Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa

West Africa is currently witnessing the most extensive Ebola virus (EBOV) outbreak so far recorded. Until now, there have been 27,013 reported cases and 11,134 deaths. The origin of the virus is thought to have been a zoonotic transmission from a bat to a two-year-old boy in December 2013 (ref. 2). From this index case the virus was spread by human-to-human contact throughout Guinea, Sierra Leone and Liberia. However, the origin of the particular virus in each country and time of transmission is not known and currently relies on epidemiological analysis, which may be unreliable owing to the difficulties of obtaining patient information. Here we trace the genetic evolution of EBOV in the current outbreak that has resulted in multiple lineages. Deep sequencing of 179 patient samples processed by the European Mobile Laboratory, the first diagnostics unit to be deployed to the epicentre of the outbreak in Guinea, reveals an epidemiological and evolutionary history of the epidemic from March 2014 to January 2015. Analysis of EBOV genome evolution has also benefited from a similar sequencing effort of patient samples from Sierra Leone. Our results confirm that the EBOV from Guinea moved into Sierra Leone, most likely in April or early May. The viruses of the Guinea/Sierra Leone lineage mixed around June/July 2014. Viral sequences covering August, September and October 2014 indicate that this lineage evolved independently within Guinea. These data can be used in conjunction with epidemiological information to test retrospectively the effectiveness of control measures, and provides an unprecedented window into the evolution of an ongoing viral haemorrhagic fever outbreak.status: publishe

L’imagerie marine aiguise le regard de la science sur l’océan

Le 4e rendez-vous mondial des spécialistes de l’imagerie marine “Marine Imaging Workshop” s’est tenu à Brest en octobre 2022, à l’invitation de l’Ifremer. Une centaine d’experts a fait le point sur ce secteur dont les avancées ne cessent d’éclairer les océans sous un jour nouveau. Les projets portés par l’Ifremer et ses partenaires dans ce domaine en apportent une belle illustration

Marine Science Videos

More and more research work on marine environment is based on the analysis of imagery. Thanks to technological development, we can now monitor ocean ecosystems using video cameras deployed on different platforms. Video acquisition provides information on organisms’ life and on environmental conditions. The sources of video data and the subjects of interest are many and varied: films from submersible dives in deep-sea environment, programmed video sequences of undersea rotary video stations in lagoons, high-frequency video data on deep-sea observatories, video observations recorded by fixed and autonomous camera devices on fishing gears, and others. The information contained in those images is essential to understand species biology and the functioning of these ecosystems, and ultimately inform environmental management policies. Because of the video data specificity (volumes, formats, diffusion…) a dedicated system has to be proposed for displaying and making accessible this huge archive of imagery, still growing every day. In spring 2015 IFREMER opened a new web portal called “Marine Science Videos” (http://video.ifremer.fr/). The first objective of this video library was to give access to recent and historical images produced during the IFREMER submersibles dives (ROV Victor 6000 and Nautile). Users can view and search videos and photos by keywords or dive information (cruise, submersible, dive, year, zone, camera…). Indeed, one or more submersibles can be deployed during oceanographic cruises in order to perform several dives lasting from some hours to some days. With their cameras catching videos throughout the dive they produce Tera Bytes of footages that are worth to be proposed to all IFREMER’S partners and to the public. The videos are available within three definitions (Low, Medium and High) in the MP4 H264 proxy format. Metadata relative to submersible dives and acquisition conditions are proposed together with this data: submersible position and attitude, temperature and salinity conditions, camera position and configuration. Comments recorded simultaneously with the videos are displayed if existing. Furthermore, images acquired during corresponding operations are accessible in addition to the videos: • Thumbnails: also called « mini-films », these images result from an automatic video sampling at a given frequency. • Images: these are photos from the submersible digital camera and video snapshots. Thumbnails, Low Definition images and videos are downloadable without restriction. Medium and High Definition versions can be used by authorised persons or on demand

L’imagerie à Ifremer: une enquête interne

Suite aux activités du groupe Imagerie en 2018 (notamment l'Atelier Imagerie en mai 2018) et à la demande de la Direction Scientifique, il a été décidé de dresser un état des lieux précis de l'utilisation de l'imagerie à Ifremer. Cet état des lieux a été réalisé grâce à une enquête basée sur un questionnaire en ligne auquel 172 personnes ont répondu entre février et mai 2019. Les résultats sont destinés à alimenter un bilan quantifié, et à envisager les perspectives en terme de définition d'une cellule Imagerie. Ils ont également permis d'identifier les collègues intéressés à participer aux sous-groupes thématiques mis en place au sein du groupe Imagerie. L’imagerie est utilisée par 61% des répondants qui se répartissent dans les différents départements avec de nombreuses applications en écologie et en halieutique et des développements technologiques. 86% des répondants sont sous statut permanent. L’imagerie est utilisée depuis plus de 10 ans par 53% des répondants. Les types d’imagerie sont variés, ainsi que les outils utilisés. L’enquête permet d’estimer à 569 To le volume approximatif de données des projets, soit une moyenne de 18 To par projet. Les besoins exprimés concernent principalement la facilitation de l’annotation des images et la gestion des données, pour lesquels il serait nécessaire de renforcer les ressources en personnel formé. Les répondants s’expriment en faveur d’un Groupe Technique Imagerie qui remplirait plusieurs fonctions : formation et assistance, développement d’outils pour gérer les données et en faciliter l’exploitation, et animation et coordination interne

Le vieillissement de la population active : quel rôle pour l'analyse extra-financière ?

The ageing of working population : what role for the extra-financial analysis ? From an analysis of existent stakes of the ageing of working population, the authors illustrate in this article the way the extra-financial analysis can supplement the traditional financial analysis of firms and bring to the investor a more complete view of medium term risks and opportunities. JEL classification : G11, J11, J26, M14À partir d’une analyse des enjeux issus du vieillissement de la population active, les auteurs cherchent à illustrer dans cet article la manière dont l’analyse extra-financière peut compléter l’analyse financière traditionnelle des entreprises et apporter à l’investisseur une vue plus complète des risques et opportunités à moyen terme. Classification JEL : G11, J11, J26, M14Guinefort Catherine, Borremans Eric, Carval Morgan. Le vieillissement de la population active : quel rôle pour l'analyse extra-financière ? . In: Revue d'économie financière, n°85, 2006. L'investissement socialement responsable. pp. 307-316

ARCHIMEDE - A new software for management of geological and biological samples

Since 2003, IFREMER manages the marine geology database of Brest (BGMB) which includes information on geological samples (sediment cores and rocks) and geotechnical measurements collected by IFREMER teams and/or resources and related analyses (stratigraphy, lithology, chemistry, grain size). In the same way, the IFREMER Deep Sea Lab database (BIOCEAN) gathers data about biological, sediment and hydrological samples collected by IFREMER biologists and ecologists since 1967. These databases which include several thousands of operations and samples require having a better visibility for the scientific community through the improvement of existing software tools and services. Indeed, according to the current scientific projects and future applications (e.g. management of mining licenses, implementation of the Nagoya Protocol, observatory of mineral raw materials, data dissemination), it becomes crucial to access to: • the geographic position of sampling operations, • the samples description (preservation, identifications,…) and related analyses, • the samples physical location. In this context, a project was initiated in order to: • improve archiving and maintenance of marine samples collected during expensive marine cruises all over the world, • make visible and accessible the available information (data and samples) to the whole scientific community, • rationalise and optimise the logistic for cruise preparation for the French and international community. As part of this, a study about management of marine geological and biological samples and related data in a unique system has been undertaken. The main objective is to save all information about the technical and scientific work during the operational phase in the field and in the lab. All metadata and data about handling and curating of sampled materials have to be collated as well. In that aim, new tools and services have been developed: • A new database was designed by merging and adapting BGMB and BIOCEAN schemas. It allows management of multi-points operations, in-situ measures and observations. Different types and subsampling levels of samples (cores, fluids, organisms…) can be stored in relation with their physical place and transfers. The analyses on samples could also be managed following this new schema. • The onboard software SEALOG allows recording and reporting events and operations and tracking samples from cruises, dives and moorings operated by biologists and geologists. Back on land, these data are loaded into the central database. However they must be completed after processing of samples and performing analyses. • The graphical user interface connected to the new database, ARCHIMEDE, can be used in the lab, downstream the early acquisition at sea. This software was developed through four structuring functions: (1) Data input; (2) Visual display of data and query; (3) Data import; (4) Data export. So far these functionalities enable processing of information about surface operations, diving operations and samples (acquisition date-time, positions, equipment, originator, description…). The marine samples physical location and movements (transfers, loans…) can already be tracked with ARCHIMEDE whereas the features for the management of analyses on samples will be added by 2017. A module dedicated to geographical sites is planned to be integrated in a longer term. • A website has been developped (soon available) in order to make visible and accessible to the whole scientific community all the information stored in the database. It is based on Sextant infrastructure (http://sextant.ifremer.fr/en/) which allows data display using the OGC Web Map Service protocol (WMS). Thanks to this website, scientists and general public will be able to locate geological and biological material from sea floor and archived in different French repositories. They will have access to related data (analyses) and images according to restriction rules. This initiative was conducted through a collaborative relationship with field operators as well as laboratory staff in order to answer their needs and to offer user-oriented solutions. Besides providing a way for scientists and data managers to enhance the currently existing data flows, this project aims to improve our capabilities in data and information security, management, use and delivery. This is of vital importance for marine researchers, industry and policy-makers in the context of various studies, from the climate change prediction, marine resources assessment, to off shore engineering, and to make evidence-based decisions in France and globally. The presentation will focus primarily on the software ARCHIMEDE, related developments and perspectives

Mg/Ca and S/Ca ratios in the skeleton of the starfish Asterias rubens

info:eu-repo/semantics/nonPublishe

A comprehensive review of artificial intelligence-based approaches for biodiversity studies in the deep sea

International audienc