Filogenia del virus linfotrópico humano htlv-1 en sudamérica

Se postula que el HTLV-I salió de África hacia otras áreas del mundo incluyendo Suramérica; sin embargo, actualmente no existe un consenso sobre las rutas de introducción ni el periodo en que ocurrieron

Data on the Amphidinium Carterae Dn241EHU Isolation and Morphological and Molecular Characterization

We present the data corresponding to the isolation and morphological and molecular characterization of a strain of Amphidinium carterae, isolated in Mallorca Island waters and now deposited in the microalgae culture collection of the Plant Biology and Ecology Department of the University of the Basque Country under the reference Dn241Ehu. The morphological characterization was made using two different techniques of microscopy and the molecular characterization by using the 28S rDNA sequences of D1 and D2 domains. This strain has been used for a culture study in an indoor LED-lighted pilot-scale raceway to determine its production of carotenoids and fatty acids, "Long-term culture of the marine dinoflagellate microalga Amphidinium carterae in an indoor LED-lighted raceway photobioreactor: Production of carotenoids and fatty acids." (Molina-Miras et al., 2018) [1]. (C) 2018 The Authors. Published by Elsevier Inc.This research was funded by the Spanish Ministry of Economy and Competitiveness (CTQ2014-55888-C3-02), the European Regional Development Fund Program, and the projects PPG17/67 from the UPV/EHU and IT1040-16 from the Basque Government

Maximizing resource usage in multifold molecular dynamics with rCUDA

[EN] The full-understanding of the dynamics of molecular systems at the atomic scale is of great relevance in the fields of chemistry, physics, materials science, and drug discovery just to name a few. Molecular dynamics (MD) is a widely used computer tool for simulating the dynamical behavior of molecules. However, the computational horsepower required by MD simulations is too high to obtain conclusive results in real-world scenarios. This is mainly motivated by two factors: (1) the long execution time required by each MD simulation (usually in the nanoseconds and microseconds scale, and beyond) and (2) the large number of simulations required in drug discovery to study the interactions between a large library of compounds and a given protein target. To deal with the former, graphics processing units (GPUs) have come up into the scene. The latter has been traditionally approached by launching large amounts of simulations in computing clusters that may contain several GPUs on each node. However, GPUs are targeted as a single node that only runs one MD instance at a time, which translates into low GPU occupancy ratios and therefore low throughput. In this work, we propose a strategy to increase the overall throughput of MD simulations by increasing the GPU occupancy through virtualized GPUs. We use the remote CUDA (rCUDA) middleware as a tool to decouple GPUs from CPUs, and thus enabling multi-tenancy of the virtual GPUs. As a working test in the drug discovery field, we studied the binding process of a novel flavonol to DNA with the GROningen MAchine for Chemical Simulations (GROMACS) MD package. Our results show that the use of rCUDA provides with a 1.21x speed-up factor compared to the CUDA counterpart version while requiring a similar power budget.The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This work was jointly supported by the Fundación Séneca (Agencia Regional de Ciencia y Tecnología, Región de Murcia) under grants (20524/PDC/18, 20813/PI/ 18, and 20988/PI/18) and by the Spanish MEC and Eur-opean Commission FEDER under grants TIN2015-66972-C5-3-R, TIN2016-78799-P, and CTQ2017-87974-R (AEI/FEDER, UE). Researchers from the Universitat Politècnica de València are supported by the Generalitat Valenciana under grant PROMETEO/2017/077.Prades, J.; Imbernon, B.; Reaño González, C.; Peña-García, J.; Cerón-Carrasco, JP.; Silla Jiménez, F.; Pérez-Sánchez, H. (2020). Maximizing resource usage in multifold molecular dynamics with rCUDA. International Journal of High Performance Computing Applications. 34(1):5-19. https://doi.org/10.1177/1094342019857131S519341Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2, 19-25. doi:10.1016/j.softx.2015.06.001Banegas-Luna, A. J., Imbernón, B., Llanes Castro, A., Pérez-Garrido, A., Cerón-Carrasco, J. P., Gesing, S., … Pérez-Sánchez, H. (2018). Advances in distributed computing with modern drug discovery. Expert Opinion on Drug Discovery, 14(1), 9-22. doi:10.1080/17460441.2019.1552936Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., … Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668-1688. doi:10.1002/jcc.20290Csermely, P., Korcsmáros, T., Kiss, H. J. M., London, G., & Nussinov, R. (2013). Structure and dynamics of molecular networks: A novel paradigm of drug discovery. Pharmacology & Therapeutics, 138(3), 333-408. doi:10.1016/j.pharmthera.2013.01.016Franco, A. A. (2013). Multiscale modelling and numerical simulation of rechargeable lithium ion batteries: concepts, methods and challenges. RSC Advances, 3(32), 13027. doi:10.1039/c3ra23502eFrisch MJ, Trucks GW, Schlegel HB, et al. (2016) Gaussian 16 Revision A.03. Wallingford, CT: Gaussian. Inc.Halder, D., & Purkayastha, P. (2018). A flavonol that acts as a potential DNA minor groove binder as also an efficient G-quadruplex loop binder. Journal of Molecular Liquids, 265, 69-76. doi:10.1016/j.molliq.2018.05.117Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. Journal of Chemical Theory and Computation, 4(3), 435-447. doi:10.1021/ct700301qHornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. 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Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926-935. doi:10.1063/1.445869Kitchen, D. B., Decornez, H., Furr, J. R., & Bajorath, J. (2004). Docking and scoring in virtual screening for drug discovery: methods and applications. Nature Reviews Drug Discovery, 3(11), 935-949. doi:10.1038/nrd1549Lagarde, N., Zagury, J.-F., & Montes, M. (2015). Benchmarking Data Sets for the Evaluation of Virtual Ligand Screening Methods: Review and Perspectives. Journal of Chemical Information and Modeling, 55(7), 1297-1307. doi:10.1021/acs.jcim.5b00090Noroozi, M., Angerson, W. J., & Lean, M. E. (1998). Effects of flavonoids and vitamin C on oxidative DNA damage to human lymphocytes. The American Journal of Clinical Nutrition, 67(6), 1210-1218. doi:10.1093/ajcn/67.6.1210Patra, M., Hyvönen, M. T., Falck, E., Sabouri-Ghomi, M., Vattulainen, I., & Karttunen, M. (2007). Long-range interactions and parallel scalability in molecular simulations. Computer Physics Communications, 176(1), 14-22. doi:10.1016/j.cpc.2006.07.017Pezeshgi Modarres, H., Dorokhov, B. D., Popov, V. O., Ravin, N. V., Skryabin, K. G., & Dal Peraro, M. (2015). Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp. 1519. Biochemistry, 54(19), 3076-3085. doi:10.1021/bi501227bPhillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., … Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781-1802. doi:10.1002/jcc.20289Prades, J., Reaño, C., Silla, F., Imbernón, B., Pérez-Sánchez, H., & Cecilia, J. M. (2018). Increasing Molecular Dynamics Simulations Throughput by Virtualizing Remote GPUs with rCUDA. Proceedings of the 47th International Conference on Parallel Processing Companion - ICPP ’18. doi:10.1145/3229710.3229734Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., … Lindahl, E. (2013). 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Determinación de la condición de riesgo para el proceso de reinyección de recortes de perforación en pozos agotados en dos plataformas costa fuera en el suroeste de la Sonda de Campeche

Potential risks associated with the cuttings re-injection process as an alternative method for drilling wastes disposal were identi- fied and assessed in two offshore platforms located at the southwest of the Campeche Sonda in Mexico. Risks were evaluated using the HAZOP methodology, to identifying hazards in 11 nodes. In addition, deviations in the process were analyzed, and each risk analyzed was categorized as tolerable or non-tolerable and providing some recommendations. Consequences derived from accidental spills of slurry and/or cuttings were analyzed using the mathematical model YAXUM 3D to simulate the pollu- tants dispersion in seawater in three different climatic periods. The results of the consequences analysis shows that even the concentrations in the discharge point exceeded the recommended criteria for protection of the marine life and seawater quality, the spill is rapidly dispersed complying with permitted levels in 8 hr as a maximum.Los riesgos potenciales asociados al proceso de reinyección de recortes como un método alternativo para la disposición de los desechos de perforación fueron identificados y calculados en dos plataformas costa fuera situadas en el suroeste de la Sonda de Campeche en México. Los riesgos fueron evaluados usando la metodología Hazop, para identificar peligros en once nodos dentro del sistema de reinyección de recortes de perforación. Además, fueron analizadas las desviaciones en el proceso y cada riesgo analizado fue categorizado como tolerable o no-tolerable; asimismo, se propusieron algunas recomendaciones. Las consecuencias derivadas de derrames accidentales de lechada y/o recortes de perforación fueron analizados usando el modelo matemático YAXUM 3D para simular la dispersión de los agentes contaminantes en agua de mar en tres periodos climáticos. Los resultados del análisis de consecuencias demuestran que aun cuando las concentraciones en el punto de descarga excedieron los criterios recomendados para la protección de la vida de marina y de la calidad del agua de mar, el derrame es rápidamente dispersado cumpliendo con los niveles permitidos en ocho horas como máxim

The wideband backend at the MDSCC in Robledo. A new facility for radio astronomy at Q- and K- bands

The antennas of NASA's Madrid Deep Space Communications Complex (MDSCC) in Robledo de Chavela are available as single-dish radio astronomical facilities during a significant percentage of their operational time. Current instrumentation includes two antennas of 70 and 34 m in diameter, equipped with dual-polarization receivers in K (18 - 26 GHz) and Q (38 - 50 GHz) bands, respectively. We have developed and built a new wideband backend for the Robledo antennas, with the objectives (1) to optimize the available time and enhance the efficiency of radio astronomy in MDSCC; and (2) to tackle new scientific cases impossible to that were investigated with the old, narrow-band autocorrelator. The backend consists of an IF processor, a FFT spectrometer (FFTS), and the software that interfaces and manages the events among the observing program, antenna control, the IF processor, the FFTS operation, and data recording. The whole system was end-to-end assembled in August 2011, at the start of commissioning activities, and the results are reported in this paper. Frequency tunings and line intensities are stable over hours, even when using different synthesizers and IF channels; no aliasing effects have been measured, and the rejection of the image sideband was characterized. The first setup provides 1.5 GHz of instantaneous bandwidth in a single polarization, using 8192 channels and a frequency resolution of 212 kHz; upgrades under way include a second FFTS card, and two high-resolution cores providing 100 MHz and 500 MHz of bandwidth, and 16384 channels. These upgrades will permit simultaneous observations of the two polarizations with instantaneous bandwidths from 100 MHz to 3 GHz, and spectral resolutions from 7 to 212 kHz.Comment: 9 pages, 8 figures. Accepted to Astronomy and Astrophysic

Detection and analysis of tumour biomarkers to strengthen the diagnosis of acute and chronic leukaemias

AbstractMolecular markers in leukaemia are essential to diagnose, establish prognosis factors and determine the correct treatment of patients; therefore, it is imperative to include molecular biology studies, so that, combined with cytomorphology and immunophenotyping studies, they constitute the differential diagnosis of these neoplasias. It is extremely important to implement a panel of molecular markers that allows us to detect oncogenes derived from chromosomal translocations, genes derived from epigenetic alterations and drug-resistant genes.A panel of molecular markers that included 11 genes derived from chromosomal translocations BCR-ABL major and minor breakpoints, E2A-PBX1, MLL-AF4, TEL-AML1, PML-RARα, AML1-ETO was standardised; cancer testis antigens (CTA) derived from NY-ESO1 and MAGE-A3 epigenetic alterations and multi-drug-resistant genes ABCB1 and ABCG2. 30 patients diagnosed with leukaemia from Mexico's General Hospital (Hospital General de Mexico) were included. They suffered from acute lymphoblastic leukaemia (ALL) and acute myeloblastic leukaemia (AML); bone marrow mononuclear cells were used, from which RNA was extracted for the synthesis of cDNA and RT-PCR for each of the markers. In acute lymphoblastic leukaemia (ALL), BCR-ABL biomarkers expressed under 30% (3/10), E2A-PBX1 10% (1/10), ABC-B1 80% (8/10), and ABC-G2 60% (6/10). Patients with acute myeloblastic leukaemia (AML) expressed 30% PML-RARα (3/10), 40% ABC-B1 (4/10), and 10% ABC-G2 (1/10). Lastly, in patients with chronic myeloid leukaemia (CML), BCR-ABL was over 100% (10/10), ABC-B1 20% (2/10), and ABC-G2 50% (5/10). The presence of transcripts from chimeric genes minor BCR-ABL and E2A-PBX1 in ALL; PML-RARα in AML; and major BCR-ABL in CML, confirms the importance that the panel of molecular markers has in strengthening the diagnosis and prognosis of these conditions

GRB 021004: Tomography of a gamma-ray burst progenitor and its host galaxy

We analyse the distribution of matter around the progenitor star of gamma-ray burst GRB 021004 as well as the properties of its host galaxy with high-resolution echelle as well as near-infrared spectroscopy. Observations were taken by the 8.2m Very Large Telescope with the Ultraviolet and Visual Echelle spectrograph (UVES) and the Infrared Spectrometer And Array Camera (ISAAC) between 10 and 14 hours after the onset of the event. We report the first detection of emission lines from a GRB host galaxy in the near-infrared, detecting H-alpha and the [O III] doublet. These allow an independent measurement of the systemic redshift (z = 2.3304 +/- 0.0005) which is not contaminated by absorption as the Ly-alpha line is, and the deduction of properties of the host galaxy. From the visual echelle spectroscopy, we find several absorption line groups spanning a range of about 3,000 km/s in velocity relative to the redshift of the host galaxy. The absorption profiles are very complex with both velocity-broadened components extending over several 100 km/s and narrow lines with velocity widths of only 20 km/s. By analogy with QSO absorption line studies, the relative velocities,widths, and degrees of ionization of the lines ("line-locking", "ionization--velocity correlation") show that the progenitor had both an extremely strong radiation field and several distinct mass loss phases (winds). These results are consistent with GRB progenitors being massive stars, such as Luminous Blue Variables (LBVs) or Wolf--Rayet stars, providing a detailed picture of the spatial and velocity structure of the GRB progenitor star at the time of explosion. The host galaxy is a prolific star-forming galaxy with a SFR of about 40 solar masses per year.Comment: 11 pages, 5 figures. Accepted for publication in Astronomy and Astrophysics

Oral chondroitin sulfate and prebiotics for the treatment of canine Inflammatory Bowel Disease: a randomized, controlled clinical trial

BACKGROUND Canine inflammatory bowel disease (IBD) is a chronic enteropathy of unknown etiology, although microbiome dysbiosis, genetic susceptibility, and dietary and/or environmental factors are hypothesized to be involved in its pathogenesis. Since some of the current therapies are associated with severe side effects, novel therapeutic modalities are needed. A new oral supplement for long-term management of canine IBD containing chondroitin sulfate (CS) and prebiotics (resistant starch, β-glucans and mannaoligosaccharides) was developed to target intestinal inflammation and oxidative stress, and restore normobiosis, without exhibiting any side effects. This double-blinded, randomized, placebo-controlled trial in dogs with IBD aims to evaluate the effects of 180 days administration of this supplement together with a hydrolyzed diet on clinical signs, intestinal histology, gut microbiota, and serum biomarkers of inflammation and oxidative stress. RESULTS Twenty-seven client-owned biopsy-confirmed IBD dogs were included in the study, switched to the same hydrolyzed diet and classified into one of two groups: supplement and placebo. Initially, there were no significant differences between groups (p > 0.05) for any of the studied parameters. Final data analysis (supplement: n = 9; placebo: n = 10) showed a significant decrease in canine IBD activity index (CIBDAI) score in both groups after treatment (p < 0.001). After treatment, a significant decrease (1.53-fold; p < 0.01) in histologic score was seen only in the supplement group. When groups were compared, the supplement group showed significantly higher serum cholesterol (p < 0.05) and paraoxonase-1 (PON1) levels after 60 days of treatment (p < 0.01), and the placebo group showed significantly reduced serum total antioxidant capacity (TAC) levels after 120 days (p < 0.05). No significant differences were found between groups at any time point for CIBDAI, WSAVA histologic score and fecal microbiota evaluated by PCR-restriction fragment length polymorphism (PCR-RFLP). No side effects were reported in any group. CONCLUSIONS The combined administration of the supplement with hydrolyzed diet over 180 days was safe and induced improvements in selected serum biomarkers, possibly suggesting a reduction in disease activity. This study was likely underpowered, therefore larger studies are warranted in order to demonstrate a supplemental effect to dietary treatment of this supplement on intestinal histology and CIBDAI