Alternative determinism principle for topological analysis of chaos

The topological analysis of chaos based on a knot-theoretic characterization of unstable periodic orbits has proved a powerful method, however knot theory can only be applied to three-dimensional systems. Still, the core principles upon which this approach is built, determinism and continuity, apply in any dimension. We propose an alternative framework in which these principles are enforced on triangulated surfaces rather than curves and show that in dimension three our approach numerically predicts the correct topological entropies for periodic orbits of the horseshoe map.Comment: Accepted for publication as Rapid Communication in Physical Review

Reduction of Electron Beam Induced Radiation Damage of Organic Material by Cooling to 4 K (Cryo Electron Microscopy)

Structure investigations of organic, in particular biological, material are frequently performed with a strong electron beam. If the dose is higher than le/Å2, as required e.g. for high resolution electron microscopy, the results are strongly influenced by radiation damage. There are no means for preventing breaking of chemical bonds and ionizing of atoms and fractures of molecules due to the electron impact. The secondary processes, however, such as diffusion or evaporation of the fragments, can be strongly reduced by cooling the specimen to 4 K (cryoprotection). A suitable instrument for experimenting with cryoprotection is a microscope equipped with a superconducting lens system. Topics relevant for cryomicroscopy are: instrumentation; determination of cryoprotection factors of various materials by electron diffraction; direct imaging in particular for information on the steric structure of the material; preparation conditions for an effective cryoprotection. Though the knowledge of the physics and chemistry causing radiation damage at 4 K is still limited, a useful application of cryoprotection is already possible

IMGT®, the international ImMunoGeneTics information system®

IMGT®, the international ImMunoGeneTics information system® (http://www.imgt.org), was created in 1989 by Marie-Paule Lefranc, Laboratoire d'ImmunoGénétique Moléculaire LIGM (Université Montpellier 2 and CNRS) at Montpellier, France, in order to standardize and manage the complexity of immunogenetics data. The building of a unique ontology, IMGT-ONTOLOGY, has made IMGT® the global reference in immunogenetics and immunoinformatics. IMGT® is a high-quality integrated knowledge resource specialized in the immunoglobulins or antibodies, T cell receptors, major histocompatibility complex, of human and other vertebrate species, proteins of the IgSF and MhcSF, and related proteins of the immune systems of any species. IMGT® provides a common access to standardized data from genome, proteome, genetics and 3D structures. IMGT® consists of five databases (IMGT/LIGM-DB, IMGT/GENE-DB, IMGT/3Dstructure-DB, etc.), fifteen interactive online tools for sequence, genome and 3D structure analysis, and more than 10 000 HTML pages of synthesis and knowledge. IMGT® is used in medical research (autoimmune diseases, infectious diseases, AIDS, leukemias, lymphomas and myelomas), veterinary research, biotechnology related to antibody engineering (phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (clonalities, detection and follow-up of residual diseases) and therapeutical approaches (graft, immunotherapy, vaccinology). IMGT is freely available at http://www.imgt.org

Topological signature of deterministic chaos in short nonstationary signals from an optical parametric oscillator

Although deterministic chaos has been predicted to occur in the triply resonant optical parametric oscillator (TROPO) fifteen years ago, experimental evidence of chaotic behavior in this system has been lacking so far, in marked contrast with most nonlinear systems, where chaos has been actively tracked and found. This situation is probably linked to the high sensitivity of the TROPO to perturbations, which adversely affects stationary operation at high power. We report the experimental observation in this system of a burst of irregular behavior of duration 80 microseconds. Although the system is highly nonstationary over this time interval, a topological analysis allows us to extract a clearcut signature of deterministic chaos from a time series segment of only 9 base cycles (3 microseconds). This result suggests that nonstationarity is not necessarily an obstacle to the characterization of chaos

Recovering probabilities for nucleotide trimming processes for T cell receptor TRA and TRG V-J junctions analyzed with IMGT tools

<p>Abstract</p> <p>Background</p> <p>Nucleotides are trimmed from the ends of variable (V), diversity (D) and joining (J) genes during immunoglobulin (IG) and T cell receptor (TR) rearrangements in B cells and T cells of the immune system. This trimming is followed by addition of nucleotides at random, forming the N regions (N for nucleotides) of the V-J and V-D-J junctions. These processes are crucial for creating diversity in the immune response since the number of trimmed nucleotides and the number of added nucleotides vary in each B or T cell. IMGT^®sequence analysis tools, IMGT/V-QUEST and IMGT/JunctionAnalysis, are able to provide detailed and accurate analysis of the final observed junction nucleotide sequences (tool "output"). However, as trimmed nucleotides can potentially be replaced by identical N region nucleotides during the process, the observed "output" represents a <it>biased </it>estimate of the "true trimming process."</p> <p>Results</p> <p>A probabilistic approach based on an analysis of the standardized tool "output" is proposed to infer the probability distribution of the "true trimmming process" and to provide plausible biological hypotheses explaining this process. We collated a benchmark dataset of TR alpha (TRA) and TR gamma (TRG) V-J rearranged sequences and junctions analysed with IMGT/V-QUEST and IMGT/JunctionAnalysis, the nucleotide sequence analysis tools from IMGT^®, the international ImMunoGeneTics information system^®, <url>http://imgt.cines.fr</url>. The standardized description of the tool output is based on the IMGT-ONTOLOGY axioms and concepts. We propose a simple first-order model that attempts to transform the observed "output" probability distribution into an estimate closer to the "true trimming process" probability distribution. We use this estimate to test the hypothesis that Poisson processes are involved in trimming. This hypothesis was not rejected at standard confidence levels for three of the four trimming processes: TRAV, TRAJ and TRGV.</p> <p>Conclusion</p> <p>By using trimming of rearranged TR genes as a benchmark, we show that a probabilistic approach, applied to IMGT^®standardized tool "outputs" opens the way to plausible hypotheses on the events involved in the "true trimming process" and eventually to an exact quantification of trimming itself. With increasing high-throughput of standardized immunogenetics data, similar probabilistic approaches will improve understanding of processes so far only characterized by the "output" of standardized tools.</p

Prospects for annihilating dark matter in the inner galactic halo by the Cherenkov Telescope Array

We compute the sensitivity to dark matter annihilations for the forthcoming large Cherenkov Telescope Array (CTA) in several primary channels and over a range of dark matter masses from 50 GeV up to 80 TeV. For all channels, we include inverse Compton scattering of e± by dark matter annihilations on the ambient photon background, which yields substantial contributions to the overall γ-ray flux. We improve the analysis over previous work by: (i) implementing a spectral and morphological analysis of the γ-ray emission; (ii) taking into account the most up-to-date cosmic ray background obtained from a full CTA Monte Carlo simulation and a description of the diffuse astrophysical emission; and (iii) including the systematic uncertainties in the rich observational CTA data sets. We find that our spectral and morphological analysis improves the CTA sensitivity by roughly a factor 2. For the hadronic channels, CTA will be able to probe thermal dark matter candidates over a broad range of masses if the systematic uncertainties in the data sets will be controlled better than the percent level. For the leptonic modes, the CTA sensitivity will be well below the thermal value of the annihilation cross-section. In this case, even with larger systematics, thermal dark matter candidates up to masses of a few TeV will be easily studied

Cooperative oscillation of non-degenerate transverse modes in an optical system: multimode operation in parametric oscillators

We show experimentally that parametric interaction can induce a cooperative oscillation of non simultaneously resonant transverse modes in an optical parametric oscillator. More generally, this effect is expected to occur in any spatially extended system subjected to boundary conditions where nonlinear wave mixing of two nonresonant spatial modes can generate a resonant oscillation

To what extent do fiscal regimes equalize opportunities for income acquisition among citizens?.

This paper employs the theory of equality of opportunity, described in Roemer’s book (Equality of Opportunity, Harvard University Press, 1998), to compute the extent to which tax-and-transfer regimes in 11 countries equalize opportunities among citizens for income acquisition. Roughly speaking, equality of opportunity for incomes has been achieved in a country when it is the case that the distributions of post-fisc income are the same for different types of citizen, where a citizen’s type is defined by the socio-economic status of his parents. Intuitively, a country will have equalized opportunity if the chances of earning high (or low) income are equal for citizens from all family backgrounds. Of course, pre-fisc income distributions, by type, will not be identical, as long as the educational system does not entirely make up for the disadvantage that children, who come from poor families face, but the tax-and-transfer system can play a role in rectifying that inequality. We include, in our computation, two numbers that summarize the extent to which each country’s current fiscal regime achieves equalization of opportunities for income, and the deadweight loss that would be incurred by moving to the regime that does.Fiscal regimes; Equal opportunities; Income acquisition;

HIV infection and aging: enhanced Interferon- and Tumor Necrosis Factor-alpha production by the CD8(+) CD28(-) T subset

BACKGROUND: T cells from HIV(+) and aged individuals show parallels in terms of suppressed proliferative activity and interleukin-2 (I1-2) production and an increased number of CD8(+) CD28(-) T cells. In order to compare cytokine production from T cells from these two states, CD4(+) and CD8(+) T cells from HIV(+) aged, and normal young donors (controls) were monitored for cytokine production by flow cytometry, quantitative PCR and ELISA upon activation by PMA and anti-CD3. In addition, the CD8(+) T cell subsets CD28(+) and CD28(-) from the HIV(+) and the aged groups were evaluated for cytokine production by flow cytometry, and compared with those from young controls. RESULTS: Flow cytometric analysis indicated that CD8(+) T cells from both HIV(+) and aged donors showed an increase of approximately 2–3 fold over controls in percentage of cells producing inflammatory cytokines IFN-γ and TNF-α. Similar analysis also revealed that the production of interleukins-4,6 and 10, production was very low (1–2% of cells) and unchanged in these cells. Quantitative PCR also showed a substantial increase (4–5 fold) in IFN-γ and TNF-α mRNA from HIV(+) and aged CD8(+) T cells, as did ELISA for secreted IFN-γ and TNF-α (2.3–4 fold). Flow cytometric analysis showed that the CD8(+) CD28(-) T cell subset accounts for approximately 80–86% of the IFN-γ and TNF-α production from the CD8(+) subset in the aged and HIV(+) states. The CD4(+) T cell, while not significantly changed in the HIV(+) or aged states in terms of IFN-γ production, showed a small but significant increase in TNF-α production in both states. CONCLUSIONS: Our data appear compatible with physiologic conditions existing in HIV(+) and aged individuals, i.e. elevated serum levels and elevated CD8(+) T cell production of IFN-γ and TNF-α. Thus, the capacity for increased production of cytokines IFN-γ and TNF-α in the aged individual by the dominant CD8(+) CD28(-) subset may have a profound influence on the clinical state by aggravating inflammatory pathologies such as rheumatoid arthritis, and possibly Alzheimer's disease and Crohn's disease. In AIDS, these cytokines may contribute to wasting and cachexia. We theorize that the predominant phenotypic change to the cytotoxic CD8(+) CD28(-) T cell subsets in both the HIV(+) and the aged states may reflect a natural "endpoint" in CD8(+) T cell differentiation induced after a lifetime of immune activity (toward viruses, etc) in the aged, and after a massive accelerated response to HIV in the HIV-positive individual