| 1. |
- Janssen, Annette B. G., et al.
(författare)
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Exploring, exploiting and evolving diversity of aquatic ecosystem models : a community perspective
- 2015
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Ingår i: Aquatic Ecology. - : Springer Science and Business Media LLC. - 1386-2588 .- 1573-5125. ; 49:4, s. 513-548
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Tidskriftsartikel (refereegranskat)abstract
- Here, we present a community perspective on how to explore, exploit and evolve the diversity in aquatic ecosystem models. These models play an important role in understanding the functioning of aquatic ecosystems, filling in observation gaps and developing effective strategies for water quality management. In this spirit, numerous models have been developed since the 1970s. We set off to explore model diversity by making an inventory among 42 aquatic ecosystem modellers, by categorizing the resulting set of models and by analysing them for diversity. We then focus on how to exploit model diversity by comparing and combining different aspects of existing models. Finally, we discuss how model diversity came about in the past and could evolve in the future. Throughout our study, we use analogies from biodiversity research to analyse and interpret model diversity. We recommend to make models publicly available through open-source policies, to standardize documentation and technical implementation of models, and to compare models through ensemble modelling and interdisciplinary approaches. We end with our perspective on how the field of aquatic ecosystem modelling might develop in the next 5-10 years. To strive for clarity and to improve readability for non-modellers, we include a glossary.
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| 2. |
- Maasri, Alain, et al.
(författare)
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A global agenda for advancing freshwater biodiversity research
- 2022
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Ingår i: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 25:2, s. 255-263
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Tidskriftsartikel (refereegranskat)abstract
- Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation.
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| 3. |
- Mooij, Wolf M., et al.
(författare)
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Modeling water quality in the Anthropocene : directions for the next-generation aquatic ecosystem models
- 2019
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Ingår i: Current Opinion in Environmental Sustainability. - : Elsevier BV. - 1877-3435 .- 1877-3443. ; 36, s. 85-95
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Forskningsöversikt (refereegranskat)abstract
- Everything changes and nothing stands still (Heraclitus). Here we review three major improvements to freshwater aquatic ecosystem models - and ecological models in general - as water quality scenario analysis tools towards a sustainable future. To tackle the rapid and deeply connected dynamics characteristic of the Anthropocene, we argue for the inclusion of eco-evolutionary, novel ecosystem and social-ecological dynamics. These dynamics arise from adaptive responses in organisms and ecosystems to global environmental change and act at different integration levels and different time scales. We provide reasons and means to incorporate each improvement into aquatic ecosystem models. Throughout this study we refer to Lake Victoria as a microcosm of the evolving novel social-ecological systems of the Anthropocene. The Lake Victoria case clearly shows how interlinked eco-evolutionary, novel ecosystem and social-ecological dynamics are, and demonstrates the need for transdisciplinary research approaches towards global sustainability.
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| 4. |
- Mooij, Wolf M., et al.
(författare)
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Serving many at once : How a database approach can create unity in dynamical ecosystem modelling
- 2014
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Ingår i: Environmental Modelling & Software. - : Elsevier BV. - 1364-8152 .- 1873-6726. ; 61, s. 266-273
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Tidskriftsartikel (refereegranskat)abstract
- Simulation modelling in ecology is a field that is becoming increasingly compartmentalized. Here we propose a Database Approach To Modelling (DATM) to create unity in dynamical ecosystem modelling with differential equations. In this approach the storage of ecological knowledge is independent of the language and platform in which the model will be run. To create an instance of the model, the information in the database is translated and augmented with the language and platform specifics. This process is automated so that a new instance can be created each time the database is updated. We describe the approach using the simple Lotka-Volterra model and the complex ecosystem model for shallow lakes PCLake, which we automatically implement in the frameworks OSIRIS, GRIND for MATLAB, ACSL, R, DUFLOW and DELWAQ. A clear advantage of working in a database is the overview it provides. The simplicity of the approach only adds to its elegance.
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| 5. |
- van Gerven, Luuk P. A., et al.
(författare)
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Advantages of concurrent use of multiple software frameworks in water quality modelling using a database approach
- 2015
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Ingår i: Fundamental and Applied Limnology. - : Schweizerbart. - 1863-9135. ; 186:1-2, s. 5-20
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Tidskriftsartikel (refereegranskat)abstract
- Water quality modelling deals with multidisciplinary questions ranging from fundamental to applied. Addressing this broad range of questions requires multiple analysis techniques and therefore multiple frameworks. Through the recently developed database approach to modelling (DATM), it has become possible to run a model in multiple software frameworks without much overhead. Here we apply DATM to the ecosystem model for ditches PCDitch and its twin model for shallow lakes PCLake. Using DATM, we run these models in six frameworks (ACSL, DELWAQ, DUFLOW, GRIND for MATLAB, OSIRIS and R), and report on the possible model analyses with tools provided by each framework. We conclude that the dynamic link between frameworks and models resulting from DATM has the following main advantages: it allows one to use the framework one is familiar with for most model analyses and eases switching between frameworks for complementary model analyses, including the switch between a 0-D and 1-D to 3-D setting. Moreover, the strength of each framework - including runtime performance - can now be easily exploited. We envision that a community-based further development of the concept can contribute to the future development of water quality modelling, not only by addressing multidisciplinary questions but also by facilitating the exchange of models and process formulations within the community of water quality modellers.
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| 6. |
- Kim, HyeJin, et al.
(författare)
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Towards a better future for biodiversity and people : Modelling Nature Futures
- 2023
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Ingår i: Global Environmental Change. - 0959-3780 .- 1872-9495. ; 82
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Tidskriftsartikel (refereegranskat)abstract
- The Nature Futures Framework (NFF) is a heuristic tool for co-creating positive futures for nature and people. It seeks to open up a diversity of futures through mainly three value perspectives on nature - Nature for Nature, Nature for Society, and Nature as Culture. This paper describes how the NFF can be applied in modelling to support decision-making. First, we describe key considerations for the NFF in developing qualitative and quantitative scenarios: i) multiple value perspectives on nature as a state space where pathways improving nature toward a frontier can be represented, ii) mutually reinforcing key feedbacks of social-ecological systems that are important for nature conservation and human wellbeing, iii) indicators of multiple knowledge systems describing the evolution of complex social-ecological dynamics. We then present three approaches to modelling Nature Futures scenarios in the review, screening, and design phases of policy processes. This paper seeks to facilitate the integration of relational values of nature in models and strengthen modelled linkages across biodiversity, nature's contributions to people, and quality of life.
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| 7. |
- Pereira, Laura M., et al.
(författare)
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Developing multiscale and integrative nature-people scenarios using the Nature Futures Framework
- 2020
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Ingår i: People and Nature. - : Wiley. - 2575-8314. ; 2:4, s. 1172-1195
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Tidskriftsartikel (refereegranskat)abstract
- 1. Scientists have repeatedly argued that transformative, multiscale global scenarios are needed as tools in the quest to halt the decline of biodiversity and achieve sustainability goals.2. As a first step towards achieving this, the researchers who participated in the scenarios and models expert group of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) entered into an iterative, participatory process that led to the development of the Nature Futures Framework (NFF).3. The NFF is a heuristic tool that captures diverse, positive relationships of humans with nature in the form of a triangle. It can be used both as a boundary object for continuously opening up more plural perspectives in the creation of desirable nature scenarios and as an actionable framework for developing consistent nature scenarios across multiple scales.4. Here we describe the methods employed to develop the NFF and how it fits into a longer term process to create transformative, multiscale scenarios for nature. We argue that the contribution of the NFF is twofold: (a) its ability to hold a plurality of perspectives on what is desirable, which enables the development of joint goals and visions and recognizes the possible convergence and synergies of measures to achieve these visions and (b), its multiscale functionality for elaborating scenarios and models that can inform decision-making at relevant levels, making it applicable across specific places and perspectives on nature.5. If humanity is to achieve its goal of a more sustainable and prosperous future rooted in a flourishing nature, it is critical to open up a space for more plural perspectives of human-nature relationships. As the global community sets out to develop new goals for biodiversity, the NFF can be used as a navigation tool helping to make diverse, desirable futures possible.
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| 8. |
- Lu, Chang, et al.
(författare)
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Identification of a gene network driving the attenuated response to lipopolysaccharide of monocytes from hypertensive coronary artery disease patients
- 2024
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Ingår i: Frontiers in Immunology. - : Frontiers Media SA. - 1664-3224. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: The impact of cardiovascular disease (CVD) risk factors, encompassing various biological determinants and unhealthy lifestyles, on the functional dynamics of circulating monocytes—a pivotal cell type in CVD pathophysiology remains elusive. In this study, we aimed to elucidate the influence of CVD risk factors on monocyte transcriptional responses to an infectious stimulus. Methods: We conducted a comparative analysis of monocyte gene expression profiles from the CTMM – CIRCULATING CELLS Cohort of coronary artery disease (CAD) patients, at baseline and after lipopolysaccharide (LPS) stimulation. Gene co-expression analysis was used to identify gene modules and their correlations with CVD risk factors, while pivotal transcription factors controlling the hub genes in these modules were identified by regulatory network analyses. The identified gene module was subjected to a drug repurposing screen, utilizing the LINCS L1000 database. Results: Monocyte responsiveness to LPS showed a highly significant, negative correlation with blood pressure levels (ρ< -0.4; P<10-80). We identified a ZNF12/ZBTB43-driven gene module closely linked to diastolic blood pressure, suggesting that monocyte responses to infectious stimuli, such as LPS, are attenuated in CAD patients with elevated diastolic blood pressure. This attenuation appears associated with a dampening of the LPS-induced suppression of oxidative phosphorylation. Finally, we identified the serine-threonine inhibitor MW-STK33-97 as a drug candidate capable of reversing this aberrant LPS response. Conclusions: Monocyte responses to infectious stimuli may be hampered in CAD patients with high diastolic blood pressure and this attenuated inflammatory response may be reversed by the serine-threonine inhibitor MW-STK33-97. Whether the identified gene module is a mere indicator of, or causal factor in diastolic blood pressure and the associated dampened LPS responses remains to be determined.
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| 9. |
- Raymond, Christopher, et al.
(författare)
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Inclusive conservation and the Post-2020 Global Biodiversity Framework : Tensions and prospects
- 2022
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Ingår i: One Earth. - : Elsevier BV. - 2590-3330 .- 2590-3322. ; 5:3, s. 252-264
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Tidskriftsartikel (refereegranskat)abstract
- The draft Post-2020 Global Biodiversity Framework commits to achievement of equity and justice outcomes and represents a “relational turn” in how we understand inclusive conservation. Although “inclusivity” is drawn on as a means to engage diverse stakeholders, widening the framing of inclusivity can create new tensions with regard to how to manage protected areas. We first offer a set of tensions that emerge in the light of the relational turn in biodiversity conservation. Drawing on global case examples applying multiple methods of inclusive conservation, we then demonstrate that, by actively engaging in the interdependent phases of recognizing hybridity, enabling conditions for reflexivity and partnership building, tensions can not only be acknowledged but softened and, in some cases, reframed when managing for biodiversity, equity, and justice goals. The results can improve stakeholder engagement in protected area management, ultimately supporting better implementation of global biodiversity targets.
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| 10. |
- Teurlincx, Sven, et al.
(författare)
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A perspective on water quality in connected systems : modelling feedback between upstream and downstream transport and local ecological processes
- 2019
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Ingår i: Current Opinion in Environmental Sustainability. - : Elsevier BV. - 1877-3435 .- 1877-3443. ; 40, s. 21-29
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Tidskriftsartikel (refereegranskat)abstract
- Food production for a growing world population relies on application of fertilisers and pesticides on agricultural lands. However, these substances threaten surface water quality and thereby endanger valued ecosystem services such as drinking water supply, food production and recreational water use. Such deleterious effects do not merely arise on the local scale, but also on the regional scale through transport of substances as well as energy and biota across the catchment. Here we argue that aquatic ecosystem models can provide a process-based understanding of how these transports by water and organisms as vectors affect - and are affected by - ecosystem state and functioning in networks of connected lakes. Such a catchment scale approach is key to setting critical limits for the release of substances by agricultural practices and other human pressures on aquatic ecosystems. Thereby, water and food production and the trade-offs between them may be managed more sustainably.
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