Simplifying the mosaic description of DNA sequences

By using the Jensen-Shannon divergence, genomic DNA can be divided into compositionally distinct domains through a standard recursive segmentation procedure. Each domain, while significantly different from its neighbours, may however share compositional similarity with one or more distant (non--neighbouring) domains. We thus obtain a coarse--grained description of the given DNA string in terms of a smaller set of distinct domain labels. This yields a minimal domain description of a given DNA sequence, significantly reducing its organizational complexity. This procedure gives a new means of evaluating genomic complexity as one examines organisms ranging from bacteria to human. The mosaic organization of DNA sequences could have originated from the insertion of fragments of one genome (the parasite) inside another (the host), and we present numerical experiments that are suggestive of this scenario.Comment: 16 pages, 1 figure, Accepted for publication in Phys. Rev.

On the reliability of merger-trees and the mass growth histories of dark matter haloes

We have used merger trees realizations to study the formation of dark matter haloes. The construction of merger-trees is based on three different pictures about the formation of structures in the Universe. These pictures include: the spherical collapse (SC), the ellipsoidal collapse (EC) and the non-radial collapse (NR). The reliability of merger-trees has been examined comparing their predictions related to the distribution of the number of progenitors, as well as the distribution of formation times, with the predictions of analytical relations. The comparison yields a very satisfactory agreement. Subsequently, >.........Comment: A&SS Accepte

Merger rates of dark matter haloes: a comparison between EPS and N-body results

We calculate merger rates of dark matter haloes using the Extended Press-Schechter approximation (EPS) for the Spherical Collapse (SC) and the Ellipsoidal Collapse (EC) models. Merger rates have been calculated for masses in the range $10^{10}M_{\odot}\mathrm{h}^{-1}$ to $10^{14}M_{\odot}\mathrm{h}^{-1}$ and for redshifts $z$ in the range 0 to 3 and they have been compared with merger rates that have been proposed by other authors as fits to the results of N-body simulations. The detailed comparison presented here shows that the agreement between the analytical models and N-body simulations depends crucially on the mass of the descendant halo. For some range of masses and redshifts either SC or EC models approximate satisfactory the results of N-body simulations but for other cases both models are less satisfactory or even bad approximations. We showed, by studying the parameters of the problem that a disagreement --if it appears-- does not depend on the values of the parameters but on the kind of the particular solution used for the distribution of progenitors or on the nature of EPS methods. Further studies could help to improve our understanding about the physical processes during the formation of dark matter haloes.Comment: 29 pages, 9 figure

assessment of disease burden in the phase iii celestial trial of cabozantinib c versus placebo p in advanced hepatocellular carcinoma hcc

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On the spin distributions of Λ\LambdaCDM haloes

We used merger trees realizations, predicted by the extended Press-Schechter theory, in order to study the growth of angular momentum of dark matter haloes. Our results showed that: 1) The spin parameter $\lambda'$ resulting from the above method, is an increasing function of the present day mass of the halo. The mean value of $\lambda'$ varies from 0.0343 to 0.0484 for haloes with present day masses in the range of $10^9\mathrm{h}^{-1}M_{\odot}$ to $10^{14}\mathrm{h}^{-1}M_{\odot}$. 2)The distribution of $\lambda'$ is close to a log-normal, but, as it is already found in the results of N-body simulations, the match is not satisfactory at the tails of the distribution. A new analytical formula that approximates the results much more satisfactorily is presented. 3) The distribution of the values of $\lambda'$ depends only weakly on the redshift. 4) The spin parameter of an halo depends on the number of recent major mergers. Specifically the spin parameter is an increasing function of this number.Comment: 10 pages, 8 figure

Temporal, spatial, and structural patterns of adult trembling aspen and white spruce mortality in Quebec's boreal forest

Temporal, spatial, and structural patterns of adult trembling aspen (Populus tremuloides Michx.) and white spruce (Picea glauca (Moench) Voss) mortality were studied in intact 150-year-old stands in the southwestern boreal forest of Quebec. For both species, mortality decreases (number of dead trees/total number of trees) with distance from the lake edge until 100-150 m, from which point it slightly increases. Strong peaks in mortality were found for 40- to 60-year-old aspen mainly between 1974 and 1992. Such mortality in relatively young aspen is likely related to competition for light from the dominant canopy trees. Also, the recruitment of this young aspen cohort is presumably the result of a stand breakup that occurred when the initial aspen-dominated stand was between 90 and 110 years old. For spruce, strong peaks in mortality were found in 110- to 150-year-old trees and they occurred mainly after 1980. No clear explanation could be found for these peaks, but we suggest that they may be related to senescence or weakening of the trees following the last spruce budworm outbreak. Suppressed and codominant aspen had a much higher mortality ratio than spruce in the same height class, while more surprisingly, no difference in mortality rate was found between dominant trees of the two species. Most spruce trees were found as standing dead, which leads us to reject the hypothesis that windthrow is an important cause of mortality for spruce in our forests

Correlations of structural, magnetic, and dielectric properties of undoped and doped CaCu3Ti4O12

The present work reports synthesis, as well as a detailed and careful characterization of structural, magnetic, and dielectric properties of differently tempered undoped and doped CaCu3Ti4O12 (CCTO) ceramics. For this purpose, neutron and x-ray powder diffraction, SQUID measurements, and dielectric spectroscopy have been performed. Mn-, Fe-, and Ni-doped CCTO ceramics were investigated in great detail to document the influence of low-level doping with 3d metals on the antiferromagnetic structure and dielectric properties. In the light of possible magnetoelectric coupling in these doped ceramics, the dielectric measurements were also carried out in external magnetic fields up to 7 T, showing a minor but significant dependence of the dielectric constant on the applied magnetic field. Undoped CCTO is well-known for its colossal dielectric constant in a broad frequency and temperature range. With the present extended characterization of doped as well as undoped CCTO, we want to address the question why doping with only 1% Mn or 0.5% Fe decreases the room-temperature dielectric constant of CCTO by a factor of ~100 with a concomitant reduction of the conductivity, whereas 0.5% Ni doping changes the dielectric properties only slightly. In addition, diffraction experiments and magnetic investigations were undertaken to check for possible correlations of the magnitude of the colossal dielectric constants with structural details or with magnetic properties like the magnetic ordering, the Curie-Weiss temperatures, or the paramagnetic moment. It is revealed, that while the magnetic ordering temperature and the effective moment of all investigated CCTO ceramics are rather similar, there is a dramatic influence of doping and tempering time on the Curie-Weiss constant.Comment: 10 pages, 11 figure

The dynamics of quark-gluon plasma and AdS/CFT

In these pedagogical lectures, we present the techniques of the AdS/CFT correspondence which can be applied to the study of real time dynamics of a strongly coupled plasma system. These methods are based on solving gravitational Einstein's equations on the string/gravity side of the AdS/CFT correspondence. We illustrate these techniques with applications to the boost-invariant expansion of a plasma system. We emphasize the common underlying AdS/CFT description both in the large proper time regime where hydrodynamic dynamics dominates, and in the small proper time regime where the dynamics is far from equilibrium. These AdS/CFT methods provide a fascinating arena interrelating General Relativity phenomenae with strongly coupled gauge theory physics.Comment: 35 pages, 3 figures. Lectures at the 5th Aegean summer school, `From gravity to thermal gauge theories: the AdS/CFT correspondence'. To appear in the proceedings in `Lecture Notes in Physics