Marisa Conte, Allen Flynn, Philip Barrison, Peter Boisvert, Zach Landis-Lewis, Charles Friedman
We present our work to develop digital objects to represent and convey a specific category of scientific knowledge: computable biomedical knowledge (CBK). Properly developed, validated, implemented and stewarded, CBK has the potential to accelerate the translation of actionable knowledge from scientific discovery to clinical application. Our research takes an infrastructural approach to CBK, initially by focusing on the creation of a conceptual model for packaging computable biomedical knowledge - the Knowledge Object (KO) - and on corresponding efforts to create an architecture for KO management and implementation. Additionally, our work is grounded in the FAIR principles, such that KO artefacts should be findable, accessible, interoperable and reusable and we are exploring aligning KOs with emerging best practices for FAIR Digital Objects (FDO). The outcomes of this work resonate in clinical contexts, health professions education, healthcare quality improvement, biomedical and translational research and population care. Our KO model is also of interest to researchers and practitioners interested in knowledge science, including those working with semantic technologies and other forms of digital objects.
我们的工作是开发数字对象，用于表示和传递特定类别的科学知识：可计算生物医学知识（CBK）。可计算生物医学知识经过适当的开发、验证、实施和管理，有可能加快可操作知识从科学发现到临床应用的转化。 我们的研究采用一种基础架构方法来处理 CBK，首先侧重于创建一个包装可计算生物医学知识的概念模型--知识对象 (KO)，并相应地努力创建一个用于 KO 管理和实施的架构。此外，我们的工作以 FAIR 原则为基础，即知识对象（KO）应是可查找、可访问、可互操作和可重复使用的，我们正在探索将知识对象与新兴的 FAIR 数字对象（FDO）最佳实践相结合。 这项工作的成果将在临床、卫生专业教育、医疗质量改进、生物医学和转化研究以及人口保健等领域产生共鸣。对知识科学感兴趣的研究人员和从业人员，包括使用语义技术和其他形式的数字对象的人员，也会对我们的 KO 模型感兴趣。
{"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}
Samuel C. Bernardes, T. von Rintelen, Serena Alexander, Fiona Lorenz, Kristina von Rintelen
Specimens in natural history museums are a valuable resource for biological research, such as taxonomic, biodiversity or evolutionary studies. However, the quality of DNA and even morphological characters can decrease over time, depending on previous fixation and long-term preservation methods. In recent years, advances in DNA extraction and sequencing techniques have allowed researchers to obtain DNA from museum specimens, even when the DNA was very fragmented. Extraction methods should ideally be morphologically non-destructive, leaving diagnostic characters intact for future taxonomic studies. Here, we assess whether the whole-body extraction widely used for several taxa would be destructive for small crustaceans kept in wet collections. We extracted the DNA from over 70 small (1-3 cm) and relatively fragile shrimps collected during the last 30 years by using: i) a piece of abdominal tissue and ii) from the entire remaining body of the animal. We photographed several samples before and after the lysis, focusing on taxonomically relevant characters. Although DNA concentration was higher in the whole-body extractions, the presence of intact DNA was not correlated to the amount of lysed tissue. The resulting genomic libraries had little to no difference in yield. The taxonomically relevant characters were primarily preserved in larger specimens, whereas smaller specimens (< 1.5 cm) became too fragile to handle or were damaged. We conclude that this method must be carried out carefully in smaller crustaceans, depending on size and taxon. We advise against using it with type specimens as the advantages do not outweigh the risks. Our experiment may provide future research with quantitative and qualitative evaluations to help scientists weigh their decisions when extracting DNA from wet collection material.
自然历史博物馆中的标本是生物研究（如分类学、生物多样性或进化研究）的宝贵资源。然而，DNA 甚至形态特征的质量会随着时间的推移而下降，这取决于以前的固定和长期保存方法。近年来，DNA 提取和测序技术的进步使研究人员能够从博物馆标本中获取 DNA，即使 DNA 非常零碎。理想的提取方法应该是形态上无损的，为未来的分类研究保留完整的诊断特征。在此，我们评估了广泛用于多个类群的全身提取法是否会对湿藏品中的小型甲壳类动物造成破坏。我们从过去 30 年中收集的 70 多只体型较小（1-3 厘米）且相对脆弱的小虾中提取了 DNA，提取方法包括：i）一片腹部组织；ii）动物的整个剩余身体。我们对裂解前后的几个样本进行了拍照，重点是分类学上的相关特征。虽然全身提取的 DNA 浓度较高，但完整 DNA 的存在与裂解组织的数量无关。由此产生的基因组文库在产量上几乎没有差别。与分类学相关的特征主要保存在较大的标本中，而较小的标本（< 1.5 厘米）则过于脆弱，无法处理或已损坏。我们的结论是，对于较小的甲壳类动物，必须根据其大小和分类群谨慎使用这种方法。我们建议不要在类型标本中使用这种方法，因为其优点并不比风险大。我们的实验可为未来的研究提供定量和定性评估，帮助科学家在从湿采集材料中提取 DNA 时权衡利弊。
{"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}
L. Fetterplace, Peter Ljungberg, Emilia Benavente Norrman, Filip Bohlin, Lisa Sörman, Per Johannesson, Daniel Rooth, Sara Königson
AquaticVID is a low-cost, long battery life video camera system for use in a wide-range of aquatic research applications. The system can be deployed for multiple day recording on a single charge, is submersible to depths of down to 950 m and can be constructed quickly using easily sourced off-the-shelf materials. The system is essentially ‘plug-and-go’, as assembly and preparation for deployment takes < 30 minutes without the need for technical build or programming skills. All of the electrical components are interchangeable with parts from multiple manufacturers and the camera system can be adapted to fit a variety of waterproof enclosure sizes depending on power and data storage requirements. Here, we describe three versions of the AquaticVID in detail and give examples of above and below water research undertaken with the system. The small size and extended battery times, coupled with ease of use and low cost (US$ 268–540) make the AquaticVID a useful option for numerous aquatic research applications.
{"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}
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
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.
{"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}
Dimitrios Malamataris, Anastasia Tsavdaridou, Dimitra C. Banti, Athanasios Malliaras, Apostolos V. Karalis, Nikolaos Theocharis, Christodoulos Michos, Antonios Mazaris
Natural resources conservation is considered indispensable for a sustainable future. A thorough managerial analysis of the current and future conservation and availability to meet future demands is both necessary and challenging. As water of adequate quantity and good quality is required for a favourable condition of natural ecosystems and for agricultural production, a comprehensive analysis which would consider hydrological, environmental and agricultural dimensions is needed to properly address their interactions and potential impacts. This study presents a Water-Ecosystems-Food (WEF) nexus methodological flamework aiming at identification and mitigation of critical challenges. The framework is tested in a highly productive water basin in north Greece, the Kokkinorema River Bain, which is also characterised by intense agriculture practices. The presented methodological approach was developed in the context of a natural resources sustainability scheme adapted by the national funded AgroClim project. The selection and prioritisation of the most efficient measures, including Nature-based Solutions, would be driven by a Decision Support System (DSS) tool which will feed upon ecological, social, economic and legislative information. The proposed DSS will also incorporate future climate scenarios to evaluate and address expected future water scarcity, ecosystems degradation and reduced agricultural productivity issues. The proposed methodology for addressing nexus challenges could be transferred to any other natural resources-stressed water basin with similar characteristics.
{"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}
Loïc Van Audenhaege, Vincent Mahamadaly, David Price, Alexandre Sneessens, Hayley Cawthra, Clément Delamare, Valentin Danet, Simon Delsol, R. Devillers, I. Gazis, I. Urbina-Barreto
For the past decades, photogrammetry has been increasingly used for monitoring spatial arrangement or temporal dynamics of submerged man-made structures and natural systems. As photogrammetry remains a nascent technique for data collection in the underwater environment, acquisition workflows have evolved constrained by specific methodological practicalities (e.g. euphotic environments vs. deep-sea waters). The annual GeoHab conference gathers a world-wide range of scientists interested in mapping and is, therefore, an adequate event to set up a state-of-the-art workshop on (underwater) photogrammetry. More specifically, a preliminary survey identified the overall lack of photogrammetry knowledge from the audience. A programme was conceptualised to explore within a day theoretical concepts, sampling design and practicalities and a wide range of case studies in various underwater environments. Furthermore, we provided manual training on data acquisition and processing. In overall, a post-survey demonstrated the audience’s satisfaction despite a remaining lack of confidence for implementing their own photogrammetry studies. As this workshop gathers a diversity of materials and a training relevant for a scientific audience, it sets the stage for a reproducible event and leaves room for future improvements. Finally, it provided relevant materials and discussions that enabled us to identify the aspects limiting photogrammetry methodology across scientific applications and institutes, in order to work towards standardisation.
{"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}
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
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.
随着全球海上交通的不断加剧，鲸鱼与船只的海上碰撞（或称 "撞船事故"）已成为鲸目动物死亡的主要原因之一，也是人类安全和经济损失方面公认的一个令人担忧的问题。地中海是全球鲸鱼与船只碰撞的热点地区，其中涉及大型鲸目动物，尤其是濒危长须鲸（Balaenoptera physalus）和抹香鲸（Physeter macrocephalus）的碰撞率最高。有证据表明，这两个物种发生致命碰撞的几率比迄今为止的预测要高，而船只撞击是该地区主要的人为威胁。区域和国际组织强调，有必要通过调查船只撞击对鲸鱼种群的预期影响，并通过确定可能的缓解措施来降低碰撞几率，从而解决这一问题。其中最受欢迎和最可行的方案是改进航行过程中的动物探测。在此，我们介绍一个名为 SEADETECT 的 LIFE 项目，该项目旨在开发一种自动探测系统，以降低船只与海洋哺乳动物和不明漂浮物（UFO）相撞的风险，将最先进的新技术与大型鲸鱼生态学研究中的现有方法相结合。该探测系统由三个部分组成：由多个传感器组成的船上自动探测系统、海上实时被动声学监测（PAM）网络以及实时探测共享和警报系统（REPCET®）。在本文中，我们提出了一个针对地中海西北部长须鲸和抹香鲸碰撞问题的缓解措施框架，该框架具有必要的可移植性，可应用于全球其他船舶碰撞高风险区域。
{"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}
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
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.
{"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}
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
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.
{"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}
Laurence Bénichou, D. Agosti, W. Egloff, Elisa Hermann, Mariko Kageyama, Patricia Mergen, Constance Rinaldo, J. Buschbom
The EU and other states have made legislative efforts to clarify data mining in copyrightable works, but the situation remains obscure and confusing, especially in a globalised field where international legislation can contribute to opacity. The present paper aims at asserting a common position of three communities representing biodiversity sciences and data specialists on this issue and to propose common and best practice guidelines so that they become universally accepted rules. As scientific data users, we take the standpoint that scientific data are not copyrightable and, furthermore, they can be accessed, shared and reused freely. Thus, once legal access has been gained to copyrighted publications, the data within those scholarly publications can be considered to be open data that is freely extractable. This set of recommendations has been reached specifically for scientific use and societal benefits.
{"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}
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