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  Subjects -> SCIENCES: COMPREHENSIVE WORKS (Total: 374 journals)
Showing 201 - 265 of 265 Journals sorted alphabetically
Jurnal MIPA     Open Access  
Jurnal Natural     Open Access  
Jurnal Sains Dasar     Open Access  
Jurnal Teknosains     Open Access  
Jurnal Udayana Mengabdi     Open Access  
Karaelmas Science and Engineering Journal     Open Access  
Karbala International Journal of Modern Science     Open Access  
Kennedy Institute of Ethics Journal     Full-text available via subscription   (Followers: 10)
LOGIKA Jurnal Ilmiah Lemlit Unswagati Cirebon     Open Access  
Logo STI Science, Technology and Innovation     Open Access   (Followers: 15)
Makara Journal of Science     Open Access  
Malawi Journal of Science and Technology     Open Access   (Followers: 6)
Maskana     Open Access  
MethodsX     Open Access  
Metode & Forskningsdesign     Open Access  
Mètode Science Studies Journal : Annual Review     Open Access  
Middle East Journal of Science     Open Access  
Middle European Scientific Bulletin     Open Access   (Followers: 4)
Modern Applied Science     Open Access   (Followers: 1)
Momona Ethiopian Journal of Science     Open Access   (Followers: 5)
MUST : Journal of Mathematics Education, Science and Technology     Open Access   (Followers: 4)
Mutis     Open Access  
National Academy Science Letters     Hybrid Journal   (Followers: 3)
National Science Review     Hybrid Journal   (Followers: 1)
Natural Sciences     Open Access  
Natural Sciences Education     Hybrid Journal   (Followers: 1)
Naturen     Full-text available via subscription  
Nepal Journal of Science and Technology     Open Access  
Network Science     Hybrid Journal   (Followers: 4)
New Directions in the Teaching of Physical Sciences     Open Access   (Followers: 2)
Nordic Journal of Science and Technology     Open Access   (Followers: 2)
Nordic Studies in Science Education     Open Access   (Followers: 3)
Nova     Open Access  
Nuncius     Hybrid Journal   (Followers: 2)
OmniScience : A Multi-disciplinary Journal     Full-text available via subscription   (Followers: 1)
Open Conference Proceedings Journal     Open Access  
Open Journal of Applied Sciences     Open Access  
Orbis Cógnita : Revista Científica     Open Access   (Followers: 2)
Patterns     Open Access   (Followers: 9)
PENDIPA : Journal of Science Education     Open Access   (Followers: 1)
People and Nature     Open Access   (Followers: 4)
Población y Desarrollo - Argonautas y caminantes     Open Access  
Politique et Sociétés     Full-text available via subscription   (Followers: 1)
Portal de la Ciencia     Open Access  
Proceedings of the Indian National Science Academy     Full-text available via subscription   (Followers: 5)
Proceedings of the Linnean Society of New South Wales     Full-text available via subscription   (Followers: 2)
Proceedings of the Royal Society of Queensland, The     Full-text available via subscription  
QScience Connect     Open Access  
Quantum Science and Technology     Hybrid Journal   (Followers: 19)
RAC: Revista Angolana de Ciências     Open Access   (Followers: 6)
Rafidain Journal of Science     Open Access  
Rehabilitation Research, Policy, and Education     Hybrid Journal   (Followers: 2)
Rekayasa     Open Access   (Followers: 2)
Reportes Científicos de la FaCEN     Open Access  
Reports in Advances of Physical Sciences     Open Access  
Research     Open Access   (Followers: 6)
Research Ideas and Outcomes     Open Access  
Research Integrity and Peer Review     Open Access  
Research Policy : X     Open Access   (Followers: 3)
Respuestas     Open Access  
Reviews in Theoretical Science     Full-text available via subscription  
Revista Bases de la Ciencia     Open Access  
Revista Binacional Brasil - Argentina: Diálogo entre as ciências     Open Access  
Revista Brasileira de Iniciação Científica     Open Access  
Revista Catarinense da Ciência Contábil     Open Access  
Revista Ciencia y Tecnología     Open Access  
Revista Ciência, Tecnologia & Ambiente     Open Access  
Revista Científica de la FAREM     Open Access  
Revista Científica de la Universidad Nacional del Este     Open Access   (Followers: 2)
Revista Cientifica Guillermo de Ockham     Open Access  
Revista Científica y Tecnológica UPSE     Open Access  
Revista Conhecimento Online     Open Access  
Revista Crítica de Ciências Sociais     Open Access  
Revista de Ciencia y Tecnología     Open Access  
Revista de Información Científica     Open Access  
Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales     Open Access  
Revista de la Sociedad Científica del Paraguay     Open Access   (Followers: 7)
Revista de la Universidad del Zulia     Open Access  
Revista Eletrônica Ludus Scientiae     Open Access  
Revista Logos Ciencia & Tecnología     Open Access  
Revista MundoFesc     Open Access  
Revista Politécnica     Open Access  
Revista Saber Digital     Open Access   (Followers: 3)
Revista Sociedad y Economía     Open Access  
Revista Tecnológica     Open Access  
Revista Theoria     Open Access   (Followers: 1)
Revista UNIMAR     Open Access  
Revista UniVap     Open Access  
Revista Vivências em Ensino de Ciências     Open Access   (Followers: 1)
Rihan Journal for Scientific Publishing     Open Access   (Followers: 1)
Royal Society Open Science     Open Access   (Followers: 7)
Ruhuna Journal of Science     Open Access  
Sainstek : Jurnal Sains dan Teknologi     Open Access  
SAINSTIS     Open Access  
Sainteknol : Jurnal Sains dan Teknologi     Open Access  
Sakarya Üniversitesi Fen Bilimleri Enstitüsü Dergisi     Open Access  
Scholedge International Journal of Multidisciplinary & Allied Studies     Open Access  
Sci     Open Access  
Science     Full-text available via subscription   (Followers: 4968)
Science & Diplomacy     Free   (Followers: 3)
Science & Technology Studies     Open Access   (Followers: 4)
Science Advances     Free   (Followers: 43)
Science and Technology     Open Access   (Followers: 2)
Science Diliman     Open Access  
Science Heritage Journal     Open Access  
Science World Journal     Open Access  
Science, Technology and Arts Research Journal     Open Access   (Followers: 1)
ScienceRise     Open Access  
Sciences du jeu     Open Access  
Sciential     Open Access  
Scientific African     Open Access  
Scientific American     Full-text available via subscription   (Followers: 497)
Scientific American Mind     Full-text available via subscription   (Followers: 10)
Scientific Bulletin     Open Access   (Followers: 1)
Scientific Data     Open Access   (Followers: 7)
Scientific Journal of Mehmet Akif Ersoy University     Open Access  
Scientific Journal of Pure and Applied Sciences     Open Access   (Followers: 1)
Scientific Reports     Open Access   (Followers: 82)
Scientific World     Open Access  
Scientonomy : Journal for the Science of Science     Open Access   (Followers: 1)
Scienze Regionali : Italian Journal of Regional Science     Full-text available via subscription   (Followers: 18)
Selforganizology     Open Access  
Seminário de Iniciação Científica e Seminário Integrado de Ensino, Pesquisa e Extensão     Open Access  
Simbiótica     Open Access  
SINET : Ethiopian Journal of Science     Open Access   (Followers: 5)
Smart Science     Open Access  
South African Journal of Science     Open Access   (Followers: 2)
South American Sciences     Open Access   (Followers: 1)
South East European University Review (SEEU Review)     Open Access   (Followers: 3)
Springer Science Reviews     Hybrid Journal   (Followers: 2)
Studies in Science Education     Hybrid Journal   (Followers: 18)
Sultan Qaboos University Journal for Science     Open Access  
Tanzania Journal of Science     Open Access   (Followers: 4)
TD : The Journal for Transdisciplinary Research in Southern Africa     Open Access  
Technologies     Open Access   (Followers: 1)
TECNOSCIENZA: Italian Journal of Science & Technology Studies     Open Access   (Followers: 2)
Temas y Debates     Open Access  
The Innovation     Open Access   (Followers: 8)
The Scientific World Journal     Open Access  
The Social Studies     Hybrid Journal   (Followers: 3)
The Winnower     Open Access  
Theoria     Open Access   (Followers: 3)
THEORIA : An International Journal for Theory, History and Foundations of Science     Full-text available via subscription   (Followers: 1)
Transactions of Tianjin University     Full-text available via subscription  
Trilogía     Open Access  
TÜBAV Bilim Dergisi     Open Access  
Türk Bilim ve Mühendislik Dergisi     Open Access  
Tydskrif vir Geesteswetenskappe     Open Access  
Uluslararası Bilimsel Araştırmalar Dergisi (IBAD)     Open Access   (Followers: 1)
UNED Research Journal / Cuadernos de Investigación UNED     Open Access   (Followers: 1)
Uni-pluriversidad     Open Access  
Uniciencia     Open Access  
Universidad, Ciencia y Tecnología     Open Access  
Universitas (León)     Open Access  
Universitas Scientiarum     Open Access  
Unnes Science Education Journal     Open Access  
Vilnius University Proceedings     Open Access  
Walailak Journal of Science and Technology     Open Access  
WikiJournal of Science     Open Access  
World Scientific Research     Open Access  
Zeitschrift für Didaktik der Naturwissenschaften     Hybrid Journal  
Образование и наука     Open Access   (Followers: 1)
Східно-Європейський журнал передових технологій : Eastern-European Journal of Enterprise Technologies     Open Access   (Followers: 3)

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Research Ideas and Outcomes
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ISSN (Online) 2367-7163
Published by Pensoft Homepage  [58 journals]
  • Open Information and Exceptions Policy of the Natural History Museum,
           London

    • Abstract: Research Ideas and Outcomes 10: e120629
      DOI : 10.3897/rio.10.e120629
      Authors : Matt Woodburn, Laurence Livermore, Esme Chapman, Ruth Benny, Nancy Chillingworth, Polly Parry, Ben Scott, Vincent Smith, Helen Hardy : There have been few, if any, open data and information management policies openly published from natural science collections. This paper contextualises the rationale for publishing the Open Information and Exceptions Policy of the Natural History Museum, London and provides the policy itself. The policy outlines how the Natural History Museum puts the principle of 'open by default' into practice; and includes sections on purpose and scope, relationship to relevant legislation (which always takes precedence over the policy), the categories of possible exceptions to open information release, what happens when exceptions are declared, relations to UK government information security classifications and definition of terms. HTML XML PDF
      PubDate: Mon, 26 Feb 2024 08:45:22 +020
       
  • Digitization Coordination Workshop Report

    • Abstract: Research Ideas and Outcomes 10: e120626
      DOI : 10.3897/rio.10.e120626
      Authors : Laurence Livermore, Holly Little, Jillian Goodwin, Sylvia Orli, Helen Hardy, Frederik Berger, Emily Braker, Jacqueline Chapman, Lauren Cohen, Sharon Grant, Jesse Grosso, David Jennings, Austin Mast, Gary Motz, Gil Nelson, Nelson Rios, Vincent Rossi, Franziska Schuster, Rebecca Snyder, Kira Sobers, Patrick Sweeney, Kimberly Watson, Alyson Wilkins, Jennifer Zaspel, Breda Zimkus, Diane Zorich : Many larger museums and archives have begun to implement a centralized approach to digitization of collections by creating Digitization Coordinator positions. This new effort has initiated a singular vision for digitization that incorporates priorities, workflows, and resources to greatly improve the efficiency and throughput of digitization in collections. Smaller institutions are now starting to see the benefit of creating a more structured cross-disciplinary approach to digitization, allowing for better awareness and resourcing of digitization needs.The workshop brought together natural sciences digitization professionals from the USA and EU, highlighting lessons learned and best practices to realize the benefits of a coordinated approach including advocacy for digitization, accelerating digitization efficiency and, ultimately, increasing digital collections access and usability to address societal challenges, such as biodiversity decline. Insights, lessons learned and initial thoughts on best practices are described, and the supporting workshop resources are shared so that others can benefit. HTML XML PDF
      PubDate: Fri, 23 Feb 2024 08:50:00 +020
       
  • Biodiversity, mental health and well-being: psychological mechanisms and
           moderators of a complex relationship (BIOWELL)

    • Abstract: Research Ideas and Outcomes 10: e116333
      DOI : 10.3897/rio.10.e116333
      Authors : Katja Liebal, Vera Denzer, Nico Eisenhauer, Immo Fritsche, Ute Kunzmann, Linda Oña, Martin F. Quaas, Ingmar Staude, Christian Wirth : Human activities and their consequences, such as environmental pollution, the exploitation of resources or deforestation, are major causes of biodiversity loss. However, humans depend on a biologically diverse and healthy environment in many ways, as it provides access to clean water, air and food. The loss of biodiversity is an ecological crisis that threatens human health, and ultimately their very existence. At the same time, there is an unwavering interest in the positive effects of "nature" on mental health. Although these examples point to a connection between biodiversity and health, little is known about the causal effects of different facets of biodiversity on mental health. Exploring these relationships and the underlying psychological mechanisms is a major goal of this project. We will build on the expertise of an interdisciplinary team involving scholars from psychology, biodiversity research, human geography, and behavioural economics and combine this expertise with a variety of methods, with a focus on quantitative research, experimental and intervention designs, and investigate participants from different age groups to understand the causal effects of different environments with varying degrees of biological diversity on mental health, and to identify the physical, social, and psychological boundary conditions of these causal effects. HTML XML PDF
      PubDate: Tue, 20 Feb 2024 11:59:45 +020
       
  • Strengthening the 2018 EU Bioeconomy Strategy through Microbiome Analysis
           and Synthetic Microbial Consortia Technologies

    • Abstract:
      DOI : 10.3897/arphapreprints.e121032
      Authors : Jens Krömer, Gabriela Popova, Katja Bühler, Peter Lindblad : The 2018 EU Bioeconomy Strategy aims to create a sustainable, circular, and low-emissions economy, based on the use of renewable biological resources. The strategy focuses on the development of new biobased products and markets, the promotion of sustainable and efficient use of resources, and the support of research, innovation, and skills development in the bioeconomy sector. The main objectives of the strategy are to: - Accelerate the deployment of bio-based products and services to reduce Europe’s dependence on fossil fuels and promote the transition to a circular economy; - Optimise the use of renewable biological resources to ensure food security, while also protecting the environment and biodiversity; - Promote sustainable and efficient use of natural resources, reduce waste, and minimize greenhouse gas emissions; - Develop innovative, sustainable, and competitive bio-based industries and value chains that create jobs and support economic growth, particularly in rural areas; - Support research, innovation, and skills development in the bioeconomy sector to drive technological advancements, enhance the competitiveness of the EU’s bio-based industries, and address societal challenges such as climate change, food security, and public health. The EU Horizon 2020 PROMICON project is a pioneering initiative that directly addresses the objectives of the 2018 EU Bioeconomy Strategy. By focusing on the production of biopolymers, energy carriers, feedstocks, and antimicrobial molecules from natural microbiomes, the project is promoting the sustainable production and use of renewable biological resources while also supporting research and innovation in the bioeconomy sector. HTML XML PDF
      PubDate: Mon, 19 Feb 2024 09:15:05 +020
       
  • Workshop report: Workshop on psychiatric prescribing and psychology
           testing and intervention in children and adults with Duchenne muscular
           dystrophy

    • Abstract: Research Ideas and Outcomes 10: e119243
      DOI : 10.3897/rio.10.e119243
      Authors : Linda Bouquillon, Dot Bindman, Jos Hendriksen, Phillipe Collin, Janet Hoskin, Rory Conn, Chloe Geagan, Ros Quinlivan : This workshop aimed at summarising knowledge and key issues in psychiatric prescribing and psychological testing in children and adults with Duchenne muscular dystrophy (DMD). It comprised clinicians and patient representatives from the UK and the Netherlands. The following topics were discussed: a model for capturing the range of non-motor problems in the domains of cognition, learning, emotion and behaviour; psychosocial screening tools for use with children and adults; assessing neurocognitive functioning in children and adults; parent and teacher perspectives on psychosocial needs; and psychopharmacological treatment for affective disorders, anxiety disorders, obsessive compulsive disorder, attention deficit hyperactivity disorder (ADHD) and insomnia. Some key considerations included: the need for tools used to assess behavioural and psychosocial functioning to consider motor aspects in DMD; to understand more about working memory performance; the need for early interventions for automatisation problems, which affect reading and arithmetic; appropriate selection of tests for neuropsychology assessments; in schools, acknowledging the range of psychosocial risks and gathering evidence of psychosocial needs; the suitability of selective serotonin reuptake inhibitors for mood and anxiety disorders; the use of stimulant medications for ADHD; melatonin use for insomnia; the cautious use of benzodiazepines; and the need for improving pathways for psychosocial care. HTML XML PDF
      PubDate: Mon, 19 Feb 2024 09:11:57 +020
       
  • LifeWatch ERIC Strategic Working Plan Outcomes

    • Abstract: Research Ideas and Outcomes 10: e119943
      DOI : 10.3897/rio.10.e119943
      Authors : Christos Arvanitidis, Alberto Basset, Peter van Tienderen, Cristina Isabel Huertas Olivares, Cristina Di Muri, Lucas de Moncuit, Wouter Los : LifeWatch ERIC has embarked on its new destination towards upgrading and (co-)constructing its Infrastructure as a response to the needs of its target communities and stakeholders. Through an industrialisation process, all independent data, software components, publications and other types of research products contributed by the Member Countries will be consolidated and integrated to enable collaborative development. The Technology Readiness Level of LifeWatch ERIC will be raised to level 9. This process is described in its new Strategic Working Plan on its second implementation period (2022-2026). Accordingly, this topical collection of papers includes articles which describe the main outcomes, that is the deliverables of this new Strategic Working Plan. The deliverables published in this topical collection are not of a confidential nature and are developed in the form of a standard, structured template. HTML XML PDF
      PubDate: Thu, 8 Feb 2024 10:46:58 +0200
       
  • WarenstromInfo: a tool for the easy extraction and visualisation of trade
           flow data

    • Abstract: Research Ideas and Outcomes 10: e112227
      DOI : 10.3897/rio.10.e112227
      Authors : Octavio Mesa-Varona, Carolina Plaza-Rodríguez, Lars Valentin, Matthias Filter : Epidemiological outbreak investigations often prove to be lengthy and inconclusive due to the time-consuming nature of the currently-used approaches. An alternative approach to address these challenges could involve the application of algorithms to support authorities and food business operators by providing timely, relevant and reliable information. Algorithms, such as gravity models, could be applied as commodity trade models, but they require a large amount of reliable and consistent data on trade for generating projections at international, national or even regional level. Several trade databases, such as UN COMTRADE, EUROSTAT, BACI, CHELEM and GTAP, provide information on trace, albeit with variations in the provided information and in the structure. However, it is worth noting that not all of these databases are freely accessible and data management can pose challenges, hampering the access to the trade data. WarenstromInfo (WI) was created as a software solution that allows easy trade data extraction and visualisation for application in different areas, such as outbreak investigations.WarenstromInfo (WI) is an application tool that automatically extracts, decodes and visually displays trade flow data from EUROSTAT "EU trade since 2002 by statistical procedure, by HS2-4-6 and CN8 (DS-059322)" (hereinafter referred to EUROSTAT) and the BACI databases, based on user input.WI was developed by using the open-source desktop software KNIME Analytics Platform. WI offers the flexibility to be executed either as a web service on a KNIME Web Server infrastructure or as a local resource.To integrate the BACI database into WI, the database is annually downloaded as csv files, rebuilt as a SQLite database and hosted locally into the KNIME Web Server Infrastructure. In order to optimise storage space on the KNIME server, this SQLite database specifically includes only agrifood data, reflecting the tool´s focus. However, if new objectives are established, this database can be expanded. Further, data of the SQLite database can be customised by executing the WI workflow locally, enabling the user to expand the database at any time.In contrast to BACI, trade data extraction from the EUROSTAT database is performed via the EUROSTAT’s API (Application Programming Interface) applying GET requests and XML data management.WI displays four User-friendly Interfaces (UIs) designed with interactive KNIME nodes that facilitate the input of variables. The extracted trade flow data are shown through interactive tables directly within the UIs. This feature enables users to easily explore the data in a structured and user-friendly manner. Additionally, WI incorporates the extracted trade flow data into maps. These maps provide a visual representation of the data, allowing users to gain insights and identify patterns and trends geographically. Both, the data table and the maps, can be downloaded as a single Excel file (containing multiple preformatted tables) and as png files, respectively. HTML XML PDF
      PubDate: Wed, 7 Feb 2024 12:14:16 +0200
       
  • Template for a Hypothesis Description paper

    • Abstract: Research Ideas and Outcomes 10: e119808
      DOI : 10.3897/rio.10.e119808
      Authors : Tina Heger, Daniel Mietchen, Jonathan M. Jeschke : Hypothesis Descriptions are a type of manuscript dedicated to the formal description of a hypothesis, as introduced in an accompanying editorial and an examplary Hypothesis Description for the Enemy Release Hypothesis that is used in invasion biology. This questionnaire provides a template for such a Hypothesis Description manuscript. The template's format was designed for simplicity to facilitate adoption, and it can be easily extended to capture additional information, e.g. instructions for falsification or generalization, taxonomic or geographic scope, etymology, or relevant information in other research fields or other languages. The template reflects the recommended structure for a Hypothesis Description manuscript in that each of its sections provides the title for a section in a Hypothesis Description manuscript and indicates whether that section is mandatory or optional. Four sections - Keywords (mandatory), Conflicts of interest (optional), Acknowledgments (optional) and References (mandatory) - are in this template filled in for the template itself but should otherwise be adjusted for the hypothesis at hand. Comments to guide authors who work on a Hypothesis Description manuscript are provided as well. HTML XML PDF
      PubDate: Thu, 1 Feb 2024 12:00:00 +0200
       
  • Hypothesis Description: Enemy Release Hypothesis

    • Abstract: Research Ideas and Outcomes 10: e107393
      DOI : 10.3897/rio.10.e107393
      Authors : Tina Heger, Jonathan Jeschke, Maud Bernard-Verdier, Camille Musseau, Daniel Mietchen : This paper provides a brief overview of a major hypothesis in invasion biology: the enemy release hypothesis. Building on a summary of different previous definitions, we provide the following revised definition: “A reduced pressure by enemies in the non-native range contributes to invasion success.” Further, we suggest formalizing the hypothesis in the basic form ‘subject - relationship - object’ to allow for disambiguating the different existing meanings and enhancing their usability by machines. HTML XML PDF
      PubDate: Thu, 1 Feb 2024 12:00:00 +0200
       
  • Introducing Hypothesis Descriptions

    • Abstract: Research Ideas and Outcomes 10: e119805
      DOI : 10.3897/rio.10.e119805
      Authors : Daniel Mietchen, Jonathan Jeschke, Tina Heger : Hypotheses play a central role in the scientific process, yet the way they are introduced often leaves much room for interpretation, which makes it difficult to use them later on: to study and test them, to delineate their scope and to explore the relationships they have to other hypotheses or concepts, to datasets, methodologies or other resources. Here, we introduce a new article type in RIO that is dedicated to them: Hypothesis Descriptions. Such articles combine a specific verbal definition of a hypothesis with a concise description of its components and provide pointers to prior work as well as alignments with formal ways of knowledge representation, optionally including relevant nanopublications. With this format, we aim to facilitate the study of hypotheses in and of themselves, to improve their testability along with the documentation and interpretability of such tests, and to stimulate efforts towards standardization and automation in this space. HTML XML PDF
      PubDate: Thu, 1 Feb 2024 12:00:00 +0200
       
  • D5.5 Short-term ecological forecasts in support of the Bioeconomy Strategy
           and EU citizens 

    • Abstract:
      DOI : 10.3897/arphapreprints.e119131
      Authors : Ana Ceia-Hasse, Judy Shamoun-Baranes, Néstor Fernández, Henrique Pereira, César Capinha : A relevant number of ecological questions raised by policymakers, managers, and citizens often pertain to the short-term future (e.g., the coming days or weeks). In this sense, short-term ecological and biological forecasts can make substantial and practical contributions to achieving policy objectives and benefit society broadly. Specifically, short-term forecasts of Essential Biodiversity Variables (EBVs) and Essential Ecosystem Service Variables (EESVs) can support decision-making by stakeholders from multiple sectors, enabling to anticipate ecological transformations and support proactive, informed decisions that promote conservation, economic activities, and human well-being.The aim of this task was to demonstrate how a European Biodiversity Observation Network can support the generation of short-term spatial forecasts of ecological and biological phenomena relevant to the Bioeconomy Strategy and to EU citizens at large. Our specific objectives included showcasing 1) a computational workflow that enables the production of days-ahead forecasts for distinct ecological or biological phenomena and 2) a specialized computational workflow for days-ahead forecasts of bird aerial biomass. The first, (‘generic’) workflow, is exemplified using two case studies: i) forecasting the fruiting of a wild mushroom of commercial and recreational relevance, and ii) forecasting the life stage of relevance for surveillance of an invasive pest species important for agriculture. These case studies aim to demonstrate specific, tangible contributions that short-term ecological forecasting can make towards the sustainable use of bio-based economy sectors, ecosystem protection, and anticipation of ecological risks. Beyond aligning with the EU Bioeconomy Strategy, our three forecasting targets also offer relevant contributions to a wider range of EU strategies and policies.We actively involved stakeholders in defining the end-products and in the development of computational modelling approaches of the workflows. This process entailed two distinct approaches. For the generic forecasting workflow, we engaged in a participatory process from the project's start, focusing on stakeholders involved in mushroom foraging and experts in mycology and ecological modelling. For the bird aerial biomass forecasting workflow, we built upon substantial developments that predated the project, with our engagement primarily drawing on insights and input from earlier initiatives. The two workflows serve complementary purposes in terms of the primary data they use. While the first (generic) workflow is based on the growing body of opportunistic biodiversity observation data, particularly from citizen science initiatives, the second workflow requires highly specialized radar data from weather stations. However, both workflows use predictor data from weather observations and forecasts and employ machine learning algorithms to correlate these data with observed variations in the phenomena being forecasted. HTML XML PDF
      PubDate: Fri, 19 Jan 2024 13:51:09 +020
       
  • Predictive modelling of total operating room time for Laparoscopic
           Cholecystectomy using pre-operatively known indicators to guide accurate
           surgical scheduling in a critical access hospital

    • Abstract: Research Ideas and Outcomes 10: e115511
      DOI : 10.3897/rio.10.e115511
      Authors : Todd Prier, Kelly Yale-Suda, Hailey Westover, Ryan Corey : The financial margin of rural and critical access hospitals highly depends on their surgical volume. An efficient operating room is necessary to maximise profit and minimise financial loss. OR utilisation is a crucial OR efficiency metric requiring accurate case duration estimates. The patient's age, ASA, BMI, Mallampati score, previous surgery, the planned surgery, the surgeon, the assistant's level of experience and the severity of the patient's disease are also associated with operative duration. Although complex machine-learning models are accurate in operative prediction, they are not always available in resource-limited hospitals. Laparoscopic cholecystectomy (LC) is one of the most common surgical procedures performed and is one of the few procedures performed at critical access and rural hospitals. The accurate estimation of the operative duration of LC is essential for efficient OR utilisation. We hypothesise that a multivariate linear regression prediction model can be constructed from a set of pre-operatively known, easily collected variables to maximise OR utilisation and improve operative scheduling accuracy for LC. We further hypothesise that this model can be implemented in resource-limited environments, such as critical access hospitals. HTML XML PDF
      PubDate: Mon, 15 Jan 2024 09:02:48 +020
       
  • Permits, contracts and their terms for biodiversity specimens

    • Abstract: Research Ideas and Outcomes 10: e114366
      DOI : 10.3897/rio.10.e114366
      Authors : Edmund Schiller, Karin Wiltschke-Schrotta, Eva Häffner, Jutta Buschbom, Frederik Leliaert, Breda Zimkus, John Dickie, Suzete Gomes, Chris Lyal, Daniel Mulcahy, Alan Paton, Gabi Droege : We present two different typologies of legal/contractual information in the context of natural history objects: the Biodiversity Permit/Contract Typology categorises permits and contracts, and the Typology of Legal/Contractual Terms for Biodiversity Specimens categorises the terms within permits and contracts. The Typologies have been developed under the EU-funded SYNTHESYS+ project with the participation of experts from outside the consortium. The document further addresses a possible technical integration of these typologies into the Distributed System of Scientific Collections (DiSSCo). The implementation in the DiSSCo data model is outlined and a concrete use case is presented to show how conditions, e.g. the Typology of Legal/Contractual Terms, can be introduced into the DiSSCo Electronic Loans and Visits System (ElViS). Finally, we give an outlook on the next steps to develop the typologies into a standard that supports compliance with legal and contractual obligations within the wider community of natural science collections. HTML XML PDF
      PubDate: Wed, 10 Jan 2024 10:27:53 +020
       
  • A report on recommendations for the most suitable financial contribution
           model for the Distributed System of Scientific Collections Research
           Infrastructure (DiSSCo-RI)

    • Abstract: Research Ideas and Outcomes 10: e117217
      DOI : 10.3897/rio.10.e117217
      Authors : Salomé Landel, Gaël Lymer, Markus Pasterk, Michel Guiraud, Katharine Worley : A key consideration during the preparatory phase project DiSSCo Prepare – which laid the foundations for the future Research Infrastructure DiSSCo (Distributed System of Scientific Collections) – was the need to establish a small number of alternative viable financial contribution models and a scalable formula which could be presented to potential funders, with a view to obtaining the minimum financial contribution necessary for DiSSCo to operate, as well as considering how the RI could grow with increased national funding.This report briefly explains the ERIC funding framework – as chosen for DiSSCo – and its legal constraints, in order to explain the key role played by national member contributions in the viability of an ERIC. An essential annex of the statutes that will be signed by all members of the ERIC is the member fee calculation. A proposal for the DiSSCo member fee calculation is set out in this document and is based on three main indicators: economic power (GDP), annual spending in research and development and population size. In the context of DiSSCo – and to ensure the ERIC can function – these indicators are connected to a fixed baseline fee of €50,000, in order to guarantee a minimum significant annual contribution from each participating country and avoid contributions that will be more expensive to manage than to benefit from. This baseline is multiplied by contribution factors which propose different ways to weight the various indicators.The method is established on an ideal scenario, whereby all 27 EU members, as well as the UK, Iceland, Norway and Switzerland sign the DiSSCo statutes and agree to the proposed member contribution calculation, amounting to €4.5 million for the annual budget of the ERIC. This scenario remains highly unlikely; therefore, a scaled approach has been envisaged, meaning the initial engagement of some countries will allow DiSSCo to begin its operation and implement its business strategy, whilst the growth of the ERIC and its activities is likely to evolve proportionally to the number of national members it is able to engage.This report also looks at the ways in which funding could be distributed amongst the DiSSCo members in order to implement decentralised services. HTML XML PDF
      PubDate: Tue, 9 Jan 2024 10:01:39 +0200
       
  • DiSSCo Transition Abridged Grant Proposal

    • Abstract: Research Ideas and Outcomes 10: e118241
      DOI : 10.3897/rio.10.e118241
      Authors : Dimitrios Koureas, Laurence Livermore, Wouter Addink, Eva Alonso, Jose Alonso, Ana Casino, François Dusoulier, Vânia Ferreira, Jonas Grieb, Quentin Groom, Sharif Islam, Urmas Kõljalg, Gaël Lymer, Karol Marhold, Carole Paleco, Stefaan Pijls, Serge Scory, Ben Scott, Claus Weiland, Katharine Worley : The Distributed System of Scientific Collections (DiSSCo) is a pan-European Research Infrastructure (RI) initiative. DiSSCo aims to bring together natural science collections from 175 museums, botanical gardens, universities and research institutes across 23 countries in a distributed infrastructure that makes these collections physically and digitally open and accessible for all forms of research and innovation. DiSSCo RI entered the ESFRI roadmap in 2018 and successfully concluded its Preparatory Phase in early 2023. The RI is now transitioning towards the constitution of its legal entity (an ERIC) and the start of its scaled-up construction (implementation) programme. This publication is an abridged version of the successful grant proposal for the DiSSCo Transition Project which has the goal of ensuring the seamless transition of the DiSSCo RI from its Preparatory Phase to the Construction Phase (expected to start in 2025). In this transition period, the Project will address five objectives building on the outcomes of the Preparatory Phase project:1) Advance the DiSSCo ERIC process and complete its policy framework, ensuring the smooth early-phase Implementation of DISSCo;2) Engage & support DiSSCo National Nodes to strengthen national commitments;3) Advance the development of core e-services to avoid the accumulation of technical debt before the start of the Implementation Phase;4) Continue international collaboration on standards & best practices needed for the DiSSCo service provision; and5) Continue supporting DiSSCo RI interim governance bodies and transition them to the DiSSCo ERIC formal governance.The Project’s impact will be measured against the increase in the RI's overall Implementation Readiness Level (IRL). More specifically, we will monitor its impact towards reaching the required level of maturity in four of the five dimensions of the IRL that can benefit from further developments. These include the organisational, financial, technological and data readiness levels. HTML XML PDF
      PubDate: Mon, 8 Jan 2024 16:15:38 +0200
       
  • PROMICON Deliverable D6.1 Project branding and communication channels
           setup and running (logo, promotional materials, website, templates, social
           media)

    • Abstract:
      DOI : 10.3897/arphapreprints.e118155
      Authors : Teodor Metodiev, Gabriela Popova : As a foundation of the future communication activities, a set of dissemination and branding tools and materials is crucial to be established within the first months of the project. Accordingly, a project logo and website were developed in the first 4 months of the PROMICON life-cycle, which form the backbone of both project branding and public visibility. In addition, various dissemination materials such as a PROMICON brochure and a poster were produced in high quality print versions for rising awareness at events. All of the materials can be found on the media center section of the website and are available to anyone interested. Document templates were also produced and made available to the consortium, in order to facilitate future dissemination and reporting activities such as letters, milestone and deliverable reports, as well as PowerPoint presentations. Accounts have been also set in two major social media channels, Twitter and Facebook, to ensure the widest possible impact and outreach of PROMICON related results, news and events, and to engage the interested parties in a virtual community. The long‐term impact of the project's results will be secured by maintaining the website for a total of 9 years – 4 years of the project duration and additional 5 years after the end of the PROMICON life-cycle. HTML XML PDF
      PubDate: Thu, 4 Jan 2024 12:00:29 +0200
       
  • Whose Ocean' Exploring multidisciplinary perspectives towards ocean
           sustainability and implications for the un(der)represented

    • Abstract: Research Ideas and Outcomes 10: e114485
      DOI : 10.3897/rio.10.e114485
      Authors : Kiara Lasch, Sabine Gollner, Alex Oude Elferink, Siren Rühs, Francesca Sangiorgi, Erik van Sebille, Junjie Wang : The ocean's significance encompasses crucial ecosystem services including climate regulation, oxygen production and food supply. The ocean is also a major player in the global economy. However, human activities continue to harm the ocean, jeopardising these vital functions. In July 2022, the United Nations Ocean Conference adopted a political declaration entitled "Our ocean, our future, our responsibility," emphasising the need for sustainable ocean management and protection. However, an important initial question arises: who are the “Our”' or, rephrased “Whose ocean” is it' This study presents first answers to this question, based on interviews with ocean professionals from diverse backgrounds. Their responses showcased the complexity of the issue, with differing opinions on ocean “ownership” and “control”. Despite the diversity of perspectives, a shared emphasis emerged: shifting from profit-driven decision-making to prioritising marine ecosystem health. Proposed approaches to build a sustainable relationship between people and the ocean include promoting ocean literacy and marine research and ensuring global accountability. These voices offered valuable insights towards ocean sustainability, guiding future academic, educational and policy-making efforts. HTML XML PDF
      PubDate: Tue, 2 Jan 2024 08:59:27 +0200
       
  • Digital objects to make computable biomedical knowledge FAIR: an
           infrastructural approach to knowledge representation, dissemination and
           implementation

    • Abstract: Research Ideas and Outcomes 9: e109307
      DOI : 10.3897/rio.9.e109307
      Authors : Marisa Conte, Allen Flynn, Philip Barrison, Peter Boisvert, Zach Landis-Lewis, Charles Friedman : We present our work to develop digital objects to represent and convey a specific category of scientific knowledge: computable biomedical knowledge (CBK). Properly developed, validated, implemented and stewarded, CBK has the potential to accelerate the translation of actionable knowledge from scientific discovery to clinical application.Our research takes an infrastructural approach to CBK, initially by focusing on the creation of a conceptual model for packaging computable biomedical knowledge - the Knowledge Object (KO) - and on corresponding efforts to create an architecture for KO management and implementation. Additionally, our work is grounded in the FAIR principles, such that KO artefacts should be findable, accessible, interoperable and reusable and we are exploring aligning KOs with emerging best practices for FAIR Digital Objects (FDO).The outcomes of this work resonate in clinical contexts, health professions education, healthcare quality improvement, biomedical and translational research and population care. Our KO model is also of interest to researchers and practitioners interested in knowledge science, including those working with semantic technologies and other forms of digital objects. HTML XML PDF
      PubDate: Mon, 18 Dec 2023 09:03:24 +020
       
  • Assessing ‘non-destructive’ DNA extraction method in small crustaceans
           kept in wet collections

    • Abstract: Research Ideas and Outcomes 9: e113299
      DOI : 10.3897/rio.9.e113299
      Authors : Samuel C. Bernardes, Thomas von Rintelen, Serena Alexander, Fiona Lorenz, Kristina von Rintelen : Specimens in natural history museums are a valuable resource for biological research, such as taxonomic, biodiversity or evolutionary studies. However, the quality of DNA and even morphological characters can decrease over time, depending on previous fixation and long-term preservation methods. In recent years, advances in DNA extraction and sequencing techniques have allowed researchers to obtain DNA from museum specimens, even when the DNA was very fragmented. Extraction methods should ideally be morphologically non-destructive, leaving diagnostic characters intact for future taxonomic studies. Here, we assess whether the whole-body extraction widely used for several taxa would be destructive for small crustaceans kept in wet collections. We extracted the DNA from over 70 small (1-3 cm) and relatively fragile shrimps collected during the last 30 years by using: i) a piece of abdominal tissue and ii) from the entire remaining body of the animal. We photographed several samples before and after the lysis, focusing on taxonomically relevant characters. Although DNA concentration was higher in the whole-body extractions, the presence of intact DNA was not correlated to the amount of lysed tissue. The resulting genomic libraries had little to no difference in yield. The taxonomically relevant characters were primarily preserved in larger specimens, whereas smaller specimens (< 1.5 cm) became too fragile to handle or were damaged. We conclude that this method must be carried out carefully in smaller crustaceans, depending on size and taxon. We advise against using it with type specimens as the advantages do not outweigh the risks. Our experiment may provide future research with quantitative and qualitative evaluations to help scientists weigh their decisions when extracting DNA from wet collection material. HTML XML PDF
      PubDate: Thu, 14 Dec 2023 17:09:31 +020
       
  • AquaticVID: a low cost, extended battery life, plug-and-go video system
           for aquatic research

    • Abstract: Research Ideas and Outcomes 9: e114134
      DOI : 10.3897/rio.9.e114134
      Authors : Lachlan Fetterplace, Peter Ljungberg, Emilia Benavente Norrman, Filip Bohlin, Lisa Sörman, Per Johannesson, Daniel Rooth, Sara Königson : AquaticVID is a low-cost, long battery life video camera system for use in a wide-range of aquatic research applications. The system can be deployed for multiple day recording on a single charge, is submersible to depths of down to 950 m and can be constructed quickly using easily sourced off-the-shelf materials. The system is essentially ‘plug-and-go’, as assembly and preparation for deployment takes < 30 minutes without the need for technical build or programming skills. All of the electrical components are interchangeable with parts from multiple manufacturers and the camera system can be adapted to fit a variety of waterproof enclosure sizes depending on power and data storage requirements. Here, we describe three versions of the AquaticVID in detail and give examples of above and below water research undertaken with the system. The small size and extended battery times, coupled with ease of use and low cost (US$ 268–540) make the AquaticVID a useful option for numerous aquatic research applications. HTML XML PDF
      PubDate: Fri, 8 Dec 2023 13:12:00 +0200
       
  • Modern Approaches to the Monitoring of Biоdiversity (MAMBO)

    • Abstract: Research Ideas and Outcomes 9: e116951
      DOI : 10.3897/rio.9.e116951
      Authors : Toke Høye, Tom August, Mario V Balzan, Koos Biesmeijer, Pierre Bonnet, Tom Breeze, Christophe Dominik, France Gerard, Alexis Joly, Vincent Kalkman, W. Daniel Kissling, Teodor Metodiev, Jesper Moeslund, Simon Potts, David Roy, Oliver Schweiger, Deepa Senapathi, Josef Settele, Pavel Stoev, Dan Stowell : EU policies, such as the EU biodiversity strategy 2030 and the Birds and Habitats Directives, demand unbiased, integrated and regularly updated biodiversity and ecosystem service data. However, efforts to monitor wildlife and other species groups are spatially and temporally fragmented, taxonomically biased, and lack integration in Europe. To bridge this gap, the MAMBO project will develop, test and implement enabling tools for monitoring conservation status and ecological requirements of species and habitats for which knowledge gaps still exist. MAMBO brings together the technical expertise of computer science, remote sensing, social science expertise on human-technology interactions, environmental economy, and citizen science, with the biological expertise on species, ecology, and conservation biology. MAMBO is built around stakeholder engagement and knowledge exchange (WP1) and the integration of new technology with existing research infrastructures (WP2). MAMBO will develop, test, and demonstrate new tools for monitoring species (WP3) and habitats (WP4) in a co-design process to create novel standards for species and habitat monitoring across the EU and beyond. MAMBO will work with stakeholders to identify user and policy needs for biodiversity monitoring and investigate the requirements for setting up a virtual lab to automate workflow deployment and efficient computing of the vast data streams (from on the ground sensors, and remote sensing) required to improve monitoring activities across Europe (WP4). Together with stakeholders, MAMBO will assess these new tools at demonstration sites distributed across Europe (WP5) to identify bottlenecks, analyze the cost-effectiveness of different tools, integrate data streams and upscale results (WP6). This will feed into the co-design of future, improved and more cost-effective monitoring schemes for species and habitats using novel technologies (WP7), and thus lead to a better management of protected sites and species. HTML XML PDF
      PubDate: Thu, 7 Dec 2023 11:01:16 +0200
       
  • PaNOSC/ExPaNDS Science Projects for EOSC Future (WP6.3): Demonstrating
           EOSC Value through cross-domain Research Science Projects

    • Abstract:
      DOI : 10.3897/arphapreprints.e116674
      Authors : Miguel Angel Gonzalez, Rudolf Dimper, Patrick Fuhrmann, Fra Schluenzen, Gianluca Santoni, Jordi Bodera, Jayesh Wagh, Irina Safiulina, Paolo Mutti, Arianna D'Angelo, Paul Millar, Krisztian Pozsa, Leonardo Sala, Alun Ashton, Giuseppe La Rocca : Photon and Neutron (PaN) user facilities serve a large variety of scientific user communities using x-rays and/or neutrons in their research projects in order to understand the structure and function of matter. The current proposal presents two concrete scientific cases intended to demonstrate the utility of FAIR data and automatic workflows in the specific domain of biological structures and processes, simplifying the access and manipulation of large sets of data and the combination of experimental and modelling tools. The final objective consists in reducing the level of expertise required to analyze and interpret data acquired at large scale neutron and synchrotron facilities. HTML XML PDF
      PubDate: Tue, 5 Dec 2023 12:45:39 +0200
       
  • ESCAPE Dark Matter Science Project for EOSC Future project (WP6.3)

    • Abstract:
      DOI : 10.3897/arphapreprints.e116673
      Authors : Pooja Bhattacharjee, Ian Bird, Francesca Calore, Caterina Doglioni, Christopher Eckner, Elena Gazzarrini, Lukas Heinrich, Tetiana Hryn'ova, Valerio Ippolito, Jared Little, Stephen Serjeant, Mikhail Smirnov : This document summarizes the design, status and results of the Dark Matter Science Project from the ESCAPE cluster within the EOSC-Future project as of November 2022.  HTML XML PDF
      PubDate: Tue, 5 Dec 2023 12:40:50 +0200
       
  • Open Imaging Data Sharing in EOSC: COVID-19 as Demonstrator

    • Abstract:
      DOI : 10.3897/arphapreprints.e116672
      Authors : Reagon Karki, Andrea Zaliani, Philip Gribbon, Carolina Simon, Jose Ramon Macias, Bugra Özdemir, Aastha Mathur : This Science Project (SP) brings together three different domains of life sciences with the aim to create reproducible workflows, tools and web-services for data visualization. This SP focuses in building resources for handling data from bioimaging, structural and bio-chemical studies. The Euro-Bioimaging will implement a community standard cloud compatible open image data format and data submission workflow for high-throughput screening data. Whereas, Instruct-ERIC will develop a user-friendly web-service to access to multi-dimensional structural and imaging data. Lastly, EU-OpenScreen/Fraunhofer ITMP will create reproducible workflow for generating Knowledge Graphs that represent phenotype-chemotype of diseases. While these resources are being developed, the collaborators will also simultaneously harmonize the resources right from the beginning to enable FAIR data principles. This SP uses COVID-19 as a demonstrator, however the resources will be generalized for any disease of interest. HTML XML PDF
      PubDate: Tue, 5 Dec 2023 12:35:16 +0200
       
  • Tracing bio-structures with serial crystallography: Facilitating the
           access to high-throughput macromolecular x-ray crystallography techniques.
           

    • Abstract:
      DOI : 10.3897/arphapreprints.e116671
      Authors : Miguel Angel Gonzalez, Rudolf Dimper, Patrick Fuhrmann, Gianluca Santoni, Jordi Bodera, Jayesh Wagh, Irina Safiulina, Arianna D'Angelo, Paolo Mutti, Paul Millar, Krisztian Pozsa, Leonardo Sala, Alun Ashton, Giuseppe La Rocca : Serial (femtosecond) X-ray-Crystallography (SFX) is a special variant of macromolecular X-ray crystallography aiming at rapid structural studies at room temperature. This highly innovative technology permits investigation of bio-structures not tractable with conventional X-ray crystallography, and is capable of studying fast in-situ biochemical processes. The method is still relatively new, but it is already one of the most prominent applications of free-electron lasers (FELs), and increasingly also of very brilliant synchrotron radiation sources. One of the unique characteristics of this type of experiments is the extremely high repetition rate combined with a quite moderate success rate. A crucial task in the rather complex data processing pipeline is the rapid and accurate classification of images: typically, only a few percent of the images contain a diffraction pattern suitable for subsequent integration and structure refinement. AI-supported image classification is hence particularly suited for drastic data reduction, saving precious storage space, compute cycles and processing time. The experimental techniques and methodologies are rapidly evolving, and the integration of emerging tools into the processing pipeline is an essential task. SFX data sets are big, require substantial storage, and computational power. The main goal of this SP is to establish and develop a data processing platform, which integrates services and developments from PaNOSC/ExPaNDS. The platform should provide integrated processing pipelines for well-established and cutting-edge applications, so that cross-disciplinary users with modest expertise gain rapid and convenient access to tools and documentation of newest developments. On the other hand, it should also provide convenient access to FAIR SFX-data, to foster developments and strengthen collaboration between experimentalists and developers of new algorithms and software implementations. This approach is of very high relevance for all PaN synchrotron and FEL facilities and their users. HTML XML PDF
      PubDate: Tue, 5 Dec 2023 12:30:49 +0200
       
  • Following biological processes combining small angle neutron and x-ray
           scattering and modelling techniques

    • Abstract:
      DOI : 10.3897/arphapreprints.e116670
      Authors : Miguel Angel Gonzalez, Irina Safiulina, Arianna D'Angelo, Paolo Mutti, Jordi Bodera, Gianluca Santoni, Rudolf Dimper, Jayesh Wagh, Patrick Fuhrmann, Paul Millar, Krisztian Pozsa, Leonardo Sala, Alun Ashton, Giuseppe La Rocca : Small-angle scattering techniques are widely used in scientific communities to determine the shape, distribution, and uniformity of particles in solution. New developments and faster acquisition will also allow for tracking the dynamics of the particles themselves. Small-Angle X-ray or Neutron Scattering (SAXS or SANS, respectively) can be very effective tools for studying, for example, the time dependence of genome release from phages, investigating entire viral life cycles, or the assembly of macromolecular complexes, providing deep insights into infection pathways. Neutrons and X-rays can be applied in a complementary mode, as is the case for the joint SANS-SAXS proposal between the ESRF and the ILL.This strategic plan aims to advance the field by providing an EOSC-based platform, enabling FAIR data and software, unified data processing pipelines featuring robust scaling algorithms for the two different sources, supporting reproducibility and automated validation, and integrating with other relevant structural databases (e.g., electron microscopy/tomography or protein structural and ligand databases). HTML XML PDF
      PubDate: Tue, 5 Dec 2023 12:25:21 +0200
       
  • BatchConvert: A command-line tool for parallelised conversion of image
           collections into the standard bioimage file formats OME-TIFF and OME-Zarr.
           

    • Abstract:
      DOI : 10.3897/arphapreprints.e116669
      Authors : Bugra Özdemir, Aastha Mathur, Johanna Bischof, John E. Eriksson, Jean-Karim Hériché, Josh Moore, Christian Tischer, Antje Keppler : File formats incompatibility has become a major obstacle in biological imaging, complicating downstream processes such as image processing and analysis. One way to address this challenge is to convert the acquired image data into standard image file formats. Here we introduce BatchConvert, a command line tool for parallelised conversion of image collections into OME-TIFF or OME-Zarr using the workflow management system Nextflow. BatchConvert offers functionalities such as remote input-output support, optional execution on Slurm clusters and pattern-based filtering of input files. Conversion can be coupled to image concatenation, allowing selected images to be merged along specified dimensions. Support for remote locations includes an option to submit the output data to S3-compatible object stores or public archives such as BioImage Archive. Overall, BatchConvert is a flexible tool for researchers who are routinely managing and analysing large multidimensional image data that is either locally or remotely stored. HTML XML PDF
      PubDate: Tue, 5 Dec 2023 12:20:54 +0200
       
  • A Jupyter notebook to explore protein conformations: An output of PaNOSC
           SP8 case

    • Abstract:
      DOI : 10.3897/arphapreprints.e116668
      Authors : Irina Safiulina, Miguel Angel Gonzalez, Paolo Mutti, Giuseppe La Rocca, Enol Fernández : Small-angle scattering techniques are widely employed across scientific communities to elucidate the morphology, spatial distribution, and uniformity of particles within liquid solutions. Recent advancements and accelerated data acquisition capabilities have extended the utility of these techniques to probe the dynamic behavior of particles over time. Small-Angle X-ray Scattering (SAXS) and Small-Angle Neutron Scattering (SANS) emerge as powerful tools in this realm, enabling the investigation of phenomena such as the time-dependent release of genomes from phages, the comprehensive exploration of viral life cycles, and the assembly dynamics of macromolecular complexes. This tandem application of X-rays and neutrons, exemplified by the collaborative SANS-SAXS initiative between the European Synchrotron Radiation Facility (ESRF) and the Institut Laue-Langevin (ILL), yields complementary insights into complex infection pathways.In this report, we present the outcomes of a software development project undertaken as part of Science Project 8: "PaNOSC Dynamics of Biological Processes" within the EOSC Future framework. The project's deliverables include a Jupyter Notebook and accompanying Python scripts, specifically sas_helper.py. The primary objective of Science Project 8 is to expand the accessibility of open Small-Angle Neutron Scattering (SANS) and Small-Angle X-ray Scattering (SAXS) data to a broader scientific community. This endeavor underscores the profound transformative potential of open-science data analysis within the European Open Science Cloud (EOSC) framework while advocating for the adoption of FAIR (Findable, Accessible, Interoperable, and Reusable) principles in scientific research.  HTML XML PDF
      PubDate: Tue, 5 Dec 2023 12:15:12 +0200
       
  • DDI-CDI-Workflow description of the EOSC Future WP6 Task 3, Science
           Project 9 ‘Climate Neutral and Smart Cities’

    • Abstract:
      DOI : 10.3897/arphapreprints.e116667
      Authors : Benjamin Beuster, Hilde Orten : The paper focuses on the technical workflow description of EOSC Future’s Science Project 9 'Climate Neutral and Smart Cities', using reputable data sources such as the European Social Survey (ESS), the European Environmental Agency (EEA), and Copernicus ERA5.A significant contribution of this project to the European Open Science Cloud (EOSC) is its demonstration of cross-domain data integration using the DDI-CDI metadata standard. This serves as a practical example of how the DDI-CDI Process model can offer a standardised methodology for detailing integration processes, thereby ensuring clarity for researchers dealing with integrated data and computed variables.The paper outlines the key elements of the CDI-Process model selected for this approach, which includes around 10 classes such as 'Activity,' 'Step,' and 'Parameter.' These classes form the structural framework for the data integration steps.Additionally, a tool developed under the project visualises the entire workflow as outlined in the CDI workflow description HTML XML PDF
      PubDate: Tue, 5 Dec 2023 12:04:08 +0200
       
  • Water-Ecosystems-Food nexus security achievement in the context of climate
           change: the case study of an agricultural Mediterranean Basin, Greece

    • Abstract: Research Ideas and Outcomes 9: e116070
      DOI : 10.3897/rio.9.e116070
      Authors : Dimitrios Malamataris, Anastasia Tsavdaridou, Dimitra Banti, Athanasios Malliaras, Apostolos Karalis, Nikolaos Theocharis, Christodoulos Michos, Antonios Mazaris : Natural resources conservation is considered indispensable for a sustainable future. A thorough managerial analysis of the current and future conservation and availability to meet future demands is both necessary and challenging. As water of adequate quantity and good quality is required for a favourable condition of natural ecosystems and for agricultural production, a comprehensive analysis which would consider hydrological, environmental and agricultural dimensions is needed to properly address their interactions and potential impacts. This study presents a Water-Ecosystems-Food (WEF) nexus methodological flamework aiming at identification and mitigation of critical challenges. The framework is tested in a highly productive water basin in north Greece, the Kokkinorema River Bain, which is also characterised by intense agriculture practices. The presented methodological approach was developed in the context of a natural resources sustainability scheme adapted by the national funded AgroClim project. The selection and prioritisation of the most efficient measures, including Nature-based Solutions, would be driven by a Decision Support System (DSS) tool which will feed upon ecological, social, economic and legislative information. The proposed DSS will also incorporate future climate scenarios to evaluate and address expected future water scarcity, ecosystems degradation and reduced agricultural productivity issues. The proposed methodology for addressing nexus challenges could be transferred to any other natural resources-stressed water basin with similar characteristics. HTML XML PDF
      PubDate: Wed, 29 Nov 2023 12:15:07 +020
       
  • Workshop on 3D mapping of habitats and biological communities with
           underwater photogrammetry

    • Abstract: Research Ideas and Outcomes 9: e115796
      DOI : 10.3897/rio.9.e115796
      Authors : Loïc Van Audenhaege, Vincent Mahamadaly, David Price, Alexandre Sneessens, Hayley Cawthra, Clément Delamare, Valentin Danet, Simon Delsol, Rodolphe Devillers, Iason-Zois Gazis, Isabel Urbina-Barreto : For the past decades, photogrammetry has been increasingly used for monitoring spatial arrangement or temporal dynamics of submerged man-made structures and natural systems. As photogrammetry remains a nascent technique for data collection in the underwater environment, acquisition workflows have evolved constrained by specific methodological practicalities (e.g. euphotic environments vs. deep-sea waters). The annual GeoHab conference gathers a world-wide range of scientists interested in mapping and is, therefore, an adequate event to set up a state-of-the-art workshop on (underwater) photogrammetry. More specifically, a preliminary survey identified the overall lack of photogrammetry knowledge from the audience. A programme was conceptualised to explore within a day theoretical concepts, sampling design and practicalities and a wide range of case studies in various underwater environments. Furthermore, we provided manual training on data acquisition and processing. In overall, a post-survey demonstrated the audience’s satisfaction despite a remaining lack of confidence for implementing their own photogrammetry studies. As this workshop gathers a diversity of materials and a training relevant for a scientific audience, it sets the stage for a reproducible event and leaves room for future improvements. Finally, it provided relevant materials and discussions that enabled us to identify the aspects limiting photogrammetry methodology across scientific applications and institutes, in order to work towards standardisation. HTML XML PDF
      PubDate: Wed, 29 Nov 2023 12:01:59 +020
       
  • Anticipating the chemical compositions of organisms across the tree of
           life.

    • Abstract:
      DOI : 10.3897/arphapreprints.e116230
      Authors : Marco Visani : This study is centered on Natural Products (NPs) - specific chemicals synthesized by living organisms. These NPs hold significant importance in various domains, notably medicine, agriculture, and ecology. A primary resource for our research is the LOTUS database, which catalogues a vast array of NPs and their occurrence. Yet, a gap exists: there are no existing model to predict the occurrence of these NPs across different species.In our initial strategy, the occurrence of natural products was viewed as a collection of observations and their associated variables. Although simple, this strategy immediately showed its limits when dealing with the complex nature of NPs. We switched to an advanced graph-based method after seeing the necessity for a more thorough strategy to accurately represent the intricate interactions governing NPs expression. When considering species in a phylogeny or molecular pathways, the graph-based method perceives data as a network of connected entities, offering a far more logical and natural way of thinking. By employing this better methodology, we have developed a more effective approach for investigating the intricate world of Natural Products. We hope that this strategy will open up new research directions and possibly result in ground-breaking NP-related findings. HTML XML PDF
      PubDate: Mon, 27 Nov 2023 12:24:35 +020
       
  • SEADETECT: developing an automated detection system to reduce whale-vessel
           collision risk

    • Abstract: Research Ideas and Outcomes 9: e113968
      DOI : 10.3897/rio.9.e113968
      Authors : Silvia Paoletti, Bob Rumes, Nino Pierantonio, Simone Panigada, Romain Jan, Thomas Folegot, Anita Schilling, Nicolas Riviere, Vincent Carrier, Antoine Dumoulin, David Van Hamme, Gildas Marquis-Laisné, François-Antoine Bruliard, Félix Petitpierre, Damien Demoor : With the continuous intensification of marine traffic worldwide, whale-vessel collisions at sea (or “ship strikes”) have become one of the primary causes of mortality for cetaceans and a widely recognised cause of concern for human safety and economic losses. The Mediterranean Sea is a global hotspot for whale-vessel collisions, with one of the highest rates involving large cetaceans, especially the endangered fin whales (Balaenoptera physalus) and sperm whales (Physeter macrocephalus). Evidence indicates that both species are experiencing higher chances of a fatal collision than what predictions have estimated so far, with ship strikes being the main human-induced threat in the area. Regional and international organisations have stressed the need to address the issue by investigating the projected impacts of ship strikes on whale populations and by identifying possible mitigation measures to reduce chances of collision. Amongst the most popular and feasible options, there is the improvement of animal detection during navigation. Here, we present SEADETECT, a LIFE project that aims at developing an automated detection system to reduce vessel collision risk with marine mammals and unidentified floating objects (UFOs), combining state-of-the-art and novel technologies with existing approaches in the study of large whale ecology. This detection system consists of three elements; an automated onboard detection system composed of several sensors, a real-time passive acoustic monitoring (PAM) network at sea and a real-time detection-sharing and alert system (REPCET®). In this paper, we propose the development of a mitigation measure framework tailored for the issue of collision with fin and sperm whales in the north-western Mediterranean Sea, but that has the transferability features necessary for its application in other high-risk areas for ship strikes worldwide. HTML XML PDF
      PubDate: Mon, 27 Nov 2023 11:05:24 +020
       
  • Enhancing Small-Medium IsLands resilience by securing the sustainability
           of Ecosystem Services: the SMILES Cost Action

    • Abstract: Research Ideas and Outcomes 9: e116061
      DOI : 10.3897/rio.9.e116061
      Authors : Ioannis Vogiatzakis, Mario Balzan, Evangelia Drakou, Stelios Katsanevakis, Emilio Padoa-Schioppa, Elli Tzirkalli, Savvas Zotos, Xana Álvarez, Mart Külvik, Catarina Fonseca, Aristides Moustakas, Javier Martínez-López, Peter Mackelworth, Dejan Mandzukovski, Liana Ricci, Bojan Srdjevic, Mirela Tase, Theano Terkenli, Shiri Zemah-Shamir, George Zittis, Paraskevi Manolaki : European islands are hotspots of biological and cultural diversity, which, compared to mainland, are more vulnerable to climate change, tourism development, uncontrolled land-use changes and the consequences of financial crisis. These drivers of change have increasingly resulted in severe impacts on socio-economic and environmental parameters. Projected climate, land-use and socio-economic change will impact on islands’ biodiversity, ecosystem services and, in turn, on the quality of life of island inhabitants. Even if the existing methods can adequately predict the abovementioned changes of the larger islands, this is not the case for small and medium-size islands, where there is a need for refinement. Although ecosystem services (ES) assessments have been carried out worldwide in different geographical areas, islands are still under-represented. Despite the recognised islands’ importance and vulnerability, efforts to date have focused solely on the pressures they face. Still, we know little about ES supply, flow and demand and their spatio-temporal variability, whilst integrated approaches that consider ES cross-island realms (terrestrial, marine and their interface) remain scarce. Even more under-represented are studies that explore the telecoupled relationship amongst islands and their mainland counterparts. Moreover, the current conceptual approaches guiding ES mapping and assessment need further refinement to account for the complex manifestations of nature and culture arising from peoples’ interaction with island spaces. This paper discusses the creation of a platform for coordinated interdisciplinary research on several aspects of mapping and assessment of ES in small and medium European islands in order to synthesise and strengthen the knowledge base for conservation of island realms and contribute to their sustainable development. HTML XML PDF
      PubDate: Thu, 23 Nov 2023 14:31:30 +020
       
  • Building an atlas of knowledge for invasion biology and beyond! 2nd
           enKORE-INAS Workshop

    • Abstract: Research Ideas and Outcomes 9: e115395
      DOI : 10.3897/rio.9.e115395
      Authors : Maud Bernard-Verdier, Tina Heger, Daniel Mietchen, Camille Musseau, Marc Brinner, Alexander Hillig, Peter Kraker, Sophie Lokatis, Ana Luisa Nunes, Nils Scheidweiler, Markus Stocker, Roxane Vial, Lars Vogt, Sven Bacher, Eya Baklouti, Harsh Bardhan Gupta, Jean-Nicolas Beisel, Sandro Bertolino, Elizabeta Briski, Gustavo Castellanos-Galindo, Franck Courchamp, Ella Daly, Wayne Dawson, James Dickey, Thomas Evans, Yuval Itescu, Birgitta Koenig-Ries, Lohith Kumar, Sabrina Kumschick, Laura Meyerson, Zarah Pattison, William Pfadenhauer, David Renault, Fiona Rickowski, Florian Ruland, Conrad Schittko, Tanja Straka, Florencia Yannelli, Jonathan Jeschke : With the exponential increase in scientific publications, new conceptual and technological tools are needed to help scientists, students, managers and policy-makers to navigate and digest current scientific knowledge. Hi Knowledge is an initiative to synthesise and visualise scientific knowledge, with an initial focus on invasion biology that is currently expanding to include urban ecology, restoration ecology and freshwater ecology. In a workshop on 5-6 June 2023 in Berlin, Germany, we discussed and tested a collection of new open tools related to this initiative in order to publish, curate, explore and synthesise concepts and results in ecology. Three main themes were discussed during in-person breakout group sessions: (1) building and using open tools for knowledge curation, exploration and synthesis; (2) making open knowledge searchable and machine friendly by improving modelling and annotation of scientific knowledge; and (3) extending beyond the field of invasion biology. We report on the discussions of all twelve sessions pertaining to these themes. A main underlying goal of our workshop was to build a community of scientists involved in openly co-designing and using these tools. Overall, the participants were enthusiastic about the usefulness of these tools and discussions gravitated around improving them and finding strategies to scale-up participation by the community. Follow-up user tests and publications are planned for individual tools and topics. HTML XML PDF
      PubDate: Wed, 22 Nov 2023 09:32:49 +020
       
  • Distributed Team Working - Approaches for DiSSCo

    • Abstract: Research Ideas and Outcomes 9: e115454
      DOI : 10.3897/rio.9.e115454
      Authors : Helen Hardy, Lisa French, Josh Humphries, Sabine von Mering, Peter Giere, Frederik Berger, Anne Koivunen, Jonas Grieb, Martin Vipp, Vincent Smith : As a highly decentralised research infrastructure, the Distributed System of Scientific Collections (DiSSCo) will need to develop cross-institutional teams, adopting work practices where individual staff are intensively working collectively on common tasks in a distributed environment. These flexible and distributed working practices will be essential to the delivery of the research infrastructure across a wide range of delivery partners and a geographically dispersed set of scarce resources and skills, particularly in more technical roles. Since work to consider secondment and distributed working in DiSSCo was first envisaged, there has been a step change in distributed working owing to the Covid-19 pandemic and lockdowns or other restrictions to where work could take place. This report examines distributed team working practices and how they have changed, through interviews with a range of key roles across DiSSCo Prepare institutions. It briefly examines key project management and technical team delivery techniques. It documents how some of these approaches have been piloted within DiSSCo Prepare for the development, testing and delivery of DiSSCo Policy and Digital Maturity tools. Finally, bringing this together with previous work on secondment policies and practices for DiSSCo, we make recommendations about how secondment and distributed team working can be approached to enhance DiSSCo capabilities and the likelihood of successful implementation of the research infrastructure. HTML XML PDF
      PubDate: Mon, 20 Nov 2023 10:22:14 +020
       
  • Joint statement by CETAF, SPNHC and BHL on DATA within scientific
           publications: clarification of [non]copyrightability

    • Abstract: Research Ideas and Outcomes 9: e115466
      DOI : 10.3897/rio.9.e115466
      Authors : Laurence Benichou, Donat Agosti, Willi Egloff, Elisa Hermann, Mariko Kageyama, Patricia Mergen, Constance Rinaldo, Jutta Buschbom : The EU and other states have made legislative efforts to clarify data mining in copyrightable works, but the situation remains obscure and confusing, especially in a globalised field where international legislation can contribute to opacity. The present paper aims at asserting a common position of three communities representing biodiversity sciences and data specialists on this issue and to propose common and best practice guidelines so that they become universally accepted rules.As scientific data users, we take the standpoint that scientific data are not copyrightable and, furthermore, they can be accessed, shared and reused freely. Thus, once legal access has been gained to copyrighted publications, the data within those scholarly publications can be considered to be open data that is freely extractable. This set of recommendations has been reached specifically for scientific use and societal benefits. HTML XML PDF
      PubDate: Mon, 20 Nov 2023 10:05:09 +020
       
  • Leaping into the future: Current application and future direction of
           computer vision and artificial intelligence in marine sciences in South
           Africa

    • Abstract: Research Ideas and Outcomes 9: e112231
      DOI : 10.3897/rio.9.e112231
      Authors : Charlene da Silva, Toufiek Samaai, Sven Kerwath, Luther Adams, Katie Watson, Anthony Bernard, Grant van der Heever, Andrea Angel, Stefan Schoombie, Guilherme Frainer, Mari-Lisa Franken, Adam Rees, Angus Paterson : The inaugural Computer Vision for Marine Scientists workshop was held at the 17th South African Marine Science Symposium, with the primary goal of establishing a community of practice for computer vision (CV) in marine sciences in South Africa. The one-day hybrid event, attended by 97 people, covered the principles of artificial intelligence (AI) techniques required for evaluating video and photographic imagery through presentations, practical demonstrations and interactive discussions. The recordings of the workshop sessions are available online, providing an opportunity to reach marine researchers both regionally and globally. The workshop highlighted that many scientists have begun to incorporate CV and AI into their research activities; however, there is little national coordination and the extent of research is lagging behind international trends. To support image-based AI research in South Africa, it is critical to maintain and expand the network established during the workshop. This would enable a more collaborative and successful approach to incorporating CV technology in the country's marine research initiatives, ultimately leading to ground-breaking discoveries and advancements in the field. HTML XML PDF
      PubDate: Thu, 16 Nov 2023 10:01:13 +020
       
  • D3.1 Framework for developing funding and finance arrangements for coastal
           restoration

    • Abstract:
      DOI : 10.3897/arphapreprints.e115410
      Authors : Fausto Favero, Lieke Hüsken, Jochen Hinkel, Heleen Vreugdenhi, Umberto Pernice, Michael Sedlmeier : This deliverable is the first contribution of Work Package 3 to the REST-COAST Project. The overarching purpose of REST-COAST is to provide the tools to address some of the key challenges faced by coastal ecosystems restoration. To achieve this objective, REST-COAST will improve coastal restoration practice and techniques through new hands-on restoration pilot projects, co-design effective governance arrangements and policies, and generate new tools and data for risk reduction assessment. In addition to these activities, Work Package 3 will design innovative financial arrangements and bankable business plans to support the implementation and thescaling up of coastal ecosystem restoration. HTML XML PDF
      PubDate: Wed, 8 Nov 2023 10:20:26 +0200
       
  • D6.12 Website and Branding

    • Abstract:
      DOI : 10.3897/arphapreprints.e115409
      Authors : Gabriela Popova, Iliyana Demirova, Boris Barov : The main goals of WP6 Dissemination, exploitation and social transformation tools, are to establish and maintain a distinct project identity, as well as to maximise the impact of project results by marketing andcommunicating them to stakeholders and the broader public. To ensure the efficient communication, Pensoft has developed a number of promotional materials reflecting the REST-COAST corporate identity, aswell as a project website. HTML XML PDF
      PubDate: Wed, 8 Nov 2023 10:18:45 +0200
       
  • D6.5 Integration guide for using common CGE/PE models with BESTMAP
           models

    • Abstract:
      DOI : 10.3897/arphapreprints.e115391
      Authors : Ruth Delzeit, Simone Markoff, Alena Schmidt, Birgit Mueller, Meike Will, Chunhui Li, Jodi Gunning, Guy Ziv : This deliverable report provides an integration guide on how information gained in BESTMAP’s agent-based model can be used in the standard economic model to improve the assessment of agricultural policies in the European Union. First, the models used in the BESTMAP are explained. The integration guide discusses in detail the preconditions and challenges when linking agent-based models with standard economic models such as partial and general equilibrium models. As a result of an expert workshop, six challenges are identified. The report also presents suggestions on how to make use of the finding and presents a way forward to integrate the two types of models. HTML XML PDF
      PubDate: Wed, 8 Nov 2023 10:06:19 +0200
       
  • D6.3 Communication Plan and Dissemination Plan

    • Abstract:
      DOI : 10.3897/arphapreprints.e115390
      Authors : Milica Trajković, Dajana Vujaklija, Pavel Stoev, Anna Sapundzhieva, Guy Ziv, Jodi Gunning : Deliverable 6.3 Communication and Dissemination plan comprises actions, tools and channels to be used throughout the BESTMAP project scope. The purpose of this document is to outline the strategy, to define means of communication, tools and actions that will be done within the BESTMAP project in order to reach a wide range of stakeholders. This plan is a living document and will be officially updated in month 24 (D6.8). The first chapter of the Communication and Dissemination Plan explains the wider context of the project and highlights how the project duration and geographical scope impact the communication and dissemination activities. The second chapter presents communication and dissemination strategy including definition of objectives and target audiences, communication tools and key messages. The third chapter presents AGRIMODELS cluster, while the fourth chapter explains Social Media Strategy. The aim of the fifth chapter is to emphasize the importance of project partners’ involvement in communication and dissemination activities, and the sixth chapter showcases the list of relevant conferences for presentation of the BESTMAP project. Seventh chapter presents an action plan for communication and dissemination activities while a list of references can be found in chapter eight. HTML XML PDF
      PubDate: Wed, 8 Nov 2023 10:00:12 +0200
       
  • D4.2 Trade-off/synthesis analyses including spatial co-occurrence of ESS
           / biodiversity socio-economic

    • Abstract:
      DOI : 10.3897/arphapreprints.e115389
      Authors : Stephanie Roilo, Anna Cord, Michael Beckmann, Anne Paulus, Katharina Schneider, Predrag Lugonja, Arjan Gosal, Rosemary Wool, George Breckenridge, Jodi Gunning, Guy Ziv : This document describes the interrelationships between the ecosystem services, biodiversity and socio-economic outputs modelled in the Work Package 3 (WP3), to identify bundles of co-occurring services. Furthermore, this document presents an analysis of how different types of Agri-Environmental Measures (AEM) drive trade-offs and synergies among different services. The analysis spans two AEM adoption scenarios, one without AEM and one reflecting the current AEM adoption levels, for all five Case Studies (CS) of BESTMAP. HTML XML PDF
      PubDate: Wed, 8 Nov 2023 09:50:04 +0200
       
  • D5.4 Mapping of vegetation indices and metrics, and their utility in
           FSA mapping at CS scale

    • Abstract:
      DOI : 10.3897/arphapreprints.e115388
      Authors : Guido Riembauer, Markus Metz, Guy Ziv, Jodi Gunning, James Bullock, Paul Evans, Tomáš Václavík, Fanny Langerwisch, Marek Bednář, Sanja Brdar, Predrag Lugonja : This deliverable provides an overview of all work conducted in the context of Activity 5.3.1 (Developing remote sensing indicators) with respect to Farming System Archetype (FSA) Mapping (Task 5.3). This work is based on the FSA definition and mapping in ‘D2.2 - Conceptual Framework’ and ‘D3.5 - Farming System Archetypes for each CS’ and investigates the potential of remote sensing methods to inform different dimensions of FSAs. Findings from this analysis will contribute to the BESTMAP roadmap (Task 5.4). Specifically, methodologies for crop type mapping, crop yield estimation, and field boundary mapping are investigated in different case study regions and their relevance for FSAs are shown. HTML XML PDF
      PubDate: Wed, 8 Nov 2023 09:40:58 +0200
       
  • D3.5 Farming System Archetypes for each CS

    • Abstract:
      DOI : 10.3897/arphapreprints.e115387
      Authors : Fanny Langerwisch, Tomáš Václavík, Marek Bednář, Guy Ziv, Jodi Gunning, Arjan Gosal, Anne Paulus, Sanja Brdar, Predrag Lugonja, Stefanija Stojkovic, Stephanie Roilo, Anna Cord : This deliverable provides an overview of the methods and data used for developing the Farming System Archetypes (FSAs) in the five case studies - Humber, Mulde, SouthMoravia, Bačka and Catalonia. Additionally, it discusses limitations as well as problems and presents solutions. The FSAs are a generalized typology of farming systems that are assumed to have similar response to policy change. FSAs are a major component of the BESTMAP modelling architecture because they provide linkages between many aspects of the project, especially connecting the biophysical and agent-based modelling in the case studies (CS), based on local data (e.g. IACS/LPIS, for explanation see Methodology), with the modelling of policy effects at the EU level, based on FADN micro-data within the FADN regions. The FSA framework defines the main farm characteristics determined by two main dimensions: firstly farm specialization and secondly economic size, both calculated and mapped for each farm in the CSs. ‘Farmer agents’ who belong to the same FSA are then assumed to have similar decision patterns regarding the adoption of agri-environmental schemes, based on the relationships revealed in the CS agent-based models. HTML XML PDF
      PubDate: Wed, 8 Nov 2023 09:36:55 +0200
       
  • D3.4 Summaries of data, obstacles and challenges from interview
           campaigns

    • Abstract:
      DOI : 10.3897/arphapreprints.e115386
      Authors : Felix Wittstock, David Hötten, Sofia Biffi, Cristina Domingo-Marimon, 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 aims at documenting the BESTMAP interview campaigns carried out to obtain data on farmers’ decision-making with regard to agri-environmental schemes (AES). 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: Wed, 8 Nov 2023 09:30:49 +0200
       
  • D2.4 Economic scenarios outputs based on policy workshops

    • Abstract:
      DOI : 10.3897/arphapreprints.e115385
      Authors : Ruth Delzeit, Simone Markoff, Sneha Thube : This deliverable report elaborates on the development and results of a set of policy scenarios that represent the outcomes of Task 2.4. After clarifying the objective of the deliverable, key features of the DART-BIO model are explained, followed by a definition of two biofuel scenarios in which the EU’s Renewable Energy Directive (RED) and in addition global biofuel policies are implemented. Further, two specifications of international climate policies are defined and their implementation explained. In the result section, the impacts of these policies on the EU’s agricultural markets and land-use change are illustrated. The results show that with the RED including a ban on palm-oil based biodiesel in place, EU’s rapeseed production and therewith also land used to cultivate rapeseed rises, while also imports of other vegetable oils increase. Land-use change outside the EU is limited. Adding biofuel policies in non-EU regions causes global land use-change towards more cropland used for biofuel feedstock (e.g. soybeans, palm fruit) at the expense of pasture land and crops not used for biofuel production. When implementing climate policies, the conversion of pasture land on the global average is reduced. Depending on the specification of climate policies (having a CO2 or all GHG emission reduction target), land-use change is affected differently. When only considering CO2 emissions, more biofuels and feedstock are imported into the EU, resulting in less area (-3 percentage points) devoted to rapeseed production compared to a situation with biofuel policies but no climate policy. Adding all GHG emissions to the reduction targets leads to a reduction of 1 percentage point in rapeseed areas in the EU since emission pricing reduces demand for livestock production. The results can serve as input into Agent-Based Modelling in case studies across the EU, changing land-use patterns and opportunity costs of participation in agri-environmental schemes. HTML XML PDF
      PubDate: Wed, 8 Nov 2023 09:26:43 +0200
       
  • D2.3 Dashboard design prototype

    • Abstract:
      DOI : 10.3897/arphapreprints.e115384
      Authors : Cristina Domingo-Marimon, Joan Masó Pau, Guy Ziv, Jodi Gunning : Dashboards for data visualisation and decision-making are information management tools that visually display, analyse and provide metrics of data, for better decisions and understanding improvement.Dashboards provide critical reporting of spatialised data and associated metrics information and are essential for displaying model results, guiding decisions and better navigating the landscape. The main aim of the dashboards is to quickly gain insights into the most relevant results of the data displayed. The main added value for users is that information is transformed into knowledge which is useful for decisions on policy making. HTML XML PDF
      PubDate: Wed, 8 Nov 2023 09:20:38 +0200
       
  • D2.2 BESTMAP Conceptual Framework Design & Architecture

    • Abstract:
      DOI : 10.3897/arphapreprints.e115383
      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. An update of the framework will be provided later in the project in Deliverable 2.4. 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: Wed, 8 Nov 2023 09:10:34 +0200
       
  • D1.2 Data Management Plan

    • Abstract:
      DOI : 10.3897/arphapreprints.e115382
      Authors : Guy Ziv, Jodi Gunning, Anna Cord, Michael Beckmann, Anne Paulus, Tomáš Václavík, Cristina Domingo-Marimon, James Bullock, Paul Evans, Milica Trajković : This document is the first version of the Data Management Plan of the H2020 BESMAP project. The Data Management Plan is intended as a living document and updated versions of this document will be produced in month 18 (D1.4) and month 36 (D1.6). The scope of the Data Management Plan is to describe the data management life cycle of all data sets that will be collected, processed or generated by the BESTMAP project. This document outlines how research data will be handled during the BESTMAP project, and after the project is completed. This Data Management Plan describes what data will be collected, processed or generated and what methodology and standards will be applied, whether and how this data will be shared and/or made open, and how it will be curated and preserved. HTML XML PDF
      PubDate: Wed, 8 Nov 2023 09:06:25 +0200
       
  • D1.1 BESTMAP website and web-based within-project communication
           system

    • Abstract:
      DOI : 10.3897/arphapreprints.e115381
      Authors : Pavel Stoev, Anna Sapundzhieva, Teodor Georgiev, Margarita Grudova, Guy Ziv, Jodi Gunning : To promote and disseminate the BESTMAP research across stakeholders and the general public, and to raise awareness of the project findings, BESTMAP launched a website at the initial phase of the project. This report describes in detail the purpose, creation process and content of the BESTMAP website – the project’s key tool for successful dissemination, communication and knowledge transfer. The deliverable also describes the current and future implementation and maintenance of the website. HTML XML PDF
      PubDate: Wed, 8 Nov 2023 09:01:49 +0200
       
  • The impacts of multiple stressors on managed bees: Novel insights from the
           PoshBee project

    • Abstract:
      DOI : 10.3897/arphapreprints.e115172
      Authors : Mark Brown, Matthias Albrecht, Pilar De la Rúa, Sara Hellström, Alexandra-Maria Klein, Denis Michez, Francesco Nazzi, Robert Paxton, Edward Straw, Dimitry Wintermantel, Simon Potts : Managed bees and other pollinators are exposed to a wide variety of stressors and these often act in combination. Historically, most risk assessments and research have focused on the impacts of individual stressors on honey bees. However, there is broad scientific consensus that there is a need for a systems-based risk assessment approach and a post-approval monitoring system. This should consider: multiple interacting stressors; a variety of pollinator species (including different subspecies, sexes, castes and life history stages); field studies as well as laboratory studies; and a diversity of end-points (molecular, physiological, behavioural, developmental, reproductive and colony health). The PoshBee project has made a significant step in our understanding of how the interactions between agrochemicals, pathogens and nutrition impact different bee species. HTML XML PDF
      PubDate: Mon, 6 Nov 2023 08:49:50 +0200
       
  • Reuse and Reproducibility: Describing Cross-Domain Research Data in the 
           Science Project Climate Neutral and Smart Cities

    • Abstract:
      DOI : 10.3897/arphapreprints.e115047
      Authors : Arofan Gregory, Joachim Wackerow, Hilde Orten : The Climate Neutral and Smart Cities project is part of the EOSC Future WP 6.3, exploring the best approaches for sharing data within cross-domain research projects. This paper looks at the implications for metadata exchange in a cross-domain research project, as explored in the project prototype. Cross-domain standard metadata is meeded to support collaborative research teams combining a mix of expertise, particularly around data lineage.  HTML XML PDF
      PubDate: Mon, 6 Nov 2023 08:34:38 +0200
       
  • Biospeckle Laser On Clouds, a digital gateway aiming at collaborative
           research improvement

    • Abstract: Research Ideas and Outcomes 9: e114736
      DOI : 10.3897/rio.9.e114736
      Authors : Roberto Braga, Robson Godinho : The Dynamic Laser Speckle (DLS) is a photonic phenomenon transformed into a technique to monitor tiny changes in many materials, particularly in biological ones (Biospeckle Laser – BSL). Its high sensitivity is key to monitor tiny changes in the tissues that can characterise biological features in medical and in agricultural samples. This work aimed to develop an environment at the world-wide-web to share raw data of BSL and to offer access to an interactively online analysis with tutorials. The gateway designed was implemented using PHP and JavaScript tools solving the challenges of managing data (images) and online interactive use. The result was an easy-to-use environment boosting the BSL research. The early results presented thousands of accesses and of more than one hundred different users from all around the world. HTML XML PDF
      PubDate: Fri, 3 Nov 2023 11:16:58 +0200
       
  • Digitisation of natural history collections: criteria for prioritisation

    • Abstract: Research Ideas and Outcomes 9: e114548
      DOI : 10.3897/rio.9.e114548
      Authors : Louise Ahl, Luca Bellucci, Philippa Brewer, Pierre-Yves Gagnier, Elspeth Haston, Laurence Livermore, Sofie De Smedt, Helen Hardy, Henrik Enghoff : There are approximately 1.5 billion specimens kept in European Natural History Collections. The mission for the Distributed System of Scientific Collections (DiSSCo) is to unite all these specimens into a one-stop e-science infrastructure of digital specimens. This is a monumental digitisation task and criteria for how to prioritise this effort are, therefore, crucial for the success of the project. In this report, we have reviewed the literature and designed and conducted surveys of the digitisation plans and criteria used by DiSSCo Partners to understand the prioritisation criteria used in the digitisation of natural history collections. As an attempt to provide some guidance for the digitisation of specimens, we suggest that an organisation (e.g. DiSSCo or an individual institution) that is planning to digitise natural history collections considers four categories of prioritisation criteria: Relevance, Data quality, Cost and Feasibility. HTML XML PDF
      PubDate: Thu, 2 Nov 2023 09:17:07 +0200
       
  • The Nekton Maldives taxonomic workshop: Exploring the biodiversity of
           shallow, mesophotic and deep-sea communities in Maldives

    • Abstract: Research Ideas and Outcomes 9: e114370
      DOI : 10.3897/rio.9.e114370
      Authors : Mohamed Ahusan, Nuria Rico-Seijo, Farah Amjad, Erika Gress, Shafiya Naeem, Toufiek Samaai, Kaveh Samimi-Namin, Lucy Woodall, Paris Stefanoudis : The Nekton Maldives Taxonomic Workshop took place at the Maniyafushi Research Station in the Maldives between 12 and 23 February 2023. This workshop had two primary objectives. Firstly, it aimed to identify species from biological samples and underwater imagery collected during the Nekton Maldives Mission in 2022. Secondly, it sought to facilitate training and knowledge exchange sessions between early career researchers from the Maldives and international taxonomists. These sessions were designed to share knowledge and introduce fundamental taxonomy concepts and enhance practical identification skills for common reef benthic groups and major zooplankton taxonomic groups. A total of 24 people from 10 different countries were directly or indirectly involved with the workshop comprising nine taxonomic experts, eleven trainees and four organisers. Collectively, we identified 278 biological specimens including potentially undescribed species of hydroids, black corals, sponges and octocorals, 318 morphotypes for underwater footage and zooplankton composition congruent with previous reports from the Indian Ocean Region. Next steps will involve depositing the specimens into a more a permanent facility to facilitate the process of specimen description and knowledge transfer. HTML XML PDF
      PubDate: Wed, 1 Nov 2023 14:13:38 +0200
       
  • Milestone MS32 The design and prototype of a workflow integrating
           Wikidata into validation and linking

    • Abstract:
      DOI : 10.3897/arphapreprints.e114920
      Authors : Mathias Dillen, Andreas Plank : In this task, the aim is to develop a workflow that should facilitate the linking process of collector name strings to PIDs for those collectors. Such a workflow should help scale up the number of links being made, make the process more efficient and should take advantage as much as possible of existing work and infrastructures, so as not to reinvent the wheel. As such, the work can be roughly split into a few subtasks:- Make existing linking workflows more easily implementable in other contexts and by other infrastructures. This includes finding ways for such workflows to produce links that can easily be published, i.e. in a standardised format compatible with existing infrastructure. The suitability of different infrastructures for making established links available should also be assessed.- Establish, document and improve the comprehensiveness, findability and interoperability of the content in PID-minting resources, in particular Wikidata as it can be edited openly.- Refine the decision making process of establishing links, by implementing and improving the methods that can be used to validate potential links.In this document, the focus lies on linking people. We will propose a workflow to 'roundtrip' links established through the Bionomia platform back to the collections holding the attributed specimens, as well as making them available for use by other BiCIKL infrastructures. We will also refine existing automated linking workflows and pilot the new functionalities on the (botanical) collections of the task partners. These refinements will be influenced by an assessment of the current state of Wikidata, investigated through shape expressions constructed from commonly used queries and from Wikidata records which have been linked in previous efforts such as the Botany Pilot, Bionomia and published specimen data to GBIF. HTML XML PDF
      PubDate: Tue, 31 Oct 2023 12:03:33 +020
       
  • How FDO attributes can support machine- and human-readability' - a
           description along three examples

    • Abstract: Research Ideas and Outcomes 9: e108737
      DOI : 10.3897/rio.9.e108737
      Authors : Ulrich Schwardmann, Tibor Kálmán : Based on the notion of a FAIR Digital Object (FDO) record, which consists of key-value pairs as attributes that are precisely defined in a Data Type Registry and selected in a profile, we show three examples of FDOs from different viewpoints how FDO records can be implemented as Handle PID records. As references to the attribute definitions, the keys determine the value space of the attribute. In the first two examples, the profiles enable human-readable keys and legacy digital objects to be integrated into FDO records. How legacy metadata from IANA media types that can be transformed into structured metadata of appropriate attribute definitions that then can be applied in profiles and FDO records, is described in the third example. HTML XML PDF
      PubDate: Mon, 30 Oct 2023 09:01:20 +020
       
  • D1.2 Technical report on barriers and enablers for coastal restoration
           upscaling: A multi-level perspective

    • Abstract:
      DOI : 10.3897/arphapreprints.e114825
      Authors : Carles Ibáñez, Alba Alemany, Ferran Bertomeu, Silvia Frias, Judith Molero, Roberto Merciai, Laura Puertolas : Coastal regions provide some of the most productive and biodiverse environments with an important and often underappreciated carbon storage potential. At the same time, they are among the areas of highest population density, natural assets, and cultural heritage in the world, yet are experiencing significant social, economic and environmental challenges, exacerbated by climate change and human pressures.The Rest-Coast Project (Large scale RESToration of COASTal ecosystems through rivers to sea connectivity) is an EU Horizon 2020 research project (Grant agreement No. 101037097) whose overall goal is to address with effective and innovative tools the key challenges faced by coastal ecosystem restoration across Europe. The approach chosen for this project will deliver a highly interdisciplinary contribution, with the demonstration of improved practices and techniques for hands-on ecosystem restoration across several pilot sites, supported by the co-design of innovative governance and financial arrangements, as well as an effective strategy for the dissemination of results. HTML XML PDF
      PubDate: Mon, 30 Oct 2023 08:21:53 +020
       
  • D5.1 Report mapping the governance status quo in pilot sites

    • Abstract:
      DOI : 10.3897/arphapreprints.e114824
      Authors : Carla Danelutti, Emmi Lindqvist, Maria del Mar Otero, Mindert de Vries, Albert Vos, Nuno Caiola, Vicente Gracia, Nil Alvarez, Laura Puertolas, Jaime Ordonez, Silvia Torresan, Caterina Dabalà, Francesca Coccon, Grzegorz Różyński, Nikolay Valchev, Nataliya Andreeva, Elitsa Hineva, Olivier Boutron, Rosaria Ester Musumeci, Massimiliano Marino, Christophe Briere, Julien Dalle, Margot Defoort-Levkov, Margot Ahr, Yael Salame-Rubin, Simon Nemtzov, Avi Uzan : Coastal regions provide some of the most productive and biodiverse environments with an important and often underappreciated carbon storage potential. At the same time, they are among the areas of highest population density, natural assets and cultural heritage in the world, yet are experiencing significant social, economic and environmental challenges, exacerbated by climate change and human pressures.The REST-COAST project (Large scale RESToration of COASTal ecosystems through rivers to sea connectivity) will demonstrate to what extent upscaled coastal restoration can provide a low-carbon adaptation, reducing risks and providing gains in biodiversity for vulnerable coastal ecosystems, such as wetlands or sea grass beds. By overcoming present technical, economic, governance and social barriers to restoration upscaling, REST-COAST will develop the large scale river-coast connectivity and increase the nearshore accommodation space for the resilient delivery of coastal ecosystem services (ESs). The selected ESs (risk reduction, environmental quality and fish provisioning) touch urgent coastal problems such as the erosion/flooding during recent storms or the accelerating coastal habitat degradation that seriously affects fisheries and aquaculture. Combining new techniques, risk assessments, innovative financial/governance arrangements and homogeneous metrics for ESs and biodiversity, REST-COAST will develop a systemic approach to coastal restoration based on a scalable coastal adaptation plan. HTML XML PDF
      PubDate: Mon, 30 Oct 2023 08:19:14 +020
       
  • Climate and Air Quality Indices for the European Social Survey

    • Abstract:
      DOI : 10.3897/arphapreprints.e114675
      Authors : Hilde Orten, David Rayner, Eirik Stavestrand, Iris Alfredsson, Ilze Lace, Irena Vipavc Brvar, Maja Dolinar, Joachim Wackerow, Hannah Clark : Knowledge of how personal experience with climate and air quality influence personal attitudes, concerns, and actions about environmental issues is increasingly important. A solid foundation for such studies is to combine interview or survey data on respondents’ attitudes and beliefs with indices created from independent meteorological or environmental monitoring data matched to the respondents location.In this project,  indicators of climate and air pollution were integrated with data from the European Social Survey for a selection of large European urban regions. A prototype provenance description application was also developed for describing the workflow for creating indicators and integrating data.Our main focus was on creating indicators that represent regional anomalies in local air quality and weather for a range of time windows up-to-and-including the dates of the interviews. The goal is to facilitate investigation of relationships between urban citizen’s attitudes and behaviors as represented in the survey responses and the conditions in their local environment.   HTML XML PDF
      PubDate: Thu, 26 Oct 2023 11:40:31 +030
       
  • D3.3 Ecosystem service, biodiversity and socio-economic models for
           each case study

    • Abstract:
      DOI : 10.3897/arphapreprints.e114653
      Authors : Anna Cord, Stephanie Roilo, Michael Beckmann, Anne Paulus, Katharina Schneider, Predrag Lugonja, Tijana Nikolić, Fanny Langerwisch, Marek Bednář, Tomáš Václavík, Paul Evans, Arjan Gosal, Rosemary Wool, George Breckenridge, Guy Ziv, Jodi Gunning : This deliverable provides a report on the biodiversity and ecosystem services (ESS) models as well as the socio-economic statistical model, generated in the Work Package 3 (WP3) - Farming System Archetypes of BESTMAP. A general overview of the research goals and guiding principles under which the models were developed is given, followed by a detailed description of the four biophysical models (biodiversity, food and fodder, carbon sequestration and water quality) and of the socio-economic model, each with case study (CS) examples. This document is accompanied by model factsheets (see Appendix) which loosely follow the structure of the ODMAP (Overview, Data, Model, Assessment and Prediction) protocol developed by Zurell et al. (2020). The deliverable also discusses the obstacles and challenges encountered during the model adaptation and implementation in the different CS, and how the model outputs will be used in various other tasks within the project. HTML XML PDF
      PubDate: Thu, 26 Oct 2023 11:36:48 +030
       
  • Developing responsible AI practices at the Smithsonian Institution

    • Abstract: Research Ideas and Outcomes 9: e113334
      DOI : 10.3897/rio.9.e113334
      Authors : Rebecca Dikow, Corey DiPietro, Michael Trizna, Hanna BredenbeckCorp, Madeline Bursell, Jenna Ekwealor, Richard Hodel, Nilda Lopez, William Mattingly, Jeremy Munro, Richard Naples, Candace Oubre, Drew Robarge, Sara Snyder, Jennifer Spillane, Melinda Jane Tomerlin, Luis Villanueva, Alexander White : Applications of artificial intelligence (AI) and machine learning (ML) have become pervasive in our everyday lives. These applications range from the mundane (asking ChatGPT to write a thank you note) to high-end science (predicting future weather patterns in the face of climate change), but, because they rely on human-generated or mediated data, they also have the potential to perpetuate systemic oppression and racism. For museums and other cultural heritage institutions, there is great interest in automating the kinds of applications at which AI and ML can excel, for example, tasks in computer vision including image segmentation, object recognition (labelling or identifying objects in an image) and natural language processing (e.g. named-entity recognition, topic modelling, generation of word and sentence embeddings) in order to make digital collections and archives discoverable, searchable and appropriately tagged.A coalition of staff, Fellows and interns working in digital spaces at the Smithsonian Institution, who are either engaged with research using AI or ML tools or working closely with digital data in other ways, came together to discuss the promise and potential perils of applying AI and ML at scale and this work results from those conversations. Here, we present the process that has led to the development of an AI Values Statement and an implementation plan, including the release of datasets with accompanying documentation to enable these data to be used with improved context and reproducibility (dataset cards). We plan to continue releasing dataset cards and for AI and ML applications, model cards, in order to enable informed usage of Smithsonian data and research products. HTML XML PDF
      PubDate: Wed, 25 Oct 2023 09:31:44 +030
       
  • Methodology to evaluate the effectiveness of hydromorphological
           restoration of rivers in Romania

    • Abstract: Research Ideas and Outcomes 9: e113991
      DOI : 10.3897/rio.9.e113991
      Authors : Gabriela Ioana-Toroimac, Gabriela Moroșanu, Dana Constantin, Cătălina Stoica, Ionuț Șandor : In the context of the requirements of the Water Framework Directive to reinstate a river’s good ecological status after being severely altered by human pressures, river restoration became a major topic in the last decade in the EU and the number of projects implemented especially on hydromorphology increased. However, it is still uncertain whether these restoration measures have positive cumulative effects, i.e. hydromorphological effectiveness, when compared to reference conditions and expectations of stakeholders, because of inconsistent methodologies. Therefore, the goal of our project is to develop a methodology to evaluate the hydromorphological effectiveness of river restoration, based on standardised indicators, at various spatial scales, appropriate for implemented measures and for restored river types, weighting the expectations of actors and adapted to case studies in Romania. This methodological protocol could become also a useful tool to create a strategy and make decisions in the practice of river restoration. Moreover, this kind of analysis could contribute to clarifying the issue of standards in environmental projects. HTML XML PDF
      PubDate: Tue, 24 Oct 2023 09:01:07 +030
       
  • Targeting Proteus mirabilis BAM Complex Proteins for Development of Novel
           Antibiotics

    • Abstract: Research Ideas and Outcomes 9: e106849
      DOI : 10.3897/rio.9.e106849
      Authors : Raphael Abban, Sarpong Kwabena, Samuel Duodu, Lydia Mosi, Isawumi Abiola : Urinary tract infections (UTIs) are frequent hospital-acquired infection, with Escherichia coli and Proteus mirabilis accounting for 90% of complicated UTIs. Emergence of multidrug-resistant (MDR) bacteria have complicated the treatment UTIs. P. mirabilis related UTIs has been associated with the production of urinary stones and long-term infections in patients with catheters. P. mirabilis and other uropathogens constitute a largely unexplored pathogen group. The pathogen is resistant to most antibiotics as a result of its impermeable outer membrane (OM). The β-barrel assemble machinery folds and inserts outer membrane proteins; however, there are no antibiotics targeting the OM assemble in clinical use currently. Therefore, this study seeks to identify drugs that will inhibit the activity of P. mirabilis B complex proteins and also determine their effects on P. mirabilis OM biogenesis. This would be achieved by screening approved drugs against the P. mirabilis Bam complex using computer-based in silico screening and cellular-based assays. First, the binding effects of drugs on P. mirabilis B complex proteins will be determined using docking algorithms. The antimicrobial and antivirulence activity of selected drugs from in silico analysis will be screened against MDR P. mirabilis. Finally, the effect of active drug(s) on the OM biogenesis of wild-type P. mirabilis and mutant P. mirabilis will be determined using peptide nucleic acids (PNA). Western lot analysis will be used to determine the abundance of proteins involved in OM biogenesis. Successful completion of this study will lead to the identification of novel antibiotics against MDR P. mirabilis and associated mechanisms while providing the foundation for future research endeavours on other uropathogens. HTML XML PDF
      PubDate: Thu, 19 Oct 2023 13:35:20 +030
       
  • Electromagnetic radiation as antiviral treatment with a focus on Rabies
           post-exposure prophylaxis

    • Abstract: Research Ideas and Outcomes 9: e107227
      DOI : 10.3897/rio.9.e107227
      Authors : Georgios Dougas : Shortwave and microwave diathermy devices are commonly used in physical therapy as heating treatment. The rise in temperature occurs due to the flow of electric current in the treated area. Ions are evenly distributed in a predicted pattern from skin to deeper tissues. We hypothesise that the diathermy physiotherapy devices (DPDs) can be repurposed as a means of neutralisation of the Rabies virus (RABV) by exploiting the generated electric charges. In order to minimise the ohmic heating of the tissue, the pulsed output of the diathermy devices is preferred where the ‘on’ time of active energy emission is considerably shorter than the ‘off’ time. RABV proteins mediating cell invasion, cytoplasmic replication and budding, contain polar components that can be adversely affected by non-thermal electric phenomena. Repurposed DPDs can replace the Rabies immunoglobulin (RIG) by targeting the site of inoculation i.e. the area of the animal bite, provided that the delivered electric charges can reduce pathogenicity by altering key viral proteins. The modality is advantageous compared to conventional RIG since it can theoretically neutralise all Lyssavirus species, is not limited by the compartment syndrome, can intercept RABV even after it gains access to the peripheral neural network where conventional post-exposure prophylaxis is ineffective and is cost-effective in the long term. The principle of physical alteration of vulnerable proteins by electricity delivered by electromagnetic radiation is not limited to RABV, but may be applied to a spectrum of viral pathogens. HTML XML PDF
      PubDate: Mon, 16 Oct 2023 09:15:18 +030
       
  • Pre-Commercial Procurement framework and European funding sources for
           European Research Infrastructure Consortiums: Insights from the DiSSCo
           ERIC development

    • Abstract: Research Ideas and Outcomes 9: e113294
      DOI : 10.3897/rio.9.e113294
      Authors : Gael Lymer, Frederik Leliaert, Patricia Mergen, Stefaan Pijls : Mechanisms and sources of funding for European Research Infrastructure Consortiums (ERICs) are diverse, complex and can be challenging to identify and to use. This paper provides a roadmap for Research & Development (R&D) within the pre-commercial procurement (PCP) framework and the landscape of funding for ERICs available from the European Union with a perspective on other tracks of funding. Our objective is to offer a starting point and underline opportunities and challenges, for existing and future ERICs. The work presented in this paper results from the research carried-out for the business model of the DiSSCo (Distributed System of Scientific Collections) ERIC, which is currently in its transition phase and will be constructed in the following years. HTML XML PDF
      PubDate: Fri, 13 Oct 2023 11:46:53 +030
       
  • Global change in above-belowground multitrophic grassland communities

    • Abstract: Research Ideas and Outcomes 9: e113960
      DOI : 10.3897/rio.9.e113960
      Authors : Malte Jochum, Vera Zizka, Stefan Scheu, Nico Eisenhauer, Melanie Pollierer : Global change is transforming Earth’s ecological communities with severe consequences for the functions and services they provide. In temperate grasslands, home to a mesmerising diversity of invertebrates controlling multiple ecosystem processes and services, land-use intensification and climate change are two of the most important global-change drivers. While we know a lot about their independent effects on grassland biodiversity and ecosystem functioning, little is known about how these stressors interact. Moreover, most research on biodiversity change focuses on decreasing biomass or species richness, while a major aspect is commonly ignored – altered ecological interactions. This is problematic because these interactions represent and control many important ecosystem processes, such as predation, herbivory or decomposition. Networks of trophic interactions, so-called food webs, link the structure and functioning of ecological communities and unravel mechanistic relationships between environmental change, ecological communities and ecosystem multifunctionality – the ability of a system to simultaneously support multiple processes. Consequently, we need to study how ecological interactions and the food webs they comprise respond to environmental change and to multiple interacting global-change drivers. Fortunately, novel tools offer unprecedented opportunities in studying trophic interactions and their impact on ecosystem processes. In addition, we know far more about how global change impacts the aboveground world than its belowground counterpart. However, belowground communities are just as important for the overall functioning of terrestrial ecosystems. Thus, to comprehensively understand global-change impacts on temperate grasslands, we need to study above- and belowground multitrophic interactions and ecosystem processes together, also accounting for their interdependencies. Here, we propose to use the Global Change Experimental Facility (GCEF, Bad Lauchstädt, Germany) to study joint impacts of land-use intensity and climate change on above-belowground multitrophic interactions and ecosystem multifunctionality in a temperate grassland global-change experiment. We will combine novel approaches to assessing trophic interactions and basal-resource dependency with an innovative method to quantify energy flux through ecological interaction networks. We will disentangle separate and interactive effects of land use and climate change and unravel how global-change driven modifications in multitrophic interactions mechanistically translate into altered ecosystem processes and multifunctionality – above and below the ground. Combining a field-experimental approach with novel molecular and quantitative techniques will allow for a leap forward in our understanding of global-change impacts on temperate grasslands, which will be crucial to manage and conserve these important ecosystems. HTML XML PDF
      PubDate: Fri, 13 Oct 2023 11:01:15 +030
       
  • DiSSCo Prepare Project: Increasing the Implementation Readiness Levels of
           the European Research Infrastructure

    • Abstract: Research Ideas and Outcomes 9: e113906
      DOI : 10.3897/rio.9.e113906
      Authors : Dimitrios Koureas, Laurence Livermore, Eva Alonso, Wouter Addink, Maria Judite Alves, Ana Casino, Luís Curral, Henrik Enghoff, Michel Guiraud, Helen Hardy, Jana Hoffmann, Salomé Landel, Carole Paleco, Mareike Petersen, Serge Scory, Vincent Smith, Claus Weiland, Karsten Wesche, Matt Woodburn : The Distributed System of Scientific Collections (DiSSCo) is a new world-class Research Infrastructure (RI) for Natural Science Collections. The DiSSCo RI aims to create a new business model for one European collection that digitally unifies all European natural science assets under common access, curation, policies and practices that ensure that all the data is easily Findable, Accessible, Interoperable and Reusable (FAIR principles). DiSSCo represents the largest ever formal agreement between natural history museums, botanic gardens and collection-holding institutions in the world.DiSSCo entered the European Roadmap for Research Infrastructures in 2018 and launched its main preparatory phase project (DiSSCo Prepare) in 2020. DiSSCo Prepare is the primary vehicle through which DiSSCo reaches the overall maturity necessary for its construction and eventual operation. DiSSCo Prepare raises DiSSCo’s implementation readiness level (IRL) across the five dimensions: technical, scientific, data, organisational and financial. Each dimension of implementation readiness is separately addressed by specific Work Packages (WP) with distinct targets, actions and tasks that will deliver DiSSCo’s Construction Masterplan. This comprehensive and integrated Masterplan will be the product of the outputs of all of its content related tasks and will be the project’s final output. It will serve as the blueprint for construction of the DiSSCo RI, including establishing it as a legal entity.DiSSCo Prepare builds on the successful completion of DiSSCo’s design study, ICEDIG and the outcomes of other DiSSCo-linked projects such as SYNTHESYS+ and MOBILISE.This paper is an abridged version of the original DiSSCo Prepare grant proposal. It contains the overarching scientific case for DiSSCo Prepare, alongside a description of our major activities. HTML XML PDF
      PubDate: Thu, 12 Oct 2023 10:31:10 +030
       
  • Establishment of a data visualization interface for the Digital Botanical
           Gardens Initiative

    • Abstract:
      DOI : 10.3897/arphapreprints.e114048
      Authors : Maëlle Wannier : The Digital Botanical Gardens Initiative (DBGI) embarks on an innovative journey to curate, manage, and disseminate digital data from living botanical collections, with an emphasis on mass spectrometric evaluations of chemodiversity. Using semantic web technology, this data is linked with relevant metadata, propelling ecosystem research and guiding biodiversity conservation efforts. Central to the success of DBGI is the creation of an interactive platform for both humans and machines to assimilate this knowledge. This report outlines our efforts to design the prototype of a data visualization portal intended to evolve into the DBGI dashboard. Starting with a Plotly Dash application, the project transitioned to a Node.js application leveraging Javascript, HTML, and CSS for enhanced customization. This provides a basis for future improvements, some of which are proposed in the report. HTML XML PDF
      PubDate: Thu, 12 Oct 2023 09:20:32 +030
       
  • Understanding the users and uses of UK Natural History Collections

    • Abstract: Research Ideas and Outcomes 9: e113378
      DOI : 10.3897/rio.9.e113378
      Authors : Helen Hardy, Laurence Livermore, Paul Kersey, Ken Norris, Vincent Smith : UK natural science collections hold over 137 million items, an unrivalled source of data about 4.56 billion years of planetary development and hundreds of years of biological change, including the differences made by humans — but the scientific, commercial, and societal benefits of these collections are constrained by the limits of physical access, and by highly fragmented digitisation efforts with less than 10% digitally available. Following work with Frontier Economics in 2021, which showed potential for £2 billion in benefits to the UK economy from digitising all UK natural science collections, in 2022–23 the Natural History Museum London worked, with analytical support from McKinsey and Company, to understand the impact of what has already been digitised and shared by UK natural science collections — what is the demand for these data, what are they used for, and how does this deliver efficient, effective and impactful research'This study focuses on usage via the Global Biodiversity Information Facility, the largest source of relevant usage data, examining 7.6 million records from twelve UK institutions. While these UK collections data are just 0.3% of total GBIF occurrences, they are cited in 12% of peer reviewed publications citing GBIF data, showing the disproportionate impact of UK collections data and the historical, geographical, and taxonomic richness that they bring. Researchers have already benefited from more than £18 million of efficiency savings from digital UK specimen data. Data from natural science collections held in the UK are uniquely impactful resources, vital to a future in which people and planet thrive, and a step change in the pace of digitisation is needed to unlock their potential for researchers, policymakers, and society. HTML XML PDF
      PubDate: Mon, 2 Oct 2023 12:34:14 +0300
       
  • Assessing the FAIR Digital Object Framework for Global Biodiversity
           Research

    • Abstract: Research Ideas and Outcomes 9: e108808
      DOI : 10.3897/rio.9.e108808
      Authors : Sharif Islam, James Beach, Elizabeth R. Ellwood, Jose Fortes, Larry Lannom, Gil Nelson, Beth Plale : In the first decades of the 21st century, there has been a global trend towards digitisation and the mobilisation of data from natural history museums and research institutions. The development of national and international aggregator systems, which focused on data standards, made it possible to access millions of museum specimen records. These records serve as an empirical foundation for research across various fields. In addition, community efforts have expanded the concept of natural history collection specimens to include physical preparations and digital resources, resulting in the Digital Extended Specimen (DES), which also includes derived and related data. Within this context, the paper proposes using the FAIR Digital Object (FDO) framework to accelerate the global vision of the DES, arguing that FDO-enabled infrastructures can reduce barriers to the discovery and access of specimens, help ensure credit back to contributors and increase the amount of research that incorporates biodiversity data. HTML XML PDF
      PubDate: Tue, 12 Sep 2023 13:38:10 +030
       
  • Mitigating multiple stressors on managed pollinators: Effectiveness and
           feasibility of implementing response options

    • Abstract:
      DOI : 10.3897/arphapreprints.e112382
      Authors : Bryony Willcox, Deepa Senapathi, Mark Brown, Simon Potts : In the real world, pollinators face multiple interacting pressures, and so response options must be tailored to this. To date, most attention has been on characterising the risks to managed pollinators from single stressors, though recently more attention has been paid to risks from multiple stressors (e.g., pesticides, pathogens and poor nutrition). The PoshBee project has developed a policy brief providing recommendations on options that mitigate against multiple stressors. HTML XML PDF
      PubDate: Fri, 8 Sep 2023 10:23:11 +0300
       
  • FAIR Research Objects for realising Open Science with the EOSC project
           RELIANCE

    • Abstract: Research Ideas and Outcomes 9: e108765
      DOI : 10.3897/rio.9.e108765
      Authors : Anne Fouilloux, Elisa Trasatti, Federica Foglini, Alejandro Coca-Castro, Jean Iaquinta : The numerous benefits of Open Science (OS) and of the four FAIR foundational principles - Findable, Accessible, Interoperable and Reusable - are increasingly valued in academia, although what OS and FAIR entail is still largely misunderstood. In such conditions, putting into practice OS and applying the FAIR principles is challenging and underrated. However, realising OS is perfectly within our grasp provided that an infrastructure supporting the management of the research lifecycle is available. ROHub (https://www.rohub.org/) is a Research Object (RO) management platform implementing three complementary technologies: Research Objects, Data Cubes and Text Mining services. ROHub enables researchers to collaboratively manage, share and preserve their research while they are still working on it (rather than after the work is finished). In this paper, three communities from Earth Sciences, namely Geohazards, Sea Monitoring and Climate Change, demonstrate how ROHub helped them to understand each other and to work openly and, more importantly, how communities of practice play an important role in facilitating reuse and interdisciplinary collaboration. These findings are illustrated with several use cases from these various communities. HTML XML PDF
      PubDate: Tue, 5 Sep 2023 09:42:17 +0300
       
  • PoshBee Toolbox: A portfolio of high quality methodologies, tools, and
           practice guides for pollinators

    • Abstract:
      DOI : 10.3897/arphapreprints.e112175
      Authors : Mark Brown, Philippe Bulet, Marie-Pierre Chauzat, Alexandra-Maria Klein, Anina Knauer, Marika Mand, Denis Michez, Francesco Nazzi, Robert Paxton, Oliver Schweiger, Jane Stout, Orlando Yanez, Simon Potts : Policies and management practices for managed bees and other pollinators are increasingly reliant on the availability of high quality data in order to inform them. This in turn requires the widespread adoption of state-of-the-art standardised methods and approaches so that new data and knowledge are both robust and trustworthy. The PoshBee project has developed, tested, and validated a wide range of new tools. These include, but are not limited to: experimental protocols, monitoring tools, technological tools and practice guides. The wide scale application of these, and other tools will help ensure that researchers, risk assessors, policymakers, beekeepers, and agri-food industry are producing data to the highest standards in a way that increases comparability and transparency. HTML XML PDF
      PubDate: Tue, 5 Sep 2023 08:44:37 +0300
       
  • How open science can support the 3Rs and improve animal research

    • Abstract: Research Ideas and Outcomes 9: e105198
      DOI : 10.3897/rio.9.e105198
      Authors : Monique Janssens, Stefan Gaillard, Judith de Haan, Wim de Leeuw, Matthew Brooke, Maura Burke, Jacques Flores, Iris Kruijen, Julia Menon, Adrian Smith, Ivo Tiebosch, Felix Weijdema : Open science in its broadest sense can make better science and provide benefits to researchers. When applied to animal experimentation, it can prevent unnecessary use of animals, because knowledge and experiences about past animal experimentation are shared openly to be consulted and used by other researchers. By extension, open science can accelerate the much anticipated transition towards animal-free innovations or New Approach Methodologies (NAMs). The purpose of this paper is to bring together and further share the preparations and findings of a symposium held at Utrecht University on aspects of open science that researchers doing animal experiments can and should take into account to improve their research and benefit themselves. The paper offers a one-figure guideline for that purpose. HTML XML PDF
      PubDate: Thu, 31 Aug 2023 16:49:51 +030
       
  • RIPARIANET - Prioritising riparian ecotones to sustain and connect
           multiple biodiversity and functional components in river networks

    • Abstract: Research Ideas and Outcomes 9: e108807
      DOI : 10.3897/rio.9.e108807
      Authors : Stefano Larsen, Jose Manuel Alvarez-Martinez, Jose Barquin, Maria Cristina Bruno, Laura Concostrina Zubiri, Luca Gallitelli, Micael Jonsson, Monika Laux, Giorgio Pace, Massimiliano Scalici, Ralf Schulz : Europe has committed to upscale ecosystems protection to include 30% of land and sea. However, due to historical overexploitation of natural assets, the available area for biodiversity protection is severely limited. Riparian zones are natural ecotones between aquatic and terrestrial ecosystems, contributing disproportionately to regional biodiversity and providing multiple ecosystem functions and services. Due to this and their branching geometry, riparian networks form a vast system of ‘blue-green arteries’ which physically and functionally connect multiple ecosystems over elevation gradients, despite covering a relatively small area of the basin. Hence, RIPARIANET argues that developing approaches able to optimise the spatial conservation of natural stream-riparian networks represent a flagship example of biodiversity protection in the EU. Although the integrity of riparian zones is fundamental for the achievement of multiple EU environmental objectives, the lack of a standardised framework for biodiversity assessment and protection across Member States has led to extensive impairment of riparian areas and frequent stakeholder conflicts.The main objective of RIPARIANET is to leverage the increasing resolution of remote sensing information to provide practitioners with evidence-based guidance and approaches to biodiversity conservation. Key questions include: i) how can we remotely assess riparian integrity and identify areas which provide effective connectivity allowing species biodiversity and ecosystem functions to persist through meta-ecological processes' ii) how can we disentangle the influence of local- and network-scale stressors and processes on riparian biodiversity to better implement river basin management schemes' iii) to what extent do currently existing protected areas in rivers account for the geometry of riparian networks and their multifunctionality'We will address these questions in riparian networks within six river basins in Europe, including Boreal, Continental, Alpine, Temperate and Mediterranean systems. First, we will gather local needs and interests from key stakeholders together with satellite imagery and GIS environmental data for all basins. Then, riparian and river ecosystems functions will be modelled and ecological hotspots will be identified through a GIS-based multi-criteria approach, including stakeholder inputs. Then, we will collect in situ data to assess multiple biodiversity and stressors at the local scale and, subsequently, scale-up this information to the network scale using geostatistical tools and advanced modelling. This knowledge will be conveyed to managers at local and EU scales in the form of decision-support tools allowing decision-makers to identify protection gaps and ecological hotspots along riparian networks, based on multiple biodiversity, functional and connectivity criteria. HTML XML PDF
      PubDate: Thu, 31 Aug 2023 16:36:29 +030
       
  • NFDI4Microbiota – national research data infrastructure for
           microbiota research

    • Abstract: Research Ideas and Outcomes 9: e110501
      DOI : 10.3897/rio.9.e110501
      Authors : Konrad U. Förstner, Anke Becker, Jochen Blom, Peer Bork, Thomas Clavel, Marius Dieckmann, Alexander Goesmann, Barbara Götz, Thomas Gübitz, Franziska Hufsky, Sebastian Jünemann, Marie-Louise Körner, Manja Marz, Ulisses Nunes Da Rocha, Jörg Overmann, Alfred Pühler, Dietrich Rebholz-Schuhmann, Alexander Sczyrba, Jens Stoye, Justine Vandendorpe, Thea Van Rossum, Alice McHardy : Microbes – bacteria, archaea, unicellular eukaryotes, and viruses – play an important role in human and environmental health. Growing awareness of this fact has led to a huge increase in microbiological research and applications in a variety of fields. Driven by technological advances that allow high-throughput molecular characterization of microbial species and communities, microbiological research now offers unparalleled opportunities to address current and emerging needs. As well as helping to address global health threats such as antimicrobial resistance and viral pandemics, it also has a key role to play in areas such as agriculture, waste management, water treatment, ecosystems remediation, and the diagnosis, treatment and prevention of various diseases. Reflecting this broad potential, billions of euros have been invested in microbiota research programs worldwide. Though run independently, many of these projects are closely related. However, Germany currently has no infrastructure to connect such projects or even compare their results. Thus, the potential synergy of data and expertise is being squandered. The goal of the NFDI4Microbiota consortium is to serve and connect this broad and heterogeneous research community by elevating the availability and quality of research results through dedicated training, and by facilitating the generation, management, interpretation, sharing, and reuse of microbial data. In doing so, we will also foster interdisciplinary interactions between researchers. NFDI4Microbiota will achieve this by creating a German microbial research network through training and community-building activities, and by creating a cloud-based system that will make the storage, integration and analysis of microbial data, especially omics data, consistent, reproducible, and accessible across all areas of life sciences. In addition to increasing the quality of microbial research in Germany, our training program will support widespread and proper usage of these services. Through this dual emphasis on education and services, NFDI4Microbiota will ensure that microbial research in Germany is synergistic and efficient, and thus excellent. By creating a central resource for German microbial research, NDFDI4Microbiota will establish a connecting hub for all NFDI consortia that work with microbiological data, including GHGA, NFDI4Biodiversity, NFDI4Agri and several others. NFDI4Microbiota will provide non-microbial specialists from these consortia with direct and easy access to the necessary expertise and infrastructure in microbial research in order to facilitate their daily work and enhance their research. The links forged through NFDI4Microbiota will not only increase the synergy between NFDI consortia, but also elevate the overall quality and relevance of microbial research in Germany. HTML XML PDF
      PubDate: Thu, 24 Aug 2023 10:44:22 +030
       
  • From implementation to application: FAIR digital objects for training data
           composition

    • Abstract: Research Ideas and Outcomes 9: e108706
      DOI : 10.3897/rio.9.e108706
      Authors : Nicolas Blumenröhr, Rossella Aversa : Composing training data for Machine Learning applications can be laborious and time-consuming when done manually. The use of FAIR Digital Objects, in which the data is machine-interpretable and -actionable, makes it possible to automate and simplify this task. As an application case, we represented labeled Scanning Electron Microscopy images from different sources as FAIR Digital Objects to compose a training data set. In addition to some existing services included in our implementation (the Typed-PID Maker, the Handle Registry, and the ePIC Data Type Registry), we developed a Python client to automate the relabeling task. Our work provides a Proof-of-Concept validation for the usefulness of FAIR Digital Objects on a specific task, facilitating further developments and future extensions to other machine learning applications. HTML XML PDF
      PubDate: Tue, 22 Aug 2023 09:38:44 +030
       
  • Mapping the Digitisation Workflow in a University Herbarium

    • Abstract: Research Ideas and Outcomes 9: e106883
      DOI : 10.3897/rio.9.e106883
      Authors : Karen Thompson, Joanne Birch : Specimens or objects in natural history collections hold substantial research and cultural value that is enhanced where these items are made digitally available. Benefits of digitisation include increasing open access to collection-based biodiversity data, increasing productivity of scientific research, enabling novel research applications of digitally accessible data, reducing preservation requirements through reduced object handling, and expanding potential for “remote curation” in collections. However, the time available for object and data digitisation is limited for most collections. Well documented digitisation workflows can ensure that curation time is efficiently applied to achieve digitisation outputs, and that digitisation standards are consistently applied within and among projects.While this case study focused on the generation of digitisation workflows in a medium-sized Australian university-based herbarium, the findings of this study are relevant to collections globally. The curation workflows comprise a set of modular steps required for the digitisation of herbarium specimen data and images. Steps are clearly identified as requiring human-mediation versus those that can be automated, those that require on-site versus remote-access, and those that require transfer or transformation of data or files. This clarity enables consideration of the opportunities and challenges for increasing efficiencies for collection-based digitisation, data and file management. The maps provide a contextual framework for herbarium-based digitisation pathways for those who work with specimen-derived biodiversity data, and an insight into these tools for those who are not familiar with herbarium protocols. HTML XML PDF
      PubDate: Fri, 18 Aug 2023 09:08:36 +030
       
  • Identifying genetic factors that increase cognitive reserve: A theoretical
           approach

    • Abstract: Research Ideas and Outcomes 9: e107939
      DOI : 10.3897/rio.9.e107939
      Authors : Daniel Neidigk, Allie Linkous, Rodney Guttmann : Studies have demonstrated that some individuals display pathological hallmarks of Alzheimer's disease (AD) but are not afflicted with cognitive decline. The ability to maintain cognitive function despite the presence of pathology is referred to as cognitive reserve. This project aims to identify the molecular pathways involved in cognitive reserve using Drosophila melanogaster (Drosophila) models of AD. Specifically, a theoretical approach using experimental evolution to drive a population of AD-like Drosophila carrying a tau mutation to develop cognitive reserve is proposed. To accomplish this, a population of AD-like Drosophila will be placed in a single population cage along with wild-type flies and forced to compete for food and water. The first generation of AD-like Drosophila will be generated using random mutagenesis of the initially isogenic AD-like fly. The selected tau mutant displays a rough eye condition which allows for easy distinction between tau mutant and wild-type flies. It is hypothesised that AD-like flies with cognitive decline will be unable to survive because their limited cognitive abilities will prevent them from effectively competing for food and water. In contrast, AD-like flies with mutations that promote cognitive reserve will be better capable of survival. After 90-99% of mutant flies have died, the surviving mutant flies will be back-crossed to the P1 mutant to maintain tau mutation stability. It is expected that artificial selection will result in the creation of a generation of tau mutant flies that demonstrate cognitive abilities comparable to those of wild-type flies despite maintaining an AD-like tau mutation. This approach will monitor the successful trajectory of the evolution of increased cognitive reserve through survival curve analysis and measures of cognition. A limitation of the method is that only a dominant mutation or series of dominant mutations would be identified using this approach. HTML XML PDF
      PubDate: Fri, 11 Aug 2023 09:02:24 +030
       
  • The energy-rush and insulin model of obesity

    • Abstract: Research Ideas and Outcomes 9: e108748
      DOI : 10.3897/rio.9.e108748
      Authors : Hangxing Jia : Obesity has been a global health problem since the twentieth century. Despite the intensive research, there is no scientific consensus on the onset of obesity. The energy balance model (EBM) and the carbohydrate-insulin model (CIM) are two competing obesity theories, each with supporting and conflicting evidence. In this essay, I propose a new model, the energy-rush and insulin model (ERIM) which integrates not only the energy intake and expenditure, but also the food composition and digestibility, to explain how the high energy-rush and insulin secretion contribute to the development of obesity. The ERIM offers a novel framework to explain how obesity occurs and proposes new recommendations which may reverse the obesity epidemic in the future. HTML XML PDF
      PubDate: Wed, 9 Aug 2023 16:08:33 +0300
       
  • Bilateral cooperation - Fostering the ability of native European beech and
           sessile oak forests in the border region against the impacts of climate
           change

    • Abstract: Research Ideas and Outcomes 9: e109816
      DOI : 10.3897/rio.9.e109816
      Authors : Erik Szamosvári, László Nagy, Heino Konrad, Norbert Móricz, Lambert Weißenbacher, Anita Bálint, Anikó Neuvirthné Bilics, Marcela van Loo : Adequate adaptions and actions to combat anthropogenic climate change (CC) are significant challenges of the 21st century. In Europe, according to the European Environmental Agency, warming of around 2°C is expected under the moderate climate scenario (RCP 4.5) by the end of the century, but the pessimistic RCP 8.5 scenario project an increase of up to 6°C. In addition to the rise in temperature, changes in precipitation and increased frequency of extreme weather events are predicted. New environmental conditions affect tree species and habitats differently; thus, forest biodiversity and local tree species compositions probably will be altered in many regions in the future. The effects may be manifold: some tree species may persist, locally adapt and migrate, while others may disappear from given regions and be replaced by native or non-native species. The native forests of the Austrian-Hungarian border region are particularly affected by the climate change. To mitigate the consequences of anthropogenic climate change to preserve forest biodiversity for future generations and to enable their use, deliberate and planned human interventions and actions are essential. These require transnational or even global efforts since nature and climate do not recognise man-made borders.The REIN-Forest project (Interreg V-A Austria-Hungary Programme - ATHU150), a bilateral project between Austria and Hungary, aimed to establish harmonised protection measures for the conservation of native forests in Northern, Central and Southern Burgenland, Vienna, Vienna Umland-South, Lower Austria South, Graz and Eastern Styria, Győr-Moson-Sopron, Vas and Zala counties (the so-called programme area). In the scope of this project, international cooperation between three project partners: the Austrian Research Centre for Forests (BFW, Austria), the Forest Research Institute – University of Sopron (SOE ERTI, Hungary) and the Vas County Government Office (VVÖH, Hungary) was established. Previous results and outputs of the SUSTREE project (Interreg Central Europe CE614), such as: a) Transnational delineation model of conservation and forest seed transfer zones in climate change, b) Report of intraspecific response function and derivation of climate transfer limits, SusSelect data, recommendations and c) Application of the species distribution models for the delineation of seed transfer zones/models in Central Europe, were put into practice during the project, focusing on two native deciduous forest tree species of the Austrian-Hungarian border region: European beech (Fagus sylvatica L.) and sessile oak (Quercus petraea (Matt.) Liebl.).During the REIN-Forest project, the following joint documents were prepared and several activities were implemented:1. Model-based document on the current state and future perspectives of European beech and sessile oak forests;2. Bilateral strategy for the transfer of forest reproductive material (FRM) and its use in the Austrian-Hungarian border region;3. Establishment of altogether six demonstration sites (three in each country) with local and climate-adapted FRM of European beech and sessile oak for long-term monitoring;4. Management and monitoring plan of the demonstration sites;5. Joint bilingual communication strategy, which included informative programmes and meetings with professionals, locals and schools and also education material for further use.REIN-Forest focused on using scientific results and outputs in the field of applied forestry and awareness-raising. Besides strategies, recommendations and reports that would facilitate forest managers' decisions for the future in the border region, events and workshops were offered for forestry practitioners, school pupils and the public and a short film and educational materials were published. HTML XML PDF
      PubDate: Wed, 9 Aug 2023 16:07:06 +0300
       
  • Digital transformation strategies for applied science domains

    • Abstract: Research Ideas and Outcomes 9: e105197
      DOI : 10.3897/rio.9.e105197
      Authors : Samuel Bentum, David Wild : The key hallmark of a digitally minded organisation today is seen in their rapid advancement, globalisation, innovation and resilience to change. Companies that wish to thrive must be prepared to adapt to the new digital reality. Being digitally minded does not mean implementing new technology, investing in tools and upgrading current systems. These stages are critical, but they are not the entire picture. If a company wants to remain competitive, it must not just be able to adapt to changes, but also anticipate and drive innovation. Companies must plan ahead and be proactive architects of their future in order to achieve this vision. This is where a digital transformation strategy is crucial. A digital transformation strategy assists organisational leadership in addressing challenges about their business, such as the present level of digitisation and a digital maturity roadmap. Although diverse data capturing technologies and data-generating assets exist, material/chemical science domains, such as R&D and Manufacturing groups, struggle to harness the full power of their data. A typical industry will have significant data sources generating large amounts of data stored in siloed databases with minimal to non-existent cross-talk. This in part creates scenarios for researchers to be able to perform a deep dive in one set of data, but unable to co-populate and harness the interdependences or relationships amongst the different datasets. This paper seeks to define, distinguish, aggregate and propose an integrative approach to utilising the various types of disparate data sources commonly encountered by researchers in the field of their material science research. The main focus here is defining strategies to harness insights across integrative data to aid in efficient research in R&D organisations as these industries seek to embrace the power of digital transformation. Although the principles described here relate to industries in the applied science domain, the general strategies proposed can be applied to other industries on a case-by-case basis. HTML XML PDF
      PubDate: Wed, 9 Aug 2023 15:47:32 +0300
       
  • Important first steps towards designing the freshwater, marine and
           terrestrial Essential Biodiversity Variable (EBV) workflows for the
           European Biodiversity Observation Network

    • Abstract: Research Ideas and Outcomes 9: e109120
      DOI : 10.3897/rio.9.e109120
      Authors : Maria Lumbierres, W. Daniel Kissling : The EuropaBON project aims to co-design a European Biodiversity Observation Network by utilising Essential Biodiversity Variables (EBVs) as the foundation for its monitoring system. To co-design the workflow steps for each EBV, the project organised a virtual workshop to engage a diverse group of experts and stakeholders. The workshop focused on describing various workflow components, identifying future needs for EBV implementation and specifying the relative importance of different monitoring techniques for each EBV. With 520 participants from 49 countries, the workshop benefited from a large stakeholder engagement and a wide range of expertise across realms, EBV classes, monitoring techniques and workflow components. During the 3-day workshop (2 hours per day), participants captured different workflows components (i.e. data collection and sampling, data integration and modelling), specified current EU or national initiatives and identified emerging tools and future needs for all 70 currently proposed EBVs. By the end of the workshop, all 70 templates of EBV workflows contained details about workflow components and future needs. Specific future needs for data collection and sampling highlighted by participants were to increase sampling efforts (e.g. number of sites, geographic coverage, sampling frequency and taxonomic scope), to develop and better incorporate novel monitoring techniques (e.g. eDNA, remote sensing and digital sensors) and to create new or improved sampling designs at a European scale. For data integration, combining and harmonising data from diverse sources and data collectors and developing standards and protocols were mentioned as key needs. For modelling, participants especially highlighted the need to develop spatially-explicit models or improve other types of existing models, ideally with open-source software and code. Next steps for designing EBV workflows are to analyse the gathered workshop information, to provide detailed descriptions of EBV workflows and to formulate specific recommendations for the development of a European Biodiversity Observation Network. Recommendations for each monitoring technique (structured in-situ monitoring, citizen science, digital sensors, genetics, satellite remote sensing and aerial remote setting) will also be identified. The gathered information will contribute to the co-design of the European Biodiversity Observation Network and to supporting the establishment of a Biodiversity Monitoring Coordination Centre in Europe. HTML XML PDF
      PubDate: Tue, 11 Jul 2023 16:14:05 +030
       
  • D3.1 Inventory of current European network for monitoring. Web-based
           database

    • Abstract:
      DOI : 10.3897/arphapreprints.e109168
      Authors : Alejandra Morán-Ordóñez, David Martí Pino, Lluís Brotons : This report describes the database on biodiversity monitoring initiatives at the European level collected by EuropaBON (WP3 - task 3.1; EuropaBON biodiversity database from hereon) and the web-based platform (website) that contains it. The website serves the dual purpose of being the platform for data entry, as well as to allow the visualisation and quick consultation of the collected data. This report also gives a brief summary of the data collected up to the date of delivery of the report (end November 2021). Previous efforts on collecting information on existing monitoring efforts in Europe have concentrated in describing programs using a generalist approach that has received criticism because of lack of completeness even for well documented groups such as birds. Including all available information on monitoring in Europe at any spatial scale is difficult because of the high number of unlinked initiatives, specially at local scales, and the dynamic nature of these projects both in terms of the emergence of new efforts and the disappearance of old ones. To address this challenge, the EuropaBON project focusses on the monitoring network concept and aims at identifying, with priority, those monitoring efforts that are coordinated and especially those in which this coordination is consistent at a supranational level and at the European scale. Coordination in the context of monitoring is related to the integration of data and information across scales which is the underlying concept of a future successful biodiversity monitoring network in Europe. HTML XML PDF
      PubDate: Mon, 10 Jul 2023 11:16:00 +030
       
  • Designing a Metascience Institute

    • Abstract: Research Ideas and Outcomes 9: e108804
      DOI : 10.3897/rio.9.e108804
      Authors : Daniel Mietchen : This proposal outlines an open, transparent and collaborative process to design a Metascience Institute that would apply the scientific method onto itself, with the mission to improve the research landscape systemically in terms of maximizing societal benefit and public documentation thereof. This facility is envisaged to engage in the systematic study of the research ecosystem, initially at a national level in Germany but later on also in other contexts. As such, the Metascience Institute would assess systemic properties, interactions of different components within and beyond the research system and how the roles played by various components are aligned with goals of relevant stakeholder groups and broader societal benefits. Collaborating with any interested stakeholders on an initially narrow yet steadily expanding range of intra- and transdisciplinary use cases and using an appropriate mix of experimental, theoretical, empirical and computational approaches, the Metascience Institute would assess existing and proposed policies and practices in the research ecosystem and engage in public discourse around them, including by assessing the relative costs, benefits and side effects of alternative parametrizations of the system. The project proposed here is to design the organizational structure of such a Metascience Institute in an evidence-based and community-led fashion, to seed it with organizational values, to establish it as an independent legal entity with open and transparent policies and practices, to provide it with an initial technical infrastructure online, to design evidence-based and sustainable mechanisms by which it prioritizes its activities, and to document the entire process in a way that would facilitate reuse and adaptation by other communities or entities aiming at evidence-based systemic improvements to the research ecosystem or selected niches within it. HTML XML PDF
      PubDate: Wed, 5 Jul 2023 17:06:19 +0300
       
  • Improving COVID-19 metadata findability and interoperability in the
           European Open Science Cloud

    • Abstract:
      DOI : 10.3897/arphapreprints.e107873
      Authors : Christian Ohmann, Steve Canham, Kurt Majcen, Petr Holub, Gary Saunders, Jing Tang, Tanushree Tunstall, Philip Gribbon, Reagon Karki, Mari Kleemola, Katja Moilanen, Walter Daelemans, Pieter Fivez, Daan Broeder, Franciska de Jong, Maria Panagiotopoulou : This publication details the workplan of the Science Project (SP) “COVID-19 metadata findability and interoperability in EOSC” (short: META-COVID) that is part of the Horizon Europe funded project EOSC Future. The COVID-19 pandemic has generated a huge variety of research activities, studies, and policies across both the life sciences (LS) and the social sciences and humanities (SSH). Useful insights from combining the data and conclusions from these different forms of research are, however, hampered by the lack of a common metadata framework with which to describe them. This is because different scientific disciplines have different ways of organising research activities. For example, the type of the research (e.g., hypothesis testing versus hypothesis generating) and the methodology chosen (e.g., experimental, survey, cohort, case study) are key elements in understanding the data generated and in supporting its secondary use. Another issue to be tackled is the integration of various sources of metadata related to parliamentary and social media metadata. In META-COVID, scientists from the LS and SSH domains gathered to discuss ways in which metadata could go beyond the description of the data itself to include the basic elements of the research process (“contextual metadata”) within the frame of the European Open Science Cloud (EOSC). The main outcomes of the SP will be: i) An inventory of metadata schemas applied across infrastructures and domains; ii) The development of a framework for a metadata model characterising the research approach and workflow across research infrastructures; iii) The application of the framework to selected COVID-19 use cases; iv) The development of an ontology of COVID-19 related topics from parliamentary data and social media. HTML XML PDF
      PubDate: Wed, 14 Jun 2023 11:20:57 +030
       
  • Climate Neutral and Smart Cities, combining data about city people and
           their physical environment

    • Abstract:
      DOI : 10.3897/arphapreprints.e107872
      Authors : Hilde Orten, Bodil Agasøster, Eric Harrison : The main objective of the Science Project (SP) Climate Neutral and Smart Cities is to demonstrate that environmental data and data about people’s attitudes, behavior and involvement can be combined for social, political and scientific analysis. In the project, scientists from the Social Sciences & Humanities Open Cloud (SSHOC) and Environmental Research Infrastructures (ENVRI) community work together with the aim of producing new and useful outputs for the benefit of the research community, such as indicators related to environmental indices, and methods and workflows for computing them. The environmental variables will be integrated with data from the European Social Survey for a selection of big European city regions. Data and metadata from the project will be accessible through a new prototype application that will be made available as an exploratory “labs” service from the European Open Science Cloud (EOSC) Portal and the EOSC Marketplace. This will allow easy access to cross-domain data for scientific analysis and their provenance, as well as to other deliverables from the project. HTML XML PDF
      PubDate: Wed, 14 Jun 2023 11:17:15 +030
       
  • Dashboard for the State of the Environment

    • Abstract:
      DOI : 10.3897/arphapreprints.e107578
      Authors : Alex Vermeulen, Dick Schaap, Angeliki Adamaki, Tjerk Krijger, Raul Bardaji, Andreu Fornos, Ivan Rodero, Damien Boulanger, Cathrine Myhre, Richard Rud, Zois Zogopoulos, Claudio D’Onofrio, Gwenaelle Moncoiffé : The Environmental Research Infrastructure (ENVRI) community is a cluster of European research infrastructures focused on the environment and Earth system science. The ENVRI-FAIR project aims to advance the FAIRness of their data and services with emphasis on interoperability and connect the ENVRI community to the European Open Science Cloud (EOSC). In this article, we present a proposal for a science project that will develop and launch a dashboard for environmental indicators as a contribution from the ENVRI cluster to the EOSC platform. The dashboard will provide easy access to environmental data and services from multiple research infrastructures and disciplines and support interdisciplinary Earth system science and societal challenges. The proposal describes the objectives, implementation, impact, and dissemination measures of the project, as well as the partners involved and the target groups that can benefit from the dashboard service. We explain how the dashboard will showcase the usefulness and relevance of the observations provided by the research infrastructures, and how it will engage a larger community of researchers and potential data providers in co-creation processes. We also discuss how the dashboard will make use of existing and new EOSC services and resources, and how it will contribute to several EU initiatives and directives related to the environment and climate change. HTML XML PDF
      PubDate: Tue, 6 Jun 2023 11:38:41 +0300
       
  • DiSSCo Prepare Project: Increasing the Implementation Readiness Levels of
           the European Research Infrastructure

    • Abstract: Research Ideas and Outcomes 9: e107220
      DOI : 10.3897/rio.9.e107220
      Authors : Dimitrios Koureas, Laurence Livermore, Eva Alonso, Wouter Addink, Ana Casino : The Distributed System of Scientific Collections (DiSSCo) is a new world-class Research Infrastructure (RI) for Natural Science Collections. The DiSSCo RI aims to create a new business model for one European collection that digitally unifies all European natural science assets under common access, curation, policies and practices that ensure that all the data is easily Findable, Accessible, Interoperable and Reusable (FAIR principles). DiSSCo represents the largest ever formal agreement between natural history museums, botanic gardens and collection-holding institutions in the world.DiSSCo entered the European Roadmap for Research Infrastructures in 2018 and launched its main preparatory phase project (DiSSCo Prepare) in 2020. DiSSCo Prepare is the primary vehicle through which DiSSCo reaches the overall maturity necessary for its construction and eventual operation. DiSSCo Prepare raises DiSSCo’s implementation readiness level (IRL) across the five dimensions: technical, scientific, data, organisational and financial. Each dimension of implementation readiness is separately addressed by specific Work Packages (WP) with distinct targets, actions and tasks that will deliver DiSSCo’s Construction Masterplan. This comprehensive and integrated Masterplan will be the product of the outputs of all of its content related tasks and will be the project’s final output. It will serve as the blueprint for construction of the DiSSCo RI, including establishing it as a legal entity.DiSSCo Prepare builds on the successful completion of DiSSCo’s design study, ICEDIG and the outcomes of other DiSSCo-linked projects such as SYNTHESYS+ and MOBILISE.This paper is an abridged version of the original DiSSCo Prepare grant proposal. It contains the overarching scientific case for DiSSCo Prepare, alongside a description of our major activities. HTML XML PDF
      PubDate: Thu, 1 Jun 2023 17:46:22 +0300
       
  • Dealiverable D1.3 Best practice manual for findability, re-use and
           accessibility of infrastructures

    • Abstract:
      DOI : 10.3897/arphapreprints.e107169
      Authors : Wouter Addink, Niki Kyriakopoulou, Lyubomir Penev, David Fichtmueller, Ben Norton, David Shorthouse : United and coordinated efforts of biodiversity data infrastructures are needed to bring together various data forms from many different scientific areas. Biodiversity data are considered of great importance and use when they form a network of knowledge that can be seamlessly integrated and presented to various audiences, promoting both research and education. The Biodiversity Community Integrated Knowledge Library (BiCIKL) project seeks to maximise the potential of integrated data sources by striving to connect fragmented data derived from biological, paleontological, and geological specimens and collections, as well as all derived information such as literature in the form of taxonomic treatments, research papers etc., taxonomic information and molecular sequences provided by these infrastructures, under the umbrella of common digital practices and policies in curation, data sharing and open data access over different scientific fields. One of the main goals of BiCIKL is to create bi-directional links between various data types, a process enabled by: a) the adoption of globally unique and persistent identifiers upon agreement among all stakeholders, that link to digital specimen objects, collections, taxonomic treatments, people, sequence data and taxa, and b) implementation of the best practices for the generation, management and curation of interlinked data by the host infrastructures. At the same time, infrastructures should be readily discoverable and accessible by end users, providing data that enable re-usability. In this manual we give an overview of the best practices and their associated recommendations for infrastructures on making the most out of their services and data, for establishing a network of knowledge with other infrastructures, for servicing researchers, data providers and other end users. These guidelines have been developed in collaboration with the infrastructures through Technical RI Forum meetings organised in the context of the BiCIKL project. Practices and recommendations were divided into six categories: 1) modalities of access, 2) building communities and trust, 3) technology and standards, 4) versioning of APIs and their data, 5) bi-directional linking between infrastructures and 6) API design patterns and naming conventions. A second division into three user groups (Infrastructures, Data providers, Users e.g. Researchers, Developers and Citizen scientists) is presented in Appendix I. HTML XML PDF
      PubDate: Tue, 30 May 2023 09:51:32 +030
       
  • Deliverable D7.1 Architecture Design for a pan-European PID system
           for Digital Specimens

    • Abstract:
      DOI : 10.3897/arphapreprints.e107168
      Authors : Wouter Addink, Sharif Islam, Mathias Dillen, Anton Güntsch, Soulaine Theocharides : Persistent Identifier (PID) systems are the foundation for achieving the FAIR Guiding Principles (“findable, accessible, interoperable and reusable”). As FAIR data and connecting different data classes (i.e. specimens, genomics, observations, taxonomy and publications) are essential aspects of the BiCIKL project, we need a PID system at least at the European level to create and maintain identifiers for the digital representation of specimens and samples, called Digital Specimens (DS) (Hardisty et al. 2022). The PID system provides the mechanism to ensure that identifiers are globally unique, persistent and resolvable. This system should also manage associated metadata, facilitate provenance, enable discovery, manage states and the life cycle of the PID, link to other derived data and digital content, and allow content providers to enforce metadata constraints. For the successful provision of a PID system, this design document has been created to guide us during the implementation and operation phases. The document is based on an earlier milestone (MS28) that was used for discussion and evaluation with potential end-users. HTML XML PDF
      PubDate: Tue, 30 May 2023 09:50:12 +030
       
  • Deliverable D8.3 Web interface for ELIXIR Contextual Data
           ClearingHouse

    • Abstract:
      DOI : 10.3897/arphapreprints.e107167
      Authors : Kessy Abarenkov, Allan Zirk, Guy Cochrane, Vishnukumar Kadhirvelu, Joana Pauperio, Olaf Bánki, Jerry Lanfear, Filipp Ivanov, Timo Piirmann, Raivo Pöhönen, Urmas Kõljalg : This deliverable report includes description of the work steps towards building a web interface for the reporting of errors and gaps in sequenced material source annotations as part of the Task 8.3 of BiCIKL. Beta version of the web interface has been published and is available for the registered users of PlutoF platform. HTML XML PDF
      PubDate: Tue, 30 May 2023 09:49:52 +030
       
  • Deliverable D11.2 Search and link association services: A RESTful API,
           which will input a link/accession number and return a ranked list of
           neighbours links with a confidence score

    • Abstract:
      DOI : 10.3897/arphapreprints.e107166
      Authors : Soulaine Theocharides, Niki Kyriakopoulou : Work package 11 of the BiCIKL project involves developing software tools to support a FAIR experience for members of the biodiversity research community. The package overall focuses on Findability, by providing tools to search and answer questions, and Accessibility, through developing links across various biodiversity data sources and research tools. Task 11.2 specifically involves prediction of new links using machine learning. We chose to demonstrate the functionality of machine learning link prediction with plant-pollinator interactions. This type of interaction was chosen due to the wealth of data available, particularly on the Global Biotic Interactions (GloBI) database, as well as this kind of interaction’s ecological and economic significance. The result was a RESTful API capable of predicting plant-pollinator interactions among a predefined set of species. Predictions are made on-the-fly, at the time of the request. The GitHub repository for the API can be found here: https://github.com/DiSSCo/BiCIKL_Linkages_APIThe API takes either a plant or a pollinator as inputs, and outputs potential matches based on a user-defined confidence score. The API’s prediction is powered by a random forest classifier stored on disk. The classifier was trained on the taxonomic hierarchy of observed plant-pollinator pairs obtained from the GloBI database. When evaluating the likelihood of an interaction, the trained classifier looks at the taxonomic hierarchy of both the plant and pollinator and outputs a confidence score. What pairs are returned is determined by the minimum confidence score set by the user. HTML XML PDF
      PubDate: Tue, 30 May 2023 09:39:22 +030
       
  • Participation as a research approach in academia: a converging field

    • Abstract: Research Ideas and Outcomes 9: e105155
      DOI : 10.3897/rio.9.e105155
      Authors : Mathilde Bessert-Nettelbeck, Andreas Bischof, Ulrike Sturm, Emilia Nagy, Martina Schraudner, Julia Backhaus, Till Bruckermann, Susanne Hecker, Justus Henke, Karola Köpferl, Sabrina Kirschke, Christin Liedtke, Felix Mahr, Arne Maibaum, Audrey Podann, Wiebke Rössig, Martina Schäfer, Carolin Schröder, Philipp Schrögel, Victoria Shennan, Norbert Steinhaus, Mhairi Stewart, Vanessa van den Bogaert, Silke Voigt-Heucke : Citizen science, transdisciplinary research, dialogic forms of science communication or public engagement: these and other research approaches and fields, often subsumed under participatory research, have in common that they enable people outside of academia to actively engage in the production of scientific knowledge. However, each of these fields sets its own goals, uses different formats and has a different scope and impact. The conference 'Opportunities and Limitations of Participation in Academia' held in September 2022 as part of the German Science Year 'Participate!' aimed to connect the various participation communities in Germany and to explore commonalities and success factors. Through intensive discussions in four working groups, a keynote speech and a panel discussion, the conference initiated an exchange of ideas and experiences amongst researchers in a converging field. This report is a summary of the key questions and outcomes of the conference. HTML XML PDF
      PubDate: Mon, 29 May 2023 09:35:50 +030
       
  • Climate Change Impact on Biodiversity and Ecosystems in Europe: Assessing
           the impact of Non-Indigenous Invasive Species (NIS) in
           European ecosystems

    • Abstract:
      DOI : 10.3897/arphapreprints.e106475
      Authors : Christos Arvanitidis, Alberto Basset, Thierry Carval, Katrina Exter, Nicola Fiore, Alessandra Giorgetti, Juan Miguel González-Aranda, Mark Hebden, Georgios Kotoulas, Joaquín López Lérida, Rory Meyer, Nikos Minadakis, Matthias Obst, Nicolas Pade, Christina Pavloudi, Marc Portier, Ioulia Santi, Dick Schaap, Peter Thijsse, Lucia Vaira, Cristina Huertas Olivares : This Science Project (SP) contributes to the estimation of the impacts of the invasive species on the European Biodiversity and Ecosystems. This topic is important for European Green Deal and the new European Biodiversity Strategy. The SP is also linked with the socio-economic issues because of the NIS implications to the local ecosystems and their services, and their societal goods and services. Since many of the above impacts may be of local scale, they may alter common practices in circular economies. The SP is implemented by: (a) Combining different sources of data and information; (b) Using a dual workflow to analyse the data; (c) Integrating its resources with core EOSC services and potentially horizontal services available; (d) Engaging the relevant scientific communities. The users will be able to: (a) Analyse distribution patterns of invasive species from different sources of data; (b) Compare the above patterns; (c) Provide managerial suggestions to relevant authorities; (d) Build on the existing infrastructure to address more complex questions (e.g. future scenarios). HTML XML PDF
      PubDate: Tue, 16 May 2023 10:15:00 +030
       
  • EOSC Future: Design and implementation of community engagement through
           Science Projects

    • Abstract:
      DOI : 10.3897/arphapreprints.e106369
      Authors : Christos Arvanitidis, Ron Dekker, Andreas Petzold, Niklas Blomberg, Giovanni Lamanna, Rudolf Dimper, Cristina Isabel Huertas Olivares, Ana Mellado, Matthew Viljoen, Sally Chambers, Montserrat González, Sophie Viscido : The Special Collection of articles on the Science Projects of the EOSC Future project, funded by the European Commission, refers to one of the essential components of the project. This editorial article explains how the Science Projects fit to the EOSC Future, the way their concept has been developed and evolved during the preparation and the implementation of the project and it also makes an introduction to the templates developed by the Science Projects as a plan to carry out their activities. HTML XML PDF
      PubDate: Mon, 15 May 2023 17:03:13 +030
       
  • D3.4 Cost-effectiveness analysis of monitoring schemes

    • Abstract:
      DOI : 10.3897/arphapreprints.e105599
      Authors : Tom Breeze, Miguel Fernandez, Ian McCallum, Alejandra Morán-Ordóñez, Henrique Pereira, Jessi Junker : Financial factors are among the most widely cited bottlenecks around biodiversity monitoring but are relatively poorly studied, compared to monitoring methodologies. The existing body of literature on the cost-effectiveness of monitoring focuses heavily on the hypothetical costs of generating data rather than the practical realities of undertaking and managing monitoring. To address this we used a combination of surveys and semi-structured interviews with 67 biodiversity monitoring managers to provide an in-depth exploration of 1) what are the main rivers of their costs, 2) how different factors affect their cost-effectiveness in generating biodiversity monitoring data, 3) What is the scale and economic value of volunteer labor and 4) what are the main cost bottlenecks and spending priorities. Analysis of these responses demonstrates that monitoring efforts are able to generate more data at a lower cost when they have a) higher numbers of volunteers, b) greater densities of sites and c) monitor a wider range of taxa and habitats. Volunteer labour was worth millions of Euros to these organizations, sometimes more than their total costs. Total budgets and volunteer recruitment and retention were the main cost related bottlenecks among respondents, while staff recruitment was the highest priority for new spending.  The results and discussion around them highlight the challenges faced by biodiversity monitoring organizations, particularly in recruiting and retaining qualified staff for the long-term. We produce a series of nine key messages and six recommendations for policy-markers and funders going forward. HTML XML PDF
      PubDate: Tue, 2 May 2023 12:30:00 +0300
       
  • Deliverable 4.2 Novel technologies for biodiversity monitoring - Final
           Report

    • Abstract:
      DOI : 10.3897/arphapreprints.e105600
      Authors : Maria Dornelas, Cher Chow, Robert Patchett, Tom Breeze, Lluís Brotons, Pedro Beja, Laurence Carvalho, Ute Jandt, Jessi Junker, W. Daniel Kissling, Ingolf Kühn, Maria Lumbierres, Anne Lyche Solheim, Marit Mjelde, Francisco Moreira, Martin Musche, Henrique Pereira, Leonard Sandin, Roy Van Grunsven : The goal of this task was to identify and characterise novel methods for biodiversity monitoring, and to assess their suitability for large scale deployment across Europe. To address this goal we combined extensive literature searches with expert consultation, namely using a survey and through an online workshop. The outcome of our searches is summarised in a metadatabase, which includes 282 methods or method components, which have been classified according to EBV classes addressed, target taxa, and broad method type the method relates to. We then consulted experts within the EuropaBON network and beyond, on the advantages and challenges associated with each of these novel methods, as well as their technology readiness level. In combination, our approaches revealed a wealth of novel methods and a highly active research field, with extensive emerging innovation on several fronts. However, it also revealed high variability in technology readiness, with lack of validation being a prevalent hurdle yet to be overcome for many applications of these methods (i.e. for some taxa and in some environments). Moreover, the opportunities for expansion in observations created by these novel approaches open new challenges associated to the standardisation, integration and storage of biodiversity monitoring data. Finally, the expansion of observations should take a designed approach, in order to deliver on its potential to improve representation and resolution of biodiversity monitoring, and should aim to complement rather than replace human observations.  HTML XML PDF
      PubDate: Tue, 2 May 2023 10:40:00 +0300
       
 
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  Subjects -> SCIENCES: COMPREHENSIVE WORKS (Total: 374 journals)
Showing 201 - 265 of 265 Journals sorted alphabetically
Jurnal MIPA     Open Access  
Jurnal Natural     Open Access  
Jurnal Sains Dasar     Open Access  
Jurnal Teknosains     Open Access  
Jurnal Udayana Mengabdi     Open Access  
Karaelmas Science and Engineering Journal     Open Access  
Karbala International Journal of Modern Science     Open Access  
Kennedy Institute of Ethics Journal     Full-text available via subscription   (Followers: 10)
LOGIKA Jurnal Ilmiah Lemlit Unswagati Cirebon     Open Access  
Logo STI Science, Technology and Innovation     Open Access   (Followers: 15)
Makara Journal of Science     Open Access  
Malawi Journal of Science and Technology     Open Access   (Followers: 6)
Maskana     Open Access  
MethodsX     Open Access  
Metode & Forskningsdesign     Open Access  
Mètode Science Studies Journal : Annual Review     Open Access  
Middle East Journal of Science     Open Access  
Middle European Scientific Bulletin     Open Access   (Followers: 4)
Modern Applied Science     Open Access   (Followers: 1)
Momona Ethiopian Journal of Science     Open Access   (Followers: 5)
MUST : Journal of Mathematics Education, Science and Technology     Open Access   (Followers: 4)
Mutis     Open Access  
National Academy Science Letters     Hybrid Journal   (Followers: 3)
National Science Review     Hybrid Journal   (Followers: 1)
Natural Sciences     Open Access  
Natural Sciences Education     Hybrid Journal   (Followers: 1)
Naturen     Full-text available via subscription  
Nepal Journal of Science and Technology     Open Access  
Network Science     Hybrid Journal   (Followers: 4)
New Directions in the Teaching of Physical Sciences     Open Access   (Followers: 2)
Nordic Journal of Science and Technology     Open Access   (Followers: 2)
Nordic Studies in Science Education     Open Access   (Followers: 3)
Nova     Open Access  
Nuncius     Hybrid Journal   (Followers: 2)
OmniScience : A Multi-disciplinary Journal     Full-text available via subscription   (Followers: 1)
Open Conference Proceedings Journal     Open Access  
Open Journal of Applied Sciences     Open Access  
Orbis Cógnita : Revista Científica     Open Access   (Followers: 2)
Patterns     Open Access   (Followers: 9)
PENDIPA : Journal of Science Education     Open Access   (Followers: 1)
People and Nature     Open Access   (Followers: 4)
Población y Desarrollo - Argonautas y caminantes     Open Access  
Politique et Sociétés     Full-text available via subscription   (Followers: 1)
Portal de la Ciencia     Open Access  
Proceedings of the Indian National Science Academy     Full-text available via subscription   (Followers: 5)
Proceedings of the Linnean Society of New South Wales     Full-text available via subscription   (Followers: 2)
Proceedings of the Royal Society of Queensland, The     Full-text available via subscription  
QScience Connect     Open Access  
Quantum Science and Technology     Hybrid Journal   (Followers: 19)
RAC: Revista Angolana de Ciências     Open Access   (Followers: 6)
Rafidain Journal of Science     Open Access  
Rehabilitation Research, Policy, and Education     Hybrid Journal   (Followers: 2)
Rekayasa     Open Access   (Followers: 2)
Reportes Científicos de la FaCEN     Open Access  
Reports in Advances of Physical Sciences     Open Access  
Research     Open Access   (Followers: 6)
Research Ideas and Outcomes     Open Access  
Research Integrity and Peer Review     Open Access  
Research Policy : X     Open Access   (Followers: 3)
Respuestas     Open Access  
Reviews in Theoretical Science     Full-text available via subscription  
Revista Bases de la Ciencia     Open Access  
Revista Binacional Brasil - Argentina: Diálogo entre as ciências     Open Access  
Revista Brasileira de Iniciação Científica     Open Access  
Revista Catarinense da Ciência Contábil     Open Access  
Revista Ciencia y Tecnología     Open Access  
Revista Ciência, Tecnologia & Ambiente     Open Access  
Revista Científica de la FAREM     Open Access  
Revista Científica de la Universidad Nacional del Este     Open Access   (Followers: 2)
Revista Cientifica Guillermo de Ockham     Open Access  
Revista Científica y Tecnológica UPSE     Open Access  
Revista Conhecimento Online     Open Access  
Revista Crítica de Ciências Sociais     Open Access  
Revista de Ciencia y Tecnología     Open Access  
Revista de Información Científica     Open Access  
Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales     Open Access  
Revista de la Sociedad Científica del Paraguay     Open Access   (Followers: 7)
Revista de la Universidad del Zulia     Open Access  
Revista Eletrônica Ludus Scientiae     Open Access  
Revista Logos Ciencia & Tecnología     Open Access  
Revista MundoFesc     Open Access  
Revista Politécnica     Open Access  
Revista Saber Digital     Open Access   (Followers: 3)
Revista Sociedad y Economía     Open Access  
Revista Tecnológica     Open Access  
Revista Theoria     Open Access   (Followers: 1)
Revista UNIMAR     Open Access  
Revista UniVap     Open Access  
Revista Vivências em Ensino de Ciências     Open Access   (Followers: 1)
Rihan Journal for Scientific Publishing     Open Access   (Followers: 1)
Royal Society Open Science     Open Access   (Followers: 7)
Ruhuna Journal of Science     Open Access  
Sainstek : Jurnal Sains dan Teknologi     Open Access  
SAINSTIS     Open Access  
Sainteknol : Jurnal Sains dan Teknologi     Open Access  
Sakarya Üniversitesi Fen Bilimleri Enstitüsü Dergisi     Open Access  
Scholedge International Journal of Multidisciplinary & Allied Studies     Open Access  
Sci     Open Access  
Science     Full-text available via subscription   (Followers: 4968)
Science & Diplomacy     Free   (Followers: 3)
Science & Technology Studies     Open Access   (Followers: 4)
Science Advances     Free   (Followers: 43)
Science and Technology     Open Access   (Followers: 2)
Science Diliman     Open Access  
Science Heritage Journal     Open Access  
Science World Journal     Open Access  
Science, Technology and Arts Research Journal     Open Access   (Followers: 1)
ScienceRise     Open Access  
Sciences du jeu     Open Access  
Sciential     Open Access  
Scientific African     Open Access  
Scientific American     Full-text available via subscription   (Followers: 497)
Scientific American Mind     Full-text available via subscription   (Followers: 10)
Scientific Bulletin     Open Access   (Followers: 1)
Scientific Data     Open Access   (Followers: 7)
Scientific Journal of Mehmet Akif Ersoy University     Open Access  
Scientific Journal of Pure and Applied Sciences     Open Access   (Followers: 1)
Scientific Reports     Open Access   (Followers: 82)
Scientific World     Open Access  
Scientonomy : Journal for the Science of Science     Open Access   (Followers: 1)
Scienze Regionali : Italian Journal of Regional Science     Full-text available via subscription   (Followers: 18)
Selforganizology     Open Access  
Seminário de Iniciação Científica e Seminário Integrado de Ensino, Pesquisa e Extensão     Open Access  
Simbiótica     Open Access  
SINET : Ethiopian Journal of Science     Open Access   (Followers: 5)
Smart Science     Open Access  
South African Journal of Science     Open Access   (Followers: 2)
South American Sciences     Open Access   (Followers: 1)
South East European University Review (SEEU Review)     Open Access   (Followers: 3)
Springer Science Reviews     Hybrid Journal   (Followers: 2)
Studies in Science Education     Hybrid Journal   (Followers: 18)
Sultan Qaboos University Journal for Science     Open Access  
Tanzania Journal of Science     Open Access   (Followers: 4)
TD : The Journal for Transdisciplinary Research in Southern Africa     Open Access  
Technologies     Open Access   (Followers: 1)
TECNOSCIENZA: Italian Journal of Science & Technology Studies     Open Access   (Followers: 2)
Temas y Debates     Open Access  
The Innovation     Open Access   (Followers: 8)
The Scientific World Journal     Open Access  
The Social Studies     Hybrid Journal   (Followers: 3)
The Winnower     Open Access  
Theoria     Open Access   (Followers: 3)
THEORIA : An International Journal for Theory, History and Foundations of Science     Full-text available via subscription   (Followers: 1)
Transactions of Tianjin University     Full-text available via subscription  
Trilogía     Open Access  
TÜBAV Bilim Dergisi     Open Access  
Türk Bilim ve Mühendislik Dergisi     Open Access  
Tydskrif vir Geesteswetenskappe     Open Access  
Uluslararası Bilimsel Araştırmalar Dergisi (IBAD)     Open Access   (Followers: 1)
UNED Research Journal / Cuadernos de Investigación UNED     Open Access   (Followers: 1)
Uni-pluriversidad     Open Access  
Uniciencia     Open Access  
Universidad, Ciencia y Tecnología     Open Access  
Universitas (León)     Open Access  
Universitas Scientiarum     Open Access  
Unnes Science Education Journal     Open Access  
Vilnius University Proceedings     Open Access  
Walailak Journal of Science and Technology     Open Access  
WikiJournal of Science     Open Access  
World Scientific Research     Open Access  
Zeitschrift für Didaktik der Naturwissenschaften     Hybrid Journal  
Образование и наука     Open Access   (Followers: 1)
Східно-Європейський журнал передових технологій : Eastern-European Journal of Enterprise Technologies     Open Access   (Followers: 3)

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