On the non-slip boundary condition enforcement in SPH methods.

The implementation of boundary conditions is one of the points where the SPH methodology still has some work to do. The aim of the present work is to provide an in-depth analysis of the most representative mirroring techniques used in SPH to enforce boundary conditions (BC) along solid profiles. We specifically refer to dummy particles, ghost particles, and Takeda et al. [1] boundary integrals. A Pouseuille flow has been used as a example to gradually evaluate the accuracy of the different implementations. Our goal is to test the behavior of the second-order differential operator with the proposed boundary extensions when the smoothing length h and other dicretization parameters as dx/h tend simultaneously to zero. First, using a smoothed continuous approximation of the unidirectional Pouseuille problem, the evolution of the velocity profile has been studied focusing on the values of the velocity and the viscous shear at the boundaries, where the exact solution should be approximated as h decreases. Second, to evaluate the impact of the discretization of the problem, an Eulerian SPH discrete version of the former problem has been implemented and similar results have been monitored. Finally, for the sake of completeness, a 2D Lagrangian SPH implementation of the problem has been also studied to compare the consequences of the particle movemen

SPH no-slip BC implementation analysis at the continous level

The aim of this paper is to discuss whether there are structural problems in three of the most representative velocity mirroring techniques used to force no-slip boundary conditions (BC) in SPH for Newtonian incompressible flows. We refer specifically to fixed fluid particles, ghost particles, and Takeda et al. [1] boundary integrals. In Newtonian incompressible flows, the viscous related terms in the momentum conservation equation depend on the evaluation of the Laplacian of the velocity field. In order to analyze such techniques, the continuous version of the Laplacian approximation by Morris et al. [2] and Monaghan Cleary-Gingold [3] viscous terms has been considered. It has been shown that there are intrinsic inaccuracies in the computation of the Laplacian close to the boundaries and the onset of singularities in such evaluation for some flows and mirroring techniques combinations. The impact of these deviations in the SPH simulation of viscous flows is not clear at this stage

Peachy Parallel Assignments (EduHPC 2018)

Peachy Parallel Assignments are a resource for instructors teaching parallel and distributed programming. These are high-quality assignments, previously tested in class, that are readily adoptable. This collection of assignments includes implementing a subset of OpenMP using pthreads, creating an animated fractal, image processing using histogram equalization, simulating a storm of high-energy particles, and solving the wave equation in a variety of settings. All of these come with sample assignment sheets and the necessary starter code.Departamento de Informática (Arquitectura y Tecnología de Computadores, Ciencias de la Computación e Inteligencia Artificial, Lenguajes y Sistemas Informáticos)Facilitar la inclusión de ejercicios prácticos de programación paralela en cursos de Computación Paralela o de alto rendimiento (HPC)Comunicación en congreso: Descripción de ejercicios prácticos con acceso a material ya desarrollado y probado

par genes in Mycobacterium bovis and Mycobacterium smegmatis are arranged in an operon transcribed from "SigGC" promoters

<p>Abstract</p> <p>Background</p> <p>The ParA/Soj and ParB/Spo0J proteins, and the <it>cis</it>-acting <it>parS </it>site, participate actively in chromosome segregation and cell cycle progression. Genes homologous to <it>parA </it>and <it>parB</it>, and two putative <it>parS </it>copies, have been identified in the <it>Mycobacterium bovis </it>BCG and <it>Mycobacterium smegmatis </it>chromosomes. As in <it>Mycobacterium tuberculosis</it>, the <it>parA </it>and <it>parB </it>genes in these two non-pathogenic mycobacteria are located near the chromosomal origin of replication. The present work focused on the determination of the transcriptional organisation of the ~6 Kb <it>orf60K-parB </it>region of <it>M. bovis </it>BCG and <it>M. smegmatis </it>by primer extension, transcriptional fusions to the green fluorescence protein (GFP) and quantitative RT-PCR.</p> <p>Results</p> <p>The <it>parAB </it>genes were arranged in an operon. However, we also found promoters upstream of each one of these genes. Seven putative promoter sequences were identified in the <it>orf60K-parB </it>region of <it>M. bovis </it>BCG, whilst four were identified in the homologous region of <it>M. smegmatis</it>, one upstream of each open reading frame (ORF).</p> <p>Real-time PCR assays showed that in <it>M. smegmatis</it>, mRNA-<it>parA </it>and mRNA-<it>parB </it>levels decreased between the exponential and stationary phases. In <it>M. bovis </it>BCG, mRNA-<it>parA </it>levels also decreased between the exponential and stationary phases. However, <it>parB </it>expression was higher than <it>parA </it>expression and remained almost unchanged along the growth curve.</p> <p>Conclusion</p> <p>The majority of the proposed promoter regions had features characteristic of <it>Mycobacterium </it>promoters previously denoted as Group D. The -10 hexamer of a strong <it>E. coli </it>σ⁷⁰-like promoter, located upstream of <it>gidB </it>of <it>M. bovis </it>BCG, overlapped with a putative <it>parS </it>sequence, suggesting that the transcription from this promoter might be regulated by the binding of ParB to <it>parS</it>.</p

High Pressure optical nanothermometer based on Er3+ photoluminescence

The optical properties of a sparsely investigated material, LaGdO3 doped with Er3+, are explored regarding its suitability as nanothermometer. Besides its excellent capabilities for dielectric applications, when doping with Er3+, this material provides a highly efficient upconversion photoluminescence (PL) for high temperature thermometry at high pressure due to its structural stability. LaGdO3 belongs to the perovskite-type ABO3 compounds with a B-type monoclinic C2/m space group (a = 14.43 Å; b = 3.69 Å; c = 9.00 Å; and ? = 100.70º) at ambient conditions. It undergoes a structural phase transition to a hexagonal ?3#?1 phase at 3GPa yielding a notable PL enhancement, thus enabling it as a potential high-pressure hightemperature nanothermometer.We acknowledge financial support from MAT2015-69508-P (MINECO/FEDER), MAT2015-71070-REDC; PGC2018-101464-B-I00 (MICIN/FEDER), IDIVAL 18/28, the European Research Council FET-OPEN NCLas H2020 Project (EU829161), and BSH Electrodomésticos España, S.A

Automatic generation of models for abdominal aortic aneurysms and intraluminal thrombus based on hexahedral meshes

To propose an automated patient-specific algorithm for the creation of accurate and smooth meshes of the aortic anatomy, to be used for evaluating rupture risk factors of abdominal aortic aneurysms (AAA). Finite element (FE) analyses and simulations require meshes to be smooth and anatomically accurate, capturing both the artery wall and the intraluminal thrombus (ILT). The two main difficulties are the modeling of the arterial bifurcations, and of the ILT, which has an arbitrary shape that is conforming to the aortic wall

Association of acid phosphatase locus 1*C allele with the risk of cardiovascular events in rheumatoid arthritis patients

Introduction: Acid phosphatase locus 1 (ACP1) encodes a low molecular weight phosphotyrosine phosphatase implicated in a number of different biological functions in the cell. The aim of this study was to determine the contribution of ACP1 polymorphisms to susceptibility to rheumatoid arthritis (RA), as well as the potential contribution of these polymorphisms to the increased risk of cardiovascular disease (CV) observed in RA patients. Methods: A set of 1,603 Spanish RA patients and 1,877 healthy controls were included in the study. Information related to the presence/absence of CV events was obtained from 1,284 of these participants. All individuals were genotyped for four ACP1 single-nucleotide polymorphisms (SNPs), rs10167992, rs11553742, rs7576247, and rs3828329, using a predesigned TaqMan SNP genotyping assay. Classical ACP1 alleles (*A, *B and *C) were imputed with SNP data. Results: No association between ACP1 gene polymorphisms and susceptibility to RA was observed. However, when RA patients were stratified according to the presence or absence of CV events, an association between rs11553742*T and CV events was found (P = 0.012, odds ratio (OR) = 2.62 (1.24 to 5.53)). Likewise, the ACP1*C allele showed evidence of association with CV events in patients with RA (P = 0.024, OR = 2.43). Conclusions: Our data show that the ACP1*C allele influences the risk of CV events in patients with R

Alternative Eco-Friendly Methods in the Control of Post-Harvest Decay of Tropical and Subtropical Fruits

The effectiveness on several fruits by the application of alternative methods against fungi is summarized in the present chapter. Several investigations have reported the efficacy of these technologies for controlling fungal infections. Currently, high post-harvest loses have been reported due to several factors such as inefficient management, lack of training for farmers, and problems with appropriate conditions for storage of fruits and vegetables. Even now, in many countries, post-harvest disease control is led by the application of chemical fungicides. However, in this time, awareness about fungi resistance, environmental, and health issues has led to the research of eco-friendly and effective alternatives for disease management. The pathogen establishment on fruits can be affected by the application of GRAS compounds like chitosan, essential oils, salts, among others; besides, their efficacy can be enhanced by their combination with other technologies like ultrasound. Thus, the applications of these alternatives are suitable approaches for post-harvest management of fruits

CHK1 expression in gastric cancer is modulated by p53 and RB1/E2F1: Implications in chemo/radiotherapy response

Radiation has a limited but relevant role in the adjuvant therapy of gastric cancer (GC) patients. Since Chk1 plays a critical function in cellular response to genotoxic agents, we aimed to analyze the role of Chk1 in GC as a biomarker for radiotherapy resistance. We analyzed Chk1 expression in AGS and MKN45 human GC cell lines by RT-QPCR and WB and in a small cohort of human patient’s samples. We demonstrated that Chk1 overexpression specifically increases resistance to radiation in GC cells. Accordingly, abrogation of Chk1 activity with UCN-01 and its expression with shChk1 increased sensitivity to bleomycin and radiation. Furthermore, when we assessed Chk1 expression in human samples, we found a correlation between nuclear Chk1 accumulation and a decrease in progression free survival. Moreover, using a luciferase assay we found that Chk1’s expression is controlled by p53 and RB/E2F1 at the transcriptional level. Additionally, we present preliminary data suggesting a posttranscriptional regulation mechanism, involving miR-195 and miR-503, which are inversely correlated with expression of Chk1 in radioresistant cells. In conclusion, Chk1/microRNA axis is involved in resistance to radiation in GC, and suggests Chk1 as a potential tool for optimal stratification of patients susceptible to receive adjuvant radiotherapy after surgeryThis work was supported by Instituto de Salud Carlos III–Fondo de Investigación Sanitaria (PS09/1988 to ISP; PI11-00949, pI014-1495 and Feder Funds to RP); Comunidad Autónoma de Madrid-Universidad Autónoma de Madrid (CCG10-UAM/BIO-5871 to ISP); Fundación Leticia Castillejo Castillo and Ministerio de Ciencia e Innovación (SAF2012-30862 to RSP), Spain