Le projet CIRDO d'assistance aux personnes âgées isolées à domicile

National audienceCIRDO RI est un projet qui vise à mettre au point un système d'assistance pour faciliter le maintien à domicile des personnes âgées et/ou dépendantes. Il a pour objectif de sécuriser les seniors et de favoriser leur autonomie pour soulager les familles et les aidants. L'idée principale du projet CIRDO est d'utiliser à la fois l'analyse vidéo et la reconnaissance de la parole et ceci dans le même processus. Afin de répondre aux contraintes fixées dans le projet CIRDO comme le respect de l'intimité, la préservation de l'information privée et la réactivité dans la détection de situations de détresse, les solutions proposées sont conçues pour opérer en tâches de fond, sans l'intervention d'un opérateur. Outre l'aspect technique, ce projet porte également sur l'évaluation psycho-sociale et psycho-ergonomique de ces technologies par des utilisateurs potentiels et leur entourage (famille, aidants...) au niveau de leur utilisabilité et de leur acceptabilité notamment. Des expérimentations conduites dans un milieu réaliste ont permis l'enregistrement de données audio et vidéo correspondant au cas d'usage

The CIRDO Corpus: Comprehensive Audio/Video Database of Domestic Falls of Elderly People

International audienceAmbient Assisted Living aims at enhancing the quality of life of older and disabled people at home thanks to Smart Homes. In particular, regarding elderly living alone at home, the detection of distress situation after a fall is very important to reassure this kind of population. However, many studies do not include tests in real settings, because data collection in this domain is very expensive and challenging and because of the few available data sets. The CIRDOcorpus is a dataset recorded in realistic conditions in DOMUS, a fully equipped Smart Home with microphones and home automation sensors, in which participants performed scenarios including real falls on a carpet and calls for help. These scenarios were elaborated thanks to a field study involving elderly persons. Experiments related in a first part to distress detection in real-time using audio and speech analysis and in a second part to fall detection using video analysis are presented. Results show the difficulty of the task. The database can be used as standardized database by researchers to evaluate and compare their systems for elderly person's assistance. Keywords: audio and video data set, multimodal corpus, natural language and multimodal interaction, Ambient Assisted Living (AAL), distress situation

CIRDO: Smart companion for helping elderly to live at home for longer

8 pagesInternational audienceCirdo project is intended to establish new healthcare systems to ensure the safety at home of seniors and people with decreasing independence. In particular, extending "e-lio" (http://www.technosens.fr/) device, Cirdo aims to develop an audio/video-based system which makes it possible for elderly to live with a sufficient degree of autonomy. To achieve this goal, generic purposes on video analysis and audio processing are discussed and implemented in the same process. Audio and video analysis algorithms are launched simultaneously and thinks to GPU implementation, the tasks are done in real time. To comply with the requirements set out in the Cirdo project namely: respect privacy and preserve personal data, the processing tasks is performed through background tasks, without any human intrusion. In order to have different types of fall for our experiences, multiple scenarios were designed and performed by several persons. Besides the technical aspect, the project also focuses on generic technology validation by potential users and their human environment (family, caregivers/care takers...). Psychological and ergonomic assessment on the use of services developed was conducted. It focused on the usefulness, usability and accessibility and acceptance of the tool. This evaluation was completed by critical investigation of knowledge acquired by professionals (geriatricians, caregivers school and associations)

Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach

As critical primary producers and recyclers of organic matter, the diversity of marine protists has been extensively explored by high-throughput barcode sequencing. However, classification of short metabarcoding sequences into traditional taxonomic units is not trivial, especially for lineages mainly known by their genetic fingerprints. This is the case for the widespread Amoebophrya ceratii species complex, parasites of their dinoflagellate congeners. We used genetic and phenotypic characters, applied to 119 Amoebophrya individuals sampled from the same geographic area, to construct practical guidelines for species delineation that could be applied in DNA/RNA based diversity analyses. Based on the internal transcribed spacer (ITS) regions, ITS2 compensatory base changes (CBC) and genome k-mer comparisons, we unambiguously defined eight cryptic species among closely related ribotypes that differed by less than 97% sequence identity in their SSU rDNA. We then followed the genetic signatures of these parasitic species during a three-year survey of Alexandrium minutum blooms. We showed that these cryptic Amoebophrya species co-occurred and shared the same ecological niche. We also observed a maximal ecological fitness for parasites having narrow tointermediate host ranges, reflecting a high cost for infecting a broader host range. This study suggests that a complete taxonomic revision of these parasitic dinoflagellates is long overdue to understand their diversity and ecological role in the marine plankton

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 (similar to 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

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

Segmentation de séquence vidéo en plans cohérents pour compositing 2D

National audienceDans le cadre d’une réalisation cinématographique, le projet Previz (FUI 15, www.previz.eu) vise à fournir au réalisateur le moyen de prévisualiser les effets spéciaux en temps réel en cours le tournage. Pour ce faire, il est nécessaire d’assurer une cohérence entre le virtuel et le réel, et plus particulièrement d’accorder les interactions entre les personnages réels et les personnages virtuels. Dans ce cas, il est indispensable, dans le flux vidéo de la caméra du réalisateur, d’une part de séparer le sujet du décor et d’autre part de reconstruire son mouvement. Ce processus est connu pour fonctionner parfaitement en environnement contraint c’est-à-dire en utilisant un fond vert ou au mieux un décor non changeant. Dans ces conditions, on a souvent recours à plusieurs caméras fixes et un éclairage contrôlé pour éviter les brusques variations de luminosités. Nous nous plaçons dans le cas où une seule caméra filme la scène. Nous n’apposons aucune contrainte sur le mouvement de la caméra et il n’est pas connu a priori mais la position de la caméra dans l’environnement est calculée en temps réel. Par ailleurs, les conditions de tournage ne permettent pas de faire un apprentissage a priori du décor. Cela amène deux difficultés. D’une part des éléments du décor peuvent apparaître et disparaître du champ de vision de la caméra et, d’autre part, le décor qui est statique apparaît en mouvement dans la séquence vidéo. Le travail présenté dans ce poster s’attache à séparer l’acteur du décor

Shape From Silhouette: Towards a Solution for Partial Visibility Problem

International audienceAcquiring human shape is a prerequisite to many applications in augmented and virtual reality, as well as in computer graphics and animation.The acquisition of a real person must be precise enough to have the best possible (realistic) rendering.To do so in real time, "Shape-from-silhouette" (SFS) methods are used. One limitation of these methods is that the acquired subject must be visible from all the camera filming it.If not, some parts of the object are not reconstructed in 3d.This paper presents a modified SFS algorithm, that extends the 3d reconstruction space.Our extension allows to build an estimation of an object's 3d shape even if it comes out of sight from one or more cameras

Real-time and Markerless 3D Human Motion Capture using Multiple Views

International audienceWe present a fully automated system for real-time and markerless 3D human motion capture. Our process is based on fast algorithms, uses simple techniques and requires low cost devices. Using input frommultiple calibrated webcams, an extended "Shape from Silhouette" algorithm reconstructs the person in real-time. Fasts 3D shape and 3D skin parts analysis provide a robust and real-time system for human full-body tracking. Animation skeleton and simple morphological constraints make easier the motion capture process. Thanks to fast and simple algorithms and low-cost cameras, our system is well suited for home entertainment device.Results on real video sequences with fast and complex movements, demonstrate our approach robustness