The conversion of supplemental greenhouse light energy into biomass is not always optimal. Recent trends in global energy prices and discussions on climate change highlight the need to reduce our ...energy footprint associated with the use of supplemental light in greenhouse crop production. This can be achieved by implementing "smart" lighting regimens which in turn rely on a good understanding of how fluctuating light influences photosynthetic physiology. Here, a simple fit-for-purpose dynamic model is presented. It accurately predicts net leaf photosynthesis under natural fluctuating light. It comprises two ordinary differential equations predicting: 1) the total stomatal conductance to CO2 diffusion and 2) the CO2 concentration inside a leaf. It contains elements of the Farquhar-von Caemmerer-Berry model and the successful incorporation of this model suggests that for tomato (Solanum lycopersicum L.), it is sufficient to assume that Rubisco remains activated despite rapid fluctuations in irradiance. Furthermore, predictions of the net photosynthetic rate under both 400ppm and enriched 800ppm ambient CO2 concentrations indicate a strong correlation between the dynamic rate of photosynthesis and the rate of electron transport. Finally, we are able to indicate whether dynamic photosynthesis is Rubisco or electron transport rate limited.
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The process of inferring parameter values from experimental data can be a cumbersome task. In addition, the collection of experimental data can be time consuming and costly. This paper covers both ...these issues by addressing the following question: "Which experimental outputs should be measured to ensure that unique model parameters can be calculated?". Stated formally, we examine the topic of minimal output sets that guarantee a model's structural identifiability. To that end, we introduce an algorithm that guides a researcher as to which model outputs to measure. Our algorithm consists of an iterative structural identifiability analysis and can determine multiple minimal output sets of a model. This choice in different output sets offers researchers flexibility during experimental design. Our method can determine minimal output sets of large differential equation models within short computational times.
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•Introduce the novice reader to the concept of structural identifiability.•Re-parameterize large ODE models, including possible state transformation that reduce the model.•Show the ...re-parameterization process in detail, even for an example that includes a non-scalable state transformation.
An efficient method that assists in the re-parametrization of structurally unidentifiable models is introduced. It significantly reduces computational demand by combining numerical and symbolic identifiability calculations. This hybrid approach facilitates the re-parametrization of large unidentifiable ordinary differential equation models, including models where state transformations are required. A model is first assessed numerically, to discover potential structurally unidentifiable parameters. We then use symbolic calculations to confirm the numerical results, after which we describe the algebraic relationships between the unidentifiable parameters. Finally, the unidentifiable parameters are substituted with new parameters and simplification ensures that all the unidentifiable parameters are eliminated from the original model structure. The novelty of this method is its utilisation of numerical results, which notably reduces the number of symbolic calculations required. We illustrate our procedure and the detailed re-parametrization process in 5 examples: (1) an immunological model, (2) a microbial growth model, (3) a lung cancer model, (4) a JAK/STAT model, and (5) a small linear model with a non-scalable re-parametrization.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Communities located in the interface between marine/brackish and freshwater habitats are likely to be early responders to climatic changes as they are exposed to both saline and freshwater ...conditions, and thus are expected to be sensitive to any change in their environmental conditions. Climatic effects are predicted to reduce the availability of groundwater, altering the hydrological balance on estuarine-aquifer interfaces. Here, we aimed to characterise the estuarine faunal community along a gradient dependent on groundwater input, under a predicted climatic scenario of reduction in groundwater discharge into the estuary. Sediment macrofauna was sampled along a salinity gradient following both the wet and dry seasons in 2009. Results indicated that species abundance varied significantly with the salinity gradient created by the groundwater discharge into the estuarine habitat and with sampling time. The isopode
Cyathura carinata (Krøyer, 1847) and the polychaetes
Heteromastus filiformis (Claparède, 1864) and
Hediste diversicolor O.F. Muller, 1776 were associated with the more saline locations, while oligochaeta and Spionidae were more abundant in areas of lower salinity. The polychaete
Alkmaria romijni Horst, 1919 was the dominant species and ubiquitous throughout sampling stations. This study provides evidence for estuarine fauna to be considered as a potentially valuable indicator of variation in the input of groundwater into marine-freshwater interface habitats, expected from climatic pressures on aquifer levels, condition and recharge rates. For instance, a reduction in the abundance of some polychaete species, found here to be more abundant in freshwater conditions, and increasing Oligochaeta found here on higher salinities, can potentially be early warnings of a reduction in the input of groundwater into estuaries. Estuarine benthic species are often the main prey for commercially important fish predators such as in our case study, making it important to monitor the aquatic habitat interfaces taking into consideration the estuarine macrobenthos and groundwater availability in the system.
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For a reconstruction of state and parameter values in a dynamic system model, first the question whether these values can be uniquely determined from the data must be answered. This structural model ...property is known as observability or, in case of parameter calibration only, identifiability. Testing a given model for observability is a well studied problem in the systems and control sciences. However, it is increasingly difficult, if not impossible, to address this property for large size models that, nowadays, are frequently used. We demonstrate the application of a recently developed algorithm that overcomes this problem and is remarkably efficient. As an illustration we show how an observability analysis for a Chinese Hamster Ovary Cell model (34 states, 117 parameters), a JAKSTAT signalling model (31 states, 51 parameters), and a MAP Kinase model (100 states, 88 parameters) can be established in a very short time.
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The paper presents a novel method for assessing the local structural identifiability question for a general non-linear state-space model. The method is a combination of (i) the application of a ...singular value decomposition to a parametric output sensitivity matrix that is created by simply integrating the model once and, (ii) a symbolic computation for a reduced model that is guided by the SVD results and allows a confirmation of the conclusions regarding identifiability obtained in the first step. In case there is a lack of identifiability, the symbolic computation quickly results in determination of the exact structure of the nullspace and a suitable re-parametrisation. The method is discussed in detail and applied to three case studies, of which the last two are considerably large, containing 22 and 43 parameters to be identified, respectively.
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Currently, over 88 million people are estimated to have adopted a vegan or vegetarian diet. Cysteine is a semi-essential amino acid, which availability is largely dependent on dietary intake of meat, ...eggs and whole grains. Vegan/vegetarian diets are therefore inherently low in cysteine. Sufficient uptake of cysteine is crucial, as it serves as substrate for protein synthesis and can be converted to taurine and glutathione. We found earlier that intermolecular cystine bridges are essential for the barrier function of the intestinal mucus layer. Therefore, we now investigate the effect of low dietary cystine on the intestine. Mice (8/group) received a high fat diet with a normal or low cystine concentration for 2 weeks. We observed no changes in plasma methionine, cysteine, taurine or glutathione levels or bile acid conjugation after 2 weeks of low cystine feeding. In the colon, dietary cystine restriction results in an increase in goblet cell numbers, and a borderline significant increase mucus layer thickness. Gut microbiome composition and expression of stem cell markers did not change on the low cystine diet. Remarkably, stem cell markers, as well as the proliferation marker Ki67, were increased upon cystine restriction in the small intestine. In line with this, gene set enrichment analysis indicated enrichment of Wnt signaling in the small intestine of mice on the low cystine diet, indicative of increased epithelial proliferation. In conclusion, 2 weeks of cystine restriction did not result in apparent systemic effects, but the low cystine diet increased the proliferative capacity specifically of the small intestine and induced the number of goblet cells in the colon.
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In this study hydrochemical, isotopic and multivariate statistical tools are combined with a recharge analysis and existing geophysical data to improve understanding of major factors controlling ...freshwater occurrence and the origins of high salinities in the multi-layered coastal aquifer system of the Great Maputo area in Mozambique. Access to freshwater in this semi-arid area is limited by an inefficient public supply network, scarce surface waters, long droughts and an increasing population growth. Groundwater has a large potential to enhance water security, but its exploitation is threatened by both coastal and inland salinization mechanisms that are poorly understood. A GIS approach is utilized to classify potential recharge zones based on hydrogeological properties and land use/cover, whereas potential recharge rates are estimated through a root zone water balance method. In combination with water stable isotope data results reveal that extreme rainfall events provide the most relevant contributions to recharge, and interception and evaporation play an important role in the low recharge areas. Hierarchical clustering of hydrochemical and isotopic data allows the classification of six water groups, varying from fresh to brackish/salt waters. Corresponding scatter plots and PHREEQC modelling show evaporation and mixing with seawater (up to 5%) as major processes affecting salinity in the area. The co-occurrence of high alkalinity and Cl concentrations, in combination with piezometric and geo-electrical data, suggests that: 1) inland brackish/salt groundwater is caused by mixing with seawater trapped within clay layers; and 2) brackish/salt surface waters result from seepage of brackish groundwater into rivers and wetlands, followed by evaporation, hence increasing salinity and δ18O values. Mixing with small fractions of trapped seawater as main salinity source, rather than halite dissolution, is further corroborated by Br/Cl ratios of brackish/salt water samples near the ocean ratio. Cation exchange upon salinization is mainly observed in the semi-confined aquifer, while freshening takes place in the phreatic aquifer, particularly in areas presenting high recharge rates.
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•Groundwater salinization in Great Maputo aquifer is caused by relic seawater.•Relic seawater is entrapped within clay layers of the aquifer system.•Seepage of salt groundwater and evaporation results in saline river and wetland.•Recharge dominated by intense rainfall is main source of freshwater.•Fresh groundwater exploitation within saline environment needs to be optimised.
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Long-term (⩽1-year) records obtained by seabed observatories (BOBO) and repeated (24-h) CTD casts show the presence of a highly energetic environment in and around two cold-water carbonate-mound ...provinces, on the Southwest and Southeast Rockall Trough (SW and SE RT) margin. Carbonate mounds, covered with a thriving coral cover, are embedded mainly in the Eastern North Atlantic Water (ENAW) and are observed in a confined bathymetric zone between 600 and 1000
m water depth. Cold-water corals seem to be restricted in their growth by temperature and food availability. The presence of living corals on top of the carbonate mounds appears linked to the presence of internal waves and tidal currents in the water column, and consequently carbonate mound structures are shaped by the local hydrodynamic regime. Mound clusters have an elongated shape perpendicular to the regional contours and corresponding to the direction of the highest current speeds. On the SW RT margin temperature, salinity and current speed reflect a diurnal tidal pattern, causing maximum temperature variations at 900
m depth of more than 3
°C. Current speeds up to 45
cm
s
−1 occur, and a residual current of 10
cm
s
−1 is directed along the slope to the southwest. At the SE RT margin the temperature of the bottom water fluctuates more than 1
°C with a semi-diurnal tidal cyclicity. Amplitudes of average and peak current speeds here are comparable with those measured on the southwest margin, but the residual current in this area is directed to the northeast. Tidal currents and internal waves at both margins force the formation of intermediate and bottom nepheloid layers and bring fresh food particles with increased velocity to the mounds. The distribution of corals in both mound areas is considered directly related to the presence of enhanced turbidity. An increase in temperature can be directly related to an increase in the amount of particles in the water column. Current velocity increases when a transition occurs from cold to warm waters. High current velocities prevent local sedimentation but provide sufficient food particles to the corals, so that the corals thrive at the mound summits.
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