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7 Research products

  • DARIAH EU
  • 2013-2022
  • Publications
  • Research software
  • Other research products
  • European Commission
  • EC|FP7
  • EC|H2020|RIA
  • EU
  • DARIAH EU

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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: Hannes Berg; Maria A. Wirtz Martin; Nadide Altincekic; Islam Alshamleh; +79 Authors

    Work at BMRZ is supported by the state of Hesse. Work in Covid19-NMR was supported by the Goethe Corona Funds, by the IWBEFRE-program 20007375 of state of Hesse, the DFG through CRC902: “Molecular Principles of RNA-based regulation.” and through infrastructure funds (project numbers: 277478796, 277479031, 392682309, 452632086, 70653611) and by European Union’s Horizon 2020 research and innovation program iNEXT-discovery under grant agreement No 871037. BY-COVID receives funding from the European Union’s Horizon Europe Research and Innovation Programme under grant agreement number 101046203. “INSPIRED” (MIS 5002550) project, implemented under the Action “Reinforcement of the Research and Innovation Infrastructure,” funded by the Operational Program “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014–2020) and co-financed by Greece and the EU (European Regional Development Fund) and the FP7 REGPOT CT-2011-285950—“SEE-DRUG” project (purchase of UPAT’s 700 MHz NMR equipment). The support of the CERM/CIRMMP center of Instruct-ERIC is gratefully acknowledged. This work has been funded in part by a grant of the Italian Ministry of University and Research (FISR2020IP_02112, ID-COVID) and by Fondazione CR Firenze. A.S. is supported by the Deutsche Forschungsgemeinschaft [SFB902/B16, SCHL2062/2-1] and the Johanna Quandt Young Academy at Goethe [2019/AS01]. M.H. and C.F. thank SFB902 and the Stiftung Polytechnische Gesellschaft for the Scholarship. L.L. work was supported by the French National Research Agency (ANR, NMR-SCoV2-ORF8), the Fondation de la Recherche Médicale (FRM, NMR-SCoV2-ORF8), FINOVI and the IR-RMN-THC Fr3050 CNRS. Work at UConn Health was supported by grants from the US National Institutes of Health (R01 GM135592 to B.H., P41 GM111135 and R01 GM123249 to J.C.H.) and the US National Science Foundation (DBI 2030601 to J.C.H.). Latvian Council of Science Grant No. VPP-COVID-2020/1-0014. National Science Foundation EAGER MCB-2031269. This work was supported by the grant Krebsliga KFS-4903-08-2019 and SNF-311030_192646 to J.O. P.G. (ITMP) The EOSC Future project is co-funded by the European Union Horizon Programme call INFRAEOSC-03-2020—Grant Agreement Number 101017536. Open Access funding enabled and organized by Projekt DEAL SARS-CoV-2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti-virals. Within the international Covid19-NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80 % of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR-detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure-based drug design against the SCoV2 proteome. 12 pags., 4 figs., 3 tabs. Peer reviewed

    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/ Angewandte Chemie In...arrow_drop_down
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    Angewandte Chemie International Edition
    Other literature type . Article . 2022 . Peer-reviewed
    License: CC BY
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    Article . 2024
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    Fraunhofer-ePrints
    Other literature type . 2022
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    Angewandte Chemie
    Article . 2022 . Peer-reviewed
    License: CC BY
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    https://doi.org/10.26083/tupri...
    Article . 2024
    License: CC BY
    Data sources: Datacite
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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/ Angewandte Chemie In...arrow_drop_down
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      Angewandte Chemie International Edition
      Other literature type . Article . 2022 . Peer-reviewed
      License: CC BY
      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/
      tuprints
      Article . 2024
      Data sources: tuprints
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      Fraunhofer-ePrints
      Other literature type . 2022
      Data sources: Fraunhofer-ePrints
      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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      Angewandte Chemie
      Article . 2022 . Peer-reviewed
      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/
      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://doi.org/10.26083/tupri...
      Article . 2024
      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/
    Authors: Berg, Hannes; Wirtz Martin, Maria A.; Altincekic, Nadide; Alshamleh, Islam; +20 Authors

    SARS-CoV-2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti-virals. Within the international Covid19-NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80 % of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR-detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure-based drug design against the SCoV2 proteome. Angewandte Chemie. International Edition, 61 (46) ISSN:0570-0833 ISSN:1433-7851 ISSN:1521-3773

    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/ Research Collectionarrow_drop_down
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    Research Collection
    Article . 2022
    License: CC BY
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      Research Collection
      Article . 2022
      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/
    Authors: Hube, Christoph; Fetahu, Besnik;

    Biased language commonly occurs around topics which are of controversial nature, thus, stirring disagreement between the different involved parties of a discussion. This is due to the fact that for language and its use, specifically, the understanding and use of phrases, the stances are cohesive within the particular groups. However, such cohesiveness does not hold across groups. In collaborative environments or environments where impartial language is desired (e.g. Wikipedia, news media), statements and the language therein should represent equally the involved parties and be neutrally phrased. Biased language is introduced through the presence of inflammatory words or phrases, or statements that may be incorrect or one-sided, thus violating such consensus. In this work, we focus on the specific case of phrasing bias, which may be introduced through specific inflammatory words or phrases in a statement. For this purpose, we propose an approach that relies on a recurrent neural networks in order to capture the inter-dependencies between words in a phrase that introduced bias. We perform a thorough experimental evaluation, where we show the advantages of a neural based approach over competitors that rely on word lexicons and other hand-crafted features in detecting biased language. We are able to distinguish biased statements with a precision of P=0.92, thus significantly outperforming baseline models with an improvement of over 30%. Finally, we release the largest corpus of statements annotated for biased language. The Twelfth ACM International Conference on Web Search and Data Mining, February 11--15, 2019, Melbourne, VIC, Australia

    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/ arXiv.org e-Print Ar...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/
    http://arxiv.org/pdf/1811.0574...
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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/10.1145/328960...
    Conference object . 2019 . Peer-reviewed
    License: ACM Copyright Policies
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    https://doi.org/10.48550/arxiv...
    Article . 2018
    License: arXiv Non-Exclusive Distribution
    Data sources: Datacite
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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/ arXiv.org e-Print Ar...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/
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      http://arxiv.org/pdf/1811.0574...
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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/10.1145/328960...
      Conference object . 2019 . Peer-reviewed
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      https://doi.org/10.48550/arxiv...
      Article . 2018
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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: Laurent Romary; Charles Riondet;

    This article tackles the issue of integrating heterogeneous archival sources in one single data repository, namely the European Holocaust Research Infrastructure (EHRI) portal, whose aim is to support Holocaust research by providing online access to information about dispersed sources relating to the Holocaust (http://portal.ehri-project.eu). In this case, the problem at hand is to combine data coming from a network of archives in order to create an interoperable data space which can be used to search for, retrieve and disseminate content in the context of archival-based research. The scholarly purpose has specific consequences on our task. It assumes that the information made available to the researcher is as close as possible to the originating source in order to guarantee that the ensuing analysis can be deemed reliable. In the EHRI network of archives, as already observed in the case of the EU Cendari project, one cannot but face heterogeneity. The EHRI portal brings together descriptions from more than 1900 institutions. Each archive comes with a whole range of idiosyncrasies corresponding to the way it has been set up and evolved over time. Cataloging practices may also differ. Even the degree of digitization may range from the absence of a digital catalogue to the provision of a full-fledged online catalogue with all the necessary APIs for anyone to query and extract content. There is indeed a contrast here with the global endeavour at the international level to develop and promote standards for the description of archival content as a whole. Nonetheless, in a project like EHRI, standards should play a central role. They are necessary for many tasks related to the integration and exploitation of the aggregated content, namely: ● Being able to compare the content of the various sources, thus being able to develop quality-checking processes; ● Defining of an integrated repository infrastructure where the content of the various archival sources can be reliably hosted; ● Querying and re-using content in a seamless way; ● Deploying tools that have been developed independently of the specificities of the information sources, for instance in order to visualise or mine the resulting pool of information. The central aspect of the work described in this paper is the assessment of the role of the EAD (Encoded Archival Description) standard as the basis for achieving the tasks described above. We have worked out how we could develop a real strategy of defining specific customization of EAD that could be used at various stages of the process of integrating heterogeneous sources. While doing so, we have developed a methodology based on a specification and customization method inspired from the extensive experience of the Text Encoding Initiative (TEI) community. In the TEI framework, as we show in section 1, one has the possibility to model specific subsets or extensions of the TEI guidelines while maintaining both the technical (XML schemas) and editorial (documentation) content within a single framework. This work has led us quite far in anticipating that the method we have developed may be of a wider interest within similar environments, but also, as we believe, for the future maintenance of the EAD standard. Finally this work, successfully tested and implemented in the framework of EHRI [Riondet 2017], can be seen as part of the wider endeavour of European research infrastructures in the humanities such as CLARIN and DARIAH to provide support for researchers to integrate the use of standards in their scholarly practices. This is the reason why the general workflow studied here has been introduced as a use case in the umbrella infrastructure project PARTHENOS which aims, among other things, at disseminating information and resources about methodological and technical standards in the humanities.

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    OpenAIRE; Archival Science
    Other literature type . Article . 2018 . Peer-reviewed
    License: Springer TDM
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    Archival Science
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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
    Authors: Emiliano Degl'Innocenti; Alfredo Cosco; Fabrizio Butini; Roberta Giacomi; +1 Authors

    TRAME is a research infrastructure for medieval manuscripts. The TRAME engine scans a set of sources for searched terms and retrieves links to a wide range of possible information, from simple reference, to detailed manuscript record, to full text transcriptions. Currently, it is possible to perform queries by: free-text, shelfmark, author, title, date, copyst or incipit, on more than 80 selected scholarly digital resources across EU and USA. Since 2014 September 1st, TRAME has entered a new phase and the current work is focused on: extending the meta-search approach to other web resources, leveraging the users interaction to define an ontology for medieval manuscripts, re-designing the front-end towards a new UX approach.

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    https://doi.org/10.1007/978-3-...
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  • Authors: Lucia Pinelli; Emiliano Degl'Innocenti;

    MIRABILE è il risultato dei processi di analisi e integrazione delle informazioni confluite nei data-base costituiti dalle singole ricerche condotte dalla SISMEL, dalla FEF e da altre istituzioni che hanno portato il loro contributo di analisi e di dati. Obiettivo di MIRABILE è fornire agli utenti della rete uno strumento informatico unitario, aperto e in costante evoluzione (sia dal punto di vista dei contenuti sia da quello tecnologico) per lo studio e la ricerca sugli autori medievali, i testi manoscritti e la loro tradizione. Si può effettuare la ricerca integrata su numerosi repertori specializzati tra cui il MEL «Medioevo latino. Bollettino bibliografico della cultura europea da Boezio a Erasmo - secoli VI-XV».

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    Authors: Vanden Daelen, Veerle; Edmond, Jennifer; Links, Petra; Priddy, Mike; +3 Authors

    International audience; One of the funded project proposals under DARIAH’s Open Humanities call 2015 was “Open History: Sustainable digital publishing of archival catalogues of twentieth-century history archives”. Based on the experiences of the Collaborative EuropeaN Digital Archival Research Infrastructure (CENDARI) and the European Holocaust Research Infrastructure (EHRI), the main goal of the “Open History” project was to enhance the dialogue between (meta-)data providers and research infrastructures. Integrating archival descriptions – when they were already available – held at a wide variety of twentieth-century history archives (from classic archives to memorial sites, libraries and private archives) into research infrastructures has proven to be a major challenge, which could not be done without some degree of limited to extensive pre-processing or other preparatory work. The “Open History” project organized two workshops and developed two tools: an easily accessible and general article on why the practice of standardization and sharing is important and how this can be achieved; and a model which provides checklists for self-analyses of archival institutions. The text that follows is the article we have developed. It intentionally remains at a general level, without much jargon, so that it can be easily read by those who are non-archivists or non-IT. Hence, we hope it will be easy to understand for both those who are describing the sources at various archives (with or without IT or archival sciences degrees), as well as decision-makers (directors and advisory boards) who wish to understand the benefits of investing in standardization and sharing of data. It is important to note is that this text is a first step, not a static, final result. Not all aspects about standardization and publication of (meta-)data are discussed, nor are updates or feedback mechanisms for annotations and comments discussed. The idea is that this text can be used in full or in part and that it will include further chapters and section updates as time goes by and as other communities begin using it. Some archives will read through much of these and see confirmation of what they have already been implementing; others – especially the smaller institutions, such as private memory institutions – will find this a low-key and hands-on introduction to help them in their efforts.

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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: Hannes Berg; Maria A. Wirtz Martin; Nadide Altincekic; Islam Alshamleh; +79 Authors

    Work at BMRZ is supported by the state of Hesse. Work in Covid19-NMR was supported by the Goethe Corona Funds, by the IWBEFRE-program 20007375 of state of Hesse, the DFG through CRC902: “Molecular Principles of RNA-based regulation.” and through infrastructure funds (project numbers: 277478796, 277479031, 392682309, 452632086, 70653611) and by European Union’s Horizon 2020 research and innovation program iNEXT-discovery under grant agreement No 871037. BY-COVID receives funding from the European Union’s Horizon Europe Research and Innovation Programme under grant agreement number 101046203. “INSPIRED” (MIS 5002550) project, implemented under the Action “Reinforcement of the Research and Innovation Infrastructure,” funded by the Operational Program “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014–2020) and co-financed by Greece and the EU (European Regional Development Fund) and the FP7 REGPOT CT-2011-285950—“SEE-DRUG” project (purchase of UPAT’s 700 MHz NMR equipment). The support of the CERM/CIRMMP center of Instruct-ERIC is gratefully acknowledged. This work has been funded in part by a grant of the Italian Ministry of University and Research (FISR2020IP_02112, ID-COVID) and by Fondazione CR Firenze. A.S. is supported by the Deutsche Forschungsgemeinschaft [SFB902/B16, SCHL2062/2-1] and the Johanna Quandt Young Academy at Goethe [2019/AS01]. M.H. and C.F. thank SFB902 and the Stiftung Polytechnische Gesellschaft for the Scholarship. L.L. work was supported by the French National Research Agency (ANR, NMR-SCoV2-ORF8), the Fondation de la Recherche Médicale (FRM, NMR-SCoV2-ORF8), FINOVI and the IR-RMN-THC Fr3050 CNRS. Work at UConn Health was supported by grants from the US National Institutes of Health (R01 GM135592 to B.H., P41 GM111135 and R01 GM123249 to J.C.H.) and the US National Science Foundation (DBI 2030601 to J.C.H.). Latvian Council of Science Grant No. VPP-COVID-2020/1-0014. National Science Foundation EAGER MCB-2031269. This work was supported by the grant Krebsliga KFS-4903-08-2019 and SNF-311030_192646 to J.O. P.G. (ITMP) The EOSC Future project is co-funded by the European Union Horizon Programme call INFRAEOSC-03-2020—Grant Agreement Number 101017536. Open Access funding enabled and organized by Projekt DEAL SARS-CoV-2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti-virals. Within the international Covid19-NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80 % of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR-detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure-based drug design against the SCoV2 proteome. 12 pags., 4 figs., 3 tabs. Peer reviewed

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    Angewandte Chemie International Edition
    Other literature type . Article . 2022 . Peer-reviewed
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    Angewandte Chemie
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    Authors: Berg, Hannes; Wirtz Martin, Maria A.; Altincekic, Nadide; Alshamleh, Islam; +20 Authors

    SARS-CoV-2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti-virals. Within the international Covid19-NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80 % of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR-detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure-based drug design against the SCoV2 proteome. Angewandte Chemie. International Edition, 61 (46) ISSN:0570-0833 ISSN:1433-7851 ISSN:1521-3773

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    Authors: Hube, Christoph; Fetahu, Besnik;

    Biased language commonly occurs around topics which are of controversial nature, thus, stirring disagreement between the different involved parties of a discussion. This is due to the fact that for language and its use, specifically, the understanding and use of phrases, the stances are cohesive within the particular groups. However, such cohesiveness does not hold across groups. In collaborative environments or environments where impartial language is desired (e.g. Wikipedia, news media), statements and the language therein should represent equally the involved parties and be neutrally phrased. Biased language is introduced through the presence of inflammatory words or phrases, or statements that may be incorrect or one-sided, thus violating such consensus. In this work, we focus on the specific case of phrasing bias, which may be introduced through specific inflammatory words or phrases in a statement. For this purpose, we propose an approach that relies on a recurrent neural networks in order to capture the inter-dependencies between words in a phrase that introduced bias. We perform a thorough experimental evaluation, where we show the advantages of a neural based approach over competitors that rely on word lexicons and other hand-crafted features in detecting biased language. We are able to distinguish biased statements with a precision of P=0.92, thus significantly outperforming baseline models with an improvement of over 30%. Finally, we release the largest corpus of statements annotated for biased language. The Twelfth ACM International Conference on Web Search and Data Mining, February 11--15, 2019, Melbourne, VIC, Australia

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    http://arxiv.org/pdf/1811.0574...
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    https://doi.org/10.1145/328960...
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    https://doi.org/10.48550/arxiv...
    Article . 2018
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      http://arxiv.org/pdf/1811.0574...
      Conference object
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      https://doi.org/10.1145/328960...
      Conference object . 2019 . Peer-reviewed
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      https://doi.org/10.48550/arxiv...
      Article . 2018
      License: arXiv Non-Exclusive Distribution
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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: Laurent Romary; Charles Riondet;

    This article tackles the issue of integrating heterogeneous archival sources in one single data repository, namely the European Holocaust Research Infrastructure (EHRI) portal, whose aim is to support Holocaust research by providing online access to information about dispersed sources relating to the Holocaust (http://portal.ehri-project.eu). In this case, the problem at hand is to combine data coming from a network of archives in order to create an interoperable data space which can be used to search for, retrieve and disseminate content in the context of archival-based research. The scholarly purpose has specific consequences on our task. It assumes that the information made available to the researcher is as close as possible to the originating source in order to guarantee that the ensuing analysis can be deemed reliable. In the EHRI network of archives, as already observed in the case of the EU Cendari project, one cannot but face heterogeneity. The EHRI portal brings together descriptions from more than 1900 institutions. Each archive comes with a whole range of idiosyncrasies corresponding to the way it has been set up and evolved over time. Cataloging practices may also differ. Even the degree of digitization may range from the absence of a digital catalogue to the provision of a full-fledged online catalogue with all the necessary APIs for anyone to query and extract content. There is indeed a contrast here with the global endeavour at the international level to develop and promote standards for the description of archival content as a whole. Nonetheless, in a project like EHRI, standards should play a central role. They are necessary for many tasks related to the integration and exploitation of the aggregated content, namely: ● Being able to compare the content of the various sources, thus being able to develop quality-checking processes; ● Defining of an integrated repository infrastructure where the content of the various archival sources can be reliably hosted; ● Querying and re-using content in a seamless way; ● Deploying tools that have been developed independently of the specificities of the information sources, for instance in order to visualise or mine the resulting pool of information. The central aspect of the work described in this paper is the assessment of the role of the EAD (Encoded Archival Description) standard as the basis for achieving the tasks described above. We have worked out how we could develop a real strategy of defining specific customization of EAD that could be used at various stages of the process of integrating heterogeneous sources. While doing so, we have developed a methodology based on a specification and customization method inspired from the extensive experience of the Text Encoding Initiative (TEI) community. In the TEI framework, as we show in section 1, one has the possibility to model specific subsets or extensions of the TEI guidelines while maintaining both the technical (XML schemas) and editorial (documentation) content within a single framework. This work has led us quite far in anticipating that the method we have developed may be of a wider interest within similar environments, but also, as we believe, for the future maintenance of the EAD standard. Finally this work, successfully tested and implemented in the framework of EHRI [Riondet 2017], can be seen as part of the wider endeavour of European research infrastructures in the humanities such as CLARIN and DARIAH to provide support for researchers to integrate the use of standards in their scholarly practices. This is the reason why the general workflow studied here has been introduced as a use case in the umbrella infrastructure project PARTHENOS which aims, among other things, at disseminating information and resources about methodological and technical standards in the humanities.

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    OpenAIRE; Archival Science
    Other literature type . Article . 2018 . Peer-reviewed
    License: Springer TDM
    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/
    Archival Science
    Article
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