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 1/Nc{1/N_c} expansion and Regge behaviour determine the structure of the lightest scalar meson

The leading $1/N_c$ behaviour of Unitarised Chiral Perturbation Theory distinguishes the nature of the $\rho$ and the $\sigma$. At one loop order the $\rho$ is a ${\bar q}q$ meson, while the $\sigma$ is not. However, semi-local duality between resonances and Regge behaviour cannot be satisfied for larger $N_c$, if such a distinction holds. While the $\sigma$ at $N_c=3$ is inevitably dominated by its di-pion component, Unitarised Chiral Perturbation Theory beyond one loop order reveals that as $N_c$ increases above 6-8, the $\sigma$ has a sub-dominant ${\bar q}q$ fraction up at 1.2 GeV. Remarkably this ensures semi-local duality is fulfilled for the range of $N_c \lesssim 15$, where the unitarisation procedure adopted applies.Comment: 22 pages, 8 figures. Version to be published in Physical Review

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

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

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