Abstract: DOI : 10.3897/arphapreprints.e134026 Authors : Claudia Fornarini, Alessandra D'Alessio, Jeremy Dertien, Néstor Fernández, Francisco Moreira, Anandi Sarita Namasivayam, Louise O'Connor, Henrique Pereira, Peter Verburg, Carlo Rondinini : A key goal of the EU Biodiversity Strategy for 2030 is the design of a connected Trans European Nature Network (TEN-N), that helps to build a coherent and resilient network of protected areas across Europe. The TEN-N will need to consider and integrate societal perspectives on future biodiversity protection in Europe, accounting for multiple values and perspectives of nature. The NaturaConnect project, through a process of co-design with stakeholders, is developing narratives on future nature protection in Europe using the Nature Futures Framework (NFF). In this framework. three value perspectives of nature are presented at each corner of a triangle: Nature for Nature, Nature as Culture, and Nature for Society. By using this framework, NaturaConnect aligns with global efforts on scenario development auspicated by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES). This report outlines the development of scenario narratives for Europe of the NaturaConnect project. The development of the narratives considered the global and European policy context as a starting point, and included a stakeholder engagement process conducted to elicit stakeholders' preferences and visions in relation to future nature conservation and management in Europe. These narratives present contrasting perspectives and priorities for seven themes: Protected areas, Connectivity and Restoration, Forestry, Freshwater ecosystems, Urban system, Agriculture, Energy. These topics are key to building a more positive future for nature and people. Besides specificities for each narrative, we also identify commonalities across the three perspectives, including macroeconomic trend assumptions, biodiversity strategic goals of the European Union and shared solutions that are necessary to achieve any positive nature future. HTML XML PDF PubDate: Wed, 7 Aug 2024 09:38:28 +0300
Abstract: Research Ideas and Outcomes 10: e131405 DOI : 10.3897/rio.10.e131405 Authors : H. Michael G. Lattorff : Pollination of crop plants is highly valued as it contributes to productivity in terms of quality and quantity. Globally, pollination is valued at more than USD 500 billion. The primary pollinators are insects and amongst them, bees. The Western honeybee (Apis mellifera) is a very generalist pollinator that is managed. Honeybees contribute up to 50% of the pollination of various crop plants. Pollinators are at risk due to land-use/land-cover changes and agricultural pesticide input.In a recently published study, research on honeybees in runner bean (Phaseolus coccineus L.) in Poland is presented. In one part of the study, the actual foraging of honeybees in beans is recorded, along with the time of day, abundance and time spent on flowers. The second part of the study investigated several apiaries concerning the potential poisoning of bees by means of pesticide exposure. The authors recorded the fitness of colonies, flight activity, behaviour, productivity and pesticide residues in bees.The manuscript, unfortunately, has several scientific flaws that are outlined in this commentary. These flaws, particularly those related to experimental planning and data collection and analysis, have the potential to compromise the conservation of pollinators. The misguidance in the implementation of measures to protect pollinators and pollination services is a cause for concern and should motivate us to address these issues. HTML XML PDF PubDate: Mon, 29 Jul 2024 10:45:00 +030
Abstract: DOI : 10.3897/arphapreprints.e132163 Authors : Marit Schnepf, Simone Prestes Dürrnagel, Giacomo Laghetto, Teresa Pastor, Carol Ritchie : NaturaConnect is a Horizon Europe research project, which aims to work closely with key stakeholders to co-develop tools and build capacity that will assist European Union Member States to design a resilient, coherent, and well-connected network of protected and conserved areas – the Trans-European Nature Network (TEN-N). The project aims to elicit stakeholder visions and to tailor knowledge and tools, resulting from engagement and dissemination efforts across Europe and in six specific case study areas. This report provides an overview of the stakeholder engagement during the first half of the project, outlines the capacity building approach and briefly discusses the main communication activities. An overview of applied methods in the stakeholder analysis, results from the stakeholder mapping and an evaluation of the engagement activities conducted until end of 2023 are described. Capacity building is a crucial project component in developing knowledge, understanding, skills and competences for users of the NaturaConnect frameworks, data and tools. The capacity building evaluation of this report focuses on the NaturaConnect Learning Platform and the NaturaConnect Training Needs Assessment. This mid-term report assesses engagement activities conducted until date in order to address any identified bottlenecks. The capacity building part provides an overview of applied methods and tools for assessing training needs and describes key features of the NaturaConnect Learning Platform. HTML XML PDF PubDate: Tue, 16 Jul 2024 09:15:00 +030
Abstract: Research Ideas and Outcomes 10: e127510 DOI : 10.3897/rio.10.e127510 Authors : James Morris : Community tutelary shrines in Taiwan have been identified as excellent resources for grassroots-level heritage. As community ritual assemblages, they are able to encode data about a settlement’s social, political and economic history in their material composition, aesthetic choices, artefacts, displays and orientations. This data paper previews a first edition dataset related to 752 such shrines found throughout the greater Taipei area in northern Taiwan. It explores the basis for such a dataset, how it can be used and what has been produced. This dataset is available on the depositar research data repository, operated out of the Institute of Information Sciences at Academia Sinica in Taipei and is publicly available for download. HTML XML PDF PubDate: Fri, 12 Jul 2024 15:30:00 +030
Abstract: Research Ideas and Outcomes 10: e129357 DOI : 10.3897/rio.10.e129357 Authors : Christiane Werner, Ulrike Wallrabe, Andreas Christen, Laura Comella, Carsten Dormann, Anna Göritz, Rüdiger Grote, Simon Haberstroh, Mazin Jouda, Ralf Kiese, Barbara Koch, Jan Korvink, Jürgen Kreuzwieser, Friederike Lang, Julian Müller, Oswald Prucker, Alexander Reiterer, Jürgen Rühe, Stefan Rupitsch, Helmer Schack-Kirchner, Katrin Schmitt, Nina Stobbe, Markus Weiler, Peter Woias, Jürgen Wöllenstein : Global climate change threatens ecosystem functioning worldwide. Forest ecosystems are particularly important for carbon sequestration, thereby buffering climate change and providing socio-economic services. However, recurrent stresses, such as heat waves, droughts and floods can affect forests with potential cascading effects on their carbon sink capacity, drought resilience and sustainability. Knowledge about the stress impact on the multitude of processes driving soil-plant-atmosphere interactions within these complex forest systems is widely lacking and uncertainty about future changes extremely high. Thus, forecasting forest response to climate change will require a dramatically improved process understanding of carbon and water cycling across various temporal (minutes to seasons) and spatial (leaf to ecosystem) scales covering atmosphere, biosphere, pedosphere and hydrosphere components.Many relevant processes controlling carbon and water exchange occur at small scales (e.g. rhizosphere, single leaf) with a high spatial and temporal variability, which is poorly constrained. However, interactions and feedback loops can be key players that amplify or dampen a system’s response to stress. Moreover, spatial and temporal scaling rules for these non-linear processes in structurally and functionally diverse ecosystems are unknown. Legacy effects, for example, altered response after previous stress and retarded recovery of forests after climate extremes, are not captured in state-of-the-art models. Currently, we are lacking the appropriate and interconnected measurement, data assimilation and modelling tools allowing for a comprehensive, real-time quantification of key processes at high spatio-temporal coverage in heterogeneous environments. Moreover, since climate impacts are highly unpredictable with respect to timing and location, future research will require novel mobile, easily deployable and cost-efficient approaches. ECOSENSE, therefore, assembles expertise from environmental and engineering sciences, both being excellently paired at the University of Freiburg.Our interdisciplinary research project will investigate all relevant scales in a next-generation ecosystem research assessment (ECOSENSE). Our vision is to detect and forecast critical changes in ecosystem functioning, based on the understanding of hierarchical process interaction. In the first phase, ECOSENSE will explore these process interactions by investigating pools and fluxes of water and carbon, i.e. CO2 exchange, isotope discrimination and volatile organic compounds (VOC), as well as stress indicators by remotely and in situ sensed chlorophyll fluorescence.To address these research tasks, ECOSENSE will develop, implement and test a distributed, autonomous, intelligent sensor network, based on novel microsensors tailored to the specific needs in remote and harsh forest environments. They will measure the spatio-temporal dynamics of ecosystem pools and fluxes in a naturally complex structured forest system with minimal physiological impact. Measured data will be transferred in real-time into a sophisticated database, which will be explored for process analysis, conducted by Artificial Intelligence and close to real-time process-based ecosystem models for now- and forecasting applications. Thereby, ECOSENSE will: i) break new ground for integrative ecosystem research by identifying hierarchies and interactions of abiotic and physiological processes of forest carbon and water exchange, ii) provide a profound understanding of complex ecosystem responses to environmental stressors and iii) enable the prediction of process-based alterations in ecosystem functioning and sustainability.Our novel ECOSENSE toolkit, tested and validated in controlled climate extreme experiments and our ECOSENSE Forest, will open new horizons for rapid assessment in vast and remote ecosystems. Thereby, ECOSENSE will allow for a unique avenue of data acquisition and, consequently, for unprecedented scale-crossing ecosystem understanding and modelling. HTML XML PDF PubDate: Fri, 12 Jul 2024 14:06:54 +030
Abstract: DOI : 10.3897/arphapreprints.e131654 Authors : Grace Kotnik, Lisa Morales, Bastiaan Willem Ibelings, Mridul Thomas, Alena Gsell, Dedmer van de Waal : Poster showing the experimental design for a laboratory assay for sinking rates of chytrid infected diatom Asterionella formosa. HTML XML PDF PubDate: Wed, 10 Jul 2024 17:05:58 +030
Abstract: Research Ideas and Outcomes 10: e130474 DOI : 10.3897/rio.10.e130474 Authors : Gabriela Ioana-Toroimac : Our report synthesizes information on (i) restoration projects along the Lower Danube River in order to show their hydrological effects and (ii) reference conditions of sites in order to better understand the evolution of riparian wetlands under present-day conditions.Our report (i) concluded on the difficulty to successfully restore the hydrology of the Lower Danube wetlands and (ii) pointed out restrictive factors for the terrestrialization of wetlands and islands in reference conditions.Overall, the report is a state of the art that shows a general picture of the present-day hydrological conditions of the Lower Danube’s wetlands. HTML XML PDF PubDate: Fri, 5 Jul 2024 10:12:00 +0300
Abstract: Research Ideas and Outcomes 10: e124977 DOI : 10.3897/rio.10.e124977 Authors : Steffen Neumann, Ann-Christin Andres, Felix Bach, Theo Bender, Christian Bonatto Minella, Franziska Eberl, Tillmann Fischer, Benjamin Golub, Shashank Harivyasi, Sonja Herres-Pawlis, Pei-Chi Huang, Johannes Hunold, John Jollife, Nicole Jung, Johannes Liermann, Venkata Nainala, Matthias Razum, Oliver Koepler, Christoph Steinbeck : The progress of the DFG-funded NFDI4Chem consortium (NFDI 4/1 - project number 441958208) in data management in chemistry is outlined in our latest report, highlighting the steps we have taken to integrate a data-centric approach within the chemistry community. This interim report offers a comprehensive overview of our data management activities, covering the reporting period from October 2020 to August 2023.The shift to digital tools in research documentation is driven by our work with Electronic Laboratory Notebooks (ELNs), such as Chemotion ELN, offering systematic data storage for easy retrieval and sharing. Additionally, we focus on developing repositories, such as Chemotion repository and RADAR4Chem, which fulfil the needs for the storage of chemical data. The NFDI4Chem Search Service ensures easy data access from our repositories. Our efforts extend to community engagement through conference visits and online presence, aimed at creating awareness for (digital) research data management and connecting to chemistry students and researchers. Our training programs have reached over 600 participants to date. Initiatives like the FAIR4Chem award and the Chemistry Data Days promote cultural change towards FAIR data. Our Editors4Chem initiative collaborates with publishers for standardised data management and the Ontologies4Chem workshops organised by our consortium promote the ontology development in the field.Apart from the consortium's engagement for chemists, NFDI4Chem members played key roles in the development of the NFDI as a whole. Being actively involved in the sections and task forces, NFDI4Chem promotes collaborative solutions across NFDI consortia. HTML XML PDF PubDate: Thu, 4 Jul 2024 08:00:25 +0300
Abstract: Research Ideas and Outcomes 10: e124288 DOI : 10.3897/rio.10.e124288 Authors : Mathias Dillen, Laura Abraham, Ann Bogaerts, Sofie De Smedt, Henry Engledow, Frederik Leliaert, Maarten Trekels, Steven Dessein, Quentin Groom : This Data Management Plan outlines a comprehensive strategy for handling, storing, and sharing of data generated by digitisation projects of the herbarium at Meise Botanic Garden with Index Herbarium code BR. Its purpose is to establish clear guidelines for both staff and external users, specifying the terms governing data usage and storage. It aims to prioritise the FAIR principles (Findable, Accessible, Interoperable and Reusable), ensure responsible data management, facilitate long-term preservation, uphold legal and ethical obligations, all while aligning with the research excellence mission of Meise Botanic Garden. This plan serves as a guiding document to effectively and efficiently achieve these goals. HTML XML PDF PubDate: Wed, 3 Jul 2024 09:34:27 +0300
Abstract: DOI : 10.3897/arphapreprints.e130555 Authors : Toke Thomas Høye, Pavel Stoev, Pierre Bonnet, W. Daniel Kissling : The MAMBO project is developing novel monitoring tools to enhance knowledge of the state of European biodiversity. Through its demonstration sites and stakeholder engagement, MAMBO is showcasing its new technologies' effectiveness and added value. It thus provides critical input on how biodiversity-related monitoring efforts can be coordinated at the EU level. As such, MAMBO has the potential to improve the ecological monitoring landscape in Europe and beyond substantially. MAMBO contributes to the aims of the EU Biodiversity Strategy for 2030 by ensuring better coordination and streamlining of biodiversity observations in Europe. HTML XML PDF PubDate: Wed, 26 Jun 2024 11:28:07 +030
Abstract: Research Ideas and Outcomes 10: e124168 DOI : 10.3897/rio.10.e124168 Authors : Franziska Taubert, Tuomas Rossi, Christoph Wohner, Sarah Venier, Tomáš Martinovič, Taimur Khan, Julian Gordillo, Thomas Banitz : European grassland management has often favoured high production through frequent mowing and heavy fertilisation over biodiversity conservation, which is typically supported by less intensive management. Besides management, climate change and extremes are increasingly affecting grassland productivity and biodiversity, requiring timely adaptation of management practices. Here, we describe the development of a prototype Digital Twin (pDT) of grassland biodiversity dynamics intended to support researchers, farmers or regulatory decision-makers in monitoring the current state of selected grassland sites and projecting their future state under various management and climate scenarios. HTML XML PDF PubDate: Thu, 20 Jun 2024 12:18:02 +030
Abstract: Research Ideas and Outcomes 10: e125523 DOI : 10.3897/rio.10.e125523 Authors : Otso Ovaskainen, Patrik Lauha, Julian Lopez Gordillo, Ossi Nokelainen, Anis Rahman, Allan Souza, Jussi Talaskivi, Gleb Tikhonov, Aurélie Vancraeyenest, Ari Lehtiö : Bird populations respond rapidly to environmental change making them excellent ecological indicators. Climate shifts advance migration, causing mismatches in breeding and resources. Understanding these changes is crucial to monitor the state of the environment. Citizen science offers vast potential to collect biodiversity data. We outline a project that combines citizen science with AI-based bird sound classification. The mobile app records bird vocalisations that are classified by AI and stored for re-analysis. Additionally, it shows a shared observation board that visualises collective classifications. By merging long-term monitoring and modern citizen science, this project harnesses the strength of both approaches for comprehensive bird population monitoring. HTML XML PDF PubDate: Thu, 20 Jun 2024 12:11:51 +030
Abstract: Research Ideas and Outcomes 10: e125521 DOI : 10.3897/rio.10.e125521 Authors : Kate Ingenloff, Syrine Ben Aziza, Claus Weiland, Nikoletta Nikolova, Hans-Hermann Thulke, Martin Lange, Adam Reichold, Dmitry Schigel : African swine fever is a transmissible virus impacting wild and domestic swine populations. In Europe, it is non-native and the recently introduced genotype affects wild boar populations with occasional outbreaks in domestic pigs. The ability to predict short-term spatial dynamics of this disease will greatly improve our ability to control and limit future spread of the virus. The BioDT disease outbreaks prototype, currently in development, implements an individual-based landscape-level mechanistic model as a digital twin aimed at providing informed support for management decisions in response to the spread of African swine fever in European wild boar populations. HTML XML PDF PubDate: Mon, 17 Jun 2024 07:05:47 +030
Abstract: Research Ideas and Outcomes 10: e125086 DOI : 10.3897/rio.10.e125086 Authors : Bekir Afsar, Kyle Eyvindson, Tuomas Rossi, Martijn Versluijs, Otso Ovaskainen : Forests are crucial in supporting biodiversity and providing ecosystem services. Understanding forest biodiversity dynamics under different management strategies and climate change scenarios is essential for effective conservation and management. This paper introduces the Forest Biodiversity Dynamics Prototype Digital Twin (pDT), integrating forest and biodiversity models to predict the effects of management options on forest ecosystems. The primary objective is to identify optimal management strategies that promote biodiversity, focusing on conservation and adaptation to different climate conditions. We start with the case of Finnish forests and bird species and plan to expand to include more European countries and a variety of species as the pDT is further developed. HTML XML PDF PubDate: Mon, 17 Jun 2024 07:03:40 +030
Abstract: Research Ideas and Outcomes 10: e125450 DOI : 10.3897/rio.10.e125450 Authors : Simon Rolph, Chris Andrews, Dylan Carbone, Julian Lopez Gordillo, Tomáš Martinovič, Nick Oostervink, Dirk Pleiter, Kata Sara-aho, John Watkins, Christoph Wohner, Will Bolton, Jan Dick : Digital twin approaches have the potential to revolutionise usage, planning and management of cultural ecosystem services i.e. the non-material benefits people obtain from ecosystems, including recreation, tourism, intellectual development, spiritual enrichment, reflection and aesthetic experiences.Here, we outline our blueprint for a prototype digital twin (pDT) for cultural ecosystem services. The pDT consists of two modelling components; a recreation potential model to quantify the cultural ecosystem services of the physical landscape and species distribution models to quantify the biodiversity component.It is envisaged that the digital twin will be used primarily by two user types: 1. those who wanted to enjoy the area and potentially contribute to citizen science programmes and 2. people who want to inform or make evidence-based management decisions (land managers, policy-makers, researchers). HTML XML PDF PubDate: Mon, 17 Jun 2024 07:01:43 +030
Abstract: Research Ideas and Outcomes 10: e124579 DOI : 10.3897/rio.10.e124579 Authors : Taimur Khan, Ahmed El-Gabbas, Marina Golivets, Allan Souza, Julian Gordillo, Dylan Kierans, Ingolf Kühn : Invasive alien species (IAS) threaten biodiversity and human well-being. These threats may increase in the future, necessitating accurate projections of potential locations and the extent of invasions. The main aim of the IAS prototype Digital Twin (IAS pDT) is to dynamically project the level of plant invasion at habitat level across Europe under current and future climates using joint species distribution models. The pDT detects updates in data sources and versions of the datasets and model outputs, implementing the FAIR principles. The pDT’s outputs will be available via an interactive dashboard. All input and output data will be freely accessible. HTML XML PDF PubDate: Mon, 17 Jun 2024 07:00:36 +030
Abstract: Research Ideas and Outcomes 10: e124978 DOI : 10.3897/rio.10.e124978 Authors : Tobias Frøslev, Robin Boyd, Dmitry Schigel : Advancements in environmental DNA (eDNA) metabarcoding have revolutionised our capacity to assess biodiversity, especially for cryptic or less-studied organisms, such as fungi, bacteria and micro-invertebrates. Despite its cost-effectiveness, the spatial selection for sampling sites remains a critical challenge due to the considerable time and resources required for processing and analysing eDNA samples. This study introduces a Biodiversity Digital Twin Prototype, aimed at optimising the selection and prioritisation of eDNA sampling locations. Leveraging available eDNA data and integrating user-defined criteria, this digital twin facilitates informed decision-making in selecting future sampling sites. Through the development of an associated data formatting tool, we also facilitate the accessibility and utility of DNA metabarcoding data for broader conservation efforts. This prototype will serve multiple end-users, from researchers and monitoring initiatives to commercial enterprises, by providing an intuitive interface for interactive exploration and prioritisation, based on estimated complementarity of future samples. The prototype offers a scalable approach to biodiversity sampling. Ultimately, this tool aims to refine our understanding of global biodiversity patterns and support targeted conservation strategies through efficient eDNA sampling. HTML XML PDF PubDate: Tue, 11 Jun 2024 11:00:44 +030
Abstract: Research Ideas and Outcomes 10: e124988 DOI : 10.3897/rio.10.e124988 Authors : Vladimir Mikryukov, Kessy Abarenkov, Thomas Jeppesen, Dmitry Schigel, Tobias Frøslev : Phylogenetic diversity (PD) represents a fundamental measure of biodiversity, encapsulating the extent of evolutionary history within species groups. This measure, pivotal for understanding biodiversity's full dimension, has gained recognition by major environmental and scientific organisations, including the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. Unlike traditional taxonomic richness, PD offers a comprehensive, evolutionary perspective on biodiversity, essential for conservation planning and biodiversity management. This manuscript describes the development of a BioDT (Biodiversity Digital Twin) prototype, aimed at facilitating the calculation and visualisation of biodiversity metrics from global, dynamic data sources. By utilising the PhyloNext pipeline and integrating with global phylogenetic and species occurrence databases like the Open Tree of Life (OToL) and the Global Biodiversity Information Facility (GBIF), the prototype aims to significantly reduce computation time and enhance user interaction. This enables dynamic visualisation and potentially hypothesis testing, making it a valuable tool for researchers, monitoring initiatives, policy-makers and the public. The prototype's development focuses on improving the PhyloNext pipeline's scalability and creating a more intuitive user interface, expanding its utility for conservation efforts and biodiversity exploration. Our work illustrates the potential impact of the BioDT prototype in supporting diverse user groups in visualising and exploring PD, thus contributing to more informed decision-making in conservation and biodiversity management. HTML XML PDF PubDate: Tue, 11 Jun 2024 11:00:23 +030
Abstract: Research Ideas and Outcomes 10: e125167 DOI : 10.3897/rio.10.e125167 Authors : Jürgen Groeneveld, Tomas Martinovic, Tuomas Rossi, Ondrej Salamon, Kata Sara-aho, Volker Grimm : Honey bees are vital to human well-being and are under multiple stresses. We need to be able to assess the viability and productivity of honey bee colonies in different landscapes and under different management and climate-change scenarios. We have developed a prototype digital twin, HONEYBEE-pDT, based on the BEEHAVE model, which simulates foraging, population dynamics and Varroa mite infestation of a single honey bee colony. The main input data are land-cover maps and daily weather data. We have developed the pDT for simulating large areas and have tested it for the whole of Germany. We have also developed a web-based GUI that users can use to run the pDT for specific sites. Hive weight data from hundreds of hives will be used for calibration and validation. HTML XML PDF PubDate: Tue, 11 Jun 2024 11:00:04 +030
Abstract: Research Ideas and Outcomes 10: e125192 DOI : 10.3897/rio.10.e125192 Authors : Desalegn Chala, Erik Kusch, Claus Weiland, Carrie Andrew, Jonas Grieb, Tuomas Rossi, Tomas Martinovic, Dag Endresen : Amidst population growth and climate-driven crop stresses such as drought, extreme weather, fungal and insect pests, as well as various crop diseases, ensuring food security demands innovative strategies. Crop wild relatives (CWR), wild plants in the same genus as the crop as well as wild populations belonging to the same species as the crop, offer novel genetic resources crucial for enhancing crop resilience against these stress factors. Here, we introduce a prototype digital twin (pDT) to aid in searching and utilising CWR genetic resources. Using the MoDGP (Modelling the Germplasm of Interest) tool, the pDT enables mapping geographic areas where stress-tolerant CWR populations can be found. With its graphical user interface, it offers flexibility in selecting genetic resources from CWR tailored to enhance resilience of various crops against diverse stress factors. HTML XML PDF PubDate: Tue, 11 Jun 2024 11:00:00 +030
Abstract: DOI : 10.3897/arphapreprints.e129447 Authors : Néstor Fernández, José Manuel Álvarez-Martínez, Lluís Brotons, Ana Ceia-Hasse, Marcel Buchhorn, César Capinha, Benoît O. L. Demars, Carlos Guerra, Ute Jandt, Borja Jimenez-Alfaro, W. Daniel Kissling, Maria Lumbierres, Andres Marmol-Guijarro, Henrique M. Pereira, Anne Lyche Solheim, Judy Shamoun-Baranes, Bruno Smets : This report discusses the potential synergies of the EBVs developed in each showcase, in conjunction with existing environmental policies, for a comprehensive assessment of European biodiversity. HTML XML PDF PubDate: Tue, 11 Jun 2024 10:43:14 +030
Abstract: Research Ideas and Outcomes 10: e126660 DOI : 10.3897/rio.10.e126660 Authors : Gonzalo Bravo, Gregorio Bigatti, María Bagur, Erasmo Macaya, Nelson Valdivia, Ariel Rodriguez, Mariela Gauna, Ian Walker, Juan Pablo Livore, María Mendez, Rocío Nieto Vilela, Fernando Lima, Rui Seabra, Enrique Montes : The Marine Biodiversity Observation Network Pole to Pole of the Americas (MBON Pole to Pole) conducted two workshops on 27-31 March 2023 and 22-26 January 2024 in the Argentinian Patagonia aiming to enhance capacity for long-term monitoring of rocky intertidal communities in Argentina and Chile by applying novel and easy-to-use methods for biodiversity observing. In these workshops, participants received training on the collection and processing of benthic photo-quadrat imagery and their analysis using open-source artificial intelligence applications. Workshop participants included park rangers, undergraduate and graduate students and scientists. These training activities covered theoretical concepts of rocky shore ecology and field exercises. The workshops promoted collaboration and knowledge exchange between users of biodiversity data and ecologists resulting in the development of a standardised biodiversity monitoring protocol for rocky intertidal communities available in the Ocean Best Practices System of the Intergovernmental Oceanographic Commission of UNESCO. Participants learned to identify dominant species and functional groups (e.g. macro-algal taxa, molluscs, barnacles) commonly present in these habitats and their zonation patterns along elevation gradients, capture high-quality benthic photographs using quadrat frames and cameras provided by the MBON Pole to Pole and compute percentage cover estimates of observed taxonomic groups using open-source automated classifiers. Emerging recommendations underscored the importance of actively involving park rangers in survey efforts and facilitating communication with decision-makers managing Marine Protected Areas. These activities were endorsed by the UN Decade as contributions to the Marine Life 2030 programme towards increasing capacity in the implementation of coordinated, standardised and sustained biodiversity observing efforts in the Americas. HTML XML PDF PubDate: Fri, 7 Jun 2024 19:41:08 +0300
Abstract: DOI : 10.3897/arphapreprints.e129021 Authors : Francisco Moreira, Filipe S. Dias, Jeremy Dertien, Ana Ceia Hasse, Luis Borda-de-Água, Silvia Carvalho, Miguel Porto, Francesca Cosentino, Luigi Maiorano, Andrea Sacchi, Luca Santini, Florian Borgwardt, Georg Gruber, Nikolaj Poulsen, Rafaela Schinegger, Carina Seliger, Néstor Fernández : Ecological connectivity is key to maintaining a coherent and resilient network of protected areas in the EU. The EU Biodiversity Strategy for 2030 has identified the unhindered movement of species, nutrients and ecological processes across connected landscapes as a key feature of a coherent Trans-European Nature Network (TEN-N) of protected and conserved areas. However, to date, streamlined guidance on planning for and implementing connectivity measures specifically at the European scale has been limited. This report presents a coherent methodological framework and guidelines for mapping functional and structural connectivity at the European scale, as part of the Horizon Europe NaturaConnect project, which is supporting EU Member States in developing a coherent TEN-N of protected and conserved areas. It describes key ecological connectivity concepts and approaches; outlines methods and tools for estimating connectivity; presents an overview of connectivity projects across Europe; identifies connectivity priorities, gaps and challenges following a stakeholder consultation process; and provides practical and operational guidelines for implementing ecological connectivity for conservation projects ranging from regional to national and European levels. The guidelines present a strategic blueprint aimed at enhancing ecological connectivity across Europe, and address the specific challenges and opportunities related to planning ecological connectivity in the European context. This report has been written for practitioners and individuals involved in the management and administration of protected areas and ecological connectivity projects across Europe. This includes professionals working in TEN-N implementation at national or regional levels, others involved in spatial planning outside protected areas, and professionals engaged in the implementation of connectivity projects and protected area management. HTML XML PDF PubDate: Thu, 6 Jun 2024 10:58:40 +0300
Abstract: DOI : 10.3897/arphapreprints.e128926 Authors : Irene Calderon Sanou, Carlos Guerra, Graciela Rusch, Sergei Põlme, Joachim Maes, Néstor Fernández : The Deliverable discusses the critical role of soil in supporting terrestrial ecosystems, agriculture, and global climate regulation. It highlights that a significant portion of European soils are currently unhealthy, which has far-reaching consequences, including risks to human health, the environment, and the economy. Soil degradation affects food security, water quality, climate change, and biodiversity. It also emphasizes the importance of soil monitoring in Europe to ensure sustainable land management, preserve biodiversity, and mitigate environmental challenges. Healthy soils are essential for agriculture, food security, and climate resilience. The European Union (EU) recognizes the importance of soil health in addressing the food needs of a growing global population increasing the need for improved soil monitoring. It also discusses the role of advanced remote sensing technologies in soil monitoring and mentions initiatives and projects focused on soil biodiversity and ecosystem functioning. This Deliverable highlights the showcase in soil restoration and climate change mitigation that is aimed at developing soil essential biodiversity variables to test the capacity of current datasets and monitoring frameworks to provide relevant information on the distribution and future trends of key soil biodiversity variables. The development process also stakeholder engagement in the context of selecting essential biodiversity variables (EBVs). Two main approaches were used: a working group involving researchers and targeted meetings with institutional stakeholders. Key meetings were held with stakeholders from organizations such as the European Environmental Agency, the Joint Research Center, and German soil and biodiversity monitoring agencies. These meetings aimed to gather input and insights on the selection of EBVs. The stakeholder engagement process revealed three key points: i) the importance of using readily available and open data to ensure data continuity and promote transparency and accessibility (this includes data from sources like the European Soil Data Centre (ESDAC) and GBIF, as well as point data from the LUCAS sampling framework); ii) the need for diversity in modeling approaches, incorporating multiple data sources and levels of expertise (the goal is to showcase the potential use of existing information and allow various stakeholders to identify their roles in producing soil-based EBVs for different functions or ecosystem services); and iii) the importance of including climate and land use prediction data in modeling frameworks when possible. Overall, the stakeholder engagement process emphasized the significance of data accessibility, diverse modeling approaches, and the incorporation of relevant future data in the selection and development of essential biodiversity variables. Furthermore, the Deliverable discusses the existing gap in the EU's legal framework concerning soil management and highlights the proposed Soil Monitoring Law as a comprehensive framework to address this gap. The outcomes of this Deliverable align with several EU environmental policy initiatives, such as the EU Biodiversity Strategy for 2030, the Zero Pollution Action Plan, the Circular Economy Action Plan, and the Chemicals Strategy for Sustainability. Finally, it proceeds with the selection of essential biodiversity variables (EBVs) for soil-related monitoring within the EuropaBON initiative. Three primary soil-related EBVs have been chosen: 'Functional Composition of soil biota' and 'Community Biomass of soil microbes' and ‘Taxonomic diversity’. These EBVs belong to the 'Community Composition' class within the 'Terrestrial' realm category. HTML XML PDF PubDate: Thu, 6 Jun 2024 10:13:38 +0300
Abstract: DOI : 10.3897/arphapreprints.e128742 Authors : Tena Radočaj, Oliver Barić, Serena Rasconi, Irena Vardić, Jurica Jug-Dujaković, Ana Gavrilović : One of the biggest challenges in the microalgae industry is the lack of reliable methods to detect and avoid biological contaminants, including parasites, which can affect cell growth and consequently lead to crash of the culture. In recent years, the metabarcoding approach has been widely used to study diversity and distribution of microalgae communities and is also a promising tool for contaminant detection in routine biomonitoring. The aim of this article presents steps of DNA extraction for molecular analysis of microalgae communities. HTML XML PDF PubDate: Mon, 3 Jun 2024 18:48:28 +0300
Abstract: DOI : 10.3897/arphapreprints.e128550 Authors : Martin Baptist, Richard Marijnissen, Grzegorz Różyński, Rosaria Ester Musumeci, Massimiliano Marino, Laura Borzi, Agata di Stefano, Morgane Jolivet, Alice Stocco, Fabienne Horneman, Silvia Rova, Silvia Torresan, Elisa Furlan, Caterina Dabalà, Francesca Coccon, Andrea Critto, Fabio Pranovi, Ferran Bertomeu, Carles Ibáñez, Nuno Caiola, Elitsa Hineva, Nataliya Andreeva, Petya Eftimova, Bogdan Prodanov, Valentina Doncheva, Nikolay Valchev, Shylee Berg, Mathis Cognat : This deliverable presents the generation of EUNIS habitat maps for Europe as a whole and for each of the pilot areas in REST-COAST. Subsequently, it presents the assignment of semi-quantitative scores for the contribution of each EUNIS (sub)habitat to the five key ecosystem services applying the rank scale 0 (none), 1 (very low contribution), 2 (low contribution), 3 (medium contribution), 4 (high contribution) to 5 (very high contribution). It also describes the assignment of the IUCN Red List of Habitats to each of the depicted EUNIS (sub)habitats in the pilot areas. And finally, to assess coastal system behaviour and restoration effects on ecosystem services and biodiversity gains under climate change, a homogenised score card methodology is presented to overcome the problem of comparing minor changes (some percents) with major changes (tens of percents) in the total scores for ESS or BDV in each pilot area. HTML XML PDF PubDate: Fri, 31 May 2024 09:37:56 +030
Abstract: Research Ideas and Outcomes 10: e127123 DOI : 10.3897/rio.10.e127123 Authors : Nico Eisenhauer, Cordula Vogel, Luiz A. Domeignoz Horta, Ana Bonato Asato, Zarah Janda, Simone Cesarz : Soil is the basis for life on Earth as we know it. Healthy and stable soil is a prerequisite for well-functioning terrestrial ecosystems and has, thus, been proposed to play a key role in plant diversity–ecosystem functioning relationships. The overall objective of this sub-project is to study multidimensional soil stability as affected by plant diversity in a long-term plant diversity experiment. We designed three coordinated work packages (WPs) to comprehensively assess soil multistability to environmental fluctuations and climate extremes by considering the biological, chemical and physical dimensions that are key for soil functioning. We will use all unique facilities and approaches of the Jena Experiment Research Unit by combining synthesis of long-term data in the Main Experiment and the ΔBEF Experiment with performing new soil analyses in the DrY Experiment, the ResCUE Experiment and a joint CoMic Experiment, to gain a better mechanistic understanding of plant diversity–ecosystem functioning relationships. In close collaboration with other sub-projects, we will assess biological, chemical and physical soil properties and stability indicators that will be used to calculate soil multifunctionality and multistability indices. In WP1, we will build on three unique datasets to explore short-term and long-term effects of plant diversity on the stability of soil (microbial) properties. In WP2, we will combine different datasets and approaches to explore if plant diversity effects on the magnitude and stability of soil properties increase with abiotic and biotic stresses. In WP3, we will combine measurements of the above-mentioned dimensions of soil stability to explore if plant diversity increases the stability of multiple soil properties under hot drought. This sub-project is at the heart of the Research Unit by testing the overarching hypotheses outlined in the Coordination Proposal of the Jena Experiment, contributing to all main experiments, sharing data and performing joint sampling campaigns with all sub-projects and, at the same time, introducing a novel concept of soil multistability as affected by plant diversity and climate extremes. We propose to use a combination of simple, high-throughput (e.g. bait-lamina test) and more sophisticated methods (e.g. extracellular polymeric substances analyses) to be able to investigate temporal dynamics of soil processes and their mechanistic basis. Taken together, the results of the three WPs will provide new insights into the stabilising mechanisms of soil properties in the long term and in relation to climate extremes through plant diversity. HTML XML PDF PubDate: Thu, 30 May 2024 10:18:45 +030
Abstract: DOI : 10.3897/arphapreprints.e128158 Authors : Helge Bruelheide, Ute Jandt, Néstor Fernández, Andres Marmol-Guijarro, Bruno Smets, Marcel Buchhorn, Lori Giagnacovo, Giorgia Milli, Borja Jimenez-Alfaro, Jose Manuel Álvarez-Martínez : The report demonstrates the potential workflows to leverage monitoring data on biodiversity to assess the status of two selected habitats of the Habitats Directive, Nardus grasslands (EU habitats directive Annex I 6230*) and forest dominated by Fagus sylvatica on acidic soils (habitat 9110). HTML XML PDF PubDate: Mon, 27 May 2024 09:10:27 +030
Abstract: DOI : 10.3897/arphapreprints.e128109 Authors : Anne Lyche Solheim, Benoît O. L. Demars, Marit Mjelde, Jannicke Moe, Andres Marmol-Guijarro, Sophie Mentzel, Jan-Erik Thrane, Jes Rasmussen, Benno Dillinger : This report provides a showcase of selected EBVs related to the EU Water Framework Directive (WFD) and possible synergies with other EU policies. The report consists of two major parts: the species level EBV on macrophyte species in Nordic lakes and the community structure EBVs for phytoplankton in lakes and benthic invertebrates in rivers based on their deviation from natural conditions measured by Ecological Quality Ratios (EQR-values). The macrophytes species level part is produced by Benoit Demars at NIVA supported by a number of co-authors, including data providers (see frontpage), while the community structure EBVs based on EQR values are produced by Jannicke Moe, Sophie Mentzel, Jan-Erik Thrane and Anne Lyche Solheim at NIVA. All EIONET data providers of EQR-values reported to WISE-2 are kindly acknowledged. HTML XML PDF PubDate: Thu, 23 May 2024 08:34:08 +030
Abstract: DOI : 10.3897/arphapreprints.e128042 Authors : Camino Liquete, Dimitrios Bormpoudakis, Joachim Maes, Ian McCallum, W. Daniel Kissling, Lluís Brotons, Tom Breeze, Alejandra Moran, Maria Lumbierres, Leonie Friedrich, Sergi Herrando, Anne Lyche Solheim, Miguel Fernandez, Néstor Fernández, Tim Hirsch, Laurence Carvalho, Petteri Vihervaara, Jessi Junker, Ivelina Georgieva, Ingolf Kühn, Roy Van Grunsven, Aino Lipsanen, Guillaume Body, Hilary Goodson, Jose Valdez, Aletta Bonn, Henrique M. Pereira : Observations are key to understanding the state of nature, the drivers of biodiversity loss and the impacts on ecosystem services and ultimately on people. Many EU policies and initiatives call for unbiased, integrated and regularly updated data on biodiversity and ecosystem services. However, biodiversity monitoring efforts are spatially and temporally fragmented, taxonomically biased and not integrated across Europe. EuropaBON has addressed this gap by developing an EU-wide framework for biodiversity monitoring. With this deliverable, EuropaBON proposes the terms of reference for an EU Biodiversity Observation Coordination Centre (EBOCC), a permanent infrastructure that could coordinate and foster the generation and use of high quality data to underpin the biodiversity knowledge-base used across EU policies, providing guidance and trainings when necessary. Such a centre represents one of the key solutions to overcome the critical challenges of biodiversity monitoring in Europe. Having this integrated and continuous monitoring capacity would allow more timely and efficient interventions that would optimise our capacity to revert biodiversity loss and prevent environmental degradation. It would also increase the value-added to the data flows, reaching high-value outputs with some existing low-value inputs. This deliverable offers a critical analysis of the existing monitoring landscape in Europe, extracting key messages about the main challenges, lessons learned and possible solutions. Based on a comprehensive analysis of needs and, most importantly, on an inclusive consultation process, the deliverable designs an EBOCC that tackles the key biodiversity monitoring challenges. The proposal specifies the mission, the tasks, the most urgent topics, the main policies and the key stakeholders that the EBOCC should serve and focus on during the first stage of its implementation. It also includes detailed analyses about governance models and potential costs. With this proposal, EuropaBON fosters the setting up and testing an operational EBOCC that could address the urgent need for coordination, integration, harmonisation and strengthening of biodiversity data collection and analysis, in order to inform policy-making at local, national, European and international level. HTML XML PDF PubDate: Wed, 22 May 2024 14:07:05 +030
Abstract: Research Ideas and Outcomes 10: e126532 DOI : 10.3897/rio.10.e126532 Authors : Andrea Weeks, Elizabeth Collins, Twanelle Majors, Zack Murrell, Deborah Paul, Matthew Sheik, David Shorthouse, Shawn Zeringue-Krosnick : We created and delivered a workshop and symposium series for biologists at all career stages focused on the skills and practices needed to sustain natural history specimen attribution and citation. The name of the workshop and symposium series, SISRIS, reflected our ultimate goal of effecting community-level change by sharing skills and practices that can support inclusive and sustainable (collections-based) research infrastructure for systematics. We report here the rationale for SISRIS, its learning objectives for participants and its results, including the assessment of outcomes from three iterations of the workshop held in 2023. The SISRIS workshops and symposia were held in person at the annual meeting of the Association for Southeastern Biologists in Winston-Salem, North Carolina and Botany 2023 in Boise, Idaho. A stand-alone SISRIS workshop was held online later to accommodate individuals who were unable to travel to the in-person events. HTML XML PDF PubDate: Mon, 20 May 2024 12:30:34 +030
Abstract: Research Ideas and Outcomes 10: e127485 DOI : 10.3897/rio.10.e127485 Authors : Christopher John Topping, Agnieszka Bednarska, Emilio Benfenati, Jordan Chetcuti, Noa Delso, Xiaodong Duan, Andreas Focks, Ryszard Laskowski, Anna Lombardo, Luna Marcussen, Teodor Metodiev, Michael Rubinigg, Maj Rundlöf, Fabio Sgolastra, Carla Stoyanova, Gregor Sušanj, James Williams, Elżbieta Ziółkowska : PollinERA aims to reverse pollinator population declines and reduce the harmful impacts of pesticides. It addresses the call through four objectives: SO1 filling ecotoxicological data gaps to enable realistic prediction of the source and routes of exposure and impact of pesticides on pollinators and their sensitivity to individual pesticides and mixtures. SO2 developing and testing a co-monitoring scheme for pesticides and pollinators across European cropping systems and landscapes, developing risk indicators and mixture exposure information. SO3 developing models for predicting pesticide toxicological effects on pollinators for chemicals and organisms, environmental fate, toxicokinetic/ toxicodynamic, and population models. SO4 developing a population-level systems-based approach to risk and policy assessment considering multiple stressors and long-term spatiotemporal dynamics at the landscape scale and generating an open database for pollinator/pesticide data and tools.This will be achieved through developing knowledge and protocols for a broad range of toxicological testing, feeding to in silico models (QSARS, toxicokinetic/toxicodynamic, and population). Using a strong stakeholder co-development approach, these models will be combined in a One System framework taking a systems view on risk assessment and policy evaluation, including an international monitoring program.The One System framework is based on EFSA’s system ERA view, expanding on the tools used for bees to include butterflies, moths and hoverflies. The consortium partners are experts in the field needed for this development and are well-placed to facilitate the uptake of tools by European bodies to guarantee the project's future impact.Expected impacts target Destination impacts of better understanding and addressing drivers of biodiversity decline, interconnected biodiversity research using digital technologies, and understanding the biodiversity and health nexus at the ecosystem level. HTML XML PDF PubDate: Thu, 16 May 2024 11:01:41 +030
Abstract: Research Ideas and Outcomes 10: e107983 DOI : 10.3897/rio.10.e107983 Authors : Katherine McLean : Since the first discoveries of Neanderthal fossils, their derived characteristics, such as increased robusticity, have engaged researchers. Adaptation to cold environments has been hypothesised to explain such traits and this hypothesis has driven the majority of discourse. This proposal seeks to examine this hypothesis and locate evidence of Neanderthals being physiologically adapted to cold at the biomolecular level. Haemoglobin is a biomolecule that has been previously demonstrated to adapt to cold in some species, driven by the inhibition of the protein’s function by low temperatures. Neanderthal haemoglobin is extinct; however, using pre-sequenced genomic data, I propose to resurrect Neanderthal haemoglobin so I can examine the consequences of lowered temperature on its function. This project could potentially detect signs of cold adaptation in the Neanderthal globin genes and provide empirical evidence for the cold adaptation hypothesis. HTML XML PDF PubDate: Mon, 13 May 2024 17:23:27 +030
Abstract: Research Ideas and Outcomes 10: e124177 DOI : 10.3897/rio.10.e124177 Authors : Eunice Ayerakwa, Isawumi Abiola : Neurocysticercosis, caused by the invasion of the central nervous system (CNS) by Taenia solium larvae, poses a significant global health burden. Despite its prevalence and severe neurological consequences, understanding of the molecular and signalling pathways facilitating parasite dissemination and CNS invasion is limited. The lack of comprehensive knowledge of host-parasite interactions and associated proteins involved in T. solium infection hinders the development of targeted interventions to mitigate its ability to cross the epithelia barrier. This is complicated by reduced oxygen availability in the intestine, a phenomenon called hypoxia. Hypoxia can result in epithelial barrier disruption and cell damage, thereby promoting the translocation and dissemination of T. solium. This study aims to establish the role of hypoxia in T. solium invasion and disseminated infections. The effect of hypoxia on the migration, viability and morphological characteristics of T. solium would be determined using transwell invasion assays, flow cytometry and microscopy. T. solium oncosphere development and dissemination under hypoxic and normoxic conditions will be monitored using animal models. Also, host-parasite transcriptome and proteome profiling will be performed to determine pathways triggered under hypoxic conditions. It is expected that hypoxia would promote the invasion and dissemination of T. solium by enhancing epithelial and endothelial cell permeability. , hypoxia will induce the expression of binding and adhesion proteins and other virulence markers such as enolase, serpin, and glutathione transferases that are involved in host invasion. Understanding the role of hypoxia in the translocation mechanism of T. solium can be leveraged to provide insights into host tissues dissemination and the development of appropriate interventions. HTML XML PDF PubDate: Mon, 13 May 2024 16:28:37 +030
Abstract: Research Ideas and Outcomes 10: e116907 DOI : 10.3897/rio.10.e116907 Authors : Tosin Senbadejo, Isawumi Abiola, Lily Paemka : Uterine fibroid (UF) is the most prevalent benign tumour that affects millions of women globally, with a high incidence of 70% amongst women of reproductive age. UF has been associated with various complications, such as recurrent surgeries, infertility, anemia and pregnancy loss. Notably, women of African descent often experience more severe symptoms and complications. Although hormones, growth factors, and genetic alterations are widely associated with UF, the precise mechanism underlying its pathogenesis is not fully understood. Recent evidence suggests altered microbiota may serve as a potential risk factor for UF development. Altered microbiota can contribute to tumorigenesis via epigenetic changes to host cells or toxic effects from invasion. The lack of curative-drug treatment poses significant challenges to patients with UF. Patients often undergo surgeries that require the removal of the uterus or tumour, which can negatively impact fertility. Furthermore, uterine fibroids’ diagnosis relies on expensive imaging technologies such as ultrasound, which may not be readily available in developing countries. Moreso, diagnosis is often conducted only after patients’ symptoms become severe. Although late presentation may contribute to severe symptoms and complications among women with UF in Africa, other factors that influence severity and increase incidence in this population remain unknown. A comprehensive assessment of UF predisposing factors in high-risk populations such as Ghana could give better insights into disease pathogenesis. Hence, this study aims to assess: UF-associated demographic factors, the role of uterine microbiota dysbiosis on UF tumorigenesis; and molecular markers associated with UF in the Ghanaian population. Epidemiological data and clinical samples (tissues, blood and cervico-vaginal swabs) will be obtained. The characterization of samples will involve metagenomics, whole genome sequencing, functional validation of SNPs and SNP genotyping. The association of risk alleles with disease phenotypes will be assessed via regression analysis using PLINK v.1.9. The findings will provide information on potential disease markers that can be explored for better management strategies for UF in high-risk populations. HTML XML PDF PubDate: Fri, 10 May 2024 08:23:20 +030
Abstract: Research Ideas and Outcomes 10: e118851 DOI : 10.3897/rio.10.e118851 Authors : Sabine von Mering, Erik Stolze, Katja Kaiser, Mareike Petersen : Linked open data on collection agents contribute to increased discoverability, accessibility and transparency of natural history collections. Despite major efforts to digitise and open up museum and university object collections, related information is often stored in internal resources. This paper describes a project conducted at the Museum für Naturkunde Berlin (MfN) contributing to its collection disclosure and development initiatives. Information on historical collectors and other collection agents was transferred from the internal MfN collector wiki to Wikidata. For a total of 600 collection agents, existing Wikidata items were enriched or new items created.Special emphasis was put on linking these people to the Museum, to document their affiliation with the MfN, its collection and its archive. Within the project, an open participatory approach was taken. Several Wikidata edit-a-thons were organised to test this collaborative and innovative format for possible future application by the Museum. By opening up institutional silos and openly sharing data on agents connected to museum holdings, these data become more widely accessible and reusable, for example, as a resource for transdisciplinary provenance research. HTML XML PDF PubDate: Wed, 8 May 2024 15:12:21 +0300
Abstract: Research Ideas and Outcomes 10: e126586 DOI : 10.3897/rio.10.e126586 Authors : Donat Agosti, Laurence Bénichou, Ana Casino, Lars Nielsen, Patrick Ruch, Puneet Kishor, Lyubomir Penev, Patricia Mergen, Christos Arvanitidis : Knowledge about biodiversity is largely embedded in a daily growing corpus of over 500 million pages of biodiversity literature that is not machine-actionable. It is thus not open to building a biodiversity knowledge graph, or facilitating the use of artificial intelligence tools. This hinders the completion of a much-needed taxonomic name reference system, prevents the discovery of the biotic interactions underpinning the prediction and understanding of global change trends and consequences, viral spillovers, annotation of genes with their respective phenotypes, and their citations in various domains dealing with biological species such as conservation, agriculture, medicine, life sciences and industry, necessary to achieve the objectives of the Green Deal and address the targets identified in the Global Biodiversity Framework. This Policy Brief highlights key actions that can liberate the scientific data published, exploit their use , promote an enhanced way to publish, and ultimately foster excellence and innovation in biodiversity science, monitoring and conservation. HTML XML PDF PubDate: Tue, 30 Apr 2024 18:25:20 +030
Abstract: Research Ideas and Outcomes 10: e126588 DOI : 10.3897/rio.10.e126588 Authors : Lyubomir Penev, Quentin Groom, Ana Casino, Boris Barov : A new community of research infrastructures has joined forces to provide scientists with seamless access to the plethora of data, services and tools in biodiversity research. New levels of technological innovation and interoperability between infrastructures foster unprecedented access to biodiversity data across all data domains and the entire research lifecycle, thus advancing open science practices and strengthening Europe's position in the global biodiversity research landscape. This policy brief highlights the potential benefits derived from enhanced connectivity and interoperability among various types of biodiversity data, fostering innovation and advancements in biodiversity science, monitoring, conservation, and policy development. HTML XML PDF PubDate: Tue, 30 Apr 2024 18:24:41 +030
Abstract: DOI : 10.3897/arphapreprints.e126021 Authors : Sergi Herrando, Sara Fraixedas, Guillem Pocull, Dani Villero, Anna Gamero, David Martí, Verena Keller, Petr Voříšek, Alena Klvaňová, Gabriel Gargallo, Lluís Brotons : This deliverable shows, using farmland birds as a demonstrative case study, how the existing European network of bird monitoring schemes could be used to regularly update the distribution of terrestrial breeding birds across the whole of EU and neighbouring countries. In addition, it shows how changes in distribution could be assessed on frequent intervals suitable for informing on the achievement of EU environmental policy targets. HTML XML PDF PubDate: Thu, 25 Apr 2024 10:08:05 +030
Abstract: Research Ideas and Outcomes 10: e124884 DOI : 10.3897/rio.10.e124884 Authors : Egon Willighagen, Marc Teunis, Alyanne De Haan : Cheminformatics is the research field that deals with information about chemical systems. This includes the chemical structure which is used in computational chemistry where quantum chemistry is too complex. The Chemistry Development Kit (CDK) was one of the first Open Science libraries in chemistry, co-founded in The Netherlands. The source code goes as far back as 1997 and has been maintained for more than 25 years. The CDK is used by many tools in drug discovery, computational toxicology, and bioinformatics. This project will develop improvements to the core library and update tools using the CDK to use the latest release. HTML XML PDF PubDate: Wed, 17 Apr 2024 17:32:57 +030
Abstract: Research Ideas and Outcomes 10: e121892 DOI : 10.3897/rio.10.e121892 Authors : Wouter Los : The original vision on what later became LifeWatch ERIC started about a quarter of a century ago in 1996. In those days, the promise of digital technologies entered biodiversity and ecosystem research. Not only by digitiing relevant information, but also with applications to process such data. While several (inter)national initiatives embarked on specific topics, there was also an idea that the upcoming view on grid computing provided attractive solutions for federated data sources, together with a strong computing capacity. This paper presents the history from conception to early actions, until actual preparations towards a research infrastructure on the European scale. HTML XML PDF PubDate: Wed, 17 Apr 2024 11:16:41 +030
Abstract: DOI : 10.3897/arphapreprints.e125515 Authors : Simon Rolph, Chris Andrews, Dylan Carbone, Julian Lopez Gordillo, Tomas Martinovic, Nick Oostervink, Dirk Pleiter, Kata Sara-aho, John Watkins, Christoph Wohner, Jan Dick : Digital twin approaches have the potential to revolutionise usage, planning and management of cultural ecosystem services i.e. the non-material benefits people obtain from ecosystems, including recreation, tourism, intellectual development, spiritual enrichment, reflection, and aesthetic experiences. Here we outline our blueprint for a prototype digital twin (pDT) for cultural ecosystem services. The pDT consists of two modelling components; a recreation potential model to quantify the cultural ecosystem services of the physical landscape and species distribution models to quantify the biodiversity component. It is envisaged that the digital twin will be used primarily by two user types 1. those who wanted to enjoy the area and potentially contribute to citizen science programs and 2. people who want to inform or make evidence-based management decisions (land managers, policy makers, researchers). HTML XML PDF PubDate: Wed, 17 Apr 2024 10:23:20 +030
Abstract: Research Ideas and Outcomes 10: e124018 DOI : 10.3897/rio.10.e124018 Authors : Marie Neumann, Franziska Ehnert : How can we re-integrate knowledge generated in real-world laboratories (RWLs) into societal practice' In the RWL “Dresden – City of the Future 2030+”, the re-integration of knowledge was central to the research design. In this Workshop Report, we focus on facilitation methods for knowledge re-integration into societal practice. This is to guide transdisciplinary research practice and help researchers in designing and facilitating such research processes. We conceptualise knowledge re-integration, based on the current literature. Further, we describe our facilitation methods (two workshop formats) to document and reflect on our experiences. A self-reflective evaluation is conducted with the help of evaluation criteria synthesised from the literature on transdisciplinary research (TDR). Our reflections confirm that the facilitation of exchange with the target group/target context can greatly enhance the transferability of knowledge gained in TDR settings. In our conclusion, we highlight the importance of facilitators and knowledge brokers, as well as co-creation with local stakeholders to reach out to the target group. HTML XML PDF PubDate: Wed, 17 Apr 2024 09:05:45 +030
Abstract: Research Ideas and Outcomes 10: e121871 DOI : 10.3897/rio.10.e121871 Authors : Sharif Islam, Dario Papale, Lucia Vaira, Ilaria Rosati, Johannes Peterseil, Christian Pichot : This paper presents a use-case conducted within the ENVRI FAIR project, examining challenges and opportunities in deploying FAIR-aligned (ensuring Findability, Accessibility, Interoperability and Reusability) scientific name-matching services across Environmental Research Infrastructures (RIs). Six services were tested using various name variations, revealing inconsistencies in match types, status reporting and handling of canonical forms and typos. These diversities pose challenges for RI data pipelines and interoperability. The paper underscores the importance of standardised tools, enhanced communication, training, collaboration and shared resources. Addressing these needs can facilitate more effective FAIR implementation within the ENVRI community and biodiversity research. This, in turn, will empower RIs to seamlessly integrate and leverage scientific names, unlocking the full potential of their data for research and policy implementation. HTML XML PDF PubDate: Fri, 5 Apr 2024 16:45:23 +0300
Abstract: DOI : 10.3897/arphapreprints.e124640 Authors : Julian Lopez Gordillo, Patrik Lauha, Ari Lehtiö, Ossi Nokelainen, Anis Rahman, Allan Souza, Jussi Talaskivi, Gleb Tikhonov, Aurélie Vancraeyenest, Otso Ovaskainen : Bird populations respond rapidly to environmental change making them excellent ecological indicators. Climate shifts advance migration, causing mismatches in breeding and resources. Understanding these changes is crucial to monitor the state of environment. Citizen science offers vast potential to collect biodiversity data. We outline a project that combines citizen science with AI-based bird sound classification. The mobile app records bird vocalizations that are classified by AI and stored for re-analysis. Also, it shows a shared observation board that visualizes collective classifications. By merging long-term monitoring and modern citizen science, this project harnesses both approaches’ strengths for comprehensive bird population monitoring. HTML XML PDF PubDate: Fri, 5 Apr 2024 09:35:41 +0300
Abstract: DOI : 10.3897/arphapreprints.e124639 Authors : Jürgen Groeneveld, Tomáš Martinovič, Tuomas Rossi, Ondrej Salamon, Kata Sara-aho, Volker Grimm : Honey bees are vital to human well-being and are under multiple stresses. We need to be able to assess the viability and productivity of honey bee colonies in different landscapes and under different management and climate change scenarios. We have developed a prototype digital twin, HONEYBEE-pDT, based on the BEEHAVE model, which simulates foraging, population dynamics and Varroa mite infestation of a single honey bee colony. The main input data are land cover maps and daily weather data. Users can run the pDT for a specific site or for larger areas, up to the whole of Germany. Hive weight data from hundreds of hives will be used for calibration and validation. HTML XML PDF PubDate: Fri, 5 Apr 2024 09:30:21 +0300
Abstract: DOI : 10.3897/arphapreprints.e124344 Authors : Milos Stupar, Wejden Gongi, Silke Van den Wyngaert, Alexandra Kraberg, Albert Reñé, Serena Rasconi : The objective of this methodological paper is to outline a microscopy protocol for detecting and observing fungal zoosporic parasites of phytoplankton in natural environments, with potential applications in algal biotechnology to enhance the success and sustainability of algal cultivation endeavors. The fluorescent dual staining with wheat germ agglutinin (WGA) and Calcofluor White (CFW) showcased during the Training School "Identification and detection of zoosporic parasites" in Neuglobsow (Germany) from 16th till 18th of May 2023 and organized and funded by COST Action ParAqua (European Cooperation in Science and Technology) illustrated its ease of implementation and suitability for diverse natural and artificial systems. HTML XML PDF PubDate: Mon, 1 Apr 2024 09:35:30 +0300
Abstract: Research Ideas and Outcomes 10: e120483 DOI : 10.3897/rio.10.e120483 Authors : Alex Borisenko, Robert Young, Robert Hanner : The adoption of environmental DNA approaches as a standard tool for biodiversity monitoring leads to the increase in the number of eDNA-based species occurrence records; however, considerable disparity remains in the nature and quality of associated information, much of it unpublished and/or poorly parametrised. A robust system for tracking biological materials from their point of origin through laboratory analyses is required to connect inferred taxon occurrences with analytical history and provenance data. The bulk of eDNA research is currently driven by small-scale operations where the tasks of digitisation, organisation and cross-referencing field records with laboratory analytical data and biomaterial sample location, are often performed manually and disconnected.We present an integrative, full-stack data management solution that provides a structured ontological concept, a minimalist data schema for eDNA research and a software application prototype designed to facilitate real-time digitisation, parsing, annotation and archival of eDNA data. The system tracks the provenance and analytical history of biological samples through a structured hierarchy of events, linked with associated digital file attachment archives, such as images and raw sequence files, and with inferred taxonomic occurrence records. The data entry process is compartmentalised and incorporated into the corresponding stages of standard operations used in fieldwork, biological collection management and laboratory analysis. Resulting data records can be integrated into various output formats required for large-scale analytics, publication and/or submission to global data aggregators. The prototype is implemented on the Microsoft 365 platform as a relational database (Access) linked to cloud-based data tables (SharePoint) and a set of associated data conversion spreadsheets (Excel). The system is designed primarily around the data management needs of small research labs; however, it is scalable to larger institutions and inter-institutional academic networks. HTML XML PDF PubDate: Thu, 28 Mar 2024 10:18:17 +020
Abstract: Research Ideas and Outcomes 10: e120899 DOI : 10.3897/rio.10.e120899 Authors : Maame Ekua Acquah, Frank Aboagye, Yvonne Ashong, Lydia Mosi : Schistosomiasis is a neglected tropical disease that affects more than 200 million people and 45% of infections have been shown to occur in school-aged children. A large percentage of the disease burden lies in Africa. In 2012, the WHO outlined a roadmap for the elimination of schistosomiasis by 2020; however, this was not achieved. Treatment for schistosomiasis is by the use of Praziquantel, a drug in use for over 30 years and there is a concern for emerging drug resistance. There are several species of the genus Schistosoma causing infection in humans. For this study, Schistosoma mansoni which causes intestinal schistosomiasis will be investigated. There are reports of lowering cure rates and suboptimal response to praziquantel following several cycles of mass drug administration (MDA). Praziquantel resistance has also been reported in some countries and laboratory-bred schistosome experiments. To address the concerns of resistance, this study aims to employ a two-part approach to assess the prevalence of S. mansoni. praziquantel resistance amongst school-aged children in schistosomiasis endemic communities in Ghana and develop a diagnostic tool to aid in field assessment of infections. To achieve this, the study will attempt to answer the following research questions: 1. Is there developing S. mansoni praziquantel resistance in communities that have undergone several mass drug administrations' 2. Is there an interplay between intermediate host exposure to praziquantel and the development of praziquantel drug resistance in the definitive host' HTML XML PDF PubDate: Fri, 22 Mar 2024 10:15:23 +020
Abstract: DOI : 10.3897/arphapreprints.e123365 Authors : Douglas Spencer, Alexandra Marques, Clara Veerkamp, Martijn van der Marel, Peter Verburg, Anandi Sarita Namasivayam, Moreno Di Marco, Martin Jung, Heini Kujala, Louise O'Connor, Piero Visconti, Aafke Schipper : Opportunity costs, the foregone economic benefits from alternative activities or uses of a resource on a particular site, represent one of multiple options to approximate costs of nature conservation and can be used alongside biodiversity and ecosystem services data in spatial conservation prioritisation analyses. However, such cost data are not yet available across Europe. We created a European opportunity cost layer for productive (arable, pastoral and forestry) and urban lands at a spatial resolution of 1 km2, using land, resource, and residential rents. We mapped the opportunity costs of productive lands based on (sub)national land and resource rent data, which we allocated to the grid level based on gridded agricultural and forestry production data combined with country-specific commodity prices. We converted empirical data on property rents specific to housing type and city into area-standardised and city-specific rents and then applied these values to all cities and urban area within the respective country. When multiple cities from a single country were represented in the empirical dataset, a mean value of all the corresponding cities was used. HTML XML PDF PubDate: Tue, 19 Mar 2024 09:24:36 +020
Abstract: Research Ideas and Outcomes 10: e119782 DOI : 10.3897/rio.10.e119782 Authors : Catherine Borremans, Jennifer Durden, Timm Schoening, Emma Curtis, Luther Adams, Alexandra Branzan Albu, Aurélien Arnaubec, Sakina-Dorothée Ayata, Reshma Baburaj, Corinne Bassin, Miriam Beck, Katharine Bigham, Rachel Boschen-Rose, Chad Collett, Matteo Contini, Paulo Correa, Carlos Dominguez-Carrió, Gautier Dreyfus, Graeme Duncan, Maxime Ferrera, Valentin Foulon, Ariell Friedman, Santosh Gaikwad, Chloe Game, Adriana Gaytán-Caballero, Fanny Girard, Michela Giusti, Mélissa Hanafi-Portier, Kerry Howell, Iryna Hulevata, Kiamuke Itiowe, Chris Jackett, Jan Jansen, Clarissa Karthäuser, Kakani Katija, Maxime Kernec, Gabriel Kim, Marcelo Kitahara, Daniel Langenkämper, Tim Langlois, Nadine Lanteri, Claude Jianping Li, Qi-Ran Li, Pierre-Olivier Liabot, Dhugal Lindsay, Ali Loulidi, Yann Marcon, Simone Marini, Ashley Marranzino, Miquel Massot-Campos, Marjolaine Matabos, Lenaick Menot, Bernabé Moreno, Marcus Morrissey, David Nakath, Tim Nattkemper, Monika Neufeld, Matthias Obst, Karine Olu, Alexa Parimbelli, Francesca Pasotti, Dominique Pelletier, Margaux Perhirin, Nils Piechaud, Oscar Pizarro, Autun Purser, Clara Rodrigues, Elena Ceballos Romero, Brian Schlining, Yifan Song, Heidi Sosik, Marc Sourisseau, Bastien Taormina, Jan Taucher, Blair Thornton, Loïc Van Audenhaege, Charles von der Meden, Guillaume Wacquet, Jack Williams, Kea Witting, Martin Zurowietz : Imaging is increasingly used to capture information on the marine environment thanks to the improvements in imaging equipment, devices for carrying cameras and data storage in recent years. In that context, biologists, geologists, computer specialists and end-users must gather to discuss the methods and procedures for optimising the quality and quantity of data collected from images. The 4th Marine Imaging Workshop was organised from 3-6 October 2022 in Brest (France) in a hybrid mode. More than a hundred participants were welcomed in person and about 80 people attended the online sessions. The workshop was organised in a single plenary session of presentations followed by discussion sessions. These were based on dynamic polls and open questions that allowed recording of the imaging community’s current and future ideas. In addition, a whole day was dedicated to practical sessions on image analysis, data standardisation and communication tools. The format of this edition allowed the participation of a wider community, including lower-income countries, early career scientists, all working on laboratory, benthic and pelagic imaging.This article summarises the topics addressed during the workshop, particularly the outcomes of the discussion sessions for future reference and to make the workshop results available to the open public. HTML XML PDF PubDate: Mon, 18 Mar 2024 09:17:24 +020
Abstract: Research Ideas and Outcomes 10: e121887 DOI : 10.3897/rio.10.e121887 Authors : Wouter Los, Magdalena Năpăruş-Aljančič, Tatyana Bileva, Eva Chatzinikolaou, Ohad Graber-Soudry, Lucas de Moncuit, Marta Neto, Graziano Pesole, Maria Vallejo Abascal, Dafinka Grozdanova : A distributed research infrastructure such as LifeWatch ERIC necessitates close cooperation among the various components that constitute the research infrastructure and contribute to the overall services, facilities and resources it offers to the user community. In-kind contributions are non-monetary contributions, consisting of labour, services, facilities and access to resources, typically provided by the distributed components of the research infrastructure. The financing for in-kind contributions is usually provided by the national funding agency on behalf of the LifeWatch member country or by the member directly, with a value being accredited towards the member's funding obligations to LifeWatch ERIC. The management and validation of in-kind contributions towards shared objectives are integral to the legal framework supporting LifeWatch ERIC. This involves a rigorous assessment process to verify each in-kind contribution. This short article outlines that process and explores the function of the In-Kind Contributions Committee (IKCC) at LifeWatch ERIC. HTML XML PDF PubDate: Thu, 14 Mar 2024 15:30:42 +020
Abstract: Research Ideas and Outcomes 10: e118244 DOI : 10.3897/rio.10.e118244 Authors : Laura Tilley, Matt Woodburn, Sarah Vincent, Ana Casino, Wouter Addink, Frederik Berger, Ann Bogaerts, Sofie De Smedt, Lisa French, Sharif Islam, Patricia Mergen, Anne Nivart, Beata Papp, Mareike Petersen, Celia Santos, Edmund Schiller, Patrick Semal, Vincent Smith, Karin Wiltschke : This paper describes the design and build of a pilot Natural Sciences Collections Digitisation Dashboard (CDD). The CDD will become a key service for the Distributed System of Scientific Collections Research Infrastructure (DiSSCo) and aims to improve the discoverability of natural science collections (NSCs) held in European institutions, both digitised and undigitised. Furthermore, it will serve as a dynamic visual assessment tool for strategic decision-making, including the prioritisation of digitisation. The CDD pilot includes high-level information from nine European NSCs, covering the number of objects, taxonomic scope, storage type, chronostratigraphy (Earth Science Collections), geographical region and level of detail in digitisation. This information is structured through a standardised Collection Classification Scheme, which uses high-level categorisation to describe physical natural science collections. HTML XML PDF PubDate: Thu, 29 Feb 2024 13:28:49 +020
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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