Particle methods parallel implementations by GP-GPU strategies

This paper outlines the problems found in the parallelization of SPH (Smoothed Particle Hydrodynamics) algorithms using Graphics Processing Units. Different results of some parallel GPU implementations in terms of the speed-up and the scalability compared to the CPU sequential codes are shown. The most problematic stage in the GPU-SPH algorithms is the one responsible for locating neighboring particles and building the vectors where this information is stored, since these specific algorithms raise many difficulties for a data-level parallelization. Because of the fact that the neighbor location using linked lists does not show enough data-level parallelism, two new approaches have been proposed to minimize bank conflicts in the writing and subsequent reading of the neighbor lists. The first strategy proposes an efficient coordination between CPU-GPU, using GPU algorithms for those stages that allow a straight forward parallelization, and sequential CPU algorithms for those instructions that involve some kind of vector reduction. This coordination provides a relatively orderly reading of the neighbor lists in the interactions stage, achieving a speed-up factor of x47 in this stage. However, since the construction of the neighbor lists is quite expensive, it is achieved an overall speed-up of x41. The second strategy seeks to maximize the use of the GPU in the neighbor’s location process by executing a specific vector sorting algorithm that allows some data-level parallelism. Although this strategy has succeeded in improving the speed-up on the stage of neighboring location, the global speed-up on the interactions stage falls, due to inefficient reading of the neighbor vectors. Some changes to these strategies are proposed, aimed at maximizing the computational load of the GPU and using the GPU texture-units, in order to reach the maximum speed-up for such codes. Different practical applications have been added to the mentioned GPU codes. First, the classical dam-break problem is studied. Second, the wave impact of the sloshing fluid contained in LNG vessel tanks is also simulated as a practical example of particle methods

Central corneal thickness and anterior chamber depth measurement by Sirius® Scheimpfug tomography and ultrasound

Background: The purpose of this study was to compare the accuracy of the new Sirius® Scheimpflug anterior segment examination device for measurement of central corneal thickness (CCT) and anterior chamber depth (ACD) with that of CCT measurements obtained by ultrasound pachymetry and ACD measurements obtained by ultrasound biometry, respectively. Methods: CCT and ACD was measured in 50 right eyes from 50 healthy subjects using a Sirius Scheimpflug camera, SP100 ultrasound pachymetry, and US800 ultrasound biometry. Results: CCT measured with the Sirius was 546 ± 39 μm and 541 ± 35 μm with SP100 ultrasound pachymetry (P = 0.003). The difference was statistically significant (mean difference 4.68 ± 10.5 μm; limits of agreement −15.8 to 25.20 μm). ACD measured with the Sirius was 2.96 ± 0.3 mm compared with 3.36 ± 0.29 mm using US800 ultrasound biometry (P , 0.001). The difference was statistically significant (mean difference -0.40 ± 0.16 mm; limits of agreement -0.72 to 0.07 mm). When the ACD values obtained using ultrasound biometry were corrected according to the values for CCT measured by ultrasound, the agreement increased significantly between both technologies for ACD measurements (mean difference 0.15 ± 0.16 mm; limits of agreement -0.16 to 0.45 mm). Conclusion: CCT and ACD measured by Sirius and ultrasound methods showing good agreement between repeated measurements obtained in the same subjects (repeatability) with either instrument. However, CCT and ACD values, even after correcting ultrasound ACD by subtracting the CCT value obtained with either technology should not be used interchangeably. Keywords: Scheimpflug corneal tomography, ultrasound biometry, ultrasound pachymetry, limits of agreement

Trypanosoma cruzi macrophage infectivity potentiator has a rotamase core and a highly exposed α-helix

The macrophage infectivity potentiator protein from Trypanosoma cruzi (TcMIP) is a major virulence factor secreted by the etiological agent of Chagas' disease. It is functionally involved in host cell invasion. We have determined the three-dimensional crystal structure of TcMIP at 1.7 Å resolution. The monomeric protein displays a peptidyl-prolyl cis-trans isomerase (PPlase) core, encompassing the characteristic rotamase hydrophobic active site, thus explaining the strong inhibition of TcMIP by the immunosuppressant FK506 and related drugs. In TcMIP, the twisted β-sheet of the core is extended by an extra β-strand, preceded by a long, exposed N-terminal α-helix, which might be a target recognition element. An invasion assay shows that the MIP protein from Legionella pneumophila (LpMIP), which has an equivalent N-terminal α-helix, can substitute for TcMIP. An additional exposed α-helix, this one unique to TcMIP, is located in the C-terminus of the protein. The high-resolution structure reported here opens the possibility for the design of new inhibitory drugs that might be useful for the clinical treatment of American trypanosomiasis.This work was supported by grants from Ministerio de Educación y Cultura (PB98-1631 and 2FD97-0518), CSIC and Generalitat de Catalunya (CERBA and 1999SGR188) to M.C., grant PB98-0479 to A.G. and by grant BIO2000-1659 to F.X.G.-R. P.J.B.P. and S.M.-R. acknowledge postdoctoral fellowships from FCT (Portugal). Data collection at DESY was supported by EC grants ERBFMGECT980134 and HPRI-CT-1999-00017 to EMBL-HamburgPeer Reviewe

Coherent state quantization of a particle in de Sitter space

We present a coherent state quantization of the dynamics of a relativistic test particle on a one-sheet hyperboloid embedded in a three-dimensional Minkowski space. The group SO_0(1,2) is considered to be the symmetry group of the system. Our procedure relies on the choice of coherent states of the motion on a circle. The coherent state realization of the principal series representation of SO_0(1,2) seems to be a new result.Comment: Journal of Physics A: Mathematical and General, vol. 37, in pres

A functional variant in the stearoyl-CoA desaturase (SCD) gene promoter affects gene expression in ovine muscle

The nutritional quality of lambs may be improved with increased stearoyl-CoA desaturase (SCD) gene expression, which increases the desaturation of stearic acid to oleic acid. The aim of this study was to evaluate the effect of the rs412429481 (FJ513370: g.31C > A) SNP located at the SCD gene on the functionality of the gene in lambs reared under different production systems. The effect of the rs412429481 SNP on gene expression in Rasa Aragonesa male lambs slaughtered at 22–24 kg was studied in two experiments. In Experiment 1 (n = 44), the semitendinosus muscle of lambs grazing alfalfa (ALF) or fed concentrates indoors (IND) was analysed; in Experiment 2 (n = 48), the semitendinosus and longissimus thoracis muscles of lambs that received supplementation with dl-a-tocopheryl acetate for different finishing periods were used. In Experiment 1, the effect of the rs412429481 SNP on the expression of the SCD gene in the semitendinosus muscle depended on the feeding group (P < 0.001), as it had no effect in ALF lambs, but CA lambs had greater SCD expression than CC lambs under the IND conditions. Moreover, ALF lambs showed lower levels of SCD gene expression than IND lambs (P < 0.05). In Experiment 2, gene expression was affected by the rs412429481 SNP in both muscles. Animals carrying the C- allele showed a lower expression rate than animals carrying the A- allele. These different expression levels were not associated with changes in the DNA methylation pattern or by the binding of specific nuclear proteins. Finally, we confirmed these results by luciferase assays, demonstrating that the SCD promoter containing the A variant had a 23.9% higher activity than the promoter containing the C variant

Evidence of telomere attrition and a potential role for DNA damage in systemic sclerosis

[Background]: To investigate the role of cell senescence in systemic sclerosis (SSc), we analyzed telomere shortening (TS) in SSc patients and the effect of targeting DNA damage in the bleomycin model of skin fibrosis. [Results]: Telomere length (TL) in blood leukocytes of 174 SSc patients and 68 healthy controls was measured by Southern blot, and we found shorter age-standardized TL in SSc patients compared to healthy controls. TL was shorter in SSc patients with ILD compared to those without ILD and in anti-topoisomerase I positive compared to anti-centromere positive patients. To analyze the potential role of DNA damage in skin fibrosis, we evaluated the effects of the DNA protective GSE4 peptide in the bleomycin mouse model of scleroderma and the fibrotic response of cultured human dermal fibroblasts. Administration of GSE4-nanoparticles attenuated bleomycin-induced skin fibrosis as measured by Masson’s staining of collagen and reduced Acta2 and Ctgf mRNA expression, whereas transduction of dermal fibroblasts with a lentiviral GSE4 expression vector reduced COL1A1, ACTA2 and CTGF gene expression after stimulation with bleomycin or TGF-β, in parallel to a reduction of the phospho-histone H2A.X marker of DNA damage. [Conclusions]: SSc is associated with TS, particularly in patients with lung disease or anti-topoisomerase I antibodies. Administration of GSE4 peptide attenuated experimental skin fibrosis and reduced fibroblast expression of profibrotic factors, supporting a role for oxidative DNA damage in scleroderma.The authors received financial support from Fondo de Investigación Sanitaria, Instituto de Salud Carlos III (PI19/01129, PI20/00335, and RIER network RD16/0012 RETICS program), co-financed by the European Regional Development Fund (FEDER)

Guidelines for the diagnosis, prevention and treatment of osteoporosis, 2012

La osteoporosis es una patología en constante crecimiento y que afecta a más de 200 millones de personas a nivel mundial. Las recomendaciones presentes son guías para el diagnóstico, la prevención y tratamiento pero no normas para las decisiones clínicas en pacientes individuales. El médico debe adaptarlas a situaciones y pacientes deferentes, incorporando factores personales que trascienden los límites de estas guías y hacen al saber y al arte del médico. Como todo conocimiento médico científico deben ser revisadas y actualizadas periódicamente a medida que se adquieran nuevas, mejores y más efectivas herramientas diagnósticas y terapéuticas.Osteoporosis is a constantly growing disease which affects over 200 million people worldwide. The present recommendations are guidelines for its diagnosis, prevention and treatment, but they do not constitute standards for clinical decisions in individual patients. The physician must adapt them to individual patients and special situations, incorporating personal factors that transcend the limits of these guidelines and are dependent on the knowledge and art of the physician. These guidelines should be reviewed and updated periodically as new, better and more effective diagnostic and therapeutic tools become available.Fil: Schurman, Leon. Grupo de Investigación en Osteopatías y Metabolismo Mineral; ArgentinaFil: Bagur, Alicia. Centro de Osteopatías Médicas; ArgentinaFil: Claus Hermberg, Heraldo. Hospital Alemán; ArgentinaFil: Messina, Osvaldo D.. Ministerio de Defensa. Ejercito Argentino. Hospital Militar Central Cirujano Mayor "Cosme Argerich"; ArgentinaFil: Negri, Armando L.. Universidad del Salvador; ArgentinaFil: Sánchez, Ariel. Centro de Endocrinología; ArgentinaFil: González, Claudio. Centro de Educación Médica e Investigaciones Clínicas; ArgentinaFil: Diehl, María. Hospital Italiano de Buenos Aires; ArgentinaFil: Rey, Paula. Universidad del Salvador; ArgentinaFil: Gamba, Julieta. Ministerio de Defensa. Ejercito Argentino. Hospital Militar Central Cirujano Mayor "Cosme Argerich"; ArgentinaFil: Chiarpenello, Javier. Universidad Nacional de Rosario; ArgentinaFil: Moggia, María Susana. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; ArgentinaFil: Mastaglia, Silvina Rosana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Inmunología, Genética y Metabolismo; Argentin