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  • Authors: Flückiger, Fabrice; Aberle, Marc; Beretta, Francesco;
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    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
    Article . 2022 . Peer-reviewed
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    https://doi.org/10.26083/tupri...
    Article . 2024
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      Angewandte Chemie International Edition
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      Angewandte Chemie
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      https://doi.org/10.26083/tupri...
      Article . 2024
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    Authors: Josh Moore; Daniela Basurto-Lozada; Sébastien Besson; John Bogovic; +65 Authors

    A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself-OME-Zarr-along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain-the file format that underlies so many personal, institutional, and global data management and analysis tasks. Histochemistry and Cell Biology, 160 (3) ISSN:0948-6143 ISSN:1432-119X

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    Histochemistry and Cell Biology
    Article . 2023 . Peer-reviewed
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    Europe PubMed Central
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    Research Collection
    Article . 2023
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      Histochemistry and Cell Biology
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      Europe PubMed Central
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      Research Collection
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    Authors: Nury, Elisa; Monier, Mina;

    {"references": ["Clivaz, Claire. \"Mk 16 im Codex Bobbiensis. Neue Materialien zur conclusio brevior des Markusevangeliums.\" Zeitschrift f\u00fcr Neues Testament 47/24 (2021), p. 59-85, https://serval.unil.ch/fr/notice/serval:BIB_4D607A256FE4", "Clivaz, Claire. \"Looking at Scribal Practices in the Endings of Mark 16\", Henoch 42 (2020/2), special issue edited by P. Pouchelle and J.-S. Rey, p. 373-387, https://serval.unil.ch/fr/notice/serval:BIB_94927C83CD64", "Clivaz, Claire. \"Returning to Mark 16,8: What's New?\" Ephemerides Theologicae Lovanienses 96/4 (2019a), p. 645-659; https://dx.doi.org/10.2143/ETL.95.4.3286928", "Clivaz, Claire, \"The Impact of Digital Research: Thinking about the MARK16 Project.\" Open Theology 5/1 (2019b): 1-12; https://doi.org/10.1515/opth-2019-0001", "Clivaz, Claire, Mina Monier and Jonathan Barda, \"MARK16 as Virtual Research Environment. Challenges and Opportunities in New Testament Studies\". In \"Ancient Manuscripts and Virtual Research Environments,\" ed. Claire Clivaz and Garrick V. Allen, special issue, Classics@ 18. [N.p.] https://classics-at.chs.harvard.edu/classics18-clivaz-monier-barda/", "Focant, Camille. \"Un silence qui fait parler (Mc 16,8).\" In Marc, un \u00e9vangile \u00e9tonnant, Recueil d'essais, Camille Focant., 194:341\u201358. BEThL. Leuven: Peeters, 2006. https://mark16material.files.wordpress.com/2021/08/focantsilence2006.pdf.", "Monier, Mina. 2022. \"Mark's Endings in Context: Paratexts and Codicological Remarks\" Religions 13, no. 6: 548. https://doi.org/10.3390/rel13060548", "Monier, Mina, \"Mark's Ending in the Digital Age: Paratextual Evidence, New Findings and Transcription Challenges\", Postscripts: The Journal of Sacred Texts, Cultural Histories, and Contemporary Contexts 12 (2021/1), p. 75-98; open access (green road): https://serval.unil.ch/fr/notice/serval:BIB_F1A56F977830; https://journal.equinoxpub.com/POST/article/view/20256", "Monier, Mina, \"GA 304, Theophylact's Commentary and the Ending of Mark.\" Filolog\u00eda Neotestamentaria 52 (2019), p. 94-106; https://reader.digitalbooks.pro/book/preview/125526/filo-8?1574842521282"]} DARIAH-CH Study Day 2022 - The SNSF MARK16 project Mina Monier and Elisa Nury (DH+, SIB) This poster will present the virtual research environment (VRE) of the five-year SNSF project MARK16, the first VRE focused on a biblical chapter (https://mark16.sib.swiss). The last chapter of Mark is a well-known enigma of New Testament textual criticism (NTTC): at least six different endings have been listed (e.g. Focant, 2006; Clivaz 2019a). We presumed that many useful manuscripts have not yet been studied, and therefore, should be explored. This led to significant primary results that were gradually documented during our research (Monier 2019, 2021 & 2022; Clivaz 2020, 2021). To support the harvest of results, we have created a VRE in four parts (Clivaz, 2019b): the main part of the MARK16 VRE holds 55 items visualized in a Manuscript Room application (https://mr-mark16.sib.swiss), with the code on Github (https://github.com/sib-swiss/dh-mr-mark16). Prepared in collaboration with the New Testament Virtual Manuscript Room (INTF, Münster), it provides folios of Mark 16 from ancient manuscripts in ten ancient languages. More than 20 international colleagues are MARK16 partners, and data have been nominally published in Nakala, the Huma-Num open public repository (https://mark16-snsf-prima-project.nakala.fr). The second part, Interpretations, presents scholarly individual opinions on Mark’s endings from the team and some colleagues (https://mark16-etalk.sib.swiss/search.php). It uses the tool eTalk, with the API on Github (https://github.com/sib-swiss/etalk-docker). The third part, Material, presents relevant material from the printed and digital cultures, like printed editions, articles, and also multimedia publications on Mark 16 (https://material-mark16.sib.swiss). The fourth part, forthcoming, Dataviz (https:// dataviz-mark16.sib.swiss) is building a geographical map in collaboration with the network Pelagios.

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    Authors: Gasser, Michael; id_orcid0000-0003-0390-1448;

    For many libraries, mass digitisation has become routine. Digitisation centres are available in many places and there is a wealth of online platforms for the presentation of a wide variety of different media. Current projects from ETH Library reveal the directions in which the enormous potential harboured in these platforms and the millions of digital copies already produced may evolve. Research partnerships play just as important a role here as active user participation and intensified outreach. HAL Archive

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    ETH Zürich Research Collection
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    ETH Zürich Research Collection
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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: Alassi, Sepideh; Rosenthaler, Lukas;

    This paper presents a novel approach to create an RDF based e-version of the correspondence network by connecting author-centric digital editions platforms without centeralizing data silos. Through one single platform that presents the network, researchers can perform advanced metadata and asynchronous full-text queries over the entire network to find resources for their research inventory and directly access the data. The advanced search tools of the platform, allow researchers to channel their expertise into the analysis of the resources and their relations rather than a quest for them. Based on this work, this paper introduces a new research method, The Network Method, to study the historical data as a graph. It also argues that visualization of the RDF based network of correspondence as web-based interactive 3D force-directed graphs empowers relational thinking by depicting the connections between resources and drawing the researcher's attention to the connection between the atoms of knowledge, data distribution, irregularities, etc. Furthermore, this paper presents a new feature that adds the time-dimension to the visualization of the correspondence data which enables researchers to study the change in the topic of correspondence over time.

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    Conference object . 2020 . Peer-reviewed
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    https://doi.org/10.5451/unibas...
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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: Nury, Elisa;

    International audience; This paper describes the workflow of the Grammateus project, from gathering data on Greek documentary papyri to the creation of a web application. The first stage is the selection of a corpus and the choice of metadata to record: papyrology specialists gather data from printed editions, existing online resources and digital facsimiles. In the next step, this data is transformed into the EpiDoc standard of XML TEI encoding, to facilitate its reuse by others, and processed for HTML display. We also reuse existing text transcriptions available on . Since these transcriptions may be regularly updated by the scholarly community, we aim to access them dynamically. Although the transcriptions follow the EpiDoc guidelines, the wide diversity of the papyri as well as small inconsistencies in encoding make data reuse challenging. Currently, our data is available on an institutional GitLab repository, and we will archive our final dataset according to the FAIR principles.

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    Authors: Nury, Elisa; Clivaz, Claire; Błaszczyńska, Marta; Kaiser, Michael; +4 Authors

    International audience; Published in OA on RESSI (http://www.ressi.ch/) at the end of Octobre 2021. We present here highlights from an enquiry on the innovations in scholarly writing in the Humanities and Social Sciences in the H2020 project OPERAS-P. This article explores the theme of Open Research Data and its role in the emergence of new models of scholarly writing. We examine more closely the obstacles and fostering conditions to the publication of research data, both from a social and a technical perspective.

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    Article . 2021
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    Authors: Timmerman, Kristof; Vanoeveren, Ine;

    Empty Mind is an audiovisual live performance that takes place in a virtual environment and is meant to be viewed online. It is inspired by the works and ideas of the American artist Agnes Martin. The work consists of 6 large movements (5 + 1), which can be performed in any order. The spectator decides this order and is able to interfere with the performance through an interactive UI-layer on top of a livestream. Empty Mind is a composition by Wim Henderickx for flutes (piccolo, flute, alto flute and bass flute) and live electronics. In each movement there is a strictly composed passage that represents a continuity between the parts and a number of free passages where the material is allowed to make its own trajectory - chosen by the soloist at that moment - creating a discontinuity. Flutist Ine Vanoeveren performs in a motion capture suit with which she controls the virtual environment. The performance in the virtual spaces is being filmed by a virtual camera and directly streamed onto Twitch. This livestream is the live feed for the audience, with the interactive layer on top of the video.

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    Presentation . 2022
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    https://dl.acm.org/doi/pdf/10....
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    https://doi.org/10.1145/349014...
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    Authors: Alliata, Giacomo; Yang, Yuchen;

    Audiovisual archives are the mnemonic records of the 20th and 21st centuries, the immense complexity of the past happenings, preserving individual and collective histories, memories, feelings, cultures and aesthetics. These collections have, in the past decades, dramatically increased in size, with, on one hand, an emergence of online video sharing services like Youtube and Vimeo, and important institutions digitising their archives, such as the BBC with its 1 million hours of footage. However, these large archives remain mostly inaccessible, due to copyright issues and to the sheer amount of content combined with the lack of a compelling system to explore them. Only 20% of the 200000 hours of the RTS audiovisual archive are accessible online for instance. Moreover, archival scholars have stressed the importance of innovative forms of engagement through compelling frameworks for the exploration of these large collections. Within this context, the Sinergia project Narratives From the Long Tail: Transforming Access to Audiovisual Archives aims to reexamine the relationship between archives, memory institutions, and general audiences through cutting edge computational and immersive technologies. We argue that, faced with the extensive amount of content available, meaningful storytelling frameworks are necessary for understanding and exploring an audiovisual collection. Thus, this paper will examine the formation of such a conceptual framework on the archival content and digital interface level. There is an increasing trend for transforming archives to be big data organisations through digitisation and state-of-art computational methods. The transformation not only enhances the management and accessibility for archives, but also unlocks the semantics in multimodal archival content as well as the potential use of domain knowledge. Such an upgrade should in theory surfacing the hidden structure, revealing and building connections between contents, allowing fast and effective curation of the archive to serve a variety of purposes. In this part of the paper, we will map different approaches used for current practises on digitally transforming archives for various storytelling purposes, and aim at identifying and addressing the opportunities, issues and challenges laying ahead brought by the methodological shift. Similarly, at the interface level, various approaches are taken to propose an immersive installation in which users can explore a large collection in a compelling way, driving their own storytelling experience. In this section, the ideas of embodiment will be leveraged to review meaningful digital installations, revealing how narrative can emerge in such frameworks. Multiple interactions and visualisations approaches can be employed to explore the semantics discovered through computational methods, using data as a sculpting material in the creation of a virtual world. Furthermore, in multi-users environments, social interactions place users as actors of the storytelling rather than mere spectators, with clear benefits in terms of enjoyment of the experience and understanding of the cultural aspect. In conclusion, this paper will propose a conceptual framework to explore a large collection of audiovisual items through the idea of storytelling in an immersive installation. Submission ID: 1032

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  • Authors: Flückiger, Fabrice; Aberle, Marc; Beretta, Francesco;
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    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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    Authors: Josh Moore; Daniela Basurto-Lozada; Sébastien Besson; John Bogovic; +65 Authors