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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: Reiner Schlitzer; Robert F. Anderson; Elena Masferrer Dodas; Maeve C. Lohan; +211 Authors

    The GEOTRACES Intermediate Data Product 2017 (IDP2017) is the second publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2016. The IDP2017 includes data from the Atlantic, Pacific, Arctic, Southern and Indian oceans, with about twice the data volume of the previous IDP2014. For the first time, the IDP2017 contains data for a large suite of biogeochemical parameters as well as aerosol and rain data characterising atmospheric trace element and isotope (TEI) sources. The TEI data in the IDP2017 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at crossover stations. The IDP2017 consists of two parts: (1) a compilation of digital data for more than 450 TEIs as well as standard hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing an on-line atlas that includes more than 590 section plots and 130 animated 3D scenes. The digital data are provided in several formats, including ASCII, Excel spreadsheet, netCDF, and Ocean Data View collection. Users can download the full data packages or make their own custom selections with a new on-line data extraction service. In addition to the actual data values, the IDP2017 also contains data quality flags and 1-σ data error values where available. Quality flags and error values are useful for data filtering and for statistical analysis. Metadata about data originators, analytical methods and original publications related to the data are linked in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2017 as section plots and rotating 3D scenes. The basin-wide 3D scenes combine data from many cruises and provide quick overviews of large-scale tracer distributions. These 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of tracer plumes near ocean margins or along ridges. The IDP2017 is the result of a truly international effort involving 326 researchers from 25 countries. This publication provides the critical reference for unpublished data, as well as for studies that make use of a large cross-section of data from the IDP2017. This article is part of a special issue entitled: Conway GEOTRACES - edited by Tim M. Conway, Tristan Horner, Yves Plancherel, and Aridane G. González. National Science Foundation (U.S.) (Grant OCE-1243377) National Science Foundation (U.S.) (Grant OCE-1546580) National Science Foundation (U.S.) (Grant OCE-0608600) National Science Foundation (U.S.) (Grant OCE0938349)

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    DSpace@MIT
    Article . 2018
    License: CC BY
    Data sources: DSpace@MIT
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    Chemical Geology
    Article . 2018 . Peer-reviewed
    License: CC BY
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    NARCIS
    Article . 2018
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    NIOZ Repository
    Article . 2018
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    Chemical Geology
    Article . 2018
    Data sources: NARCIS
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    Oxford University Research Archive
    Other literature type . 2018
    License: CC BY
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    HAL AMU
    Article . 2018
    Data sources: HAL AMU
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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: Böhmová, Katerina; Mihalák, Matús; Pröger, Tobias; Srámek, Rastislav; +1 Authors

    We study the problem of robust routing in urban public transportation networks. In order to propose solutions that are robust for typical delays, we assume that we have past observations of real traffic situations available. In particular, we assume that we have "daily records" containing the observed travel times in the whole network for a few past days. We introduce a new concept to express a solution that is feasible in any record of a given public transportation network. We adapt the method of Buhmann et al. [Buhmann et al., ITCS 2013] for optimization under uncertainty, and develop algorithms that allow its application for finding a robust journey from a given source to a given destination. The performance of the algorithms and the quality of the predicted journey are evaluated in a preliminary experimental study. We furthermore introduce a measure of reliability of a given journey, and develop algorithms for its computation. The robust routing concepts presented in this work are suited specially for public transportation networks of large cities that lack clear hierarchical structure and contain services that run with high frequencies. 13th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2013) OpenAccess Series in Informatics (OASIcs), 33 ISBN:978-393-98975-8-3 ISSN:2190-6807

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    Conference object . 2013
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    Conference object . 2013
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    ETH Zürich Research Collection
    Conference object . 2013
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    Authors: Yuan, Yufei; Duret, Aurélien; van Lint, Hans;

    EWGT 2015 - 18thEuro Working Group on Transportation, DELFT, PAYS-BAS, 13-/07/2015 - 16/07/2015; This paper proposes a new model-based traffic state estimation framework using the LWR model formulated in vehicle number - space (Lagrangian - space) coordinates. This formulation inherits the numerical benefits and modelling flexibility from Lagrangian (vehicle number - time) models. Specifically, a variational formulation of the LWR model is selected as the underlying process model. Compared to the traditional conservation law approach in the same coordinate system, the current formulation entitles a simplified expression (no complex state updating originated from different traffic conditions), and provides more accurate numerical results in the prediction step of the data assimilation framework (exact solution to the continuous model when the fundamental diagram is bi-linear). More importantly, this formulation is particularly convenient for data assimilation, because in reality, the flow characteristics are mostly observed at fixed point (spatial fixed) or along vehicle trajectories (vehicle number fixed). These observations are located on cell boundaries of the Lagrangian-space grid, which makes any traffic state estimation method convenient with this approach. Its corresponding observation models are also defined to incorporate both spatial-fixed and moving observations. A Kalman filter framework is applied with the underlying traffic system model. Moreover, travel time can be directly derived from system estimates, and no state transformation is required compared to other estimation approaches. Model validation experiment based on a synthetic traffic network has demonstrated the feasibility of the proposed framework, and suggested promising extensions for future applications.

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    Hal-Diderot
    Conference object . 2015
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      Conference object . 2015
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    Authors: Rubbens, Peter; Brodie, Stephanie; Cordier, Tristan; Destro Barcellos, Diogo; +35 Authors

    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. Machine learning in marine ecology: an overview of techniques and applications

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    OceanRep
    Article . 2023 . Peer-reviewed
    Data sources: OceanRep
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    Lille Open Archive
    Review . 2023
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    Research@WUR
    Other literature type . 2023
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    Brage IMR
    Article . 2023
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      Article . 2023 . Peer-reviewed
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      Review . 2023
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      Research@WUR
      Other literature type . 2023
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      HAL AMU
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    Authors: Frangoulidis, D.; Rodolakis, Annie; Heiser, V.; Landt, O.; +2 Authors

    Coxiella burnetii is an obligate intracellular bacterium causing Q-fever, a zoonotic disease that is ubiquitous throughout the world with the exception of New Zealand. Cattle, goats, sheep and ticks are the primary reservoirs, but many other species, including fish, birds, rodents and cats, are known to become infected. Especially in small ruminants, infection can lead to abortion associated with exceptionally high amounts of C. burnetii in amniotic fluids and the placenta. Furthermore, C. burnetii may be excreted in milk, urine and faeces of infected animals. Human infections frequently follow contact with infected sheep, especially during lambing, or via the inhalation of dried tick faeces during shearing. Most cases of human infection with C. burnetii are self-limiting, associated with fever, fatigue, headache and myalgia. Acute Q-fever is frequently accompanied by atypical pneumonia and ⁄ or hepatitis. Persistence of infection exceeding 6 months in duration is regarded as chronic Q-fever. Commonly, endocarditis is seen, but chronic hepatitis, osteomyelitis, septic arthritis or infection of aneurysm and vascular grafts can also occur. During pregnancy, Q-fever has been associated with premature birth, abortion and neonatal death. Diagnosis mostly relies on serology, but, especially in the early clinical stages, PCR offers substantial benefits for the identification of C. burnetii infection [1]. In our study, we investigated the suitability of a new rapid ‘low cost and density’ (LCD) DNA microarray chip for the detection of C. burnetii (Coxiella 2.5). Besides the commonly used IS1111 genomic target (Genebank accession number: M80806), we coated a recently described genomic marker proposed to be diagnostic of acute Q-fever (acute disease antigen A (adaA), CBU_0952, GenBank ID AAO90475.1) on the chip [2]. The results were compared with those of both conventional, gel-based and a real-time LightCyclerHyprobe– PCR assay in terms of specificity and sensitivity. Clinical materials of both human and animal origin were also used for evaluation.

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    Clinical Microbiology and Infection
    Article
    License: Elsevier Non-Commercial
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    Clinical Microbiology and Infection
    Article . 2009 . Peer-reviewed
    License: Elsevier Non-Commercial
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      Clinical Microbiology and Infection
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      Clinical Microbiology and Infection
      Article . 2009 . Peer-reviewed
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    Authors: Pietro Aricò; Pietro Aricò; Pietro Aricò; Maxime Reynal; +23 Authors

    New solutions in operational environments are often, among objective measurements, evaluated by using subjective assessment and judgment from experts. Anyhow, it has been demonstrated that subjective measures suffer from poor resolution due to a high intra and inter-operator variability. Also, performance measures, if available, could provide just partial information, since an operator could achieve the same performance but experiencing a different workload. In this study, we aimed to demonstrate: (i) the higher resolution of neurophysiological measures in comparison to subjective ones; and (ii) how the simultaneous employment of neurophysiological measures and behavioral ones could allow a holistic assessment of operational tools. In this regard, we tested the effectiveness of an electroencephalography (EEG)-based neurophysiological index (WEEG index) in comparing two different solutions (i.e., Normal and Augmented) in terms of experienced workload. In this regard, 16 professional air traffic controllers (ATCOs) have been asked to perform two operational scenarios. Galvanic Skin Response (GSR) has also been recorded to evaluate the level of arousal (i.e., operator involvement) during the two scenarios execution. NASA-TLX questionnaire has been used to evaluate the perceived workload, and an expert was asked to assess performance achieved by the ATCOs. Finally, reaction times on specific operational events relevant for the assessment of the two solutions, have also been collected. Results highlighted that the Augmented solution induced a local increase in subjects performance (Reaction times). At the same time, this solution induced an increase in the workload experienced by the participants (WEEG). Anyhow, this increase is still acceptable, since it did not negatively impact the performance and has to be intended only as a consequence of the higher engagement of the ATCOs. This behavioral effect is totally in line with physiological results obtained in terms of arousal (GSR), that increased during the scenario with augmentation. Subjective measures (NASA-TLX) did not highlight any significant variation in perceived workload. These results suggest that neurophysiological measure provide additional information than behavioral and subjective ones, even at a level of few seconds, and its employment during the pre-operational activities (e.g., design process) could allow a more holistic and accurate evaluation of new solutions.

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    Frontiers in Human Neuroscience
    Article
    License: CC BY
    Data sources: UnpayWall
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    DOAJ
    Article . 2019
    Data sources: DOAJ
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    Authors: Yacine Ben Chehida; Roisin Loughnane; Julie Thumloup; Kristin Kaschner; +3 Authors

    AbstractUnderstanding a species response to past environmental changes can help forecast how they will cope with ongoing climate changes. Harbor porpoises are widely distributed in the North Atlantic and were deeply impacted by the Pleistocene changes with the split of three sub-species. Despite major impacts of fisheries on natural populations, little is known about population connectivity and dispersal, how they reacted to the Pleistocene changes and how they will evolve in the future. Here, we used phylogenetics, population genetics, and predictive habitat modelling to investigate population structure and phylogeographic history of the North Atlantic porpoises. A total of 925 porpoises were characterized at 10 microsatellite loci and one-quarter of the mitogenome (mtDNA). A highly divergent mtDNA lineage was uncovered in one porpoise off Western Greenland, suggesting that a cryptic group may occur and could belong to a recently discovered mesopelagic ecotype off Greenland. Aside from it and the southern sub-species, spatial genetic variation showed that porpoises from both sides of the North Atlantic form a continuous system belonging to the same subspecies (Phocoena phocoena phoceona). Yet, we identified important departures from random mating and restricted intergenerational dispersal forming a highly significant isolation-by-distance (IBD) at both mtDNA and nuclear markers. A ten times stronger IBD at mtDNA compared to nuclear loci supported previous evidence of female philopatry. Together with the lack of spatial trends in genetic diversity, this IBD suggests that migration-drift equilibrium has been reached, erasing any genetic signal of a leading-edge effect that accompanied the predicted recolonization of the northern habitats freed from Pleistocene ice. These results illuminate the processes shaping porpoise population structure and provide a framework for designing conservation strategies and forecasting future population evolution.

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    Evolutionary Applications
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      Evolutionary Applications
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    Authors: Roemmich, Dean; Alford, Matthew; Claustre, Hervé; Johnson, Kenneth; +76 Authors

    The Argo Program has been implemented and sustained for almost two decades, as a global array of about 4000 profiling floats. Argo provides continuous observations of ocean temperature and salinity versus pressure, from the sea surface to 2000 dbar. The successful installation of the Argo array and its innovative data management system arose opportunistically from the combination of great scientific need and technological innovation. Through the data system, Argo provides fundamental physical observations with broad societally-valuable applications, built on the cost-efficient and robust technologies of autonomous profiling floats. Following recent advances in platform and sensor technologies, even greater opportunity exists now than 20 years ago to (i) improve Argo’s global coverage and value beyond the original design, (ii) extend Argo to span the full ocean depth, (iii) add biogeochemical sensors for improved understanding of oceanic cycles of carbon, nutrients, and ecosystems, and (iv) consider experimental sensors that might be included in the future, for example to document the spatial and temporal patterns of ocean mixing. For Core Argo and each of these enhancements, the past, present, and future progression along a path from experimental deployments to regional pilot arrays to global implementation is described. The objective is to create a fully global, top-to-bottom, dynamically complete, and multidisciplinary Argo Program that will integrate seamlessly with satellite and with other in situ elements of the Global Ocean Observing System (Legler et al., 2015). The integrated system will deliver operational reanalysis and forecasting capability, and assessment of the state and variability of the climate system with respect to physical, biogeochemical, and ecosystems parameters. It will enable basic research of unprecedented breadth and magnitude, and a wealth of ocean-education and outreach opportunities. Sí

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    OceanRep
    Article . 2019 . Peer-reviewed
    Data sources: OceanRep
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    Brage IMR
    Article . 2019
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    Bergen Open Research Archive - UiB
    Article . 2019 . Peer-reviewed
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    Bergen Open Research Archive - UiB
    Article . 2019 . Peer-reviewed
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    DOAJ
    Article . 2019
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    Authors: Vigano, Nicola; Tanguy, Alexandre; Hallais, Simon; Dimanov, Alexandre; +3 Authors

    AbstractA previously introduced mathematical framework for full-field X-ray orientation microscopy is for the first time applied to experimental near-field diffraction data acquired from a polycrystalline sample. Grain by grain tomographic reconstructions using convex optimization and prior knowledge are carried out in a six-dimensional representation of position-orientation space, used for modelling the inverse problem of X-ray orientation imaging. From the 6D reconstruction output we derive 3D orientation maps, which are then assembled into a common sample volume. The obtained 3D orientation map is compared to an EBSD surface map and local misorientations, as well as remaining discrepancies in grain boundary positions are quantified. The new approach replaces the single orientation reconstruction scheme behind X-ray diffraction contrast tomography and extends the applicability of this diffraction imaging technique to material micro-structures exhibiting sub-grains and/or intra-granular orientation spreads of up to a few degrees. As demonstrated on textured sub-regions of the sample, the new framework can be extended to operate on experimental raw data, thereby bypassing the concept of orientation indexation based on diffraction spot peak positions. This new method enables fast, three-dimensional characterization with isotropic spatial resolution, suitable for time-lapse observations of grain microstructures evolving as a function of applied strain or temperature.

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    Scientific Reports
    Article . 2016 . Peer-reviewed
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      Scientific Reports
      Article . 2016 . Peer-reviewed
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      Article . 2016
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    Authors: Wagner, Bernd; Wilke, Thomas; Francke, Alexander; Albrecht, Christian; +49 Authors

    International audience; This study reviews and synthesises existing information generated within the SCOPSCO (Scientific Collaboration on Past Speciation Conditions in Lake Ohrid) deep drilling project. The four main aims of the project are to infer (i) the age and origin of Lake Ohrid (Former Yu-goslav Republic of Macedonia/Republic of Albania), (ii) its regional seismotectonic history, (iii) volcanic activity and climate change in the central northern Mediterranean region, and (iv) the influence of major geological events on the evolution of its endemic species. The Ohrid basin formed by transtension during the Miocene, opened during the Pliocene and Pleistocene, and the lake established de novo in the still relatively narrow valley between 1.9 and 1.3 Ma. The lake history is recorded in a 584 m long sediment sequence, which was recovered within the framework of the International Continental Scientific Drilling Program (ICDP) from the central part (DEEP site) of the lake in spring 2013. To date, 54 tephra and cryptotephra horizons have been found in the upper 460 m of this sequence. Tephrochronology and tuning biogeochemical proxy data to orbital parameters revealed that the upper 247.8 m represent the last 637 kyr. The multi-proxy data set covering these 637 kyr indicates long-term variability. Some proxies show a change from generally cooler and wetter to drier and warmer glacial and in-terglacial periods around 300 ka. Short-term environmental change caused, for example, by tephra deposition or the climatic impact of millennial-scale Dansgaard-Oeschger and Heinrich events are superimposed on the long-term trends. Evolutionary studies on the extant fauna indicate that Lake Ohrid was not a refugial area for regional freshwater animals. This differs from the surrounding catchment, where the mountainous setting with relatively high water availability provided a refuge for temperate and montane trees during the relatively cold and dry glacial periods. Although Lake Ohrid experienced significant environmental change over the last 637 kyr, preliminary molecular data from extant microgas-tropod species do not indicate significant changes in diversification rate during this period. The reasons for this constant rate remain largely unknown, but a possible lack of environmentally induced extinction events in Lake Ohrid and/or the high resilience of the ecosystems may have played a role.

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    OceanRep
    Article . 2017 . Peer-reviewed
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    Biogeosciences
    Article . Preprint
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    Biogeosciences
    Article . 2017
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    Biogeosciences
    Article . 2017
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    https://doi.org/10.5194/bg-201...
    Preprint . 2016 . Peer-reviewed
    License: CC BY
    Data sources: Crossref
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    https://doi.org/10.7892/boris....
    Other literature type . 2017
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    DOAJ
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    CNR ExploRA
    Article . 2017
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    Authors: Reiner Schlitzer; Robert F. Anderson; Elena Masferrer Dodas; Maeve C. Lohan; +211 Authors

    The GEOTRACES Intermediate Data Product 2017 (IDP2017) is the second publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2016. The IDP2017 includes data from the Atlantic, Pacific, Arctic, Southern and Indian oceans, with about twice the data volume of the previous IDP2014. For the first time, the IDP2017 contains data for a large suite of biogeochemical parameters as well as aerosol and rain data characterising atmospheric trace element and isotope (TEI) sources. The TEI data in the IDP2017 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at crossover stations. The IDP2017 consists of two parts: (1) a compilation of digital data for more than 450 TEIs as well as standard hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing an on-line atlas that includes more than 590 section plots and 130 animated 3D scenes. The digital data are provided in several formats, including ASCII, Excel spreadsheet, netCDF, and Ocean Data View collection. Users can download the full data packages or make their own custom selections with a new on-line data extraction service. In addition to the actual data values, the IDP2017 also contains data quality flags and 1-σ data error values where available. Quality flags and error values are useful for data filtering and for statistical analysis. Metadata about data originators, analytical methods and original publications related to the data are linked in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2017 as section plots and rotating 3D scenes. The basin-wide 3D scenes combine data from many cruises and provide quick overviews of large-scale tracer distributions. These 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of tracer plumes near ocean margins or along ridges. The IDP2017 is the result of a truly international effort involving 326 researchers from 25 countries. This publication provides the critical reference for unpublished data, as well as for studies that make use of a large cross-section of data from the IDP2017. This article is part of a special issue entitled: Conway GEOTRACES - edited by Tim M. Conway, Tristan Horner, Yves Plancherel, and Aridane G. González. National Science Foundation (U.S.) (Grant OCE-1243377) National Science Foundation (U.S.) (Grant OCE-1546580) National Science Foundation (U.S.) (Grant OCE-0608600) National Science Foundation (U.S.) (Grant OCE0938349)

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    DSpace@MIT
    Article . 2018
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    Data sources: DSpace@MIT
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    Chemical Geology
    Article . 2018 . Peer-reviewed
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    Chemical Geology
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    Oxford University Research Archive
    Other literature type . 2018
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    Authors: Böhmová, Katerina; Mihalák, Matús; Pröger, Tobias; Srámek, Rastislav; +1 Authors

    We study the problem of robust routing in urban public transportation networks. In order to propose solutions that are robust for typical delays, we assume that we have past observations of real traffic situations available. In particular, we assume that we have "daily records" containing the observed travel times in the whole network for a few past days. We introduce a new concept to express a solution that is feasible in any record of a given public transportation network. We adapt the method of Buhmann et al. [Buhmann et al., ITCS 2013] for optimization under uncertainty, and develop algorithms that allow its application for finding a robust journey from a given source to a given destination. The performance of the algorithms and the quality of the predicted journey are evaluated in a preliminary experimental study. We furthermore introduce a measure of reliability of a given journey, and develop algorithms for its computation. The robust routing concepts presented in this work are suited specially for public transportation networks of large cities that lack clear hierarchical structure and contain services that run with high frequencies. 13th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2013) OpenAccess Series in Informatics (OASIcs), 33 ISBN:978-393-98975-8-3 ISSN:2190-6807

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    Authors: Yuan, Yufei; Duret, Aurélien; van Lint, Hans;

    EWGT 2015 - 18thEuro Working Group on Transportation, DELFT, PAYS-BAS, 13-/07/2015 - 16/07/2015; This paper proposes a new model-based traffic state estimation framework using the LWR model formulated in vehicle number - space (Lagrangian - space) coordinates. This formulation inherits the numerical benefits and modelling flexibility from Lagrangian (vehicle number - time) models. Specifically, a variational formulation of the LWR model is selected as the underlying process model. Compared to the traditional conservation law approach in the same coordinate system, the current formulation entitles a simplified expression (no complex state updating originated from different traffic conditions), and provides more accurate numerical results in the prediction step of the data assimilation framework (exact solution to the continuous model when the fundamental diagram is bi-linear). More importantly, this formulation is particularly convenient for data assimilation, because in reality, the flow characteristics are mostly observed at fixed point (spatial fixed) or along vehicle trajectories (vehicle number fixed). These observations are located on cell boundaries of the Lagrangian-space grid, which makes any traffic state estimation method convenient with this approach. Its corresponding observation models are also defined to incorporate both spatial-fixed and moving observations. A Kalman filter framework is applied with the underlying traffic system model. Moreover, travel time can be directly derived from system estimates, and no state transformation is required compared to other estimation approaches. Model validation experiment based on a synthetic traffic network has demonstrated the feasibility of the proposed framework, and suggested promising extensions for future applications.

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    Authors: Rubbens, Peter; Brodie, Stephanie; Cordier, Tristan; Destro Barcellos, Diogo; +35 Authors

    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. Machine learning in marine ecology: an overview of techniques and applications

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    OceanRep
    Article . 2023 . Peer-reviewed
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    Research@WUR
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    Authors: Frangoulidis, D.; Rodolakis, Annie; Heiser, V.; Landt, O.; +2 Authors

    Coxiella burnetii is an obligate intracellular bacterium causing Q-fever, a zoonotic disease that is ubiquitous throughout the world with the exception of New Zealand. Cattle, goats, sheep and ticks are the primary reservoirs, but many other species, including fish, birds, rodents and cats, are known to become infected. Especially in small ruminants, infection can lead to abortion associated with exceptionally high amounts of C. burnetii in amniotic fluids and the placenta. Furthermore, C. burnetii may be excreted in milk, urine and faeces of infected animals. Human infections frequently follow contact with infected sheep, especially during lambing, or via the inhalation of dried tick faeces during shearing. Most cases of human infection with C. burnetii are self-limiting, associated with fever, fatigue, headache and myalgia. Acute Q-fever is frequently accompanied by atypical pneumonia and ⁄ or hepatitis. Persistence of infection exceeding 6 months in duration is regarded as chronic Q-fever. Commonly, endocarditis is seen, but chronic hepatitis, osteomyelitis, septic arthritis or infection of aneurysm and vascular grafts can also occur. During pregnancy, Q-fever has been associated with premature birth, abortion and neonatal death. Diagnosis mostly relies on serology, but, especially in the early clinical stages, PCR offers substantial benefits for the identification of C. burnetii infection [1]. In our study, we investigated the suitability of a new rapid ‘low cost and density’ (LCD) DNA microarray chip for the detection of C. burnetii (Coxiella 2.5). Besides the commonly used IS1111 genomic target (Genebank accession number: M80806), we coated a recently described genomic marker proposed to be diagnostic of acute Q-fever (acute disease antigen A (adaA), CBU_0952, GenBank ID AAO90475.1) on the chip [2]. The results were compared with those of both conventional, gel-based and a real-time LightCyclerHyprobe– PCR assay in terms of specificity and sensitivity. Clinical materials of both human and animal origin were also used for evaluation.

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    Clinical Microbiology and Infection
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    Clinical Microbiology and Infection
    Article . 2009 . Peer-reviewed
    License: Elsevier Non-Commercial
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      Clinical Microbiology and Infection
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      Clinical Microbiology and Infection
      Article . 2009 . Peer-reviewed
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    Authors: Pietro Aricò; Pietro Aricò; Pietro Aricò; Maxime Reynal; +23 Authors

    New solutions in operational environments are often, among objective measurements, evaluated by using subjective assessment and judgment from experts. Anyhow, it has been demonstrated that subjective measures suffer from poor resolution due to a high intra and inter-operator variability. Also, performance measures, if available, could provide just partial information, since an operator could achieve the same performance but experiencing a different workload. In this study, we aimed to demonstrate: (i) the higher resolution of neurophysiological measures in comparison to subjective ones; and (ii) how the simultaneous employment of neurophysiological measures and behavioral ones could allow a holistic assessment of operational tools. In this regard, we tested the effectiveness of an electroencephalography (EEG)-based neurophysiological index (WEEG index) in comparing two different solutions (i.e., Normal and Augmented) in terms of experienced workload. In this regard, 16 professional air traffic controllers (ATCOs) have been asked to perform two operational scenarios. Galvanic Skin Response (GSR) has also been recorded to evaluate the level of arousal (i.e., operator involvement) during the two scenarios execution. NASA-TLX questionnaire has been used to evaluate the perceived workload, and an expert was asked to assess performance achieved by the ATCOs. Finally, reaction times on specific operational events relevant for the assessment of the two solutions, have also been collected. Results highlighted that the Augmented solution induced a local increase in subjects performance (Reaction times). At the same time, this solution induced an increase in the workload experienced by the participants (WEEG). Anyhow, this increase is still acceptable, since it did not negatively impact the performance and has to be intended only as a consequence of the higher engagement of the ATCOs. This behavioral effect is totally in line with physiological results obtained in terms of arousal (GSR), that increased during the scenario with augmentation. Subjective measures (NASA-TLX) did not highlight any significant variation in perceived workload. These results suggest that neurophysiological measure provide additional information than behavioral and subjective ones, even at a level of few seconds, and its employment during the pre-operational activities (e.g., design process) could allow a more holistic and accurate evaluation of new solutions.

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    Frontiers in Human Neuroscience
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    Article . 2019
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    Authors: Yacine Ben Chehida; Roisin Loughnane; Julie Thumloup; Kristin Kaschner; +3 Authors

    AbstractUnderstanding a species response to past environmental changes can help forecast how they will cope with ongoing climate changes. Harbor porpoises are widely distributed in the North Atlantic and were deeply impacted by the Pleistocene changes with the split of three sub-species. Despite major impacts of fisheries on natural populations, little is known about population connectivity and dispersal, how they reacted to the Pleistocene changes and how they will evolve in the future. Here, we used phylogenetics, population genetics, and predictive habitat modelling to investigate population structure and phylogeographic history of the North Atlantic porpoises. A total of 925 porpoises were characterized at 10 microsatellite loci and one-quarter of the mitogenome (mtDNA). A highly divergent mtDNA lineage was uncovered in one porpoise off Western Greenland, suggesting that a cryptic group may occur and could belong to a recently discovered mesopelagic ecotype off Greenland. Aside from it and the southern sub-species, spatial genetic variation showed that porpoises from both sides of the North Atlantic form a continuous system belonging to the same subspecies (Phocoena phocoena phoceona). Yet, we identified important departures from random mating and restricted intergenerational dispersal forming a highly significant isolation-by-distance (IBD) at both mtDNA and nuclear markers. A ten times stronger IBD at mtDNA compared to nuclear loci supported previous evidence of female philopatry. Together with the lack of spatial trends in genetic diversity, this IBD suggests that migration-drift equilibrium has been reached, erasing any genetic signal of a leading-edge effect that accompanied the predicted recolonization of the northern habitats freed from Pleistocene ice. These results illuminate the processes shaping porpoise population structure and provide a framework for designing conservation strategies and forecasting future population evolution.

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    Evolutionary Applications
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      Evolutionary Applications
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    Authors: Roemmich, Dean; Alford, Matthew; Claustre, Hervé; Johnson, Kenneth; +76 Authors

    The Argo Program has been implemented and sustained for almost two decades, as a global array of about 4000 profiling floats. Argo provides continuous observations of ocean temperature and salinity versus pressure, from the sea surface to 2000 dbar. The successful installation of the Argo array and its innovative data management system arose opportunistically from the combination of great scientific need and technological innovation. Through the data system, Argo provides fundamental physical observations with broad societally-valuable applications, built on the cost-efficient and robust technologies of autonomous profiling floats. Following recent advances in platform and sensor technologies, even greater opportunity exists now than 20 years ago to (i) improve Argo’s global coverage and value beyond the original design, (ii) extend Argo to span the full ocean depth, (iii) add biogeochemical sensors for improved understanding of oceanic cycles of carbon, nutrients, and ecosystems, and (iv) consider experimental sensors that might be included in the future, for example to document the spatial and temporal patterns of ocean mixing. For Core Argo and each of these enhancements, the past, present, and future progression along a path from experimental deployments to regional pilot arrays to global implementation is described. The objective is to create a fully global, top-to-bottom, dynamically complete, and multidisciplinary Argo Program that will integrate seamlessly with satellite and with other in situ elements of the Global Ocean Observing System (Legler et al., 2015). The integrated system will deliver operational reanalysis and forecasting capability, and assessment of the state and variability of the climate system with respect to physical, biogeochemical, and ecosystems parameters. It will enable basic research of unprecedented breadth and magnitude, and a wealth of ocean-education and outreach opportunities. Sí

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    OceanRep
    Article . 2019 . Peer-reviewed
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    Brage IMR
    Article . 2019
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    Bergen Open Research Archive - UiB
    Article . 2019 . Peer-reviewed
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    Article . 2019 . Peer-reviewed
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    Article . 2019
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    Authors: Vigano, Nicola; Tanguy, Alexandre; Hallais, Simon; Dimanov, Alexandre; +3 Authors

    AbstractA previously introduced mathematical framework for full-field X-ray orientation microscopy is for the first time applied to experimental near-field diffraction data acquired from a polycrystalline sample. Grain by grain tomographic reconstructions using convex optimization and prior knowledge are carried out in a six-dimensional representation of position-orientation space, used for modelling the inverse problem of X-ray orientation imaging. From the 6D reconstruction output we derive 3D orientation maps, which are then assembled into a common sample volume. The obtained 3D orientation map is compared to an EBSD surface map and local misorientations, as well as remaining discrepancies in grain boundary positions are quantified. The new approach replaces the single orientation reconstruction scheme behind X-ray diffraction contrast tomography and extends the applicability of this diffraction imaging technique to material micro-structures exhibiting sub-grains and/or intra-granular orientation spreads of up to a few degrees. As demonstrated on textured sub-regions of the sample, the new framework can be extended to operate on experimental raw data, thereby bypassing the concept of orientation indexation based on diffraction spot peak positions. This new method enables fast, three-dimensional characterization with isotropic spatial resolution, suitable for time-lapse observations of grain microstructures evolving as a function of applied strain or temperature.

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    Scientific Reports
    Article . 2016 . Peer-reviewed
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    Authors: Wagner, Bernd; Wilke, Thomas; Francke, Alexander; Albrecht, Christian; +49 Authors

    International audience; This study reviews and synthesises existing information generated within the SCOPSCO (Scientific Collaboration on Past Speciation Conditions in Lake Ohrid) deep drilling project. The four main aims of the project are to infer (i) the age and origin of Lake Ohrid (Former Yu-goslav Republic of Macedonia/Republic of Albania), (ii) its regional seismotectonic history, (iii) volcanic activity and climate change in the central northern Mediterranean region, and (iv) the influence of major geological events on the evolution of its endemic species. The Ohrid basin formed by transtension during the Miocene, opened during the Pliocene and Pleistocene, and the lake established de novo in the still relatively narrow valley between 1.9 and 1.3 Ma. The lake history is recorded in a 584 m long sediment sequence, which was recovered within the framework of the International Continental Scientific Drilling Program (ICDP) from the central part (DEEP site) of the lake in spring 2013. To date, 54 tephra and cryptotephra horizons have been found in the upper 460 m of this sequence. Tephrochronology and tuning biogeochemical proxy data to orbital parameters revealed that the upper 247.8 m represent the last 637 kyr. The multi-proxy data set covering these 637 kyr indicates long-term variability. Some proxies show a change from generally cooler and wetter to drier and warmer glacial and in-terglacial periods around 300 ka. Short-term environmental change caused, for example, by tephra deposition or the climatic impact of millennial-scale Dansgaard-Oeschger and Heinrich events are superimposed on the long-term trends. Evolutionary studies on the extant fauna indicate that Lake Ohrid was not a refugial area for regional freshwater animals. This differs from the surrounding catchment, where the mountainous setting with relatively high water availability provided a refuge for temperate and montane trees during the relatively cold and dry glacial periods. Although Lake Ohrid experienced significant environmental change over the last 637 kyr, preliminary molecular data from extant microgas-tropod species do not indicate significant changes in diversification rate during this period. The reasons for this constant rate remain largely unknown, but a possible lack of environmentally induced extinction events in Lake Ohrid and/or the high resilience of the ecosystems may have played a role.

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    Biogeosciences
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