Transmission behaviors of single mode hollow metallic waveguides dedicated to mid-infrared nulling interferometry

This paper reports the characterization of hollow metallic waveguides (HMW) to be used as single-mode wavefront filters for nulling interferometry in the 6-20 microns range. The measurements presented here were performed using both single-mode and multimode conductive waveguides at 10.6 microns. We found propagation losses of about 16dB/mm, which are mainly due to the theoretical skin effect absorption in addition to the roughness of the waveguide metallic walls. The input and output coupling efficiency of our samples has been improved by adding tapers to minimize the impedance mismatch. A proper distinction between propagation losses and coupling losses is presented. Despite their elevate propagation losses, HMW show excellent spatial filtering capabilities in a spectral range where photonics technologies are only emerging.Comment: This paper was published in Optics Express and can be found at http://www.opticsinfobase.org/abstract.cfm?URI=oe-15-26-1800

M-lines characterization of selenide and telluride waveguides for mid-infrared interferometry

Nulling interferometry is an astronomical technique that combines equal wavefronts to achieve a deep rejection ratio of an on-axis star, and that could permit to detect Earth-like planets in the mid-infrared band 5 -- 20 microns. Similarly to what is done in the near-infrared, high frequencies spatial filtering of the incoming beams can be achieved using single-mode waveguides operating in the mid-infrared. An appreciable reduction of the instrumental complexity is also possible using integrated optics (IO) devices in this spectral range. The relative lack of single-mode guided optics in the mid-infrared has motivated the present technological study to demonstrate the feasibility of dielectric waveguides functioning at longer wavelengths. We propose to use selenide and telluride components to pursue the development of more complex IO functions.Comment: accepted in OSA Optics Express, 11 pages, 4 figure

First fringes with an integrated-optics beam combiner at 10 um - A new step towards instrument miniaturization for mid-infrared interferometry

Observations at mas-resolution scales and high dynamic range hold a central place in achieving, for instance, the spectroscopic characterization of exo-Earths or the detailed mapping of their protoplanetary disc birthplace. Ground or space-based multi-aperture infrared interferometry is a promising technique to tackle these goals. But significant efforts still need to be undertaken to achieve a simplification of these instruments if we want to combine the light from a large number of telescopes. Integrated-optics appears as an alternative to the current conventional designs, especially if its use can be extended to a higher number of astronomical bands. This article reports for the first time the experimental demonstration of the feasibility of an integrated-optics approach to mid-infrared beam combination for single-mode stellar interferometry. We have fabricated a 2-telescope beam combiner prototype integrated on a substrate of chalcogenide glasses, a material transparent from 1 to 14 um. We have developed laboratory tools to characterize the modal properties and the interferometric capabilities of our device. We obtain fringes at 10 um and measure a mean contrast V=0.981 \pm 0.001 with high repeatability over one week and high stability over 5h. We show experimentally - as well as on the basis of modeling considerations - that the component has a single-mode behavior at this wavelength, which is essential to achieve high-accuracy interferometry. From previous studies, the propagation losses are estimated to 0.5 dB/cm for such components. We also discuss possible issues that may impact the interferometric contrast. The IO beam combiner performs well at 10. We also anticipate the requirement of a better matching between the numerical apertures of the component and the (de)coupling optics to optimize the total throughput. The next step foreseen is the achievement of wide-band interferograms.Comment: Accepted in A&A; 7 pages; 7 figure

Demographic consequences of heavy metals and persistent organic pollutants in a vulnerable long-lived bird, the wandering albatross

International audienceSeabirds are top predators of the marine environment that accumulate contaminants over a long life-span. Chronic exposure to pollutants is thought to compromise survival rate and long-term reproductive outputs in these long-lived organisms, thus inducing population decline. However, the demographic consequences of contaminant exposure are largely theoretical because of the dearth of long-term datasets. This study aims to test whether adult survival rate, return to the colony and long-term breeding performance were related to blood mercury (Hg), cadmium (Cd) and persistent organic pollutants (POPs), by using a capture–mark–recapture dataset on the vulnerable wandering albatross Diomedea exulans. We did not find evidence for any effect of contaminants on adult survival probability. However, blood Hg and POPs negatively impacted long-term breeding probability, hatching and fledging probabilities. The proximate mechanisms underlying these deleterious effects are likely multifaceted, through physiological perturbations and interactions with reproductive costs. Using matrix population models, we projected a demographic decline in response to an increase in Hg or POPs concentrations. This decline in population growth rate could be exacerbated by other anthropogenic perturbations, such as climate change, disease and fishery bycatch. This study gives a new dimension to the overall picture of environmental threats to wildlife populations

Advances in the Development of Mid-Infrared Integrated Devices for Interferometric Arrays

This article reports the advances on the development of mid-infrared integrated optics for stellar interferometry. The devices are fabricated by laser writing techniques on chalcogenide glasses. Laboratory characterizaton is reported and analyzed.Comment: 12 pages, 9 figures, SPIE Astronomical Telescopes and Instrumentatio

High precision astrometry mission for the detection and characterization of nearby habitable planetary systems with the Nearby Earth Astrometric Telescope (NEAT)

(abridged) A complete census of planetary systems around a volume-limited sample of solar-type stars (FGK dwarfs) in the Solar neighborhood with uniform sensitivity down to Earth-mass planets within their Habitable Zones out to several AUs would be a major milestone in extrasolar planets astrophysics. This fundamental goal can be achieved with a mission concept such as NEAT - the Nearby Earth Astrometric Telescope. NEAT is designed to carry out space-borne extremely-high-precision astrometric measurements sufficient to detect dynamical effects due to orbiting planets of mass even lower than Earth's around the nearest stars. Such a survey mission would provide the actual planetary masses and the full orbital geometry for all the components of the detected planetary systems down to the Earth-mass limit. The NEAT performance limits can be achieved by carrying out differential astrometry between the targets and a set of suitable reference stars in the field. The NEAT instrument design consists of an off-axis parabola single-mirror telescope, a detector with a large field of view made of small movable CCDs located around a fixed central CCD, and an interferometric calibration system originating from metrology fibers located at the primary mirror. The proposed mission architecture relies on the use of two satellites operating at L2 for 5 years, flying in formation and offering a capability of more than 20,000 reconfigurations (alternative option uses deployable boom). The NEAT primary science program will encompass an astrometric survey of our 200 closest F-, G- and K-type stellar neighbors, with an average of 50 visits. The remaining time might be allocated to improve the characterization of the architecture of selected planetary systems around nearby targets of specific interest (low-mass stars, young stars, etc.) discovered by Gaia, ground-based high-precision radial-velocity surveys.Comment: Accepted for publication in Experimental Astronomy. The full member list of the NEAT proposal and the news about the project are available at http://neat.obs.ujf-grenoble.fr. The final publication is available at http://www.springerlink.co

Unconventional Repertoire Profile Is Imprinted during Acute Chikungunya Infection for Natural Killer Cells Polarization toward Cytotoxicity

Chikungunya virus (CHIKV) is a worldwide emerging pathogen. In humans it causes a syndrome characterized by high fever, polyarthritis, and in some cases lethal encephalitis. Growing evidence indicates that the innate immune response plays a role in controlling CHIKV infection. We show here that CHIKV induces major but transient modifications in NK-cell phenotype and function soon after the onset of acute infection. We report a transient clonal expansion of NK cells that coexpress CD94/NKG2C and inhibitory receptors for HLA-C1 alleles and are correlated with the viral load. Functional tests reveal cytolytic capacity driven by NK cells in the absence of exogenous signals and severely impaired IFN-γ production. Collectively these data provide insight into the role of this unique subset of NK cells in controlling CHIKV infection by subset-specific expansion in response to acute infection, followed by a contraction phase after viral clearance

Supporting work practices through telehealth: impact on nurses in peripheral regions

<p>Abstract</p> <p>Background</p> <p>In Canada, workforce shortages in the health care sector constrain the ability of the health care system to meet the needs of its population and of its health care professionals. This issue is of particular importance in peripheral regions of Quebec, where significant inequalities in workforce distribution between regions has lead to acute nursing shortages and increased workloads. Information and communication technologies (ICTs) are innovative solutions that can be used to develop strategies to optimise the use of available resources and to design new nursing work practices. However, current knowledge is still limited about the real impact of ICTs on nursing recruitment and retention. Our aim is to better understand how work practice reorganization, supported by ICTs, and particularly by telehealth, may influence professional, educational, and organizational factors relating to Quebec nurses, notably those working in peripheral regions.</p> <p>Methods/Design</p> <p>First, we will conduct a descriptive study on the issue of nursing recruitment. Stratified sampling will be used to select approximately twenty innovative projects relating to the reorganization of work practices based upon ICTs. Semi-structured interviews with key informants will determine professional, educational, and organizational recruitment factors. The results will be used to create a questionnaire which, using a convenience sampling method, will be mailed to 600 third year students and recent graduates of two Quebec university nursing faculties. Descriptive, correlation, and hierarchical regression analyses will be performed to identify factors influencing nursing graduates' intentions to practice in peripheral regions. Secondly, we will conduct five case studies pertaining to the issue of nursing retention. Five ICT projects in semi-urban, rural, and isolated regions have been identified. Qualitative data will be collected through field observation and approximately fifty semi-structured interviews with key stakeholders.</p> <p>Discussion</p> <p>Data from both parts of this research project will be jointly analysed using triangulation of researchers, theoretical approaches, methods, and results. Continuous exchanges with decision makers and periodic knowledge transfer activities are planned to facilitate the dissemination and utilization of research results in policies regarding the nursing recruitment and retention.</p

Chikungunya Disease: Infection-Associated Markers from the Acute to the Chronic Phase of Arbovirus-Induced Arthralgia

At the end of 2005, an outbreak of fever associated with joint pain occurred in La Réunion. The causal agent, chikungunya virus (CHIKV), has been known for 50 years and could thus be readily identified. This arbovirus is present worldwide, particularly in India, but also in Europe, with new variants returning to Africa. In humans, it causes a disease characterized by a typical acute infection, sometimes followed by persistent arthralgia and myalgia lasting months or years. Investigations in the La Réunion cohort and studies in a macaque model of chikungunya implicated monocytes-macrophages in viral persistence. In this Review, we consider the relationship between CHIKV and the immune response and discuss predictive factors for chronic arthralgia and myalgia by providing an overview of current knowledge on chikungunya pathogenesis. Comparisons of data from animal models of the acute and chronic phases of infection, and data from clinical series, provide information about the mechanisms of CHIKV infection–associated inflammation, viral persistence in monocytes-macrophages, and their link to chronic signs

Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

BACKGROUND : Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in corals or as parasites infecting other protists and animals. Dinoflagellates harbor atypically large genomes (~ 3 to 250 Gb), with gene organization and gene expression patterns very different from closely related apicomplexan parasites. Here we sequenced and analyzed the genomes of two early-diverging and co-occurring parasitic dinoflagellate Amoebophrya strains, to shed light on the emergence of such atypical genomic features, dinoflagellate evolution, and host specialization. RESULTS : We sequenced, assembled, and annotated high-quality genomes for two Amoebophrya strains (A25 and A120), using a combination of Illumina paired-end short-read and Oxford Nanopore Technology (ONT) MinION long-read sequencing approaches. We found a small number of transposable elements, along with short introns and intergenic regions, and a limited number of gene families, together contribute to the compactness of the Amoebophrya genomes, a feature potentially linked with parasitism. While the majority of Amoebophrya proteins (63.7% of A25 and 59.3% of A120) had no functional assignment, we found many orthologs shared with Dinophyceae. Our analyses revealed a strong tendency for genes encoded by unidirectional clusters and high levels of synteny conservation between the two genomes despite low interspecific protein sequence similarity, suggesting rapid protein evolution. Most strikingly, we identified a large portion of non-canonical introns, including repeated introns, displaying a broad variability of associated splicing motifs never observed among eukaryotes. Those introner elements appear to have the capacity to spread over their respective genomes in a manner similar to transposable elements. Finally, we confirmed the reduction of organelles observed in Amoebophrya spp., i.e., loss of the plastid, potential loss of a mitochondrial genome and functions. CONCLUSION : These results expand the range of atypical genome features found in basal dinoflagellates and raise questions regarding speciation and the evolutionary mechanisms at play while parastitism was selected for in this particular unicellular lineage.ADDITIONAL FILE 1: FIGURE S1. Phylogeny of Alveolata. Proteomes from 89 alveolates genomes and transcriptome assemblies from the MMETSP project (https://zenodo.org/record/257026/files/) were used to create orthologous groups using orthofinder v2.2 with the diamond BLAST similarity search. Single ortholog alignments were pruned using PhyloTreePruner v.1.0 (minimum taxa to keep 44 and support value 0.9) and realigned using mafft v7 and filtered with Gblocks v.0.91b (−b5 = a -p = n). Filtered alignments were concatenated using seqCat.pl and a phylogenetic tree was produced under Maximum Likelihood framework using RAxML v8.2.9 with the PROTGAMMALGF model of sequence evolution and 101 bootstraps. Asterics represent support values of 95 and above. A detailed method can be found in Kayal et al. 2018 BMC Evol. Biol. (https://doi.org/10.1186/s12862-018-1142-0). The full tree can be found at http://mmo.sb-roscoff.fr/jbrowseAmoebophrya/. FIGURE S2. SSU rDNA sequence identity (in percentage, relative to A25 and A120 compared to other species). FIGURE S3. Distribution of k-mer in A25 and A120 genomes. FIGURE S4. Classification of repeated elements in 3 Amoebophrya genomes (AT5, A25, and A120) using REPET. The x-axis represents the cumulated number of bases of repeated elements in the genome. FIGURE S5. Conserved motif of the putative splice leader (SL) in A25 and A120. FIGURE S6. Alignments of gene encoding the putative spliced leader (SL) gene in A25 and A120. FIGURE S7. Gene orientation change rate in 3 Amoebophrya genomes. FIGURE S8. Number of orthologs genes shared by selected taxa. FIGURE S9. Boxplot of the dN/dS ratios of orthologous genes between A25 and A120, calculated using the model average method (MA). FIGURE S10. Synteny dot-plot obtained by comparison between Amoebophrya A25 and AT5 genomes. FIGURE S11. Synteny dot-plot obtained by comparison between Amoebophrya A120 and AT5 genomes. FIGURE S12. Intron length distribution. FIGURE S13. GC content distribution. FIGURE S14. Multiple alignments of U2 snRNAs. FIGURE S15. Multiple alignments of U4 snRNAs. FIGURE S16. Multiple alignments of U5 snRNAs. FIGURE S17. Multiple alignments of U6 snRNAs. FIGURE S18. Secondary structure of Amoebophrya snRNA. FIGURE S19. Example of introner elements (IEs) in Amoebophrya. FIGURE S20. Distribution the direct repeats with size ranging between 3 and 8 nucleotides in A25. FIGURE S21. Distribution of the direct repeats with size ranging between 3 and 8 nucleotides in A120. FIGURE S22. Composition of direct repeats in introners elements. The diversity in composition of the three (a, b, c) most abundant of direct repeats in introner elements in A25 (up) and A120 (down). FIGURE S23. Terminal inverted repeat locations around the splicing sites in A25 and A120. The position of inverted repeats according to the location of the splice sites in A25 and A120. Left, the inverted repeats of A120 are located at 1–5 the nucleotides upstream and downstream of the splice sites. Right, the inverted repeats of A25 are located at the 1–6 nucleotides in upstream and downstream of the splice sites. FIGURE S24. The flowchart for the in silico search of introner elements. FIGURE S25. Hierarchical clustering analysis (pairwise similarity and OrthoMCL) of all intron families and of the inverted repeats in A25 and A120. FIGURE S26. Percentage of genes with assigned functions in relation with introns composition. FIGURE S27. Difference in the proportion of IEs-containing-genes compared to their KEGG assignment in A25 and A120. FIGURE S28. Distribution of conserved introns. TABLE S1. RCC number, date and site of isolation of strains considered in this study. TABLE S2. Metrics of Nanopore runs for the two Amoebophrya strains. TABLE S3. Search for pathways involved in plastidial functions that are entirely independent of plastid-encoded gene content. TABLE S4. Number of the different types of introns identified in A25 and A120 genomes. TABLE S5. Search for RNA editing in A25 and A120 introns. TABLE S6. Putative Amoebophrya A25 and A120 snRNP homologs. TABLE S7. Classification into families of non-canonical introns in A25 and A120. TABLE S8. RNAseq read assembly statistics of Amoebophrya A25 and A120 corresponding samples from the different time of infection and to the freeliving stage (dinospore only). TABLE S9. Total number of contigs belonging to samples from different stages of infection and the proportion of them that were aligned against the genomes of both Amoebophrya A25 and A120. ND corresponds to “not determined” when no measurement was done. TABLE S10. Metabolic pathway screened in A25 and A120 proteomes.This research was funded by the ANR (Agence Nationale de la Recherche) Grant ANR-14-CE02-0007 HAPAR, the CEA and the Région Bretagne (RC doctoral grant ARED PARASITE 9450 and EK postdoctoral grant SAD HAPAR 9229), and the CNRS (X-life SEAgOInG).http://www.mdpi.com/journal/biomedicinesam2022BiochemistryGeneticsMicrobiology and Plant Patholog