73 research outputs found

    Exploiting hybrid parallelism in the kinematic analysis of multibody systems based on group equations

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    Computational kinematics is a fundamental tool for the design, simulation, control, optimization and dynamic analysis of multibody systems. The analysis of complex multibody systems and the need for real time solutions requires the development of kinematic and dynamic formulations that reduces computational cost, the selection and efficient use of the most appropriated solvers and the exploiting of all the computer resources using parallel computing techniques. The topological approach based on group equations and natural coordinates reduces the computation time in comparison with well-known global formulations and enables the use of parallelism techniques which can be applied at different levels: simultaneous solution of equations, use of multithreading routines, or a combination of both. This paper studies and compares these topological formulation and parallel techniques to ascertain which combination performs better in two applications. The first application uses dedicated systems for the real time control of small multibody systems, defined by a few number of equations and small linear systems, so shared-memory parallelism in combination with linear algebra routines is analyzed in a small multicore and in Raspberry Pi. The control of a Stewart platform is used as a case study. The second application studies large multibody systems in which the kinematic analysis must be performed several times during the design of multibody systems. A simulator which allows us to control the formulation, the solver, the parallel techniques and size of the problem has been developed and tested in more powerful computational systems with larger multicores and GPU.This work was supported by the Spanish MINECO, as well as European Commission FEDER funds, under grant TIN2015-66972-C5-3-

    GSK-3 is an RNA polymerase II phospho-CTD kinase

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    We have previously found that UV-induced DNA damage causes hyperphosphorylation of the carboxy terminal domain (CTD) of RNA polymerase II (RNAPII), inhibition of transcriptional elongation and changes in alternative splicing (AS) due to kinetic coupling between transcription and splicing. In an unbiased search for protein kinases involved in the AS response to DNA damage, we have identified glycogen synthase kinase 3 (GSK-3) as an unforeseen participant. Unlike Cdk9 inhibition, GSK-3 inhibition only prevents CTD hyperphosphorylation triggered by UV but not basal phosphorylation. This effect is not due to differential degradation of the phospho-CTD isoforms and can be reproduced, at the AS level, by overexpression of a kinase-dead GSK-3 dominant negative mutant. GSK-3 inhibition abrogates both the reduction in RNAPII elongation and changes in AS elicited by UV. We show that GSK-3 phosphorylates the CTD in vitro, but preferentially when the substrate is previously phosphorylated, consistently with the requirement of a priming phosphorylation reported for GSK-3 efficacy. In line with a role for GSK-3 in the response to DNA damage, GSK-3 inhibition prevents UV-induced apoptosis. In summary, we uncover a novel role for a widely studied kinase in key steps of eukaryotic transcription and pre-mRNA processing.Fil: Nieto Moreno, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Villafañez, Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; ArgentinaFil: Giono, Luciana Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Cuenca, Carmen. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Soria, Gastón. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; ArgentinaFil: Muñoz, Manuel Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Fondazione Istituto FIRC di Oncologia Molecolare; Italia. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Biodiversidad y Biología Experimental; ArgentinaFil: Kornblihtt, Alberto Rodolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentin

    On the Statistical and Temporal Dynamics of Sentiment Analysis

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    Despite the broad interest and use of sentiment analysis nowadays, most of the conclusions in current literature are driven by simple statistical representations of sentiment scores. On that basis, the generated sentiment evaluation consists nowadays of encoding and aggregating emotional information from a number of individuals and their populational trends. We hypothesized that the stochastic processes aimed to be measured by sentiment analysis systems will exhibit nontrivial statistical and temporal properties. We established an experimental setup consisting of analyzing the short text messages (tweets) of 6 user groups with different nature (universities, politics, musicians, communication media, technological companies, and financial companies), including in each group ten high-intensity users in their regular generation of traffic on social networks. Statistical descriptors were checked to converge at about 2000 messages for each user, for which messages from the last two weeks were compiled using a custom-made tool. The messages were subsequently processed for sentiment scoring in terms of different lexicons currently available and widely used. Not only the temporal dynamics of the resulting score time series per user was scrutinized, but also its statistical description as given by the score histogram, the temporal autocorrelation, the entropy, and the mutual information. Our results showed that the actual dynamic range of lexicons is in general moderate, and hence not much resolution is given within their end-of-scales. We found that seasonal patterns were more present in the time evolution of the number of tweets, but to a much lesser extent in the sentiment intensity. Additionally, we found that the presence of retweets added negligible effects over standard statistical modes, while it hindered informational and temporal patterns. The innovative Compounded Aggregated Positivity Index developed in this work proved to be characteristic for industries and at ..

    Study of the orpiment and anorpiment phases of As2S3 under pressure

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    [EN] In this work we study the pressure behaviour of the orpiment (monoclinic) and anorpiment (triclinic) layered structures of As2S3 by means of ab initio calculations performed within the density functional theory, as part of an ongoing theoretical and experimental joint effort to provide a comprehensive picture of the bonding of this interesting material and the evolution of its structural, electronic, and vibrational properties under pressure.The authors acknowledge the financial support from the Ministerio de Economia y Competitividad (MINECO) of Spain through Projects No. MAT2013-46649-C04-02-P and MAT2013-46649-C04-03-P. Computer time in the MALTA computer cluster at the University of Oviedo, Spain, is also gratefully acknowledged (MINECO Project No. CSD2007-00045).Randescu, S.; Mújica, A.; Rodríguez-Hernández, P.; Muñoz, A.; Ibañez, J.; Sans-Tresserras, JÁ.; Cuenca Gotor, VP.... (2017). Study of the orpiment and anorpiment phases of As2S3 under pressure. Journal of Physics: Conference Series. 950:042018-042018. https://doi.org/10.1088/1742-6596/950/4/042018S042018042018950Brazhkin, V. V., Katayama, Y., Kondrin, M. V., Lyapin, A. G., & Saitoh, H. (2010). Structural transformation yielding an unusual metallic state in liquidAs2S3under high pressure. Physical Review B, 82(14). doi:10.1103/physrevb.82.140202Gibbs, G. V., Wallace, A. F., Zallen, R., Downs, R. T., Ross, N. L., Cox, D. F., & Rosso, K. M. (2010). Bond Paths and van der Waals Interactions in Orpiment, As2S3. The Journal of Physical Chemistry A, 114(23), 6550-6557. doi:10.1021/jp102391aKampf, A. R., Downs, R. T., Housley, R. M., Jenkins, R. A., & Hyršl, J. (2011). Anorpiment, As2S3, the triclinic dimorph of orpiment. Mineralogical Magazine, 75(6), 2857-2867. doi:10.1180/minmag.2011.075.6.2857Bolotina, N. B., Brazhkin, V. V., Dyuzheva, T. I., Katayama, Y., Kulikova, L. F., Lityagina, L. V., & Nikolaev, N. A. (2014). High-pressure polymorphism of As2S3 and new AsS2 modification with layered structure. JETP Letters, 98(9), 539-543. doi:10.1134/s0021364013220025Bolotina, N. B., Brazhkin, V. V., Dyuzheva, T. I., Lityagina, L. M., Kulikova, L. F., Nikolaev, N. A., & Verin, I. A. (2013). Crystal structure of new AsS2 compound. Crystallography Reports, 58(1), 61-64. doi:10.1134/s1063774513010069Kresse, G., & Hafner, J. (1993). Ab initiomolecular dynamics for liquid metals. Physical Review B, 47(1), 558-561. doi:10.1103/physrevb.47.558Kresse, G., & Furthmüller, J. (1996). Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set. Computational Materials Science, 6(1), 15-50. doi:10.1016/0927-0256(96)00008-0Kresse, G., & Furthmüller, J. (1996). Efficient iterative schemes forab initiototal-energy calculations using a plane-wave basis set. Physical Review B, 54(16), 11169-11186. doi:10.1103/physrevb.54.11169Perdew, J. P., Burke, K., & Ernzerhof, M. (1996). Generalized Gradient Approximation Made Simple. Physical Review Letters, 77(18), 3865-3868. doi:10.1103/physrevlett.77.3865Perdew, J. P., Ruzsinszky, A., Csonka, G. I., Vydrov, O. A., Scuseria, G. E., Constantin, L. A., … Burke, K. (2008). Restoring the Density-Gradient Expansion for Exchange in Solids and Surfaces. Physical Review Letters, 100(13). doi:10.1103/physrevlett.100.136406Kresse, G., & Joubert, D. (1999). From ultrasoft pseudopotentials to the projector augmented-wave method. Physical Review B, 59(3), 1758-1775. doi:10.1103/physrevb.59.1758Blöchl, P. E. (1994). Projector augmented-wave method. Physical Review B, 50(24), 17953-17979. doi:10.1103/physrevb.50.17953Monkhorst, H. J., & Pack, J. D. (1976). Special points for Brillouin-zone integrations. Physical Review B, 13(12), 5188-5192. doi:10.1103/physrevb.13.5188Grimme, S. (2006). Semiempirical GGA-type density functional constructed with a long-range dispersion correction. Journal of Computational Chemistry, 27(15), 1787-1799. doi:10.1002/jcc.20495Grimme, S., Antony, J., Ehrlich, S., & Krieg, H. (2010). A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. The Journal of Chemical Physics, 132(15), 154104. doi:10.1063/1.3382344Birch, F. (1947). Finite Elastic Strain of Cubic Crystals. Physical Review, 71(11), 809-824. doi:10.1103/physrev.71.809Mujica, A., Rubio, A., Muñoz, A., & Needs, R. J. (2003). High-pressure phases of group-IV, III–V, and II–VI compounds. Reviews of Modern Physics, 75(3), 863-912. doi:10.1103/revmodphys.75.863Alfè, D. (2009). PHON: A program to calculate phonons using the small displacement method. Computer Physics Communications, 180(12), 2622-2633. doi:10.1016/j.cpc.2009.03.01

    Cloud Computing en salud: Sistema para Administrar Imagenes Biomedicas

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    En el campo de la biomedicina se genera una inmensa cantidad de imágenes diariamente. Para administrarlas es necesaria la creación de sistemas informáticos robustos y ágiles, que necesitan gran cantidad de recursos computacionales. El presente artículo presenta un servicio de cloud computing capaz de manejar grandes colecciones de imágenes biomédicas. Gracias a este servicio organizaciones y usuarios podrían administrar sus imágenes biomédicas sin necesidad de poseer grandes recursos informáticos. El servicio usa un sistema distribuido multi agente donde las imágenes son procesadas y se extraen y almacenan en una estructura de datos las regiones que contiene junto con sus características. Una característica novedosa del sistema es que una misma imagen puede ser dividida, y las sub-imágenes resultantes pueden ser almacenadas por separado por distintos agentes. Esta característica ayuda a mejorar el rendimiento del sistema a la hora de buscar y recuperar las imágenes almacenadas

    Trabeculated Myocardium in Hypertrophic Cardiomyopathy: Clinical Consequences

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    Aims: Hypertrophic cardiomyopathy (HCM) is often accompanied by increased trabeculated myocardium (TM)-which clinical relevance is unknown. We aim to measure the left ventricular (LV) mass and proportion of trabeculation in an HCM population and to analyze its clinical implication. Methods and Results: We evaluated 211 patients with HCM (mean age 47.8 +/- 16.3 years, 73.0% males) with cardiac magnetic resonance (CMR) studies. LV trabecular and compacted mass were measured using dedicated software for automatic delineation of borders. Mean compacted myocardium (CM) was 160.0 +/- 62.0 g and trabecular myocardium (TM) 55.5 +/- 18.7 g. The percentage of trabeculated myocardium (TM%) was 26.7% +/- 6.4%. Females had significantly increased TM% compared to males (29.7 +/- 7.2 vs. 25.6 +/- 5.8, p < 0.0001). Patients with LVEF < 50% had significantly higher values of TM% (30.2% +/- 6.0% vs. 26.6% +/- 6.4%, p = 0.02). Multivariable analysis showed that female gender and neutral pattern of hypertrophy were directly associated with TM%, while dynamic obstruction, maximal wall thickness and LVEF% were inversely associated with TM%. There was no association between TM% with arterial hypertension, physical activity, or symptoms. Atrial fibrillation and severity of hypertrophy were the only variables associated with cardiovascular death. Multivariable analysis failed to demonstrate any correlation between TM% and arrhythmias. Conclusions: Approximately 25% of myocardium appears non-compacted and can automatically be measured in HCM series. Proportion of non-compacted myocardium is increased in female, non-obstructives, and in those with lower contractility. The amount of trabeculation might help to identify HCM patients prone to systolic heart failure

    Structural and Lattice-Dynamical Properties of Tb2O3 under Compression: A Comparative Study with Rare Earth and Related Sesquioxides

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    [EN] We report a joint experimental and theoretical investigation of the high pressure structural and vibrational properties of terbium sesquioxide (Tb2O3). Powder X-ray diffraction and Raman scattering measurements show that cubic Ia (3 ) over bar (C-type) Tb2O3 undergoes two phase transitions up to 25 GPa. We observe a first irreversible reconstructive transition to the monoclinic C2/m (B-type) phase at similar to 7 GPa and a subsequent reversible displacive transition from the monoclinic to the trigonal P (3) over bar m1 (A-type) phase at similar to I-2 GPa. Thus, Tb2O3 is found to follow the well- known C -> B -> A phase transition sequence found in other cubic rare earth sesquioxides with cations of larger atomic mass than Tb. Our ab initio theoretical calculations predict phase transition pressures and bulk moduli for the three phases in rather good agreement with experimental results. Moreover, Raman-active modes of the three phases have been monitored as a function of pressure, while lattice-dynamics calculations have allowed us to confirm the assignment of the experimental phonon modes in the C- and A-type phases as well as to make a tentative assignment of the symmetry of most vibrational modes in the B-type phase. Finally, we extract the bulk moduli and the Raman-active mode frequencies together with their pressure coefficients for the three phases of Tb2O3 . These results are thoroughly compared and discussed in relation to those reported for rare earth and other related sesquioxides as well as with new calculations for selected sesquioxides. It is concluded that the evolution of the volume and bulk modulus of all the three phases of these technologically relevant compounds exhibit a nearly linear trend with respect to the third power of the ionic radii of the cations and that the values of the bulk moduli for the three phases depend on the filling of the f orbitals.The authors are thankful for the financial support of Generalitat Valenciana under Project PROMETEO 2018/123-EFIMAT and of the Spanish Ministerio de Economia y Competitividad under Projects MAT2015-71035-R, MAT2016-75586-C4-2/3/4-P, and FIS2017-2017-83295-P as well as MALTA Consolider Team research network under project RED2018-102612-T. J.A.S. also acknowledges the Ramon y Cajal program for funding support through RYC-2015-17482. A.M. and P.R.-H. acknowledge computing time provided by Red Española de Supercomputación (RES) and the MALTA Consolider Team cluster. HP-XRD experiments were performed at MPSD beamline of Alba Synchrotron (experiment no. 2016071772). We would like to thank Oriol Blázquez (Universitat de Barcelona) for his contribution to the Raman measurements.Ibañez, J.; Sans-Tresserras, JÁ.; Cuenca-Gotor, VP.; Oliva, R.; Gomis, O.; Rodríguez-Hernández, P.; Muñoz, A.... (2020). Structural and Lattice-Dynamical Properties of Tb2O3 under Compression: A Comparative Study with Rare Earth and Related Sesquioxides. Inorganic Chemistry. 59(14):9648-9666. https://doi.org/10.1021/acs.inorgchem.0c00834S964896665914Pan, T.-M., Chen, F.-H., & Jung, J.-S. (2010). Structural and electrical characteristics of high-k Tb2O3 and Tb2TiO5 charge trapping layers for nonvolatile memory applications. Journal of Applied Physics, 108(7), 074501. doi:10.1063/1.3490179Kao, C. H., Liu, K. C., Lee, M. H., Cheng, S. N., Huang, C. H., & Lin, W. K. (2012). High dielectric constant terbium oxide (Tb2O3) dielectric deposited on strained-Si:C. Thin Solid Films, 520(8), 3402-3405. doi:10.1016/j.tsf.2011.10.173Gray, N. W., Prestgard, M. C., & Tiwari, A. (2014). 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    Pressure-induced order-disorder transitions in beta-In2S3: an experimental and theoretical study of structural and vibrational properties.

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    [EN] This joint experimental and theoretical study of the structural and vibrational properties of beta-In2S3 upon compression shows that this tetragonal defect spinel undergoes two reversible pressure-induced order¿disorder transitions up to 20 GPa. We propose that the first high-pressure phase above 5.0 GPa has the cubic defect spinel structure of alpha-In2S3 and the second high-pressure phase (phi-In2S3) above 10.5 GPa has a defect alpha-NaFeO2-type (R-3m) structure. This phase, related to the NaCl structure, has not been previously observed in spinels under compression and is related to both the tetradymite structure of topological insulators and to the defect LiTiO2 phase observed at high pressure in other thiospinels. Structural characterization of the three phases shows that alpha-In2S3 is softer than beta-In2S3 while phi-In2S3 is harder than beta-In2S3. Vibrational characterization of the three phases is also provided, and their Raman active modes are tentatively assigned. Our work shows that the metastable a phase of In2S3 can be accessed not only by high temperature or varying composition, but also by high pressure. On top of that, the pressure-induced beta¿alpha¿phi sequence of phase transitions evidences that beta-In2S3, a BIII2XV3 compound with an intriguing structure typical of AIIBIII2XVI4 compounds (intermediate between thiospinels and ordered-vacancy compounds) undergoes: (i) a first phase transition at ambient pressure to a disordered spinel-type structure (alpha-In2S3), isostructural with those found at high pressure and high temperature in other BIII2XV3 compounds; and (ii) a second phase transition to the defect alpha-NaFeO2-type structure (phi-In2S3), a distorted NaCl-type structure that is related to the defect NaCl phase found at high pressure in AIIBIII2XVI4 ordered-vacancy compounds and to the defect LiTiO2-type phase found at high pressure in AIIBIII2XVI4 thiospinels. This result shows that In2S3 (with its intrinsic vacancies) has a similar pressure behaviour to thiospinels and ordered-vacancy compounds of the AIIBIII2XVI4 family, making beta-In2S3 the union link between such families of compounds and showing that group-13 thiospinels have more in common with ordered-vacancy compounds than with oxospinels and thiospinels with transition metals.This publication is part of the project MALTA Consolider Team network (RED2018-102612-T), financed by MINECO/AEI/10.13039/501100003329; by I+D+i projects PID2019-106383GB41/42/43, financed by MCIN/AEI/10.13039/501100011033; by project PROMETEO/2018/123 (EFIMAT), financed by Generalitat Valenciana; and by projects DMREF-NSF 1434897 and DOE DE-SC0016176, financed from US agencies. A. M., and P. R.-H. acknowledge computing time provided by Red Espanola de Supercomputacion (RES) and MALTA-Cluster, and we also thank ALBA synchrotron light source for funded experiment 2017022088 at the MSPD-BL04 beamline. A. H. R. acknowledges the computational resources awarded by XSEDE, a project supported by National Science Foundation grant number ACI-1053575, as well as the time from the Super Computing System (Thorny Flat) at WVU, which is funded in part by the National Science Foundation (NSF) Major Research Instrumentation Program (MRI) Award #1726534, and West Virginia University. The authors also acknowledge the support from the Texas Advances Computer Center (with the Stampede2 and Bridges supercomputers). A. M. and R. A. acknowledge the support from Olle Engkvists stiftelse, Sweden, Carl Tryggers Stiftelse for Vetenskaplig Forskning (CTS) and the Swedish Research Council (Grant no. VR-2016-06014 and VR-2020-04410). SNIC and HPC2N are also acknowledged for providing computing resources.Gallego-Parra, S.; Gomis, O.; Vilaplana Cerda, RI.; Cuenca-Gotor, VP.; Martínez-García, D.; Rodríguez-Hernández, P.; Muñoz, A.... (2021). Pressure-induced order-disorder transitions in beta-In2S3: an experimental and theoretical study of structural and vibrational properties. Physical Chemistry Chemical Physics. 23(41):23625-23642. https://doi.org/10.1039/d1cp02969j2362523642234

    Ludus: Juegos aplicados al aprendizaje de las Ciencias y Técnicas Historiográficas

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    Proyecto de Innovación Docente (convocatoria 2019/20, nº 261) basado en una propuesta de ludificación de la docencia a través de la utilización de dos juegos en el aula, uno consistente en la resolución de crucigramas y otro que plantea una mecánica de preguntas-respuestas mediante un modelo inspirado en el Trivial
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