2,155 research outputs found

    Image and Volume Segmentation by Water Flow

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    A general framework for image segmentation is presented in this paper, based on the paradigm of water flow. The major water flow attributes like water pressure, surface tension and capillary force are defined in the context of force field generation and make the model adaptable to topological and geometrical changes. A flow-stopping image functional combining edge- and region-based forces is introduced to produce capability for both range and accuracy. The method is assessed qualitatively and quantitatively on synthetic and natural images. It is shown that the new approach can segment objects with complex shapes or weak-contrasted boundaries, and has good immunity to noise. The operator is also extended to 3-D, and is successfully applied to medical volume segmentation

    Inversion formula of multifractal energy dissipation in 3D fully developed turbulence

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    The concept of inverse statistics in turbulence has attracted much attention in the recent years. It is argued that the scaling exponents of the direct structure functions and the inverse structure functions satisfy an inversion formula. This proposition has already been verified by numerical data using the shell model. However, no direct evidence was reported for experimental three dimensional turbulence. We propose to test the inversion formula using experimental data of three dimensional fully developed turbulence by considering the energy dissipation rates in stead of the usual efforts on the structure functions. The moments of the exit distances are shown to exhibit nice multifractality. The inversion formula between the direct and inverse exponents is then verified.Comment: 3 RevTex pages including 3 eps figure

    Distances and classification of amino acids for different protein secondary structures

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    Window profiles of amino acids in protein sequences are taken as a description of the amino acid environment. The relative entropy or Kullback-Leibler distance derived from profiles is used as a measure of dissimilarity for comparison of amino acids and secondary structure conformations. Distance matrices of amino acid pairs at different conformations are obtained, which display a non-negligible dependence of amino acid similarity on conformations. Based on the conformation specific distances clustering analysis for amino acids is conducted.Comment: 15 pages, 8 figure

    A progressive diagonalization scheme for the Rabi Hamiltonian

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    A diagonalization scheme for the Rabi Hamiltonian, which describes a qubit interacting with a single-mode radiation field via a dipole interaction, is proposed. It is shown that the Rabi Hamiltonian can be solved almost exactly using a progressive scheme that involves a finite set of one variable polynomial equations. The scheme is especially efficient for lower part of the spectrum. Some low-lying energy levels of the model with several sets of parameters are calculated and compared to those provided by the recently proposed generalized rotating-wave approximation and full matrix diagonalization.Comment: 8pages, 1 figure, LaTeX. Accepted for publication in J. Phys. B: At. Mol. Opt. Phy

    Reconstructing generalized ghost condensate model with dynamical dark energy parametrizations and observational datasets

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    Observations of high-redshift supernovae indicate that the universe is accelerating at the present stage, and we refer to the cause for this cosmic acceleration as ``dark energy''. In particular, the analysis of current data of type Ia supernovae (SNIa), cosmic large-scale structure (LSS), and the cosmic microwave background (CMB) anisotropy implies that, with some possibility, the equation-of-state parameter of dark energy may cross the cosmological-constant boundary (w=1w=-1) during the recent evolution stage. The model of ``quintom'' has been proposed to describe this w=1w=-1 crossing behavior for dark energy. As a single-real-scalar-field model of dark energy, the generalized ghost condensate model provides us with a successful mechanism for realizing the quintom-like behavior. In this paper, we reconstruct the generalized ghost condensate model in the light of three forms of parametrization for dynamical dark energy, with the best-fit results of up-to-date observational data.Comment: 8 pages, 3 figures; references added; accepted for publication in Mod. Phys. Lett.

    GWAS and co-expression network combination uncovers multigenes with close linkage effects on the oleic acid content accumulation in Brassica napus

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    Background: Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS combination with haplotype analysis has evolved as an effective method to dissect the genetic architecture of complex traits in crop species. Results: We used the 60 K Brassica Infinium SNP array to perform a genome-wide analysis of haplotype blocks associated with oleic acid (C18:1) in rapeseed. Six haplotype regions were identified as significantly associated with oleic acid (C18:1) that mapped to chromosomes A02, A07, A08, C01, C02, and C03. Additionally, whole-genome sequencing of 50 rapeseed accessions revealed three genes (BnmtACP2-A02, BnABCI13-A02 and BnECI1-A02) in the A02 chromosome haplotype region and two genes (BnFAD8-C02 and BnSDP1-C02) in the C02 chromosome haplotype region that were closely linked to oleic acid content phenotypic variation. Moreover, the co-expression network analysis uncovered candidate genes from these two different haplotype regions with potential regulatory interrelationships with oleic acid content accumulation. Conclusions: Our results suggest that several candidate genes are closely linked, which provides us with an opportunity to develop functional haplotype markers for the improvement of the oleic acid content in rapeseed

    Statistical Properties of Charmonium Spectrum and a New Mechanism of J/\psi Suppression

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    The statistical properties of Charmonium energy spectrum determined by the Bethe-Salpeter equation are investigated. It is found that the regular motion of the ccˉc\bar{c} system can be expected at a small value of color screening mass but the chaotic motion at a large one. It is shown that the level mixing due to color screening serves as a new mechanism resulting in the J/ψ\psi suppression. Moreover, this kind of suppression can occur before the color screening mass reaches its critical value for J/ψ\psi dissociation. It implies that a strong J/ψ\psi suppression is possible in the absence of dissociation of J/ψ\psi.Comment: 13 latex pages, 2 figures. Phys. Rev. C in pres

    Four myriapod relatives – but who are sisters? No end to debates on relationships among the four major myriapod subgroups

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    BackgroundPhylogenetic relationships among the myriapod subgroups Chilopoda, Diplopoda, Symphyla and Pauropoda are still not robustly resolved. The first phylogenomic study covering all subgroups resolved phylogenetic relationships congruently to morphological evidence but is in conflict with most previously published phylogenetic trees based on diverse molecular data. Outgroup choice and long-branch attraction effects were stated as possible explanations for these incongruencies. In this study, we addressed these issues by extending the myriapod and outgroup taxon sampling using transcriptome data.ResultsWe generated new transcriptome data of 42 panarthropod species, including all four myriapod subgroups and additional outgroup taxa. Our taxon sampling was complemented by published transcriptome and genome data resulting in a supermatrix covering 59 species. We compiled two data sets, the first with a full coverage of genes per species (292 single-copy protein-coding genes), the second with a less stringent coverage (988 genes). We inferred phylogenetic relationships among myriapods using different data types, tree inference, and quartet computation approaches. Our results unambiguously support monophyletic Mandibulata and Myriapoda. Our analyses clearly showed that there is strong signal for a single unrooted topology, but a sensitivity of the position of the internal root on the choice of outgroups. However, we observe strong evidence for a clade Pauropoda+Symphyla, as well as for a clade Chilopoda+Diplopoda.ConclusionsOur best quartet topology is incongruent with current morphological phylogenies which were supported in another phylogenomic study. AU tests and quartet mapping reject the quartet topology congruent to trees inferred with morphological characters. Moreover, quartet mapping shows that confounding signal present in the data set is sufficient to explain the weak signal for the quartet topology derived from morphological characters. Although outgroup choice affects results, our study could narrow possible trees to derivatives of a single quartet topology. For highly disputed relationships, we propose to apply a series of tests (AU and quartet mapping), since results of such tests allow to narrow down possible relationships and to rule out confounding signal

    Novel role for the innate immune receptor toll-like receptor 4 (TLR4) in the regulation of the wnt signaling pathway and photoreceptor apoptosis

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    Recent evidence has implicated innate immunity in regulating neuronal survival in the brain during stroke and other neurodegenerations. Photoreceptors are specialized light-detecting neurons in the retina that are essential for vision. In this study, we investigated the role of the innate immunity receptor TLR4 in photoreceptors. TLR4 activation by lipopolysaccharide (LPS) significantly reduced the survival of cultured mouse photoreceptors exposed to oxidative stress. With respect to mechanism, TLR4 suppressed Wnt signaling, decreased phosphorylation and activation of the Wnt receptor LRP6, and blocked the protective effect of the Wnt3a ligand. Paradoxically, TLR4 activation prior to oxidative injury protected photoreceptors, in a phenomenon known as preconditioning. Expression of TNFα and its receptors TNFR1 and TNFR2 decreased during preconditioning, and preconditioning was mimicked by TNFα antagonists, but was independent of Wnt signaling. Therefore, TLR4 is a novel regulator of photoreceptor survival that acts through the Wnt and TNFα pathways. © 2012 Yi et al