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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Investigating the variance of edge-of-field deposits of spray drift
Holterman, H.J. ; Michielsen, J.M.G.P. ; Stallinga, H. ; Velde, P. van; Zande, J.C. van de - \ 2018
pesticide - statistics - risk assessment - systems analysis
Spray applications in arable crops often lead to off-target spray deposits downwind from the treated field. Throughout several decades, many experiments have been carried out by different researchers to quantify the downwind spray deposits. Relations between downwind spray deposits and parameters like sprayer settings, field conditions and environmental conditions were investigated. Still, there is a large variance in the observed data that cannot be explained satisfactorily by the experimental and environmental conditions. Sprayer boom movements and local fluctuations in driving speed, wind speed and wind direction are the most likely factors affecting variance in downwind spray deposits.
In this study variations in downwind deposits of spray drift caused by sprayer boom movements are investigated both experimentally and based on simulations using the spray drift model IDEFICS. Downwind deposits of spray drift were measured alongside a treated potato field, at 2 m and 5 m off the edge. Wind speed and direction were recorded during the experiments. Horizontal and vertical movements of the sprayer boom were recorded as well. Variance of spray deposits at 2 m downwind from the field edge was about 50%. At 5 m downwind variance was about 30%.
A quasi-dynamic model was developed based on the IDEFICS spray drift model. In the new model the effect of both horizontal and vertical boom movements on downwind spray deposits was studied. From the above mentioned experiments, the most important frequencies and amplitudes of boom movements were derived. Using these frequencies, the model simulations resulted in variances of spray drift deposits similar to those established experimentally. Effects of fluctuating wind directions are to be investigated in the near future.
Exposure assessment for edge-of-field watercourses next to tree nurseries regarding spray drift deposits
Holterman, H.J. ; Zande, J.C. van de - \ 2018
pesticide - statistics - risk assessment - systems analysis - surface water - spatial
Spray applications in arable crops often lead to off-target spray deposits downwind from the treated field. Throughout several decades, many experiments have been carried out by different researchers to quantify the downwind spray deposits. Relations between downwind spray deposits and parameters like sprayer settings, field conditions and environmental conditions were investigated. Still, there is a large variance in the observed data that cannot be explained satisfactorily by the experimental and environmental conditions. Sprayer boom movements and local fluctuations in driving speed, wind speed and wind direction are the most likely factors affecting variance in downwind spray deposits.
In this study variations in downwind deposits of spray drift caused by sprayer boom movements are investigated both experimentally and based on simulations using the spray drift model IDEFICS. Downwind deposits of spray drift were measured alongside a treated potato field, at 2 m and 5 m off the edge. Wind speed and direction were recorded during the experiments. Horizontal and vertical movements of the sprayer boom were recorded as well. Variance of spray deposits at 2 m downwind from the field edge was about 50%. At 5 m downwind variance was about 30%.
A quasi-dynamic model was developed based on the IDEFICS spray drift model. In the new model the effect of both horizontal and vertical boom movements on downwind spray deposits was studied. From the above mentioned experiments, the most important frequencies and amplitudes of boom movements were derived. Using these frequencies, the model simulations resulted in variances of spray drift deposits similar to those established experimentally. Effects of fluctuating wind directions are to be investigated in the near future.
Systems analysis of Mycoplasma hyopneumoniae to improve vaccine production
Kamminga, Tjerko - \ 2017
University. Promotor(en): Vitor Martins dos Santos, co-promotor(en): Peter Schaap; J.J.E. Bijlsma. - Wageningen : Wageningen University - ISBN 9789463436519 - 152
interdisciplinary research - molecular biology - mycoplasma hyopneumoniae - vaccines - systems biology - systems analysis - pigs - pneumonia - animals - interdisciplinair onderzoek - moleculaire biologie - vaccins - systeembiologie - systeemanalyse - varkens - longontsteking - dieren

Mycoplasma hyopneumoniae (M. hyopneumoniae) is a bacterial pathogen that has evolved from a gram-positive ancestor and specifically colonizes the lower respiratory tract of pigs where it causes enzootic pneumonia and plays a major role in the development of respiratory disease in pigs. Whole-cell inactivated vaccines are available that lower the severity of disease and are widely applied in pig industry to prevent clinical signs and improve pig herd health. However, production of these vaccines is challenging because it is not known which bacterial components are needed for protection and complex cultivation media are needed because growth requirements are not completely understood. The aim of this thesis was to understand growth and survival strategies of M. hyopneumoniae during infection, to integrate this knowledge with metabolic modeling under conditions used for vaccine production and apply this knowledge to improve the current production process for M. hyopneumoniae vaccines.

Chapter 1 provides a general introduction into the disease, treatment and prevention methods with a focus on vaccines. I then introduce the characteristics of the M. hyopneumoniae genome, transcriptome and review the current knowledge on infectious mechanisms and the response of the pig to infection and vaccination. Finally, I discuss the challenges related to vaccine production and introduce systems biology tools that will be applied in the thesis. In chapter 2 we define a strategy for risk-based process development of bacterial vaccines which provided the framework for future studies performed during this thesis. We propose to integrate the academic workflow for rational strain design with the industry standard for process design. Systems biology tools, especially genome-scale metabolic models, play an essential role in this strategy because application of these tools reduces process risks and increases process understanding. Therefore, in line with this strategy, we created a manually curated genome-scale metabolic model of M. hyopneumoniae which we applied to dynamically model the cultivation step in the vaccine production process (chapter 3). We found that only 16% of cellular energy in a standard fermentation was used for growth and 84% was used for non-growth associated maintenance. By model-driven experimentation we were able to increase the fraction of cellular energy used for growth by addition of pyruvate to the production medium, and showed in dedicated fermentor experiments that the improved process reached a 2.3 times higher biomass yield. Although the metabolic model helped to increase process yield, it did not allow prediction of a defined cultivation medium without components from porcine origin. Therefore, to better understand the dependency of M. hyopneumoniae on host derived components, we performed a functional comparison of 80 mycoplasma genomes and used multivariate and machine-learning algorithms to relate functional capability to the specific host and niche of mycoplasma species (chapter 4). This analysis allowed us to identify protein domains possibly needed for growth and survival in the pig lung. In addition, we found that protein domains expected to be essential for bacterial growth were not persistently present in mycoplasma genomes suggesting that alternative domain configurations exist that bypass their essentiality. To better understand whether the proteins we identified as possibly important for survival in pigs actually play a role during M. hyopneumoniae infection, we sequenced the bacterial mRNA during infection in chapter 5 and compared the in vivo transcriptome to that of broth grown mycoplasma. We found 22 up-regulated and 30 down-regulated genes during infection (FDR<0.01 and fold change >2LOG2) and identified differentially expressed ncRNAs. In chapter 6 we build upon our mycoplasma basis to further analyse the role of ncRNAs in bacterial genomes. We identified an exponential relationship between the AT content of genomes and the number of ncRNAs and propose that this relation is the result of spurious transcription, which is more likely to occur in AT rich genomes. This hypothesis is further substantiated by showing that spurious transcription demands minimal cellular energy and that overexpression of cis-binding ncRNAs in M. pneumoniae did not influence the level of proteins translated from their overlapping mRNAs. Finally, in chapter 7 I discuss four system strategies, identified in this thesis and derived from recent literature, and discuss how these strategies could be integrated in the metabolic model of M. hyopneumoniae. Lastly, I provide an outlook on the next steps needed for improvement of the production process for M. hyopneumoniae vaccines.

In conclusion, this work provided novel insight in the metabolic capability of M. hyopneumoniae based on the proteome domain content, captured in a genome-scale metabolic model and studied under in vitro and in vivo conditions. Biomass yield of the cultivation step for vaccine production was increased and the basis was laid to further improve the production process for M. hyopneumoniae vaccines using model-based experimentation.

Nat zandlandschap van de 21e eeuw : kennisagenda
Schouten, M.G.C. ; Jansen, A.A.M. ; Tweel-Groot, Loekie van - \ 2016
Landschap : tijdschrift voor Landschapsecologie en Milieukunde 33 (2016)2. - ISSN 0169-6300 - p. 118 - 121.
natuurbeheer - natuurgebieden - biodiversiteit - zandgronden - duurzame ontwikkeling - landschapsecologie - kennismanagement - soortendiversiteit - ecotypen - systeemanalyse - ecosystemen - toegepast onderzoek - bodems van waterrijke gebieden - nature management - natural areas - biodiversity - sandy soils - sustainable development - landscape ecology - knowledge management - species diversity - ecotypes - systems analysis - ecosystems - applied research - wetland soils
Hoe ziet een duurzaam en biodivers nat zandlandschap van de 21e eeuw eruit en hoe ontwikkelen we dat? Dat landschap zal ongetwijfeld een ander zijn dan dat van de 19e en de eerste helft van de 20e eeuw, maar de uitdaging is de totale soortenrijkdom hierin weer voldoende plaats te bieden. Dit artikel biedt een overzicht van de kennis die daartoe ontwikkeld moet worden.
Ecologisch raamwerk voor aquatische ecosystemen
Verdonschot, P.F.M. - \ 2015
Amersfoort : Stowa (Rapport / STOWA 2015-29) - ISBN 9789057737039 - 118
kaderrichtlijn water - aquatische ecologie - ecologische beoordeling - natuurbeleid - waterbeheer - zoetwaterorganismen - ecosystemen - modelleren - systeemanalyse - aquatische ecosystemen - water framework directive - aquatic ecology - ecological assessment - nature conservation policy - water management - freshwater organisms - ecosystems - modeling - systems analysis - aquatic ecosystems
Het doel van de KRW is het in waterlichamen bereiken van de goede ecologische toestand met, vanuit oogpunt van natuurbeleid, een hoge biodiversiteit. Om deze doelen te halen worden maatregelen uitgevoerd. Bij het nemen van maatregelen worden de omstandigheden in oppervlaktewaterecosystemen zo gewijzigd dat een verbetering van de ecologische toestand optreedt. De keuze van maatregelen vraagt kennis van (de toestand van) die factoren en van de achterliggende processen die deze verbetering bewerkstelligen. Om het juiste doel te kunnen bepalen en de juiste maatregelen te kunnen kiezen is begrip nodig van het systeemfunctioneren. Het doel van het ecologisch raamwerk is het geven van een onderbouwing aan de keuze van (kosten-)effectieve en in samenhang probleem-oplossende maatregelen en het afleiden van passende doelen. Om dit doel te bereiken is kennis nodig van de factoren en achterliggende processen die verbetering bewerkstelligen.
Toolkit for a systems analysis framework of the EU bioeconomy : overview of WP2 in the EU FP 7 SAT-BBE project: systems analysis tools framework for the EU Bio-Based Economy Strategy
Leeuwen, M.G.A. van; Meijl, J.C.M. van; Smeets, E.M.W. - \ 2014
Den Haag : LEI Wageningen UR - 30
economische ontwikkeling - monitoring - biobased economy - economische analyse - economische evaluatie - systeemanalyse - analytische methoden - europese unie - economic development - economic analysis - economic evaluation - systems analysis - analytical methods - european union
The objective of the SAT-BBE project is to describe, monitor and model the bioeconomy part of the economic system, by the development of an appropriate conceptual toolkit. In WP1, the concepts of bioeconomy and non-bioeconomy sectors have been defined, the major interactions and feedback effects between the bioeconomy and other parts of the system have been identified and analysed. Also, the likely impacts and trade-offs of the bioeconomy drivers (e.g. economic growth, climate change) have been studied. On its turn, the objective of WP 2 in the SAT-BBE project is to provide an inventory of tools for evaluation and monitoring the EU bioeconomy, according to the data bases required, the indicators available, and the quantitative and qualitative models currently used or under development.
Overview of the Systems Analysis Framework for the EU Bioeconomy. Deliverable 1.4 of the EU FP 7 SAT-BBE project Systems Analysis Tools Framework for the EU Bio-Based Economy Strategy (SAT BBE)
Leeuwen, M.G.A. van; Meijl, H. van; Smeets, E.M.W. ; Tabeau-Kowalska, E.W. - \ 2014
Den Haag : SAT-BBE / LEI Wageningen UR (Report Deliverable 1.4) - 23
economische analyse - biobased economy - economische ontwikkeling - analytische methoden - economische evaluatie - systeemanalyse - europese unie - economic analysis - economic development - analytical methods - economic evaluation - systems analysis - european union
In November 2012 the Systems Analysis Tools Framework for the EU Bio-Based Economy Strategy project (SAT-BBE) was launched with the purpose to design an analysis tool useful to monitoring the evolution and impacts of the bioeconomy. In the SAT-BBE project the development of the analysis tool for the EU bioeconomy strategy is structured in three phases: scoping and definition of the systems analysis framework (WP 1); tools for evaluating and monitoring (WP 2); systems analysis protocols (WP 3).
Panarchy rules? : rethinking resilience of agroecosystems
Apeldoorn, D.F. van - \ 2014
University. Promotor(en): Ken Giller, co-promotor(en): Kasper Kok; Marthijn Sonneveld. - Wageningen : Wageningen University - ISBN 9789461739179 - 137
agro-ecosystemen - duurzaamheid (sustainability) - bedrijfssystemen - organisch bodemmateriaal - wiskundige modellen - systeemanalyse - nederland - zimbabwe - agroecosystems - sustainability - farming systems - soil organic matter - mathematical models - systems analysis - netherlands

This thesis explores the applicability of the resilience perspective on agro-ecosystems dynamics. It start out by using the five heuristics of the resilience perspective on intensive agricultural systems. Simulations with a dynamic farm model suggest that conventional farming short cuts the adaptive cycle leading to an ‘incremental adaptation’ trap. Panarchy is therefore claimed as a leading heuristic to understand long-term dynamics and current management characteristics. This interaction of long-term dynamics with current management leads to an asymmetry in the landscape. This asymmetry leads to windows of opportunities for farmers. However, disregarding the cross-scale nature of the asymmetry might also lead to a cascade of events that undermine the resilience of the landscape as whole. The cross-scale interactions of landscape dynamics and farm management suggest a co-evolution of production intensity and landscape pattern. Moreover trajectories of intensification might even be linked to certain tipping points of combinations of landscape characteristics and management. Therefore the landscape asymmetry might yield insight in agro-ecosystem functioning. The landscape asymmetry potentially provides a level of self-organisation above the farm. However, identifying the asymmetry appeared to be problematic. Next to scale issues, the current pattern does not necessary result from current management, leading to a de-coupling of pattern and process. A re-coupling of management and landscape asymmetry can exploit positive feedbacks. I suggest the use of identity to locate asymmetries and to use space-time substitutions to experiment with the typical slow variables that shape the asymmetry.

The theory developed in this thesis is grounded on empirical farm management data and dynamical model simulation of intensive dairy farming in the Netherlands and small-holder systems in Zimbabwe.

Perspectives in hindsight
Rabbinge, R. - \ 2012
Wageningen : Wageningen University, Wageningen UR - ISBN 9789461731654 - 28
systeemanalyse - hulpbronnenbeheer - voedselzekerheid - duurzaamheid (sustainability) - ontwikkeling - landbouwproductie - systems analysis - resource management - food security - sustainability - development - agricultural production
Klimaatbestendig Nederland : systeemanalyse
Koomen, A.J.M. ; Nieuwenhuizen, W. ; Kater, E. ; Maas, G.J. ; Jansen, P. ; Massop, H.T.L. ; Grashof-Bokdam, C.J. ; Boers, J. - \ 2011
Utrecht : Programmabureau Kennis voor Klimaat - 106
klimaatverandering - klimaatadaptatie - watersystemen - systeemanalyse - climatic change - climate adaptation - water systems - systems analysis
De systeemanalyse waar deze rapportage over gaat, probeert antwoorden te vinden op vragen als: hoe is een systeem opgebouwd?; wat zijn de diverse (hiërarchische) schaalniveaus en hoe is de samenhang tussen deze schaalniveaus?; wat zijn de onderdelen en wat zijn de kenmerken daarvan? En ten slotte hoe werkt het systeem (op diverse schaalniveaus)?
Bewogen toestand : systeemdynamica in het groen
Straten, G. van - \ 2011
Wageningen : Wageningen University - ISBN 9789461731586 - 40
automatische regeling - regeltheorie - regelsystemen - systeemanalyse - dynamisch modelleren - agrotechnologie - automatic control - control theory - control systems - systems analysis - dynamic modeling - agrotechnology
Nutriëntenhuishouding in de bodem en het oppervlaktewater van de Drentse Aa : bronnen, routes en sturingsmogelijkheden
Roelsma, J. ; Grift, B. van der; Mulder, H.M. ; Tol-Leenders, T.P. van - \ 2011
Wageningen : Alterra (Reeks monitoring stroomgebieden 25-I) - 82
stroomgebieden - beekdalen - nutriëntenuitspoeling - oppervlaktewaterkwaliteit - bodemchemie - systeemanalyse - drenthe - watersheds - brook valleys - nutrient leaching - surface water quality - soil chemistry - systems analysis
Deze rapportage richt zich op het stroomgebied de Drentse Aa. Om zicht te krijgen op de nutriëntenhuishouding in het gebied is er vanaf 2004 aanvullend op het reguliere meetnet van het waterschap in het oppervlaktewater gemeten. Voor de interpretatie van deze meetgegevens en het leggen van relaties om de bronnen en transportroutes van nutriënten in beeld te brengen waren modellen en aanvullende metingen noodzakelijk. In dit syntheserapport wordt de nutriëntenhuishouding in de bodem en het oppervlaktewater van de Drentse Aa beschreven, met als doel het totale systeem te doorgronden (waaronder de bronnen en routes van nutriënten in het systeem) en vanuit die positie de sturingsmogelijkheden om de waterkwaliteit te verbeteren aan te geven.
From food production to food security: developing interdisciplinary, regional-level research
Ingram, J.S.I. - \ 2011
University. Promotor(en): Rudy Rabbinge. - [S.l.] : S.n. - ISBN 9789461730022 - 152
voedselproductie - voedselzekerheid - systeemanalyse - interdisciplinair onderzoek - klimaatverandering - landbouwkundig onderzoek - regionale ontwikkeling - multi-stakeholder processen - food production - food security - systems analysis - interdisciplinary research - climatic change - agricultural research - regional development - multi-stakeholder processes
Le lait, de l'or blanc? : amélioration de la productivité des exploitations mixtes cultures-élevage à travers une meilleure gestion et alimentation des vaches laitières dans la zone de Koutiala, Mali
Sanogo, O. - \ 2011
University. Promotor(en): Herman van Keulen; Ken Giller; Nico de Ridder; Mariana Rufino. - S.l. : s.n. - ISBN 9789085859505 - 157
bedrijfssystemen - melkveehouderij - veehouderij - dry farming - dierlijke productie - diervoedering - systeemanalyse - simulatiemodellen - mali - farming systems - dairy farming - livestock farming - animal production - animal feeding - systems analysis - simulation models
Robuustheid
Goede, D.M. de - \ 2010
In: Over zorgvuldige veehouderij. Veel instrumenten, één concert / Eijsackers, H., Scholten, M., Wageningen : Wageningen UR (Essaybundel 2010 ) - ISBN 9789085858959 - p. 104 - 113.
dierenwelzijn - veehouderij - duurzaamheid (sustainability) - systeemanalyse - diergezondheid - dierlijke productie - animal welfare - livestock farming - sustainability - systems analysis - animal health - animal production
Hoewel de term robuustheid steeds vaker wordt gebruikt om een ‘niet-kwetsbare’ staat van een systeem te omschrijven, blijft de precieze betekenis meestal onduidelijk. Robuustheid heeft betrekking op de relatieve kwetsbaarheid van een systeem in relatie tot een specifieke verstoring. Dit essay gaat in op de conceptualisering van robuustheid in de veehouderij en onderzoekt in hoeverre robuustheid kan bijdragen aan een zorgvuldige veehouderij. Drie verschillende robuustheidtoestanden en -strategieën worden gerelateerd aan één extern en twee interne aspecten van systeemkwetsbaarheid, namelijk blootstelling, weerstand en veerkracht. Dit essay beargumenteert dat robuustheid in de veehouderij als systeemeigenschap in enge zin gebruikt wordt op dierniveau in relatie tot dierenwelzijn en diergezondheid, en dat de robuustheidstrategie zich beperkt tot het dierlijke subsysteem en het sociale duurzaamheidaspect
Exploring the potential of high technological and eco-efficient agriculture
Visser, C.L.M. de; Hengsdijk, H. ; Ittersum, M.K. van; Meijerink, G.W. ; Pol, A. van den; Slingerland, M.A. - \ 2010
Wageningen : Applied Plant Research (PPO publication 395) - 154
landbouwproductie - voedselzekerheid - populatiegroei - landbouwkundig onderzoek - duurzaamheid (sustainability) - systeemanalyse - agro-ecologie - agricultural production - food security - population growth - agricultural research - sustainability - systems analysis - agroecology
A framework to introduce flexibility in crop modelling: from conceptual modelling to software engineering and back
Adam, M.Y.O. - \ 2010
University. Promotor(en): Herman van Keulen; J. Wery, co-promotor(en): F.A. Ewert; Peter Leffelaar. - [S.l. : S.n. - ISBN 9789085857648 - 190
systeemanalyse - computersimulatie - wiskundige modellen - computer software - engineering - gewasproductie - gewasopbrengst - systems analysis - computer simulation - mathematical models - crop production - crop yield

Keywords: model structure, uncertainty, modularity, software design patterns, good modelling practices, crop growth and development.

This thesis is an account of the development and use of a framework to introduce flexibility in crop modelling. The construction of such a framework is supported by two main beams: the implementation and the modelling beam. Since the beginning of the 1990s, the implementation beam has gained increasing attention in the crop modelling field, notably with the development of APSIM (Agricultural Production Systems sIMulator) in Australia, OMS (Object Modelling System) in the United States, and APES (Agricultural Production and Externalities Simulator) in Europe. The main focus of this thesis is on the modelling beam and how to combine it with the implementation beam. I first explain how flexibility is adopted in crop modelling and what is required for the implementation beam of the framework, namely libraries of modules representing the basic crop growth and development processes and of crop models (i.e. modelling solutions). Then, I define how to deal with this flexibility (i.e. modelling beam) and more specifically I describe systematic approaches to facilitate the selection of the appropriate model structure (i.e. a combination of modules) for a specific simulation objective. While developing the framework, I stress the need for better documentation of the underlying assumptions of the modules and of the criteria applied in the selection of these modules for a particular simulation objective. Such documentation should help to point out the sources of uncertainties associated with the development of crop models and to reinforce the role of the crop modeller as an intermediary between the software engineer, coding the modules, and the end users, using the model for a specific objective. Finally, I draw conclusions for the prospects of such a framework in the crop modelling field. I see its main contribution to (i) a better understanding in crop physiology through easier testing of alternatives hypotheses, and (ii) integrated studies by facilitating model reuse.



Kennisleemten in de concept-kennisagenda gezien door de bril van systeeminnovatie: de Uitvoeringsagenda centraal
Spoelstra, S.F. - \ 2010
Lelystad : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research 351) - 28
duurzame veehouderij - veehouderij - duurzaamheid (sustainability) - systeemanalyse - kennismanagement - wetenschappelijke methode - innovaties - sustainable animal husbandry - livestock farming - sustainability - systems analysis - knowledge management - scientific method - innovations
An overview is given of 1. research that supports the policies of the Ministry towards sustainable livestock production and 2. initiatives mentioned in the policy agenda. Sustainable Livestock. Based on these overviews gaps in knowledge are identified including system analyses to identify chances and barriers for sustainable development, formulation of concrete visions of integral sustainable livestock production and performance of "real world" experiments to advance sustainable development
29th Benelux Meeting on Systems and Control - Book of Abstracts, Heeze, The Netherlands, 30 March-1 April 2010
Stigter, J.D. ; Meinsma, G. - \ 2010
Wageningen : Wageningen University - ISBN 9789085856726 - 301
automatische regeling - systeemanalyse - systemen - regeltechniek - regeltheorie - regelsystemen - automatic control - systems analysis - systems - control engineering - control theory - control systems
Adaptation science for agriculture : solutions for a changing planet
Meinke, H.B. - \ 2010
Wageningen : Wageningen UR - ISBN 9789085852711 - 32
gewasproductie - plantenfysiologie - plantenecologie - systeemanalyse - agro-ecologie - agro-ecosystemen - crop production - plant physiology - plant ecology - systems analysis - agroecology - agroecosystems
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