1,440 research outputs found

    Marmal-aid - a database for Infinium HumanMethylation450

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    This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated

    A Study of Archiving Strategies in Multi-Objective PSO for Molecular Docking

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    Molecular docking is a complex optimization problem aimed at predicting the position of a ligand molecule in the active site of a receptor with the lowest binding energy. This problem can be formulated as a bi-objective optimization problem by minimizing the binding energy and the Root Mean Square Deviation (RMSD) difference in the coordinates of ligands. In this context, the SMPSO multi-objective swarm-intelligence algorithm has shown a remarkable performance. SMPSO is characterized by having an external archive used to store the non-dominated solutions and also as the basis of the leader selection strategy. In this paper, we analyze several SMPSO variants based on different archiving strategies in the scope of a benchmark of molecular docking instances. Our study reveals that the SMPSOhv, which uses an hypervolume contribution based archive, shows the overall best performance.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

    Ecological Niche Dimensionality and the Evolutionary Diversification of Stick Insects

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    The degree of phenotypic divergence and reproductive isolation between taxon pairs can vary quantitatively, and often increases as evolutionary divergence proceeds through various stages, from polymorphism to population differentiation, ecotype and race formation, speciation, and post-speciational divergence. Although divergent natural selection promotes divergence, it does not always result in strong differentiation. For example, divergent selection can fail to complete speciation, and distinct species pairs sometimes collapse (‘speciation in reverse’). Widely-discussed explanations for this variability concern genetic architecture, and the geographic arrangement of populations. A less-explored possibility is that the degree of phenotypic and reproductive divergence between taxon pairs is positively related to the number of ecological niche dimensions (i.e., traits) subject to divergent selection. Some data supporting this idea stem from laboratory experimental evolution studies using Drosophila, but tests from nature are lacking. Here we report results from manipulative field experiments in natural populations of herbivorous Timema stick insects that are consistent with this ‘niche dimensionality’ hypothesis. In such insects, divergent selection between host plants might occur for cryptic colouration (camouflage to evade visual predation), physiology (to detoxify plant chemicals), or both of these niche dimensions. We show that divergent selection on the single niche dimension of cryptic colouration can result in ecotype formation and intermediate levels of phenotypic and reproductive divergence between populations feeding on different hosts. However, greater divergence between a species pair involved divergent selection on both niche dimensions. Although further replication of the trends reported here is required, the results suggest that dimensionality of selection may complement genetic and geographic explanations for the degree of diversification in nature

    Estreptococos beta-hemolítico en tilapias del Nilo (Oreochromis niloticus) cultivadas en Sullana, Piura - Perú

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    Objective. This investigation aimed to study the presence of Streptococcus spp. in tilapia (Oreochromis niloticus) from fish farm located in Sullana-Piura, Peru. Materials and methods. 150 fish with clinical signs of streptococcal disease were sampled, and the bacterium isolation was performed on blood agar, correlated to histopathological lesions description and molecular confirmation by real-time PCR. Results. The necropsy revealed exophthalmia, hyphema, congestion and/or haemorrhagic meninges, ascites, splenomegaly, hepatomegaly and diffuse haemorrhagic zones throughout the body. 102 isolated positives (54 tilapias) to Streptococcus spp. were identified in the microbiological analysis (prevalence of 26%), the brain was the organ with the highest percentage of this bacteria (34.31%), and 19 isolates were beta-haemolytic (18.63%) with prevalence of 10.12%. Fish beta-haemolytic streptococci presented epicarditis, perisplenitis and chronic meningitis, panophthalmitis, coagulative necrosis of skeletal muscle and granulomas formation. In the confirmatory test by real-time PCR, any positive tilapia to S. iniae was obtained. The results were analysed using a stochastic simulation of beta distribution using @Risk program uncertainty, reporting an average prevalence of 0.66% in sick tilapias. Conclusions. The analysed fishes were positive to bacteria of the genus Streptococcus, which confirms its presence in the fish farm. However, 19 isolates were beta-haemolytic, and the presence of S. iniae was not positive to the limit prevalence of 2.7% in real-time PCR.Objetivo. Esta investigación objetivó estudiar la presencia de Streptococcus spp. en tilapia (Oreochromis niloticus) de la piscifactoría localizada en Sullana-Piura, Perú. Materiales y Métodos. 150 peces con signos clínicos de la enfermedad estreptocócica fueron analizados, el aislamiento bacteriano se realizó en agar sangre, en correlación con las lesiones histopatológicas y diagnóstico molecular mediante PCR en tiempo real. Resultados. A la necropsia se observó exoftalmia, hifema, congestión y/o meninges hemorrágicas, ascitis, esplenomegalia, hepatomegalia y zonas hemorrágicas difusas en todo el cuerpo. 102 aislados positivos (54) tilapias para Streptococcus spp. fueron identificados en el análisis microbiológico (prevalencia del 26%), el cerebro fue el órgano con el más alto porcentaje del género de esta bacteria (34.31%), 19 aislados fueron beta-hemolítico (18.63%), con prevalencia de 10.12%. Peces con Streptococcus beta-hemolíticos presentaron epicarditis, perisplenitis y meningitis crónica, panoftalmitis, necrosis coagulativa del músculo esquelético y formación de granulomas. En el análisis de PCR en tiempo real, no se obtuvo ninguna tilapia positiva para S. iniae. Los resultados se analizaron mediante una simulación estocástica de la distribución beta usando el programa de incertidumbre @Risk, reportando una prevalencia media de 0.66% en tilapias enfermas. Conclusiones. Los peces analizados fueron positivos para bacterias del género Streptococcus, lo que confirma su presencia en la piscifactoría. Sin embargo, 19 aislados fueron beta-hemolíticos, y la presencia de S. iniae no fue positiva para la prevalencia límite de 2.7% en PCR en tiempo real

    Two-pion Bose-Einstein correlations in central Pb-Pb collisions at sNN\sqrt{s_{\rm NN}} = 2.76 TeV

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    The first measurement of two-pion Bose-Einstein correlations in central Pb-Pb collisions at sNN=2.76\sqrt{s_{\rm NN}} = 2.76 TeV at the Large Hadron Collider is presented. We observe a growing trend with energy now not only for the longitudinal and the outward but also for the sideward pion source radius. The pion homogeneity volume and the decoupling time are significantly larger than those measured at RHIC.Comment: 17 pages, 5 captioned figures, 1 table, authors from page 12, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/388

    Suppression of charged particle production at large transverse momentum in central Pb-Pb collisions at sNN=2.76\sqrt{s_{\rm NN}} = 2.76 TeV

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    Inclusive transverse momentum spectra of primary charged particles in Pb-Pb collisions at sNN\sqrt{s_{_{\rm NN}}} = 2.76 TeV have been measured by the ALICE Collaboration at the LHC. The data are presented for central and peripheral collisions, corresponding to 0-5% and 70-80% of the hadronic Pb-Pb cross section. The measured charged particle spectra in η<0.8|\eta|<0.8 and 0.3<pT<200.3 < p_T < 20 GeV/cc are compared to the expectation in pp collisions at the same sNN\sqrt{s_{\rm NN}}, scaled by the number of underlying nucleon-nucleon collisions. The comparison is expressed in terms of the nuclear modification factor RAAR_{\rm AA}. The result indicates only weak medium effects (RAAR_{\rm AA} \approx 0.7) in peripheral collisions. In central collisions, RAAR_{\rm AA} reaches a minimum of about 0.14 at pT=6p_{\rm T}=6-7GeV/cc and increases significantly at larger pTp_{\rm T}. The measured suppression of high-pTp_{\rm T} particles is stronger than that observed at lower collision energies, indicating that a very dense medium is formed in central Pb-Pb collisions at the LHC.Comment: 15 pages, 5 captioned figures, 3 tables, authors from page 10, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/98

    Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV

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    The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of √s = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pT≥20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60≤pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2≤{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration

    Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

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    Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente
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