Analytic continuation by averaging Pad\'e approximants

The ill-posed analytic continuation problem for Green's functions and self-energies is investigated by revisiting the Pad\'{e} approximants technique. We propose to remedy the well-known problems of the Pad\'{e} approximants by performing an average of several continuations, obtained by varying the number of fitted input points and Pad\'{e} coefficients independently. The suggested approach is then applied to several test cases, including Sm and Pr atomic self-energies, the Green's functions of the Hubbard model for a Bethe lattice and of the Haldane model for a nano-ribbon, as well as two special test functions. The sensitivity to numerical noise and the dependence on the precision of the numerical libraries are analysed in detail. The present approach is compared to a number of other techniques, i.e. the non-negative least-square method, the non-negative Tikhonov method and the maximum entropy method, and is shown to perform well for the chosen test cases. This conclusion holds even when the noise on the input data is increased to reach values typical for quantum Monte Carlo simulations. The ability of the algorithm to resolve fine structures is finally illustrated for two relevant test functions.Comment: 10 figure

L'analyse des distributions d'énergie cinétique par la méthode du maximum d'entropie.

Energy is not always fully randomized in an activated molecule because of the existence of dynamical constraints. An analysis of kinetic energy release distributions (KERDs) of dissociation fragments by the maximum entropy method (MEM) provides information on the efficiency of the energy flow between the reaction coordinate and the remaining degrees of freedom during the fragmentation. For example, for barrierless cleavages, large translational energy releases are disfavoured while energy channeling into the rotational and vibrational degrees of freedom of the pair of fragments is increased with respect to a purely statistical partitioning. Hydrogen atom loss reactions provide an exception to this propensity rule. An ergodicity index, F, can be derived. It represents an upper bound to the ratio between two volumes of phase space: that effectively explored during the reaction and that in principle available at the internal energy E. The function F(E) has been found to initially decrease and to level off at high internal energies. For an atom loss reaction, the orbiting transition state version of phase space theory (OTST) is especially valid for low internal energies, low total angular momentum, large reduced mass of the pair of fragments, large rotational constant of the fragment ion, and large polarizability of the released atom. For barrierless dissociations, the major constraint that results from conservation of angular momentum is a propensity to confine the translational motion to a two-dimensional space. For high rotational quantum numbers, the influence of conservation of angular momentum cannot be separated from effects resulting from the curvature of the reaction path. The nonlinear relationship between the average translational energy and the internal energy E is determined by the density of vibrational-rotational states of the pair of fragments and also by non-statistical effects related to the incompleteness of phase space exploration. The MEM analysis of experimental KERDs suggests that many simple reactions can be described by the reaction path Hamiltonian (RPH) model and provides a criterion for the validity of this method. Chemically oriented problems can also be solved by this approach. A few examples are discussed: determination of branching ratios between competitive channels, reactions involving a reverse activation barrier, nonadiabatic mechanisms, and isolated state decay. (c) 2005 Elsevier B.V. All rights reserved

Predominance of Ancestral Lineages of Mycobacterium tuberculosis in India

Molecular epidemiologic findings suggest an ancient focus of TB

Highlights of the 11th International Bordetella Symposium: from Basic Biology to Vaccine Development

ABSTRACT Pertussis is a severe respiratory disease caused by infection with the bacterial pathogen Bordetella pertussis . The disease affects individuals of all ages but is particularly severe and sometimes fatal in unvaccinated young infants. Other Bordetella species cause diseases in humans, animals, and birds. Scientific, clinical, public health, vaccine company, and regulatory agency experts on these pathogens and diseases gathered in Buenos Aires, Argentina from 5 to 8 April 2016 for the 11th International Bordetella Symposium to discuss recent advances in our understanding of the biology of these organisms, the diseases they cause, and the development of new vaccines and other strategies to prevent these diseases. Highlights of the meeting included pertussis epidemiology in developing nations, genomic analysis of Bordetella biology and evolution, regulation of virulence factor expression, new model systems to study Bordetella biology and disease, effects of different vaccines on immune responses, maternal immunization as a strategy to prevent newborn disease, and novel vaccine development for pertussis. In addition, the group approved the formation of an International Bordetella Society to promote research and information exchange on bordetellae and to organize future meetings. A new Bordetella.org website will also be developed to facilitate these goals

Live Attenuated B. pertussis as a Single-Dose Nasal Vaccine against Whooping Cough

Pertussis is still among the principal causes of death worldwide, and its incidence is increasing even in countries with high vaccine coverage. Although all age groups are susceptible, it is most severe in infants too young to be protected by currently available vaccines. To induce strong protective immunity in neonates, we have developed BPZE1, a live attenuated Bordetella pertussis strain to be given as a single-dose nasal vaccine in early life. BPZE1 was developed by the genetic inactivation or removal of three major toxins. In mice, BPZE1 was highly attenuated, yet able to colonize the respiratory tract and to induce strong protective immunity after a single nasal administration. Protection against B. pertussis was comparable to that induced by two injections of acellular vaccine (aPV) in adult mice, but was significantly better than two administrations of aPV in infant mice. Moreover, BPZE1 protected against Bordetella parapertussis infection, whereas aPV did not. BPZE1 is thus an attractive vaccine candidate to protect against whooping cough by nasal, needle-free administration early in life, possibly at birth

Detection of Pathogenic Mycobacteria Based on Functionalized Quantum Dots Coupled with Immunomagnetic Separation

Mycobacteria have always proven difficult to identify due to their low growth rate and fastidious nature. Therefore molecular biology and more recently nanotechnology, have been exploited from early on for the detection of these pathogens. Here we present the first stage of development of an assay incorporating cadmium selenide quantum dots (QDs) for the detection of mycobacterial surface antigens. The principle of the assay is the separation of bacterial cells using magnetic beads coupled with genus-specific polyclonal antibodies and monoclonal antibodies for heparin-binding hemagglutinin. These complexes are then tagged with anti-mouse biotinylated antibody and finally streptavidin-conjugated QDs which leads to the detection of a fluorescent signal. For the evaluation of performance, the method under study was applied on Mycobacterium bovis BCG and Mycobacterium tuberculosis (positive controls), as well as E. coli and Salmonella spp. that constituted the negative controls. The direct observation of the latter category of samples did not reveal fluorescence as opposed to the mycobacteria mentioned above. The minimum detection limit of the assay was defined to 104 bacteria/ml, which could be further decreased by a 1 log when fluorescence was measured with a spectrofluorometer. The method described here can be easily adjusted for any other protein target of either the pathogen or the host, and once fully developed it will be directly applicable on clinical samples

Distinct virulence ranges for infection of mice by Bordetella pertussis revealed by engineering of the sensor-kinase BvgS

The whooping cough agent Bordetella pertussis coordinately regulates the expression of its virulence factors with the two-component system BvgAS. In laboratory conditions, specific chemical modulators are used to trigger phenotypic modulation of B. pertussis from its default virulent Bvg+ phase to avirulent Bvg- or intermediate Bvgi phases, in which no virulence factors or only a subset of them are produced, respectively. Whether phenotypic modulation occurs in the host remains unknown. In this work, recombinant B. pertussis strains harboring BvgS variants were tested in a mouse model of infection and analyzed using transcriptomic approaches. Recombinant BP-BvgΔ65, which is in the Bvgi phase by default and can be up-modulated to the Bvg+ phase in vitro, could colonize the mouse nose but was rapidly cleared from the lungs, while Bvg+-phase strains colonized both organs for up to four weeks. These results indicated that phenotypic modulation, which might have restored the full virulence capability of BP-BvgΔ65, does not occur in mice or is temporally or spatially restricted and has no effect in those conditions. Transcriptomic analyses of this and other recombinant Bvgi and Bvg+-phase strains revealed that two distinct ranges of virulence gene expression allow colonization of the mouse nose and lungs, respectively. We also showed that a recombinant strain expressing moderately lower levels of the virulence genes than its wild type parent was as efficient at colonizing both organs. Altogether, genetic modifications of BvgS generate a range of phenotypic phases, which are useful tools to decipher host-pathogen interactions