Quantum fluctuations and correlations of spatial scalar or multimode vector solitons in Kerr media

International audienceWe apply the Green\'s function method to determine theglobal degree of squeezing and the transverse spatial distributionof quantum fluctuations of solitons in Kerr media. We show thatboth scalar bright solitons and multimode vector solitonsexperience strong squeezing on the optimal quadrature. For vectorsolitons, this squeezing is shown to result from an almost perfectanti-correlation between the fluctuations on the twoincoherently-coupled circular polarisations

Ground motion prediction at gravitational wave observatories using archival seismic data

Gravitational wave observatories have always been affected by tele-seismic earthquakes leading to a decrease in duty cycle and coincident observation time. In this analysis, we leverage the power of machine learning algorithms and archival seismic data to predict the ground motion and the state of the gravitational wave interferometer during the event of an earthquake. We demonstrate improvement from a factor of 5 to a factor of 2.5 in scatter of the error in the predicted ground velocity over a previous model fitting based approach. The level of accuracy achieved with this scheme makes it possible to switch control configuration during periods of excessive ground motion thus preventing the interferometer from losing lock. To further assess the accuracy and utility of our approach, we use IRIS seismic network data and obtain similar levels of agreement between the estimates and the measured amplitudes. The performance indicates that such an archival or prediction scheme can be extended beyond the realm of gravitational wave detector sites for hazard-based early warning alerts.Comment: 10 pages, 7 figures; matches published versio

Noncanonical splicing junctions between exons and transposable elements represent a source of immunogenic recurrent neo-antigens in patients with lung cancer

Although most characterized tumor antigens are encoded by canonical transcripts (such as differentiation or tumor-testis antigens) or mutations (both driver and passenger mutations), recent results have shown that noncanonical transcripts including long noncoding RNAs and transposable elements (TEs) can also encode tumor-specific neo-antigens. Here, we investigate the presentation and immunogenicity of tumor antigens derived from noncanonical mRNA splicing events between coding exons and TEs. Comparing human non-small cell lung cancer (NSCLC) and diverse healthy tissues, we identified a subset of splicing junctions that is both tumor specific and shared across patients. We used HLA-I peptidomics to identify peptides encoded by tumor-specific junctions in primary NSCLC samples and lung tumor cell lines. Recurrent junction-encoded peptides were immunogenic in vitro, and CD8+ T cells specific for junction-encoded epitopes were present in tumors and tumor-draining lymph nodes from patients with NSCLC. We conclude that noncanonical splicing junctions between exons and TEs represent a source of recurrent, immunogenic tumor-specific antigens in patients with NSCLC

Serendipitous meta-transcriptomics : the fungal community of Norway Spruce (Picea abies)

After performing de novo transcript assembly of >1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active. Here, we show that these serendipitously sequenced transcripts need not be considered merely as contamination, as is common, but that they provide insight into the plant’s phyllosphere. Notably, we could classify these transcripts as originating predominantly fromDothideomycetes and Leotiomycetes species, with functional annotation of gene families indicating active growth and metabolism, with particular regards to glucose intake and processing, as well as gene regulation.S1 Fig. Samples collected from Norway spruce. For each sample a brief description and sample ID are shown below a representative image of the associated plant tissue, while the sampling date is shown above.S2 Fig. Bioinformatics workflow of RNA data processing. We assembled reads from all samples into a single assembly (left column), computed Tau scores, GC content, and mapped the transcripts to the genome as well as to the Uniref90 protein database. For enriching for fungal transcripts (right column), we applied GC content and expression breadth filters to the reads and assembly respectively, clustered sequences by similarity, and performed functional annotation as well as phylogenetic analyses.S3 Fig. Putative taxonomic characterization of transcripts via protein alignments. Bar plot showing the number of transcripts by taxonomy (super)kingdoms. Parent summarises taxons hierarchically higher than the represented (super)kingdoms, NA summarises transcripts with no sequence similarity in the UniRef90 database. The number of transcripts is indicated at the top of every bar.S4 Fig. Taxonomic class and phylum of the fungal transcripts. (a) Number of transcripts per fungal phylum. The phylum are sorted by abundance top to bottom with Ascomycota (n = 81,181) and Basidiomycota (n = 4,839) being the most represented; the remaining phyla varying from n = 11 to n = 2. (b) A graph of the taxonomic hierarchy from species to phylum of the fungal transcripts, showing the broad species diversity of the largest clusters: Ascomycota (bottom) and Basidiomycota (top). (c) Similar to (a) for the fungal classes, with the Eurotiomycetes and Dothideomycetes classes being over-represented among the fungal transcripts. (d) Similar to (b) for the fungal classes (n = 24).S5 Fig. Characterisation of transcripts lacking taxonomic assignment by their GMAP alignments to the P. abies genome. (a) Boxplot of the tau scores for the no taxon transcripts split based on their GMAP alignments to the P. abies genome. The tau score ranges from 1 for complete specificity to 0 for equal expression in all samples. The transcripts having a GMAP alignment in the genome (99% of the GMAP hits cover 80% of the transcripts with at least a 90% identity) show a wide tau score distribution indicative of the presence of ubiquitously expressed transcripts as well as that of more tissue-specific transcripts. The transcripts having no GMAP alignment show a distribution typical of only tissue-specific expression (mean tau score of 0.98). (b) Percentage GC density distribution of the no taxon transcripts split based on their GMAP alignments to the P. abies genome. Transcripts having a GMAP alignment to the genome present a GC distribution typical of the P. abies transcripts. The transcripts without a GMAP alignment show a distribution enriched for higher percentage GC, similar to that of fungi. The shoulder observed under the peak of transcripts with GMAP alignments may indicate transcripts where the assembly contained gaps or created chimeras. (c) Scatterplot of log2 FPKM expression values vs. the percentage GC content for the transcripts with a GMAP alignment. Colouring indicates density, which is shaded from yellow (high) to blue (low). The expression of transcripts with a GMAP alignment resembles that of the Embryophita phylum. (d) Scatterplot of log2 FPKM expression values vs. the percentage GC content for transcripts with a GMAP alignment. Colouring as in (c). The expression of transcripts with no GMAP alignment resembled that of the fungal kingdom.S6 Fig. Phylogeny built on four nuclear genes. Shown are maximum-likelihood phylogenies based on fungal nucleotide sequences assembled from the spruce samples in context of known sequences, with highest sequence similarity to: (a) phosphoenolpyruvate carboxykinase; (b) NADP-dependent medium chain alcohol dehydrogenase; (c) beta lactamase; and (d) unspecific lipid transporter. Only branch with support values > 0.9 are shown. While clusters with more representative sequences yield better branch support (a, b), placement of clusters with fewer sequences is less certain (c, d). However, in all cases, at least one sequence is grouped with Dothideomycetes, and for (a,b) with Leotiomycetes.S1 Table. Sample IDs, description, and ENA submission IDs. Correspondence between the sample IDs as described in Nystedt et al., (2013), this manuscript and the ENA are shown in columns one to three. The fourth column contains a succinct description of the samples, refer to Nystedt et al., (2013) for full details.http://www.plosone.orgam201

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

Search for gravitational-lensing signatures in the full third observing run of the LIGO-Virgo network

Gravitational lensing by massive objects along the line of sight to the source causes distortions of gravitational wave-signals; such distortions may reveal information about fundamental physics, cosmology and astrophysics. In this work, we have extended the search for lensing signatures to all binary black hole events from the third observing run of the LIGO--Virgo network. We search for repeated signals from strong lensing by 1) performing targeted searches for subthreshold signals, 2) calculating the degree of overlap amongst the intrinsic parameters and sky location of pairs of signals, 3) comparing the similarities of the spectrograms amongst pairs of signals, and 4) performing dual-signal Bayesian analysis that takes into account selection effects and astrophysical knowledge. We also search for distortions to the gravitational waveform caused by 1) frequency-independent phase shifts in strongly lensed images, and 2) frequency-dependent modulation of the amplitude and phase due to point masses. None of these searches yields significant evidence for lensing. Finally, we use the non-detection of gravitational-wave lensing to constrain the lensing rate based on the latest merger-rate estimates and the fraction of dark matter composed of compact objects

Search for eccentric black hole coalescences during the third observing run of LIGO and Virgo

Despite the growing number of confident binary black hole coalescences observed through gravitational waves so far, the astrophysical origin of these binaries remains uncertain. Orbital eccentricity is one of the clearest tracers of binary formation channels. Identifying binary eccentricity, however, remains challenging due to the limited availability of gravitational waveforms that include effects of eccentricity. Here, we present observational results for a waveform-independent search sensitive to eccentric black hole coalescences, covering the third observing run (O3) of the LIGO and Virgo detectors. We identified no new high-significance candidates beyond those that were already identified with searches focusing on quasi-circular binaries. We determine the sensitivity of our search to high-mass (total mass M>70 M⊙) binaries covering eccentricities up to 0.3 at 15 Hz orbital frequency, and use this to compare model predictions to search results. Assuming all detections are indeed quasi-circular, for our fiducial population model, we place an upper limit for the merger rate density of high-mass binaries with eccentricities 0<e≤0.3 at 0.33 Gpc−3 yr−1 at 90\% confidence level

Ultralight vector dark matter search using data from the KAGRA O3GK run

Among the various candidates for dark matter (DM), ultralight vector DM can be probed by laser interferometric gravitational wave detectors through the measurement of oscillating length changes in the arm cavities. In this context, KAGRA has a unique feature due to differing compositions of its mirrors, enhancing the signal of vector DM in the length change in the auxiliary channels. Here we present the result of a search for U(1)B−L gauge boson DM using the KAGRA data from auxiliary length channels during the first joint observation run together with GEO600. By applying our search pipeline, which takes into account the stochastic nature of ultralight DM, upper bounds on the coupling strength between the U(1)B−L gauge boson and ordinary matter are obtained for a range of DM masses. While our constraints are less stringent than those derived from previous experiments, this study demonstrates the applicability of our method to the lower-mass vector DM search, which is made difficult in this measurement by the short observation time compared to the auto-correlation time scale of DM

Role of the P2Y1,P2Y4 and P2Y12 receptor in a mouse in vivo angiogenesis model and role of the P2Y1 receptor in the endothelial cell function

En plus de leur rôle dans l’hémostase et la thrombose, les nucléotides extracellulaires interviennent dans différents processus physiologiques et physio-pathologiques tels que la prolifération cellulaire et la modulation de l’apoptose, le contrôle du tonus vasculaire et la réponse inflammatoire, en agissant sur les cellules endothéliales, les cellules musculaires lisses et les leucocytes. L’inflammation, la prolifération cellulaire et les plaquettes sanguines tiennent une place importante dans l’angiogenèse ce qui suggère que ces nucléotides pourraient jouer un rôle dans ce processus. Les récepteurs P2Y aux nucléotides sont exprimés sur la plupart des cellules qui participent aux étapes de la formation des vaisseaux sanguins, à savoir les plaquettes sanguines, les cellules endothéliales, les cellules musculaires lisses et les leucocytes, et leur rôle dans l’angiogenèse a été ainsi envisagé. L’objectif de ce travail a été d’étudier le rôle des récepteurs P2 des nucléotides dans l’angiogenèse. Pour cela, nous avons d’abord mis au point un modèle d’étude in vivo chez la souris. Nous avons aussi été amenés, au cours de ce travail, à établir des lignées immortalisées de cellules endothéliales de souris. Les principaux résultats de ces travaux sont que, parmi les récepteurs étudiés, le récepteur P2Y4 semble avoir un rôle important dans l’angiogenèse. Concernant le récepteur P2Y1, son rôle n’a pas pu être mis en évidence dans le modèle in vivo. En revanche, dans les cellules endothéliales immortalisées en culture, il semble participer à la régulation de la prolifération. Enfin, pour étudier le rôle du récepteur P2Y12, nous avons utilisé le clopidogrel, l’inhibiteur sélectif de ce récepteur, ainsi que son énantiomère inactif. Les deux molécules ayant le même impact dans notre modèle in vivo, à savoir la formation de zones hémorragiques et une diminution du nombre de vaisseaux formés, nous ne pouvons pas attribuer cet effet à l’inhibition du récepteur P2Y12. En conclusion, notre travail a permis de mettre à disposition du laboratoire, deux modèles d’étude : un modèle d’angiogenèse in vivo et un modèle de culture de cellules endothéliales immortalisées. Concernant les récepteurs P2, seul le récepteur P2Y4 semble jouer un rôle dans l’angiogenèse. Des expériences complémentaires permettront d’indiquer l’importance du rôle d’autres récepteurs P2Y, comme les récepteurs P2Y2 et P2Y6, ainsi que les récepteurs P2X, dans la formation des vaisseaux sanguins. Leur identification à la surface des cellules endothéliales et des autres cellules participant à l’angiogenèse, permettra non seulement d’étudier leurs fonctions dans la régulation de ces cellules, mais aussi d’envisager leur rôle dans des pathologies dépendantes de l’angiogenèse.In addition to their role in haemostasis and thrombosis, extracellular nucleotides regulate various physiological and physiopathological processes such as the cellular proliferation and the modulation of apoptosis, the control of vascular tone and inflammation, by acting on endothelial cells, smooth muscle cells and leucocytes. Inflammation, cellular proliferation and blood platelets hold an important place in angiogenesis suggesting that nucleotides could play a role in this process. Extracellular nucleotides receptors, the P2Y receptors, are expressed on the majority of the cells involved in the blood vessels formation, for example the blood platelets, endothelial cells, smooth muscle cells and leucocytes, and their role in angiogenesis was thus considered. The aim of this work was to study the role of the extracellular nucleotides P2 receptors in angiogenesis. First, we developed an in vivo mouse model of angiogenesis then we established immortalized mouse endothelial cell lines. The major results of this work are that, among the receptors studied, the P2Y4 receptor seems to have an important role in angiogenesis. Concerning the P2Y1 receptor, its role could not be highlighted in the in vivo model. On the other hand, in the immortalized endothelial cells in culture, this receptor seems to play a role in the control of the proliferation. Lastly, to study the role of the P2Y12 receptor, we used the clopidogrel, the selective inhibitor of this receptor and also its inactive enantiomer. These two molecules having the same impact in our in vivo model, the formation of hemorrhagic zones and a reduction in the number of new vessels formed, we cannot allot this effect to the P2Y12 receptor inhibition. In conclusion, thanks to this work, the laboratory has now two models of study: an in vivo model of angiogenesis and a model of culture of immortalized endothelial cells. Concerning the P2 receptors, only the P2Y4 receptor seems to be important in angiogenesis. Additional experiments are required to highlight the importance of the role of other P2Y receptors, like the P2Y2 and P2Y6 receptors, as well as the P2X receptors, in the formation of blood vessels. Their identification on the surface of endothelial cells and other cells involved in angiogenesis will not only make it possible to study their functions in the regulation of these cells, but also to consider their role in pathologies dependent on angiogenesis