Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Using yield gap analysis to give sustainable intensification local meaning
Silva, João Vasco - \ 2017
University. Promotor(en): Martin van Ittersum, co-promotor(en): Ken Giller; Pytrik Reidsma. - Wageningen : Wageningen University - ISBN 9789463437141 - 361
crops - yields - crop yield - modeling - simulation models - cereals - farming systems - yield losses - gewassen - opbrengsten - gewasopbrengst - modelleren - simulatiemodellen - graansoorten - bedrijfssystemen - oogstverliezen

Yield gap analysis is useful to understand the relative contribution of growth-defining, -limiting and -reducing factors to actual yields. This is traditionally performed at the field level using mechanistic crop growth simulation models, and directly up-scaled to the regional and global levels without considering a range of factors intersecting at farm and farming system levels. As an example, these may include farmers' objectives and resource constraints, farm(er) characteristics, rotational effects between subsequent crops or decisions on resource allocation and prioritization of crop management. The objective of this thesis is to gain insights into yield gaps from a farm(ing) systems perspective in order to identify opportunities for sustainable intensification at local level.

Three contrasting case studies representing a gradient of intensification and capturing a diversity of agricultural systems were selected for this purpose, namely mixed crop-livestock systems in Southern Ethiopia, rice based-farming systems in Central Luzon (Philippines) and arable farming systems in the Netherlands. A theoretical framework combining concepts of production ecology and methods of frontier analysis was developed to decompose yield gaps into efficiency, resource and technology yield gaps. This framework was applied and tested for the major crops in each case study using crop-specific input-output data for a large number of individual farms. In addition, different statistical methods and data analyses techniques were used in each case study to understand the contribution of farmers' objectives, farm(er) characteristics, cropping frequency and resource constraints to yield gaps and management practices at crop level.

Yield gaps were largest for maize and wheat in Southern Ethiopia (ca. 80\\\\% of the water-limited yield), intermediate for rice in Central Luzon (ca. 50\\\\% of the climatic potential yield) and smallest for the major arable crops in the Netherlands (ca. 30\\\\% of the climatic potential yield). The underlying causes of these yield gaps also differed per case study. The technology yield gap explained most of the yield gap observed in Southern Ethiopia, which points to a lack of adoption of technologies able to reach the water-limited yield. The efficiency yield gap was most important for different arable crops in the Netherlands, which suggests a sub-optimal timing, space and form of the inputs applied. The three intermediate yield gaps contributed similarly to the rice yield gap in Central Luzon meaning that sub-optimal quantities of inputs used are as important in this case study as the causes mentioned for the other case studies.

Narrowing the yield gap of the major crops does not seem to entail trade-offs with gross margin per unit land in each case study. However, the opposite seems to be true for N use efficiency and labour productivity particularly in Southern Ethiopia and Central Luzon, and to a less extent in the Netherlands. This means that (sustainable) intensification of smallholder agriculture in the tropics needs to go hand-in-hand with agronomic interventions that increase land productivity while ensuring high resource use efficiency and with labour-saving technologies that can reduce the drudgery of farming without compromising crop yields.

Other insights at farm(ing) system level were clearer in Southern Ethiopia than in Central Luzon or in the Netherlands. For example, alleviating capital constraints was positively associated with intensification of maize-based farming systems around Hawassa and increases in oxen ownership (an indicator of farm power) was associated with extensification of wheat-based farming systems around Asella. In Central Luzon, farm and regional factors did not lead to different levels of intensification within the variation of rice farms investigated and the most striking effect was that direct-seeding (and thus slightly lower rice yields) was mostly adopted in larger farms, and used lower amounts of hired labour, compared to transplanting. In the Netherlands, the analysis of rotational effects on crop yields provided inconclusive results but confounding effects with e.g. rented land do not allow to conclude that these are not at stake in this farming system.

This thesis broadens the discussion on yield gaps by moving from the technical aspects underlying their estimation towards the broader farm level opportunities and constraints undermining their closure. Overall, insights from contrasting case studies support conventional wisdom that intensification of agriculture needs to occur in the 'developing South', where yield gaps are large and resource use efficiency low, while a focus on improving sustainability based on sustainable intensification (or even extensification) is more appropriate in the 'developed North', where yield gaps are small and resource use efficiency high.

Simulating pigs : Understanding their motivations, behaviour, welfare and productivity
Boumans, Iris - \ 2017
University. Promotor(en): Imke de Boer, co-promotor(en): Eddy Bokkers; Gert Jan Hofstede. - Wageningen : Wageningen University - ISBN 9789463432122 - 200
pigs - pig farming - sustainability - motivation - animal behaviour - behaviour disorders - animal welfare - simulation models - animal production - varkens - varkenshouderij - duurzaamheid (sustainability) - motivatie - diergedrag - gedragsstoornissen - dierenwelzijn - simulatiemodellen - dierlijke productie

The transition towards sustainable pig production systems is receiving increasing attention nowadays. Pig behaviour plays a central role in sustainability, as it is an important indicator for pig welfare and can also affect other sustainability issues. Understanding behaviour and related welfare consequences requires to understand motivations underlying behaviour. The two aims of this thesis were: 1) to assess the use of agent-based modelling for understanding pig behaviour and underlying motivation, and 2) to apply agent-based modelling for increasing our understanding of pig behaviour, and related animal welfare and productivity performance.

We first explored the use of agent-based modelling with tail biting behaviour in pigs as a case study. An agent-based model was developed to understand the causation of tail biting behaviour. Subsequently, we developed a mechanistic and dynamic simulation model to gain more understanding of feeding behaviour and internal (physiological) factors. The model integrates knowledge from physiology and ethology, and combines growth with a behavioural decision model based on motivation. This model included motivations underlying feeding behaviour and various feeding patterns of an individually housed growing pig. To deepen our understanding of mechanisms underlying feeding patterns of pigs within 24 hours, hormonal circadian rhythms were included in the model in a follow-up study. The circadian rhythms of cortisol and melatonin explained the alternans pattern, a small peak of feed intake at the beginning of the day and a larger peak at the end of the day, of feeding in pigs. Next, an agent-based model of feeding and social interaction in commercially group-housed pigs was developed to deepen our understanding of the complex interaction between internal physiological factors and external social factors. Social factors (e.g. competition level and social facilitation) and behavioural strategies (e.g. avoidance and approach) affected social interactions among pigs and feeding behaviour. The causation of variation among pigs was further explored in this model. Pig characteristics were important in various feeding, social interaction and growth patterns in pigs.

In general, agent-based modelling proved to be a useful method to understand animal behaviour and underlying motivations. It contributed to further understanding of tail biting, feeding and social behaviour in pigs. Furthermore, agent-based modelling showed to be a novel method to find and assess behaviours as welfare indicators, and to contribute to understanding trade-offs and synergies between sustainability issues, such as animal welfare and productivity.

SWAP version 4
Kroes, J.G. ; Dam, J.C. van; Bartholomeus, R.P. ; Groenendijk, P. ; Heinen, M. ; Hendriks, R.F.A. ; Mulder, H.M. ; Supit, I. ; Walsum, P.E.V. van - \ 2017
Wageningen : Wageningen Environmental Research (Wageningen Environmental Research report 2780) - 243
agrohydrology - irrigation - drainage - surface water - soil water - water management - simulation models - salinization - agrohydrologie - irrigatie - oppervlaktewater - bodemwater - waterbeheer - simulatiemodellen - verzilting
Theory description and user manual
Systeemstap naar minimaal energieverbruik Alstroemeria : metingen op praktijkbedrijven en een energiezuinige teeltconcept
Garcia Victoria, N. ; Zwart, Feije de; Weel, Peter van; Steenhuizen, Johan ; Groot, Marco de - \ 2017
Bleiswijk : Wageningen University & Research, BU Glastuinbouw (Rapport GTB 1372) - 66
kasgewassen - glastuinbouw - kastechniek - kassen - alstroemeria - energiebehoeften - energiebesparing - verwarming - aanvullend licht - kunstlicht - simulatiemodellen - isolatie (insulation) - evaporatie - greenhouse crops - greenhouse horticulture - greenhouse technology - greenhouses - energy requirements - energy saving - heating - supplementary light - artificial light - simulation models - insulation - evaporation
Alstroemeria cultivation in The Netherlands requires energy for heating, supplementary light and root cooling. For the program “Greenhouse as Source of Energy” we calculated to which extent the energy demand for growing this crop can be reduced with existing energy saving innovations. Some innovations were tested in practice, others were calculated by means of the greenhouse climate simulation model Kaspro. Results showed that it is possible to save up to 34% energy for heating compared to the reference situation. 40% energy can be saved on electricity for supplementary light and root cooling. However, this strategy leads to a reduced amount of PAR-light in the winter, and 4% less flowers in comparison with the reference. The greatest impact can be achieved by increasing the insulation of the greenhouse by using double screens, reducing the evaporation from the soil, improving the crop hygiene to avoid extra evaporation from crop debris and reduce pest pressure, and implementing controlled dehumidification of the greenhouse air.
Simulation nitrogen-limited crop growth with SWAP/WOFOST : process descriptions and user manual
Groenendijk, Piet ; Boogaard, Hendrik ; Heinen, Marius ; Kroes, J.G. ; Supit, Iwan ; Wit, Allard de - \ 2016
Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2721) - 59
crops - growth - soil - nitrogen - organic matter - mineralization - leaching - simulation models - nitrates - gewassen - groei - bodem - stikstof - organische stof - mineralisatie - uitspoelen - simulatiemodellen - nitraten
This report describes a soil nitrogen module (Soil-N), which is combined with the agro-hydrological model, SWAP, and the crop growth model, WOFOST. The core of the Soil-N module is a description of the nitrogen cycle, which is coupled to the organic matter cycle based upon the RothC-26.3 model. Nitrogen can be supplied to the soil as different types of fertilizer applications and through mineralisation of organic nitrogen. Ammonium and nitrate balances are calculated including uptake by plant roots, de-nitrification and leaching of nitrate. Data exchange is on a daily base. The partitioning of nitrogen within crops and the nitrogen contents of crop residues are calculated by WOFOST and passed to the Soil-N module. SWAP generates the data for establishing the water balance of the soil compartment for which the Soil-N perform the simulations. Nitrogen uptake by the crop is calculated as the minimum of the demand by the crop and the availability of nitrogen in the soil. The crop production rate is reduced when the mineral nitrogen stock is limited. Nitrogen-fixation is based on a simple approach. An improved sub-model for phenological stages of soybean was implemented. Increasing atmospheric CO2 concentrations can be accounted for. The innovated integrated model was tested using data sets from The Netherlands, China and Argentina, for which examples are given. This new model can be used as a tool in studies, in which both water and nitrogen can be limited for crop growth.
Lubrication and perception of foods : tribological, rheological and sensory properties of particle-filled food system
Liu, K. - \ 2016
University. Promotor(en): Erik van der Linden, co-promotor(en): Markus Stieger; Fred van de Velde. - Wageningen : Wageningen University - ISBN 9789462576803 - 236 p.
rheological properties - tribology - fat globules - particles - lubrication - sensory evaluation - simulation models - food - gels - rice - reologische eigenschappen - tribologie - vetbolletjes - deeltjes - smering - sensorische evaluatie - simulatiemodellen - voedsel - rijst

Background and aims

Food structure is determined by its composition and the interaction between the compositional or structural elements. Both food structure and the texture perception of foods undergo dynamic changes during different phases of oral processing. During oral processing, both rheological and tribological properties of foods are relevant for sensory perception. The general aim of this thesis was to understand the relationship between the structural properties, rheological and tribological properties during food breakdown, and the sensory perception of foods. More specifically, this thesis aimed to link the properties of food particles in liquid and semi-solid matrices to the tribological and rheological properties, and in this way, understand the sensory perception of these systems.


Fat droplets and micro-particle fat replacers based on protein and starch were investigated. These particles varied in size, morphology, deformability and stability, as well as their interaction with the surrounding matrix. These particles were dispersed in liquid or semi-solid gel phases, forming the food model systems under consideration. The friction and microstructural evolution of food model systems under shear was determined using a mouth-mimicking tribometer connected to a confocal laser scanning microscopy. The viscosities of liquid systems were analyzed using a rheometer, and the large deformation properties of semi-solid gel systems were determined during uniaxial compression tests. The sensory perception of the food model systems were measured using quantitative descriptive analysis. The release and deposition of fat droplets on the tongue were determined using in vivo fluorescence.


Food structural elements could be manipulated to control the tribological properties of food model systems. Morphology, size, and deformability of food particles determine the lubrication behavior of the food systems. Spherical particles with micrometer size were able to reduce friction through a ball bearing mechanism, while irregularly shaped particles increased friction by increasing apparent surface asperity contacts. Deformable particles could flatten the surface by filling asperities, thus reduced friction. Coalescence of unstable droplets could plate-out on the surface and form film patches, thus reduced friction. Other structural elements, such as emulsifiers and sticky molecules, also influenced tribological properties of the systems. Interactions between the food structural elements could influence the rheological properties of liquid and semi-solid food systems. These properties as well as tribological properties were inter-related and all of them affect sensory perception. The inter-relations between physical and sensory properties of food systems were influenced by oral processing, such as oral processing duration and temperature. Furthermore, several fat reduction and replacement strategies were suggested, including increasing the availability of fat that is in contact with oral surfaces, improving the lubrication by ball bearing of particles, and reducing perception of negative attributes such as roughness.


This thesis showed the importance of food particle properties in both the tribological properties and sensory perception of foods, and emphasized the different lubrication mechanisms of different structure elements and their relation to perception. The differences in behavior of food particles between liquid and semi-solid gel systems were highlighted. These findings would enable a better understanding of relationship between food structure and their physical and sensory properties, and this would allow designing or modifying food products with targeted texture and sensory perception.

Statistical modelling for exposure measurement error with application to epidemiological data
Agogo, G.O. - \ 2016
University. Promotor(en): Hendriek Boshuizen; Fred van Eeuwijk, co-promotor(en): Hilko van der Voet. - Wageningen : Wageningen University - ISBN 9789462576223 - 160 p.
calibration - regression analysis - exposure assessment - validity - simulation models - statistical bias - epidemiology - kalibratie - regressieanalyse - blootstellingsbepaling - geldigheid - simulatiemodellen - statistische vertekening - epidemiologie

Background Measurement error in exposure variables is an important issue in epidemiological studies that relate exposures to health outcomes. Such studies, however, usually pay limited attention to the quantitative effects of exposure measurement error on estimated exposure-outcome associations. Therefore, the estimators for exposure-outcome associations are prone to bias. Existing methods to adjust for the bias in the associations require a validation study with multiple replicates of a reference measurement. Validation studies with multiple replicates are quite costly and therefore, in some cases only a single–replicate validation study is conducted besides the main study. For a study that does not include an internal validation study, the challenge in dealing with exposure measurement error is even bigger. The challenge is how to use external data from other similar validation studies to adjust for the bias in the exposure-outcome association. In accelerometry research, various accelerometer models have currently been developed. However, some of these new accelerometer models have not been properly validated in field situations. Despite the widely recognized measurement error in the accelerometer, some accelerometers have been used to validate other instruments, such as physical activity questionnaires, in measuring physical activity. Consequently, if an instrument is validated against the accelerometer, and the accelerometer itself has considerable measurement error, the observed validity in the instrument being validated will misrepresent the true validity.

Methodology In this thesis, we adapted regression calibration to adjust for exposure measurement error for a single-replicate validation study with zero-inflated reference measurements and assessed the adequacy of the adapted method in a simulation study. For the case where there is no internal validation study, we showed how to combine external data on validity for self-report instruments with the observed questionnaire data to adjust for the bias in the associations caused by measurement error in correlated exposures. In the last part, we applied a measurement error model to assess the measurement error in physical activity as measured by an accelerometer in free-living individuals in a recently concluded validation study.

Results The performance of the proposed two-part model was sensitive to the form of continuous independent variables and was minimally influenced by the correlation between the probability of a non-zero response and the actual non-zero response values. Reducing the number of covariates in the model seemed beneficial, but was not critical in large-sample studies. We showed that if the confounder is strongly linked with the outcome, measurement error in the confounder can be more influential than measurement error in the exposure in causing the bias in the exposure-outcome association, and that the bias can be in any direction. We further showed that when accelerometers are used to monitor the level of physical activity in free-living individuals, the mean level of physical activity would be underestimated, the associations between physical activity and health outcomes would be biased, and there would be loss of statistical power to detect associations.

Conclusion The following remarks were made from the work in this thesis. First, when only a single-replicate validation study with zero-inflated reference measurements is available, a correctly specified regression calibration can be used to adjust for the bias in the exposure-outcome associations. The performance of the proposed calibration model is influenced more by the assumption made on the form of the continuous covariates than the form of the response distribution. Second, in the absence of an internal validation study, carefully extracted validation data that is transportable to the main study can be used to adjust for the bias in the associations. The proposed method is also useful in conducting sensitivity analyses on the effect of measurement errors. Lastly, when “reference” instruments are themselves marred by substantial bias, the effect of measurement error in an instrument being validated can be seriously underestimated.

Extra light and save energy in ideal winter-light greenhouse : effect of condensation still being researched
Arkesteijn, Marleen - \ 2015
In Greenhouses : the international magazine for greenhouse growers (2015)4. - ISSN 2215-0633 - p. 26 - 27.
horticulture - greenhouse horticulture - greenhouse technology - innovations - lighting - light transmission - physical models - energy saving - winter - simulation models - humidity - tuinbouw - glastuinbouw - kastechniek - innovaties - verlichting - lichtdoorlating - fysische modellen - energiebesparing - simulatiemodellen - vochtigheid
A consortium of companies, together with Wageningen UR, is developing a greenhouse that will maximise the amount of light entering between October and March. The goal is to achieve 10% extra yield during these months. The gain in light should come from a combination of various adjustments and improvements. Following the theoretical simulation models and physical scale models, the first winter-light greenhouse will be built next year as ‘proof of principle’ at the Innovation- and Demonstration centre in Bleiswijk, the Netherlands.
Logistics network design & control : managing product quality in a blooming sector
Keizer, M. de - \ 2015
University. Promotor(en): Jack van der Vorst, co-promotor(en): Jacqueline Bloemhof-Ruwaard; Rene Haijema. - Wageningen : Wageningen University - ISBN 9789462576025 - 239
logistiek - netwerkanalyse - sierteelt - kwaliteitszorg - kwaliteit - productie - tuinbouw - verse producten - voedselproducten - simulatiemodellen - simulatie - logistics - network analysis - ornamental horticulture - quality management - quality - production - horticulture - fresh products - food products - simulation models - simulation
PermVeg: a generic tool to design and assess crop rotations for permanent vegetable production systems; User manual
Wassink, B. ; Berg, W. van den; Putter, H. de; Hengsdijk, H. - \ 2015
Wageningen : Wageningen UR (vegIMPACT report 9) - 10
rotatie - groenteteelt - computersimulatie - simulatiemodellen - handbediening - vietnam - indonesië - rentabiliteit - arbeidskosten - pesticiden - handleidingen - rotation - vegetable growing - computer simulation - simulation models - manual operation - indonesia - profitability - labour costs - pesticides - guide books
This manual describes a generic tool to design and assess alternative vegetable rotations. The model combines vegetable crops to generate all possible crop rotations for a given period, based on a number of explicit criteria (objectives and restrictions) controlled by the user. The criteria eliminate in early stages those crop rotations that are undesirable. The criteria relate among others to the most important socio-economic and environmental factors in vegetable production, i.e. profitability, labor requirements and costs of pesticide use.
Investigation of a growth model incorporating density dependence for the mackerel management plan simulations
Brunel, T.P.A. - \ 2015
IJmuiden : IMARES (Report / IMARES Wageningen UR C134/15) - 12
trachurus - density dependence - growth - models - simulation models - fish culture - dichtheidsafhankelijkheid - groei - modellen - simulatiemodellen - visteelt
This report presents a framework to model density dependent growth for the North East Atlantic mackerel. The model used is the classical von Bertalanffy equation, but modified so that growth is reduced when stock size increases. The model developed was able to reproduce quite closely the trends in the observed historical weight-at-age data. This framework can therefore be incorporated in the simulation tool used for the mackerel management plan evaluation. But since the actual mechanisms through which stock size affects growth are not identified, density dependent growth should not be used as the base case scenario in simulations. However it can be used in sensitivity tests which can be conducted to assess the potential impact of density dependent growth on simulation output, such as Fmsy.
The African Greenhouse : a toolbox
Elings, A. ; Hemming, S. ; Os, E.A. van; Campen, J.B. ; Bakker, J.C. - \ 2015
Bleiswijk : Wageningen UR Glastuinbouw (Rapport GTB 1360) - 52
greenhouse horticulture - greenhouses - greenhouse crops - greenhouse technology - protected cultivation - decision models - crop growth models - simulation models - africa - glastuinbouw - kassen - kasgewassen - kastechniek - teelt onder bescherming - beslissingsmodellen - gewasgroeimodellen - simulatiemodellen - afrika
There is demand for a decision support tool to design greenhouse production systems in various climate zones and locations in Africa: the ‘Toolbox Adaptive Greenhouse Systems for Africa’. Selection of a limited number of climate zones that are representative for Africa limits the variation in designs to be evaluated and makes the approach more effective for the Netherlands supply industry. The toolbox will result in a number of greenhouse cultivation systems that are most suitable for a given location, weighing perspectives such as greenhouse type, greenhouse installation, climate, production and economic viability. The toolkit will follow the ‘adaptive greenhouse approach’ in which models for greenhouse, crop and finances are combined. This report provides a basis for the toolbox. An overview of African climates is given, followed by options for greenhouse design which are placed in the context of a number of production systems. The expected future developments and the transitions from current situations to likely future situations are briefly described. Anticipating likely future developments enables an analysis of the potential of a certain farm type, the requirements for further development, and the options for Netherlands involvement.
Modeling studies of biological gas desulfurization under haloalkaline conditions
Klok, J.B.M. - \ 2015
University. Promotor(en): Albert Janssen, co-promotor(en): Karel Keesman. - Wageningen : Wageningen University - ISBN 9789462572980 - 158
biogas - aardgas - ontzwaveling - sulfiden - oxidatie - bioreactoren - wiskundige modellen - simulatiemodellen - natural gas - desulfurization - sulfides - oxidation - bioreactors - mathematical models - simulation models


Biogas, synthesis and natural gas streams often require treatment because of the presence of gaseous hydrogen sulphide (H2S). About 25 years ago, a biotechnological gas treatment process was developed as an alternative to the conventionally applied technologies. This process is known as the Thiopaq process and offers a number of advantages compared to the existing physical-chemical processes. Depending on the process conditions, H2S is oxidized to elemental bio-sulfur (90-94 mol%) and sulphate (6-10 mol%). In order to enable cost effective large scale applications, the selectivity for sulfur production should be increased to more than 97 mol%. Hence, a better understanding of the combined effect of abiotic and biological reaction kinetics and the relation to hydrodynamic characteristics is required.

The first part of this PhD study focuses on biological reaction kinetics and biological pathways for sulphide oxidation that occur in the process at haloalkaline conditions. It was found that two different sulfide oxidizing enzyme systems are present in haloalkaline sulfide oxidizing bacteria. It has been hypothesized that the different enzymatic routes are determined by the process conditions. Both enzyme systems were taken into account to propose and validate a new physiological mathematical model that can handle multi-substrates and multi-products.

In the second part of the thesis, this model was evaluated via a normalized sensitivity method and it was demonstrated that certain key parameters affect the activity of the biomass at different substrate levels. Furthermore, from CSTR simulations it has been demonstrated that non-linear effects are of importance when scaling up from lab-scale to full-scale industrial units.

Finally, the developed kinetic models have been incorporated in a full-scale biodesulfurization model that includes the effects of turbulent flow regimes and mass transfer of oxygen. This enables us to better understand the overall process. Moreover, the model can also be used as a tool to design model-based control strategies which will lead to better overall process performance, i.e. maximize sulfur production and minimize chemical consumption rates.

Physiologically based in silico modelling to examine DNA adduct formation by different food-borne a,ß-unsaturated aldehydes at realistic low dietary exposure levels
Kiwamoto, R. - \ 2015
University. Promotor(en): Ivonne Rietjens, co-promotor(en): Ans Punt. - Wageningen : Wageningen University - ISBN 9789462572843 - 200
aldehyden - dna - ontgifting - voedseladditieven - aromatische stoffen - genotoxiciteit - carcinogenen - modellen - wiskundige modellen - fysiologie - simulatiemodellen - toxicologie - aldehydes - detoxification - food additives - flavourings - genotoxicity - carcinogens - models - mathematical models - physiology - simulation models - toxicology

Abstract (R.Kiwamoto ISBN 978-94-6257-284-3)

Various α,β-unsaturated aldehydes are present in fruits, vegetables, spices, or processed products containing these items as natural constituents or as added food flavouring agents. Because of the α,β-unsaturated aldehyde moiety the β carbon in the molecule becomes electron deficient and the aldehydes react with electron rich molecules including DNA via Michael addition. The formation of DNA adducts raises a concern for genotoxicity, although formation of DNA adducts may not be significant at low doses relevant for dietary exposure in vivo because of adequate detoxification. This thesis therefore aimed at determining dose-dependent detoxification and DNA adduct formation of food-borne α,β-unsaturated aldehydes by using a physiologically based in silico modelling approach in order to contribute to the safety assessment of these aldehydes used as food flavourings instead of performing animal experiments.

Physiologically based in silico models were developed for 18 α,β-unsaturated aldehydes. The model outcomes indicated that the DNA adduct formation by the 18 α,β-unsaturated aldehydes as food flavourings is negligible and does not raise a safety concern at their levels of intake resulting from their use as food flavourings. The application of QSAR models strongly accelerated the development process of the PBK/D models of the group of 18 compounds. Also, it was illustrated that physiologically based in silico models provide a very useful and powerful tool to facilitate a group evaluation and read-across for food-borne DNA reactive agents. PBK/D models developed for the group of compounds supported read-across from cinnamaldehyde which is known not to be genotoxic or carcinogenic in vivo to other aldehydes, by allowing comparison of dose-dependent DNA adduct formations. Altogether this thesis presented physiologically based in silico modelling as an approach to test relevance of positive in vitro genotoxicity results by DNA reactive compounds in vivo without using animal experiments.

A model based method for evaluation of crop operation scenarios in greenhouses
Ooster, A. van 't - \ 2015
University. Promotor(en): Eldert van Henten, co-promotor(en): Jan Bontsema; Silke Hemming. - Wageningen : Wageningen University - ISBN 9789462573024 - 169
kastechniek - glastuinbouw - simulatie - discrete simulatie - simulatiemodellen - arbeid (werk) - rozen - greenhouse technology - greenhouse horticulture - simulation - discrete simulation - simulation models - labour - roses


This research initiated a model-based method to analyse labour in crop production systems and to quantify effects of system changes in order to contribute to effective greenhouse crop cultivation systems with efficient use of human labour and technology. This method was gradually given shape in the discrete event simulation model GWorkS, acronym for Greenhouse Work Simulation. Model based evaluation of labour in crop operations is relatively new in greenhouse horticulture and could allow for quantitative evaluation of existing greenhouse crop production systems, analysis of improvements, and identification of bottlenecks in crop operations. The modelling objective was a flexible and generic approach to quantify effects of production system changes. Cut-rose was selected as a case-study representative for many cut-flowers and fruit vegetables.

The first focus was a queueing network model of the actions of a worker harvesting roses in a mobile cultivation system. Data and observations from a state-of-art mobile rose production system were used to validate and test the harvesting model. Model experiments addressed target values of operational parameters for best system performance. The model exposed effects of internal parameters not visible in acquired data. This was illustrated for operator and gutter speed as a function of crop yield. The structure and setup of the GWorkS model was generic where possible and system specific where inevitable.

The generic concept was tested by transferring GWorkS to harvesting a greenhouse section in a static growing system for cut-roses and extending it with navigation in the greenhouse, product handling, and multiple operator activity (up to 3 workers). Also for rose harvesting in a static growing system, the model reproduced harvesting accurately. A seven workday validation for an average skilled harvester showed a relative root mean squared error (RRMSE) under 5% for both labour time and harvest rate. A validation for 96 days with various harvesters showed a higher RRMSE, 15.2% and 13.6% for labour time and harvest rate respectively. This increase was mainly caused by the absence of model parameters for individual harvesters. Work scenarios were simulated to examine effects of skill, equipment, and harvest management. For rose yields of 0.5 and 3 harvested roses per m2, harvest rate was 346 and 615 stems h-1 for average skilled harvesters, 207 and 339 stems h-1 for new harvesters and 407 and 767 stems h-1 for highly skilled harvesters. Economic effects of trolley choice are small, 0-2 € per 1000 stems and two harvest cycles per day was only feasible if yield quality effects compensate for extra costs of 0.2-1.1 eurocents per stem.

In a sensitivity analysis and uncertainty analysis, parameters with strong influence on labour performance in harvesting roses in a static system were identified as well as effects of parameter uncertainty on key performance indicators. Differential sensitivity was analysed, and results were tested for linearity and superposability and verified using the robust Monte Carlo method. The model was not extremely sensitive for any of the 22 tested input parameters. Individual sensitivities changed with crop yield. Labour performance was most affected by greenhouse section dimensions, single rose cut time, and yield. Throughput was most affected by cut time of a single rose, yield, number of harvest cycles, greenhouse length and operator transport velocity. In uncertainty analysis the coefficient of variation for the most important outputs labour time and throughput is around 5%. The main sources of model uncertainty were in parallel execution of actions and trolley speed. The uncertainty effect of these parameters in labour time, throughput and utilisation of the operator is acceptably small with CV less than 5%. The combination of differential sensitivity analysis and Monte Carlo analysis gave full insight in both individual and total sensitivity of key performance indicators.

To realise the objective of model based improvement of the operation of horticultural production systems in resources constrained system, the GWorkS-model was extended for simultaneous crop operations by multiple workers analysis. This objective was narrowed down to ranking eight scenarios with worker skill as a central theme including a labour management scenario applied in practise. The crop operations harvest, disbudding and bending were considered, which represent over 90% of crop-bound labour time. New sub-models on disbudding and bending were verified using measured data. The integrated scenario study on harvest, disbudding and bending showed differences between scenarios of up to 5 s per harvested rose in simulated labour time and up to 7.1 € m-2 per year in labour costs. The simulated practice of the grower and the scenario with minimum costs indicated possible savings of 4 € m-2 per year, which equals 15% of labour cost for harvest, disbudding and bending. Multi-factorial assessment of scenarios pointed out that working with low skilled, low paid workers is not effective. Specialised workers were most time effective with -17.5% compared to the reference, but overall a permanent team of skilled generalists ranked best. Reduced diversity in crop operations per day improved labour organisational outputs but ranked almost indifferent. The reference scenario was outranked by 5 scenarios.

Discrete event simulation, as applied in the GWorkS-model, described greenhouse crop operations mechanistically correct and predicts labour use accurately. This model-based method was developed and validated by means of data sets originating from commercial growers. The model provided clear answers to research questions related to operations management and labour organisation using the full complexity of crop operations and a multi-factorial criterion. To the best of our knowledge, the GWorkS-model is the first model that is able to simulate multiple crop operations with constraints on available staff and resources. The model potentially supports analysis and evaluation of design concepts for system innovation.

Interactions between aerosal and convective boundary-layer dynamics over land
Wilde Barbaro, E. - \ 2015
University. Promotor(en): Maarten Krol; Bert Holtslag, co-promotor(en): Jordi Vila-Guerau de Arellano. - Wageningen : Wageningen University - ISBN 9789462572652 - 182
aërosolen - atmosferische grenslaag - grenslaagmeteorologie - aardoppervlak - modellen - simulatiemodellen - straling - atmosfeer - aerosols - atmospheric boundary-layer - boundary-layer meteorology - land surface - models - simulation models - radiation - atmosphere

In this Section, we summarize the most important findings and relevant issues treated in detail in Chapters 2 to 5.

The primary conclusion of this thesis is that it is necessary to take aerosols into account to accurately describe the convective atmospheric boundary-layer (CBL) dynamics and the land-surface processes. We reached this conclusion by systematically studying the land-CBL system and its couplings, and employed a hierarchy of models ranging from an eddy-resolving model (large-eddy simulation; LES) to non-eddy resolving models (mixed-layer model, and single column model). In addition to the numerical component, we used a complete observational data set to help us design and evaluate our numerical framework.

Chapter 2 was devoted to the explanation of the radiative transfer code used in Chapters 4 and 5. We showed that despite the simplified treatment of solar radiation and its interactions with aerosols, our radiative code is in general agreement with a more sophisticated radiative transfer code, even for extreme aerosol loads. Moreover, our results reproduce observations of direct and diffuse radiation at the surface accordingly - as shown in Chapter 4.

Regarding the longwave band, we showed that aerosols are not relevant for the estimation of the incoming longwave radiation at the surface. We concluded that Brunt's formula, depending only on screen level temperature and vapor pressure, is the most adequate to represent the incoming longwave radiation at the surface for the cases relevant for our studies.

In Chapter 3 we investigated the impact of aerosol heat absorption on the dynamics of an idealized CBL with prescribed surface fluxes. We found that the structure and evolution of the CBL were influenced by the vertical distribution of the aerosols. Moreover, we showed that the aerosols influence the exchange of heat between the CBL and the free troposphere by (i) extinction of radiation and consequently reduced surface fluxes, and by (ii) deepening the entrainment zone depth. We highlighted the importance of high-resolution models to properly represent the effects of aerosol absorption of radiation on the dynamics of the CBL, especially in the entrainment zone. We demonstrated that, in addition to the properties of the aerosols, the vertical distribution is an important characteristic to properly describe the CBL height evolution and the dynamics of the upper part of the CBL. To further support the analysis of the LES results, we used a mixed-layer (MXL) model to calculate boundary-layer depth and the potential temperature jump at the inversion layer. In spite of the simplicity of this model, the mixed-layer results obtained for boundary-layer height and the inversion layer jump agreed well with the LES results.

Extending the knowledge acquired with the academical prototypical experiments performed in Chapter 3, in Chapter 4 we quantified the effects of aerosol scattering and absorption of shortwave (SW) radiation both on the surface energy budget and on the CBL dynamics. To this end, we coupled our LES model and the MXL model to (i) a land-surface model and (ii) a broadband SW radiative transfer model, (described in Chapter 2). We successfully validated the results obtained with the LES model and MXL model using measurements of (thermo)dynamic variables and aerosol properties observed in Cabauw (the Netherlands). Our LES results showed that for Cabauw (over well-watered grassland) aerosols significantly alter the magnitude of the available energy at the surface and its partitioning. Under well-watered conditions, the sensible heat flux was more strongly reduced compared to the latent heat flux. Given the satisfactory agreement between the LES results and MXL model results, we further explored the sensitivity of the land-CBL system to a wide range of aerosol optical depths and single scattering albedos using the MXL model. Our results showed that higher loads of aerosols impose an energy restriction at the surface. As a result, we calculated a delay in the morning onset of the CBL and an advance in the CBL afternoon collapse. We also found that entrainment of aerosols from the residual layer plays a significant role in the development of the CBL dynamics during the day. An important aspect of Chapter 4 is the investigation of the different responses of the CBL dynamics depending on aerosol optical properties. Strongly absorbing aerosols deepened and warmed the CBL, while purely scattering aerosols shallowed and cooled the CBL.

We highlighted that the results presented in Chapter 4 can be used as a benchmark to evaluate coupling and performance of the parametrizations for SW radiation, land-surface and boundary-layer schemes, implemented in mesoscale or global chemistry transport models.

In Chapter 5 we increased the complexity of our land-CBL system representation by studying the formation and transport of ammonium nitrate aerosols. In doing so, we coupled in our LES radiation, chemistry, aerosols, CBL dynamics, and surface exchange processes of chemicals, heat and moisture. Our fully coupled LES model was again evaluated against observations of chemistry and aerosol fields and showed a good correspondence. In particular, our results showed a satisfactory agreement between the simulated and observed nitrate partitioning at the surface.

We showed that gas-aerosol conversion of nitrate leads to highly non-linear profiles of nitrate concentrations and turbulent fluxes. Moreover, the shapes of the simulated profiles depended strongly on the time scale of gas-aerosol conversions. Note that the typical timescale of turbulent motions in the CBL is around 10-20 minutes. For shorter time scales of gas-aerosol conversion compared to the CBL dynamics timescale, we found that turbulent fluxes are larger and concentration profiles more tilted within the CBL. These results have a significant impact on the nitrate deposition flux at the surface. Our LES results confirmed that the large deposition velocities for aerosol nitrate close to the surface are actually due to outgassing of aerosol nitrate rather than a real deposition process.

An important aspect discussed in Chapter 5 concerns the inability of non-eddy resolving models to accurately model the turbulent transport of nitrate within the CBL. Based on a detailed analysis of the flux budget equation, we showed that the exchange coefficient of heat used in our 1D model has to be increased to better account for the complex interaction between gas-aerosol conversion of nitrate and 3D turbulence within the CBL. Indeed, the new exchange coefficient also improved the comparison between gas-aerosol partitioning of nitrate calculated with our 1D model and surface observations.

The results discussed in this thesis demonstrate the need for considering the influence of aerosols on the CBL dynamics. Specifically, aerosols influence important phenomena for the CBL evolution namely radiation, surface-atmosphere interactions, chemistry, and (thermo)dynamics. In addition to that, the availability of high-resolution numerical simulations is crucial to validate and evaluate results obtained by numerical models that do not explicitly resolve the turbulent field.

Plant plasticity in intercropping: mechanisms and consequences
Zhu, J. - \ 2015
University. Promotor(en): Niels Anten, co-promotor(en): Jochem Evers; Wopke van der Werf. - Wageningen : Wageningen University - ISBN 9789462572195 - 196
tussenteelt - concurrentie tussen planten - simulatiemodellen - intercropping - plant competition - simulation models


Diverse agricultural system such as intercrop is practised widely in developing countries and is gaining increasing interest for sustainable agriculture in developed countries. Plants in intercrops grow differently from plants in single crops, due to interspecific plant interactions and heterogeneous resource distribution, but adaptive plant morphological responses to competition in intercrops have not been studied in detail. This thesis aims to link the performance of an intercropping system with plasticity in plant traits.

Grain yield of border-row wheat of an intercrop was 141% higher than in sole wheat. The yield increase was mainly associated with plasticity in tillering and leaf sizes. Compared to maize in monoculture, maize in intercrops had lower leaf and collar appearance rates, larger blade and sheath sizes at low ranks and smaller ones at high ranks. The data suggest many of those changes are linked to each other through feedback mechanisms both at plant level and at phytomer level. A model of maize development was further developed based on three coordination rules between leaf emergence events and dynamics of organ extension. Flexible timing of organ development can emerge from the model as well as the distribution of leaf sizes over ranks. A wheat-maize architectural model was developed for quantifying the role of architectural trait plasticity in light capture in intercrop. Simulated light capture was 23% higher in intercrop with plasticity in traits than the expected value weighted from the light capture in sole crops. Thirty-six percentage of the light increase was due to intercrop configuration alone and 64% was due to plasticity.

Overall, this thesis clearly shows the importance of plasticity in architectural traits for overyielding in wheat-maize intercropping and probably in diversified cropping systems in general. Thus it points to a previously under-appreciated mechanism driving the relationship between species diversity and overyielding of plant communities.

The MAGNET Model: Module description
Woltjer, G.B. ; Kuiper, M. ; Kavallari, A. ; Meijl, H. van; Powell, J.P. ; Rutten, M.M. ; Shutes, L.J. ; Tabeau, A.A. - \ 2014
The Hague : LEI Wageningen UR (Manual / LEI 14-57) - 146
modellen - modelleren - databanken - simulatiemodellen - evenwicht - models - modeling - databases - simulation models - equilibrium
Voedselverspilling terugdringen: Simulatietool berekent effect verbetermaatregelen
Janssen, A. ; Snels, J.C.M.A. - \ 2014
Voedingsmiddelentechnologie 2014 (2014)3. - ISSN 0042-7934 - p. 16 - 18.
voedselverspilling - simulatiemodellen - supermarkten - houdbaarheid (kwaliteit) - bewaartijd - verse producten - voedselkwaliteit - voedselketens - food wastage - simulation models - supermarkets - keeping quality - storage life - fresh products - food quality - food chains
In de strijd tegen voedselverspilling in de supermarkt is een nieuw hulpmiddel in de maak. een simulatietool waarmee het effect van verbetermaatregelen in versketens wordt gekwantificeerd. Onderzoekers van TI Food and Nutrition en projectpartners CBl en FNLI hebben hiermee een krachtig gereedschap in handen om derving verder te beperken.
Climate variability and change in Ethiopia : exploring impacts and adaptation options for cereal production
Kassie, B.T. - \ 2014
University. Promotor(en): Martin van Ittersum, co-promotor(en): R.P. Rötter; Huib Hengsdijk; S. Asseng. - Wageningen : Wageningen University - ISBN 9789461738370 - 183
zea mays - maïs - klimaatverandering - klimaatadaptatie - simulatiemodellen - onzekerheid - ethiopië - maize - climatic change - climate adaptation - simulation models - uncertainty - ethiopia

Key words: Climate change, Adaptation, Crop modelling, Uncertainty, Maize (Zea mays), Central Rift Valley.

Smallholder farmers in Ethiopia have been facing severe climate related hazards, in particular highly variable rainfall and severe droughts that negativelyaffect their livelihoods.Anticipated climate change is expected to aggravate some of the existing challenges and impose new risks beyond the range of current experiences. This study aimed at understanding current climate variability and future climate change and associated impacts, and providing insights on current climate risk management strategies and future adaptation options for adapting agriculture, in particular maize production.The study was conducted in the Central Rift Valley, which represents major cereal-based farming systems of the semi-arid environments of Ethiopia. A second case study area, Kobo Valley was also used for additional analysis in part of the study. Empirical statistical analyses, field survey methods, and a systems analytical approach, using field experimental data in combination with crop-climate simulation modelling were used to achieve the objectives of the study.Crop growth simulation modelling was carried out using two well-accepted crop models, which is an innovative feature of the methodology used in this thesis.

The analysis revealed that rainfall exhibited high inter-annual variability (coefficient of variation 15-40%) during the period 1977-2007 in the CRV. The mean annual temperature significantly increased with 0.12 to 0.54 oC per decade during 1977-2007. Projections for future climate suggested that annual rainfall will change by -40 to +10% and the annual temperature is expected to increase in the range of 1.4 to 4.1 oC by 2080s. Simulated water-limited yields are characterized by high inter-annual variability (coefficient of variation 36%) and about 60% of this variability is explained by the variation in growing season rainfall. Actual yields of maize in the CRV are only 28-30% of the simulated water-limited yield. Analysis of climate change scenarios showed that maize yield will decrease on average by 20% in the 2050s relative to a baseline climate due to an increase in temperature and a decrease in growing season rainfall. The negative impact of climate change is very likely, however, the extent of the negative impact has some uncertainties ranging from -2 to -29% depending on crop model and climate change scenario. From the selection of models used, it was concluded that General Circulation Models to assess future climate are the most important source of uncertainty in this study.

In response to perceived impacts, farm households are implementing various coping and adaptation strategies. The most important current adaptive strategies include crop selection, adjusting planting time, in situ moisture conservation and income diversification. Lack of affordable technologies, high costs for agricultural inputs, lack of reliable information on weather forecasts, and insecure land tenure systems were identified as limiting factors of farmers’ adaptive capacity. The crop model-based evaluation of future adaptation options indicates that increasing nitrogen fertilization, use of irrigation and changes in planting dates can compensate for some of the negative impacts of climate change on maize production. Developing more heat tolerant and high yielding new cultivars is critical to sustain crop production under future climate change. It was clear from the study that enabling strategies targeted at agricultural inputs, credit supply, market access and strengthening of local knowledge and information services need to become an integral part of government policies to assist farmers in adapting to the impacts of current climate variability and future climate change.

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