679 research outputs found
Propagation on networks: an exact alternative perspective
By generating the specifics of a network structure only when needed
(on-the-fly), we derive a simple stochastic process that exactly models the
time evolution of susceptible-infectious dynamics on finite-size networks. The
small number of dynamical variables of this birth-death Markov process greatly
simplifies analytical calculations. We show how a dual analytical description,
treating large scale epidemics with a Gaussian approximations and small
outbreaks with a branching process, provides an accurate approximation of the
distribution even for rather small networks. The approach also offers important
computational advantages and generalizes to a vast class of systems.Comment: 8 pages, 4 figure
Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics
Motivation: Lateral gene transfer is a major mechanism contributing to bacterial genome dynamics and pathovar emergence via pathogenicity island (PAI) spreading. However, since few of these genomic exchanges are experimentally reproducible, it is difficult to establish evolutionary scenarios for the successive PAI transmissions between bacterial genera. Methods initially developed at the gene and/or nucleotide level for genomics, i.e. comparisons of concatenated sequences, ortholog frequency, gene order or dinucleotide usage, were combined and applied here to homologous PAIs: we call this approach comparative PAI genometrics. Results: YAPI, a Yersinia PAI, and related islands were compared with measure evolutionary relationships between related modules. Through use of our genometric approach designed for tracking codon usage adaptation and gene phylogeny, an ancient inter-genus PAI transfer was oriented for the first time by characterizing the genomic environment in which the ancestral island emerged and its subsequent transfers to other bacterial genera. Contact: [email protected] Supplementary informatio
Is Gravitational Lensing by Intercluster Filaments Always Negligible?
Intercluster filaments negligibly contribute to the weak lensing signal in
general relativity (GR), . In the context of
relativistic modified Newtonian dynamics (MOND) introduced by Bekenstein,
however, a single filament inclined by from the line of
sight can cause substantial distortion of background sources pointing towards
the filament's axis (); this is rigorous
for infinitely long uniform filaments, but also qualitatively true for short
filaments (Mpc), and even in regions where the projected matter
density of the filament is equal to zero. Since galaxies and galaxy clusters
are generally embedded in filaments or are projected on such structures, this
contribution complicates the interpretation of the weak lensing shear map in
the context of MOND. While our analysis is of mainly theoretical interest
providing order-of-magnitude estimates only, it seems safe to conclude that
when modeling systems with anomalous weak lensing signals, e.g. the "bullet
cluster" of Clowe et al., the "cosmic train wreck" of Abell 520 from Mahdavi et
al., and the "dark clusters" of Erben et al., filamentary structures might
contribute in a significant and likely complex fashion. On the other hand, our
predictions of a (conceptual) difference in the weak lensing signal could, in
principle, be used to falsify MOND/TeVeS and its variations.Comment: 11 pages, 6 figures, published versio
Analysis of electron-positron momentum spectra of metallic alloys as supported by first-principles calculations
Electron-positron momentum distributions measured by the coincidence Doppler
broadening method can be used in the chemical analysis of the annihilation
environment, typically a vacancy-impurity complex in a solid. In the present
work, we study possibilities for a quantitative analysis, i.e., for
distinguishing the average numbers of different atomic species around the
defect. First-principles electronic structure calculations self-consistently
determining electron and positron densities and ion positions are performed for
vacancy-solute complexes in Al-Cu, Al-Mg-Cu, and Al-Mg-Cu-Ag alloys. The
ensuing simulated coincidence Doppler broadening spectra are compared with
measured ones for defect identification. A linear fitting procedure, which uses
the spectra for positrons trapped at vacancies in pure constituent metals as
components, has previously been employed to find the relative percentages of
different atomic species around the vacancy [A. Somoza et al. Phys. Rev. B 65,
094107 (2002)]. We test the reliability of the procedure by the help of
first-principles results for vacancy-solute complexes and vacancies in
constituent metals.Comment: Submitted to Physical Review B on September 19 2006. Revised version
submitted on November 8 2006. Published on February 14 200
Adsorption and reaction of CO on (Pd–)Al2O3 and (Pd–)ZrO2: vibrational spectroscopy of carbonate formation
γ-Alumina is widely used as an oxide support in catalysis, and palladium nanoparticles supported by alumina represent one of the most frequently used dispersed metals. The surface sites of the catalysts are often probed via FTIR spectroscopy upon CO adsorption, which may result in the formation of surface carbonate species. We have examined this process in detail utilizing FTIR to monitor carbonate formation on γ-alumina and zirconia upon exposure to isotopically labelled and unlabelled CO and CO2. The same was carried out for well-defined Pd nanoparticles supported on Al2O3 or ZrO2. A water gas shift reaction of CO with surface hydroxyls was detected, which requires surface defect sites and adjacent OH groups. Furthermore, we have studied the effect of Cl synthesis residues, leading to strongly reduced carbonate formation and changes in the OH region (isolated OH groups were partly replaced or were even absent). To corroborate this finding, samples were deliberately poisoned with Cl to an extent comparable to that of synthesis residues, as confirmed by Auger electron spectroscopy. For catalysts prepared from Cl-containing precursors a new CO band at 2164 cm−1 was observed in the carbonyl region, which was ascribed to Pd interacting with Cl. Finally, the FTIR measurements were complemented by quantification of the amount of carbonates formed via chemisorption, which provides a tool to determine the concentration of reactive defect sites on the alumina surface
Structural preferential attachment: Network organization beyond the link
We introduce a mechanism which models the emergence of the universal
properties of complex networks, such as scale independence, modularity and
self-similarity, and unifies them under a scale-free organization beyond the
link. This brings a new perspective on network organization where communities,
instead of links, are the fundamental building blocks of complex systems. We
show how our simple model can reproduce social and information networks by
predicting their community structure and more importantly, how their nodes or
communities are interconnected, often in a self-similar manner.Comment: 4 pages, 3 figures, 1 tabl
Oscillating epidemics in a dynamic network model: stochastic and mean-field analysis
An adaptive network model using SIS epidemic propagation with link-type-dependent link activation and deletion is considered. Bifurcation analysis of the pairwise ODE approximation and the network-based stochastic simulation is carried out, showing that three typical behaviours may occur; namely, oscillations can be observed besides disease-free or endemic steady states. The oscillatory behaviour in the stochastic simulations is studied using Fourier analysis, as well as through analysing the exact master equations of the stochastic model. By going beyond simply comparing simulation results to mean-field models, our approach yields deeper insights into the observed phenomena and help better understand and map out the limitations of mean-field models
An order-to-disorder structural switch activates the FoxM1 transcription factor
Intrinsically disordered transcription factor transactivation domains (TADs) function through structural plasticity, adopting ordered conformations when bound to transcriptional co-regulators. Many transcription factors contain a negative regulatory domain (NRD) that suppresses recruitment of transcriptional machinery through autoregulation of the TAD. We report the solution structure of an autoinhibited NRD-TAD complex within FoxM1, a critical activator of mitotic gene expression. We observe that while both the FoxM1 NRD and TAD are primarily intrinsically disordered domains, they associate and adopt a structured conformation. We identify how Plk1 and Cdk kinases cooperate to phosphorylate FoxM1, which releases the TAD into a disordered conformation that then associates with the TAZ2 or KIX domains of the transcriptional co-activator CBP. Our results support a mechanism of FoxM1 regulation in which the TAD undergoes switching between disordered and different ordered structures
On negative higher-order Kerr effect and filamentation
As a contribution to the ongoing controversy about the role of higher-order
Kerr effect (HOKE) in laser filamentation, we first provide thorough details
about the protocol that has been employed to infer the HOKE indices from the
experiment. Next, we discuss potential sources of artifact in the experimental
measurements of these terms and show that neither the value of the observed
birefringence, nor its inversion, nor the intensity at which it is observed,
appear to be flawed. Furthermore, we argue that, independently on our values,
the principle of including HOKE is straightforward. Due to the different
temporal and spectral dynamics, the respective efficiency of defocusing by the
plasma and by the HOKE is expected to depend substantially on both incident
wavelength and pulse duration. The discussion should therefore focus on
defining the conditions where each filamentation regime dominates.Comment: 22 pages, 11 figures. Submitted to Laser physics as proceedings of
the Laser Physics 2010 conferenc
Novel Bradykinin Analogues Modified in the N-Terminal Part of the Molecule with a Variety of Acyl Substituents
In the current work we present some pharmacological characteristics of ten new analogues of bradykinin (Arg–Pro–Pro–Gly–Phe–Ser–Pro–Phe–Arg) modified in the N-terminal part of the molecule with a variety of acyl substituents. Of the many acylating agents used previously with B2 receptor antagonists, the following residues were chosen: 1-adamantaneacetic acid (Aaa), 1-adamantanecarboxylic acid (Aca), 4-tert-butylbenzoic acid (t-Bba), 4-aminobenzoic acid (Aba), 12-aminododecanoic acid (Adc), succinic acid (Sua), 4-hydroxybenzoic acid, 4-hydroxy-3-methoxybenzoic acid, 3-(4-hydroxyphenyl)propionic acid and 6-hydroxy-2-naphthoic acid. Biological activity of the compounds was assessed in the in vivo rat blood pressure test and the in vitro rat uterus test. Surprisingly, N-terminal substitution of the bradykinin peptide chain itself with aforementioned groups resulted in antagonists of bradykinin in the pressor test and suppressed agonistic potency in the uterotonic test. These interesting findings need further studies as they can be helpful for designing more potent B2 receptor blockers
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