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  • 1
    Publication Date: 2015-05-10
    Description: Massive young star clusters contain dozens or hundreds of massive stars that inject mechanical energy in the form of winds and supernova explosions, producing an outflow which expands into their surrounding medium, shocking it and forming structures called superbubbles. The regions of shocked material can have temperatures in excess of 10 6  K, and emit mainly in thermal X-rays (soft and hard). This X-ray emission is strongly affected by the action of thermal conduction, as well as by the metallicity of the material injected by the massive stars. We present three-dimensional numerical simulations exploring these two effects, metallicity of the stellar winds and supernova explosions, as well as thermal conduction.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 2
    Publication Date: 2015-10-15
    Description: We present the results of the multi-frequency scatter time measurements for 10 radio pulsars that were relatively less studied in this regard. The observations were performed using the Giant Metrewave Radio Telescope at the observing frequencies of 150, 235, 325, 610 and 1060 MHz. The data we collected, in conjunction with the results from other frequencies published earlier, allowed us to estimate the scatter time frequency scaling indices for eight of these sources. For PSR J1852–0635, it became evident that its profile undergoes a strong evolution with frequency, which makes the scatter time measurements difficult to perform, and for PSR J1835–1020 we were able to obtain reliable pulse broadening estimates at only two frequencies. We used the eight frequency scaling indices to estimate both: the electron density fluctuation strengths along the respective lines of sight and the standardized amount of scattering at the frequency of 1 GHz. Combining the new data with the results published earlier by Lewandowski et al., we revisited the scaling index versus the dispersion measure (DM) relation, and similarly to some of the earlier studies, we show that the average value of the scaling index deviates from the theoretical predictions for large-DM pulsars; however, it reaches the magnitude claimed by Löhmer et al. only for pulsars with very large DMs (〉650 pc cm –3 ). We also investigated the dependence of the scattering strength indicators on the pulsar distance, DM and the position of the source in the Milky Way Galaxy.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 3
    Publication Date: 2015-04-12
    Description: Background: The performance of the single particle tracking (SPT) nearest-neighbor algorithm is determined by parameters that need to be set according to the characteristics of the time series under study. Inhomogeneous systems, where these characteristics fluctuate spatially, are poorly tracked when parameters are set globally. Results: We present a novel SPT approach that adapts the well-known nearest-neighbor tracking algorithm to the local density of particles to overcome the problems of inhomogeneity. Conclusions: We demonstrate the performance improvement provided by the proposed method using numerical simulations and experimental data and compare its performance with state of the art SPT algorithms. Availability and implementation : The algorithms proposed here, are released under the GNU General Public License and are freely available on the web at http://sourceforge.net/p/adaptivespt . Contact: javier.mazzaferri@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 4
    Publication Date: 2012-07-17
    Description: Natural temperature gradient (NTG) can be a significant problem in thermal sap flow measurements, particularly in dry environments with sparse vegetation. To resolve this problem, we propose a novel correction method called cyclic heat dissipation (CHD) in its thermal dissipation probe (TDP) application. The CHD method is based on cyclic, switching ON/OFF power schema measurements and a three-exponential model, extrapolating measured signal to steady state thermal equilibrium. The extrapolated signal OFF represents NTG, whereas the extrapolated signal ON represents standard TDP signal, biased by NTG. Therefore, subtraction of the OFF signal from the ON signal allows defining the unbiased TDP signal, finally processed according to standard Granier calibration. The in vivo Kalahari measurements were carried out in three steps on four different tree species, first as NTG, then as standard TDP and finally in CHD mode, each step for ~1–2 days. Afterwards, each tree was separated from its stem following modified Roberts' (1977) procedure, and CHD verification was applied. The typical NTG varying from ~0.5 °C during night-time to –1 °C during day-time, after CHD correction, resulted in significant reduction of sap flux densities ( J p ) as compared with the standard TDP, particularly distinct for low J p . The verification of the CHD method indicated ~20% agreement with the reference method, largely dependent on the sapwood area estimate. The proposed CHD method offers the following advantages: (i) in contrast to any other NTG correction method, it removes NTG bias from the measured signal by using in situ, extrapolated to thermal equilibrium signal; (ii) it does not need any specific calibration making use of the standard Granier calibration; (iii) it provides a physical background to the proposed NTG correction; (iv) it allows for power savings; (v) it is not tied to TDP, and so can be adapted to other thermal methods. In its current state, the CHD data processing is not yet fully automated.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 5
    Publication Date: 2013-12-06
    Description: We present 3D hydrodynamical simulations of the Galactic supernova remnant G352.7–0.1. This remnant is peculiar for having a shell-like inner ring structure and an outer arc in radio observations. In our model, the supernova explosion producing the remnant occurs inside and near the border of a spherical cloud with a density higher than that of the surrounding interstellar medium. A blowout is produced when the remnant reaches the border of the cloud. We have then used the results of our hydrodynamical simulations to calculate synthetic synchrotron radio emission maps, as well as synthetic X-ray maps. For some combinations of the particle acceleration mechanism and the direction of the line of sight, our radio maps display the peculiar morphology of G352.7–0.1 and reproduce the correct relative sizes of the main observed features. At the same time, the calculated X-ray maps reproduce the centrally peaked morphology of the observations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 6
    Publication Date: 2014-10-10
    Description: In this paper, we develop a semi-analytic model of a supernova which goes off in the centre of a stellar cluster. The supernova remnant interacts with a stratified, pre-existent outflow produced by the winds of the cluster stars. We compare our semi-analytic model with numerical simulations using the spherically symmetric Euler equations with appropriate mass and energy source terms. We find good agreement between these two approaches, and we find that for typical parameters the blast wave is likely to reach the Taylor–Sedov regime outside the cluster radius. We also calculate the predicted X-ray luminosity of the flow as a function of time, and we obtain its dependence on the outer radius and the number of stars of the cluster.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 7
    Publication Date: 2014-06-06
    Description: We present new 3D numerical simulations for Kepler's supernova remnant. In this work we revisit the possibility that the asymmetric shape of the remnant in X-rays is the product of a Type Ia supernova explosion which occurs inside the wind bubble previously created by an AGB companion star. Due to the large peculiar velocity of the system, the interaction of the strong AGB wind with the interstellar medium results in a bow shock structure. In this new model we propose that the AGB wind is anisotropic, with properties such as mass-loss rate and density having a latitude dependence, and that the orientation of the polar axis of the AGB star is not aligned with the direction of motion. The ejecta from the Type Ia supernova explosion is modelled using a power-law density profile, and we let the remnant evolve for 400 yr. We computed synthetic X-ray maps from the numerical results. We find that the estimated size and peculiar X-ray morphology of Kepler's supernova remnant are well reproduced by considering an AGB mass-loss rate of 10 –5 M  yr –1 , a wind terminal velocity of 10 km s –1 , an ambient medium density of 10 –3  cm –3 and an explosion energy of 7 10 50  erg. The obtained total X-ray luminosity of the remnant in this model reaches 6 10 50  erg, which is within a factor of 2 of the observed value, and the time evolution of the luminosity shows a rate of decrease in recent decades of ~2.4 per cent yr –1 that is consistent with the observations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 8
    Publication Date: 2014-07-19
    Description: Disease progression in cancer can vary substantially between patients. Yet, patients often receive the same treatment. Recently, there has been much work on predicting disease progression and patient outcome variables from gene expression in order to personalize treatment options. Despite first diagnostic kits in the market, there are open problems such as the choice of random gene signatures or noisy expression data. One approach to deal with these two problems employs protein–protein interaction networks and ranks genes using the random surfer model of Google’s PageRank algorithm. In this work, we created a benchmark dataset collection comprising 25 cancer outcome prediction datasets from literature and systematically evaluated the use of networks and a PageRank derivative, NetRank, for signature identification. We show that the NetRank performs significantly better than classical methods such as fold change or t -test. Despite an order of magnitude difference in network size, a regulatory and protein–protein interaction network perform equally well. Experimental evaluation on cancer outcome prediction in all of the 25 underlying datasets suggests that the network-based methodology identifies highly overlapping signatures over all cancer types, in contrast to classical methods that fail to identify highly common gene sets across the same cancer types. Integration of network information into gene expression analysis allows the identification of more reliable and accurate biomarkers and provides a deeper understanding of processes occurring in cancer development and progression.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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  • 9
    Publication Date: 2013-06-30
    Description: The Giant Metrewave Radio Telescope Epoch of Reionization experiment is an ongoing effort to measure the power spectrum from neutral hydrogen at high redshift. We have previously reported an upper limit of (70 mK) 2 at wavenumbers of k 0.65 h Mpc –1 using a basic piecewise-linear foreground subtraction. In this paper, we explore the use of a singular value decomposition to remove foregrounds with fewer assumptions about the foreground structure. Using this method, we also quantify, for the first time, the signal loss due to the foreground filter and present new power spectra adjusted for this loss, providing a revised measurement of a 2 upper limit at (248 mK) 2 for k  = 0.50 h Mpc –1 . While this revised limit is larger than previously reported, we believe it to be more robust and still represents the best current constraint on reionization at z 8.6.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 10
    Publication Date: 2013-10-29
    Description: Hypertension, the most frequently diagnosed clinical condition world-wide, predisposes individuals to morbidity and mortality, yet its underlying pathological etiologies are poorly understood. So far, a large number of quantitative trait loci (QTLs) have been identified in both humans and animal models, but how they function together in determining overall blood pressure (BP) in physiological settings is unknown. Here, we systematically and comprehensively performed pair-wise comparisons of individual QTLs to create a global picture of their functionality in an inbred rat model. Rather than each of numerous QTLs contributing to infinitesimal BP increments, a modularized pattern arises: two epistatic ‘blocks’ constitute basic functional ‘units’ for nearly all QTLs, designated as epistatic module 1 (EM1) and EM2. This modularization dictates the magnitude and scope of BP effects. Any EM1 member can contribute to BP additively to that of EM2, but not to those of the same module. Members of each EM display epistatic hierarchy, which seems to reflect a related functional pathway. Rat homologues of 11 human BP QTLs belong to either EM1 or EM2. Unique insights emerge into the novel genetic mechanism and hierarchy determining BP in the Dahl salt-sensitive SS/Jr (DSS) rat model that implicate a portion of human QTLs. Elucidating the pathways underlying EM1 and EM2 may reveal the genetic regulation of BP.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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