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  • Authors: Mensah-Ankrah, Chris;
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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: Soiland-Reyes, Stian; Sefton, Peter; Crosas, Mercè; Castro, Leyla Jael; +12 Authors

    An increasing number of researchers support reproducibility by including pointers to and descriptions of datasets, software and methods in their publications. However, scientific articles may be ambiguous, incomplete and difficult to process by automated systems. In this paper we introduce RO-Crate, an open, community-driven, and lightweight approach to packaging research artefacts along with their metadata in a machine readable manner. RO-Crate is based on Schema$.$org annotations in JSON-LD, aiming to establish best practices to formally describe metadata in an accessible and practical way for their use in a wide variety of situations. An RO-Crate is a structured archive of all the items that contributed to a research outcome, including their identifiers, provenance, relations and annotations. As a general purpose packaging approach for data and their metadata, RO-Crate is used across multiple areas, including bioinformatics, digital humanities and regulatory sciences. By applying "just enough" Linked Data standards, RO-Crate simplifies the process of making research outputs FAIR while also enhancing research reproducibility. An RO-Crate for this article is available at https://www.researchobject.org/2021-packaging-research-artefacts-with-ro-crate/ Comment: 42 pages. Submitted to Data Science

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    arXiv.org e-Print Archive
    Other literature type . Preprint . 2021
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    Article . 2022 . Peer-reviewed
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    https://doi.org/10.48550/arxiv...
    Article . 2021
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      Article . 2022 . Peer-reviewed
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      arXiv.org e-Print Archive
      Other literature type . Preprint . 2021
      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/
      ZENODO
      Article . 2022 . Peer-reviewed
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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
      https://doi.org/10.48550/arxiv...
      Article . 2021
      License: CC BY
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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/

    With the increasing adoption of technology, more and more systems become target to information security breaches. In terms of readily identifying zero-day vulnerabilities, a substantial number of news outlets and social media accounts reveal emerging vulnerabilities and threats. However, analysts often spend a lot of time looking through these decentralized sources of information in order to ensure up-to-date countermeasures and patches applicable to their organisation’s information systems. Various automated processing pipelines grounded in Natural Language Processing techniques for text classification were introduced for the early identification of vulnerabilities starting from Open-Source Intelligence (OSINT) data, including news websites, blogs, and social media. In this study, we consider a corpus of more than 1600 labeled news articles, and introduce an interpretable approach to the subject of cyberthreat early detection. In particular, an interpretable classification is performed using the Longformer architecture alongside prototypes from the ProSeNet structure, after performing a preliminary analysis on the Transformer’s encoding capabilities. The best interpretable architecture achieves an 88% F2-Score, arguing for the system’s applicability in real-life monitoring conditions of OSINT data.

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    Conference object . 2021 . Peer-reviewed
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      Conference object . 2021 . Peer-reviewed
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  • Authors: Acosta Reveles, Irma Lorena;
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    Other literature type . Preprint . 2021 . 2020
    https://doi.org/10.48779/dyp8-...
    Part of book or chapter of book . 2021
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      Other literature type . Preprint . 2021 . 2020
      https://doi.org/10.48779/dyp8-...
      Part of book or chapter of book . 2021
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    Authors: Mitchell, Jeffrey J; Bowers, Jeffrey S;

    Recently, domain-general recurrent neural networks, without explicit linguistic inductive biases, have been shown to successfully reproduce a range of human language behaviours, such as accurately predicting number agreement between nouns and verbs. We show that such networks will also learn number agreement within unnatural sentence structures, i.e. structures that are not found within any natural languages and which humans struggle to process. These results suggest that the models are learning from their input in a manner that is substantially different from human language acquisition, and we undertake an analysis of how the learned knowledge is stored in the weights of the network. We find that while the model has an effective understanding of singular versus plural for individual sentences, there is a lack of a unified concept of number agreement connecting these processes across the full range of inputs. Moreover, the weights handling natural and unnatural structures overlap substantially, in a way that underlines the non-human-like nature of the knowledge learned by the network.

    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/ Explore Bristol Rese...arrow_drop_down
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    Contribution for newspaper or weekly magazine . Conference object . 2020
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    https://doi.org/10.18653/v1/20...
    Other literature type . Conference object . 2020 . Peer-reviewed
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      Contribution for newspaper or weekly magazine . Conference object . 2020
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    The topic of my research is "Learning and Upgrading in Global Value Chains: An Analysis of India's Manufacturing Sector". To analyse India's learning and upgrading through position, functions, specialisation & value addition of manufacturing GVCs, it is required to quantify the extent, drivers, and impacts of India's Manufacturing links in GVCs. I have transformed this overall broad objective into three fundamental questions: (1) What is the extent of India's Manufacturing Links in GVCs? (2) What are the determinants of India's Manufacturing Links in GVCs? (3) What are the impacts of India's Manufacturing Links in GVCs? These three objectives represent my three chapters in my PhD thesis. 26 pages, PhD Proposal

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    arXiv.org e-Print Archive
    Other literature type . Preprint . 2021
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    https://doi.org/10.48550/arxiv...
    Article . 2021
    License: CC BY
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    https://doi.org/10.31219/osf.i...
    Preprint . 2021
    License: CC BY
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    SSRN Electronic Journal
    Article . 2018 . 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: Anders Svensson; Dorthe Dahl-Jensen; Jørgen Peder Steffensen; Thomas Blunier; +22 Authors

    The last glacial period is characterized by a number of millennial climate events that have been identified in both Greenland and Antarctic ice cores and that are abrupt in Greenland climate records. The mechanisms governing this climate variability remain a puzzle that requires a precise synchronization of ice cores from the two hemispheres to be resolved. Previously, Greenland and Antarctic ice cores have been synchronized primarily via their common records of gas concentrations or isotopes from the trapped air and via cosmogenic isotopes measured on the ice. In this work, we apply ice core volcanic proxies and annual layer counting to identify large volcanic eruptions that have left a signature in both Greenland and Antarctica. Generally, no tephra is associated with those eruptions in the ice cores, so the source of the eruptions cannot be identified. Instead, we identify and match sequences of volcanic eruptions with bipolar distribution of sulfate, i.e. unique patterns of volcanic events separated by the same number of years at the two poles. Using this approach, we pinpoint 82 large bipolar volcanic eruptions throughout the second half of the last glacial period (12–60 ka). This improved ice core synchronization is applied to determine the bipolar phasing of abrupt climate change events at decadal-scale precision. In response to Greenland abrupt climatic transitions, we find a response in the Antarctic water isotope signals (δ18O and deuterium excess) that is both more immediate and more abrupt than that found with previous gas-based interpolar synchronizations, providing additional support for our volcanic framework. On average, the Antarctic bipolar seesaw climate response lags the midpoint of Greenland abrupt δ18O transitions by 122±24 years. The time difference between Antarctic signals in deuterium excess and δ18O, which likewise informs the time needed to propagate the signal as described by the theory of the bipolar seesaw but is less sensitive to synchronization errors, suggests an Antarctic δ18O lag behind Greenland of 152±37 years. These estimates are shorter than the 200 years suggested by earlier gas-based synchronizations. As before, we find variations in the timing and duration between the response at different sites and for different events suggesting an interaction of oceanic and atmospheric teleconnection patterns as well as internal climate variability. International audience

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    https://doi.org/10.5194/cp-202...
    Preprint . 2020
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    Article . 2020
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    https://doi.org/10.57694/7175...
    Article . 2020
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    Other literature type . 2020
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    Climate of the Past; Climate of the Past (CP)
    Article . Preprint . 2020
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      https://doi.org/10.5194/cp-202...
      Preprint . 2020
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      https://doi.org/10.57694/7175...
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      Climate of the Past; Climate of the Past (CP)
      Article . Preprint . 2020
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    Authors: Irene Malmierca-Vallet; Louise C. Sime; Paul J. Valdes; Julia Tindall;

    <p><strong>Abstract.</strong> Changes in the Greenland ice sheet (GIS) affect global sea level. Greenland stable water isotope (δ<sup>18</sup>O) records from ice cores offer information on past changes in the surface of the GIS. Here, we use the isotope-enabled HadCM3 climate model to simulate a set of Last Interglacial (LIG) idealised GIS surface elevation change scenarios focusing on GIS ice core sites. We investigate how δ<sup>18</sup>O depends on the magnitude and sign of GIS elevation change and evaluate how the response is altered by sea ice changes. We find that modifying GIS elevation induces changes in Northern Hemisphere atmospheric circulation, sea ice and precipitation patterns. These climate feedbacks lead to ice core-averaged isotopic lapse rates of 0.49 ‰ per 100 m for the lowered GIS states and 0.29 ‰ per 100 m for the enlarged GIS states. This is lower than the spatially derived Greenland lapse rates of 0.62–0.72 ‰ per 100 m. These results thus suggest non-linearities in the isotope-elevation relationship, and have consequences for the interpretation of past elevation and climate changes across Greenland. In particular, our results suggest that winter sea ice changes may significantly influence isotopic-elevation gradients: winter sea ice effect can decrease (increase) modelled core-averaged isotopic lapse rate values by about -19 % (and +28 %) for the lowered (enlarged) GIS states respectively. The largest influence of sea ice on δ<sup>18</sup>O changes is found in coastal regions like the Camp Century site.</p>

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    Climate of the Past; Climate of the Past (CP)
    Article . Preprint . 2020
    License: CC BY
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    https://doi.org/10.5194/cp-202...
    Preprint . 2020
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    DOAJ
    Article . 2020
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      Climate of the Past; Climate of the Past (CP)
      Article . Preprint . 2020
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      https://doi.org/10.5194/cp-202...
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    Authors: Oswaldo Solarte-Pabon; Ernestina Menasalvas; Alejandro Rodríguez-González;

    Electronic health records contain valuable information written in narrative form. A relevant challenge in clinical narrative text is that concepts commonly appear negated. Several proposals have been developed to detect negation in clinical text written in Spanish. Much of these proposals have adapted the Negex algorithm to Spanish, but obtained results indicating lower performance than NegEx implementations in other languages. Moreover, in most of these proposals, the validation process could be improved using a shared test corpus focused on negation in clinical text. This paper proposes Spa-neg, an approach to improve negation detection in clinical text written in Spanish. Spa-neg combines three elements: (i) an exploratory data analysis of how negation is written in the clinical text, (ii) use of regular expressions best adapted to the way in which negation is expressed in Spanish, (iii) experiments, and validation using a shared annotated corpus focused on negation. Our findings suggest that the combination of these elements improves the process of negation detection. The tests performed have shown 92% F-Score using IULA Spanish, an annotated corpus for negation in clinical text.

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    https://doi.org/10.1007/978-3-...
    Part of book or chapter of book . 2020 . Peer-reviewed
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      https://doi.org/10.1007/978-3-...
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    Authors: Reveles, Irma Lorena Acosta; Quezada, Miguel Ángel Jesus Salas;

    The environmental topic arrived on the political agenda questioning citizens, groups and institutions. From this concert of actors, universities are relevant due to its social incidence and critical tradition. Today, Mexican Universities claim the sustainability. This paper aims to determine the moments that mark the gradual assimilation of the environmental issue in public universities, and characterize the scope of this appropriation in its substantive tasks. The supplies are secondary documental data, public politic and specialized articles. As a conclusion, the environmental issue has penetrated on university through a formal and informal way, being displayed in three core areas, but those are not articulated each other.

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  • Authors: Mensah-Ankrah, Chris;
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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: Soiland-Reyes, Stian; Sefton, Peter; Crosas, Mercè; Castro, Leyla Jael; +12 Authors

    An increasing number of researchers support reproducibility by including pointers to and descriptions of datasets, software and methods in their publications. However, scientific articles may be ambiguous, incomplete and difficult to process by automated systems. In this paper we introduce RO-Crate, an open, community-driven, and lightweight approach to packaging research artefacts along with their metadata in a machine readable manner. RO-Crate is based on Schema$.$org annotations in JSON-LD, aiming to establish best practices to formally describe metadata in an accessible and practical way for their use in a wide variety of situations. An RO-Crate is a structured archive of all the items that contributed to a research outcome, including their identifiers, provenance, relations and annotations. As a general purpose packaging approach for data and their metadata, RO-Crate is used across multiple areas, including bioinformatics, digital humanities and regulatory sciences. By applying "just enough" Linked Data standards, RO-Crate simplifies the process of making research outputs FAIR while also enhancing research reproducibility. An RO-Crate for this article is available at https://www.researchobject.org/2021-packaging-research-artefacts-with-ro-crate/ Comment: 42 pages. Submitted to Data Science

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    Data Science
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    https://doi.org/10.48550/arxiv...
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      https://doi.org/10.48550/arxiv...
      Article . 2021
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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/

    With the increasing adoption of technology, more and more systems become target to information security breaches. In terms of readily identifying zero-day vulnerabilities, a substantial number of news outlets and social media accounts reveal emerging vulnerabilities and threats. However, analysts often spend a lot of time looking through these decentralized sources of information in order to ensure up-to-date countermeasures and patches applicable to their organisation’s information systems. Various automated processing pipelines grounded in Natural Language Processing techniques for text classification were introduced for the early identification of vulnerabilities starting from Open-Source Intelligence (OSINT) data, including news websites, blogs, and social media. In this study, we consider a corpus of more than 1600 labeled news articles, and introduce an interpretable approach to the subject of cyberthreat early detection. In particular, an interpretable classification is performed using the Longformer architecture alongside prototypes from the ProSeNet structure, after performing a preliminary analysis on the Transformer’s encoding capabilities. The best interpretable architecture achieves an 88% F2-Score, arguing for the system’s applicability in real-life monitoring conditions of OSINT data.

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  • Authors: Acosta Reveles, Irma Lorena;
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    https://doi.org/10.48779/dyp8-...
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    Authors: Mitchell, Jeffrey J; Bowers, Jeffrey S;

    Recently, domain-general recurrent neural networks, without explicit linguistic inductive biases, have been shown to successfully reproduce a range of human language behaviours, such as accurately predicting number agreement between nouns and verbs. We show that such networks will also learn number agreement within unnatural sentence structures, i.e. structures that are not found within any natural languages and which humans struggle to process. These results suggest that the models are learning from their input in a manner that is substantially different from human language acquisition, and we undertake an analysis of how the learned knowledge is stored in the weights of the network. We find that while the model has an effective understanding of singular versus plural for individual sentences, there is a lack of a unified concept of number agreement connecting these processes across the full range of inputs. Moreover, the weights handling natural and unnatural structures overlap substantially, in a way that underlines the non-human-like nature of the knowledge learned by the network.

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    https://doi.org/10.18653/v1/20...
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    The topic of my research is "Learning and Upgrading in Global Value Chains: An Analysis of India's Manufacturing Sector". To analyse India's learning and upgrading through position, functions, specialisation & value addition of manufacturing GVCs, it is required to quantify the extent, drivers, and impacts of India's Manufacturing links in GVCs. I have transformed this overall broad objective into three fundamental questions: (1) What is the extent of India's Manufacturing Links in GVCs? (2) What are the determinants of India's Manufacturing Links in GVCs? (3) What are the impacts of India's Manufacturing Links in GVCs? These three objectives represent my three chapters in my PhD thesis. 26 pages, PhD Proposal

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    arXiv.org e-Print Archive
    Other literature type . Preprint . 2021
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    https://doi.org/10.48550/arxiv...
    Article . 2021
    License: CC BY
    Data sources: Datacite
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    https://doi.org/10.31219/osf.i...
    Preprint . 2021
    License: CC BY
    Data sources: Crossref
    SSRN Electronic Journal
    Article . 2018 . Peer-reviewed
    Data sources: Crossref
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    Authors: Anders Svensson; Dorthe Dahl-Jensen; Jørgen Peder Steffensen; Thomas Blunier; +22 Authors

    The last glacial period is characterized by a number of millennial climate events that have been identified in both Greenland and Antarctic ice cores and that are abrupt in Greenland climate records. The mechanisms governing this climate variability remain a puzzle that requires a precise synchronization of ice cores from the two hemispheres to be resolved. Previously, Greenland and Antarctic ice cores have been synchronized primarily via their common records of gas concentrations or isotopes from the trapped air and via cosmogenic isotopes measured on the ice. In this work, we apply ice core volcanic proxies and annual layer counting to identify large volcanic eruptions that have left a signature in both Greenland and Antarctica. Generally, no tephra is associated with those eruptions in the ice cores, so the source of the eruptions cannot be identified. Instead, we identify and match sequences of volcanic eruptions with bipolar distribution of sulfate, i.e. unique patterns of volcanic events separated by the same number of years at the two poles. Using this approach, we pinpoint 82 large bipolar volcanic eruptions throughout the second half of the last glacial period (12–60 ka). This improved ice core synchronization is applied to determine the bipolar phasing of abrupt climate change events at decadal-scale precision. In response to Greenland abrupt climatic transitions, we find a response in the Antarctic water isotope signals (δ18O and deuterium excess) that is both more immediate and more abrupt than that found with previous gas-based interpolar synchronizations, providing additional support for our volcanic framework. On average, the Antarctic bipolar seesaw climate response lags the midpoint of Greenland abrupt δ18O transitions by 122±24 years. The time difference between Antarctic signals in deuterium excess and δ18O, which likewise informs the time needed to propagate the signal as described by the theory of the bipolar seesaw but is less sensitive to synchronization errors, suggests an Antarctic δ18O lag behind Greenland of 152±37 years. These estimates are shorter than the 200 years suggested by earlier gas-based synchronizations. As before, we find variations in the timing and duration between the response at different sites and for different events suggesting an interaction of oceanic and atmospheric teleconnection patterns as well as internal climate variability. International audience

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    https://doi.org/10.5194/cp-202...
    Preprint . 2020
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    DOAJ
    Article . 2020
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    https://doi.org/10.57694/7175...
    Article . 2020
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    Other literature type . 2020
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    Climate of the Past; Climate of the Past (CP)
    Article . Preprint . 2020
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      https://doi.org/10.5194/cp-202...
      Preprint . 2020
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      DOAJ
      Article . 2020
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      https://doi.org/10.57694/7175...
      Article . 2020
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      Other literature type . 2020
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      Climate of the Past; Climate of the Past (CP)
      Article . Preprint . 2020
      License: CC BY
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    Authors: Irene Malmierca-Vallet; Louise C. Sime; Paul J. Valdes; Julia Tindall;

    <p><strong>Abstract.</strong> Changes in the Greenland ice sheet (GIS) affect global sea level. Greenland stable water isotope (δ<sup>18</sup>O) records from ice cores offer information on past changes in the surface of the GIS. Here, we use the isotope-enabled HadCM3 climate model to simulate a set of Last Interglacial (LIG) idealised GIS surface elevation change scenarios focusing on GIS ice core sites. We investigate how δ<sup>18</sup>O depends on the magnitude and sign of GIS elevation change and evaluate how the response is altered by sea ice changes. We find that modifying GIS elevation induces changes in Northern Hemisphere atmospheric circulation, sea ice and precipitation patterns. These climate feedbacks lead to ice core-averaged isotopic lapse rates of 0.49 ‰ per 100 m for the lowered GIS states and 0.29 ‰ per 100 m for the enlarged GIS states. This is lower than the spatially derived Greenland lapse rates of 0.62–0.72 ‰ per 100 m. These results thus suggest non-linearities in the isotope-elevation relationship, and have consequences for the interpretation of past elevation and climate changes across Greenland. In particular, our results suggest that winter sea ice changes may significantly influence isotopic-elevation gradients: winter sea ice effect can decrease (increase) modelled core-averaged isotopic lapse rate values by about -19 % (and +28 %) for the lowered (enlarged) GIS states respectively. The largest influence of sea ice on δ<sup>18</sup>O changes is found in coastal regions like the Camp Century site.</p>

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    Climate of the Past; Climate of the Past (CP)
    Article . Preprint . 2020
    License: CC BY
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    https://doi.org/10.5194/cp-202...
    Preprint . 2020
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    DOAJ
    Article . 2020
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      Climate of the Past; Climate of the Past (CP)
      Article . Preprint . 2020
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      https://doi.org/10.5194/cp-202...
      Preprint . 2020
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    Authors: Oswaldo Solarte-Pabon; Ernestina Menasalvas; Alejandro Rodríguez-González;

    Electronic health records contain valuable information written in narrative form. A relevant challenge in clinical narrative text is that concepts commonly appear negated. Several proposals have been developed to detect negation in clinical text written in Spanish. Much of these proposals have adapted the Negex algorithm to Spanish, but obtained results indicating lower performance than NegEx implementations in other languages. Moreover, in most of these proposals, the validation process could be improved using a shared test corpus focused on negation in clinical text. This paper proposes Spa-neg, an approach to improve negation detection in clinical text written in Spanish. Spa-neg combines three elements: (i) an exploratory data analysis of how negation is written in the clinical text, (ii) use of regular expressions best adapted to the way in which negation is expressed in Spanish, (iii) experiments, and validation using a shared annotated corpus focused on negation. Our findings suggest that the combination of these elements improves the process of negation detection. The tests performed have shown 92% F-Score using IULA Spanish, an annotated corpus for negation in clinical text.

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    https://doi.org/10.1007/978-3-...
    Part of book or chapter of book . 2020 . Peer-reviewed
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      https://doi.org/10.1007/978-3-...
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    Authors: Reveles, Irma Lorena Acosta; Quezada, Miguel Ángel Jesus Salas;

    The environmental topic arrived on the political agenda questioning citizens, groups and institutions. From this concert of actors, universities are relevant due to its social incidence and critical tradition. Today, Mexican Universities claim the sustainability. This paper aims to determine the moments that mark the gradual assimilation of the environmental issue in public universities, and characterize the scope of this appropriation in its substantive tasks. The supplies are secondary documental data, public politic and specialized articles. As a conclusion, the environmental issue has penetrated on university through a formal and informal way, being displayed in three core areas, but those are not articulated each other.

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