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Research Ideas and Outcomes
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  This is an Open Access Journal Open Access journal
ISSN (Online) 2367-7163
Published by Pensoft Homepage  [58 journals]
  • Current cave monitoring practices, their variation and recommendations for
           future improvement in Europe: A synopsis from the 6th EuroSpeleo
           Protection Symposium

    • Abstract: Research Ideas and Outcomes 8: e85859
      DOI : 10.3897/rio.8.e85859
      Authors : Alexander Weigand, Szilárd-Lehel Bücs, Stanimira Deleva, Lada Lukić Bilela, Pierrette Nyssen, Kaloust Paragamian, Axel Ssymank, Hannah Weigand, Valerija Zakšek, Maja Zagmajster, Gergely Balázs, Shalva Barjadze, Katharina Bürger, William Burn, Didier Cailhol, Amélie Decrolière, Ferdinando Didonna, Azdren Doli, Tvrtko Drazina, Joerg Dreybrodt, Lana Ðud, Csaba Egri, Markus Erhard, Sašo Finžgar, Dominik Fröhlich, Grant Gartrell, Suren Gazaryan, Michel Georges, Jean-Francois Godeau, Ralf Grunewald, John Gunn, Jeff Hajenga, Peter Hofmann, Lee Knight, Hannes Köble, Nikolina Kuharic, Christian Lüthi, Cristian Munteanu, Rudjer Novak, Dainis Ozols, Matija Petkovic, Fabio Stoch, Bärbel Vogel, Ines Vukovic, Meredith Hall Weberg, Christian Zaenker, Stefan Zaenker, Ute Feit, Jean-Claude Thies : This manuscript summarizes the outcomes of the 6th EuroSpeleo Protection Symposium. Special emphasis was laid on presenting and discussing monitoring activities under the umbrella of the Habitats Directive (EU Council Directive 92/43/EEC) for habitat type 8310 "Caves not open to the public" and the Emerald Network. The discussions revealed a high level of variation in the currently conducted underground monitoring activities: there is no uniform definition of what kind of underground environments the "cave" habitat should cover, how often a specific cave has to be monitored, and what parameters should be measured to evaluate the conservation status. The variation in spatial dimensions in national definitions of caves further affects the number of catalogued caves in a country and the number of caves to be monitored. Not always participants are aware of the complete national monitoring process and that data sets should be freely available or easily accessible. The discussions further showed an inherent dilemma between an anticipated uniform monitoring approach with a coherent assessment methodology and, on the contrary, the uniqueness of caves and subterranean biota to be assessed – combined with profound knowledge gaps and a lack of resources. Nevertheless, some good practices for future cave monitoring activities have been identified by the participants: (1) Cave monitoring should focus on bio- and geodiversity elements alike; (2) Local communities should be involved, and formal agreements envisaged; (3) Caves must be understood as windows into the subterranean realm; (4) Touristic caves should not be excluded ad-hoc from regular monitoring; (5) New digital tools and open FAIR data infrastructures should be implemented; (6) Cave biomonitoring should focus on a large(r) biological diversity; and (7) DNA-based tools should be integrated. Finally, the importance of the 'forgotten' Recommendation No. 36 from the Bern Convention as a guiding legal European document was highlighted. HTML XML PDF
      PubDate: Wed, 4 May 2022 12:46:42 +0300
  • An idea on Smart Farming: IoT monitoring of water production from
           dihydrogen combustion

    • Abstract: Research Ideas and Outcomes 8: e82995
      DOI : 10.3897/rio.8.e82995
      Authors : Radia Belkeziz : Smart Farming is a concept developing rapidly and gaining momentum. The management of livestock and farm products is done in an automated way thanks to IoT technology. The large field of data at hand offers the possibility of analysis for a better understanding of issues and more efficient decision-making. The management of water consumption is one of the most relevent Smart Farming use cases. In the event of drought, the pressure on water resources becomes increasingly strong. What if we produced water then' The idea of not worrying about the consequence of drought on agricultural production would be interesting.One of the first experiences you learn in a chemistry class is that the combustion of dihydrogen produces water. However, it is necessary to follow this experience closely because of the risk of explosion. Dihydrogen can be produced by the gasification of (agricultural) biomass. Here, the technology takes over, by the means of a supervising IoT system. This system will manage the overall process from biomass production, then dihydrogen production (biomass-to-hydrogen), to water production (dihydrogen-to-water).If the idea proves to be viable on a large scale, the result would be valuable in reducing the issue of water scarcity, in times of drought, in agricultural areas, and even in allowing energy autonomy on farms. HTML XML PDF
      PubDate: Mon, 18 Apr 2022 09:08:57 +030
  • FID Civil Engineering, Architecture and Urbanism digital - A platform for
           science (BAUdigital)

    • Abstract: Research Ideas and Outcomes 8: e82563
      DOI : 10.3897/rio.8.e82563
      Authors : Susanne Arndt, Anna Beer, Ina Blümel, Carsten Elsner, Christian Hauschke, Dagmar Holste, Benjamin Kampe, Micky Lindlar, Gelareh Mofakhamsanie, Andreas Noback, Hedda Saemann, Stephan Tittel, Friedmar Voormann, Katja Wermbter, Roger Winkler : University Library Braunschweig (UB Braunschweig), University and State Library Darmstadt (ULB Darmstadt), TIB – Leibniz Information Centre for Technology and Natural Sciences and the Fraunhofer Information Centre for Planning and Building (Fraunhofer IRB) are jointly establishing a specialised information service (FID, "Fachinformationsdienst") for the disciplines of civil engineering, architecture and urbanism. The FID BAUdigital, which is funded by the German Research Foundation (DFG, "Deutsche Forschungsgemeinschaft"), will provide researchers working on digital design, planning and production methods in construction engineering with a joint information, networking and data exchange platform and support them with innovative services for documentation, archiving and publication in their data-based research. HTML XML PDF
      PubDate: Wed, 6 Apr 2022 08:10:41 +0300
  • Europa Biodiversity Observation Network: User and Policy Needs Assessment

    • Abstract: Research Ideas and Outcomes 8: e84480
      DOI : 10.3897/arphapreprints.e84517
      Authors : Hannah Moersberger, Juliette G. C. Martin, Jessi Junker, Ivelina Georgieva, Silke Bauer, Pedro Beja, Tom Breeze, Lluís Brotons, Helge Bruelheide, Néstor Fernández, Miguel Fernandez, Ute Jandt, Christian Langer, Anne Lyche Solheim, Joachim Maes, Francisco Moreira, Guy Pe'er, Joana Santana, Judy Shamoun-Baranes, Bruno Smets, Jose Valdez, Ian McCallum, Henrique M. Pereira, Aletta Bonn : In this report, we present the analysis of the different available biodiversity data streams at the EU and national level, both baseline biodiversity data and monitoring data. We assess how these biodiversity data inform and trigger policy action and identify the related challenges the different European countries and relevant EU agencies face and the solutions to overcome them. To do this, we consulted with more than 350 expert stakeholders from policy, research and practice. The assessment identified a fragmented biodiversity data landscape that cannot currently easily answer all relevant policy questions. Quantity and quality of biodiversity baseline datasets differ for the different countries, ranging from non-existent biodiversity monitoring due to capacity issues, to regular monitoring of ecosystem processes and state. By engaging stakeholders and experts in both member states and non-member states and from several EU bodies, we identified key challenges and ways to address these with targeted solutions towards building a joint European Biodiversity Monitoring Network. Solutions include focussing on cooperation and coordination, enhanced data standardisation and sharing, as well as the use of models and new technologies. These solutions can however only be realised with dedicated funding and capacity building, in coordination with all stakeholders in partnership. HTML XML PDF
      PubDate: Wed, 30 Mar 2022 07:57:25 +030
  • The Ecological Observing System of the Adriatic Sea (ECOAdS): structure
           and perspectives within the main European biodiversity and environmental

    • Abstract: Research Ideas and Outcomes 8: e82597
      DOI : 10.3897/rio.8.e82597
      Authors : Alessandra Pugnetti, Elisabetta Manea, Ivica Vilibić, Alessandro Sarretta, Lucilla Capotondi, Bruno Cataletto, Elisabeth De Maio, Carlo Franzosini, Ivana Golec, Marco Gottardi, Jelena Kurtović Mrčelić, Hrvoje Mihanovic, Alessandro Oggioni, Grgur Pleslic, Mariangela Ravaioli, Silvia Rova, Andrea Valentini, Caterina Bergami : This Policy Brief succinctly presents the Ecological Observing System of the Adriatic Sea (ECOAdS), aimed at integrating the ecological and oceanographic dimensions within the conservation strategy of the Natura 2000 network, and to propose a way to go for its future development and maintenance. After a definition of marine ecological observatories, we describe the current structure of ECOAdS, its key components and potential relevance in relation to the main European strategies for biodiversity and marine observation for the next decade. Finally, we suggest some actions that could be undertaken for the future development of ECOAdS, targeting possible perspectives in different regional, macro-regional, national and European strategic contexts. This Policy Brief is one of the outcomes of the Interreg Italy-Croatia Project ECOSS (ECological Observing System in the Adriatic Sea: oceanographic observations for biodiversity; https://www.italy-croatia.eu/web/ecoss), which had the main purpose to design and carry out the first steps for the establishment of ECOAdS. HTML XML PDF
      PubDate: Fri, 25 Mar 2022 09:08:20 +020
  • B-GOOD: Giving Beekeeping Guidance by cOmputatiOnal-assisted Decision

    • Abstract: Research Ideas and Outcomes 8: e84129
      DOI : 10.3897/rio.8.e84129
      Authors : Dirk de Graaf, Martin Bencsik, Lina De Smet, Peter Neumann, Marten Schoonman, José Paulo Sousa, Christopher Topping, Wim Verbeke, James Williams, Coby van Dooremalen : A key to healthy beekeeping is the Health Status Index (HIS) inspired by EFSA’s Healthy-B toolbox which we will make fully operational, with the active collaboration of beekeepers, by facilitating the coordinated and harmonised flow of data from various sources and by testing and validating each component thoroughly. We envisage a step-by-step expansion of participating apiaries, and will eventually cover all EU biogeographic regions. The key to a sustainable beekeeping is a better understanding of its socio-economics, particularly within local value chains, its relationship with bee health and the human-ecosystem equilibrium of the beekeeping sector and to implement these insights into the data processing and decision making. We will fully integrate socio-economic analyses, identify viable business models tailored to different contexts for European beekeeping and determine the carrying capacity of the landscape. In close cooperation with the EU Bee Partnership, an EU-wide bee health and management data platform and affiliated project website will be created to enable sharing of knowledge and learning between scientists and stakeholders within and outside the consortium. We will utilise and further expand the classification of the open source IT-application for digital beekeeping, BEEP, to streamline the flow of data related to beekeeping management, the beehive and its environment (landscape, agricultural practices, weather and climate) from various sources. The dynamic bee health and management data platform will allow us to identify correlative relationships among factors impacting the HSI, assess the risk of emerging pests and predators, and enable beekeepers to develop adaptive management strategies that account for local and EU-wide issues. Reinforcing and establishing, where necessary, new multi-actor networks of collaboration will engender a lasting learning and innovation system to ensure social-ecological resilient and sustainable beekeeping. HTML XML PDF
      PubDate: Wed, 23 Mar 2022 08:49:02 +020
  • SKG4EOSC - Scholarly Knowledge Graphs for EOSC: Establishing a backbone of
           knowledge graphs for FAIR Scholarly Information in EOSC

    • Abstract: Research Ideas and Outcomes 8: e83789
      DOI : 10.3897/rio.8.e83789
      Authors : Markus Stocker, Tina Heger, Artur Schweidtmann, Hanna Ćwiek-Kupczyńska, Lyubomir Penev, Milan Dojchinovski, Egon Willighagen, Maria-Esther Vidal, Houcemeddine Turki, Daniel Balliet, Ilaria Tiddi, Tobias Kuhn, Daniel Mietchen, Oliver Karras, Lars Vogt, Sebastian Hellmann, Jonathan Jeschke, Paweł Krajewski, Sören Auer : In the age of advanced information systems powering fast-paced knowledge economies that face global societal challenges, it is no longer adequate to express scholarly information - an essential resource for modern economies - primarily as article narratives in document form. Despite being a well-established tradition in scholarly communication, PDF-based text publishing is hindering scientific progress as it buries scholarly information into non-machine-readable formats. The key objective of SKG4EOSC is to improve science productivity through development and implementation of services for text and data conversion, and production, curation, and re-use of FAIR scholarly information. This will be achieved by (1) establishing the Open Research Knowledge Graph (ORKG, orkg.org), a service operated by the SKG4EOSC coordinator, as a Hub for access to FAIR scholarly information in the EOSC; (2) lifting to EOSC of numerous and heterogeneous domain-specific research infrastructures through the ORKG Hub’s harmonized access facilities; and (3) leverage the Hub to support cross-disciplinary research and policy decisions addressing societal challenges. SKG4EOSC will pilot the devised approaches and technologies in four research domains: biodiversity crisis, precision oncology, circular processes, and human cooperation. With the aim to improve machine-based scholarly information use, SKG4EOSC addresses an important current and future need of researchers. It extends the application of the FAIR data principles to scholarly communication practices, hence a more comprehensive coverage of the entire research lifecycle. Through explicit, machine actionable provenance links between FAIR scholarly information, primary data and contextual entities, it will substantially contribute to reproducibility, validation and trust in science. The resulting advanced machine support will catalyse new discoveries in basic research and solutions in key application areas. HTML XML PDF
      PubDate: Tue, 15 Mar 2022 14:47:20 +020
  • The WIO Regional Benthic Imagery Workshop: Lessons from past IIOE-2

    • Abstract: Research Ideas and Outcomes 8: e81563
      DOI : 10.3897/rio.8.e81563
      Authors : Tanya Haupt, Jamie Ceasar, Paris Stefanoudis, Charles von der Meden, Robyn Payne, Luther Adams, Darrell Anders, Anthony Bernard, Willem Coetzer, Wayne Florence, Liesl Janson, Ashley Johnson, Roxanne Juby, Alison Kock, Daniel Langenkämper, Ahmed Nadjim, Denham Parker, Toufiek Samaai, Laurenne Snyders, Leshia Upfold, Grant van der Heever, Lauren Williams : Originating from the Second International Indian Ocean Expedition (IIOE-2), the main goal of the Western Indian Ocean (WIO) Regional Benthic Imagery Workshop, was to provide information and training on the use of various underwater imagery platforms in benthic research. To date, attempts made to explore the bottom of the ocean range from simple diving bells to more advanced camera systems, and the rapidly expanding field of underwater image-based research has supported marine exploration in many forms, from biodiversity surveys, spatial analyses and temporal studies, to monitoring schemes. Alongside the increasing use of underwater camera systems worldwide, there is an evident need to improve training and access to these techniques for students and researchers from institutes within the WIO. The week-long virtual event was conducted between 30 August and 3 September 2021 with 266 participants. Sessions consisted of lessons, practical demonstrations and interactive discussions which covered the steps required to conduct underwater imagery surveys, taking participants through elements of sampling design, data acquisition and processing, considerations for statistical analysis and, effective managment of data. The session recordings from the workshop are available online as a teaching aid which has the potential to reach marine researchers both regionally and globally. It is crucial that we build on this momentum by continuing to develop and strengthen the network established through this initiative for standardised benthic-image-based research within the WIO. HTML XML PDF
      PubDate: Tue, 8 Mar 2022 14:14:19 +0200
  • BridgeDb and Wikidata: a powerful combination generating interoperable
           open research (BridgeDb)

    • Abstract: Research Ideas and Outcomes 8: e83031
      DOI : 10.3897/rio.8.e83031
      Authors : Egon Willighagen, Martina Kutmon, Marvin Martens, Denise Slenter : Like humans have a unique social security number and different phone numbers from various providers, so do proteins and metabolites have a unique structure but different identifiers from various databases. BridgeDb is an interoperability platform that allows combining these databases, by matching database-specific identifiers. These matches are called identifier mappings, and they are indispensable when combining experimental (omics) data with knowledge in reference databases. BridgeDb takes care of this interoperability between gene, protein, metabolite, and other databases, thus enabling seamless integration of many knowledge bases and wet-lab results. Since databases get updated continuously, so should the Open Science BridgeDb project. HTML XML PDF
      PubDate: Mon, 7 Mar 2022 11:50:37 +0200
  • Sharing taxonomic expertise between natural history collections using
           image recognition

    • Abstract: Research Ideas and Outcomes 8: e79187
      DOI : 10.3897/rio.8.e79187
      Authors : Michael Greeff, Max Caspers, Vincent Kalkman, Luc Willemse, Barry Sunderland, Olaf Bánki, Laurens Hogeweg : Natural history collections play a vital role in biodiversity research and conservation by providing a window to the past. The usefulness of the vast amount of historical data depends on their quality, with correct taxonomic identifications being the most critical. The identification of many of the objects of natural history collections, however, is wanting, doubtful or outdated. Providing correct identifications is difficult given the sheer number of objects and the scarcity of expertise. Here we outline the construction of an ecosystem for the collaborative development and exchange of image recognition algorithms designed to support the identification of objects. Such an ecosystem will facilitate sharing taxonomic expertise among institutions by offering image datasets that are correctly identified by their in-house taxonomic experts. Together with openly accessible machine learning algorithms and easy to use workbenches, this will allow other institutes to train image recognition algorithms and thereby compensate for the lacking expertise. HTML XML PDF
      PubDate: Tue, 1 Mar 2022 10:02:21 +0200
  • D6.1 Analysis of needs and capacity of different audiences including
           policy makers, expert practitioners and other modellers

    • Abstract:
      DOI : 10.3897/arphapreprints.e82715
      Authors : Milica Trajković, Dajana Vujaklija, Guy Ziv, Arjan Gosal, Jiaqi Ge, Jodi Gunning, Birgit Mueller, Annabelle Williams, Elisabet Nadeu : This document has five main sections: the first one, “Developing the needs assessment protocol” which explains how we approached to different stakeholders in order to define and analyse their needs and capacities; the second section contains the report of of the interviews conducted by RISE and present the needs of Policy Makers; section three explains the needs of expert practitioners identified during the online workshop (14th and 15th of July 2020);  section four presents the needs of biophysical modeling community and section five explains the needs of ABM modellers identified from recent scholarly workshops. The results of this analysis will be taken under consideration and co-design and co-development processes. HTML XML PDF
      PubDate: Fri, 25 Feb 2022 16:30:00 +020
  • Deliverable D2.2 BESTMAP Conceptual Framework Design &

    • Abstract:
      DOI : 10.3897/arphapreprints.e82404
      Authors : Guy Ziv, Jodi Gunning, Tomáš Václavík, Michael Beckmann, Anne Paulus, Birgit Mueller, Meike Will, Anna Cord, Stephanie Roilo, James Bullock, Paul Evans, Cristina Domingo-Marimon, Joan Masó Pau : This deliverable provides a General Framework for the BESTMAP Policy Impact Assessment Modelling (BESTMAP-PIAM) toolset. The BESTMAP-PIAM is based on the notion of defining (a) a typology of agricultural systems, with one (or more) representative case study (CS) in each major system; (b) mapping all individual farms within the case study to a Farm System Archetype (FSA) typology; (c) model the adoption of agri-environmental schemes (AES) within the spatially-mapped FSA population using Agent Based Models (ABM), based on literature and a survey with sufficient representative sample in each FSA of each CS, to elucidate the non-monetary drivers underpinning AES adoption and the relative importance of financial and non-financial/social/identity drivers; (d) linking AES adoption to a set of biophysical, ecological and socio-economic impact models; (e) upscaling the CS level results to EU scale; (f) linking the outputs of these models to indicators developed for the post-2020 CAP output, result and impact reports; (g) visualizing outputs and providing a dashboard for policy makers to explore a range of policy scenarios, focusing on cost-effectiveness of different AES. HTML XML PDF
      PubDate: Fri, 25 Feb 2022 15:30:00 +020
  • Use of Worksheet events in Excel to save solver objective cell value from
           each iteration

    • Abstract: Research Ideas and Outcomes 8: e79006
      DOI : 10.3897/rio.8.e79006
      Authors : Prasanth Sambaraju : Solver is a Microsoft Excel add-in program which is used to find an optimal value for a formula in the objective cell. Solver accomplishes this either by maximizing, minimizing or setting the objective cell value to a specific value. The article presents the utility of in built worksheet events in Excel VBA to save the value of objective cell from each iteration when solver is used for optimization. HTML XML PDF
      PubDate: Fri, 25 Feb 2022 08:43:38 +020
  • Unifying approaches to Functional Marine Connectivity for improved marine
           resource management: the European SEA-UNICORN COST Action

    • Abstract: Research Ideas and Outcomes 8: e80223
      DOI : 10.3897/rio.8.e80223
      Authors : Audrey Darnaude, Sophie Arnaud-Haond, Ewan Hunter, Oscar Gaggiotti, Anna Sturrock, Maria Beger, Filip Volckaert, Angel Pérez-Ruzafa, Lucía López-López, Susanne E. Tanner, Cemal Turan, Servet Ahmet Doğdu, Stelios Katsanevakis, Federica Costantini : Truly sustainable development in a human-altered, fragmented marine environment subject to unprecedented climate change, demands informed planning strategies in order to be successful. Beyond a simple understanding of the distribution of marine species, data describing how variations in spatio-temporal dynamics impact ecosystem functioning and the evolution of species are required. Marine Functional Connectivity (MFC) characterizes the flows of matter, genes and energy produced by organism movements and migrations across the seascape. As such, MFC determines the ecological and evolutionary interdependency of populations, and ultimately the fate of species and ecosystems. Gathering effective MFC knowledge can therefore improve predictions of the impacts of environmental change and help to refine management and conservation strategies for the seas and oceans. Gathering these data are challenging however, as access to, and survey of marine ecosystems still presents significant challenge. Over 50 European institutions currently investigate aspects of MFC using complementary methods across multiple research fields, to understand the ecology and evolution of marine species. The aim of SEA-UNICORN, a COST Action within the European Union Horizon 2020 framework programme, is to bring together this research effort, unite the multiple approaches to MFC, and to integrate these under a common conceptual and analytical framework. The consortium brings together a diverse group of scientists to collate existing MFC data, to identify knowledge gaps, to enhance complementarity among disciplines, and to devise common approaches to MFC. SEA-UNICORN will promote co-working between connectivity practitioners and ecosystem modelers to facilitate the incorporation of MFC data into the predictive models used to identify marine conservation priorities. Ultimately, SEA-UNICORN will forge strong forward-working links between scientists, policy-makers and stakeholders to facilitate the integration of MFC knowledge into decision support tools for marine management and environmental policies. HTML XML PDF
      PubDate: Tue, 22 Feb 2022 14:49:46 +020
  • Deliverable D3.4 Summaries of data, obstacles and challenges from
           interview campaigns

    • Abstract:
      DOI : 10.3897/arphapreprints.e81787
      Authors : Felix Wittstock, David Hötten, Sofia Biffi, Cristina Domingo, Bořivoj Šarapatka, Marek Bednář, Minučer Mesaroš : This deliverable presents a Summaries of data, obstacles and challenges from interview campaigns of the H2020 BESTMAP project. It covers a detailed description of methodology, reporting on the concrete steps taken to collect and analyze interview data. It also discusses obstacles and challenges to BESTMAP interview campaigns. Finally, the deliverable presents the main qualitative and quantitative findings of the interview analysis, with a focus on qualitative content analysis of open interview questions. HTML XML PDF
      PubDate: Mon, 7 Feb 2022 10:15:00 +0200
  • D1.3 Guidelines and protocols harmonizing activities across case

    • Abstract:
      DOI : 10.3897/arphapreprints.e81337
      Authors : Tomáš Václavík, Fanny Langerwisch, Guy Ziv, Jodi Gunning, Arjan Gosal, Michael Beckmann, Anne Paulus, Felix Wittstock, Anna Cord, Stephanie Roilo, Cristina Domingo-Marimon, Anabel Sanchez, Annelies Broekman, Dajana Vujaklija : This document is the first version of the Guidelines and protocols harmonizing activities across case studies of the H2020 BESTMAP project. It is intended to be updated in month 40 (D1.8). HTML XML PDF
      PubDate: Fri, 28 Jan 2022 10:00:00 +020
  • Europa Biodiversity Observation Network: integrating data streams to
           support policy

    • Abstract:
      DOI : 10.3897/arphapreprints.e81207
      Authors : Henrique M. Pereira, Jessi Junker, Néstor Fernández, Joachim Maes, Pedro Beja, Aletta Bonn, Tom Breeze, Lluís Brotons, Helge Bruelheide, Marcel Buchhorn, César Capinha, Cher Chow, Karolin Dietrich, Maria Dornelas, Grégoire Dubois, Miguel Fernandez, Mark Frenzel, Nikolai Friberg, Steffen Fritz, Ivelina Georgieva, Anne Gobin, Carlos Guerra, Sigrid Haande, Sergi Herrando, Ute Jandt, W. Daniel Kissling, Ingolf Kühn, Christian Langer, Camino Liquete, Anne Lyche Solheim, David Martí, Juliette G. C. Martin, Annett Masur, Ian McCallum, Marit Mjelde, Jannicke Moe, Hannah Moersberger, Alejandra Morán-Ordóñez, Francisco Moreira, Martin Musche, Laetitia M. Navarro, Alberto Orgiazzi, Robert Patchett, Lyubomir Penev, Joan Pino, Gabriela Popova, Simon Potts, Anna Ramon, Leonard Sandin, Joana Santana, Anna Sapundzhieva, Linda See, Judy Shamoun-Baranes, Bruno Smets, Pavel Stoev, Leho Tedersoo, Liis Tiimann, Jose Valdez, Sara Vallecillo, Roy H. A. Van Grunsven, Ruben Van De Kerchove, Dani Villero, Piero Visconti, Claudia Weinhold, Annika M. Zuleger : Observations are key to understand the drivers of biodiversity loss, and the impacts on ecosystem services and ultimately on people. Many EU policies and initiatives demand unbiased, integrated and regularly updated biodiversity and ecosystem service data. However, efforts to monitor biodiversity are spatially and temporally fragmented, taxonomically biased, and lack integration in Europe. EuropaBON aims to bridge this gap by designing an EU-wide framework for monitoring biodiversity and ecosystem services. EuropaBON harnesses the power of modelling essential variables to integrate different reporting streams, data sources, and monitoring schemes. These essential variables provide consistent knowledge about multiple dimensions of biodiversity change across space and time. They can then be analyzed and synthesized to support decision-making at different spatial scales, from the sub-national to the European scale, through the production of indicators and scenarios. To develop essential biodiversity and ecosystem variables workflows that are policy relevant, EuropaBON is built around stakeholder engagement and knowledge exchange (WP2). EuropaBON will work with stakeholders to identify user and policy needs for biodiversity monitoring and investigate the feasibility of setting up a center to coordinate monitoring activities across Europe (WP2). Together with stakeholders, EuropaBON will assess current monitoring efforts to identify gaps, data and workflow bottlenecks, and analyse cost-effectiveness of different schemes (WP3). This will be used to co-design improved monitoring schemes using novel technologies to become more representative temporally, spatially and taxonomically, delivering multiple benefits to users and society (WP4). Finally, EuropaBON will demonstrate in a set of showcases how workflows tailored to the Birds Directive, Habitats Directive, Water Framework Directive, Climate and Restoration Policy, and the Bioeconomy Strategy, can be implemented (WP5). HTML XML PDF
      PubDate: Wed, 26 Jan 2022 18:15:00 +020
  • Biodiversity Community Integrated Knowledge Library (BiCIKL)

    • Abstract: Research Ideas and Outcomes 8: e81136
      DOI : 10.3897/rio.8.e81136
      Authors : Lyubomir Penev, Dimitrios Koureas, Quentin Groom, Jerry Lanfear, Donat Agosti, Ana Casino, Joe Miller, Christos Arvanitidis, Guy Cochrane, Donald Hobern, Olaf Banki, Wouter Addink, Urmas Kõljalg, Kyle Copas, Patricia Mergen, Anton Güntsch, Laurence Benichou, Jose Benito Gonzalez Lopez, Patrick Ruch, Corinne Martin, Boris Barov, Kristina Hristova : BiCIKL is an European Union Horizon 2020 project that will initiate and build a new European starting community of key research infrastructures, establishing open science practices in the domain of biodiversity through provision of access to data, associated tools and services at each separate stage of and along the entire research cycle. BiCIKL will provide new methods and workflows for an integrated access to harvesting, liberating, linking, accessing and re-using of subarticle-level data (specimens, material citations, samples, sequences, taxonomic names, taxonomic treatments, figures, tables) extracted from literature. BiCIKL will provide for the first time access and tools for seamless linking and usage tracking of data along the line: specimens > sequences > species > analytics > publications > biodiversity knowledge graph > re-use. HTML XML PDF
      PubDate: Wed, 26 Jan 2022 17:00:00 +020
  • INAS: Interactive Argumentation Support for the Scientific Domain of
           Invasion Biology

    • Abstract: Research Ideas and Outcomes 8: e80457
      DOI : 10.3897/rio.8.e80457
      Authors : Tina Heger, Sina Zarrieß, Alsayed Algergawy, Jonathan Jeschke, Birgitta König-Ries : Developing a precise argument is not an easy task. In real-world argumentation scenarios, arguments presented in texts (e.g. scientific publications) often constitute the end result of a long and tedious process. A lot of work on computational argumentation has focused on analyzing and aggregating these products of argumentation processes, i.e. argumentative texts. In this project, we adopt a complementary perspective: we aim to develop an argumentation machine that supports users during the argumentation process in a scientific context, enabling them to follow ongoing argumentation in a scientific community and to develop their own arguments. To achieve this ambitious goal, we will focus on a particular phase of the scientific argumentation process, namely the initial phase of claim or hypothesis development. According to argumentation theory, the starting point of an argument is a claim, and also data that serves as a basis for the claim. In scientific argumentation, a carefully developed and thought-through hypothesis (which we see as Toulmin's "claim'' in a scientific context) is often crucial for researchers to be able to conduct a successful study and, in the end, present a new, high-quality finding or argument. Thus, an initial hypothesis needs to be specific enough that a researcher can test it based on data, but, at the same time, it should also relate to previous general claims made in the community. We investigate how argumentation machines can (i) represent concrete and more abstract knowledge on hypotheses and their underlying concepts, (ii) model the process of hypothesis refinement, including data as a basis of refinement, and (iii) interactively support a user in developing her own hypothesis based on these resources. This project will combine methods from different disciplines: natural language processing, knowledge representation and semantic web, philosophy of science and -- as an example for a scientific domain -- invasion biology. Our starting point is an existing resource in invasion biology that organizes and relates core hypotheses in the field and associates them to meta-data for more than 1000 scientific publications, which was developed over the course of several years based on manual analysis. This network, however, is currently static (i.e. needs substantial manual curation to be extended to incorporate new claims) and, moreover, is not easily accessible for users who miss specific background and domain knowledge in invasion biology. Our goal is to develop (i) a semantic model for representing knowledge on concepts and hypotheses, such that also non-expert users can use the network; (ii) a tool that automatically computes links from publication abstracts (and data) to these hypotheses; and (iii) an interactive system that supports users in refining their initial, potentially underdeveloped hypothesis. HTML XML PDF
      PubDate: Tue, 25 Jan 2022 10:00:00 +020
  • Securing Biodiversity, Functional Integrity, and Ecosystem Services in
           Drying River Networks (DRYvER)

    • Abstract: Research Ideas and Outcomes 7: e77750
      DOI : 10.3897/rio.7.e77750
      Authors : Thibault Datry, Daniel Allen, Roger Argelich, Jose Barquin, Nuria Bonada, Andrew Boulton, Flora Branger, Yongjiu Cai, Miguel Cañedo-Argüelles, Núria Cid, Zoltán Csabai, Martin Dallimer, José Carlos de Araújo, Steven Declerck, Thijs Dekker, Petra Döll, Andrea Encalada, Maxence Forcellini, Arnaud Foulquier, Jani Heino, Franck Jabot, Patrícia Keszler, Leena Kopperoinen, Sven Kralisch, Annika Künne, Nicolas Lamouroux, Claire Lauvernet, Virpi Lehtoranta, Barbora Loskotová, Rafael Marcé, Julia Martin Ortega, Christine Matauschek, Marko Miliša, Szilárd Mogyorósi, Nabor Moya, Hannes Müller Schmied, Antoni Munné, François Munoz, Heikki Mykrä, Irina Pal, Riikka Paloniemi, Petr Pařil, Polona Pengal, Bálint Pernecker, Marek Polášek, Carla Rezende, Sergi Sabater, Romain Sarremejane, Guido Schmidt, Lisette Senerpont Domis, Gabriel Singer, Esteban Suárez, Matthew Talluto, Sven Teurlincx, Tim Trautmann, Amélie Truchy, Emmanouil Tyllianakis, Sari Väisänen, Liisa Varumo, Jean-Philippe Vidal, Annika Vilmi, Dolors Vinyoles : River networks are among Earth’s most threatened hot-spots of biodiversity and provide key ecosystem services (e.g., supply drinking water and food, climate regulation) essential to sustaining human well-being. Climate change and increased human water use are causing more rivers and streams to dry, with devastating impacts on biodiversity and ecosystem services. Currently, more than a half of the global river networks consist of drying channels, and these are expanding dramatically. However, drying river networks (DRNs) have received little attention from scientists and policy makers, and the public is unaware of their importance. Consequently, there is no effective integrated biodiversity conservation or ecosystem management strategy of DRNs.A multidisciplinary team of 25 experts from 11 countries in Europe, South America, China and the USA will build on EU efforts to assess the cascading effects of climate change on biodiversity, ecosystem functions and ecosystem services of DRNs through changes in flow regimes and water use. DRYvER (DRYing riVER networks) will gather and upscale empirical and modelling data from nine focal DRNs (case studies) in Europe (EU) and Community of Latin American and Caribbean States (CELAC) to develop a meta-system framework applicable to Europe and worldwide. It will also generate crucial knowledge-based strategies, tools and guidelines for economically-efficient adaptive management of DRNs. Working closely with stakeholders and end-users, DRYvER will co-develop strategies to mitigate and adapt to climate change impacts in DRNs, integrating hydrological, ecological (including nature-based solutions), socio-economic and policy perspectives. The end results of DRYvER will contribute to reaching the objectives of the Paris Agreement and placing Europe at the forefront of research on climate change. HTML XML PDF
      PubDate: Fri, 31 Dec 2021 17:00:00 +020
  • Documentation of a public communication project by German-speaking
           scientists prior to the September 2021 climate demonstrations

    • Abstract: Research Ideas and Outcomes 7: e79061
      DOI : 10.3897/rio.7.e79061
      Authors : Gregor Hagedorn, Kirsten von Elverfeldt : English: Documentation of a communication project by German-speaking scientists encouraging their peers to participate in the September 2021 climate demonstrations by means of short statements or appeals (German, with English and French translations).Deutsch: Dokumentation eines Kommunikationsprojekts deutschsprachiger Wissenschaftler:innen, ihre Kolleg:innen mit kurzen Statements oder Aufrufen zur Teilnahme an den Klimademonstrationen im September 2021 zu ermuntern (deutsch, mit englischer und französischer Übersetzung).Français: Documentation d'un projet de communication de scientifiques germanophones visant à encourager leurs collègues à participer aux manifestations pour le climat en septembre 2021 par de courtes déclarations ou des appels (en allemand, avec traduction en anglais et en français). HTML XML PDF
      PubDate: Mon, 13 Dec 2021 12:00:00 +020
  • The Value of Digitising Natural History Collections

    • Abstract: Research Ideas and Outcomes 7: e78844
      DOI : 10.3897/rio.7.e78844
      Authors : Danail Popov, Priyanka Roychoudhury, Helen Hardy, Laurence Livermore, Ken Norris : The Natural History Museum, London has been creating digital data about collections for many years, with a formal Digital Collections Programme since 2014. Efforts to monitor the outcomes and impact of this work have focused on metrics of digital access, such as download events, and on citations of digital specimens as a measure of use. Digitisation projects and resulting research have also been used as impact case studies, highlighting areas such as human health and conservation. In 2021, the Museum decided to explore the economic impacts of collections data in more depth, and commissioned Frontier Economics to undertake modelling, resulting in this report. While the methods in this report are relevant to collections globally, this modelling focuses on benefits to the UK, and is intended to support the Museum’s own digitisation work, as well as a current scoping study funded by the Arts & Humanities Research Council about the case for digitising all UK natural science collections as a research infrastructure. This study focuses on digitisation in the round, not distinguishing between different collection types or levels of data creation at this stage. Three methods have been used: first, analysing five key thematic areas or sectors where data from natural science collections are likely to lead to benefits; secondly, analysing typical returns on investment in scientific research; and thirdly, examining the efficiency savings that can be reinvested in research if data are available freely and openly. Together, these methods confirm benefits in excess of £2 billion over 30 years, representing a seven to ten times return on investment. HTML XML PDF
      PubDate: Tue, 7 Dec 2021 12:00:00 +0200
  • RECLAMO: Unlocking the potential of wastewater reuse for agricultural
           irrigation in Spain 

    • Abstract: Research Ideas and Outcomes 7: e76793
      DOI : 10.3897/rio.7.e76793
      Authors : Irene Blanco-Gutiérrez, Paloma Esteve, Alberto Garrido, Almudena Gómez-Ramos, Augusto Arce, Sergio Zubelzu, Carlos Díaz-Ambrona, Raúl Sánchez, Javier Calatrava, Juan López-Correa : Increasing water scarcity is encouraging the use of unconventional water resources. In recent years, the European Union has launched numerous initiatives to promote and facilitate water reuse for agricultural irrigation. Today, the use of reclaimed water for agriculture has become an alternative, reliable and safe source of water supply and an indispensable water planning tool, especially in the area of southern Europe. However, water reuse for irrigation is currently far below its potential. Numerous barriers prevent its development and call for a detailed analysis of the different aspects affecting reclaimed water reuse, through an integrated and multidisciplinary approach.A multidisciplinary research team from Universidad Politécnica de Madrid, consisting of agronomists, hydrologists, chemists and agricultural economists, will work on the RECLAMO Project (https://blogs.upm.es/reclamo/), with the aim of providing solutions and recommendations aimed at promoting the full development and use of reclaimed water for irrigation in areas of Spain with marked water stress.For this purpose, project activities will be developed in two selected case studies (the Segura Basin, leader in water reuse in Spain and the Guadiana Basin, with success stories, but low levels of water reuse) and organised according to five axes: 1) development of a comprehensive knowledge-base covering the regulatory, technical, socio-economic and environmental aspects of reclaimed water reuse in agriculture; 2) participatory development of future scenarios exploring possible strategies, barriers and opportunities, in relation to the expansion of the use of reclaimed water for irrigation; 3) impact analysis of  the strategies identified at different scales (crop, farm, (sub-)basin), through the development of an integrated modelling platform (hydrologic-agronomic-economic models); 4) Development of a roadmap and policy recommendations to achieve the full development and use of reclaimed water reuse for irrigation; 5) Dissemination of knowledge and promotion of science-policy-society dialogue.To this end, RECLAMO will collaborate closely with experts and stakeholder groups that will play a key role in the project in co-creating the scenarios and modelling tools and validating the results. The project will also seek for synergies and complementarities with other similar projects and explore new ways of collaborating with companies and research groups that allow research to continue and expand beyond the spatial and temporal limits of the project.RECLAMO’s results will promote an integrated approach to the sustainable management of water resources in water-stressed areas, including reclaimed water management. The integrated modelling platform developed in the project will allow policy-makers and water users to benefit from an improved understanding of the interactions between the social, economic and environmental aspects of water systems, in the context of climate and socio-economic change that will lead to better informed decision-making to address future water challenges. In addition, RECLAMO is expected to contribute to raising awareness about the use of reclaimed water reuse in agriculture as a safe and sustainable practice and to improve its social acceptance by producing science-based knowledge that provide evidence on the benefits derived from its use. HTML XML PDF
      PubDate: Fri, 26 Nov 2021 19:00:00 +020
  • Dataset: Feedback on the Path2Integrity learning cards for research
           integrity (2020)

    • Abstract: Research Ideas and Outcomes 7: e78118
      DOI : 10.3897/rio.7.e78118
      Authors : Ina Berg, Julia Prieß-Buchheit : This dataset is drawn from feedback given by participants, lecturers, and experts on the Path2Integrity learning cards programme for research integrity in 2020. Positive as well as negative feedback is presented, thus recording what went well, what did not, and what must be improved. The data collected is viewed as crucial for the further development of tools for teaching and learning research integrity, in particular Path2Integrity’s learning cards. HTML XML PDF
      PubDate: Thu, 18 Nov 2021 11:00:00 +020
  • Epidemiological Trends for Cryptococcosis in Swaziland (Eswatini),
           Southern Africa

    • Abstract: Research Ideas and Outcomes 7: e77736
      DOI : 10.3897/rio.7.e77736
      Authors : Ibraheem Alimi, Emmanuel Keku : Cryptococcosis is a fungal disease that is characterized by inflammation of the lungs and central nervous system, and it is commonly associated with HIV/AIDS. Even though the disease accounts for roughly 15% of all AIDS-related deaths, it is relatively neglected. This is most especially true in Southern Africa which has the highest HIV/AIDS cases in the world and accounts for more than 10% of all HIV/AIDS cases worldwide most especially in Southern African countries such as Swaziland (Eswatini) which has the highest HIV/AIDS adult prevalence rate in the world. Despite this, there are little or no previous studies with regards to the epidemiological trends for cryptococcosis in Swaziland (Eswatini) which further suggests that it is relatively neglected. With the increasing spread of virulent strains of the fungus such as Cryptococcus gattii causing outbreaks in several countries around the world, it is important to have a concrete understanding of the epidemiological trends for cryptococcosis in Swaziland (Eswatini). This is also important during the current coronavirus outbreak as previous studies have reported higher morbidity and mortality rates among COVID-19 patients that are also co-infected with HIV/AIDS, cryptococcus as well as other secondary infections. This is further supported by the fact that Southern Africa has the highest number of COVID-19 cases in Africa as well as one of the highest in the world. As a result, the purpose of this study is to determine the epidemiological trends for cryptococcosis in Swaziland (Eswatini) as this will enable adequate control, management, assessment, policies, and regulations that will be useful during outbreaks. This will be achieved by performing a repeated cross-sectional study to determine the epidemiological changes and trends for cryptococcosis in Swaziland (Eswatini) over a 5-year period from 2023 to 2028. HTML XML PDF
      PubDate: Wed, 10 Nov 2021 13:30:00 +020
  • EnTIRE: Mapping Normative Frameworks for EThics and Integrity of REsearch

    • Abstract: Research Ideas and Outcomes 7: e76240
      DOI : 10.3897/rio.7.e76240
      Authors : Natalie Evans, Marc van Hoof, Laura Hartman, Ana Marusic, Bert Gordijn, Kris Dierickx, Lex Bouter, Guy Widdershoven : Background: The areas of Research Ethics and Research Integrity (RE+RI) are rapidly evolving. In the EU and internationally, new legislation, codes of conduct and good practices are constantly being developed. New technologies (e.g. gene editing), complex statistical methods (e.g. biostatistics), pressure to publish and obtain grants, and growing emphasis on stakeholder driven science (e.g. public-private partnerships) increase the complexity of conducting science. In this complex and dynamic environment, researchers cannot easily identify the correct rules and best tools for responsible conduct of research. This also increasingly constitutes a challenge for RE+RI experts.Aim: Our aim is to create a platform that makes the normative framework governing RE+RI easily accessible, supports application in research and evaluation, and involves all stakeholders in a participatory way, thus achieving sustainability. The platform will foster uptake of ethical standards and responsible conduct of research, and ultimately support research excellence and strengthen society’s confidence in research and its findings.Vision: Our vision is that in order to make the normative framework governing RE+RI accessible, a dynamic online Wiki-platform, owned by the community of RE+RI stakeholders, is needed. The value of this platform will lie in the availability of practical information on how to comply with EU, national and discipline-specific RE+RI standards and legislation, including information on rules and procedures, educational materials, and illustrative cases and scenarios. Adopting open science (open source and open data) approaches, the platform will be easy to use, by applying novel techniques for data collection and comparison, enabling users to navigate quickly and intuitively to appropriate content. In order to keep the platform up-to-date and sustainable, it will be based upon active involvement of the RE+RI community, and will contribute to further development of this community by providing a podium for reflection and dialogue on RE+RI norms and practices.Objectives: EnTIRE’s work packages (WP) will: undertake an in-depth stakeholder consultation across EU countries exploring RE+RI experiences and practices in order to define the boundaries of data to be collected, and developing a mapping structure adapted to user needs (WP 2); assemble the relevant normative elements, including RE+RI rules and procedures, educational materials, and illustrative casuistry, and identify relevant institutions across EU countries (WP 3-5); develop a user-friendly Wiki-platform and online resources to foster and facilitate responsible research practices and to promote compliance amongst European researchers with RE+RI standards and pertinent legislation and regulations (WP 6); and foster further development of the RE+RI community, that will support the platform and be supported by it, will keep the information up-to-date, disseminate the project’s findings and develop innovative strategies for maintaining the platform and building relationships to relevant organisations for further dissemination, including sustainable funding (WP 7).Relevance to the work programme: The proposed project responds directly to the core requirement of call SwafS-16-2016 to ‘provide a dynamic mapping of the RE+RI normative framework which applies to scientific research conducted in the EU and beyond’. Our proposal does this by using a participatory approach, stimulating knowledge transfer regarding codes and regulations, resources and institutions, and cases, by applying innovative ICT solutions and open science approaches, and by further developing a community of active users, to enable sustainability after the end of the project. HTML XML PDF
      PubDate: Tue, 9 Nov 2021 12:45:00 +0200
  • Capacity-building as an instrument to foster the implementation of
           nature-based solutions

    • Abstract: Research Ideas and Outcomes 7: e77666
      DOI : 10.3897/rio.7.e77666
      Authors : Judita Tomaskinova, Davide Geneletti, Lynn Dicks, Miriam Grace, Marcus Collier, Davide Longato, Pavel Stoev, Anna Sapundzhieva, Mario Balzan : This article presents teaching and learning material from three strategically designed ReNature Horizon 2020 project training activities. A total of twelve presentations covering different aspects of NbS implementation are presented with this article. Additionally, this article also includes materials produced by learners, throughout their work within self-organised groups carried out during the Second ReNature Training School. This is the second article publishing teaching and learning material arising from the ReNature project. HTML XML PDF
      PubDate: Mon, 8 Nov 2021 14:30:00 +0200
  • Sedation-Led chEmotherapy Evades Pain (S.L.E.E.P.)

    • Abstract: Research Ideas and Outcomes 7: e71271
      DOI : 10.3897/rio.7.e71271
      Authors : Marco Cirillo : Chemotherapy and other invasive therapies are often limited by side effects, pain and negative experiences that can limit adherence to the therapy itself. Such negative components add to the patient's depressive state due to the disease. This research project proposes the use of deep sedation during chemotherapy sessions or other disabling therapies in the treatment of tumors or other severe diseases. The proposed protocol provides for an ad hoc hospitalization which could be during the night, during the day or limited to a few hours. Administration during sleep eliminates the memory and the negative impact the treatment has on the rest of the patient's daily life. This approach also agrees with the evidence of the circadian rhythm of cellular repair processes, which is greater at sunrise and sunset and linked to a good quantity and quality of sleep. In conclusion, this project aims to reduce the negative impact and increase the adherence to and efficacy of the therapy itself. HTML XML PDF
      PubDate: Thu, 28 Oct 2021 14:30:00 +030
  • The contribution of Area-Based Fisheries Management Measures to Fisheries
           Sustainability and Marine Conservation: a global scoping review protocol

    • Abstract: Research Ideas and Outcomes 7: e70486
      DOI : 10.3897/rio.7.e70486
      Authors : Dimitra Petza, Panagiotis Anastopoulos, Marta Coll, Serge Garcia, Michel Kaiser, Stefanos Kalogirou, Irene Lourdi, Jake Rice, Marija Sciberras, Stelios Katsanevakis : Objective: This scoping review (ScR) aims to identify and map the evidence base on the contribution of area-based fisheries management measures (ABFMs) to fisheries sustainability and marine conservation. Emphasis will be given to the research that has been conducted in terms of the methodologies applied and the key findings acknowledged.Introduction: ABFMs have been used for centuries and are present in modern fisheries management plans and regulations. Although ABFMs are commonly related to the sustainable exploitation of the target species of the managed fishery, they may also be considered as wider conservation measures, in the cases where their outcomes include the protection or reduction of impact on biodiversity or ecosystem structures and functions.Inclusion criteria: Studies that perform an assessment of the contribution of ABFMs on either fisheries sustainability or on area-based marine conservation (or both) will be considered. All types of ABFMs in the marine realm globally, which are established as management measures by any type of designation authority or jurisdiction and for any type of fishing activity, gear, target species and/or habitats will be considered. Peer-reviewed and grey literature will be included. There will be no search limitations applied by year of publication. Studies in English, French, Greek, Italian, Spanish and Swedish will be reviewed.Methods: The ScR will be conducted in accordance with the JBI (Joanna Briggs Institute) methodology. The PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) extension for ScRs will guide the protocol. The bibliographic databases to be searched include Scopus and Web of Science. Sources of grey literature will include databases, pre-print archives, organisational websites and web-based search engines. The design of the search strategy will be guided by a librarian/ information specialist. The Zotero software, Sysrev platform and EviAtlas tool will be used for data management, extraction and presentation. Data will be extracted by two reviewers. Tables, graphs and maps along with a narrative summary of the outcomes will be presented. HTML XML PDF
      PubDate: Tue, 26 Oct 2021 13:00:00 +030
  • Geology collection policy of the Finnish Museum of Natural History

    • Abstract: Research Ideas and Outcomes 7: e76875
      DOI : 10.3897/rio.7.e76875
      Authors : Arto Luttinen, Risto Väinölä, Jaana Halla, Björn Kröger, Kari Lintulaakso, Aino Juslén, Markku Oinonen, Pasi Sihvonen, Marko-Tapio Hyvärinen : The Geology Collection is part of the national collections of the Finnish Museum of Natural History Luomus. General principles and guidelines for the collections are defined in the General Collection Policy of Luomus. The Geology Collection Policy is subordinate to the General Collection Policy of Luomus, clarifying its content with reference to the special characteristics of the geological collections. The Geological Collection includes mineral, rock, and meteorite specimens worldwide and from all geologic ages to support Finnish research and educational projects. The coverage emphasizes specimens from Finland, Scandinavia, Africa, and Antarctica. The Geology Collection Policy defines the purpose of the collections, the objectives, the distribution of responsibilities for collection management and maintenance in the organisation, and the principles of collection accumulation, preservation, accessibility and use to public. HTML XML PDF
      PubDate: Mon, 25 Oct 2021 12:15:00 +030
  • Dataset for Mosquitoes (Diptera: Culicidae) from Cross Key, Monroe County,
           Florida, USA

    • Abstract: Research Ideas and Outcomes 7: e73768
      DOI : 10.3897/rio.7.e73768
      Authors : Lawrence J. Hribar : The Florida Keys Mosquito Control District deploys dry ice-baited light traps to monitor mosquito populations throughout the Florida Keys. Cross Key is an island directly north of Key Largo and via bridges it serves as a link between Key Largo and mainland Florida.This paper describes a data set compiled from trap collections on Cross Key, Florida, between September 23, 2002 and March 1, 2016. HTML XML PDF
      PubDate: Fri, 22 Oct 2021 09:00:00 +030
  • Idea of an experimental technique for quantitative passive gamma emission
           tomography on irradiated nuclear fuel assemblies

    • Abstract: Research Ideas and Outcomes 7: e71320
      DOI : 10.3897/rio.7.e71320
      Authors : Peter Jansson : An idea is presented in which passive gamma emission tomography of irradiated nuclear fuel is developed to enable quantitative information of the spatial activity distribution of selected isotopes within the fuel rods of the assembly. The idea is based on using well-known calibration sources mounted in the measurement device during measurement. The image reconstruction would include the sources, thereby enable quantification of the activity distribution. Should the idea be proven viable, the outcome would be valuable to the global community dealing with characterisation of nuclear fuel in terms of safety, security, safeguards and fuel development. HTML XML PDF
      PubDate: Wed, 29 Sep 2021 12:15:00 +030
  • A modeler's manifesto: Synthesizing modeling best practices with social
           science frameworks to support critical approaches to data science

    • Abstract: Research Ideas and Outcomes 7: e71553
      DOI : 10.3897/rio.7.e71553
      Authors : M.V. Eitzel : In the face of the "crisis of reproducibility" and the rise of "big data" with its associated issues, modeling needs to be practiced more critically and less automatically. Many modelers are discussing better modeling practices, but to address questions about the transparency, equity, and relevance of modeling, we also need the theoretical grounding of social science and the tools of critical theory. I have therefore synthesized recent work by modelers on better practices for modeling with social science literature (especially feminist science and technology studies) to offer a "modeler’s manifesto": a set of applied practices and framings for critical modeling approaches. Broadly, these practices involve 1) giving greater context to scientific modeling through extended methods sections, appendices, and companion articles, clarifying quantitative and qualitative reasoning and process; 2) greater collaboration in scientific modeling via triangulation with different data sources, gaining feedback from interdisciplinary teams, and viewing uncertainty as openness and invitation for dialogue; and 3) directly engaging with justice and ethics by watching for and mitigating unequal power dynamics in projects, facing the impacts and implications of the work throughout the process rather than only afterwards, and seeking opportunities to collaborate directly with people impacted by the modeling. HTML XML PDF
      PubDate: Wed, 8 Sep 2021 09:15:00 +0300
  • A digital dietary assessment tool may help identify malnutrition and
           nutritional deficiencies in hospitalized patients

    • Abstract: Research Ideas and Outcomes 7: e70642
      DOI : 10.3897/rio.7.e70642
      Authors : Adam Bernstein, Randall Moore, Lauren Rhee, Dina Aronson, David Katz : Malnutrition is common among hospitalized patients and associated with longer hospital stays, higher rates of rehospitalization, and increased mortality. Validated questionnaires of varying sensitivity and specificity to help identify patients at risk of malnutrition have been developed, but none has been broadly adopted. Tools to identify patients at risk for malnutrition should be quick, inexpensive, easy to administer and use, not require specialized nutrition knowledge, and provide results which can be entered into an electronic medical record; ideally, the tool should be deployed within 24 hours of admission and repeated if warranted. We hypothesize that a novel digital nutrition assessment tool which uses the Diet Quality Photo Navigation (DQPN) method, can help triage hospitalized patients toward further evaluation of nutritional status. We further propose that micronutrient deficiencies may be identified at the same time as malnutrition and that the reimbursement and cost savings from DQPN will prove substantially greater than the combined costs of its use and triggered dietitian consult. Deploying DQPN upon admission will represent an addition to standard hospital intake procedure that is frictionless for patients and health professionals, and one which may be overseen by clerical rather than clinical staff. The digital format of DQPN, which can be integrated into electronic medical records, will facilitate easier tracking and management of nutritional status over the course of hospitalization and post-discharge. To evaluate the hypotheses, DQPN will be deployed in a hospital setting to a group of patients who will also be seen by a registered dietitian to assess the nutritional status of each patient. Receiver operating characteristic curves will determine the point, or criterion, at which maximal true positivity rate and least false positivity rate for a diagnosis of malnutrition and specific nutrient deficiencies align. The study cohort will also be compared to a matched historical cohort to compare total medical spend and reimbursement between the intervention cohort and matched control. Testing of these hypotheses will thus allow for insight into whether DQPN may be used to identify malnutrition and nutrient deficiencies in hospitalized patients and, in so doing, improve patient outcomes, reduce healthcare utilization, and bring financial benefit to hospitals. HTML XML PDF
      PubDate: Wed, 8 Sep 2021 09:00:00 +0300
  • Polish network of research infrastructure for plant phenotyping

    • Abstract: Research Ideas and Outcomes 7: e73858
      DOI : 10.3897/rio.7.e73858
      Authors : Hanna Ćwiek-Kupczyńska, Paweł Krajewski : This document is an edited version of the original application for inclusion of a strategic research infrastructure project in the Polish Roadmap for Research Infrastructures. The application entitled "Polish network of research infrastructure for plant phenotyping" was submitted to the Polish Ministry of Science and Higher Education in June 2018; the project was not included in the Roadmap published in January 2020. The original document did not contain this abstract. HTML XML PDF
      PubDate: Fri, 3 Sep 2021 17:45:00 +0300
  • PoshBee: Pan-European Assessment, Monitoring, and Mitigation of Stressors
           on the Health of Bees

    • Abstract:
      DOI : 10.3897/arphapreprints.e72231
      Authors : Mark Brown, Tom Breeze, Philippe Bulet, Marie-Pierre Chauzat, Iliyana Demirova, Joachim de Miranda, Alexandra-Maria Klein, Marika Mand, Teodor Metodiev, Denis Michez, Franceso Nazzi, Peter Neumann, Robert Paxton, Simon Potts, Jane Stout, Gail Turney, Orlando Yañez : PoshBee is a 5-year funded project (2018-2023) that aims to support healthy bee populations, sustainable beekeeping, and consequently pollination for crops and wildflowers across Europe. To do this we take a range of approaches, from the laboratory to the field, from molecules to ecosystems, and from fundamental science to risk assessment. This document is an edited version of the original funding proposal that was submitted to the European Commission. HTML XML PDF
      PubDate: Tue, 17 Aug 2021 16:30:00 +030
  • The Glossaryfication Web Service: an automated glossary creation tool to
           support the One Health community

    • Abstract: Research Ideas and Outcomes 7: e70183
      DOI : 10.3897/rio.7.e70183
      Authors : Nazareno Scaccia, Taras Günther, Estibaliz Lopez de Abechuco, Matthias Filter : In many interdisciplinary research domains, the creation of a shared understanding of relevant terms is considered the foundation for efficient cross-sector communication and interpretation of data and information. This is also true for the domain of One Health (OH) where many One Health Surveillance (OHS) documents rarely contain glossaries with a list of terms for which their specific meaning in the context of the given document is defined (Cornelia et al. 2018, Buschhardt et al. 2021). The absence of glossaries within these documents may lead to misinterpretation of surveillance results due to the wrong interpretation of terminology specifically when term definitions differ across OH sectors. Under the One Health EJP project ORION, the OHEJP Glossary was recently created. The OHEJP Glossary is a tool to improve communication and collaboration amongst OH sectors by providing an easy-to-use online resource that lists relevant OH terms and sector-specific definitions. To improve the accessibility of content from the OHEJP Glossary and support the creation of integrative glossaries in future OHS-related documents, the OHEJP Glossaryfication Web Service was created. This service can support the practical use of the OHEJP Glossary and other relevant online glossaries by OH professionals.The Glossaryfication Web Service (GWS) is an application that automatically identifies terms in any uploaded text-based document and creates a document-specific list of matching definitions in selected online glossaries. This auto-generated document-specific glossary can easily be adjusted by the user, for example, by selecting the desired definition in case multiple definitions were found for a specific term. The document-specific glossary could then be downloaded, manually adjusted and finally included into the original document where it supports the correct interpretation of terminology used. Especially in sector-specific reports, such as from animal health or public health authorities, this can be beneficial to ensure the correct interpretation by other OH sectors in the future. The GWS was developed with the open-source desktop software KNIME Analytics Platform and runs as a web service on a KNIME Web Server infrastructure. The core data processing functionality in the GWS is based on KNIME’s Text Processing extension. KNIME's JavaScript nodes provided the basis for an interactive user interface where users can easily upload their files and select between different reference glossaries, such as the OHEJP Glossary, the CDC Glossary, the WHO Glossary or the EFSA Glossary. After retrieval of the user input settings, the GWS tags words within the provided document and maps these tagged words with matching entries in the selected glossaries. As the main output, the user receives a downloadable list of matching terms with their corresponding definitions, sectorial assignments and references, which can then be added by the user to the original document. The GWS is freely accessible via this link as well as the underlying KNIME workflow. HTML XML PDF
      PubDate: Fri, 6 Aug 2021 15:30:00 +0300
  • A Good Practice Guide for the Use of DGTs. Sampling of metals in
           transitional and coastal waters by Diffusive Gradient in Thin films (DGT)

    • Abstract:
      DOI : 10.3897/arphapreprints.e70983
      Authors : Blánaid White, Fiona Regan, Miguel Caetano, German Rodriguez, Iratxe Mentxaka, Joana Larreta, Maria Jesus Belzunce, Florence Menet-Nedelec, Isabelle Amouroux, Jean-Louis Gonzalez, Stephane Guesdon, Philippe Bersuder, Thi Bolam, Barbara Marras, Marco Schintu, Natalia Montero, Margarida Correia dos Santos, Craig D. Robinson, Brendan McHugh, Gary R. Fones, Hao Zhang : This good practice guide is focused on the DGT devices, which are the most widely used passive sampler for metals, covering the following aspects:■ Principle■ Handling passive sampling devices for metals■ Estimation of appropriate field deployment time■ A Good Practice Guide for the Use of DGTs■ Passive sampling device preparation and assembly■ Selection of sampling site and safety precautions■ Passive sampling device deployment and retrieval■ Extraction of analytes from passive sampling devices■ Analysis■ Calculations HTML XML PDF
      PubDate: Wed, 14 Jul 2021 17:00:00 +030
  • A choice of persistent identifier schemes for the Distributed System of
           Scientific Collections (DiSSCo)

    • Abstract: Research Ideas and Outcomes 7: e67379
      DOI : 10.3897/rio.7.e67379
      Authors : Alex Hardisty, Wouter Addink, Falko Glöckler, Anton Güntsch, Sharif Islam, Claus Weiland : Persistent identifiers (PID) to identify digital representations of physical specimens in natural science collections (i.e., digital specimens) unambiguously and uniquely on the Internet are one of the mechanisms for digitally transforming collections-based science. Digital Specimen PIDs contribute to building and maintaining long-term community trust in the accuracy and authenticity of the scientific data to be managed and presented by the Distributed System of Scientific Collections (DiSSCo) research infrastructure planned in Europe to commence implementation in 2024. Not only are such PIDs valid over the very long timescales common in the heritage sector but they can also transcend changes in underlying technologies of their implementation. They are part of the mechanism for widening access to natural science collections. DiSSCo technical experts previously selected the Handle System as the choice to meet core PID requirements.Using a two-step approach, this options appraisal captures, characterises and analyses different alternative Handle-based PID schemes and the possible operational modes of use. In a first step a weighting and ranking the options has been applied followed by a structured qualitative assessment of social and technical compliance across several assessment dimensions: levels of scalability, community trust, persistence, governance, appropriateness of the scheme and suitability for future global adoption. The results are discussed in relation to branding, community perceptions and global context to determine a preferred PID scheme for DiSSCo that also has potential for adoption and acceptance globally.DiSSCo will adopt a ‘driven-by
      DOI ’ persistent identifier (PID) scheme customised with natural sciences community characteristics. Establishing a new Registration Agency in collaboration with the International
      DOI Foundation is a practical way forward to support the FAIR (findable, accessible interoperable, reusable) data architecture of DiSSCo research infrastructure. This approach is compatible with the policies of the European Open Science Cloud (EOSC) and is aligned to existing practices across the global community of natural science collections. HTML XML PDF
      PubDate: Tue, 6 Jul 2021 12:00:00 +0300
  • Wikipedia for multilingual COVID-19 vaccine education at scale

    • Abstract: Research Ideas and Outcomes 7: e70042
      DOI : 10.3897/rio.7.e70042
      Authors : Lane Rasberry, Daniel Mietchen : We present the design of a project to develop Wikipedia content on general vaccine safety and the COVID-19 vaccines, specifically. This proposal describes what a team would need to distribute public health information in Wikipedia in multiple languages in response to a disaster or crisis, and to measure and report the communication impact of the same. Researchers at the School of Data Science at the University of Virginia made this proposal in response to a February 2021 call from a sponsor which was seeking to share public health information to respond globally to vaccine hesitancy related to the COVID-19 vaccines. This proposal was not selected for funding, and now the research team is sharing the proposal here with an open copyright license for anyone to reuse and remix. Most of the text here is from the original proposal, but there are modifications to remove the names of the funder, named partners, and for other details to make this text more reusable. The budget in this proposal has been converted from a dollar amount to equivalent descriptions in terms of labor hours, and the timeline was adapted from absolute to relative months. HTML XML PDF
      PubDate: Thu, 1 Jul 2021 08:50:43 +0300
  • Virtue-based ethics and integrity of research: train-the-trainer programme
           for upholding the principles and practices of the European Code of Conduct
           for Research Integrity (VIRT2UE)

    • Abstract: Research Ideas and Outcomes 7: e68258
      DOI : 10.3897/rio.7.e68258
      Authors : Natalie Evans, Ana Marusic, Nicole Foeger, Erika Lofstrom, Marc van Hoof, Sabine Vrijhoef-Welten, Giulia Inguaggiato, Kris Dierickx, Lex Bouter, Guy Widdershoven : Background: Recognising the importance of addressing ethics and research integrity (ERI) in Europe, in 2017, the All European Academies (ALLEA) published a revised and updated European Code of Conduct for Research Integrity (ECoC). Consistent application of the ECoC by researchers across Europe will require its widespread dissemination, as well as an innovative training programme and novel tools to enable researchers to truly uphold and internalise the principles and practices listed in the Code.Aim: VIRT2UE aims to develop a sustainable train-the-trainer blended learning programme enabling contextualised ERI teaching across Europe focusing on understanding and upholding the principles and practices of the ECoC.Vision: The VIRT2UE project recognises that researchers not only need to have knowledge of the ECoC, but also to be able to truly uphold and internalise the principles underpinning the code. They need to learn how to integrate them into their everyday practice and understand how to act in concrete situations. VIRT2UE addresses this challenge by providing ERI trainers and researchers with an innovative blended (i.e. combined online and off-line approaches) learning programme that draws on a toolbox of educational resources and incorporates an e-learning course (including a YouTube channel) and face-to-face sessions designed to foster moral virtues. ERI trainers and researchers from academia and industry will have open access to online teaching material. Moreover, ERI trainers will learn how to facilitate face-to-face sessions of researchers, which focus on learning how to apply the content of the teaching material to concrete situations in daily practice.Objectives: VIRT2UE’s work packages (WP) will: conduct a conceptual mapping amongst stakeholders to identify and rank the virtues which are essential for good scientific practice and their relationship to the principles and practices of the ECoC (WP1); identify and consult ERI trainers and the wider scientific community to understand existing capacity and deficiencies in ERI educational resources (WP2); develop the face-to-face component of the train-the-trainer programme which provides trainers with tools to foster researchers’ virtues and promote the ECoC and iteratively develop the programme based on evaluations (WP3); produce educational materials for online learning by researchers and trainers (WP4); implement and disseminate the train-the-trainer programme across Europe, ensuring the training of sufficient trainers for each country and build capacity and consistency by focusing on underdeveloped regions and unifying fragmented efforts (WP5); and develop the online training platform and user interface, which will be instrumental in evaluation of trainers’ and researchers’ needs and project sustainability (WP6).Impact: The VIRT2UE training programme will promote consistent application of the ECoC across Europe. The programme will affect behaviour on the individual level of trainers and researchers – simultaneously developing an understanding of the ECoC and other ERI issues, whilst also developing scientific virtues, enabling the application of the acquired knowledge to concrete situations and complex moral dilemmas. Through a dedicated embedding strategy, the programme will also have an impact on an institutional level. The train-the-trainer approach multiplies the impact of the programme by reaching current and future European ERI trainers and, subsequently, the researchers they train. HTML XML PDF
      PubDate: Mon, 21 Jun 2021 15:00:00 +030
  • AlpConv Atlas: The Geospatial Content Management System of the Alpine

    • Abstract: Research Ideas and Outcomes 7: e66106
      DOI : 10.3897/rio.7.e66106
      Authors : Stefano Della Chiesa, Andrea Vianello, Simone Tritini, Aureliano Piva : The Alpine Convention (AC) promotes research, cooperation and monitoring activities in the Alpine region. In this framework, the AC Atlas is the official content management system for geographical data published by the Alpine Convention. The AC Atlas' final goal is to promote, collect, organize, and disseminate the results of research activities carried out by the Alpine Convention, its Working Groups and by European projects in the Alpine region.The system is based on the open-source GeoNode platform supporting standard OGC services. Hence, the AlpConv Atlas allows for browsing, searching, editing documents, layers, maps, and related metadata by an intuitive web-based graphical user interface. The AC Atlas is finally a collaborative platform for managing various geographical data and the related documentation, which can be of great interest to several stakeholders. HTML XML PDF
      PubDate: Wed, 16 Jun 2021 17:00:00 +030
  • Developing a scalable framework for partnerships between health agencies
           and the Wikimedia ecosystem

    • Abstract: Research Ideas and Outcomes 7: e68121
      DOI : 10.3897/rio.7.e68121
      Authors : Daniel Mietchen, Lane Rasberry, Thais Morata, John Sadowski, Jeanette Novakovich, James Heilman : In this era of information overload and misinformation, it is a challenge to rapidly translate evidence-based health information to the public. Wikipedia is a prominent global source of health information with high traffic, multilingual coverage, and acceptable quality control practices. Viewership data following the Ebola crisis and during the COVID-19 pandemic reveals that a significant number of web users located health guidance through Wikipedia and related projects, including its media repository Wikimedia Commons and structured data complement, Wikidata.The basic idea discussed in this paper is to increase and expedite health institutions' global reach to the general public, by developing a specific strategy to maximize the availability of focused content into Wikimedia’s public digital knowledge archives. It was conceptualized from the experiences of leading health organizations such as Cochrane, the World Health Organization (WHO) and other United Nations Organizations, Cancer Research UK, National Network of Libraries of Medicine, and Centers for Disease Control and Prevention (CDC)'s National Institute for Occupational Safety and Health (NIOSH). Each has customized strategies to integrate content in Wikipedia and evaluate responses.We propose the development of an interactive guide on the Wikipedia and Wikidata platforms to support health agencies, health professionals and communicators in quickly distributing key messages during crisis situations. The guide aims to cover basic features of Wikipedia, including adding key health messages to Wikipedia articles, citing expert sources to facilitate fact-checking, staging text for translation into multiple languages; automating metrics reporting; sharing non-text media; anticipating offline reuse of Wikipedia content in apps or virtual assistants; structuring data for querying and reuse through Wikidata, and profiling other flagship projects from major health organizations.In the first phase, we propose the development of a curriculum for the guide using information from prior case studies. In the second phase, the guide would be tested on select health-related topics as new case studies. In its third phase, the guide would be finalized and disseminated. HTML XML PDF
      PubDate: Wed, 16 Jun 2021 16:30:00 +030
  • Policy and objectives of the New Zealand Arthropod Collection

    • Abstract: Research Ideas and Outcomes 7: e69765
      DOI : 10.3897/rio.7.e69765
      Authors : Darren Ward, Sarah Tassell : The New Zealand Arthropod Collection (NZAC) is the world’s largest taxonomic collection of terrestrial invertebrates from New Zealand. The NZAC policy is presented that defines the vision for the collection of being managed to the highest international standards, connected through a global infrastructure, and providing high quality, authoritative, and trusted information. The policy also provides context and guidelines for collection activities, and twenty-two objectives are outlined that will be completed over the next 5 years. HTML XML PDF
      PubDate: Tue, 15 Jun 2021 13:15:00 +030
  • Identifying SOX2-OT transcript that is responsible for regulating SOX2 in
           cancer cells and embryonic stem cells

    • Abstract: Research Ideas and Outcomes 7: e69726
      DOI : 10.3897/rio.7.e69726
      Authors : Dao-Yin Dong, Pu-Yu Li : SOX2 overlapping transcript (SOX2-OT) is an evolutionarily conserved long non-coding RNA (lncRNA) whose intronic region contains the transcript of pluripotency gene SRY-box transcription factor 2 (SOX2). It has been suggested that SOX2-OT can regulate its overlapping gene, SOX2. Studies demonstrated that elevated SOX2-OT promotes SOX2 expression in cancer cells, whereas levels of SOX2-OT are inversely correlated with levels of SOX2 in embryonic stem cells. It is not clear why there is a tremendous discrepancy in the regulation of SOX2 by SOX2-OT in cancer cells and embryonic stem cells. Due to the diversified transcription of the SOX2-OT gene, we hypothesize that differential expression of transcripts of the SOX2-OT gene in cancer cells and embryonic stem cells may contribute to the divergence in the regulatory relationship of SOX2-OT and SOX2. A CRISPR screening platform can be leveraged to systemic evaluate which transcript of the SOX2-OT gene may be responsible for upregulation or downregulation of SOX2 in cancer cells and embryonic stem cells, respectively. HTML XML PDF
      PubDate: Tue, 8 Jun 2021 17:00:00 +0300
  • Taxonomy at Face Value: An assessment of entomological postage stamps as
           effective teaching aids for science educators

    • Abstract: Research Ideas and Outcomes 7: e68056
      DOI : 10.3897/rio.7.e68056
      Authors : Vazrick Nazari : Entomological postage stamps are unique means of communication of science with the public and have been suggested as effective teaching tools in primary and secondary education. A survey of the taxonomic and other information contained on insect- and arachnid-themed stamps issued globally from 1891 to 2020 reveals that 30% of these stamps contain various errors and are scientifically unreliable. In addition, representations of insects are highly biased towards only two orders (Lepidoptera and Odonata), while other mega-diverse orders (e.g. Coleoptera, Diptera, Hymenoptera) are poorly represented or not represented at all. This phenomenon can negatively affect public perception of priorities in biodiversity and conservation. Standardization of taxonomic information on entomological stamps and implementation of rigorous quality control measures are encouraged to assure dissemination of accurate scientific information. HTML XML PDF
      PubDate: Fri, 4 Jun 2021 14:30:00 +0300
  • ORKG: Facilitating the Transfer of Research Results with the Open Research
           Knowledge Graph

    • Abstract: Research Ideas and Outcomes 7: e68513
      DOI : 10.3897/rio.7.e68513
      Authors : Sören Auer, Markus Stocker, Lars Vogt, Grischa Fraumann, Alexandra Garatzogianni : This document is an edited version of the original funding proposal entitled 'ORKG: Facilitating the Transfer of Research Results with the Open Research Knowledge Graph' that was submitted to the European Research Council (ERC) Proof of Concept (PoC) Grant in September 2020 (https://erc.europa.eu/funding/proof-concept). The proposal was evaluated by five reviewers and has been placed after the evaluations on the reserve list. The main document of the original proposal did not contain an abstract. HTML XML PDF
      PubDate: Wed, 26 May 2021 17:00:00 +030
  • A Test Collection for Dataset Retrieval in Biodiversity Research

    • Abstract: Research Ideas and Outcomes 7: e67887
      DOI : 10.3897/rio.7.e67887
      Authors : Felicitas Löffler, Andreas Schuldt, Birgitta König-Ries, Helge Bruelheide, Friederike Klan : Searching for scientific datasets is a prominent task in scholars' daily research practice. A variety of data publishers, archives and data portals offer search applications that allow the discovery of datasets. The evaluation of such dataset retrieval systems requires proper test collections, including questions that reflect real world information needs of scholars, a set of datasets and human judgements assessing the relevance of the datasets to the questions in the benchmark corpus. Unfortunately, only very few test collections exist for a dataset search. In this paper, we introduce the BEF-China test collection, the very first test collection for dataset retrieval in biodiversity research, a research field with an increasing demand in data discovery services. The test collection consists of 14 questions, a corpus of 372 datasets from the BEF-China project and binary relevance judgements provided by a biodiversity expert. HTML XML PDF
      PubDate: Wed, 26 May 2021 17:00:00 +030
  • Commentary - Methods to find all the edges on any of the shortest paths
           between two given nodes of a directed acyclic graph

    • Abstract: Research Ideas and Outcomes 7: e68600
      DOI : 10.3897/rio.7.e68600
      Authors : Deepak Ahire, Omkar Jadhav : This article puts forth all the existing methods proposed by the various authors of the Stack Exchange community to find all the edges on any shortest path between two given nodes of a directed acyclic graph. For a directed acyclic graph with N number of nodes, an exponential number of paths are possible between any two given nodes and, thus, it is not feasible to compute every path and find the shortest ones in polynomial time to generate a set of all edges that contribute or make any of the shortest paths. The methods discussed in this article are not limited only to this specific use case, but have a much broader scope in graph theory, dynamic programming and counting problems. Generally, various other questions and answers, raised on the community portal having similar scope to those that the users specifically seek, do not receive sufficient hits and, hence, enough attention and votes for various reasons worth contemplating. Therefore, this article also aims to highlight the various scopes of the methods discussed in this article and acknowledge the efforts of the authors, moderators and contributors of the Stack Exchange community for their expertise and time to write precise answers and share their opinions and advice. Finally, it also appeals to all the other beneficiaries in the community to use their privileges responsibly and upvote the posted answers, if they helped solve their queries, as one upvote is free of cost. HTML XML PDF
      PubDate: Tue, 25 May 2021 12:00:00 +030
  • Open science in practice: 300 published research ideas and outcomes
           illustrate how RIO Journal facilitates engagement with the research

    • Abstract: Research Ideas and Outcomes 7: e68595
      DOI : 10.3897/rio.7.e68595
      Authors : Daniel Mietchen, Lyubomir Penev, Teodor Georgiev, Boriana Ovcharova, Iva Kostadinova : Since Research Ideas and Outcomes was launched in late 2015, it has stimulated experimentation around the publication of and engagement with research processes, especially those with a strong open science component. Here, we zoom in on the first 300 RIO articles that have been published and elucidate how they relate to the different stages and variants of the research cycle, how they help address societal challenges and what forms of engagement have evolved around these resources, most of which have a nature and scope that would prevent them from entering the scholarly record via more traditional journals. Building on these observations, we describe some changes we recently introduced in the policies and peer review process at RIO to further facilitate engagement with the research process, including the establishment of an article collections feature that allows us to bring together research ideas and outcomes from within one research cycle or across multiple ones, irrespective of where they have been published. HTML XML PDF
      PubDate: Wed, 12 May 2021 17:30:00 +030
  • Evolutionary explanations for religion: An interdisciplinary critical

    • Abstract: Research Ideas and Outcomes 7: e66132
      DOI : 10.3897/rio.7.e66132
      Authors : Patrik Lindenfors, Jonas Svensson : Some form of religion exists in every documented society on earth. However, ‘religion’ is a multifaceted phenomenon commonly including aspects, such as rituals, myths, rules and regulations concerning ethical behaviour, social practices and some form of belief in the supernatural (e.g. gods, spirits or souls). Due to its pervasiveness, many researchers of biological and cultural evolution have suggested that religion needs a universal evolutionary explanation. However, most proposed explanations have either treated religion as a single all-encompassing entity or only focused on a single or a few aspects of religion. We propose, instead, to carry out an extensive review of such suggested evolutionary explanations with the express aim of pairing up proposed explanations with religious components in order to form a more comprehensive depiction of causation and how religion and human cognition both have evolved, each influenced by the other. We also propose to summarise predictions and hypotheses that spring from each explanation, with the express aim of stating how each may be evaluated and tested. Crucially, different aspects of religion may have different explanations and different explanations may apply to several aspects of religion. Proposed explanations will be summarised in a series of thematically oriented scientific articles, as well as in a summary monograph. Our dual competencies, in evolutionary theory and religious studies, provide us with a unique opportunity to evaluate these issues from both a natural and a humanistic point of view. HTML XML PDF
      PubDate: Tue, 20 Apr 2021 15:30:00 +030
  • OPTIMETA – Strengthening the Open Access publishing system through open
           citations and spatiotemporal metadata 

    • Abstract: Research Ideas and Outcomes 7: e66264
      DOI : 10.3897/rio.7.e66264
      Authors : Christian Hauschke, Daniel Nüst, Anette Cordts, Svantje Lilienthal : The BMBF project OPTIMETA aims to strengthen the Open Access publishing system by connecting open citations and spatiotemporal metadata from open access journals with openly accessible data sources. For this purpose, we will extend Open Journal Systems (OJS) to give it functionalities for collecting and distributing open data by developing two OJS plugins for capturing citation networks and articles' spatial and temporal properties as machine-readable and accessible metadata. We will ensure the target group-orientated design of the plugins by performing a comprehensive needs analysis for key stakeholders: the editors or operators of OA journals and the researchers, as authors and readers of articles. The developments will be designed and tested in cooperation with several independent journals and OA publishers. Overall, OPTIMETA supports the attraction of independent OA journals as publication venues by substantially improving the discoverability and visibility of OA publications through enrichment and interlinking of article metadata. HTML XML PDF
      PubDate: Wed, 14 Apr 2021 13:15:00 +030
  • Path2Integrity Learning Cards & Handbook for Trainers and Lecturers:

    • Abstract:
      DOI : 10.3897/arphapreprints.e66719
      Authors : Julia Prieß-Buchheit, Lisa Häberlein, Tom Lindemann : Do you want to teach future researchers how to integrate their knowledge into their own research activities, as well as help them understand how important reliable research is for society' This handbook accompanies the Path2Integrity learning cards (P2ILC) on six topics (https://www.path2integrity.eu/ri-materials) and introduces you to an easy and fun learning programme that has been evaluated in over 15 training sessions. The Path2Integrity learning cards M-series is especially designed for graduates who already have a university degree. They learn how responsible research needs to be conducted in order to be reliable and thus useful for society. HTML XML PDF
      PubDate: Tue, 30 Mar 2021 17:30:00 +030
  • Path2Integrity Learning Cards & Handbook for Trainers and Lecturers:

    • Abstract:
      DOI : 10.3897/arphapreprints.e66720
      Authors : Julia Prieß-Buchheit, Lisa Häberlein, Tom Lindemann : Do you want to teach researchers how to clarify their own role in research, as well as help them understand how important reliable research is for society' This handbook accompanies the Path2Integrity learning cards (P2ILC) on eight topics (https://www.path2integrity.eu/ri-materials) and introduces you to an easy and fun learning programme that has been evaluated in over 20 training sessions. The Path2Integrity learning cards Y-series is especially designed for early career and active researchers to learn how responsible research must necessarily be conducted in order to be reliable and in this sense useful for society. HTML XML PDF
      PubDate: Tue, 30 Mar 2021 17:30:00 +030
  • Path2Integrity Learning Cards & Handbook for Teacher and Trainers:

    • Abstract:
      DOI : 10.3897/arphapreprints.e66718
      Authors : Julia Prieß-Buchheit, Lisa Häberlein : Do you want to teach your students how to do research, as well as help them understand how important reliable research is for society' This handbook accompanies the Path2Integrity learning cards (P2ILC) on five topics (https://www.path2integrity.eu/ri-materials) and introduces you to an easy and fun learning programme that has been evaluated in over 25 training sessions. The Path2Integrity learning cards S-series is especially designed for secondary school students and undergraduates. Through this series, students learn how research results must be produced in order to be reliable and thus useful for society. HTML XML PDF
      PubDate: Tue, 30 Mar 2021 17:15:00 +030
  • Data Browser Matsch Mazia: Web Application to access microclimatic time
           series of an ecological research site

    • Abstract: Research Ideas and Outcomes 7: e63748
      DOI : 10.3897/rio.7.e63748
      Authors : Martin Palma, Alessandro Zandonai, Luca Cattani, Johannes Klotz, Giulio Genova, Christian Brida, Norbert Andreatta, Georg Niedrist, Stefano Della Chiesa : Easily accessible data is an essential requirement for scientific data analysis. The Data Browser Matsch Mazia was designed to provide a fast and comprehensible solution to access, visualize and download the microclimatic measurements of the IT 25 LT(S)ER Match  Mazia research site in South Tyrol, Northern Italy, with the overall aim to provide straightforward data accessibility and enhance dissemination.Data Browser Matsch Mazia is a user-friendly web-based application to visualize and download micrometeorological and biophysical time series of the Long-Term Socio-Ecological Research site Matsch Mazia in South Tyrol, Italy. It is designed both for the general public and researchers. The Data Browser Matsch Mazia drop-down menus allow the user to query the InfluxDB database in the backend by selecting the measurements, time range, land use and elevation. Interactive Grafana dashboards show dynamic graphs of the time series. HTML XML PDF
      PubDate: Mon, 29 Mar 2021 11:00:00 +030
  • FAIR and open multilingual clinical trials in Wikidata and Wikipedia

    • Abstract: Research Ideas and Outcomes 7: e66490
      DOI : 10.3897/rio.7.e66490
      Authors : Lane Rasberry, Daniel Mietchen : This project seeks to conduct language translation on metadata labels for research publications, attribution data, and clinical trials information to make data about medical research queriable in underserved languages through Wikidata and the Linked Open Web. This project has the benefit of distributing content through Wikipedia and Wikidata, which already have an annual userbase of a billion users and which already have established actionable standards to practice diversity, inclusion, openness, FAIRness, and transparency about program development. The impact will be localized access to basic research information in various Global South languages to integrate with existing community efforts for establishing the same. Although Wikidata development in this direction seems inevitable, the cultural and social exchange required to establish global multilingual research partnerships could begin now with support rather than later as a second phase effort for including the developing world. Wikipedia and Wikidata are established forums with an existing active userbase for multilingual research collaboration, but the research practices there still are immature. By applying metadata expertise through this project, we will elevate the current amateur development with more stable Linked Open Data compatibility to English language databases. Using the wiki distribution and discussion platform to develop the global conversation about data sharing will set good precedents for the trend of global research collaboration. HTML XML PDF
      PubDate: Thu, 25 Mar 2021 18:30:00 +020
  • Mental health crisis in midlife – a proposed research agenda

    • Abstract: Research Ideas and Outcomes 7: e66204
      DOI : 10.3897/rio.7.e66204
      Authors : Dawid Gondek, Bettina Moltrecht, George Ploubidis : There is a growing amount of evidence indicating increased levels of psychological distress, suicide rates and decreased well-being in midlife (age 45-55). We refer to this phenomenon as the ‘midlife mental health crisis’. As there is little empirical evidence or theoretical grounds to explain the midlife mental health crisis, we propose a research agenda.In order to facilitate further research, we consulted members of public, mental health professionals and researchers on potential reasons for the midlife mental health crisis. Subsequently, we translated those into research questions testable with the British birth cohorts. We propose a series of studies using three statistical modelling approaches: descriptive (what is the midlife mental health crisis'), predictive (who is at increased risk of experiencing the midlife mental health crisis') and explanatory (what are the processes leading to the midlife mental health crisis'). HTML XML PDF
      PubDate: Mon, 22 Mar 2021 10:35:00 +020
  • Mental health crisis in midlife – a proposed research agenda

    • Abstract: Research Ideas and Outcomes 7: e62024
      DOI : 10.3897/rio.7.e62024
      Authors : Dawid Gondek, Bettina Moltrecht, George Ploubidis : There is a growing amount of evidence indicating increased levels of psychological distress, suicide rates and decreased well-being in midlife (age 45-55). We refer to this phenomenon as the ‘midlife mental health crisis’. As there is little empirical evidence or theoretical grounds to explain the midlife mental health crisis, we propose a research agenda.In order to facilitate further research, we consulted members of public, mental health professionals and researchers on potential reasons for the midlife mental health crisis. Subsequently, we translated those into research questions testable with the British birth cohorts. We propose a series of studies using three statistical modelling approaches: descriptive (what is the midlife mental health crisis'), predictive (who is at increased risk of experiencing the midlife mental health crisis') and explanatory (what are the processes leading to the midlife mental health crisis'). HTML XML PDF
      PubDate: Wed, 10 Mar 2021 12:30:00 +020
  • Data management plan for CIVOIR project - Circulation of knowledge in
           education - through "CoopLa"

    • Abstract: Research Ideas and Outcomes 7: e60614
      DOI : 10.3897/rio.7.e60614
      Authors : Amelie Derobert, Françoise Lantheaume : This data management plan was created using the OPIDoR (Optimiser le partage et l'interopérabilié des données de la recherche/ Tools and services to support french research data mangement). It describes all data collected and created as part of the postdoctoral research for the project "Circulation of knowledge: between sciences, policies, and practices in education (CIVOIR)" under the scientific direction of Professor Françoise Lantheaume and with the participation of German Fernandez Vavrik, University Lumiere Lyon 2, France. The data produced in this survey was collected through a mechanism specifically created for this project: the cooperative laboratory - CoopLa. HTML XML PDF
      PubDate: Mon, 8 Mar 2021 11:00:00 +0200
  • Prejudice Against Citizens with Right-aligned Political Views in Western
           Cosmopolitan Cities, and Possible Interventions

    • Abstract: Research Ideas and Outcomes 7: e64121
      DOI : 10.3897/rio.7.e64121
      Authors : Vincent Weidlich : Prejudice against citizens with right-aligned political views in western cosmopolitan cities was explored, and possible interventions proposed. Literature and theories were reviewed, with social psychological and sociological theories compiled that explain the reasons for this prejudice and an intervention to solve this problem. Scientific research in social sciences is dominated by bias from left-aligned researchers in social psychology and psychology. Dysfunctional scientific processes prominent in this area of sciences are due to the sacralization of social science. A significantly small percent of social and personality psychologists identify as politically conservative. A significant amount of errors and distortions were found in sociology textbooks. Media and corporation biases toward left-aligned political views were found, and right-aligned individuals are out-group members in cosmopolitan cities. Inoculation by media assignments and critical literacy education is proposed, that could prevent school students from being influenced by stealth messages and propaganda. Media campaigns targeting the full spectrum of political views is proposed, that could help reduce biases of citizens. A family and community health class is proposed, that could improve student’s psychological, family, and social health. Youth and adult clubs are proposed, that could help reduce animosity between social groups, and promote solidarity and community health. HTML XML PDF
      PubDate: Fri, 19 Feb 2021 13:55:00 +020
  • Palaeontology Collection Policy

    • Abstract: Research Ideas and Outcomes 7: e62808
      DOI : 10.3897/rio.7.e62808
      Authors : Björn Kröger, Anniina Kuusijärvi, Leena Myllys, Pasi Sihvonen, Gunilla Ståhls-Mäkelä, Henry Väre, Markku Oinonen, Aino Juslén, Leif Schulman, Marko-Tapio Hyvärinen : The Paleontological Collection (PalCo) is one of partial collections of the Finnish Museum of Natural History Luomus. General principles and guidelines for the collections are defined in the General Collection Policy of Luomus. The PalCo Policy is subordinate to the General Collection Policy of Luomus, clarifying its content with reference to the special characteristics of the paleontological collections. The PalCo includes fossil plant, invertebrate and vertebrate specimens worldwide in scope and from all geologic ages to support Finnish research and educational projects. The coverage emphasizes Paleozoic and Quaternary specimens from Finland, the Baltic countries and Scandinavia. The PalCo Policy defines the purpose of the collections, the objectives, the distribution of responsibilities for collection management and maintenance in the organisation, and the principles of collection accumulation, preservation, accessibility and use. HTML XML PDF
      PubDate: Fri, 19 Feb 2021 11:30:00 +020
  • BII-Implementation: The causes and consequences of plant biodiversity
           across scales in a rapidly changing world

    • Abstract: Research Ideas and Outcomes 7: e63850
      DOI : 10.3897/rio.7.e63850
      Authors : Jeannine Cavender-Bares, Peter Reich, Philip Townsend, Arindam Banerjee, Ethan Butler, Ankur Desai, Amanda Gevens, Sarah Hobbie, Forest Isbell, Etienne Laliberté, José Eduardo Meireles, Holly Menninger, Ryan Pavlick, Jesús Pinto-Ledezma, Caitlin Potter, Meredith Schuman, Nathan Springer, Artur Stefanski, Pankaj Trivedi, Amy Trowbridge, Laura Williams, Charles Willis, Ya Yang : The proposed Biology Integration Institute will bring together two major research institutions in the Upper Midwest—the University of Minnesota (UMN) and University of Wisconsin-Madison (UW)—to investigate the causes and consequences of plant biodiversity across scales in a rapidly changing world—from genes and molecules within cells and tissues to communities, ecosystems, landscapes and the biosphere. The Institute focuses on plant biodiversity, defined broadly to encompass the heterogeneity within life that occurs from the smallest to the largest biological scales. A premise of the Institute is that life is envisioned as occurring at different scales nested within several contrasting conceptions of biological hierarchies, defined by the separate but related fields of physiology, evolutionary biology and ecology. The Institute will emphasize the use of ‘spectral biology’—detection of biological properties based on the interaction of light energy with matter—and process-oriented predictive models to investigate the processes by which biological components at one scale give rise to emergent properties at higher scales. Through an iterative process that harnesses cutting edge technologies to observe a suite of carefully designed empirical systems—including the National Ecological Observatory Network (NEON) and some of the world’s longest running and state-of-the-art global change experiments—the Institute will advance biological understanding and theory of the causes and consequences of changes in biodiversity and at the interface of plant physiology, ecology and evolution.INTELLECTUAL MERITThe Institute brings together a diverse, gender-balanced and highly productive team with significant leadership experience that spans biological disciplines and career stages and is poised to integrate biology in new ways. Together, the team will harness the potential of spectral biology, experiments, observations and synthetic modeling in a manner never before possible to transform understanding of how variation within and among biological scales drives plant and ecosystem responses to global change over diurnal, seasonal and millennial time scales. In doing so, it will use and advance state-of-the-art theory. The institute team posits that the designed projects will unearth transformative understanding and biological rules at each of the various scales that will enable an unprecedented capacity to discern the linkages between physiological, ecological and evolutionary processes in relation to the multi-dimensional nature of biodiversity in this time of massive planetary change. A strength of the proposed Institute is that it leverages prior federal investments in research and formalizes partnerships with foreign institutions heavily invested in related biodiversity research. Most of the planned projects leverage existing research initiatives, infrastructure, working groups, experiments, training programs, and public outreach infrastructure, all of which are already highly synergistic and collaborative, and will bring together members of the overall research and training team.BROADER IMPACTSA central goal of the proposed Institute is to train the next generation of diverse integrative biologists. Post-doctoral, graduate student and undergraduate trainees, recruited from non-traditional and underrepresented groups, including through formal engagement with Native American communities, will receive a range of mentoring and training opportunities. Annual summer training workshops will be offered at UMN and UW as well as training experiences with the Global Change and Biodiversity Research Priority Program (URPP-GCB) at the University of Zurich (UZH) and through the Canadian Airborne Biodiversity Observatory (CABO). The Institute will engage diverse K-12 audiences, the general public and Native American communities through Market Science modules, Minute Earth videos, a museum exhibit and public engagement and educational activities through the Bell Museum of Natural History, the Cedar Creek Ecosystem Science Reserve (CCESR) and the Wisconsin Tribal Conservation Association. HTML XML PDF
      PubDate: Fri, 5 Feb 2021 10:30:00 +0200
  • Open comments on the Task Force SIRS report: Scholarly Infrastructures for
           Research Software (EOSC Executive Board, EOSCArchitecture)

    • Abstract: Research Ideas and Outcomes 7: e63872
      DOI : 10.3897/rio.7.e63872
      Authors : Teresa Gomez-Diaz, Tomas Recio : The goal of this document is to openly contribute with our comments to the EOSCArchitecture report: Scholarly Infrastructures for Research Software (SIRS), and thus, to participate in the European Open Science Cloud (EOSC) architecture design. HTML XML PDF
      PubDate: Fri, 5 Feb 2021 09:30:00 +0200
  • Conservation of saproxylic beetles in the Carpathians

    • Abstract: Research Ideas and Outcomes 7: e63874
      DOI : 10.3897/rio.7.e63874
      Authors : Marian Mirea, Steluta Manolache, Cristiana Pioarca-Ciocanea, Andreea Nita, Iulia Miu, Viorel Popescu, Bekka Brodie, Matei Dragomir, Ion Militaru, Silviu Chiriac, Laurentiu Rozylowicz : Romanian Carpathians are considered a biodiversity hotspot in Europe, with large forested areas, including old-growth forests. Past forestry practices, such as selective logging resulting in forest high grading and removal of ancient or decaying trees, reduced the heterogeneity of forest structure and composition. These practices led to forest habitats with few veteran trees and a small amount of deadwood, which protected saproxylic beetles rely on for completing their complex life cycles. Moreover, saproxylic species are considered pest species under traditional forestry practices, as they reduce the value of timber. As such, Romanian forestry practices have actively sought to reduce the amount of deadwood in an effort to decrease the presence of saproxylic species, thus effectively isolating stands with a high diversity of saproxylic beetles.The European Commission will finance the project LIFE19 NAT/RO/000023 Conservation of saproxylic beetles in the Carpathians LIFE ROsalia. The project aims to stop and reverse the loss of protected saproxylic beetles (Rosalia longicorn Rosalia alpina, the hermit beetle Osmoderma eremita, great capricorn beetle Cerambyx cerdo, grey beetle Morimus funereus, and stag beetle Lucanus cervus) in the Carpathians by demonstrating conservation actions for increasing the connectivity of favorable habitats in the ROSCI0208 Putna-Vrancea (Eastern Carpathians, Romania), and transferring and replicating best management practices in other Romanian Natura 2000 sites.LIFE ROsalia will be implemented between 2020 and 2025 by the Environmental Protection Agency Vrancea, the Center for Environmental Research at the University of Bucharest, the Putna-Vrancea Natural Park Administration, and the Association for Biodiversity Conservation. HTML XML PDF
      PubDate: Wed, 3 Feb 2021 16:30:00 +0200
  • ConservePlants: An integrated approach to conservation of threatened
           plants for the 21st Century

    • Abstract: Research Ideas and Outcomes 7: e62810
      DOI : 10.3897/rio.7.e62810
      Authors : Živa Fišer, Giovanna Aronne, Tsipe Aavik, Meleksen Akin, Paraskevi Alizoti, Filippos Aravanopoulos, Gianluigi Bacchetta, Manica Balant, Dalibor Ballian, Oz Barazani, Andrea Francesca Bellia, Nadine Bernhardt, Magda Bou Dagher Kharrat, Adrian Bugeja Douglas, Michael Burkart, Dušica Ćalić, André Carapeto, Tor Carlsen, Sílvia Castro, Guy Colling, Joana Cursach, Sara Cvetanoska, Cvetanka Cvetkoska, Renata Ćušterevska, Laura Daco, Kalina Danova, Aida Dervishi, Gordana Djukanović, Snežana Dragićević, Andreas Ensslin, Marianne Evju, Giuseppe Fenu, Ana Francisco, Pedro Pablo Gallego, Marta Galloni, Anatolie Ganea, Birgit Gemeinholzer, Peter Glasnović, Sandrine Godefroid, Mette Goul Thomsen, Melinda Halassy, Aveliina Helm, Marko Hyvärinen, Jasmin Joshi, Amra Kazić, Michael Kiehn, Marcin Klisz, Anneleen Kool, Marcin Koprowski, Anna Kövendi-Jakó, Karel Kříž, Matthias Kropf, Tiiu Kull, Sandro Lanfranco, Predrag Lazarević, Maja Lazarević, Merav Lebel Vine, Ligita Liepina, João Loureiro, Diana Lukminė, Nathalie Machon, Conor Meade, Detlev Metzing, Đorđije Milanović, Luis Navarro, Saša Orlović, Bart Panis, Hana Pankova, Taras Parpan, Ondřej Pašek, Dhimiter Peci, Theodora Petanidou, Kristina Plenk, Radosław Puchałka, Ivan Radosavljević, Hassan Rankou, Valerijus Rašomavičius, Gabriela Romanciuc, Anna Ruotsalainen, Nina Šajna, Terezia Salaj, Carolina Sánchez-Romero, Murat Sarginci, Deborah Schäfer, Ole Seberg, Suzanne Sharrock, Jozef Šibík, Mária Šibíková, Olav Skarpaas, Milena Stanković Neđić, Srdjan Stojnic, Boštjan Surina, Katalin Szitár, Aco Teofilovski, Rannveig Thoroddsen, Ivaylo Tsvetkov, Domas Uogintas, Koenraad Van Meerbeek, Nils van Rooijen, Loukia Vassiliou, Rita Verbylaitė, Philippine Vergeer, Petr Vít, Margareta Walczak, Alex Widmer, Justyna Wiland-Szymańska, Goran Zdunić, Elke Zippel : Even though plants represent an essential part of our lives offering exploitational, supporting and cultural services, we know very little about the biology of the rarest and most threatened plant species, and even less about their conservation status. Rapid changes in the environment and climate, today more pronounced than ever, affect their fitness and distribution causing rapid species declines, sometimes even before they had been discovered. Despite the high goals set by conservationists to protect native plants from further degradation and extinction, the initiatives for the conservation of threatened species in Europe are scattered and have not yielded the desired results. The main aim of this Action is to improve plant conservation in Europe through the establishment of a network of scientists and other stakeholders who deal with different aspects of plant conservation, from plant taxonomy, ecology, conservation genetics, conservation physiology and reproductive biology to protected area's managers, not forgetting social scientists, who are crucial when dealing with the general public. HTML XML PDF
      PubDate: Mon, 25 Jan 2021 12:45:00 +020
  • SARS-CoV-2 Structural Analysis of Receptor Binding Domain New Variants
           from United Kingdom and South Africa

    • Abstract: Research Ideas and Outcomes 7: e62936
      DOI : 10.3897/rio.7.e62936
      Authors : Victor Padilla-Sanchez : SARS-CoV-2 has caused more than 80 million infections and close to 2 million deaths worldwide as of January 2021. This pandemic has caused an incredible damage to humanity being it medically and/or financially halting life as we know it. If it were not enough, the current virus is changing to a more deadly form because of the mutations that are arising on its genome. Importantly, two variants have emerged in recent months, one in United Kingdom and the other in South Africa that are more infectious and escape antibody binding. These two variants have mutations in the receptor binding domain of the spike glycoprotein namely N501Y (UK, SA), K417N (SA) and E484K (SA). Here, I present a structural analysis of spike glycoprotein bound to ACE2 (angiotensin converting enzyme 2) where the mutations have been introduced in silico showing the reason why these variants bind better to ACE2 receptors. HTML XML PDF
      PubDate: Fri, 15 Jan 2021 14:15:00 +020
  • The Genomic Resources Collection Policy of the Finnish Museum of Natural

    • Abstract: Research Ideas and Outcomes 7: e61664
      DOI : 10.3897/rio.7.e61664
      Authors : Gunilla Ståhls, Alexandre Aleixo, Marko-Tapio Hyvärinen, Anniina Kuusijärvi, Leena Myllys, Henry Väre, Pasi Sihvonen, Arto Luttinen, Björn Kröger, Markku Oinonen, Leif Schulman, Aino Juslén : The Genomic Resources Collection is a separate, independently managed part of the natural history collections of the Finnish Museum of Natural History Luomus specifically intended for consumptive research. The GRC policy deals with the materials that are archived for the very purpose of enabling the study of biological diversity at the genome level, DNA extractions of animal, fungal and plant specimens, and animal tissue samples stored deep-frozen for purposes of future DNA extraction. The GRC policy defines the purpose of the collections, the objectives and content of the procedures and activities related to them, the distribution of responsibilities for collection management and maintenance in Luomus, and the principles of collection accumulation, preservation and accessibility.The aim of the GRC is to store and loan genomic samples for research purposes. In taxonomic coverage the collection overlaps with all the taxonomically delimited specimen collections managed by the Zoology and Botany Units, but is distinguished as being directed to preserve the genomic (DNA) information irrespective of the phenotypic variation that are the focus of specimen collections. The GRC includes both Finnish and foreign samples, all legally and ethically obtained, mostly linked to a specimen voucher in the taxonomic collections. The GRC samples are documented and trackable in Luomus collections management system. In accordance with the Universities Act, the GRC belongs to the national natural science collections of Luomus. For their part, the GRC collection implement the mission of Luomus, which is to be “responsible for the preservation, accumulation and exhibition of the national natural history collections and for research and education relating to them”. HTML XML PDF
      PubDate: Mon, 11 Jan 2021 11:35:00 +020
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