00630nas a2200181 4500008004100000022001300041245014500054210006900199260001600268300001400284490000800298100002200306700002200328700002100350700002100371700002000392856003600412 2019 eng d a0959652600aMussels or tunicates: That is the question. Evaluating efficient and sustainable resource use by low-trophic species in aquaculture settings0 aMussels or tunicates That is the question Evaluating efficient a cJan-09-2019 a132 - 1430 v2311 aFilgueira, Ramón1 aStrople, Leah, C.1 aStrohmeier, Tore1 aRastrick, Samuel1 aStrand, Øivind u//www.simulistics.com/node/439001967nas a2200169 4500008004100000022001300041245007200054210006900126260001600195300001200211490000700223520128000230100001901510700001901529700001601548856023301564 2017 eng d a1364815200aModular and spatially explicit: A novel approach to system dynamics0 aModular and spatially explicit A novel approach to system dynami cJan-08-2017 a48 - 620 v943 a

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.

1 aWingo, Patrick1 aBrookes, Allen1 aBolte, John uhttps://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/plain01250nas a2200217 4500008004100000022001400041245013200055210006900187260001600256300001400272490000700286520052500293100002400818700002300842700002100865700002600886700002000912700002300932700002200955856005500977 2016 eng d a0921-297300aMulti-scale feedbacks between tree regeneration traits and herbivore behavior explain the structure of pasture-woodland mosaics0 aMultiscale feedbacks between tree regeneration traits and herbiv cJan-05-2016 a913 - 9270 v313 a

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.

1 aPeringer, Alexander1 aSchulze, Kiowa, A.1 aStupariu, Ileana1 aStupariu, Mihai-Sorin1 aRosenthal, Gert1 aButtler, Alexandre1 aGillet, François uhttp://link.springer.com/10.1007/s10980-015-0308-z02003nas a2200181 4500008003900000022001300039245013200052210006900184260001200253300001200265490000700277520134100284100002001625700001501645700001701660700001701677856012701694 2015 d a2212041600aThe Multiscale Integrated Model of Ecosystem Services (MIMES): Simulating the interactions of coupled human and natural systems0 aMultiscale Integrated Model of Ecosystem Services MIMES Simulati c04/2015 a30 - 410 v123 aIn 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.1 aBoumans, Roelof1 aRoman, Joe1 aAltman, Irit1 aKaufman, Les u//www.simulistics.com/publications/multiscale-integrated-model-ecosystem-services-mimes-simulating-interactions-coupled-hu02611nas a2200277 4500008003900000022001400039245008700053210006900140520178500209100001401994700001402008700001202022700001402034700001402048700001502062700001402077700001402091700001602105700001402121700001302135700001602148700002002164700001802184700001602202856011502218 2014 d a1091-649000aMultiscale digital Arabidopsis predicts individual organ and whole-organism growth0 aMultiscale digital Arabidopsis predicts individual organ and who3 aUnderstanding 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.1 aChew, Y H1 aWenden, B1 aFlis, A1 aMengin, V1 aTaylor, J1 aDavey, C L1 aTindal, C1 aThomas, H1 aOugham, H J1 aReffye, P1 aStitt, M1 aWilliams, M1 aMuetzelfeldt, R1 aHalliday, K J1 aMillar, A J uhttp://www.pnas.org/content/early/2014/08/27/1410238111.full.pdf+html?sid=66edb45d-8e99-4d84-a072-a47729a65e1408328nas a2200145 4500008003900000245008900039210006900128260002600197300001000223490000700233520784400240100002008084700002008104856005808124 2009 d00aModeling the soil system: Bridging the gap between pedology and soil–water physics0 aModeling the soil system Bridging the gap between pedology and s bElsevier B.Vc05/2009 a51-610 v673 a

 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).

1 aBraudeaua, Erik1 aMohtar, Rabi, H uhttp://dx.doi.org/10.1016/j.gloplacha.2008.12.002 03051nas a2200133 4500008003900000245008400039210006900123300001400192490000600206520257100212100005802783700001402841856006202855 2009 d00aA multi-scale ''soil water structure'' model based on the pedostructure concept0 amultiscale soil water structure model based on the pedostructure a1111-11630 v63 a

 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.

1 aBraudeau, Mohtar El Ghezal Crayol Salahat, R H N 1 aMartin, P uhttp://www.hydrol-earth-syst-sci-discuss.net/6/1111/2009/03699nas a2200193 4500008003900000245016300039210006900202260001200271300001400283490000800297520302600305653001403331653002603345653002003371653002303391653001903414100001903433856005303452 2008 d00aModelling the impacts of various thinning intensities on tree growth and survival in a mixed species eucalypt forest in central Gippsland, Victoria, Australia0 aModelling the impacts of various thinning intensities on tree gr c12/2008 a2007-20170 v2563 a

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.

10aAustralia10aDiameter distribution10aDiameter growth10aThinning intensity10aTree mortality1 aKariuki, Maina uhttp://dx.doi.org/10.1016/j.foreco.2008.07.035