Philippe JEAN-PIERRE

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• Type de publi. : Article dans une revue
• Date de publi. : 16/03/2024
• Auteurs : Michaël Luciano TantelySoa Fy AndriamandimbyMaminirina Fidelis AmbinintsoaManou Rominah RaharinirinaJean Théophile RafisandratantsoaJean-Pierre RavaloheryAina Nirina HarimananaNirina Nantenaina RanoelisonJudickaelle IrinantenainaMiamina Fidy AnkasitrahanaDany Bakoly RanoaritianaLaurence RandrianasoloRindra Vatosoa RandremananaVincent LacostePhilippe DussartRomain Girod
• Organismes : Institut Pasteur de Madagascar Institut Pasteur de Madagascar Institut Pasteur de Madagascar Institut Pasteur de Madagascar Institut Pasteur de Madagascar Institut Pasteur de Madagascar Institut Pasteur de Madagascar Institut Pasteur de Madagascar Institut Pasteur de Madagascar Ministère de la Santé Publique - Ministry of Public Health [Antananarivo, Madagascar] Ministère de la Santé Publique - Ministry of Public Health [Antananarivo, Madagascar] Institut Pasteur de Madagascar Institut Pasteur de Madagascar Institut Pasteur de Madagascar Institut Pasteur de Madagascar Institut Pasteur de Madagascar
• Publié dans Pathogens le 26/10/2020

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Résumé : A Rift Valley fever (RVF) outbreak occurred in at least five regions of Madagascar in 2021. The aim of this study was to provide an overview of the richness, abundance, ecology, and trophic preferences of mosquitoes in the Mananjary district and to investigate the distribution of mosquitoes that were RT-PCR-positive for RVFV. Three localities were prospected from 26 April to 4 May 2021, using light traps, BG-Sentinel traps baited with an artificial human odor, Muirhead-Thomson pit traps, and indoor pyrethroid spray catches. A total of 2806 mosquitoes belonging to at least 26 species were collected. Of 512 monospecific pools of mosquitoes tested with real-time RT-PCR, RVFV was detected in 37 pools representing 10 mosquito species. The RVFV-positive species were as follows: Aedes albopictus, Ae. argenteopunctatus, Anopheles coustani, An. gambiae s.l., An. mascarensis, An. squamosus/cydippis, Culex antennatus, Cx. decens, Cx. Tritaeniorhynchus, and Uranotaenia spp. Of the 450 tested engorged females, 78.7% had taken a blood meal on humans, 92.9% on cattle, and 71.6% had taken mixed (human–cattle) blood meals. This investigation suggests the potential role of mosquitoes in RVFV transmission within this epizootic/epidemic context and that the human populations at the three study sites were highly exposed to mosquitoes. Therefore, the use of impregnated mosquito nets as an appropriate prevention method is recommended.

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Fichiers liés : pathogens-13-00258.pdf

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• Type de publi. : Communication dans un congrès
• Date de publi. : 15/03/2024
• Auteurs : Jean-Pierre ChevrotTristan DumasJean-Philippe MaguéLouise Tarrade
• Organismes : LInguistique et DIdactique des Langues Étrangères et Maternelles LInguistique et DIdactique des Langues Étrangères et Maternelles Institut Rhône-Alpin des systèmes complexes Interactions, Corpus, Apprentissages, Représentations Interactions, Corpus, Apprentissages, Représentations

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Résumé : L’inférence démograpique est un ensemble de méthodes computationnelles permettant de déduire les attributs sociodémographiques (genre, niveau d’éducation, revenu, etc.) d’utilisateurs (d’Instagram, de téléphones portables), à partir des contenus (textes, images) et comportements qu’ils produisent en ligne et de données associées (localisation GPS, réseau de contacts). Les enjeux sont commerciaux, pour cibler publicités et offres, mais ils concernent aussi l’épidémiologie numérique, la prévention ou les sciences politiques (Abitbol et al., 2018; Abitbol & Karsai, 2020, 2020; Ciot et al., 2013; Lasri et al., 2023; Wang et al., 2019). Dans le champ sociolinguistique, la capacité d’inférer des informations à partir des usages du langage renvoie à la notion d’indexicalité. Les traits indexicaux sont les aspects d’une langue associés à des informations sociales (origine régionale, affiliation à un groupe), individuelles (émotion, état de santé) ou contextuelles (nature de la situation) (Foulkes, 2010). Même si la notion reste débattue du fait des conceptions simplistes qui pourraient en découler (Eckert, 2008), elle fournit une base conceptuelle et des outils pour mettre en perspective les travaux computationnels sur l’inférence démographique. Alors que les travaux du domaine computationnel testent l’efficacité des algorithmes ou utilisent leurs sorties à d’autres fins, nous allons comparer les décisions prises par des Modèles de langage fondés sur l’IA à propos du profil social d’utilisateurs de X (ex-Twitter) aux mêmes décisions prises par un échantillon de locuteurs. Dans la base SoSweet (www.ortolang.fr/market/corpora/sosweet) comptant 658 747 413 tweets produits par 2 878 562 utilisateurs, nous avons utilisé un sous-corpus de 4 974 utilisateurs dont le genre, l’âge, et le statut économique ont été estimés par observation directe des profils et par projection des coordonnées GPS sur une carte de France des revenus (INSEE). D’une part, ce sous-corpus a permis l’examen des relations entre traits langagiers (fréquence des émojis, des graphies non-standard…) et profils sociaux des utilisateurs. D’autre part il a servi de base pour entrainer un modèle de langage (CamemBERT, Martin et al., 2020) à identifier genre, revenu et âge des utilisateurs. Les décisions de ce Modèle de langage ainsi que celles d’autres modèles plus récents (Chat GPT, etc.) seront comparées aux jugements effectués sur le même matériel par environ 200 participants lors d’une enquête réalisée en ligne et utilisant plusieurs méthodes d’exploration des perceptions en sociolinguistique. Nous centrerons notre présentation sur les divergences et les convergences dans les décisions prises par les Modèles de langage et les échantillons de locuteurs. Nous nous demanderons si ces divergences et convergences dépendent des trois catégories testées (âge, revenu, genre), d’un usage particulier de la variété de français numérique (contenu lexical, présence d’émojis...) ou du profil des répondants à l’enquête (genre, niveau de diplôme, familiarité avec les médias sociaux). Notre objectif est d’améliorer notre connaissance globale du fonctionnement de l’indexicalité.

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• Type de publi. : Article dans une revue
• Date de publi. : 14/03/2024
• Auteurs : Anne Santerre HenriksenKaty JeannotAntonio OliverJohn D PerryMathias W PletzStefania StefaniIan MorrisseyChristopher LongshawBirgit WillingerDavid LeysseneChristian CattoenCorentine AlauzetPierre BoyerVéronique DuboisKaty JeannotStephane CorvecJean-Philippe LavigneThomas GuillardAudrey Merens GontierThierry NaasHolger RohdeStefan ZiesingCan ImirzaliogluKlaus-Peter HunfeldJette JungSören GatermannMathias W PletzGabriele BiancoAnna GiammancoDavide CarcioneGiammarco RaponiCaterina MatinatoEnea Gino Di DomenicoPaolo GaibaniAnna MarcheseFabio ArenaClaudia NiccolaiStefania StefaniCristina PitartJose Luis BarriosEmilia CercenadoGerman BouAlicia Beteta LopezRafael CantonJose Lopez HontangasIrene Gracia-AhufingerAntonio OliverLorena Lopez-CereroNieves LarrosaDavid WarehamJohn D PerryAnna CaseyJasvir NahlDaniel HughesMichael CoyneMichelle ListerMarie Attwood
• Organismes : Shionogi & Co Laboratoire Chrono-environnement (UMR 6249) Centre National de Référence de la Résistance aux Antibiotiques Centre Hospitalier Régional Universitaire de Besançon Université Marie et Louis Pasteur Fundació Institut d'Investigació Sanitària Illes Balears Freeman Hospital Universitätsklinikum Jena = Jena University Hospital [Jena, Germany] Università degli studi di Catania = University of Catania Antimicrobial Focus Ltd Shionogi & Co Stress, Immunité, Pathogènes Laboratoire Chrono-environnement (UMR 6249) Centre National de Référence de la Résistance aux Antibiotiques Centre Hospitalier Régional Universitaire de Besançon Université Marie et Louis Pasteur Virulence Bactérienne et Infections Chroniques Centre Hospitalier Universitaire de Nîmes
• Publié dans Microbiology Spectrum le 26/10/2020

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Résumé : Carbapenem-resistant Pseudomonas aeruginosa and Acinetobacter spp. represent major threats and have few approved therapeutic options. Non-fermenting Gram-negative isolates were collected from hospitalized inpatients from 49 sites in 6 European countries between 01 January 2020 and 31 December 2020 and underwent susceptibility testing against cefiderocol and β-lactam/β-lactamase inhibitor combinations. Meropenem-resistant (MIC >8 mg/L), cefiderocol-susceptible susceptiblecefiderocol-susceptibleisolates were analyzed by PCR, and cefiderocol-resistant isolates were analyzed by whole-genome sequencing to identify resistance mechanisms. Overall, 1,451 (950 P. aeruginosa; 501 Acinetobacter spp.) isolates were collected, commonly from the respiratory tract (42.0% and 39.3%, respectively). Cefiderocol susceptibility was higher than β-lactam/β-lactamase inhibitor combinations against P. aeruginosa (98.9% vs 83.3%–91.4%), and P. aeruginosa resistant to meropenem (n = 139; 97.8% vs 12.2%–59.7%), β-lactam/β-lactamase inhibitor combinations (93.6%–98.1% vs 10.7%–71.8%), and both meropenem and ceftazidime-avibactam (96.7% vs 5.0%–45.0%) or ceftolozane-tazobactam (98.4% vs 8.1%–54.8%), respectively. Cefiderocol and sulbactam-durlobactam susceptibilities were high against Acinetobacter spp. (92.4% and 97.0%) and meropenem-resistant Acinetobacter spp. (n = 227; 85.0% and 93.8%) but lower against sulbactam-durlobactam- (n = 15; 13.3%) and cefiderocol- (n = 38; 65.8%) resistant isolates, respectively. Among meropenem-resistant P. aeruginosa and Acinetobacter spp., the most common β-lactamase genes were metallo-β-lactamases [30/139; blaVIM-2 (15/139)] and oxacillinases [215/227; blaOXA-23 (194/227)], respectively. Acquired β-lactamase genes were identified in 1/10 and 32/38 of cefiderocol-resistant P. aeruginosa and Acinetobacter spp., and pirA-like or piuA mutations in 10/10 and 37/38, respectively. Conclusion: cefiderocol susceptibility was high against P. aeruginosa and Acinetobacter spp., including meropenem-resistant isolates and those resistant to recent β-lactam/β-lactamase inhibitor combinations common in first-line treatment of European non-fermenters.

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Fichiers liés : Henriksen et al,pseudomonas Microbiology spectrum, 2024.pdf

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• Type de publi. : Article dans une revue
• Date de publi. : 14/03/2024
• Auteurs : Pierre KalfonWissam El-HageMarie-Agnès GeantotConstance FavierLaëtitia Bodet-ContentinKhaldoun KuteifanPierre-Yves OlivierDidier ThéveninJulien PottecherJullien Crozon-ClauzelBénédicte MauchienArnaud GalboisRoland de VaraxSabine ValeraPhilippe EstagnasieAudrey BerricMartine NyungaNathalie RevelGeorges SimonBenjamin KowalskiAchille SossouThomas SignouretMarc LeoneCharles DelaléAurélien SeemannSigismond LasockiJean-Pierre QuenotAntoine MonselOlivier MichelMathieu PageRené-Gilles PatrigeonWalid NicolaArnaud ThilleGuillaume HékimianPascal AuquierKarine Baumstarck
• Organismes : Hôpital Louis Pasteur [Chartres] Centre d'études et de recherche sur les services de santé et la qualité de vie Hôpital Privé La Casamance [Marseille] Imaging, Brain & Neuropsychiatry Centre Hospitalier Régional Universitaire de Tours Service d'anesthésie - réanimation chirurgicale [CHU de Dijon] Centre d'études et de recherche sur les services de santé et la qualité de vie methodS in Patients-centered outcomes and HEalth ResEarch Centre d’Investigation Clinique [CHRU Tours] Réseau CRICS-TRIGGERSEP [Clinical Research in Intensive Care and Sepsis - TRIal Group for Global Evaluation and Research in SEPsis – Labellisé F-CRIN (French Clinical Research Infrastructure Network)] Groupe hospitalier de la région de Mulhouse et Sud-Alsace Centre Hospitalier Universitaire d'Angers Centre Hospitalier de Lens Hôpital de Hautepierre [Strasbourg] Hôpital Edouard Herriot [CHU - HCL] Hôpital Louis Pasteur [Chartres] Centre Hospitalier Privé Claude Galien - Ramsay Santé Centre hospitalier Les Chanaux [Mâcon] Hôpital Nord [CHU - APHM] Clinique Ambroise Paré [Centres Médico-Chirurgicaux Ambroise Paré, Pierre Cherest, Hartmann] Centre Hospitalier Intercommunal Toulon-La Seyne sur Mer - Hôpital Sainte-Musse Hôpital Victor Provo [Roubaix] Hôpital Pasteur [Nice] Centre hospitalier de Troyes Centre Hospitalier de Douai [Douai, Nord] Centre Hospitalier Emile Roux [Le Puy-en-Velay] Hôpital Européen [Fondation Ambroise Paré - Marseille] Hôpital Nord [CHU - APHM] Centre Hospitalier Simone-Veil de Blois [Blois] Nouvelle Clinique de Tours Saint Gatien-Alliance [Tours] Centre Hospitalier Universitaire d'Angers Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand Groupe de Recherche Clinique en Anesthésie Réanimation médecine PEriopératoire Centre Hospitalier Jacques Coeur [Bourges] Clinique Convert [Bourg-en-Bresse] Centre hospitalier d'Auxerre Centre Hospitalier de l'Agglomération Montargoise [Amilly] Centre hospitalier universitaire de Poitiers = Poitiers University Hospital CHU Pitié-Salpêtrière [AP-HP] Centre d'études et de recherche sur les services de santé et la qualité de vie Centre d'études et de recherche sur les services de santé et la qualité de vie
• Publié dans Critical Care le 31/10/2020

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Résumé : Abstract Background Posttraumatic stress disorder (PTSD) after a stay in the intensive care unit (ICU) can affect one in five ICU survivors. At the beginning of the coronavirus disease 2019 (COVID-19) pandemic, admission to the ICU for COVID-19 was stressful due to the severity of this disease. This study assessed whether admission to the ICU for COVID-19 was associated with a higher prevalence of PTSD compared with other causes of ICU admission after adjustment for pre-ICU psychological factors. Methods This prospective observational comparative cohort study included 31 ICUs. Eligible patients were adult ICU survivors hospitalized during the first wave of COVID-19 pandemic in France, regardless of the reason for admission. The prevalence of presumptive diagnosis of PTSD at 6 months was assessed using the PTSD Checklist for DSM-5 (PCL-5). Sociodemographics, clinical data, history of childhood trauma (Childhood Trauma Questionnaire [CTQ]), and exposure to potentially traumatic events (Life Events Checklist for DSM-5 [LEC-5]) were assessed. Results Of the 778 ICU survivors included during the first wave of COVID-19 pandemic in France, 417 and 361 were assigned to the COVID-19 and non-COVID-19 cohorts, respectively. Fourteen (4.9%) and 11 (4.9%), respectively, presented with presumptive diagnosis of PTSD at 6 months ( p = 0.976). After adjusting for age, sex, severity score at admission, use of invasive mechanical ventilation, ICU duration, CTQ and LEC-5, COVID-19 status was not associated with presumptive diagnosis of PTSD using the PCL-5. Only female sex was associated with presumptive diagnosis of PTSD. However, COVID-19 patients reported significantly more intrusion and avoidance symptoms than non-COVID patients (39% vs. 29%, p = 0.015 and 27% vs. 19%, p = 0.030), respectively. The median PCL-5 score was higher in the COVID-19 than non-COVID-19 cohort (9 [3, 20] vs. 4 [2, 16], p = 0.034). Conclusion Admission to the ICU for COVID-19 was not associated with a higher prevalence of PTSD compared with admission for another cause during the first wave of the COVID-19 pandemic in France. However, intrusion and avoidance symptoms were more frequent in COVID-19 patients than in non-COVID-19 patients. Trial Registration : Clinicaltrials.gov Identifier NCT03991611, registered on June 19, 2019.

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• Type de publi. : Article dans une revue
• Date de publi. : 14/03/2024
• Auteurs : Jiaying HeWei LiZhe ZhaoLei ZhuXiaomeng DuYidi XuMinxuan SunJiaxin ZhouPhilippe CiaisWigneron J.-P.Ronggao LiuGuanghui LinLei Fan
• Organismes : Chinese Academy of Sciences [Beijing] Qing hua da xue = Tsinghua University = Université Tsinghoua [Beijing] Qing hua da xue = Tsinghua University = Université Tsinghoua [Beijing] Qing hua da xue = Tsinghua University = Université Tsinghoua [Beijing] Qing hua da xue = Tsinghua University = Université Tsinghoua [Beijing] Qing hua da xue = Tsinghua University = Université Tsinghoua [Beijing] Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] Qing hua da xue = Tsinghua University = Université Tsinghoua [Beijing] Qing hua da xue = Tsinghua University = Université Tsinghoua [Beijing] Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] Interactions Sol Plante Atmosphère Chinese Academy of Sciences [Beijing] Chinese Academy of Forestry Southwest University [Chongqing]
• Publié dans Frontiers in Remote Sensing le 16/08/2021

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Résumé : Tropical moist forests have been severely affected by natural and anthropogenic disturbances, leading to substantial changes in global carbon cycle and climate. These effects have received great attention in scientific research and debates. Here we review recent progress on drivers and ecological impacts of tropical moist forest disturbances, and their monitoring and modeling methods. Disturbances in tropical moist forests are primarily driven by clearcutting, selective logging, fire, extreme drought, and edge effects. Compound disturbances such as fire and edge effects aggravate degradation in the edge forests. Drought can result in terrestrial carbon loss via physiological impacts. These disturbances lead to direct carbon loss, biophysical warming and microclimate change. Remote sensing observations are promising for monitoring forest disturbances and revealing mechanisms, which will be useful for implementing disturbance processes in dynamic vegetation models. Yet, constrained spatiotemporal coverages and resolutions limit the application of these data in process-based models. It is also challenging to represent physical processes derived from fine-resolution remote sensing data in coarse-resolution models. We highlight the need to continuously integrate new datasets and physical processes in forest disturbance modeling to advance understanding of disturbance patterns and impacts. Interactions and impacts of climate change and anthropogenic activities should also be considered for modeling and assessing feedbacks of tropical moist forest disturbances.

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Fichiers liés : frsen-05-1332728.pdf

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• Type de publi. : Article dans une revue
• Date de publi. : 13/03/2024
• Auteurs : Nina GrandremyPaul BourriauEdwin DachéMarie-Madeleine DanielouMathieu DorayChristine DupuyBertrand ForestLaetitia JalabertMartin HuretSophie Le MestreAntoine NowaczykPierre PetitgasPhilippe PineauJustin RouxelMorgan TardivelJean-Baptiste Romagnan
• Organismes : Dynamique et durabilité des écosystèmes : de la source à l’océan Dynamique et durabilité des écosystèmes : de la source à l’océan Biologie et Ecologie des Ecosystèmes Marins Profonds Unité Dynamiques des Écosystèmes Côtiers Dynamique et durabilité des écosystèmes : de la source à l’océan La Rochelle Université LIttoral ENvironnement et Sociétés Unité Recherches et Développements Technologiques Institut de la Mer de Villefranche Dynamique et durabilité des écosystèmes : de la source à l’océan Dynamique et durabilité des écosystèmes : de la source à l’océan Environnements et Paléoenvironnements OCéaniques Institut Français de Recherche pour l'Exploitation de la Mer LIttoral ENvironnement et Sociétés Unité Recherches et Développements Technologiques Institut Français de Recherche pour l'Exploitation de la Mer Unité Recherches et Développements Technologiques Dynamique et durabilité des écosystèmes : de la source à l’océan
• Publié dans Earth System Science Data le 23/10/2020

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Résumé : This paper presents two metazoan zooplankton datasets obtained by imaging samples collected on the Bay of Biscay continental shelf in spring during the PELGAS (PELagique GAScogne) integrated surveys over the 2004–2019 period. The samples were collected at night with a 200 µm mesh-size WP2 net fitted with a Hydrobios (back-run stop) mechanical flowmeter and hauled vertically from the sea floor to the surface, with the maximum depth set at 100 m when the bathymetry was deeper than this. The first dataset originates from samples collected from 2004 to 2016 and imaged on land with the ZooScan and is composed of 1 153 507 imaged and measured objects. The second dataset originates from samples collected from 2016 to 2019 and imaged onboard the R/V Thalassa with the ZooCAM and is composed of 702 111 imaged and measured objects. The imaged objects are composed of zooplankton individuals, zooplankton pieces, non-living particles and imaging artefacts ranging from 300 µm to 3.39 mm in equivalent spherical diameter which were individually imaged, measured and identified. Each imaged object is geolocated and associated with a station, a survey, a year and other metadata. Each object is described by a set of morphological and grey-level-based features (8 bit encoding, 0 = black, 255 = white), including size, that were automatically extracted from each individual image. Each object was taxonomically identified using the web-based application Ecotaxa with built-in random-forest and CNN-based semi-automatic sorting tools, which was followed by expert validation or correction. The objects were sorted into 172 taxonomic and morphological groups. Each dataset features a table combining metadata and data at individual-object granularity from which one can easily derive quantitative population and community descriptors such as abundances, mean sizes, biovolumes, biomasses and size structure. Each object's individual image is provided along with the data. These two datasets can be used in combination for ecological studies, as the two instruments are interoperable, or they can be used as training sets for ZooScan and ZooCAM users. The data presented here are available at the SEANOE dataportal: https://doi.org/10.17882/94052 (ZooScan dataset, Grandremy et al., 2023c) and https://doi.org/10.17882/94040 (ZooCAM dataset, Grandremy et al., 2023d).

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Fichiers liés : essd-16-1265-2024.pdf

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• Type de publi. : Article dans une revue
• Date de publi. : 13/03/2024
• Auteurs : Nina GrandremyPaul BourriauEdwin DachéMarie-Madeleine DanielouMathieu DorayChristine DupuyBertrand ForestLaetitia JalabertMartin HuretSophie Le MestreAntoine NowaczykPierre PetitgasPhilippe PineauJustin RouxelMorgan TardivelJean-Baptiste Romagnan
• Organismes : Dynamique et durabilité des écosystèmes : de la source à l’océan Dynamique et durabilité des écosystèmes : de la source à l’océan Biologie et Ecologie des Ecosystèmes Marins Profonds Unité Dynamiques des Écosystèmes Côtiers Dynamique et durabilité des écosystèmes : de la source à l’océan LIttoral ENvironnement et Sociétés Unité Recherches et Développements Technologiques Institut de la Mer de Villefranche Dynamique et durabilité des écosystèmes : de la source à l’océan Dynamique et durabilité des écosystèmes : de la source à l’océan Environnements et Paléoenvironnements OCéaniques Institut Français de Recherche pour l'Exploitation de la Mer LIttoral ENvironnement et Sociétés Unité Recherches et Développements Technologiques Unité Recherches et Développements Technologiques Dynamique et durabilité des écosystèmes : de la source à l’océan
• Publié dans Earth System Science Data le 11/09/2023

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Résumé : This paper presents two metazoan zooplankton datasets obtained by imaging samples collected on the Bay of Biscay continental shelf in spring during the PELGAS integrated surveys, over the 2004–2019 period. The samples were collected at night, with a WP2 200 µm mesh size fitted with a Hydrobios (back-run stop) mechanical flowmeter, hauled vertically from the sea floor to the surface with a maximum depth set at 100 m when the bathymetry is deeper. The first dataset originates from samples collected from 2004 to 2016, imaged on land with the ZooScan and is composed of 1,153,507 imaged and measured objects. The second dataset originates from samples collected from 2016 to 2019, imaged on board the R/V Thalassa with the ZooCAM and is composed of 702,111 imaged and measured objects. The imaged objects is composed of zooplankton individuals, zooplankton pieces, non-living particles and imaging artefacts, ranging from 300 µm to 3.39 mm Equivalent Spherical Diameter, individually imaged, measured and identified. Each imaged object is geolocated, associated to a station, a survey, a year and other metadata. Each object is described by a set of morphological and grey level based features (8 bits encoding, 0 = black, 255 = white), including size, automatically extracted on each individual image. Each object was taxonomically identified using the web based application Ecotaxa with built-in, random forest and CNN based, semi-automatic sorting tools followed by expert validation or correction. The objects were sorted in 172 taxonomic and morphological groups. Each dataset features a table combining metadata and data, at the individual object granularity, from which one can easily derive quantitative population and communities descriptors such as abundances, mean sizes, biovolumes, biomasses, and size structure. Each object’s individual image is provided along with the data. These two datasets can be used combined together for ecological studies as the two instruments are interoperable, or as training sets for ZooScan and ZooCAM users.

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Fichiers liés : essd-16-1265-2024.pdf

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• Type de publi. : Communication dans un congrès
• Date de publi. : 11/03/2024
• Auteurs : Boubacar DiarraKarine GuillouardMeryem OuzzifPhilippe MerleJean-Bernard Stefani
• Organismes : Orange Innovation Orange Innovation Orange Innovation Self-adaptation for distributed services and large software systems Sound Programming of Adaptive Dependable Embedded Systems

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Résumé : Kubernetes has emerged as the leading platform for orchestrating cloud-native network functions (CNF). The description of the hardware and software architecture of systems to be deployed with Kubernetes is defined in configuration files called manifests. In order to address the errors that these manifests may contain, manifest verification tools have been developed. However, evaluating and selecting the most appropriate verification tool for a given project is a difficult task. To facilitate this evaluation process, we identified and characterized the most relevant verification capabilities, useful also in the CNF context. The selected capabilities serve as criteria for the evaluation of manifest verification tools. In total, we have identified 13 criteria, like the variety of verification types or the ability to carry out JSON Schema-based verification. The identified criteria were used to evaluate 16 of the most commonly used verification tools in the Kubernetes community. This evaluation revealed several shortcomings in the existing tools.

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Fichiers liés : icin-camera-ready.pdf

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• Type de publi. : Article dans une revue
• Date de publi. : 09/03/2024
• Auteurs : Oumaima MoubsetDenis FillouxHugo FontèsCharlotte JulianEmmanuel FernandezSerge GalziLaurence BlondinSélim Ben ChehidaJean-Michel LettFrançois MesléardSimona KrabergerJoy M CusterAndrew SalywonElizabeth MakingsArmelle MaraisFrédéric ChiroleuPierre LefeuvreDarren MartinThierry CandresseArvind VarsaniVirginie RavignéPhilippe Roumagnac
• Organismes : Plant Health Institute of Montpellier Département Systèmes Biologiques Plant Health Institute of Montpellier Institut méditerranéen de biodiversité et d'écologie marine et continentale Institut de recherche de la Tour du Valat Plant Health Institute of Montpellier Plant Health Institute of Montpellier Plant Health Institute of Montpellier Département Systèmes Biologiques Plant Health Institute of Montpellier Peuplements végétaux et bioagresseurs en milieu tropical Peuplements végétaux et bioagresseurs en milieu tropical Département Systèmes Biologiques Institut méditerranéen de biodiversité et d'écologie marine et continentale Institut de recherche de la Tour du Valat Arizona State University [Tempe] Arizona State University [Tempe] Desert Botanical Garden Arizona State University [Tempe] Biologie du fruit et pathologie Peuplements végétaux et bioagresseurs en milieu tropical Peuplements végétaux et bioagresseurs en milieu tropical Laboratoire de Matériaux Céramiques et de Mathématiques University of Cape Town Biologie du fruit et pathologie Arizona State University [Tempe] University of Cape Town Plant Health Institute of Montpellier Plant Health Institute of Montpellier
• Publié dans Virus Evolution le 25/01/2017

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Résumé : The increase in human-mediated introduction of plant species to new regions has resulted in a rise of invasive exotic plant species (IEPS) that has had significant effects on biodiversity and ecosystem processes. One commonly accepted mechanism of invasions is that proposed by the enemy release hypothesis (ERH), which states that IEPS free from their native herbivores and natural enemies in new environments can outcompete indigenous species and become invasive. We here propose the virome release hypothesis (VRH) as a virus-centered variant of the conventional ERH that is only focused on enemies. The VRH predicts that vertically transmitted plant-associated viruses (PAV, encompassing phytoviruses and mycoviruses) should be co-introduced during the dissemination of the IEPS, while horizontally transmitted PAV of IEPS should be left behind or should not be locally transmitted in the introduced area due to a maladaptation of local vectors. To document the VRH, virome richness and composition as well as PAV prevalence, co-infection, host range, and transmission modes were compared between indigenous plant species and an invasive grass, cane bluestem (Bothriochloa barbinodis), in both its introduced range (southern France) and one area of its native range (Sonoran Desert, Arizona, USA). Contrary to the VRH, we show that invasive populations of B. barbinodis in France were not associated with a lower PAV prevalence or richness than native populations of B. barbinodis from the USA. However, comparison of virome compositions and network analyses further revealed more diverse and complex plant-virus interactions in the French ecosystem, with a significant richness of mycoviruses. Setting mycoviruses apart, only one putatively vertically transmitted phytovirus (belonging to the Amalgaviridae family) and one putatively horizontally transmitted phytovirus (belonging to the Geminiviridae family) were identified from B. barbinodis plants in the introduced area. Collectively, these characteristics of the B. barbinodis-associated PAV community in southern France suggest that a virome release phase may have immediately followed the introduction of B. barbinodis to France in the 1960s or 1970s, and that, since then, the invasive populations of this IEPS have already transitioned out of this virome release phase, and have started interacting with several local mycoviruses and a few local plant viruses.

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Fichiers liés : Moubset-VE-2024-CC-BY-NC.pdf

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• Type de publi. : Article dans une revue
• Date de publi. : 05/03/2024
• Auteurs : Sybren de HoogThomas WalshSarah A AhmedAna Alastruey-IzquierdoBarbara D AlexanderMaiken Cavling ArendrupEsther BabadyFeng-Yan BaiJoan-Miquel Balada-LlasatAndrew BormanAnuradha ChowdharyAndrew ClarkRobert C ColgroveOliver A CornelyTanis C DinglePhilippe J DufresneJeff FullerJean-Pierre GangneuxConnie GibasHeather GlasgowYvonne GraserJacques GuillotAndreas H. GrollGerhard HaaseKimberly HansonAmanda HarringtonDavid L HawksworthRandall T HaydenMartin HoeniglVit HubkaKristie JohnsonJulianne V KusRuoyu LiJacques MeisMichaela LacknerFanny LanternierSixto Leal Jr.Francesca LeeShawn LockhartPaul LuethyIsabella MartinKyung J Kwon-ChungWieland MeyerM. Hong NguyenLuis Ostrosky-ZeichnerElizabeth PalavecinoPreeti PancholiPeter G PappasGary W ProcopScott A RedheadDaniel D RhoadsStefan RiedelBryan StevensKaede Ota SullivanPaschalis VergidisEmmanuel RoilidesAmir SeyedmousaviLili TaoVania A VicenteRoxana G VitaleQi-Ming WangNancy L WengenackLars WestbladeNathan P WiederholdP. Lewis WhiteChristina M WojewodaSean X Zhang
• Organismes : Radboud University Medical Center [Nijmegen] Peking University [Beijing] University of Maryland School of Medicine National Institute of Neurological Disorders and Stroke [Bethesda] Instituto de Salud Carlos III [Madrid] Duke University [Durham] Copenhagen University Hospital [Denmark] = Københavns Universitetshospital [Danmark] Memorial Sloan Kettering Cancer Center Chinese Academy of Sciences [Beijing] University of Delhi University of Glasgow Universität zu Köln = University of Cologne Archéosciences Bordeaux Archéosciences Bordeaux Institut de recherche en santé, environnement et travail Centre Hospitalier Universitaire de Rennes [CHU Rennes] = Rennes University Hospital [Pontchaillou] Archéosciences Bordeaux Charité - UniversitätsMedizin = Berlin University Medicine École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique SFR UA 4208 Interactions Cellulaires et Applications Thérapeutiques Infections Respiratoires Fongiques University of Delhi RWTH Aachen University = Rheinisch-Westfälische Technische Hochschule Aachen Institut Pasteur [Paris] University of Texas Health Science Center University of Vermont [Burlington] Johns Hopkins University School of Medicine [Baltimore]
• Publié dans Journal of Clinical Microbiology le 01/11/2020

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Fichiers liés : de Hoog et al. - 2024 - Reply to Kidd et al., Inconsistencies within the .pdf

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