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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    Heuvelink, E. ; Okello, R.C.O. ; Peet, M. ; Giovannoni, J.J. ; Dorais, M. - \ 2020
    In: The physiology of vegetable crops / Wien, H.C., Stutzel, H., CABI - ISBN 9781786393777 - p. 138 - 178.
    This chapter focuses on the history and botany, global industry, model plant species, genetics, plant breeding, biotechonology, plant development, vegetative growth, reproductive growth, fruit growth, fruit quality components, and environmental and cultural factors affecting growth and productivity of tomato.
    Vrijwilligers leveren betrouwbare fenologische waarnemingen voor klimaatonderzoek
    Vliet, A.J.H. van; Mehdipoor, Hamed ; Zurita-Milla, Raúl ; Augustijn, Ellen-Wien - \ 2019
    Nature Today
    Uit een nieuwe ruimtelijke analyse van 13 jaar Natuurkalenderwaarnemingen van bloei en bladontplooiing blijkt dat de waarnemingen betrouwbaar zijn. Ze kunnen dus goed gebruikt worden om het effect van klimaatverandering op natuur vast te leggen. Het blijkt ook dat bloei en bladontplooiing veel meer varieert tussen individuele planten van dezelfde soort in warme winters en voorjaren.
    A Successful Model to fight Food Waste. Experiences from EU FUSIONS and REFRESH
    Timmermans, Toine - \ 2018
    Checking the consistency of volunteered phenological observations while analysing their synchrony
    Mehdipoor, Hamed ; Zurita-Milla, Raul ; Augustijn, Ellen-Wien ; Vliet, Arnold J.H. van - \ 2018
    ISPRS International Journal of Geo-Information 7 (2018)12. - ISSN 2220-9964
    Citizen science - Climate change - Constraint satisfaction - Data quality - Geocomputation - Phenology - Synchrony - Volunteered geographical information

    The increasing availability of volunteered geographic information (VGI) enables novel studies in many scientific domains. However, inconsistent VGI can negatively affect these studies. This paper describes a workflow that checks the consistency of Volunteered Phenological Observations (VPOs) while considering the synchrony of observations (i.e., the temporal dispersion of a phenological event). The geographic coordinates, day of the year (DOY) of the observed event, and the accumulation of daily temperature until that DOY were used to: (1) spatially group VPOs by connecting observations that are near to each other, (2) define consistency constraints, (3) check the consistency of VPOs by evaluating the defined constraints, and (4) optimize the constraints by analysing the effect of inconsistent VPOs on the synchrony models derived from the observations. This workflow was tested using VPOs collected in the Netherlands during the period 2003–2015. We found that the average percentage of inconsistent observations was low to moderate (ranging from 1% for wood anemone and pedunculate oak to 15% for cow parsley species). This indicates that volunteers provide reliable phenological information. We also found a significant correlation between the standard deviation of DOY of the observed events and the accumulation of daily temperature (with correlation coefficients ranging from 0.78 for lesser celandine, and 0.60 for pedunculate oak). This confirmed that colder days in late winter and early spring lead to synchronous flowering and leafing onsets. Our results highlighted the potential of synchrony information and geographical context for checking the consistency of phenological VGI. Other domains using VGI can adapt this geocomputational workflow to check the consistency of their data, and hence the robustness of their analyses.

    Auxin regulation of embryo development
    Rios, Alejandra Freire ; Yoshida, Saiko ; Weijers, Dolf - \ 2014
    In: Auxin and Its Role in Plant Development Springer-Verlag Wien - ISBN 9783709115251 - p. 171 - 189.

    Important steps in plant development are made shortly after fertilization. In a brief succession of cell divisions, the zygote is transformed into an embryo, a multicellular structure carrying all fundamental tissue types and the meristems. Hence, embryogenesis offers excellent opportunities to dissect the molecular control and cellular mechanisms underlying plant development. In the past decades, forward and reverse genetics studies have revealed that the plant hormone auxin plays a central role in the establishment of pattern and polarity in the Arabidopsis embryo. Here, we review the roles that localized auxin biosynthesis, directional transport and cell type-specific response play in embryo development. We focus on the molecular mechanisms, as well as the feedbacks that connect these disparate levels of regulation. Finally, we discuss the potential for hormonal cross-talk in auxin-dependent control of the key events during the earliest, formative phase of plant life.

    Introductory Remarks
    Kiefer, F. ; Schulte-Merker, S. - \ 2014
    In: Developmental Aspects of the Lymphatic Vascular System / Kiefer, F., Schulte-Merker, S., Wien : Springer-Verlag (Advances in Anatomy, Embryology and Cell Biology Volume 214) - ISBN 9783709116456 - p. 1 - 4.
    This introductory section briefly highlights the subsequent chapters in the context of recent findings and open questions in lymphatic vessel biology. It aims to provide a quick overview and orientation in the contents of this monograph collection.
    Evaluating OpenMI as a model integration platform across disciplines
    Knapen, M.J.R. ; Janssen, S.J.C. ; Roosenschoon, O.R. ; Verweij, P.J.F.M. ; Winter, W.P. de; Uiterwijk, M. ; Wien, J.J.F. - \ 2013
    Environmental Modelling & Software 39 (2013). - ISSN 1364-8152 - p. 274 - 282.
    simulation - communication - management - frameworks - interface - systems - science
    For decision makers in the domains of agriculture and environment, for instance in government agencies, farmers, environmental NGOs and farmers' unions, it is beneficial to evaluate ex-post or to asses ex-ante the impacts of their choices. To research these interdisciplinary relationships, models developed by different scientific disciplines and often operating at different scales can be integrated into model chains that cover processes across disciplines. In order to assemble models into an operational model chain conceptual, semantic and technical levels of integration have to be taken into account. The main focus of this paper is on technical integration to ensure repeatability and reproducibility of model chain runs and to optimize use of computer hardware for model simulations. Technical integration itself can be achieved by different approaches (i.e. manual, scripting, building or using a proprietary framework, using an open framework based on standards). From the many available modelling frameworks (e.g. OMS, TIME, KEPLER, FRAMES, MODCOM, OpenMI) the emphasis will be on OpenMI, the Open Modelling Interface and its use and usefulness as a readily available, generally accepted and open standards based framework. OpenMI is an open source software standard for dynamically linking models at runtime, which can potentially be used in many domains, but is currently mainly applied in the water and environmental domains. This paper describes and evaluates the use of OpenMI in several multi-disciplinary large projects that worked on integrated models. These projects operated in the disciplines of agriculture, land use, nitrogen cycling, forestry, hydrology and economics. To this end two workshops were organized to acquire feedback from both software developers and modellers that contributed to the aforementioned projects on the use of OpenMI. Perceived advantages and disadvantages of OpenMI differed between modellers and software engineers, although both identified the lack of standard functionality as a major disadvantage and the prescription of a way of working through OpenMI as a standard as a major advantage. In conclusion, OpenMI can be used as a standard for technical model integration across disciplines, and it is not limited to one particular discipline. (C) 2012 Elsevier Ltd. All rights reserved.
    Polysaccharides: Molecular and Supramolecular Structures. Terminology.
    Heinze, Thomas ; Petzold-Welcke, Katrin ; Dam, J.E.G. van - \ 2012
    In: The European Polysaccharide network of Excellence (EPNOE) / Navard, Patrick, Wien : Springer Verlag - ISBN 9783709104200 - p. 23 - 64.
    This chapter summarises important issues about the molecular and supramolecular structure of polysaccharides. It describes the terminology of polysaccharides systematically. The polysaccharides are divided regarding the molecular structures in glucans, polyoses, polysaccharides with amino functions, polysaccharides with acid functions and some miscellaneous. The most important glucans cellulose, (1 → 3)-β-d-glucans, starch, glycogen, dextran and pullulan are discussed. For polyoses, xylans, mannans, xyloglucans and mixed-linkage β-glucans are described. Polysaccharides with amino functions include the description of chitin and chitosan, hyaluronan or hyaluronic acid, glycosaminoglycans and murein. The polysaccharides with acid functions are described including pectins, alginates, agar-agar and carrageenan. Moreover, inulin, levan and xanthan gum are described.
    Bridging the gap between modellers and model users, why does this gap exist and what can we do about it?
    Roosenschoon, O.R. ; Reis, S. ; Turnpenny, J. ; Adele, C. ; Jacob, K. ; Wascher, D. ; Weiland, S. ; Helming, K. ; Podhora, A. ; Wien, J.J.F. - \ 2012
    In: Proceedings of the sixth biannial meeting of the International Environmental Modelling and Software Society. - Leipzig : - ISBN 9788890357428 - p. 1936 - 1943.
    An IT perspective on integrated environmental modelling: The SIAT case
    Verweij, P.J.F.M. ; Knapen, M.J.R. ; Winter, W.P. de; Wien, J.J.F. ; Roller, J.A. te; Sieber, S. ; Jansen, J.M.L. - \ 2010
    Ecological Modelling 221 (2010)18. - ISSN 0304-3800 - p. 2167 - 2176.
    decision-support-systems - management - methodology - interface - issues - tools
    Policy makers have a growing interest in integrated assessments of policies. The Integrated Assessment Modelling (IAM) community is reacting to this interest by extending the application of model development from pure scientific analysis towards application in decision making or policy context by giving tools a higher capability for analysis targeted at non-experts, but intelligent users. Many parties are involved in the construction of such tools including modellers, domain experts and tool users, resulting in as many views on the proposed tool. During tool development research continues which leads to advanced understanding of the system and may alter early specifications. Accumulation of changes to the initial design obscures the design, usually vastly increasing the number of defects in the software. The software engineering community uses concepts, methods and practices to deal with ambiguous specifications, changing requirements and incompletely conceived visions, and to design and develop maintainable/extensible quality software. The aim of this paper is to introduce modellers to software engineering concepts and methods which have the potential to improve model and tool development using experiences from the development of the Sustainability Impact Assessment Tool. These range from choosing a software development methodology for planning activities and coordinating people, technical design principles impacting maintainability, quality and reusability of the software to prototyping and user involvement. It is argued that adaptive development methods seem to best fit research projects, that typically have unclear upfront and changing requirements. The break-down of a system into elements that overlap as little as possible in features and behaviour helps to divide the work across teams and to achieve a modular and flexible system. However, this must be accompanied by proper automated testing methods and automated continuous integration of the elements. Prototypes, screen sketches and mock-ups are useful to align the different views, build a shared vision of required functionality and to match expectations.
    Semantic mediation of an integrated assessment tool for agicultural systems
    Janssen, S.J.C. ; Athanasiadis, I.N. ; Andersen, E. ; Rizzoli, A.E. ; Wien, J.J.F. ; Ittersum, M.K. van - \ 2010
    Using the SEAMLESS Integrated Framework for ex-ante assessment of trade policies
    Bezlepkina, I. ; Adenäuer, M. ; Kuiper, M.H. ; Janssen, S.J.C. ; Knapen, M.J.R. ; Kanellopoulos, A. ; Brouwer, F.M. ; Wien, J.J.F. ; Wolf, J. ; Ittersum, M.K. van - \ 2010
    In: Towards effective food chains; models and applications / Trienekens, J., Top, J., van der Vorst, J., Beulens, A., Wageningen : Wageningen Academic Publishers - ISBN 9789086861484 - p. 251 - 271.
    A web-based software system for model integration in impact assessments of agricultural and environmental policies
    Wien, J.E. ; Rizzoli, A. ; Knapen, M.J.R. ; Athanasiadis, I. ; Janssen, S.J.C. ; Ruinelli, L. ; Villa, F. ; Svensson, M. ; Wallman, P. ; Jonsson, B. ; Ittersum, M.K. van - \ 2010
    In: Environmental and Agricultural Modelling: Integrated Approaches for Policy Impact Assessment / Brouwer, F.M., van Ittersum, M.K., Dordrecht : Springer - ISBN 9789048136186 - p. 207 - 234.
    Probability distribution on the causal bacteria of clinical mastitis in dairy cows using naive Bayesian Networks
    Steeneveld, W. ; Gaag, M.A. van der; Barkema, H.W. ; Hogeveen, H. - \ 2009
    In: EFITA conference ’09 / Bregt, A., Wolfert, S., Wien, J.E., Lokhorst, C., Wageningen : Wageningen Academic Publishers - p. 49 - 56.
    Modeling precision dairy farming technology investment decisions
    Bewley, J.M. ; Boehlje, M.D. ; Gray, A.W. ; Hogeveen, H. - \ 2009
    In: Precision Livestock Farming ‘09 / Bregt, A., Wolfert, S., Wien, J.E., Lokhorst, C., Wageningen : Wageningen Academic Publishers - ISBN 9789086861125 - p. 107 - 14.
    Robust performance: principles and potential application in livestock production systems
    Veen, A.A. van der; Napel, J. ten; Oosting, S.J. ; Bontsema, J. ; Zijpp, A.J. van der; Groot Koerkamp, P.W.G. - \ 2009
    In: Joint International Agricultural Conference,(JIAC2009), Wageningen, The Netherlands, 6-8 July 2009. - Wageningen : Wageningen Academic Publishers - p. 173 - 180.
    Geographic management and monitoring of livestock disease events
    Janssen, H. ; Vanmeulebrouk, B. ; Staritsky, I.G. ; Os, J. van; Wal, T. van der; Leijs, P. - \ 2009
    In: Proceedings of the 7th EFITA Conference, Wageningen, The Netherlands, July 6-8, 2009. - Wageningen : Wageningen Academic Publishers - p. 727 - 734.
    Updated version of final design and of the architecture of SEAMLESS-IF
    Rizzoli, A.E. ; Wien, J.J.F. ; Knapen, M.J.R. ; Ruinelli, L. ; Athanasiadis, I. ; Jonsson, B. - \ 2009
    [S.l.] : SEAMLESS (Report / SEAMLESS no. 47) - ISBN 9789085855903 - 31
    Towards outside-in development of integrated assessment systems
    Knapen, M.J.R. ; Verweij, P.J.F.M. ; Wien, J.J.F. - \ 2009
    In: EFITA conference '09. Proceedings of the 7th EFITA Conference, July 6-8, 2009, Wageningen, The Netherlands. - Wageningen : Academic Publishers - p. 181 - 188.
    OpenMI - The universal glue for integrated modelling?
    Knapen, M.J.R. ; Verweij, P.J.F.M. ; Wien, J.J.F. ; Hummel, S. - \ 2009
    In: 18th World IMACS Congress and MODSIM09 International Congress on Modelling and Simulation, Cairns, Australia, 13 - 17 July, 2009. - Cairns : Modelling and Simulation Society of Australia and New Zealand and International Association for Mathematics and Computers in Simulation - ISBN 9780975840078 - p. 895 - 901.
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