Integration of datasets for individual prediction of DNA methylation-based biomarkers

BACKGROUND: Epigenetic scores (EpiScores) can provide biomarkers of lifestyle and disease risk. Projecting new datasets onto a reference panel is challenging due to separation of technical and biological variation with array data. Normalisation can standardise data distributions but may also remove population-level biological variation.RESULTS: We compare two birth cohorts (Lothian Birth Cohorts of 1921 and 1936 - nLBC1921 = 387 and nLBC1936 = 498) with blood-based DNA methylation assessed at the same chronological age (79 years) and processed in the same lab but in different years and experimental batches. We examine the effect of 16 normalisation methods on a novel BMI EpiScore (trained in an external cohort, n = 18,413), and Horvath's pan-tissue DNA methylation age, when the cohorts are normalised separately and together. The BMI EpiScore explains a maximum variance of R2=24.5% in BMI in LBC1936 (SWAN normalisation). Although there are cross-cohort R2 differences, the normalisation method makes a minimal difference to within-cohort estimates. Conversely, a range of absolute differences are seen for individual-level EpiScore estimates for BMI and age when cohorts are normalised separately versus together. While within-array methods result in identical EpiScores whether a cohort is normalised on its own or together with the second dataset, a range of differences is observed for between-array methods.CONCLUSIONS: Normalisation methods returning similar EpiScores, whether cohorts are analysed separately or together, will minimise technical variation when projecting new data onto a reference panel. These methods are important for cases where raw data is unavailable and joint normalisation of cohorts is computationally expensive.</p

Advancing marine conservation in European and contiguous seas with the MarCons Action

Cumulative human impacts have led to the degradation of marine ecosystems and the decline of biodiversity in the European and contiguous seas. Effective conservation measures are urgently needed to reverse these trends. Conservation must entail societal choices, underpinned by human values and worldviews that differ between the countries bordering these seas. Social, economic and political heterogeneity adds to the challenge of balancing conservation with sustainable use of the seas. Comprehensive macro-regional coordination is needed to ensure effective conservation of marine ecosystems and biodiversity of this region. Under the European Union Horizon 2020 framework programme, the MarCons COST action aims to promote collaborative research to support marine management, conservation planning and policy development. This will be achieved by developing novel methods and tools to close knowledge gaps and advance marine conservation science. This action will provide support for the development of macro-regional and national policies through six key actions: to develop tools to analyse cumulative human impacts; to identify critical scientific and technical gaps in conservation efforts; to improve the resilience of the marine environment to global change and biological invasions; to develop frameworks for integrated conservation planning across terrestrial, freshwater, and marine environments; to coordinate marine conservation policy across national boundaries; and to identify effective governance approaches for marine protected area management. Achieving the objectives of these actions will facilitate the integration of marine conservation policy into macro-regional maritime spatial planning agendas for the European and contiguous seas, thereby offsetting the loss of biodiversity and ecosystem services in this region

Workshop on Stakeholder Engagement Strategy (WKSHOES)

The ICES Workshop on Stakeholder Engagement Strategy (WKSHOES) met online 22-24 June 2021 with the objective to organize the background information needed for SCICOM and ACOM to develop a formal ICES Stakeholder Engagement Strategy. Stakeholder engagement has taken an increasingly important role in ICES. There was a strong consensus in the workshop that stakeholder engagement is essential to ICES’ work, as has been captured by the most recent ICES Strategic, Science, and Advisory Plans. The question is how to do it best. While WKSHOES recognized the essential nature of stakeholder engagement for addressing environmental challenges, understanding human impacts and values, the group discussed the valid concern that if stakeholder engagement is done incorrectly, it could compromise the perceived objectivity of ICES science and its independence. Workshop participants challenged the idea of objective or “pure” science, but also recognized the practical need to have ICES advice be transparent and science-based. Participants also understand that when providing advice, tradeoffs have to be made that are informed by the different weights that stakeholders place on various management objectives. A key question related to a potential stakeholder engagement strategy is “Who is a stakeholder?” This report discusses several definitions and roles. A central challenge for ICES is recognizing that the network of stakeholders is a subset of the people impacted by ICES science and advice. The Stakeholder Engagement Strategy should therefore primarily focus on ensuring that people who are part of the ICES network have clear roles and responsibilities and that ICES performs its work fairly and transparently. However, participants also recognize the need to increase opportunities for diverse resource users and citizens to have clear avenues to engage with the different aspects of the ICES network. Considering and promoting diversity and inclusion and avoiding implicit bias are crucial in this process. It is also essential to define clear goals for stakeholder engagement in general, and tangible objectives for each engagement activity in particular. Engagement objectives already formulated in various ICES documents are outlined in this report, as well as recommendations for guiding principles that provide the overarching frame of reference for engagement. This Report serves as the primary output from WKSHOES, and represents the knowledge and opinions of workshop participants. WKSHOES recommends that in order to both complete the development of the strategy and conduct successful stakeholder engagement about it, a suite of communication activities is needed that should best be coordinated from a central contact point within ICES. WKSHOES recommends that after ACOM and SCICOM draft the strategy and obtain input from the ICES Council, a diversity of stakeholders should be invited to provide input on the WKSHOES report and the development of the Engagement Strategy. ICES should solicit input from stakeholders by early 2022 to agree on the contents of the Strategy and how it will be implemented. WKSHOES also recommends that a future Expert Group address the ongoing need to develop and communicate effective stakeholder engagement methods within the ICES network.Peer reviewe

Deliverable 3.6 zoning plan of case studies : evaluation of spatial management options for the case studies

Within MESMA, nine case studies (CS) represent discrete marine European spatial entities, at different spatial scales, where a spatial marine management framework is in place, under development or considered. These CS (described in more details below) are chosen in such a way (MESMA D. 3.1 ) that they encompass the complexity of accommodating the various user functions of the marine landscape in various regions of the European marine waters. While human activities at sea are competing for space, there is also growing awareness of the possible negative effects of these human activities on the marine ecosystem. As such, system specific management options are required, satisfying current and future sectoral needs, while safeguarding the marine ecosystem from further detoriation. This integrated management approach is embedded in the concept of ecosystem based management (EBM). The goal of marine EBM is to maintain marine ecosystems in a healthy, productive and resilient condition, making it possible that they sustain human use and provide the goods and services required by society (McLeod et al. 2005). Therefore EBM is an environmental mangagement approach that recognises the interactions within a marine ecosystem, including humans. Hence, EBM does not consider single issues, species or ecosystems good and services in isolation. Operationalisation of EBM can be done through place-based or spatial management approaches (Lackey 1998), such as marine spatial planning (MSP). MSP is a public process of analysing and allocating the spatial and temporal distribution of human activities aiming at achieving ecological, economic and social objectives. These objectives are usually formulated through political processes (Douvere et al. 2007, Douvere 2008). Within MESMA, a spatially managed area (SMA) is then defined as “a geographical area within which marine spatial planning initiatives exist in the real world”. Marine spatial planning initiatives refer to existing management measures actually in place within a defined area, or in any stage of a process of putting management in place, e.g. plans or recommendations for a particular area. Management can include management for marine protection (e.g. in MPAs), or management for sectoral objectives (e.g. building a wind farm to meet renewable energy objectives). Within MESMA, SMAs can have different spatial scales. A SMA can be a small, specific area that is managed/planned to be managed for one specific purpose, but it can also be a larger area within which lots of plans or ‘usage zones’ exist. This definition is different from the definition mentioned in the DoW (page 60). The original definition was adapted during a CS leader workshop (2-4 May 2012 in Gent, Belgium) and formally accepted by the MESMA ExB during the ExB meeting in Cork (29-30 May 2012). MSP should result in a marine spatial management plan that will produce the desired future trough explicit decisions about the location and timing of human activities. Ehler & Douvere (2009) consider this spatial management as a beginning toward the the implementation of desired goals and objectives. They describe the spatial management plan as a comprehensive, strategic document that provides the framework and direction for marine spatial management decisions. The plan should identify when, where and how goals and objectives will be met. Zoning (the development of zoning plans) is often an important management measure to implement spatial management plans. The purpose of a zoning plan (Ehler & Douvere 2009) is: To provide protection for biologically and ecologically important habitats, ecosystems, and ecological processes. To seperate conflicting human activities, or to combine compatible activities. To protect the natural values of the marine management area (in MESMA terminology: the SMA) while allowing reasonable human uses of the area. To allocate areas for reasonable human uses while minimising the effects of these human uses on each other, and nature. To preserve some areas of the SMA in their natural state undisturbed by humans except for scientific and educational purposes.peer-reviewe

What does nature feel like? Using embodied walking interviews to discover cultural ecosystem services

The development of cultural ecosystem services (CES) concept has progressed beyond the common categories of economic benefits from tourism and recreation, and yet definitions of CES remain vague and often shallow. It is necessary to develop methodologies that can more fully express the depth of meaning of non-material benefits humans receive from nature to both strengthen the conceptual foundation of CES, and to support the evaluation, management, and decision-making processes pertaining to protected areas and other environments. This study demonstrates how embodied interviews, conducted with informants while walking in nature, capture real-time intuitive and grounded perceptions of, and reactions to, four different ecosystem types and their associated services. The results provide a deeper and more nuanced understanding of diverse human-nature relationships and reflect two distinct groups of CES values or themes: general (common across research sites) and local (site-specific). The twelve General CES include cognitive and psychological services, among them calmness and newness, heightened imagination and curiosity, increased energy and motivation, and gaining new perspectives. Local themes differed from one ecosystem to another and included more biodiversity- and geodiversity-related values pertaining to local species and geology, as well as more sensory-based experiences

What does nature feel like? Using embodied walking interviews to discover cultural ecosystem services

The development of cultural ecosystem services (CES) concept has progressed beyond the common categories of economic benefits from tourism and recreation, and yet definitions of CES remain vague and often shallow. It is necessary to develop methodologies that can more fully express the depth of meaning of non-material benefits humans receive from nature to both strengthen the conceptual foundation of CES, and to support the evaluation, management, and decision-making processes pertaining to protected areas and other environments. This study demonstrates how embodied interviews, conducted with informants while walking in nature, capture real-time intuitive and grounded perceptions of, and reactions to, four different ecosystem types and their associated services. The results provide a deeper and more nuanced understanding of diverse human-nature relationships and reflect two distinct groups of CES values or themes: general (common across research sites) and local (site specific). The twelve General CES include cognitive and psychological services, among them calmness and newness, heightened imagination and curiosity, increased energy and motivation, and gaining new perspectives. Local themes differed from one ecosystem to another and included more biodiversity-and geodiversity-related values pertaining to local species and geology, as well as more sensory-based experiences.Peer reviewe