7,116 research outputs found
Parallel Metropolis chains with cooperative adaptation
Monte Carlo methods, such as Markov chain Monte Carlo (MCMC) algorithms, have
become very popular in signal processing over the last years. In this work, we
introduce a novel MCMC scheme where parallel MCMC chains interact, adapting
cooperatively the parameters of their proposal functions. Furthermore, the
novel algorithm distributes the computational effort adaptively, rewarding the
chains which are providing better performance and, possibly even stopping other
ones. These extinct chains can be reactivated if the algorithm considers
necessary. Numerical simulations shows the benefits of the novel scheme
Orthogonal parallel MCMC methods for sampling and optimization
Monte Carlo (MC) methods are widely used for Bayesian inference and
optimization in statistics, signal processing and machine learning. A
well-known class of MC methods are Markov Chain Monte Carlo (MCMC) algorithms.
In order to foster better exploration of the state space, specially in
high-dimensional applications, several schemes employing multiple parallel MCMC
chains have been recently introduced. In this work, we describe a novel
parallel interacting MCMC scheme, called {\it orthogonal MCMC} (O-MCMC), where
a set of "vertical" parallel MCMC chains share information using some
"horizontal" MCMC techniques working on the entire population of current
states. More specifically, the vertical chains are led by random-walk
proposals, whereas the horizontal MCMC techniques employ independent proposals,
thus allowing an efficient combination of global exploration and local
approximation. The interaction is contained in these horizontal iterations.
Within the analysis of different implementations of O-MCMC, novel schemes in
order to reduce the overall computational cost of parallel multiple try
Metropolis (MTM) chains are also presented. Furthermore, a modified version of
O-MCMC for optimization is provided by considering parallel simulated annealing
(SA) algorithms. Numerical results show the advantages of the proposed sampling
scheme in terms of efficiency in the estimation, as well as robustness in terms
of independence with respect to initial values and the choice of the
parameters
Chiral Perturbation Theory, the expansion and Regge behaviour determine the structure of the lightest scalar meson
The leading behaviour of Unitarised Chiral Perturbation Theory
distinguishes the nature of the and the . At one loop order the
is a meson, while the is not. However, semi-local
duality between resonances and Regge behaviour cannot be satisfied for larger
, if such a distinction holds. While the at is inevitably
dominated by its di-pion component, Unitarised Chiral Perturbation Theory
beyond one loop order reveals that as increases above 6-8, the
has a sub-dominant fraction up at 1.2 GeV. Remarkably this ensures
semi-local duality is fulfilled for the range of , where the
unitarisation procedure adopted applies.Comment: 22 pages, 8 figures. Version to be published in Physical Review
Voltage-dependent anion-selective channels VDAC2 and VDAC3 are abundant proteins in bovine outer dense fibers, a cytoskeletal component of the sperm flagellum
Outer dense fibers (ODF) are specific subcellular components of the sperm flagellum. The functions of ODF have not yet been clearly elucidated. We have investigated the protein composition of purified ODF from bovine spermatozoa and found that one of the most abundant proteins is a 30-32-kDa polypeptide. This protein was analyzed by sequencing peptides derived following limited proteolysis. Peptide sequences were found to match VDAC2 and VDAC3. VDACs (voltage-dependent, anion-selective channels) or eukaryotic porins are a group of proteins first identified in the mitochondrial outer membrane that are able to form hydrophilic pore structures in membranes. In mammals, three VDAC isoforms (VDAC1, -2, -3) have been identified by cDNA cloning and sequencing. Antibodies against synthetic peptides specific for the three mammal VDAC isoforms were generated in rabbits. Their specificity was demonstrated by immunoblotting using recombinant VDAC1, -2, and -3. In protein extracts of bovine spermatozoa, VDAC1, -2, and -3 were detected by specific antibodies, while only VDAC2 and -3 were found as solubilized proteins derived from purified bovine ODFs. Immunofluorescence microscopy of spermatozoa revealed that anti-VDAC2 and anti-VDAC3 antibodies clearly bound to the sperm flagellum, in particular to the ODF. Transmission electron immunomicroscopy supported the finding that VDAC2 protein is abundant in the ODF. Since the ODF does not have any known membranous structure, it is tempting to speculate that VDAC2 and VDAC3 might have an alternative structural organization and different functions in ODF than in mitochondria
Anisotropic pinning enhancement in Nb films with arrays of submicrometric Ni lines
Arrays of submicrometric Ni lines have been fabricated in superconducting Nb films by electron beam lithography. In the mixed state, these arrays induce strong anisotropy in the dissipation behavior. The dissipation is reduced several orders of magnitude, in the whole applied magnetic field range, when the vortex motion is perpendicular to the Ni lines (applied current parallel to them) in comparison with dissipation of vortices moving parallel to the lines. In addition, for the samples studied in this work, a change in the slope of the rho(B) curves is observed when the vortices move perpendicular to the lines and the vortex lattice parameter matches the width of the Ni lines
Layered adaptive importance sampling
Monte Carlo methods represent the de facto standard for approximating complicated integrals involving multidimensional target distributions. In order to generate random realizations from the target distribution, Monte Carlo techniques use simpler proposal probability densities to draw candidate samples. The performance of any such method is strictly related to the specification of the proposal distribution, such that unfortunate choices easily wreak havoc on the resulting estimators. In this work, we introduce a layered (i.e., hierarchical) procedure to generate samples employed within a Monte Carlo scheme. This approach ensures that an appropriate equivalent proposal density is always obtained automatically (thus eliminating the risk of a catastrophic performance), although at the expense of a moderate increase in the complexity. Furthermore, we provide a general unified importance sampling (IS) framework, where multiple proposal densities are employed and several IS schemes are introduced by applying the so-called deterministic mixture approach. Finally, given these schemes, we also propose a novel class of adaptive importance samplers using a population of proposals, where the adaptation is driven by independent parallel or interacting Markov chain Monte Carlo (MCMC) chains. The resulting algorithms efficiently combine the benefits of both IS and MCMC methods.Peer reviewe
Kinetic behavior of Desulfovibrio gigas aldehyde oxidoreductase encapsulated in reverse micelles
Biochemical and Biophysical Research Communications 308 (2003) 73–78We report the kinetic behavior of the enzyme aldehyde oxidoreductase (AOR) from the sulfate reducing bacterium Desulfovibrio
gigas (Dg) encapsulated in reverse micelles of sodium bis-(2-ethylhexyl) sulfosuccinate in isooctane using benzaldehyde, octaldehyde,
and decylaldehyde as substrates. Dg AOR is a 200-kDa homodimeric protein that catalyzes the conversion of aldehydes to carboxylic
acids. Ultrasedimentation analysis of Dg AOR-containing micelles showed the presence of 100-kDa molecular weight species, confirming that the Dg AOR subunits can be dissociated. UV–visible spectra of encapsulated Dg AOR are indistinguishable
from the enzyme spectrum in solution, suggesting that both protein fold and metal cofactor are kept intact upon encapsulation. The catalytic constant (kcat) profile as a function of the micelle size W0 (W0 ¼ ½H2O /[AOT]) using benzaldehyde as substrate showed two bell-shaped activity peaks at W0 ¼ 20 and 26. Furthermore, enzymatic activity for octaldehyde and decylaldehyde was detected only in reverse micelles. Like for the benzaldehyde kinetics, two peaks with both similar kcat values and W0 positions were obtained. EPR studies using spin-labeled reverse micelles indicated that octaldehyde and benzaldehyde are intercalated in the micelle membrane.
This suggests that, though Dg AOR is found in the cytoplasm of bacterial cells, the enzyme may catalyze the reaction of substrates incorporated into a cell membrane
Limits on WWgamma and WWZ Couplings from W Boson Pair Production
The results of a search for W boson pair production in pbar-p collisions at
sqrt{s}=1.8 TeV with subsequent decay to emu, ee, and mumu channels are
presented. Five candidate events are observed with an expected background of
3.1+-0.4 events for an integrated luminosity of approximately 97 pb^{-1}.
Limits on the anomalous couplings are obtained from a maximum likelihood fit of
the E_T spectra of the leptons in the candidate events. Assuming identical
WWgamma and WWZ couplings, the 95 % C.L. limits are -0.62<Delta_kappa<0.77
(lambda = 0) and -0.53<lambda<0.56 (Delta_kappa = 0) for a form factor scale
Lambda = 1.5 TeV.Comment: 10 pages, 1 figure, submitted to Physical Review
Pine Pitch Canker and Insects: Regional Risks, Environmental Regulation, and Practical Management Options
Producción CientíficaPine pitch canker (PPC), caused by the pathogenic fungus Fusarium circinatum (Nirenberg
and O’ Donnell), is a serious threat to pine forests globally. The recent introduction of the pathogen to Southern Europe and its spread in Mediterranean region is alarming considering the immense
ecological and economic importance of pines in the region. Pines in forests and nurseries can be
infected, resulting in severe growth losses and mortality. The pathogen is known to spread in plants
for planting and in seeds, and results from recent studies have indicated that F. circinatum may also
spread through phoretic associations with certain insects. With this review, we aim to expand the
current understanding of the risk of insect-mediated spread of PPC in different parts of Europe.
Through the joint action of a multinational researcher team, we collate the existing information about
the insect species spectrum in different biogeographic conditions and scrutinize the potential of
these insects to transmit F. circinatum spores in forests and nurseries. We also discuss the impact of
environmental factors and forest management in this context. We present evidence for the existence of
a high diversity of insects with potential to weaken pines and disseminate PPC in Europe, including
several common beetle species. In many parts of Europe, temperatures are projected to rise, which
may promote the activity of several insect species, supporting multivoltinism and thus, further
amplifying the risk of insect-mediated dissemination of PPC. Integrated pest management (IPM)
solutions that comply with forest management practices need to be developed to reduce this risk.
We recommend careful monitoring of insect populations as the basis for successful IPM. Improved
understanding of environmental control of the interaction between insects, the pathogen, and host
trees is needed in order to support development of bio-rational strategies to safeguard European pine
trees and forests against F. circinatum in future.European Cooperation in Science and Technology (COST Action FP1406 PINESTRENGTH)Ministerio de Economía, Industria y Competitividad - Fondo Europeo de Desarrollo Regional (project AGL2015-69370-R)Portuguese Foundation for Science and Technology (contract IF/00471/2013/CP1203/CT0001)Russian Foundation for Basic Research (grant 17-04-01486)Saint Petersburg State Polytechnical University (project 2019-0420
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