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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Walker, Emily; Monestiez, Pascal; Gomez, Cécile; Lagacherie, Philippe;

    The limited availability of soil information has been recognized as a main limiting factor in digital soil mapping (DSM) studies. It is therefore important to optimize the joint use of the three sources of soil data that can be used as inputs of DSM models, namely spatial sets of measured sites, soil maps and soil sensing products.In this paper, we propose to combine these three inputs, through a cokriging with a categorical external drift (CKCED). This new interpolation technique was applied for mapping seven soil properties over a 24.6 km2 area located in the vineyard plain of Languedoc (Southern France), using an hyperspectral imagery product as example of a soil sensing data. Cross-validation results of CKCED were compared with those of five spatial and non-spatial techniques using one of these inputs or a combination of two of them.The results obtained in the La Peyne Catchment showed i) the utility of soil map and hyperspectral imagery products as auxiliary data for improving soil property predictions ii) the greater added-value of the latter against the former in most situations and iii) the feasibility and the interest of CKCED in a limited number of soil properties and data configurations. Testing CKCED in case study with soil maps of better quality and soil sensing techniques covering more area and depths should be necessary to better evaluate the benefits of this new technique. International audience

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Mémoires en Sciences...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Geoderma
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ProdInra
    Article . 2017
    License: CC BY SA
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Horizon / Pleins textes
    Other literature type . 2017
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Geoderma
    Article . 2017 . Peer-reviewed
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Mémoires en Sciences...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Geoderma
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ProdInra
      Article . 2017
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Horizon / Pleins textes
      Other literature type . 2017
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Geoderma
      Article . 2017 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Daniel Montoya; Sabrina Gaba; Claire de Mazancourt; Vincent Bretagnolle; +1 Authors

    Efficient management of agricultural management should consider multiple services and stakeholders. Yet, it remains unclear how to guarantee ecosystem services for multiple stakeholders' demands, especially considering the observed biodiversity decline following reductions in semi-natural habitat (SNH), and global change. Here, we use an ecosystem service model of intensively-managed agricultural landscapes to derive the best landscape compositions for different stakeholders' demands, and how they vary with stochasticity and the degree of pollination dependence of crops. We analyse three groups of stakeholders assumed to value different ecosystem services most-individual farmers (crop yield per area), agricultural unions (landscape production) and con-servationists (biodiversity). Additionally, we consider a social average scenario that aims at maximizing mul-tifunctionality. Trade-offs among stakeholders' demands strongly depend on the degree of pollination dependence of crops, the strength of environmental and demographic stochasticity, and the relative amount of an ecosystem service demanded by each stakeholder. Intermediate amounts of SNH deliver relatively high levels of the three services (social average). Our analysis further suggests that the current levels of SNH protection lie below these intermediate amounts of SNH in intensively-managed agricultural landscapes. Given the worldwide trends in agriculture and global change, current policies should start to consider factors such as crop type and stochasticity, as they can strongly influence best landscape compositions for different stakeholders. Our results suggest ways of managing landscapes to reconcile several actors' demands and ensure for biodiversity conservation and food production. International audience

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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    Europe PubMed Central
    Other literature type . 2019
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Ecological Modelling
    Other literature type . Article . 2020 . Peer-reviewed
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Europe PubMed Central
      Other literature type . 2019
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Ecological Modelling
      Other literature type . Article . 2020 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Tritsch, Isabelle; Arvor, Damien;

    Highlights • We emphasize the end of the boom-and-bust development pattern in the Brazilian Amazon. • Deforestation and socioeconomic development follow an inverted U-shape relationship. • Household incomes are greater in stabilized areas than in areas undergoing deforestation. • Environmental governance efforts fostered the emergence of EKC. Abstract Socioeconomic development in the Brazilian Amazon is currently reaching national averages although deforestation activity has been declining for a decade. As a consequence, recent studies rejected the widely agreed boom-and-bust development hypothesis that deforestation first generates an economic boom, which is then followed by a collapse as forest resources are depleted. Here, we confirm these studies that there is no boom-bust cycle and suggest that a new pattern of relationship between deforestation and socioeconomic development has emerged following an environmental Kuznets curve (EKC). In this scenario, environmental degradation increases in the early stages of economic development and decreases in later stages as the economy develops and wellbeing increases. To validate this assumption, we conducted the first sub-municipal analysis of socioeconomic development and deforestation in the Brazilian Amazon for the 2000–2010 period. Our results confirm the emergence of an EKC relationship with a turning point beyond which socioeconomic growth does not appear anymore to be a driver of deforestation. We also emphasize that areas subjected to active deforestation in 2010 present lower socio-Author manuscript version economic indicators than stabilized areas, pointing to the precarious socioeconomic situation of areas still undergoing active deforestation. We put these results in perspective by considering Brazilian efforts to ensure a transition in environmental governance with the objective of promoting land use sustainability through control of deforestation at the same time as supporting socioeconomic development. International audience

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ HAL Descartes; Mémoi...arrow_drop_down
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Land Use Policy
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Land Use Policy
    Other literature type . Article . 2016 . Peer-reviewed
    License: Elsevier TDM
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ HAL Descartes; Mémoi...arrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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      Other literature type . Article . 2016 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Courbot, Jean-Baptiste; Mazet, Vincent; Monfrini, Emmanuel; Collet, Christophe;

    Circum-Galactic Medium surrounding galaxies has been punctually detected, but its morphology remains largely unknown. The Multi-Unit Spectroscopic Explorer (MUSE) spectro-imager provides for the first time both spectral and spatial resolution to spatially map such features. The problem lies in the statistical detection of faint spatially-extended sources in massive hyperspectral images such as provided by MUSE, and has not been previously handled. This paper presents a statistical detection method based on hypothesis testing tackling this problem. The proposed strategy is step-by-step validated over alternative ways with simulations. Then, results on MUSE observations are presented. International audience

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ https://hal.archives...arrow_drop_down
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    https://doi.org/10.1109/icassp...
    Conference object . 2016 . Peer-reviewed
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    Authors: Zeller, Bernd; Legout, Arnaud; Bienaimé, Séverine; Gratia, Bruno; +3 Authors

    AbstractDouglas fir trees presumable stimulate nitrification in the soil. We studied in 21 French Douglas fir forests if and how nitrification is modulated by soil properties, past land use and current forest management. Soil (0–10 cm depth) was collected and initial concentrations of N-NH4+ and N-NO3−, potential net nitrogen mineralization (PNM) and net nitrification (PNN) rates and microbial biomass were measured. At 11 of the 21 sites, annual nitrate fluxes in the soil were measured using anion exchange resin bags. Soils contained between 2.3 to 29.4 mg N-NO3− kg soil−1. About 86% (±14%) of mineral N was nitrate. The proportion of nitrate increased to almost 100% during incubation. PNN varied from 0.10 mg N kg soil−1 day−1 to 1.05 mg N kg soil−1 day−1 (21 sites). Neither the initial nitrate concentration nor PNN was related to soil chemistry (pH, % C, %N, P, CEC), microbial biomass, texture, past land use or thinning. In situ net nitrate accumulation (NNA) estimated with resins beds varied from 4 to 100 kg N-NO3− ha−1 yr−1 (11 sites). It was positively correlated with base saturation, clay content, ELLENBERG N, temperature and negatively with soil organic N, C/N ratio and precipitation.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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    Scientific Reports
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    ProdInra
    Article . 2019
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    Scientific Reports
    Article . 2019 . Peer-reviewed
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      ProdInra
      Article . 2019
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      Scientific Reports
      Article . 2019 . Peer-reviewed
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    Authors: Andreas Wunsch; Tanja Liesch; Guillaume Cinkus; Nataša Ravbar; +4 Authors

    Despite many existing approaches, modeling karst water resources remains challenging as conventional approaches usually heavily rely on distinct system knowledge. Artificial neural networks (ANNs), however, require only little prior knowledge to automatically establish an input-output relationship. For ANN modeling in karst, the temporal and spatial data availability is often an important constraint, as usually no or few climate stations are located within or near karst spring catchments. Hence, spatial coverage is often not satisfactory and can result in substantial uncertainties about the true conditions in the catchment, leading to lower model performance. To overcome these problems, we apply convolutional neural networks (CNNs) to simulate karst spring discharge and to directly learn from spatially distributed climate input data (combined 2D-1D CNNs). We investigate three karst spring catchments in the Alpine and Mediterranean region with different meteorological-hydrological characteristics and hydrodynamic system properties. We compare the proposed approach both to existing modeling studies in these regions and to our own 1D CNN models that are conventionally trained with climate station input data. Our results show that all the models are excellently suited to modeling karst spring discharge (NSE: 0.73-0.87, KGE: 0.63-0.86) and can compete with the simulation results of existing approaches in the respective areas. The 2D models show a better fit than the 1D models in two of three cases and automatically learn to focus on the relevant areas of the input domain. By performing a spatial input sensitivity analysis, we can further show their usefulness in localizing the position of karst catchments. International audience

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    https://doi.org/10.5194/hess-2...
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    https://doi.org/10.5445/ir/100...
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      https://doi.org/10.5194/hess-2...
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    Authors: Caracciolo, C.; Aubin, S.; Jonquet, C.; Amdouni, E.; +6 Authors

    In this paper, we report on the outputs and adoption of the Agrisemantics Working Group of the Research Data Alliance (RDA), consisting of a set of recommendations to facilitate the adoption of semantic technologies and methods for the purpose of data interoperability in the field of agriculture and nutrition. From 2016 to 2019, the group gathered researchers and practitioners at the crossing point between information technology and agricultural science, to study all aspects in the life cycle of semantic resources: Conceptualization, edition, sharing, standardization, services, alignment, long term support. First, the working group realized a landscape study, a study of the uses of semantics in agrifood, then collected use cases for the exploitation of semantics resources a generic term to encompass vocabularies, terminologies, thesauri, ontologies. The resulting requirements were synthesized into 39 hints for users and developers of semantic resources, and providers of semantic resource services. We believe adopting these recommendations will engage agrifood sciences in a necessary transition to leverage data production, sharing and reuse and the adoption of the FAIR data principles. The paper includes examples of adoption of those requirements, and a discussion of their contribution to the field of data science. © 2020 The Author(s). Brandon Whitehead acknowledges with thanks the support of the CABI Development Fund. CABI is an international intergovernmental organization and we gratefully acknowledge the core financial support from our member countries (and lead agencies) including the United Kingdom (Department for International Development), China (Chinese Ministry of Agriculture), Australia (Australian Center for International Agricultural Research), Canada (Agriculture and Agri-Food Canada), Netherlands (Directorate-General for International Cooperation), and Switzerland (Swiss Agency for Development and Cooperation). See https:// www.cabi.org/about-cabi/who-we-work-with/key-donors/ for details. Sophie Aubin, Clement Jonquet, Emna Amdouni, Romain David and Catherine Roussey were supported, in part, by the French National Research Agency (ANR) Data to Knowledge in Agronomy and Biodiversity (D2KAB – www.d2kab.org – ANR-18-CE23-0017). Romain David was partly supported by the EPPN2020 project (H2020 grant N°731013), the EOSC-Life european program (grant agreement N°824087), the ‘Infrastructure Biologie Sante’ PHENOME-EMPHASIS project funded by the French National Research Agency (ANR-11-INBS-0012) and the ‘Programme d’Investissements d’Avenir’.

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    Data Science Journal
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    Article . 2020
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    arXiv.org e-Print Archive
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    Authors: Yi-Chen Chen; Wei-Che Chang; Shau-Ping Lin; Masataka Minami; +6 Authors

    Scalable production of avian cell lines exhibits a valuable potential on therapeutic application by producing recombinant proteins and as the substrate for virus growth due to the special glycosylation occurs in avian species. Chicken primordial germ cells (cPGCs), a germinal pluripotent avian cell type, present the ability of self-renewal, an anchorage-independent cell growth and the ability to be genetically modified. This cell type could be an interesting bioreactor system for industrial purposes. This study sought to establish an expandable culture system with defined components for three-dimensional (3D) culture of cPGCs. cPGCs were cultured in medium supplemented with the functional polymer FP003. Viscoelasticity was low in this medium but cPGCs did not sediment in culture and efficiencies of space and nutrient utilization were thus enhanced and consequently their expansion was improved. The total number of cPGCs increased by 17-fold after 1 week of culture in 3D-FAot medium, an aseric defined medium containing FP003 polymer, FGF2 and Activin A as growth factors and Ovotransferrin as protein. Moreover, cPGC cell lines stably expressed the germline-specific reporter VASA:tdTOMATO, as well as other markers of cPGCs, for more than 1 month upon culture in 3D-FAot medium, indicating that the characteristics of these cells are maintained. In summary, this novel 3D culture system can be used to efficiently expand cPGCs in suspension without mechanical stirring, which is available for long-term culture and no loss of cellular properties was found. This system provides a platform for large-scale culture of cPGCs.

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      PLoS ONE
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    Authors: Guitet, Stéphane; Herault, Bruno; Molto, Quentin; Brunaux, Olivier; +1 Authors

    Precise mapping of above-ground biomass (AGB) is a major challenge for the success of REDD+ processes in tropical rainforest. The usual mapping methods are based on two hypotheses: a large and long-ranged spatial autocorrelation and a strong environment influence at the regional scale. However, there are no studies of the spatial structure of AGB at the landscapes scale to support these assumptions. We studied spatial variation in AGB at various scales using two large forest inventories conducted in French Guiana. The dataset comprised 2507 plots (0.4 to 0.5 ha) of undisturbed rainforest distributed over the whole region. After checking the uncertainties of estimates obtained from these data, we used half of the dataset to develop explicit predictive models including spatial and environmental effects and tested the accuracy of the resulting maps according to their resolution using the rest of the data. Forest inventories provided accurate AGB estimates at the plot scale, for a mean of 325 Mg.ha-1. They revealed high local variability combined with a weak autocorrelation up to distances of no more than10 km. Environmental variables accounted for a minor part of spatial variation. Accuracy of the best model including spatial effects was 90 Mg.ha-1 at plot scale but coarse graining up to 2-km resolution allowed mapping AGB with accuracy lower than 50 Mg.ha-1. Whatever the resolution, no agreement was found with available pan-tropical reference maps at all resolutions. We concluded that the combined weak autocorrelation and weak environmental effect limit AGB maps accuracy in rainforest, and that a trade-off has to be found between spatial resolution and effective accuracy until adequate “wall-to-wall” remote sensing signals provide reliable AGB predictions. Waiting for this, using large forest inventories with low sampling rate (<0.5%) may be an efficient way to increase the global coverage of AGB maps with acceptable accuracy at kilometric resolution

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    Horizon / Pleins textes
    Other literature type . 2015
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    PLoS ONE
    Article . 2015 . Peer-reviewed
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    DOAJ; PLoS ONE
    Article . 2015
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      Horizon / Pleins textes
      Other literature type . 2015
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      Article . 2015
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    Authors: Rubbens, Peter; Brodie, Stephanie; Cordier, Tristan; Destro Barcellos, Diogo; +35 Authors

    Abstract Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks to the increase in the amount of data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine learning is needed in marine ecology. Then we provide a quick primer on machine learning techniques and vocabulary. We built a database of ∼1000 publications that implement such techniques to analyse marine ecology data. For various data types (images, optical spectra, acoustics, omics, geolocations, biogeochemical profiles, and satellite imagery), we present a historical perspective on applications that proved influential, can serve as templates for new work, or represent the diversity of approaches. Then, we illustrate how machine learning can be used to better understand ecological systems, by combining various sources of marine data. Through this coverage of the literature, we demonstrate an increase in the proportion of marine ecology studies that use machine learning, the pervasiveness of images as a data source, the dominance of machine learning for classification-type problems, and a shift towards deep learning for all data types. This overview is meant to guide researchers who wish to apply machine learning methods to their marine datasets. 80 7

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    OceanRep
    Article . 2023 . Peer-reviewed
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    Lille Open Archive
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    Research@WUR
    Article . 2023
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      Lille Open Archive
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    Authors: Walker, Emily; Monestiez, Pascal; Gomez, Cécile; Lagacherie, Philippe;

    The limited availability of soil information has been recognized as a main limiting factor in digital soil mapping (DSM) studies. It is therefore important to optimize the joint use of the three sources of soil data that can be used as inputs of DSM models, namely spatial sets of measured sites, soil maps and soil sensing products.In this paper, we propose to combine these three inputs, through a cokriging with a categorical external drift (CKCED). This new interpolation technique was applied for mapping seven soil properties over a 24.6 km2 area located in the vineyard plain of Languedoc (Southern France), using an hyperspectral imagery product as example of a soil sensing data. Cross-validation results of CKCED were compared with those of five spatial and non-spatial techniques using one of these inputs or a combination of two of them.The results obtained in the La Peyne Catchment showed i) the utility of soil map and hyperspectral imagery products as auxiliary data for improving soil property predictions ii) the greater added-value of the latter against the former in most situations and iii) the feasibility and the interest of CKCED in a limited number of soil properties and data configurations. Testing CKCED in case study with soil maps of better quality and soil sensing techniques covering more area and depths should be necessary to better evaluate the benefits of this new technique. International audience

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    Geoderma
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    ProdInra
    Article . 2017
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    Horizon / Pleins textes
    Other literature type . 2017
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    Geoderma
    Article . 2017 . Peer-reviewed
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      Horizon / Pleins textes
      Other literature type . 2017
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      Geoderma
      Article . 2017 . Peer-reviewed
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    Authors: Daniel Montoya; Sabrina Gaba; Claire de Mazancourt; Vincent Bretagnolle; +1 Authors

    Efficient management of agricultural management should consider multiple services and stakeholders. Yet, it remains unclear how to guarantee ecosystem services for multiple stakeholders' demands, especially considering the observed biodiversity decline following reductions in semi-natural habitat (SNH), and global change. Here, we use an ecosystem service model of intensively-managed agricultural landscapes to derive the best landscape compositions for different stakeholders' demands, and how they vary with stochasticity and the degree of pollination dependence of crops. We analyse three groups of stakeholders assumed to value different ecosystem services most-individual farmers (crop yield per area), agricultural unions (landscape production) and con-servationists (biodiversity). Additionally, we consider a social average scenario that aims at maximizing mul-tifunctionality. Trade-offs among stakeholders' demands strongly depend on the degree of pollination dependence of crops, the strength of environmental and demographic stochasticity, and the relative amount of an ecosystem service demanded by each stakeholder. Intermediate amounts of SNH deliver relatively high levels of the three services (social average). Our analysis further suggests that the current levels of SNH protection lie below these intermediate amounts of SNH in intensively-managed agricultural landscapes. Given the worldwide trends in agriculture and global change, current policies should start to consider factors such as crop type and stochasticity, as they can strongly influence best landscape compositions for different stakeholders. Our results suggest ways of managing landscapes to reconcile several actors' demands and ensure for biodiversity conservation and food production. International audience

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    Europe PubMed Central
    Other literature type . 2019
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    Ecological Modelling
    Other literature type . Article . 2020 . Peer-reviewed
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      Ecological Modelling
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    Authors: Tritsch, Isabelle; Arvor, Damien;

    Highlights • We emphasize the end of the boom-and-bust development pattern in the Brazilian Amazon. • Deforestation and socioeconomic development follow an inverted U-shape relationship. • Household incomes are greater in stabilized areas than in areas undergoing deforestation. • Environmental governance efforts fostered the emergence of EKC. Abstract Socioeconomic development in the Brazilian Amazon is currently reaching national averages although deforestation activity has been declining for a decade. As a consequence, recent studies rejected the widely agreed boom-and-bust development hypothesis that deforestation first generates an economic boom, which is then followed by a collapse as forest resources are depleted. Here, we confirm these studies that there is no boom-bust cycle and suggest that a new pattern of relationship between deforestation and socioeconomic development has emerged following an environmental Kuznets curve (EKC). In this scenario, environmental degradation increases in the early stages of economic development and decreases in later stages as the economy develops and wellbeing increases. To validate this assumption, we conducted the first sub-municipal analysis of socioeconomic development and deforestation in the Brazilian Amazon for the 2000–2010 period. Our results confirm the emergence of an EKC relationship with a turning point beyond which socioeconomic growth does not appear anymore to be a driver of deforestation. We also emphasize that areas subjected to active deforestation in 2010 present lower socio-Author manuscript version economic indicators than stabilized areas, pointing to the precarious socioeconomic situation of areas still undergoing active deforestation. We put these results in perspective by considering Brazilian efforts to ensure a transition in environmental governance with the objective of promoting land use sustainability through control of deforestation at the same time as supporting socioeconomic development. International audience

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    Land Use Policy
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    Land Use Policy
    Other literature type . Article . 2016 . Peer-reviewed
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      Other literature type . Article . 2016 . Peer-reviewed
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    Authors: Courbot, Jean-Baptiste; Mazet, Vincent; Monfrini, Emmanuel; Collet, Christophe;

    Circum-Galactic Medium surrounding galaxies has been punctually detected, but its morphology remains largely unknown. The Multi-Unit Spectroscopic Explorer (MUSE) spectro-imager provides for the first time both spectral and spatial resolution to spatially map such features. The problem lies in the statistical detection of faint spatially-extended sources in massive hyperspectral images such as provided by MUSE, and has not been previously handled. This paper presents a statistical detection method based on hypothesis testing tackling this problem. The proposed strategy is step-by-step validated over alternative ways with simulations. Then, results on MUSE observations are presented. International audience

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    https://doi.org/10.1109/icassp...
    Conference object . 2016 . Peer-reviewed
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    Authors: Zeller, Bernd; Legout, Arnaud; Bienaimé, Séverine; Gratia, Bruno; +3 Authors

    AbstractDouglas fir trees presumable stimulate nitrification in the soil. We studied in 21 French Douglas fir forests if and how nitrification is modulated by soil properties, past land use and current forest management. Soil (0–10 cm depth) was collected and initial concentrations of N-NH4+ and N-NO3−, potential net nitrogen mineralization (PNM) and net nitrification (PNN) rates and microbial biomass were measured. At 11 of the 21 sites, annual nitrate fluxes in the soil were measured using anion exchange resin bags. Soils contained between 2.3 to 29.4 mg N-NO3− kg soil−1. About 86% (±14%) of mineral N was nitrate. The proportion of nitrate increased to almost 100% during incubation. PNN varied from 0.10 mg N kg soil−1 day−1 to 1.05 mg N kg soil−1 day−1 (21 sites). Neither the initial nitrate concentration nor PNN was related to soil chemistry (pH, % C, %N, P, CEC), microbial biomass, texture, past land use or thinning. In situ net nitrate accumulation (NNA) estimated with resins beds varied from 4 to 100 kg N-NO3− ha−1 yr−1 (11 sites). It was positively correlated with base saturation, clay content, ELLENBERG N, temperature and negatively with soil organic N, C/N ratio and precipitation.

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    Authors: Andreas Wunsch; Tanja Liesch; Guillaume Cinkus; Nataša Ravbar; +4 Authors

    Despite many existing approaches, modeling karst water resources remains challenging as conventional approaches usually heavily rely on distinct system knowledge. Artificial neural networks (ANNs), however, require only little prior knowledge to automatically establish an input-output relationship. For ANN modeling in karst, the temporal and spatial data availability is often an important constraint, as usually no or few climate stations are located within or near karst spring catchments. Hence, spatial coverage is often not satisfactory and can result in substantial uncertainties about the true conditions in the catchment, leading to lower model performance. To overcome these problems, we apply convolutional neural networks (CNNs) to simulate karst spring discharge and to directly learn from spatially distributed climate input data (combined 2D-1D CNNs). We investigate three karst spring catchments in the Alpine and Mediterranean region with different meteorological-hydrological characteristics and hydrodynamic system properties. We compare the proposed approach both to existing modeling studies in these regions and to our own 1D CNN models that are conventionally trained with climate station input data. Our results show that all the models are excellently suited to modeling karst spring discharge (NSE: 0.73-0.87, KGE: 0.63-0.86) and can compete with the simulation results of existing approaches in the respective areas. The 2D models show a better fit than the 1D models in two of three cases and automatically learn to focus on the relevant areas of the input domain. By performing a spatial input sensitivity analysis, we can further show their usefulness in localizing the position of karst catchments. International audience

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    https://doi.org/10.5194/hess-2...
    Preprint . 2021 . Peer-reviewed
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    Authors: Caracciolo, C.; Aubin, S.; Jonquet, C.; Amdouni, E.; +6 Authors

    In this paper, we report on the outputs and adoption of the Agrisemantics Working Group of the Research Data Alliance (RDA), consisting of a set of recommendations to facilitate the adoption of semantic technologies and methods for the purpose of data interoperability in the field of agriculture and nutrition. From 2016 to 2019, the group gathered researchers and practitioners at the crossing point between information technology and agricultural science, to study all aspects in the life cycle of semantic resources: Conceptualization, edition, sharing, standardization, services, alignment, long term support. First, the working group realized a landscape study, a study of the uses of semantics in agrifood, then collected use cases for the exploitation of semantics resources a generic term to encompass vocabularies, terminologies, thesauri, ontologies. The resulting requirements were synthesized into 39 hints for users and developers of semantic resources, and providers of semantic resource services. We believe adopting these recommendations will engage agrifood sciences in a necessary transition to leverage data production, sharing and reuse and the adoption of the FAIR data principles. The paper includes examples of adoption of those requirements, and a discussion of their contribution to the field of data science. © 2020 The Author(s). Brandon Whitehead acknowledges with thanks the support of the CABI Development Fund. CABI is an international intergovernmental organization and we gratefully acknowledge the core financial support from our member countries (and lead agencies) including the United Kingdom (Department for International Development), China (Chinese Ministry of Agriculture), Australia (Australian Center for International Agricultural Research), Canada (Agriculture and Agri-Food Canada), Netherlands (Directorate-General for International Cooperation), and Switzerland (Swiss Agency for Development and Cooperation). See https:// www.cabi.org/about-cabi/who-we-work-with/key-donors/ for details. Sophie Aubin, Clement Jonquet, Emna Amdouni, Romain David and Catherine Roussey were supported, in part, by the French National Research Agency (ANR) Data to Knowledge in Agronomy and Biodiversity (D2KAB – www.d2kab.org – ANR-18-CE23-0017). Romain David was partly supported by the EPPN2020 project (H2020 grant N°731013), the EOSC-Life european program (grant agreement N°824087), the ‘Infrastructure Biologie Sante’ PHENOME-EMPHASIS project funded by the French National Research Agency (ANR-11-INBS-0012) and the ‘Programme d’Investissements d’Avenir’.

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    Authors: Yi-Chen Chen; Wei-Che Chang; Shau-Ping Lin; Masataka Minami; +6 Authors

    Scalable production of avian cell lines exhibits a valuable potential on therapeutic application by producing recombinant proteins and as the substrate for virus growth due to the special glycosylation occurs in avian species. Chicken primordial germ cells (cPGCs), a germinal pluripotent avian cell type, present the ability of self-renewal, an anchorage-independent cell growth and the ability to be genetically modified. This cell type could be an interesting bioreactor system for industrial purposes. This study sought to establish an expandable culture system with defined components for three-dimensional (3D) culture of cPGCs. cPGCs were cultured in medium supplemented with the functional polymer FP003. Viscoelasticity was low in this medium but cPGCs did not sediment in culture and efficiencies of space and nutrient utilization were thus enhanced and consequently their expansion was improved. The total number of cPGCs increased by 17-fold after 1 week of culture in 3D-FAot medium, an aseric defined medium containing FP003 polymer, FGF2 and Activin A as growth factors and Ovotransferrin as protein. Moreover, cPGC cell lines stably expressed the germline-specific reporter VASA:tdTOMATO, as well as other markers of cPGCs, for more than 1 month upon culture in 3D-FAot medium, indicating that the characteristics of these cells are maintained. In summary, this novel 3D culture system can be used to efficiently expand cPGCs in suspension without mechanical stirring, which is available for long-term culture and no loss of cellular properties was found. This system provides a platform for large-scale culture of cPGCs.

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    Authors: Guitet, Stéphane; Herault, Bruno; Molto, Quentin; Brunaux, Olivier; +1 Authors

    Precise mapping of above-ground biomass (AGB) is a major challenge for the success of REDD+ processes in tropical rainforest. The usual mapping methods are based on two hypotheses: a large and long-ranged spatial autocorrelation and a strong environment influence at the regional scale. However, there are no studies of the spatial structure of AGB at the landscapes scale to support these assumptions. We studied spatial variation in AGB at various scales using two large forest inventories conducted in French Guiana. The dataset comprised 2507 plots (0.4 to 0.5 ha) of undisturbed rainforest distributed over the whole region. After checking the uncertainties of estimates obtained from these data, we used half of the dataset to develop explicit predictive models including spatial and environmental effects and tested the accuracy of the resulting maps according to their resolution using the rest of the data. Forest inventories provided accurate AGB estimates at the plot scale, for a mean of 325 Mg.ha-1. They revealed high local variability combined with a weak autocorrelation up to distances of no more than10 km. Environmental variables accounted for a minor part of spatial variation. Accuracy of the best model including spatial effects was 90 Mg.ha-1 at plot scale but coarse graining up to 2-km resolution allowed mapping AGB with accuracy lower than 50 Mg.ha-1. Whatever the resolution, no agreement was found with available pan-tropical reference maps at all resolutions. We concluded that the combined weak autocorrelation and weak environmental effect limit AGB maps accuracy in rainforest, and that a trade-off has to be found between spatial resolution and effective accuracy until adequate “wall-to-wall” remote sensing signals provide reliable AGB predictions. Waiting for this, using large forest inventories with low sampling rate (<0.5%) may be an efficient way to increase the global coverage of AGB maps with acceptable accuracy at kilometric resolution

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    Horizon / Pleins textes
    Other literature type . 2015
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    PLoS ONE
    Article
    License: CC BY
    Data sources: UnpayWall
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    PLoS ONE
    Article . 2015 . Peer-reviewed
    License: CC BY
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    DOAJ; PLoS ONE
    Article . 2015
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    ProdInra
    Article . 2015
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      Horizon / Pleins textes
      Other literature type . 2015
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      PLoS ONE
      Article . 2015 . Peer-reviewed
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      DOAJ; PLoS ONE
      Article . 2015
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    Authors: Rubbens, Peter; Brodie, Stephanie; Cordier, Tristan; Destro Barcellos, Diogo; +35 Authors

    Abstract Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks to the increase in the amount of data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine learning is needed in marine ecology. Then we provide a quick primer on machine learning techniques and vocabulary. We built a database of ∼1000 publications that implement such techniques to analyse marine ecology data. For various data types (images, optical spectra, acoustics, omics, geolocations, biogeochemical profiles, and satellite imagery), we present a historical perspective on applications that proved influential, can serve as templates for new work, or represent the diversity of approaches. Then, we illustrate how machine learning can be used to better understand ecological systems, by combining various sources of marine data. Through this coverage of the literature, we demonstrate an increase in the proportion of marine ecology studies that use machine learning, the pervasiveness of images as a data source, the dominance of machine learning for classification-type problems, and a shift towards deep learning for all data types. This overview is meant to guide researchers who wish to apply machine learning methods to their marine datasets. 80 7

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    OceanRep
    Article . 2023 . Peer-reviewed
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    Lille Open Archive
    Review . 2023
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    Research@WUR
    Article . 2023
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    Brage IMR
    Article . 2023
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    Article . 2023
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      Article . 2023 . Peer-reviewed
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