Research ideas and outcomes最新文献

{"title":"Digital objects to make computable biomedical knowledge FAIR: an infrastructural approach to knowledge representation, dissemination and implementation","authors":"Marisa Conte, Allen Flynn, Philip Barrison, Peter Boisvert, Zach Landis-Lewis, Charles Friedman","doi":"10.3897/rio.9.e109307","DOIUrl":"https://doi.org/10.3897/rio.9.e109307","url":null,"abstract":"We present our work to develop digital objects to represent and convey a specific category of scientific knowledge: computable biomedical knowledge (CBK). Properly developed, validated, implemented and stewarded, CBK has the potential to accelerate the translation of actionable knowledge from scientific discovery to clinical application. Our research takes an infrastructural approach to CBK, initially by focusing on the creation of a conceptual model for packaging computable biomedical knowledge - the Knowledge Object (KO) - and on corresponding efforts to create an architecture for KO management and implementation. Additionally, our work is grounded in the FAIR principles, such that KO artefacts should be findable, accessible, interoperable and reusable and we are exploring aligning KOs with emerging best practices for FAIR Digital Objects (FDO). The outcomes of this work resonate in clinical contexts, health professions education, healthcare quality improvement, biomedical and translational research and population care. Our KO model is also of interest to researchers and practitioners interested in knowledge science, including those working with semantic technologies and other forms of digital objects.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"40 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139174977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing ‘non-destructive’ DNA extraction method in small crustaceans kept in wet collections","authors":"Samuel C. Bernardes, T. von Rintelen, Serena Alexander, Fiona Lorenz, Kristina von Rintelen","doi":"10.3897/rio.9.e113299","DOIUrl":"https://doi.org/10.3897/rio.9.e113299","url":null,"abstract":"Specimens in natural history museums are a valuable resource for biological research, such as taxonomic, biodiversity or evolutionary studies. However, the quality of DNA and even morphological characters can decrease over time, depending on previous fixation and long-term preservation methods. In recent years, advances in DNA extraction and sequencing techniques have allowed researchers to obtain DNA from museum specimens, even when the DNA was very fragmented. Extraction methods should ideally be morphologically non-destructive, leaving diagnostic characters intact for future taxonomic studies. Here, we assess whether the whole-body extraction widely used for several taxa would be destructive for small crustaceans kept in wet collections. We extracted the DNA from over 70 small (1-3 cm) and relatively fragile shrimps collected during the last 30 years by using: i) a piece of abdominal tissue and ii) from the entire remaining body of the animal. We photographed several samples before and after the lysis, focusing on taxonomically relevant characters. Although DNA concentration was higher in the whole-body extractions, the presence of intact DNA was not correlated to the amount of lysed tissue. The resulting genomic libraries had little to no difference in yield. The taxonomically relevant characters were primarily preserved in larger specimens, whereas smaller specimens (< 1.5 cm) became too fragile to handle or were damaged. We conclude that this method must be carried out carefully in smaller crustaceans, depending on size and taxon. We advise against using it with type specimens as the advantages do not outweigh the risks. Our experiment may provide future research with quantitative and qualitative evaluations to help scientists weigh their decisions when extracting DNA from wet collection material.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"32 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138972318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AquaticVID: a low cost, extended battery life, plug-and-go video system for aquatic research","authors":"L. Fetterplace, Peter Ljungberg, Emilia Benavente Norrman, Filip Bohlin, Lisa Sörman, Per Johannesson, Daniel Rooth, Sara Königson","doi":"10.3897/rio.9.e114134","DOIUrl":"https://doi.org/10.3897/rio.9.e114134","url":null,"abstract":"AquaticVID is a low-cost, long battery life video camera system for use in a wide-range of aquatic research applications. The system can be deployed for multiple day recording on a single charge, is submersible to depths of down to 950 m and can be constructed quickly using easily sourced off-the-shelf materials. The system is essentially ‘plug-and-go’, as assembly and preparation for deployment takes < 30 minutes without the need for technical build or programming skills. All of the electrical components are interchangeable with parts from multiple manufacturers and the camera system can be adapted to fit a variety of waterproof enclosure sizes depending on power and data storage requirements. Here, we describe three versions of the AquaticVID in detail and give examples of above and below water research undertaken with the system. The small size and extended battery times, coupled with ease of use and low cost (US$ 268–540) make the AquaticVID a useful option for numerous aquatic research applications.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"22 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138587684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modern Approaches to the Monitoring of Biоdiversity (MAMBO)","authors":"Toke Høye, Tom August, Mario V Balzan, Koos Biesmeijer, Pierre Bonnet, Tom Breeze, Christophe Dominik, France Gerard, Alexis Joly, Vincent Kalkman, W. Kissling, Teodor Metodiev, Jesper Moeslund, Simon G. Potts, David Roy, Oliver Schweiger, D. Senapathi, J. Settele, Pavel Stoev, Dana T Stowell","doi":"10.3897/rio.9.e116951","DOIUrl":"https://doi.org/10.3897/rio.9.e116951","url":null,"abstract":"EU policies, such as the EU biodiversity strategy 2030 and the Birds and Habitats Directives, demand unbiased, integrated and regularly updated biodiversity and ecosystem service data. However, efforts to monitor wildlife and other species groups are spatially and temporally fragmented, taxonomically biased, and lack integration in Europe. To bridge this gap, the MAMBO project will develop, test and implement enabling tools for monitoring conservation status and ecological requirements of species and habitats for which knowledge gaps still exist. MAMBO brings together the technical expertise of computer science, remote sensing, social science expertise on human-technology interactions, environmental economy, and citizen science, with the biological expertise on species, ecology, and conservation biology. MAMBO is built around stakeholder engagement and knowledge exchange (WP1) and the integration of new technology with existing research infrastructures (WP2). MAMBO will develop, test, and demonstrate new tools for monitoring species (WP3) and habitats (WP4) in a co-design process to create novel standards for species and habitat monitoring across the EU and beyond. MAMBO will work with stakeholders to identify user and policy needs for biodiversity monitoring and investigate the requirements for setting up a virtual lab to automate workflow deployment and efficient computing of the vast data streams (from on the ground sensors, and remote sensing) required to improve monitoring activities across Europe (WP4). Together with stakeholders, MAMBO will assess these new tools at demonstration sites distributed across Europe (WP5) to identify bottlenecks, analyze the cost-effectiveness of different tools, integrate data streams and upscale results (WP6). This will feed into the co-design of future, improved and more cost-effective monitoring schemes for species and habitats using novel technologies (WP7), and thus lead to a better management of protected sites and species.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"41 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138593408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Water-Ecosystems-Food nexus security achievement in the context of climate change: the case study of an agricultural Mediterranean Basin, Greece","authors":"Dimitrios Malamataris, Anastasia Tsavdaridou, Dimitra C. Banti, Athanasios Malliaras, Apostolos V. Karalis, Nikolaos Theocharis, Christodoulos Michos, Antonios Mazaris","doi":"10.3897/rio.9.e116070","DOIUrl":"https://doi.org/10.3897/rio.9.e116070","url":null,"abstract":"Natural resources conservation is considered indispensable for a sustainable future. A thorough managerial analysis of the current and future conservation and availability to meet future demands is both necessary and challenging. As water of adequate quantity and good quality is required for a favourable condition of natural ecosystems and for agricultural production, a comprehensive analysis which would consider hydrological, environmental and agricultural dimensions is needed to properly address their interactions and potential impacts. This study presents a Water-Ecosystems-Food (WEF) nexus methodological flamework aiming at identification and mitigation of critical challenges. The framework is tested in a highly productive water basin in north Greece, the Kokkinorema River Bain, which is also characterised by intense agriculture practices. The presented methodological approach was developed in the context of a natural resources sustainability scheme adapted by the national funded AgroClim project. The selection and prioritisation of the most efficient measures, including Nature-based Solutions, would be driven by a Decision Support System (DSS) tool which will feed upon ecological, social, economic and legislative information. The proposed DSS will also incorporate future climate scenarios to evaluate and address expected future water scarcity, ecosystems degradation and reduced agricultural productivity issues. The proposed methodology for addressing nexus challenges could be transferred to any other natural resources-stressed water basin with similar characteristics.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"55 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139210954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Workshop on 3D mapping of habitats and biological communities with underwater photogrammetry","authors":"Loïc Van Audenhaege, Vincent Mahamadaly, David Price, Alexandre Sneessens, Hayley Cawthra, Clément Delamare, Valentin Danet, Simon Delsol, R. Devillers, I. Gazis, I. Urbina-Barreto","doi":"10.3897/rio.9.e115796","DOIUrl":"https://doi.org/10.3897/rio.9.e115796","url":null,"abstract":"For the past decades, photogrammetry has been increasingly used for monitoring spatial arrangement or temporal dynamics of submerged man-made structures and natural systems. As photogrammetry remains a nascent technique for data collection in the underwater environment, acquisition workflows have evolved constrained by specific methodological practicalities (e.g. euphotic environments vs. deep-sea waters). The annual GeoHab conference gathers a world-wide range of scientists interested in mapping and is, therefore, an adequate event to set up a state-of-the-art workshop on (underwater) photogrammetry. More specifically, a preliminary survey identified the overall lack of photogrammetry knowledge from the audience. A programme was conceptualised to explore within a day theoretical concepts, sampling design and practicalities and a wide range of case studies in various underwater environments. Furthermore, we provided manual training on data acquisition and processing. In overall, a post-survey demonstrated the audience’s satisfaction despite a remaining lack of confidence for implementing their own photogrammetry studies. As this workshop gathers a diversity of materials and a training relevant for a scientific audience, it sets the stage for a reproducible event and leaves room for future improvements. Finally, it provided relevant materials and discussions that enabled us to identify the aspects limiting photogrammetry methodology across scientific applications and institutes, in order to work towards standardisation.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139214938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SEADETECT: developing an automated detection system to reduce whale-vessel collision risk","authors":"Silvia Paoletti, Bob Rumes, N. Pierantonio, S. Panigada, Romain Jan, Thomas Folegot, Anita Schilling, Nicolas Riviere, Vincent Carrier, Antoine Dumoulin, David Van Hamme, Gildas Marquis-Laisné, François-Antoine Bruliard, Félix Petitpierre, Damien Demoor","doi":"10.3897/rio.9.e113968","DOIUrl":"https://doi.org/10.3897/rio.9.e113968","url":null,"abstract":"With the continuous intensification of marine traffic worldwide, whale-vessel collisions at sea (or “ship strikes”) have become one of the primary causes of mortality for cetaceans and a widely recognised cause of concern for human safety and economic losses. The Mediterranean Sea is a global hotspot for whale-vessel collisions, with one of the highest rates involving large cetaceans, especially the endangered fin whales (Balaenoptera physalus) and sperm whales (Physeter macrocephalus). Evidence indicates that both species are experiencing higher chances of a fatal collision than what predictions have estimated so far, with ship strikes being the main human-induced threat in the area. Regional and international organisations have stressed the need to address the issue by investigating the projected impacts of ship strikes on whale populations and by identifying possible mitigation measures to reduce chances of collision. Amongst the most popular and feasible options, there is the improvement of animal detection during navigation. Here, we present SEADETECT, a LIFE project that aims at developing an automated detection system to reduce vessel collision risk with marine mammals and unidentified floating objects (UFOs), combining state-of-the-art and novel technologies with existing approaches in the study of large whale ecology. This detection system consists of three elements; an automated onboard detection system composed of several sensors, a real-time passive acoustic monitoring (PAM) network at sea and a real-time detection-sharing and alert system (REPCET®). In this paper, we propose the development of a mitigation measure framework tailored for the issue of collision with fin and sperm whales in the north-western Mediterranean Sea, but that has the transferability features necessary for its application in other high-risk areas for ship strikes worldwide.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139234295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing Small-Medium IsLands resilience by securing the sustainability of Ecosystem Services: the SMILES Cost Action","authors":"Ioannis N. Vogiatzakis, Mario V Balzan, Evangelia Drakou, S. Katsanevakis, Emilio Padoa-Schioppa, E. Tzirkalli, S. Zotos, Xana Álvarez, M. Külvik, Catarina Fonseca, A. Moustakas, Javier Martínez-López, P. Mackelworth, D. Mandžukovski, Liana Ricci, Bojan Srdjevic, M. Tase, T. Terkenli, Shiri Zemah-Shamir, G. Zittis, Paraskevi Manolaki","doi":"10.3897/rio.9.e116061","DOIUrl":"https://doi.org/10.3897/rio.9.e116061","url":null,"abstract":"European islands are hotspots of biological and cultural diversity, which, compared to mainland, are more vulnerable to climate change, tourism development, uncontrolled land-use changes and the consequences of financial crisis. These drivers of change have increasingly resulted in severe impacts on socio-economic and environmental parameters. Projected climate, land-use and socio-economic change will impact on islands’ biodiversity, ecosystem services and, in turn, on the quality of life of island inhabitants. Even if the existing methods can adequately predict the abovementioned changes of the larger islands, this is not the case for small and medium-size islands, where there is a need for refinement. Although ecosystem services (ES) assessments have been carried out worldwide in different geographical areas, islands are still under-represented. Despite the recognised islands’ importance and vulnerability, efforts to date have focused solely on the pressures they face. Still, we know little about ES supply, flow and demand and their spatio-temporal variability, whilst integrated approaches that consider ES cross-island realms (terrestrial, marine and their interface) remain scarce. Even more under-represented are studies that explore the telecoupled relationship amongst islands and their mainland counterparts. Moreover, the current conceptual approaches guiding ES mapping and assessment need further refinement to account for the complex manifestations of nature and culture arising from peoples’ interaction with island spaces. This paper discusses the creation of a platform for coordinated interdisciplinary research on several aspects of mapping and assessment of ES in small and medium European islands in order to synthesise and strengthen the knowledge base for conservation of island realms and contribute to their sustainable development.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"46 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139242632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Building an atlas of knowledge for invasion biology and beyond! 2nd enKORE-INAS Workshop","authors":"Maud Bernard‐Verdier, Tina Heger, D. Mietchen, Camille Musseau, Marc Brinner, Alexander Hillig, Peter Kraker, Sophie Lokatis, A. L. Nunes, Nils Scheidweiler, Markus Stocker, Roxane Vial, Lars Vogt, Sven Bacher, Eya Baklouti, Harsh Bardhan Gupta, J. Beisel, Sandro Bertolino, Elizabeta Briski, Gustavo Castellanos-Galindo, Franck Courchamp, Ella Z. Daly, Wayne Dawson, James W. E. Dickey, Thomas Evans, Y. Itescu, Birgitta Koenig-ries, Lohith Kumar, Sabrina Kumschick, L. Meyerson, Zarah Pattison, William G. Pfadenhauer, David Renault, Fiona Rickowski, F. Ruland, Conrad Schittko, T. Straka, F. Yannelli, J. Jeschke","doi":"10.3897/rio.9.e115395","DOIUrl":"https://doi.org/10.3897/rio.9.e115395","url":null,"abstract":"With the exponential increase in scientific publications, new conceptual and technological tools are needed to help scientists, students, managers and policy-makers to navigate and digest current scientific knowledge. Hi Knowledge is an initiative to synthesise and visualise scientific knowledge, with an initial focus on invasion biology that is currently expanding to include urban ecology, restoration ecology and freshwater ecology. In a workshop on 5-6 June 2023 in Berlin, Germany, we discussed and tested a collection of new open tools related to this initiative in order to publish, curate, explore and synthesise concepts and results in ecology. Three main themes were discussed during in-person breakout group sessions: (1) building and using open tools for knowledge curation, exploration and synthesis; (2) making open knowledge searchable and machine friendly by improving modelling and annotation of scientific knowledge; and (3) extending beyond the field of invasion biology. We report on the discussions of all twelve sessions pertaining to these themes. A main underlying goal of our workshop was to build a community of scientists involved in openly co-designing and using these tools. Overall, the participants were enthusiastic about the usefulness of these tools and discussions gravitated around improving them and finding strategies to scale-up participation by the community. Follow-up user tests and publications are planned for individual tools and topics.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"626 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139246688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Joint statement by CETAF, SPNHC and BHL on DATA within scientific publications: clarification of [non]copyrightability","authors":"Laurence Bénichou, D. Agosti, W. Egloff, Elisa Hermann, Mariko Kageyama, Patricia Mergen, Constance Rinaldo, J. Buschbom","doi":"10.3897/rio.9.e115466","DOIUrl":"https://doi.org/10.3897/rio.9.e115466","url":null,"abstract":"The EU and other states have made legislative efforts to clarify data mining in copyrightable works, but the situation remains obscure and confusing, especially in a globalised field where international legislation can contribute to opacity. The present paper aims at asserting a common position of three communities representing biodiversity sciences and data specialists on this issue and to propose common and best practice guidelines so that they become universally accepted rules. As scientific data users, we take the standpoint that scientific data are not copyrightable and, furthermore, they can be accessed, shared and reused freely. Thus, once legal access has been gained to copyrighted publications, the data within those scholarly publications can be considered to be open data that is freely extractable. This set of recommendations has been reached specifically for scientific use and societal benefits.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"130 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139256332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}