5,357 research outputs found
Anomalous behavior of trapping on a fractal scale-free network
It is known that the heterogeneity of scale-free networks helps enhancing the
efficiency of trapping processes performed on them. In this paper, we show that
transport efficiency is much lower in a fractal scale-free network than in
non-fractal networks. To this end, we examine a simple random walk with a fixed
trap at a given position on a fractal scale-free network. We calculate
analytically the mean first-passage time (MFPT) as a measure of the efficiency
for the trapping process, and obtain a closed-form expression for MFPT, which
agrees with direct numerical calculations. We find that, in the limit of a
large network order , the MFPT behaves superlinearly as with an exponent 3/2 much larger than 1, which is in sharp contrast
to the scaling with , previously obtained
for non-fractal scale-free networks. Our results indicate that the degree
distribution of scale-free networks is not sufficient to characterize trapping
processes taking place on them. Since various real-world networks are
simultaneously scale-free and fractal, our results may shed light on the
understanding of trapping processes running on real-life systems.Comment: 6 pages, 5 figures; Definitive version accepted for publication in
EPL (Europhysics Letters
Trapping in scale-free networks with hierarchical organization of modularity
A wide variety of real-life networks share two remarkable generic topological
properties: scale-free behavior and modular organization, and it is natural and
important to study how these two features affect the dynamical processes taking
place on such networks. In this paper, we investigate a simple stochastic
process--trapping problem, a random walk with a perfect trap fixed at a given
location, performed on a family of hierarchical networks that exhibit
simultaneously striking scale-free and modular structure. We focus on a
particular case with the immobile trap positioned at the hub node having the
largest degree. Using a method based on generating functions, we determine
explicitly the mean first-passage time (MFPT) for the trapping problem, which
is the mean of the node-to-trap first-passage time over the entire network. The
exact expression for the MFPT is calculated through the recurrence relations
derived from the special construction of the hierarchical networks. The
obtained rigorous formula corroborated by extensive direct numerical
calculations exhibits that the MFPT grows algebraically with the network order.
Concretely, the MFPT increases as a power-law function of the number of nodes
with the exponent much less than 1. We demonstrate that the hierarchical
networks under consideration have more efficient structure for transport by
diffusion in contrast with other analytically soluble media including some
previously studied scale-free networks. We argue that the scale-free and
modular topologies are responsible for the high efficiency of the trapping
process on the hierarchical networks.Comment: Definitive version accepted for publication in Physical Review
Orphan Nuclear Receptor Nur77 Inhibits Cardiac Hypertrophic Response to Beta-Adrenergic Stimulation.
The orphan nuclear receptor Nur77 plays critical roles in cardiovascular diseases, and its expression is markedly induced in the heart after beta-adrenergic receptor (β-AR) activation. However, the functional significance of Nur77 in β-AR signaling in the heart remains unclear. By using Northern blot, Western blot, and immunofluorescent staining assays, we showed that Nur77 expression was markedly upregulated in cardiomyocytes in response to multiple hypertrophic stimuli, including isoproterenol (ISO), phenylephrine (PE), and endothelin-1 (ET-1). In a time- and dose-dependent manner, ISO increases Nur77 expression in the nuclei of cardiomyocytes. Overexpression of Nur77 markedly inhibited ISO-induced cardiac hypertrophy by inducing nuclear translocation of Nur77 in cardiomyocytes. Furthermore, cardiac overexpression of Nur77 by intramyocardial injection of Ad-Nur77 substantially inhibited cardiac hypertrophy and ameliorated cardiac dysfunction after chronic infusion of ISO in mice. Mechanistically, we demonstrated that Nur77 functionally interacts with NFATc3 and GATA4 and inhibits their transcriptional activities, which are critical for the development of cardiac hypertrophy. These results demonstrate for the first time that Nur77 is a novel negative regulator for the β-AR-induced cardiac hypertrophy through inhibiting the NFATc3 and GATA4 transcriptional pathways. Targeting Nur77 may represent a potentially novel therapeutic strategy for preventing cardiac hypertrophy and heart failure
PACT-mediated pkr activation acts as a hyperosmotic stress intensity sensor weakening osmoadaptation and enhancing inflammation
The inability of cells to adapt to increased environmental tonicity can lead to inflammatory gene expression and pathogenesis. The Rel family of transcription factors TonEBP and NF-κB p65 play critical roles in the switch from osmoadaptive homeostasis to inflammation, respectively. Here we identified PACT-mediated PKR kinase activation as a marker of the termination of adaptation and initiation of inflammation in Mus musculus embryonic fibroblasts. We found that high stress-induced PACT-PKR activation inhibits the interaction between NF-κB c-Rel and TonEBP essential for the increased expression of TonEBP-dependent osmoprotective genes. This resulted in enhanced formation of TonEBP/NF-κB p65 complexes and enhanced proinflammatory gene expression. These data demonstrate a novel role of c-Rel in the adaptive response to hyperosmotic stress, which is inhibited via a PACT/PKR-dependent dimer redistribution of the Rel family transcription factors. Our results suggest that inhibiting PACT-PKR signaling may prove a novel target for alleviating stress-induced inflammatory diseases
Analytical methods in wineries: is it time to change?
A review of the methods for the most common parameters determined in wine—namely, ethanol, sulfur dioxide, reducing sugars, polyphenols, organic acids, total and volatile acidity, iron, soluble solids, pH, and color—reported in the last 10 years is presented here. The definition of the given parameter, official and usual methods in wineries appear at the beginning of each section, followed by the methods reported in the last decade divided into discontinuous and continuous methods, the latter also are grouped in nonchromatographic and chromatographic methods because of the typical characteristics of each subgroup. A critical comparison between continuous and discontinuous methods for the given parameter ends each section. Tables summarizing the features of the methods and a conclusions section may help users to select the most appropriate method and also to know the state-of-the-art of analytical methods in this area
Interdependent network reciprocity in evolutionary games
Besides the structure of interactions within networks, also the interactions between networks are of the outmost
importance. We therefore study the outcome of the public goods game on two interdependent networks that are
connected by means of a utility function, which determines how payoffs on both networks jointly influence the
success of players in each individual network. We show that an unbiased coupling allows the spontaneous
emergence of interdependent network reciprocity, which is capable to maintain healthy levels of public
cooperation even in extremely adverse conditions. The mechanism, however, requires simultaneous formation of
correlated cooperator clusters on both networks. If this does not emerge or if the coordination process is
disturbed, network reciprocity fails, resulting in the total collapse of cooperation. Network interdependence can
thus be exploited effectively to promote cooperation past the limits imposed by isolated networks, but only if the
coordination between the interdependent networks is not disturbe
SIRT6 protein deacetylase interacts with MYH DNA glycosylase, APE1 endonuclease, and Rad9-Rad1-Hus1 checkpoint clamp
Background: SIRT6, a member of the NAD+-dependent histone/protein deacetylase family, regulates genomic stability, metabolism, and lifespan. MYH glycosylase and APE1 are two base excision repair (BER) enzymes involved in mutation avoidance from oxidative DNA damage. Rad9-Rad1-Hus1 (9-1-1) checkpoint clamp promotes cell cycle checkpoint signaling and DNA repair. BER is coordinated with the checkpoint machinery and requires chromatin remodeling for efficient repair. SIRT6 is involved in DNA double-strand break repair and has been implicated in BER. Here we investigate the direct physical and functional interactions between SIRT6 and BER enzymes. Results: We show that SIRT6 interacts with and stimulates MYH glycosylase and APE1. In addition, SIRT6 interacts with the 9-1-1 checkpoint clamp. These interactions are enhanced following oxidative stress. The interdomain connector of MYH is important for interactions with SIRT6, APE1, and 9-1-1. Mutagenesis studies indicate that SIRT6, APE1, and Hus1 bind overlapping but different sequence motifs on MYH. However, there is no competition of APE1, Hus1, or SIRT6 binding to MYH. Rather, one MYH partner enhances the association of the other two partners to MYH. Moreover, APE1 and Hus1 act together to stabilize the MYH/SIRT6 complex. Within human cells, MYH and SIRT6 are efficiently recruited to confined oxidative DNA damage sites within transcriptionally active chromatin, but not within repressive chromatin. In addition, Myh foci induced by oxidative stress and Sirt6 depletion are frequently localized on mouse telomeres. Conclusions: Although SIRT6, APE1, and 9-1-1 bind to the interdomain connector of MYH, they do not compete for MYH association. Our findings indicate that SIRT6 forms a complex with MYH, APE1, and 9-1-1 to maintain genomic and telomeric integrity in mammalian cells
Met promotes the formation of double minute chromosomes induced by Sei-1 in NIH-3T3 murine fibroblasts
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