@article {4407, title = {Water-food-energy nexus for transboundary cooperation in Eastern Africa}, journal = {Water Supply}, year = {2022}, month = {Mar-01-2022}, abstract = {Establishing cooperation in transboundary rivers is challenging especially with the weak or non-existent river basin institutions. A nexus-based approach is developed to explore cooperation opportunities in transboundary river basins while considering system operation and coordination under uncertain hydrologic river regimes. The proposed approach is applied to the Nile river basin with a special focus on the Grand Ethiopian Renaissance Dam (GERD), assuming two possible governance positions: with or without cooperation. A cooperation mechanism is developed to allocate additional releases from the GERD when necessary, while a unilateral position assumes that the GERD is operated to maximize hydropower generation regardless of downstream users{\textquoteright} needs. The GERD operation modes were analysed considering operation of downstream reservoirs and varying demands in Egypt. Results show that average basin-wide hydropower generation is likely to increase by about 547 GWh/year (1\%) if cooperation is adopted when compared to the unilateral position. In Sudan, hydropower generation and water supply are expected to enhance in the unilateral position and would improve further with cooperation. Furthermore, elevated low flows by the GERD are likely to improve the WFE nexus outcomes in Egypt under full cooperation governance scenario with a small reduction in GERD hydropower generation (2,000 GWh/year (19\%)). }, issn = {1606-9749}, doi = {10.2166/ws.2022.001}, url = {https://iwaponline.com/ws/article/doi/10.2166/ws.2022.001/86211/Water-food-energy-nexus-for-transboundary}, author = {Elsayed, Hamdy and Djordjevi{\'c}, Slobodan and Savic, Dragan and Tsoukalas, Ioannis and Makropoulos, Christos} } @article {4394, title = {The Nile Water-Food-Energy Nexus under Uncertainty: Impacts of the Grand Ethiopian Renaissance Dam}, journal = {Journal of Water Resources Planning and Management}, volume = {146}, year = {2020}, month = {Jan-11-2020}, pages = {04020085}, abstract = {

Achieving a water, food, and energy (WFE) nexus balance through policy interventions is challenging in a transboundary river basin because of the dynamic nature and intersectoral complexity that may cross borders. The Nile basin is shared by a number of riparian countries and is currently experiencing rapid population and economic growth. This has sparked new developments to meet the growing water, food, and energy demands, alleviate poverty, and improve the livelihood in the basin. Such developments could result in basinwide cooperation or trigger conflicts among the riparian countries. A system dynamics model was developed for the entire Nile basin and integrated with the food and energy sectors in Egypt to investigate the future of the WFE nexus with and without the Grand Ethiopian Renaissance Dam (GERD) during filling and subsequent operation using basinwide stochastically generated flows. Different filling rates from 10\% to 100\% of the average monthly flow are considered during the filling process. Results suggest that the GERD filling and operation would affect the WFE nexus in Egypt, with the impact likely to be significant if the filling process occurred during a dry period. Food production from irrigated agriculture would be reduced by 9\%\–19\% during filling and by about 4\% during GERD operation compared with the case without it. The irrigation water supply and hydropower generation in Sudan will be reduced during the filling phase of the GERD, but this is expected to be improved during the dam operation phase as a result of the regulation afforded by the GERD. Ethiopian hydropower generation is expected to be boosted by the GERD during the filling and operation of the dam, adding an average of 15,000\ \ GWh/year15,000\ \ GWh/year once GERD comes online. Lastly, the results reveal the urgency of cooperation and coordination among the riparian countries to minimize the regional risks and maximize the regional rewards associated with the GERD.

}, issn = {0733-9496}, doi = {10.1061/(ASCE)WR.1943-5452.0001285}, url = {http://ascelibrary.org/doi/10.1061/\%28ASCE\%29WR.1943-5452.0001285http://ascelibrary.org/doi/pdf/10.1061/\%28ASCE\%29WR.1943-5452.0001285}, author = {Elsayed, Hamdy and Djordjevi{\'c}, Slobodan and Savi{\'c}, Dragan A. and Tsoukalas, Ioannis and Makropoulos, Christos} } @article {4401, title = {Land Use Guidelines to Maintain Habitat Diversity of Wood- Pastures in the Southern Carpathians Under Projected Climate Change}, journal = {Landscape Online}, volume = {74}, year = {2019}, month = {Oct-09-2019}, pages = {1 - 24}, abstract = {

The biodiversity of wood-pastures depends on a balance between human interference and natural vegetation succession, which however is undergoing changes driven by socio-economic factors and climate change. Widely spread throughout Europe, wood-pastures were subject to either intensification or abandonment, leading to habitat segregation and loss. This is currently the fate of large Romanian remnant woodpastures and climate warming further complicates management adaptation.
In a series of simulation experiments, we compared the long-term effects of different land use and climate change scenarios on the habitat diversity of a wood-pasture in the Southern Carpathians (Fundata village, Romania). We tested livestock densities according to management guidelines, complemented with shrub-cutting in order to maintain a structurally-diverse landscape with high habitat values in the light of climate change. We found that significant losses of open pastureland and inclusion into forest, as well as landscape structural simplification and loss of complex habitats can be expected from climate warming, with more severe consequences in a hotter climate perspective. We arguefor the re-establishment of the traditional multi-use of wood-pastures at optimum livestock densities in combination with low-intensity shrubcutting, because our study demonstrated that traditional practices offer a balanced compromise between agricultural use and maintaining habitat mosaics that are robust to climate change.

}, doi = {10.3097/LO.201974}, url = {https://www.landscape-online.org/index.php/lo/article/view/LO.201974https://www.landscape-online.org/index.php/lo/article/download/LO.201974/87https://www.landscape-online.org/index.php/lo/article/download/LO.201974/87}, author = {Stoicescu, Iona and P{\u a}tru-Stupariu, Ileana and Hossu, Constantina Alina and Peringer, Alexander} } @article {4396, title = {Linking Spatial and Temporal Modeling: A Case Study from the Eastern Pamir, TJ}, journal = {International Journal of Geoinformatics}, volume = {15}, year = {2019}, month = {10/2019}, pages = {29-41}, abstract = {

The Eastern Pamir of Tajikistan is a remote high mountain region located in the east of Tajikistan. Today, a great share of the Eastern Pamir\’s local energy demand is satisfied by dwarf shrubs (Krascheninnikovia ceratoides and Artemisia spp.) and animal manure. Besides of their energetic potential, dwarf shrubs are an important nutrient source for local livestock. It is assumed that overuse of local dwarf shrub stands leads to a degradation of pastures. With decreasing pasture quality, potentially, less livestock can be kept by locals. Besides of the economic losses associated with a decrease in livestock numbers, yields of manure also decline. In order to compensate the missing manure yields, locals may harvest even more dwarf shrubs. Thus, potentially a self-reinforcing functional chain exists in this system. BRECKLE AND WUCHERER (2006) refer to the degradation of pasturelands due to excessive dwarf shrub harvest in the Pamir Mountains as teresken syndrome. In a field study, we identified typical current energy carrier usage patterns in the village of Alichur, the second largest settlement in the Eastern Pamir. We then used a System Dynamics and Geographical Information Systems combining hybrid approach to analyze the energy system of Alichur and we modeled two scenarios of the system: one pessimistic in terms of dwarf shrub growth and one optimistic. Both scenarios show that in the short to medium term a collapse of the energy system of Alichur is unlikely to happen. The optimistic scenario indicates that resource consumption currently is sustainable in terms of pasture quality and dwarf shrub balance. The assumed self-reinforcing functional chain could not be confirmed. After all, the model provides strong indications that the teresken syndrome does not apply for Alichur. In addition to these findings, the case study shows, that combining SD and GIS in one model, allows for a conceptual understanding of the modeled system (mainly SD part), mass-balance simulations (SD and GIS parts) and visualization of model results (GIS part). Thereby, in addition to the case study results, this work demonstrates that System Dynamics and Geographical Information Systems combining hybrid approaches are a powerful tool for case study analysis, model simulation and result presentation. The approach is able to clarify structural assumption on the regional Social-Ecological-System and to support management decision.

}, author = {Hohberg, G. and Schwarz-v Raumer, H. G.} } @article {4390, title = {Mussels or tunicates: That is the question. Evaluating efficient and sustainable resource use by low-trophic species in aquaculture settings}, journal = {Journal of Cleaner Production}, volume = {231}, year = {2019}, month = {Jan-09-2019}, pages = {132 - 143}, issn = {09596526}, doi = {10.1016/j.jclepro.2019.05.173}, author = {Filgueira, Ram{\'o}n and Strople, Leah C. and Strohmeier, Tore and Rastrick, Samuel and Strand, {\O}ivind} } @article {4389, title = {The effect of environmental conditions on Atlantic salmon smolts{\textquoteright} (Salmo salar) bioenergetic requirements and migration through an inland sea}, journal = {Environmental Biology of Fishes}, volume = {101}, year = {2018}, month = {Jan-10-2018}, pages = {1467 - 1482}, issn = {0378-1909}, doi = {10.1007/s10641-018-0792-5}, url = {http://link.springer.com/10.1007/s10641-018-0792-5http://link.springer.com/content/pdf/10.1007/s10641-018-0792-5.pdfhttp://link.springer.com/article/10.1007/s10641-018-0792-5/fulltext.htmlhttp://link.springer.com/content/pdf/10.1007/s10641-018-0792-5.pdf}, author = {Strople, Leah C. and Filgueira, Ram{\'o}n and Hatcher, Bruce G. and Denny, Shelley and Bordeleau, Xavier and Whoriskey, Frederick G. and Crossin, Glenn T.} } @article {4403, title = {Intermediate foraging large herbivores maintain semi-open habitats in wilderness landscape simulations}, journal = {Ecological Modelling}, volume = {379}, year = {2018}, month = {Jan-07-2018}, pages = {10 - 21}, abstract = {

In the context of the rewilding Europe debate, the German national strategy on biodiversity aims to dedicate two percent of the German state area to wilderness development until 2020. Many of these potential large wilderness reserves harbor open habitats that require protection according to the Flora-Fauna-Habitat-directive of the European Union. As forests prevail in potential natural vegetation, research is required, to which extent wild large herbivores and natural disturbances may create semi-open landscape patterns in the long-term. We used the spatially explicit process-based model of pasture-woodland ecosystem dynamics WoodPaM, to analyze the long-term interactions between intermediate foraging large wild herbivores and vegetation dynamics in edaphically heterogeneous forest-grassland mosaic landscapes. We newly implemented a routine for intermediate foraging herbivores. We determined herbivore impact on vegetation from the quantitative balance between the demand and supply of herbaceous forage and woody browse. In abstract landscapes that represent the conditions in the established German wilderness area \"D\öberitzer Heide\", we simulated potential future landscape dynamics on open land, in forest and along forest edges with and without intermediate foraging large herbivores and for a climate change scenario. In our simulations the currently open landscape was conserved and even more the opening of current oak and beech forest was promoted. Canopy thinning and patch-mosaics of oak, birch, poplar and pine stands increased the overall nature conservation value in the long-term. To the contrary, open habitats were lost in simulations without herbivores. Moreover, our simulations suggested that intermediate foraging herbivores are especially suitable to maintain semi-open landscapes in wilderness areas, because (i) no additional winter forage was required, the natural availability of browse was sufficient. (ii) Their grazing maintained open land and their browsing thinned tree canopies even on poor sites that were unattractive for foraging. Here, habitat was maintained for threatened species from dry grasslands.

}, issn = {03043800}, doi = {10.1016/j.ecolmodel.2018.04.002}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0304380018301133}, author = {Schulze, Kiowa Alraune and Rosenthal, Gert and Peringer, Alexander} } @article {4402, title = {Shifts in wind energy potential following land-use driven vegetation dynamics in complex terrain}, journal = {Science of The Total Environment}, volume = {639}, year = {2018}, month = {Jan-10-2018}, pages = {374 - 384}, abstract = {

Many mountainous regions with high wind energy potential are characterized by multi-scale variabilities of vegetation in both spatial and time dimensions, which strongly affect the spatial distribution of wind resource and its time evolution. To this end, we developed a coupled interdisciplinary modeling framework capable of assessing the shifts in wind energy potential following land-use driven vegetation dynamics in complex mountain terrain. It was applied to a case study area in the Romanian Carpathians. The results show that the overall shifts in wind energy potential following the changes of vegetation pattern due to different land-use policies can be dramatic. This suggests that the planning of wind energy project should be integrated with the land-use planning at a specific site to ensure that the expected energy production of the planned wind farm can be reached over its entire lifetime. Moreover, the changes in the spatial distribution of wind and turbulence under different scenarios of land-use are complex, and they must be taken into account in the micro-siting of wind turbines to maximize wind energy production and minimize fatigue loads (and associated maintenance costs). The proposed new modeling framework offers, for the first time, a powerful tool for assessing long-term variability in local wind energy potential that emerges from land-use change driven vegetation dynamics over complex terrain. Following a previously unexplored pathway of cause-effect relationships, it demonstrates a new linkage of agro- and forest policies in landscape development with an ultimate trade-off between renewable energy production and biodiversity targets. Moreover, it can be extended to study the potential effects of micro-climatic changes associated with wind farms on vegetation development (growth and patterning), which could in turn have a long-term feedback effect on wind resource distribution in mountainous regions.

}, issn = {00489697}, doi = {10.1016/j.scitotenv.2018.05.083}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969718317182https://api.elsevier.com/content/article/PII:S0048969718317182?httpAccept=text/xmlhttps://api.elsevier.com/content/article/PII:S0048969718317182?httpAccept=text/plain}, author = {Fang, Jiannong and Peringer, Alexander and Stupariu, Mihai-Sorin and P{\u a}tru-Stupariu, Ileana and Buttler, Alexandre and Golay, Francois and Port{\'e}-Agel, Fernando} } @article {4404, title = {Disturbance-grazer-vegetation interactions maintain habitat diversity in mountain pasture-woodlands}, journal = {Ecological Modelling}, volume = {359}, year = {2017}, month = {Jan-09-2017}, pages = {301 - 310}, abstract = {

Low-intensity livestock grazing is a widespread management tool in order to maintain habitat diversity in mountain pasture-woodlands for nature conservation purposes. Historical photographs indicate that forest disturbance significantly contributed to forest-grassland mosaic pattern formation. Disturbance-grazer interactions are however poorly understood and the effects of logging or windthrow are rarely considered in management plans. Moreover, disturbance-grazer interactions are crucial for the maintenance of open habitats in the upcoming \“rewilding\” approach of nature conservation. We aimed to understand the effects of forest gap creation by the breakdown of senile trees or by single-tree cutting and of large forest openings by windthrow or logging on mosaic pattern formation in pasture-woodlands that were grazed by cattle and dominated by tree species with distinct regeneration ecology (Picea abies vs. Fagus sylvatica). We used the process-based model of pasture-woodland vegetation dynamics WoodPaM and newly implemented a forest disturbance routine. We simulated disturbance and grazing scenarios in an artificial mountain landscape and analyzed mosaic patterns with landscape metrics. We found that grazing in absence of disturbance promoted simply structured mosaics that were preconditioned by topography. Only large-scale forest disturbance disrupted this pattern and maintained the historical heterogeneous distribution of grassland communities across all habitat conditions (especially species-rich mountain grasslands on poor soil). This prerequisite is stronger in pasture-woodlands where the ecology of the dominant tree species promotes forest-grassland segregation (F. sylvatica in our case) and less in naturally thin-canopy mountain forest close to the tree line (P. abies). In wilderness areas, the very low density of grazers may limit the maintenance of open habitats regardless disturbance.

}, issn = {03043800}, doi = {10.1016/j.ecolmodel.2017.06.012}, url = {https://linkinghub.elsevier.com/retrieve/pii/S030438001730100Xhttps://api.elsevier.com/content/article/PII:S030438001730100X?httpAccept=text/xmlhttps://api.elsevier.com/content/article/PII:S030438001730100X?httpAccept=text/plain}, author = {Peringer, Alexander and Buttler, Alexandre and Gillet, Fran{\c c}ois and P{\u a}tru-Stupariu, Ileana and Schulze, Kiowa A. and Stupariu, Mihai-Sorin and Rosenthal, Gert} } @article {4400, title = {An integrated model to evaluate water-energy-food nexus at a household scale}, journal = {Environmental Modelling \& Software}, volume = {93}, year = {2017}, month = {Jan-07-2017}, pages = {366 - 380}, abstract = {

To achieve a sustainable supply and effectively manage water, energy and food (WEF) demand, interactions between WEF need to be understood. This study developed an integrated model, capturing the interactions between WEF at end-use level at a household scale. The model is based on a survey of 419 households conducted to investigate WEF over winter and summer for the city of Duhok, Iraq. A bottom-up approach was used to develop this system dynamics-based model. The model estimates WEF demand and the generated organic waste and wastewater quantities. It also investigates the impact of change in user behaviour, diet, income, family size and climate.

The simulation results show a good agreement with the historical data. Using the model, the impact of Global Scenario Group (GSG) scenarios was investigated. The results suggest that the \‘fortress world\’ scenario (an authoritarian response to the threat of breakdown) had the highest impact on WEF.

}, issn = {13648152}, doi = {10.1016/j.envsoft.2017.03.034}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1364815216306594https://api.elsevier.com/content/article/PII:S1364815216306594?httpAccept=text/xmlhttps://api.elsevier.com/content/article/PII:S1364815216306594?httpAccept=text/plain}, author = {Hussien, Wa{\textquoteright}el A. and Memon, Fayyaz A. and Savi{\'c}, Dragan A.} } @article {4399, title = {Modular and spatially explicit: A novel approach to system dynamics}, journal = {Environmental Modelling \& Software}, volume = {94}, year = {2017}, month = {Jan-08-2017}, pages = {48 - 62}, abstract = {

The Open Modeling Environment (OME) is an\ open-source System\ Dynamics (SD) simulation engine which has been created as a joint project between Oregon State University and the US\ Environmental Protection Agency. It is designed around a modular implementation, and provides a standardized interface for interacting with spatially explicit data while still supporting the standard SD model components. OME can be run as a standalone simulation or as a plugin to a larger simulation framework, and is capable of importing Models from several SD model formats, including Simile model files, Vensim model files, and the XMILE interchange format. While it has been released, OME is still under development, and a number of potential future improvements are discussed. To help illustrate the utility of OME, an example model design process is provided as an Appendix.

}, issn = {13648152}, doi = {10.1016/j.envsoft.2017.03.012}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1364815216308453https://api.elsevier.com/content/article/PII:S1364815216308453?httpAccept=text/xmlhttps://api.elsevier.com/content/article/PII:S1364815216308453?httpAccept=text/plain}, author = {Wingo, Patrick and Brookes, Allen and Bolte, John} } @mastersthesis {4388, title = {Using an individual based model to evaluate the effects of climate change on the reproductive phenology of eelgrass (Zostera marina L.) along a latitudinal gradient (master{\textquoteright}s thesis).}, volume = {Master of Science}, year = {2017}, pages = {253}, abstract = {

I explored the effects of climate change on the reproductive biology of the clonal
marine angiosperm Zostera marina L. (eelgrass) using an individual-based model.
The model captures whole plant ontogeny, morphology, and ecophysiology from seed
to reproductive adult to simulate the plasticity of eelgrass in response to
environmental variables. Using a latitudinal gradient as a proxy for climate change,
virtual seeding experiments were performed in three locations along the East coast of
the United States. I simulated the impacts of increased temperatures on Z. marina\’s
biomass, reproductive phenology, and life history. Warmer temperatures resulted in a
modeled decrease of Z. marina\’s total biomass, as well as altered reproductive timing
and strategy. These results have implications for long term predictions of Z. marina
persistence in its traditional biogeographic range, and indicate adaptation via shifts in
phenology and reproductive strategy may interact to dampen some negative
consequences of increased temperatures.

}, author = {Foley, J. L.} } @article {4356, title = {Intermediate tree cover can maximize groundwater recharge in the seasonally dry tropics}, journal = {Scientific Reports}, volume = {6}, year = {2016}, month = {Jan-04-2016}, doi = {10.1038/srep21930}, url = {http://www.nature.com/articles/srep21930http://www.nature.com/articles/srep21930.pdfhttp://www.nature.com/articles/srep21930.pdfhttp://www.nature.com/articles/srep21930}, author = {Ilstedt, U. and Bargu?s Tobella, A. and Bazi?, H. R. and Bayala, J. and Verbeeten, E. and Nyberg, G. and Sanou, J. and Benegas, L. and Murdiyarso, D. and Laudon, H. and Sheil, D. and Malmer, A.} } @article {4405, title = {Landscape-scale simulation experiments test Romanian and Swiss management guidelines for mountain pasture-woodland habitat diversity}, journal = {Ecological Modelling}, volume = {330}, year = {2016}, month = {Jan-06-2016}, pages = {41 - 49}, abstract = {

Distinct guidelines have been proposed in Romania and Switzerland for the management of pasture-woodlands that either focused on the regulation of grazing pressure (Romanian production perspective) or overall tree cover (Swiss conservation perspective). However, the landscape structural diversity and the cover of forest-grassland ecotones, which are both crucial for nature conservation value, were not explicitly considered.

We aimed to compare the country-specific management guidelines regarding their efficiency for the conservation of the structurally diverse forest-grassland mosaics in the light of recent land-use and climate change.

In strategic simulation experiments using the process-based model of pasture-woodland ecosystems WoodPaM, we analyzed the relationships among drivers for the formation of mosaic patterns (grazing intensity, climate change) and the resulting landscape properties (tree cover, forest-grassland ecotones, mosaic structure) during the past until today (2000 AD).

The results showed that tree canopy densification following recent climate warming is likely to trigger landscape structural shifts. Medium grazing pressure promoted the development of the full range of pasture-woodland habitats and is therefore confirmed as a management strategy that balances agronomic demands and nature conservation value. Tree cover is rejected as a criteria to monitor pasture-woodland conservation status, because its relationship to landscape structural diversity and to the cover of forest-grassland ecotones did not hold for changing climate.

Our results suggest \“experimental-retrospective\” analysis as a useful tool to test conclusions from expert knowledge.

}, issn = {03043800}, doi = {10.1016/j.ecolmodel.2016.03.013}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0304380016300795}, author = {Peringer, Alexander and Gillet, Fran{\c c}ois and Rosenthal, Gert and Stoicescu, Ioana and P{\u a}tru-Stupariu, Ileana and Stupariu, Mihai-Sorin and Buttler, Alexandre} } @article {4406, title = {Multi-scale feedbacks between tree regeneration traits and herbivore behavior explain the structure of pasture-woodland mosaics}, journal = {Landscape Ecology}, volume = {31}, year = {2016}, month = {Jan-05-2016}, pages = {913 - 927}, abstract = {

The pasture-woodlands of Central Europe are low-intensity grazing systems in which the structural richness of dynamic forest-grassland mosaics is causal for their high biodiversity. Distinct mosaic patterns in Picea abies- and Fagus sylvatica-dominated pasture-woodlands in the Swiss Jura Mountains suggest a strong influence of tree species regeneration ecology on landscape structural properties. At the landscape scale, however, cause-effect relationships are complicated by habitat selectivity of livestock.

}, issn = {0921-2973}, doi = {10.1007/s10980-015-0308-z}, url = {http://link.springer.com/10.1007/s10980-015-0308-z}, author = {Peringer, Alexander and Schulze, Kiowa A. and Stupariu, Ileana and Stupariu, Mihai-Sorin and Rosenthal, Gert and Buttler, Alexandre and Gillet, Fran{\c c}ois} } @article {4342, title = {Informing Marine Spatial Planning (MSP) with numerical modelling: A case-study on shellfish aquaculture in Malpeque Bay (Eastern Canada)}, journal = {Marine Pollution Bulletin}, volume = {100}, year = {2015}, month = {11/2015}, pages = {200 - 216}, issn = {0025326X}, doi = {10.1016/j.marpolbul.2015.08.048}, author = {Ram{\'o}n Filgueira and Guyondet, Thomas and C{\'e}dric Bacher and Comeau, Luc A.} } @article {4282, title = {The Multiscale Integrated Model of Ecosystem Services (MIMES): Simulating the interactions of coupled human and natural systems}, journal = {Ecosystem Services}, volume = {12}, year = {2015}, month = {04/2015}, pages = {30 - 41}, abstract = {In coupled human and natural systems ecosystem services form the link between ecosystem function and what humans want and need from their surroundings. Interactions between natural and human components are bidirectional and define the dynamics of the total system. Here we describe the MIMES, an analytical framework designed to assess the dynamics associated with ecosystem service function and human activities. MIMES integrate diverse types of knowledge and elucidate how benefits from ecosystem services are gained and lost. In MIMES, users formalize how materials are transformed between natural, human, built, and social capitals. This information is synthesized within a systems model to forecast ecosystem services and human-use dynamics under alternative scenarios. The MIMES requires that multiple ecological and human dynamics be specified, and that outputs may be understood through different temporal and spatial lenses to assess the effects of different actions in the short and long term and at different spatial scales. Here we describe how MIMES methodologies were developed in association with three case studies: a global application, a watershed model, and a marine application. We discuss the advantages and disadvantage of the MIMES approach and compare it to other broadly used ecosystem service assessment tools.}, issn = {22120416}, doi = {10.1016/j.ecoser.2015.01.004}, author = {Boumans, Roelof and Roman, Joe and Altman, Irit and Kaufman, Les} } @article {4263, title = {A fully-spatial ecosystem-DEB model of oyster (Crassostrea virginica) carrying capacity in the Richibucto Estuary, Eastern Canada}, journal = {Journal of Marine Systems}, volume = {136}, year = {2014}, month = {08/2014}, pages = {42 - 54}, abstract = {The success of shellfish aquaculture as well as its sustainability relies on adjusting the cultured biomass to local ecosystem characteristics. Oyster filter-feeding activity can control phytoplankton concentration, reaching severe depletion in extreme situations, which can threaten ecological sustainability. A better understanding of oyster{\textendash} phytoplankton interaction can be achieved by constructing ecosystem models. In this study, a fully-spatial hydro- dynamic biogeochemical model has been constructed for the Richibucto Estuary in order to explore oyster carry- ing capacity. The biogeochemical model was based on a classical nutrient{\textendash}phytoplankton{\textendash}zooplankton{\textendash}detritus (NPZD) approach with the addition of a Dynamic Energy Budget (DEB) model of Crassostrea virginica. Natural variation of chlorophyll was used as a benchmark to define a sustainability threshold based on a resilience frame- work. Scenario building was applied to explore carrying capacity of the system. However, the complex geomor- phology of the Richibucto Estuary and the associated heterogeneity in water residence time, which is integral in estuarine functioning, indicate that the carrying capacity assessment must be specific for each area of the system. The model outcomes suggest that water residence time plays a key role in carrying capacity estimations through its influence on ecological resistance.}, issn = {09247963}, doi = {10.1016/j.jmarsys.2014.03.015}, author = {R. Filgueira and Guyondet, T. and Comeau, L.A. and J. Grant} } @article {4264, title = {Implementation of marine spatial planning in shellfish aquaculture management: modeling studies in a Norwegian fjord}, journal = {Ecological Applications}, volume = {24}, year = {2014}, pages = {832{\textendash}843}, abstract = {Shellfish carrying capacity is determined by the interaction of a cultured species with its ecosystem, which is strongly influenced by hydrodynamics. Water circulation controls the exchange of matter between farms and the adjacent areas, which in turn establishes the nutrient supply that supports phytoplankton populations. The complexity of water circulation makes necessary the use of hydrodynamic models with detailed spatial resolution in carrying capacity estimations. This detailed spatial resolution also allows for the study of processes that depend on specific spatial arrangements, e.g., the most suitable location to place farms, which is crucial for marine spatial planning, and consequently for decision support systems. In the present study, a fully spatial physical-biogeochemical model has been combined with scenario building and optimization techniques as a proof of concept of the use of ecosystem modeling as an objective tool to inform marine spatial planning. The object of this exercise was to generate objective knowledge based on an ecosystem approach to establish new mussel aquaculture areas in a Norwegian fjord. Scenario building was used to determine the best location of a pump that can be used to bring nutrient-rich deep waters to the euphotic layer, increasing primary production, and consequently, carrying capacity for mussel cultivation. In addition, an optimization tool, parameter estimation (PEST), was applied to the optimal location and mussel standing stock biomass that maximize production, according to a preestablished carrying capacity criterion. Optimization tools allow us to make rational and transparent decisions to solve a well-defined question, decisions that are essential for policy makers. The outcomes of combining ecosystem models with scenario building and optimization facilitate planning based on an ecosystem approach, highlighting the capabilities of ecosystem modeling as a tool for marine spatial planning.}, doi = {10.1890/13-0479.1}, url = {http://www.esajournals.org/doi/pdf/10.1890/13-0479.1}, author = {Ram{\'o}n Filgueira and Jon Grant and {\O}ivind Strand} } @article {4262, title = {Multiscale digital Arabidopsis predicts individual organ and whole-organism growth}, journal = {Proceedings of the National Academy of Sciences}, year = {2014}, abstract = {Understanding how dynamic molecular networks affect whole-organism physiology, analogous to mapping genotype to phenotype, remains a key challenge in biology. Quantitative models that represent processes at multiple scales and link understanding from several research domains can help to tackle this problem. Such integrated models are more common in crop science and ecophysiology than in the research communities that elucidate molecular networks. Several laboratories have modeled particular aspects of growth in Arabidopsis thaliana, but it was unclear whether these existing models could productively be combined. We test this approach by constructing a multiscale model of Arabidopsis rosette growth. Four existing models were integrated with minimal parameter modification (leaf water content and one flowering parameter used measured data). The resulting framework model links genetic regulation and biochemical dynamics to events at the organ and whole-plant levels, helping to understand the combined effects of endogenous and environmental regulators on Arabidopsis growth. The framework model was validated and tested with metabolic, physiological, and biomass data from two laboratories, for five photoperiods, three accessions, and a transgenic line, highlighting the plasticity of plant growth strategies. The model was extended to include stochastic development. Model simulations gave insight into the developmental control of leaf production and provided a quantitative explanation for the pleiotropic developmental phenotype caused by overexpression of miR156, which was an open question. Modular, multiscale models, assembling knowledge from systems biology to ecophysiology, will help to understand and to engineer plant behavior from the genome to the field.}, issn = {1091-6490}, doi = {10.1073/pnas.1410238111}, url = {http://www.pnas.org/content/early/2014/08/27/1410238111.full.pdf+html?sid=66edb45d-8e99-4d84-a072-a47729a65e14}, author = {Chew, Y. H. and Wenden, B. and Flis, A. and Mengin, V. and Taylor, J. and Davey, C. L. and Tindal, C. and Thomas, H. and Ougham, H. J. and de Reffye, P. and Stitt, M. and Williams, M. and Muetzelfeldt, R. and Halliday, K. J. and Millar, A. J.} } @article {4243, title = {Physiological indices as indicators of ecosystem status in shellfish aquaculture sites}, journal = {Ecological Indicators}, volume = {39}, year = {2014}, month = {04/2014}, pages = {134 - 143}, abstract = {The filtration activity of cultured mussels may exert a strong control on phytoplankton populations. Given that phytoplankton constitutes the base of marine food webs, carrying capacity in shellfish aquaculture sites has been commonly studied in terms of phytoplankton depletion. However, spatial and temporal variability of phytoplankton concentration in coastal areas present a methodological constraint for using phytoplankton depletion as an indicator in monitoring programs, and necessitates intensive field campaigns. The main goal of this study is to explore the potential of different bivalve performance indices for use as alternatives to phytoplankton depletion as cost-effective indicators of carrying capacity. For that, a fully spatial hydrodynamic{\textendash}biogeochemical coupled model of Tracadie Bay, an intensive mussel culture embayment located in Prince of Edward Island (Canada), has been constructed and scenario building has been used to explore the relationship between phytoplankton depletion and bivalve performance. Our underlying premise is that overstocking of bivalves leads to increased competition for food resources, i.e. phytoplankton, which may ultimately have a significant effect on bivalve growth rate and performance. Following this working hypothesis, the relationships among bay-scale phytoplankton depletion and three bivalve physiological indices, one static, condition index, and two dynamic, tissue mass and shell length growth rates, have been simulated. These three metrics present methodological advantages compared to phytoplankton depletion for incorporation into monitoring programs. Although significant correlations among phytoplankton depletion and the three physiological indices have been observed, shell length growth rate is shown as the most sensitive indicator of carrying capacity, followed by tissue mass growth rate and then by condition index. These results demonstrate the potentiality of using bivalve physiological measurements in monitoring programs as indicators of ecosystem status.}, issn = {1470160X}, doi = {10.1016/j.ecolind.2013.12.006}, url = {http://www.sciencedirect.com/science/article/pii/S1470160X13004962}, author = {R. Filgueira and Guyondet, T. and Comeau, L.A. and J. Grant} } @article {4242, title = {Storm-induced changes in coastal geomorphology control estuarine secondary productivity}, journal = {Earth{\textquoteright}s Future}, year = {2014}, month = {01/2014}, pages = {n/a - n/a}, abstract = {Estuarine ecosystems are highly sensitive not only to projected effects of climate change such as ocean warming, acidification, and sea-level rise but also to the incidence of nor{\textquoteright}easter storms and hurricanes. The effects of storms and hurricanes can be extreme, with immediate impact on coastal geomorphology and water circulation, which is integral to estuarine function and consequently to provision of ecosystem services. In this article, we present the results of a natural estuarine-scale experiment on the effects of changes in coastal geomorphology on hydrodynamics and aquaculture production. A bay in Prince Edward Island, Canada, was altered when a nor{\textquoteright}easter storm eroded a second tidal inlet through a barrier island. Previous field and modeling studies allowed a comparison of prestorm and post-storm circulation, food limitation by cultured mussels, and aquaculture harvest. Dramatic increases in mussel production occurred in the year following the opening of the new inlet. Model studies showed that post-storm circulation reduced food limitation for cultured mussels, allowing greater growth. Climate change is expected to have severe effects on the delivery of marine ecosystem services to human populations by changing the underlying physical-biological coupling inherent to their functioning.}, doi = {10.1002/2013EF000145}, url = {http://onlinelibrary.wiley.com/doi/10.1002/2013EF000145/abstract;jsessionid=DBD0FB7B2443BD9C9D658F85A42F41FD.f04t04}, author = {Ram{\'o}n Filgueira and Guyondet, Thomas and Comeau, Luc A. and Jon Grant} } @article {4241, title = {Ecosystem modelling for ecosystem-based management of bivalve aquaculture sites in data-poor environment}, journal = {Aquacult Environ Interact}, volume = {4}, year = {2013}, pages = {117-133}, chapter = {117}, abstract = {Although models of carrying capacity have been around for some time, their use in aquaculture management has been limited. This is partially due to the cost involved in generating and testing the models. However, the use of more generic and flexible models could facilitate the implementation of modelling in management. We have built a generic core for coupling biogeochemical and hydrodynamic models using Simile (www.simulistics.com), a visual simulation environment software that is well-suited to accommodate fully spatial models. Specifically, Simile integrates PEST (model-independent parameter estimation, Watermark Numerical Computing, www.pesthomepage.org), an optimization tool that uses the Gauss-Marquardt-Levenberg algorithm and can be used to estimate the value of a parameter, or set of parameters, in order to minimize the discrepancies between the model results and a dataset chosen by the user. The other critical aspect of modelling exercises is the large amount of data necessary to set up, tune and groundtruth the ecosystem model. However, ecoinformatics and improvements in remote sensing procedures have facilitated acquisition of these datasets, even in data-poor environments. In this paper we describe the required datasets and stages of model development necessary to build a biogeochemical model that can be used as a decision-making tool for bivalve aquaculture management in data-poor environments.}, doi = {10.3354/aei00078}, url = {http://www.int-res.com/abstracts/aei/v4/n2/p117-133/}, author = {R. Filgueira and J. Grant and R. Stuart and M. S. Brown} } @article {4222, title = {Ein Ansatz zur r{\"a}umlich- dynamischen Modellierung am Beispiel der Tereskenernte im Ostpamir }, year = {2013}, url = {http://gispoint.de/fileadmin/user_upload/paper_gis_open/537533033.pdf}, author = {Georg HOHBERG} } @article {4213, title = {A physical{\textendash}biogeochemical coupling scheme for modeling marine coastal ecosystems}, journal = {Ecological Informatics}, volume = {7}, year = {2012}, pages = {71-80}, doi = {http://dx.doi.org/10.1016/j.ecoinf.2011.11.007}, url = {http://www.sciencedirect.com/science/article/pii/S1574954111000975}, author = {Ram{\'o}n Filgueira and Jon Grant and C{\'e}dric Bacher and Michel Carreau} } @article {4379, title = {Uncovering land-use dynamics driven by human decision-making {\textendash} A combined model approach using cellular automata and system dynamics}, journal = {Environmental Modelling \& Software}, volume = {27-28}, year = {2012}, month = {Jan-01-2012}, pages = {71 - 82}, issn = {13648152}, doi = {10.1016/j.envsoft.2011.09.005}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1364815211002039https://api.elsevier.com/content/article/PII:S1364815211002039?httpAccept=text/xmlhttps://api.elsevier.com/content/article/PII:S1364815211002039?httpAccept=text/plain}, author = {Lauf, S. and Haase, D. and Hostert, P. and Lakes, T. and Kleinschmit, B.} } @article {4216, title = {An assessment of the Economics, Implementation and Modelling of Universal MRSA Screening}, number = {2}, year = {2011}, url = {http://www.documents.hps.scot.nhs.uk/hai/mrsa-screening/pathfinder-programme/mrsa-pathfinder-vol2-2011-02-23.pdf} } @article {4391, title = {Spatiotemporal dynamics of landscape pattern and hydrologic process in watershed systems}, journal = {Journal of Hydrology}, volume = {404}, year = {2011}, month = {Jan-06-2011}, pages = {1 - 12}, issn = {00221694}, doi = {10.1016/j.jhydrol.2011.03.019}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0022169411001880https://api.elsevier.com/content/article/PII:S0022169411001880?httpAccept=text/xmlhttps://api.elsevier.com/content/article/PII:S0022169411001880?httpAccept=text/plain}, author = {Randhir, Timothy O. and Tsvetkova, Olga} } @article {1899, title = {A Box Model for Ecosystem-Level Management of Mussel Culture Carrying Capacity in a Coastal Bay}, journal = {Ecosystems}, year = {2009}, abstract = {

The carrying capacity of shellfish aquaculture is determined by the interaction of cultured species with the ecosystem, particularly food availability to suspension feeders. A multiple box dynamic ecosystem model was constructed to examine the carrying capacity for mussel (Mytilus edulis) aquaculture in Tracadie Bay, Prince of Edward Island, Canada. Criteria for carrying capacity were based on chlorophyll concentration. The model was run in two different years (1998 and 1999) in which time series for three points inside the bay and a point outside the bay were available. This data set allows spatial validation of the ecosystem model and assessment of its sensitivity to changes in boundary conditions. The model validation process indicated that the differential equations and parameters used in the simulation provided robust prediction of the ecological dynamics within the bay. Results verified that mussel biomass exerts top-down control of phytoplankton populations.

}, doi = {10.1007/s10021-009-9289-6}, author = {Ramon Filgueira and Jon Grant} } @article {1557, title = {Modeling the soil system: Bridging the gap between pedology and soil{\textendash}water physics}, journal = {Global and Planetary Change}, volume = {67}, year = {2009}, month = {05/2009}, pages = {51-61}, publisher = {Elsevier B.V}, abstract = {

The biological and geochemical processes in soil such as organic matter mineralization, microbiological activity, and plant alimentation can be accurately assessed and modeled only with the knowledge of the thermodynamic status of the soil medium where these processes take place. However, current soil water models do not define and characterize the soil structure or the thermodynamic state of the soil water interacting with this structure. This article presents a new paradigm in characterizing and\ previous termmodelingnext term\ the organized soil medium and the physical properties resulting from this organization. It describes a framework of the\ previous termmodelingnext term\ approach as a contribution to the General Systems theory. The basic concept of Representative Elementary Volume (REV) in soil physics and hydrology was transformed into the concept of Structure Representative Volume (SREV) which takes into account the hierarchical organization of the structured soil medium. The pedostructure is defined as the SREV of the soil medium and this concept is at the basis of the new paradigm including variables, equations, parameters, and units in soil physics, in a similar way that the REV is at the basis of the continuous porous media mechanics applied to soils. The paradigm allows for a thermodynamic characterization of the structured soil medium with respect to soil water content then bridging the gap between pedology and soil physics. We show that the two points of view (REV and SREV) are complementary and must be used in the scaling of information. This approach leads to a new dimension in soil\–water properties characterization that ensures a physically based\ previous termmodelingnext term\ of processes in soil and the transfer of information from the physical scale of processes (pedostructure or laboratory measurements scale) to the application scale of the other disciplines (previous termmodelingnext term\ and mapping scale).

}, doi = {10.1016/j.gloplacha.2008.12.002 }, url = {http://dx.doi.org/10.1016/j.gloplacha.2008.12.002 }, author = {Erik Braudeaua and Rabi H. Mohtar} } @article {1558, title = {A multi-scale {\textquoteright}{\textquoteright}soil water structure{\textquoteright}{\textquoteright} model based on the pedostructure concept}, journal = {Hydrol. Earth Syst. Sci. Discuss.}, volume = {6}, year = {2009}, pages = {1111-1163}, abstract = {

Current soil water models do not take into account the internal organization of the soil medium and, a fortiori, the physical interaction between the water film surrounding the solid particles of the soil structure, and the surface charges of this structure. In that sense they empirically deal with the physical soil properties that are all generated from this soil water-structure interaction. As a result, the thermodynamic state of the soil water medium, which constitutes the local physical conditions, namely the pedo-climate, for biological and geo-chemical processes in soil, is not defined in these models. The omission of soil structure from soil characterization and modeling does not allow for coupling disciplinary models for these processes with soil water models. This article presents a soil water structure model, Kamel, which was developed based on a new paradigm in soil physics where the hierarchical soil structure is taken into account allowing for defining its thermodynamic properties. After a review of soil physics principles which forms the basis of the paradigm, we describe the basic relationships and functionality of the model. Kamel\ runs with a set of 15 soil input parameters, the pedohydral parameters, which are parameters of the physically-based equations of four soil characteristic curves that can be measured in the laboratory. For cases where some of these parameters are not available, we show how to estimate these parameters from commonly available soil information using published pedotransfer functions. A published field experimental study on the dynamics of the soil moisture profile following a pounded infiltration rainfall event was used as an example to demonstrate soil characterization and Kamel\ simulations. The simulated soil moisture profile for a period of 60 days showed very good agreement with experimental field data. Simulations using input data calculated from soil texture and pedotransfer functions were also generated and compared to simulations of the more ideal characterization. The later comparison illustrates how Kamel\ can be used and adapt to any case of soil data availability. As physically based model on soil structure, it may be used as a standard reference to evaluate other soil-water models and also pedotransfer functions at a given location or agronomical situation.

}, url = {http://www.hydrol-earth-syst-sci-discuss.net/6/1111/2009/}, author = {Braudeau, E. , Mohtar, R. H. , El Ghezal, N. , Crayol, M. , Salahat, M. , and Martin, P} } @article {4215, title = {NHS Scotland MRSA Screening Pathfinder Programme Interim Report}, number = {1}, year = {2009}, url = {www.hps.scot.nhs.uk/haiic/sshaip/publicationsdetail.aspx?id=40925} } @inbook {1536, title = {Chapter Seven Integrated Modelling Frameworks for Environmental Assessment and Decision Support}, booktitle = {Developments in Integrated Environmental Assessment}, volume = {3}, year = {2008}, pages = {101-118}, publisher = { Elsevier}, organization = { Elsevier}, chapter = {7}, abstract = {

In this chapter we investigate the motivation behind the development of modelling frameworks that explicitly target the environmental domain. Despite many commercial and industrial-strength frameworks being available, we claim that there is a definite niche for environmental-specific frameworks. We first introduce a general definition of what is an environmental integrated modelling framework, leading to an outline of the requirements for a generic software architecture for such frameworks. This identifies the need for a knowledge layer to support the modelling layer and an experimentation layer to support the execution of models.

The chapter then focuses on the themes of knowledge representation, model management and model execution. We advocate that appropriate knowledge representation and management tools can facilitate model integration and linking. We stress that a model development process adhering to industry standards and good practices, called \“model engineering,\” is to be pursued. We focus on the requirements of the experimental frame, which can ensure transparency and traceability in the execution of simulation scenarios and optimisation problems associated with complex integrated assessment studies.

A promising trend for knowledge representation is the use of ontologies that have the capacity to elicit the meaning of knowledge in a manner that is logical, consistent and understandable by computers and the knowledge worker community. This new path in knowledge-based computing will support retention of institutional knowledge, while putting modelling back in the hands of modellers. Environmental modelling will then become a conceptual activity, focusing on model design rather than model implementation, with code generation being delegated to some degree to ontology-aware tools. In this respect, we envision the whole model lifecycle to change drastically, becoming more of a theoretical activity and less of a coding-intensive, highly engineering-oriented task.

}, keywords = {environmental integrated modelling frameworks, knowledge representation, model engineering, model management, modelling frameworks}, isbn = {9780080568867}, doi = {doi:10.1016/S1574-101X(08)00607-8}, author = {A. E. Rizzoli and G. Leavesley and J. C. Ascough II and R. M. Argent and I. N. Athanasiadis and V. Brilhante and F. H. A. Claeys and O. David and M. Donatelli and P. Gijsbers and D. Havlik and A. Kassahun and P. Krause and N. W. T. Quinn and H. Scholten and R. S. Sojda and F. Villa}, editor = {A. J. Jakeman and A. A. Voinov and A. E. Rizzoli and S. H. Chen} } @proceedings {1560, title = {CONCEPT MAPS FOR COMBINING HARD AND SOFT SYSTEM THINKING IN THE MANAGEMENT OF SOCIO-ECOSYSTEMS}, year = {2008}, url = {http://cmc.ihmc.us/cmc2008papers/cmc2008-p190.pdf}, author = {Franco Salerno and Emanuele Cuccillato and Robert Muetzelfeldt and Francesco Giannino and Birendra Bajracharya and Paolo Caroli and Gaetano Viviano and Anna Staiano and Fabrizio Carten{\`\i}, and Stefano Mazzoleni and Gianni Tartari} } @article {1534, title = {The effect of vegetation on pesticide dissipation from ponded treatment wetlands: Quantification using a simple model}, journal = {Chemosphere}, volume = {72}, year = {2008}, month = {07/2008}, pages = {999-1005}, chapter = {999}, abstract = {

Field data shows that plants accelerate pesticide dissipation from aquatic systems by increasing sedimentation, biofilm contact and photolysis. In this study, a graphical model was constructed and calibrated with site-specific and supplementary data to describe the loss of two pesticides, endosulfan and fluometuron, from a vegetated and a non-vegetated pond. In the model, the major processes responsible for endosulfan dissipation were alkaline hydrolysis and sedimentation, with the former process being reduced by vegetation and the latter enhanced. Fluometuron dissipation resulted primarily from biofilm reaction and photolysis, both of which were increased by vegetation. Here, greater photolysis under vegetation arose from faster sedimentation and increased light penetration, despite shading. Management options for employing constructed wetlands to polish pesticide-contaminated agricultural runoff are discussed. The lack of easily fulfilled sub-models and data describing the effect of aquatic vegetation on water chemistry and sedimentation is also highlighted.

}, keywords = {Cotton, Herbicide, Insecticide, Macrophyte, Phytoremediation, Runoff water}, doi = {10.1016/j.chemosphere.2008.04.059}, url = {http://dx.doi.org/10.1016/j.chemosphere.2008.04.059}, author = {Michael T. Rose and Angus N. Crossan and Ivan R. Kennedy} } @article {1544, title = {Modelling the impacts of various thinning intensities on tree growth and survival in a mixed species eucalypt forest in central Gippsland, Victoria, Australia}, journal = {Forest Ecology and Management}, volume = {256}, year = {2008}, month = {12/2008}, pages = {2007-2017}, abstract = {

The response of tree survival and diameter growth to thinning treatments was examined over 29 years, in various thinning treatments established in a 21-year-old even-aged mixed species regenerating forest in Victoria, Australia. The treatments were control, crown release, strip thinning and three different intensities of thinning from below (light, moderate, and heavy). Each treatment was replicated three times in a complete randomised design. Logistic and multilevel regression analyses showed that tree survival, growth and thinning response (change of tree growth due to a thinning treatment) were functions of tree species, size, age, removed and remaining competition, as well as time since the treatment. Mean annual tree diameter growth in unthinned stands was highest for Eucalyptus sieberi L. Johnson (1.9\ mm) followed by Eucalyptus baxteri (Benth.) Maiden \& Blakely ex J. Black (1.6\ mm), and lowest for both Eucalyptus consideniana (Maiden) and Eucalyptus radiata (Sieber ex DC) combined (0.7\ mm). Diameter growth increased with tree size for both E. sieberi and E. baxteri, but not for E. consideniana and E. radiata. Smaller trees were more likely to die due to shading and suppression than their larger counterparts. A mortality model suggested, however, that both shading and suppression had very little effect on trees in both E. consideniana and E. radiata species, which were less likely to die compared to trees in the other species. This result indicates that both E. consideniana and E. radiata species may be relatively shade tolerant compared with the other species. Total thinning response was a sum of positive (increased growing space) and negative (thinning stress) effects. Following thinning, smaller trees showed signs of thinning stress for the first one or two years, after which the highest percentage thinning response was observed. While larger trees were initially less responsive to thinning, the rate of decrease in the response for subsequent years was greater in smaller trees than larger ones. The average amount of thinning response showed similar trends to diameter growth increasing from E. sieberi (1.7\ mm) through E. baxteri (0.6\ mm) to both E. consideniana and E. radiata (0.5\ mm). This translates into low average percentage thinning response in E. baxteri (34\%), twice as much in both E. consideniana and E. radiata (69\%) and highest overall percentage response in E. sieberi (87\%). Thinning response and the duration of this response appeared to increase with thinning intensity and was still evident 29 years after thinning. Heavy thinning did, however, reduce the number of trees to a severely under-stocked condition, which prohibited optimum site occupancy, requiring 29 years of post-thinning development for the heavily thinned stands to regain their pre-thinning stand basal area.

}, keywords = {Australia, Diameter distribution, Diameter growth, Thinning intensity, Tree mortality}, doi = {http://dx.doi.org/10.1016/j.foreco.2008.07.035 }, url = {http://dx.doi.org/10.1016/j.foreco.2008.07.035 }, author = {Maina Kariuki} } @article {1535, title = {Semantic links in integrated modelling frameworks}, journal = {Mathematics and Computers in Simulation}, volume = {78}, year = {2008}, month = {07/2008}, pages = {412-423}, abstract = {

It is commonly accepted that modelling frameworks offer a powerful tool for modellers, researchers and decision makers, since they allow the management, re-use and integration of mathematical models from various disciplines and at different spatial and temporal scales. However, the actual re-usability of models depends on a number of factors such as the accessibility of the source code, the compatibility of different binary platforms, and often it is left to the modellers own discipline and responsibility to structure a complex model in such a way that it is decomposed in smaller re-usable sub-components. What reusable and interchangeable means is also somewhat vague; although several approaches to build modelling frameworks have been developed, little attention has been dedicated to the intrinsic re-usability of components, in particular between different modelling frameworks. In this paper, we focus on how models can be linked together to build complex integrated models. We stress that even if a model component interface is clear and reusable from a software standpoint, this is not a sufficient condition for reusing a component across different integrated modelling frameworks. This reveals the need for adding rich semantics in model interfaces.

}, keywords = {Integrated modelling frameworks, Model linking, Model reuse, Ontologies}, doi = {dx:10.1016/j.matcom.2008.01.017 }, author = {Andrea E. Rizzoli and Marcello Donatelli and Ioannis N. Athanasiadis and Ferdinando Villa and David Huber} } @article {1898, title = {A spatiotemporal model of shifting cultivation and forest cover dynamics}, journal = {Environment and Development Economics 13: }, volume = {13}, year = {2008}, pages = {28}, chapter = {643}, abstract = {

Sustainable use of humid forest resources as a source of fertile land for cultivation requires long periods of fallow and the ability to move the zone of active cultivation from one location to another over time. At the individual field level, shifting cultivation is essentially a resource extraction problem akin to a pulse fishery \– a short period of intensive use of the stock of soil fertility followed by a long idle period permitting regeneration. This paper describes a spatiotemporal model of resource extraction adapted to the use of forest resources by shifting cultivators. Theoretically grounded in the spatial and household modelling literature, it is a structural simulation model of household decision-making, and includes a demonstration of the conceptwith a limited data set from southern Cameroon. Use of a stated preference approach to modelling decision-making identifies individual preferences and spatial path-dependency as important sources of shortened fallows and resource degradation.

}, author = {Douglas R Brown} } @proceedings {1559, title = {System Dynamics Modelling: A Tool for Participatory Simulation of Complex Water Systems within AquaStress}, year = {2008}, month = {07/07/2008}, keywords = {Decision making, Participatory process, Simulation, System Dynamics Modelling, Water Systems}, url = {http://centres.exeter.ac.uk/cws/downloads/cat_view/43-aquastress}, author = {L. S. Vamvakeridou-Lyroudiaa, D. A. Savic} } @book {2754, title = {Systems Science and Modeling for Ecological Economics}, year = {2008}, pages = {432}, publisher = {Academic Press}, organization = {Academic Press}, abstract = {

Modeling is a key component to sciences from mathematics to life science, including environmental and ecological studies. By looking at the underlying concepts of the software, we can make sure that we build mathematically feasible models and that we get the most out of the data and information that we have. This book shows how models can be analyzed using simple math and software to generate meaningful qualitative descriptions of system dynamics. This book shows that even without a full analytical, mathematically rigorous analysis of the equations, there may be ways to derive some qualitative understanding of general behavior of a system. By relating some of the modeling approaches and systems theory to real world examples the book illustrates how these approaches can help understand concepts such as sustainability, peak oil, adaptive management, optimal harvest and other practical applications.

* Relates modeling approaches and systems theory to real world examples
* Teaches students to build mathematically feasible models and get the most of our the data and information available
* Wide range of applications in hydrology, population dynamics, market cycles, sustainability theory, management, and more

}, isbn = {978-0123725837}, author = {Alexey A. Voinov} } @article {1539, title = {A box model of carrying capacity for suspended mussel aquaculture in Lagune de la Grande-Entr{\'e}e, Iles-de-la-Madeleine, Qu{\'e}bec }, journal = {Ecological Modelling,}, volume = {200}, year = {2007}, month = {1/2007}, pages = {193-206}, abstract = {

An object-oriented model of environment\–mussel aquaculture interactions and mussel carrying-capacity within Lagune de la Grande-Entr\ée (GEL), Iles-de-la-Madeleine, Qu\ébec, was constructed to assist in development of sustainable mussel culture in this region. A multiple box ecosystem model for GEL tied to the output of a hydrodynamic model was constructed using Simile software, which has inherent ability to represent spatial elements and specify water exchange between modelled regions. Mussel growth and other field data were used for model validation. Plackett\–Burman sensitivity analysis demonstrated that a variety of bioenergetic parameters of zooplankton and phytoplankton submodels were important in model outcomes. Model results demonstrated that mussel aquaculture can be further developed throughout the lagoon. At present culture densities, phytoplankton depletion is minimal, and there is little food limitation of mussel growth. Results indicated that increased stocking density of mussels in the existing farm will lead to decreased mass per individual mussel. Depending on the location of new farm emplacement within the lagoon, implementation of new aquaculture sites either reduced mussel growth in the existing farm due to depletion of phytoplankton, or exhibited minimum negative impact on the existing farm. With development throughout GEL, an excess of phytoplankton was observed during the year in all modelled regions, even at stocking densities as high as 20\ mussels\ m\−3. Although mussels cultured at this density do not substantially impact the ecosystem, their growth is controlled by the flux of phytoplankton food and abundance of zooplankton competitors. This model provides an effective tool to examine expansion of shellfish farming to new areas, balancing culture location and density.

}, keywords = {Aquaculture, Carrying-capacity, Ecosystem model, Magdalen Islands, Mussels}, doi = {doi:10.1016/j.ecolmodel.2006.07.026}, author = {Jon Grant and Kristian J. Curran and Thomas L. Guyondet and Guglielmo Tita and C{\'e}dric Bacher and Vladimir Koutitonsky and Michael Dowd} } @article {4214, title = {The clinical and cost effectiveness of screening for meticillin-resistant Staphylococcus aureus (MRSA)}, year = {2007}, issn = {HTA 9}, url = {http://www.healthcareimprovementscotland.org/his/idoc.ashx?docid=4cd58ffa-afdb-45bb-b0d5-22782b3f327d\&version=-1}, author = {Ritchie K and Bradbury I and Craig J and Eastgate J and Foster L and Kohli H and Iqbal K and MacPherson K and McCarthy T and McIntosh H and Nic Lochlainn E and Reid M and Taylor J} } @article {1538, title = {The EROI of U.S. offshore energy extraction: A net energy analysis of the Gulf of Mexico}, journal = {Ecological Economics}, volume = {63}, year = {2007}, month = {08/2007}, pages = {355-364}, abstract = {

In 2004, the U.S. Department of the Interior{\textquoteright}s Minerals Management Service estimated that 49\% of the oil and 57\% of the natural gas yet to be discovered offshore in the United States are located in the Gulf of Mexico Outer Continental Shelf region. While the existence of these energy resources is critical to the nation{\textquoteright}s future economic well being, of equal importance is the amount of already extracted energy that will be required to deliver the new fuel to society in a useful form. The difference between the two energy quantities is the net supply. In many respects, net energy is the most relevant measure of fuel supply because it represents the energy available to produce final-demand economic goods and services. Unfortunately, there currently exists no standard procedure for determining net energy, and so the data are extremely limited and inconsistent. In this paper, we present an \“energy return on investment\”, or \“EROI\”-based approach. EROI is defined as the ratio of gross energy produced by an energy supply process to the total, direct plus indirect, energy cost of its production. If the EROI of an energy supply process is known, then it{\textquoteright}s net energy output can be derived easily given gross production data. Below, we specify an empirical computer model programmed to simulate the productivity dynamics of offshore energy extraction in the Gulf of Mexico and estimate the EROI of the \"offshore process\" over a twenty-year period (1985\–2004). At the conclusion of the simulation, the model calculates the EROI of the process to range from 10 to 25, depending on how energy costs have been defined. In comparison, it has been estimated that the EROI of U.S. domestic petroleum extraction in the 1930s was approximately 100.

}, keywords = {EROI, Net energy, Offshore energy extraction}, doi = {doi:10.1016/j.ecolecon.2007.02.015}, author = {Mark Gately} } @article {1537, title = {Evaluation and comparison of models and modelling tools simulating nitrogen processes in treatment wetlands }, journal = {Simulation Modelling Practice and Theory}, volume = {16}, year = {2007}, note = {

From Bachelor thesis, http://liu.diva-portal.org/smash/record.jsf?pid=diva2:20221

Modelica was compared with Simile, Stella and PowerSim

It would be interesting to evaluate the comments on Simile.

}, pages = {26-49}, publisher = {Elsevier}, abstract = {

In this paper, two ecological models of nitrogen processes in treatment wetlands have been evaluated and compared. These models were implemented, simulated, and visualized using the Modelica modelling and simulation language [P. Fritzson, Principles of Object-Oriented Modelling and Simulation with Modelica 2.1 (Wiley-IEEE Press, USA, 2004).] and an associated tool. The differences and similarities between the MathModelica Model Editor and three other ecological modelling tools have also been evaluated. The results show that the models can well be modelled and simulated in the MathModelica Model Editor, and that nitrogen decrease in a constructed treatment wetland should be described and simulated using the Nitrification/Denitrification model as this model has the highest overall quality score and provides a more variable environment.

}, keywords = {Denitrification, Ecological modelling, Evaluation, Modelica, Nitrification, Nitrogen, Treatment wetlands}, doi = {doi:10.1016/j.simpat.2007.08.010 }, author = {Stina Edelfeldt and Peter Fritzson} } @article {1542, title = {Corrigendum to {\textquotedblleft}It was an artefact not the result: A note on systems dynamic{\textquotedblright} [Environ. Model. Softw. 20 (2005) 1543{\textendash}1548] }, journal = {Environmental Modelling \& Software}, volume = {21}, year = {2006}, month = {05/2006}, pages = {756-758 }, doi = {doi:10.1016/j.envsoft.2006.01.003 }, author = {R. Seppelta and O. Richterb} } @article {1897, title = {Personal preferences and intensification of land use: their impact on southern Cameroonian slash-and-burn agroforestry systems}, journal = {Agroforestry Systems}, volume = {68}, year = {2006}, month = {03/2006}, pages = {53{\textendash}67}, publisher = {Springer}, abstract = {

Where long forest-fallows are no longer practiced, productivity declines in the absence of input substitution, as does the ability of subsistence farmers to earn an adequate livelihood from shifting cultivation. Land availability, population density and productivity-related factors such as soil fertility and labour requirements are not the only factors that affect fallow length and land use intensification in shifting cultivation agroforestry systems. Households surveyed indicated that various other decision criteria (e.g., proximity to other fields and the protection of land use rights) are important in land use decisions. Even though one quarter of households reported insufficient land resources to maintain soil fertility, few actually indicated that their choices were constrained by land availability. In fact, many cleared much younger fallows than strictly necessary based on the age of fallows available in their land holdings \– even those with fallows of sufficient age to maintain long-term productivity. This paper outlines an approach to quantify information about the household preferences that influence land use decisions, discusses the implications of these decision criteria for land use intensification and uses them to model household decision-making in a way that effectively simulates the spatial and dynamic mosaic of land use characteristic of shifting cultivation. Not only are non-productivity related decision criteria important in land use decisions in general; they also have a significant impact on land use intensification. In fact, the research described here demonstrates that both household-specific preferences and household-specific initial conditions can lead to intensification of land use apart from that arising due to increasing population density.

}, keywords = {Household modelling, Intensification, Preferences, Shifting cultivation, Spatiotemporal modelling, Sustainable forest use}, doi = {10.1007/s10457-006-0003-9}, author = {Douglas R Brown} } @book {1583, title = {Realizing Community Futures: A Practical Guide to Harnessing Natural Resources}, year = {2006}, publisher = {EarthScan}, organization = {EarthScan}, abstract = {

Through an easy-to-read narrative style and using real examples from Africa and Asia, this revolutionary book--part argument for the limitless power of human imagination and part practical manual for turning visions into reality--explains how to use a process of participatory modelling\" to structure people\’s learning and understanding of the natural systems they depend upon and how this can lead to better social and environmental outcomes.

}, isbn = {978-1844073849}, url = {http://www.cifor.cgiar.org/realizingfutures/_ref/home/index.htm}, author = {Jerry Vanclay and Ravi Prabhu and Fergus Sinclair} } @article {1540, title = {Spatially-explicit competition indices and the analysis of mixed-species plantings with the Simile modelling environment }, journal = {Forest Ecology and Management}, volume = {233}, year = {2006}, pages = {295-302}, abstract = {

Individual-based modelling and analysis of forest experiments has been made more accessible to researchers with the advent of modelling environments like Simile from www.simulistics.com. Individual-based analyses of tree growth data offer insights not possible with plot-based analyses, especially when the original experimental design has been compromised by mortality or other unforeseen events. The paper illustrates how Simile can be used for individual-based analyses of mixed plantings, and how it can be used to explore the consequences of the resulting statistical models. A mixed-species planting of Eucalyptus pellita and Acacia peregrina is used to illustrate possibilities.

}, keywords = {Acacia, Distance-dependent competition index, Eucalyptus, Individual-based modelling, Mixed-species, Powersim; Stella; Systems dynamics, Simile, Vensim}, doi = {doi:10.1016/j.foreco.2006.05.020 }, author = {Jerome K. VanclayCorresponding Author Contact Information} } @article {1541, title = {{\textquotedblleft}It was an artefact not the result{\textquotedblright}: A note on systems dynamic model development tools}, journal = {Environmental Modelling \& Software}, volume = {20}, year = {2005}, note = {

07 October: Integration methods test model added to the model catalogue, Lotka-Volterra predator-prey model (Seppelt and Richter, 2005).
The model is included in response to the call by Seppelt and Richter (2005) for evaluation of the numerical methods of simulation modelling tools. Such evaluation is to be welcomed as it is required to provide confidence in results, though of course, the model itself must also represent the target system adequately for confidence. If either the model representation or numerical methods are flawed, the results will be flawed. Unfortunately, Seppelt and Richter (2005) report aberrant behaviour of Simile 3.2 though neither the authors nor we can reproduce the flawed behaviour. A corrigendum has been published.

}, month = {12/2005}, pages = {1543-1548}, abstract = {

Environmental modelling is done more and more by practising ecologists rather than computer scientists or mathematicians. This is because there is a broad spectrum of development tools available that allows graphical coding of complex models of dynamic systems and help to abstract from the mathematical issues of the modelled system and the related numerical problems for estimating solutions. In this contribution, we study how different modelling tools treat a test system, a highly non-linear predator\–prey model, and how the numerical solutions vary. We can show that solutions (a) differ if different development tools are chosen but the same numerical procedure is selected; (b) depend on undocumented implementation details; (c) vary even for the same tool but for different versions; and (d) are generated but with no notifications on numerical problems even if these could be identified. We conclude that improved documentation of numeric methods used in the modelling software is essential to make sure that process based models formulated in terms of these modelling packages do not become \“black box\” models due to uncertainty in integration methods.

}, keywords = {Lotka-Volterra equation; Predator-prey modelling, MATEMATICA, MATLAB, Model analysis, MODELMAKER, Numerical ODE solvers, Simile, STELLA, Stiff systems}, doi = {doi:10.1016/j.envsoft.2004.12.004 }, author = {R. Seppelt and O. Richter} } @article {1585, title = {CamFlores: A FLORES-type model for the humid forest margin in Cameroon}, journal = {Small-Scale Forestry}, volume = {2}, year = {2003}, month = {2003/05/07/}, pages = {211 - 223}, abstract = {Abstract\ \ A FLORES-type model in the Simile modelling environment is being developed for three villages in the Humid Forest Benchmark area of southern Cameroon. The modelling project seeks to investigate the effects of introduction of new crop varieties and improved farming systems on the long-term maintenance of stable mosaics of forest and agriculture, within the context of the international Alternatives to Slash and Burn programme. Biophysical data have been collated, and socio-econnomic and tenure data have been acquired in spatially-explicit ways. Maps of land-cover at village and benchmark scale are being prepared from detailed and semi-detailed satellite imagery, using a nested legend system that allows linking of maps at different scales. These data enable the initial construction and parameterisation of the model, and will permit the extrapolation of the results of modelling from the villages to the benchmark, and ultimately to the whole of the Congo Basin humid forests. The prototype version of the model involves 10 households and about 500 land patches, and includes the three agricultural systems dominant in the southern more forested portion of the Benchmark (mixed food-fallow systems, forest melon fields, cocoa plantations) with no rental, sale or other transfer of land. Decision-making at the household level is essentially modelled deterministically, and labour productivity is assumed to be constant between households. This model is now complete, and once it has been adjusted and suitably parameterised, it will be applied to real data from the three test villages. This will require the addition of new farming systems, the introduction of modes of permanent or temporary transfer of land, and modification of the decision model to render it more realistic. ER - }, url = {http://dx.doi.org/10.1007/s11842-003-0016-4}, author = {Legg, Christopher} } @book {1594, title = {Environmental Modelling: Finding Simplicity in Complexity}, year = {2003}, pages = {430}, publisher = {Wiley}, organization = {Wiley}, keywords = {environmental modelling, GIS}, isbn = {978-0471496182}, url = {http://eu.wiley.com/WileyCDA/WileyTitle/productCd-0471496189.html}, author = {John Wainwright and Mark Mulligan} } @article {1543, title = {The Simile visual modelling environment.}, journal = {European Journal of Agronomy}, volume = {18}, year = {2003}, pages = {345-358 }, abstract = {

Simile is a visual modelling environment that has been developed to overcome the problems involved in implementing agro-ecological simulation models using conventional programming languages: problems such as the effort and skill needed to program the models, the lack of transparency in models implemented as programs, and the lack of reuseability of models and submodels. It combines the familiar System Dynamics (compartment-flow) paradigm with an object-based paradigm, allowing many forms of disaggregation to be handled, as well as spatial modelling and individual-based modelling. Its visual modelling interface makes it accessible to non-programmers, at the same time allowing models to be largely self-documenting. Models can be run very efficiently as compiled C++ programs, and users can develop new visualisation tools for displaying model results. Simile has been used in international research programmes, including the modelling of Mediterranean vegetation dynamics and modelling the interaction between households and land at the forest margin in developing countries. Simile has been developed in a spirit of open standards for model sharing. Models are saved as a text file in a structured format, with a view to enable model sharing with other modelling environments and to encourage others to develop additional tools for working with models.

}, keywords = {Declarative modelling, Modelling, Modelling environment, Simile}, url = {http://www.simulistics.com/files/documents/SimilePaper.pdf}, author = {Muetzelfeldt, R. I and Massheder, J.} }