-state and transient conditions have been considered. The goal of this numerical example has been the comparison between different sub-grid scale stabilization methods for the velocity and temperature equations. In particular, using a GLS stabilization method for the pressure equation, a comparison between SUPG and OSGS convective stabilization methods has been performed. Additionally, using a SUPG stabilization method for the temperature equation, a comparison between GLS and OSGS pressure stabilization methods has been done. The second example deals with the 3D numerical simulation of a representative FSW process. Numerical results obtained have been compared with experimental results available in the literature. A good agreement on the temperature distribution has been obtained and predicted peak temperatures compare well, both in value and position, with the experimental results available

Expectation maximization (EM) algorithms using polar symmetriesfor computed tomography(CT) image reconstruction

We suggest a symmetric-polar pixellation scheme which makes possible a reduction of the computational cost for expectation maximization (EM) iterative algorithms. The proposed symmetric-polar pixellation allows us to deal with 3D images as a whole problem without dividing the 3D problem into 2D slices approach. Performance evaluation of each approach in terms of stability and image quality is presented. Exhaustive comparisons between all approaches were conducted in a 2D based image reconstruction model. From these 2D approaches, that showing the best performances were finally implemented and evaluated in a 3D based image reconstruction model. Comparison to 3D images reconstructed with FBP is also presented. Although the algorithm is presented in the context of computed tomography (CT) image reconstruction, it can be applied to any other tomographic technique as well, due to the fact that the only requirement is a scanning geometry involving measurements of an object under different projection angles. Real data have been acquired with a small animal (CT) scanner to verify the proposed mathematical description of the CT system.This work was supported by the Spanish Plan Nacional de Investigacion Cientifica, Desarrollo e Innovacion Tecnologica (I+D+I) under Grant, FIS2010-21216-CO2-01, Valencian Local Government under Grant Nos. PROMETEO 2008/114 and APOSTD/2010/012. The authors would like to thank Brennan Holt for checking and correcting the text.Rodríguez Álvarez, MJ.; Soriano Asensi, A.; Iborra Carreres, A.; Sánchez Martínez, F.; González Martínez, AJ.; Conde, P.; Hernández Hernández, L.... (2013). Expectation maximization (EM) algorithms using polar symmetriesfor computed tomography(CT) image reconstruction. Computers in Biology and Medicine. 43(8):1053-1061. https://doi.org/10.1016/j.compbiomed.2013.04.015S1053106143

Identification of conserved gene clusters in multiple genomes based on synteny and homology

<p>Abstract</p> <p>Background</p> <p>Uncovering the relationship between the conserved chromosomal segments and the functional relatedness of elements within these segments is an important question in computational genomics. We build upon the series of works on <it>gene teams</it> and <it>homology teams.</it></p> <p>Results</p> <p>Our primary contribution is a local sliding-window SYNS (SYNtenic teamS) algorithm that refines an existing family structure into orthologous sub-families by analyzing the neighborhoods around the members of a given family with a locally sliding window. The neighborhood analysis is done by computing conserved gene clusters. We evaluate our algorithm on the existing homologous families from the Genolevures database over five genomes of the Hemyascomycete phylum.</p> <p>Conclusions</p> <p>The result is an efficient algorithm that works on multiple genomes, considers paralogous copies of genes and is able to uncover orthologous clusters even in distant genomes. Resulting orthologous clusters are comparable to those obtained by manual curation.</p

MEDLEM database, a data collection on large elasmobranchs in the Mediterranean and Black Seas

The Mediterranean Large Elasmobranchs Monitoring (MEDLEM) database contains more than 3,000 records (with more than 4,000 individuals) of large elasmobranch species from 21 different countries around the Mediterranean and Black seas, observed from 1666 to 2017. The principal species included in the archive are the devil ray (1,868 individuals), the basking shark (935 individuals), the blue shark (622 individuals), and the great white shark (342 individuals). In the last decades, other species such as the thresher shark (187 individuals), the shortfin mako (180 individuals), and the spiny butterfly ray (138) were reported with increasing frequency. This was possibly due to increased public awareness on the conservation status of sharks, and the consequent development of new monitoring programs. MEDLEM does not have homogeneous reporting coverage throughout the Mediterranean and Black seas and it should be considered as a database of observed species presence. Scientific monitoring efforts in the south-eastern Mediterranean and Black seas are generally lower than in the northern sectors and the absence of some species in our database does not imply their actual absence in these regions. However, the available data allowed us to analyse the frequency and spatial distribution of records, the size frequencies for a few selected the available data allowed us to analyse the frequency and spatial distribution of records, the size frequencies for a few selected species, the overall area coverage, and which species are involved as bycatch by different fishing gears

Diet and Physical Activity for the Prevention of Noncommunicable Diseases in Low- and Middle-Income Countries: A Systematic Policy Review

Background: Diet-related noncommunicable diseases (NCDs) are increasing rapidly in low-and middle-income countries (LMICs) and constitute a leading cause of mortality. Although a call for global action has been resonating for years, the progress in national policy development in LMICs has not been assessed. This review of strategies to prevent NCDs in LMICs provides a benchmark against which policy response can be tracked over time. Methods and Findings: We reviewed how government policies in LMICs outline actions that address salt consumption, fat consumption, fruit and vegetable intake, or physical activity. A structured content analysis of national nutrition, NCDs, and health policies published between 1 January 2004 and 1 January 2013 by 140 LMIC members of the World Health Organization (WHO) was carried out. We assessed availability of policies in 83% (116/140) of the countries. NCD strategies were found in 47% (54/116) of LMICs reviewed, but only a minority proposed actions to promote healthier diets and physical activity. The coverage of policies that specifically targeted at least one of the risk factors reviewed was lower in Africa, Europe, the Americas, and the Eastern Mediterranean compared to the other two World Health Organization regions, South-East Asia and Western Pacific. Of the countries reviewed, only 12% (14/116) proposed a policy that addressed all four risk factors, and 25% (29/116) addressed only one of the risk factors reviewed. Strategies targeting the private sector were less frequently encountered than strategies targeting the general public or policy makers. Conclusions: This review indicates the disconnection between the burden of NCDs and national policy responses in LMICs. Policy makers urgently need to develop comprehensive and multi-stakeholder policies to improve dietary quality and physical activity

Antagonistic Changes in Sensitivity to Antifungal Drugs by Mutations of an Important ABC Transporter Gene in a Fungal Pathogen

Fungal pathogens can be lethal, especially among immunocompromised populations, such as patients with AIDS and recipients of tissue transplantation or chemotherapy. Prolonged usage of antifungal reagents can lead to drug resistance and treatment failure. Understanding mechanisms that underlie drug resistance by pathogenic microorganisms is thus vital for dealing with this emerging issue. In this study, we show that dramatic sequence changes in PDR5, an ABC (ATP-binding cassette) efflux transporter protein gene in an opportunistic fungal pathogen, caused the organism to become hypersensitive to azole, a widely used antifungal drug. Surprisingly, the same mutations conferred growth advantages to the organism on polyenes, which are also commonly used antimycotics. Our results indicate that Pdr5p might be important for ergosterol homeostasis. The observed remarkable sequence divergence in the PDR5 gene in yeast strain YJM789 may represent an interesting case of adaptive loss of gene function with significant clinical implications