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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    Sustainable development of agriculture: contribution of farm-level assessment tools
    Olde, Evelien de - \ 2017
    Wageningen University. Promotor(en): I.J.M. de Boer, co-promotor(en): E.A.M. Bokkers; F.W. Oudshoorn. - Wageningen : Wageningen University - ISBN 9789463430685 - 152
    sustainable agriculture - sustainability - sustainability indicators - sustainability criteria - assessment - tools - reliability - validity - farming systems - duurzame landbouw - duurzaamheid (sustainability) - duurzaamheidsindicatoren - duurzaamheidscriteria - beoordeling - gereedschappen - betrouwbaarheid - geldigheid - bedrijfssystemen

    Current environmental, economic and social challenges urge agriculture to change to more sustainable modes of production. Insight in the impact of a system or a potential innovation on sustainability could support decision makers in identifying actions towards sustainable development. Over the past decade, therefore, a large number of tools have been developed to assess sustainability performance at farm level. Several concerns, however, have been raised whether assessment results provide reliable and valid conclusions about the sustainability performance of farms, and whether these conclusions can be implemented in practice. To evaluate the contribution of farm-level assessment tools to sustainable development of agriculture, this thesis analyzed current approaches to assessing sustainability. One of these approaches is the sustainability assessment tool RISE 2.0, which was used to assess the sustainability performance of 37 organic farms in Denmark. Analysis of the assessment results showed the impact of decisions, made during the development of a tool (e.g. selection of themes, indicators, reference values, scoring and aggregation method), on the assessment results. This emphasizes the importance of transparency in sustainability assessment tools to understand assessment results and identify actions to improve. Subsequently, a comparison of sustainability assessment tools in practice was made to gain insight into practical requirements, procedures and relevance perceived by farmers. Of 48 indicator-based sustainability assessment tools, only four tools (RISE, SAFA, PG and IDEA) complied to the selection criteria and were applied to assess the sustainability performance of five Danish farms. Characteristics including data requirements, assessment time, complexity, transparency and output accuracy varied between tools. Critical factors in farmers’ perception of tool relevance were context specificity, user-friendliness, complexity of the tool, language use, and a match between value judgements of tool developers and farmers. Farmers, moreover, indicated that implementing conclusions derived from sustainability assessments is challenging given the complex organization of agricultural systems. A more in-depth analysis of the four tools revealed a high diversity in selected indicators, themes, reference values, and scoring and aggregation methods. This results in different conclusions on the sustainability performance of farms, which does not only cause confusion but also affects the trust in, and reliability and implementation of, sustainability assessments. Variability in tools is caused by different perspectives on how to assess sustainability and is related to differences in context, priorities and value judgements of tool developers. These differences also play a role in the prioritization of criteria for indicator selection. To explore whether sustainability experts agreed on which criteria are most important in the selection of indicators and indicators sets for sustainability assessments, two ranking surveys were carried out. Both surveys showed a lack of consensus amongst experts about how best to measure agricultural sustainability. This thesis revealed variability in approaches to assess sustainability at farm level. This makes current assessment tools less suitable for functions that require a high reliability and validity, such as certification. Instead, current assessment tools present a useful starting point for discussion, reflection and learning on sustainable development of farming. To enhance the contribution of tools towards sustainable development of agriculture, more attention should be paid to increasing reliability and validity of tools, and improving transparency, harmonization, participation and implementation of assessments.

    Molecular design, synthesis and evaluation of chemical biology tools
    Hoogenboom, Jorin - \ 2017
    Wageningen University. Promotor(en): Han Zuilhof, co-promotor(en): Tom Wennekes. - Wageningen : Wageningen University - ISBN 9789463430388 - 206
    chemical biology - biology - tools - synthesis - organic chemistry - molecules - design - chemische biologie - biologie - gereedschappen - synthese - organische scheikunde - moleculen - ontwerp

    Chapter 1 provides a perspective of synthetic organic chemistry as a discipline involved in the design, synthesis and evaluation of complex molecules. The reader is introduced with a brief history of synthetic organic chemistry, all the while dealing with different aspects of synthetic organic chemistry. These aspects include design, synthesis and evaluation of complex molecules, which are described with representative examples. For instance, chapter 1 described different strategies to design antibiotics like penicillin. Furthermore, efforts at the interface of chemistry and biology has led to the emerging of a new subdisciplines such as chemical biology. Although this discipline is relatively new, the scientific community has witnessed many breakthrough discoveries and some of these discoveries are highlighted in this chapter. After the general introduction presented in chapter 1, the following chapters of this thesis focus on the design, synthesis and evaluation of small molecular probes towards the study of proteins and glycans in plant and mammalian cells. Most of these probes are complex glycomimetic small molecules that in many instances are prepared with a nitrone-olefin [3+2] cycloaddition as a key step.

    In chapter 2, a novel nitrone is presented for the nitrone-olefin [3+2] cycloaddition reaction. This reaction is a powerful tool in synthetic organic chemistry for the synthesis of a wide range of complex molecules. The versatile nature of the reaction is illustrated by the synthesis of several classes of natural product such as vitamins and alkaloids – all complex molecules containing multiple neighboring chiral centers – through the nitrone-olefin [3+2] cycloaddition. However, most nitrones that show good regio- and stereoselectivity are limited in their synthetic versatility, as subsequent synthetic modification of the cycloaddition products are limited. The nitrone described in chapter 2 is a novel masked aldehyde-containing nitrone. This nitrone is prepared by a simple and scalable procedure and can be combined with a diverse set of olefins and other dipolarophiles to afford a broad range of cycloadducts. These cycloadducts can be considered as a masked form of amino-aldehydes, which makes them interesting from a synthetic point of view as illustrated by several postcycloaddition modifications.

    The nitrone-olefin [3+2] cycloaddition is also utilized in chapter 3 for the synthesis of glycomimetic building blocks. Glycomimetics such as iminosugars and pipecolic acids are found in nature and possess a variety of biological activities. The potential of glycomimetics have led to the development of drugs for the treatment of diseases such as type 2 diabetes, Gaucher disease and HIV. Chapter 3 describes how glycomimetic building blocks can be obtained through a nitrone-olefin [3+2] cycloaddition, providing different bicyclic isoxazolidines. These cycloadducts are synthetically versatile, as we report a set of reactions that allow selective modification at each functional position. Accordingly, these versatile bicyclic isoxazolidines enable the synthesis of different glycomimetic building blocks. For example, we were able to make a library of pipecolic acid derivatives – a popular drug-motif – via a one-pot Staudinger/aza-Wittig/Ugi three-component reaction.

    The bicyclic isoxazolidines, discussed in chapter 3, are also reported in chapter 4. This chapter describes the development of a synthetic route towards an activity-based probe (ABP) to study the enzymatic activity of neuraminidases. Neuraminidases are a class of enzymes found in a range of organisms including mammals. The importance of neuraminidases is illustrated by the existence of a neuraminidase-related genetic disease, sialidosis. With no cure for this fatal disease being very limited, there is keen interest in the discovery of novel mechanisms to restore neuraminidase activity. The poor enzyme-activity of a different enzyme-related disease, Gaucher disease, could be improved through the identification of a small molecule that stabilizes and/or promotes the folding of the active enzyme. The validation of this small molecule was aided greatly by the development of a sensitive ABP targeting this disease specific enzyme. Accordingly, the development of a neuramidase-ABP would provide a diagnostic tool to study the activity of neuramidases and ultimately help identify small molecules that could increase the activity of mutant-neuraminidase molecules by stabilizing and/or promoting the folding of this enzyme. The synthesis of a carbocyclic neuraminidase ABP was the goal of chapter 4 and was approached by starting with the nitrone-olefin [3+2] cycloaddition as the key-step. This reaction provided a bicyclic cycloadduct that was used for the development of a synthetic route, which led to a high yielding and practical synthesis of an advance intermediate possessing the majority of the stereochemistry of the required carbocyclic neuraminidase ABP.

    Chapter 5 describes the synthesis and evaluation of chemical tools to study phoshatidyl ethanolamine-binding proteins (PEBPs). This family of proteins is found in a variety of organisms including mammals and plants. This family includes FLOWERING LOCUS T (FT), a signaling protein that acts as a vital flowering hormone in plants. No small molecule inhibitors for FT are known, but an inhibitor called locostatin has been reported to bind in the highly conserved ligand binding site of a structurally related protein. Based on this conservation and overall structurally similarity with FT it was hypothesized that locostatin or derivatives thereof could covalently bind in the ligand binding pocket of FT and hence affect flowering. Chapter 5 reports on the synthesis of novel locostatin-based chemical PEBP probes, followed by evaluation for their ability and selectivity towards FT and a mammalian PEBP.

    Chemical tools were also used to study plants in chapter 6, although different aspects of plants were investigated. This chapter describes the direct molecular imaging of carbohydrates (glycans) in Arabidopsis thaliana. Glycans play a crucial but not fully understood role in plant health and development. The formation of glycans is not genetically encoded, which makes it impossible to image them in vivo using genetically encoded fluorescent tags and related molecular biology approaches. A solution to this problem is the use of tailor-made glycans that are metabolically incorporated in plants via the roots, which may then be visualized with copper-catalyzed click labeling. However, this labelling-technique is toxic to plants and future applications would benefit from bio-orthoganol copper-free labeling techniques. Chapter 6 shows, for the first time in metabolic labeling and imaging of plant glycans, the potential of two copper-free click chemistry methods. These methods are bio-orthogonal and lead to more uniform labeling. Furthermore, this chapter also describes the metabolic incorporation of five novel monosaccharide probes in Arabidopsis thaliana roots and their imaging after (copper-free) fluorescent labeling.

    Finally, chapter 7 contains a general discussion, critically summarizing the body of this thesis along with additional ideas and recommendations for further research.

    Sustainability assessment tools for organic greenhouse horticulture
    Foresi, Lucia ; Schmutz, U. ; Anton, Assumpcio ; Vieweger, Anja ; Bavec, Martina ; Meier, Matthias ; Shadid, Muhammad ; Pena, Nancy ; Petrasek, Richard ; Stajnko, Denis ; Vukamaniĉ, T. ; Landert, Jan ; Weißhaidinger, Rainier ; Meijer, R.J.M. - \ 2016
    [Netherlands] : BioGreenhouse - ISBN 9789462575370 - 50
    greenhouse horticulture - organic farming - tools - life cycle assessment - sustainability - ecological assessment - glastuinbouw - biologische landbouw - gereedschappen - levenscyclusanalyse - duurzaamheid (sustainability) - ecologische beoordeling
    This booklet describes different tools currently employed for sustainability evaluation, according to the field of expertise and experience of the authors. Each method serves a different purpose and covers different aspects of sustainability (environmental, economic, social or all together). This body of work will attempt to show the complexity of assessing sustainability in a comprehensive way, by giving a short background and describing the main features of each tool, and supplying the reader with a practical example of application whenever possible.
    McGraze : Concept model for modern continuous stocking
    Klein Koerkamp, Pim ; Li, Peiyun ; Oostdam, Marieke ; El-Din Sherif, Mohie ; Stienezen, M.W.J. ; Philipsen, A.P. - \ 2015
    Wageningen UR Livestock Research - 31
    dairy farms - grasslands - grazing - pastures - weather - management - stocking density - tools - dairy farming - melkveebedrijven - graslanden - begrazing - weiden - weer - bedrijfsvoering - bezettingsdichtheid - gereedschappen - melkveehouderij
    This report analysed the modern continuous stocking system for dairy farms in the Netherlands. This system has to deal with a minimum grass height of 8 or 10cm (depending on the season) in order to obtain maximum grass production. A model should predict the available herbage mass under changing weather conditions and therefore the available fresh grass and the related amount of additional feed needed for the cows. A concept model, called McGraze, is developed for farmers in order to manage modern continuous stocking (Figure 1). McGraze consists of a grass production section and a stoking related section. The grass production section is based on an existing grass production model called LINGRA, which resulted from a literature review to be the most accurate model to predict grass production. LINGRA needs some minor changes in order to fit into McGraze. The stocking related section is key to the final hours of stocking and the related additional feeding, which are the outputs of McGraze. All values used to predict the outputs are a result of a literature study on grass height, grass quality, grass intake and the effect of stocking on grass growth.
    New tools in modulating Maillard reaction from model systems to food
    Troise, A.D. - \ 2015
    Wageningen University. Promotor(en): Vincenzo Fogliano, co-promotor(en): Claire Berton-Carabin; P. Vitaglione. - Wageningen : Wageningen University - ISBN 9789462575455 - 129
    maillard-reactie - maillard-reactieproducten - modulatie - controle - inkapselen - olijfolie - melk - emulsies - modellen - voedsel - gereedschappen - maillard reaction - maillard reaction products - modulation - control - encapsulation - olive oil - milk - emulsions - models - food - tools
    New tools in modulating Maillard reaction from model systems to food

    The Maillard reaction (MR) supervises the final quality of foods and occupies a prominent place in food science. The first stable compounds, the Amadori rearrangement products (APs) and Heyns rearrangement products (HPs), represent the key molecules from which a myriad of reactions takes place and each of them contributes to the formation of Maillard reaction end-products (MRPs) or advanced glycation end products (AGEs).

    Several papers have dealt with the control of the MR in foods ranging from the thermal loading reduction, to the use of alternative process technologies, reactants impact or enzymes, as well as to the monitoring of the end-products formation by multiresponse modeling. The strategies used up to now aim at common goals: the reduction of potentially toxic compounds and the promotion of desired molecules formation as well as flavor, aroma, color and texture attributes. In other words the ultimate target is the promotion of food quality by tuning the MR.

    This thesis introduces four alternative strategies that are able to control the final extent of the MR in foods.

    The possibility to segregate reactants by encapsulating some minor components and thus delaying the MR was highlighted in Chapter 2. The encapsulation of sodium chloride, ascorbic acid, PUFA and iron inside hydrophobic capsules was used as a possible example: the core material release over the time delayed the reaction rates.

    The results obtained through the treatment with the enzyme fructosamine oxidase (Faox) I and II which is able to deglycate free Amadori products and capitalize the local unfolding of lysine peptide bound residues were reported in Chapter 3. Data showed that Faox can reduce the formation ofNε-(Carboxymethyl)-L-lysine and bound hydroxymethylfurfural in model system and in low lactose milk.

    The effects obtained with the addition of spray-dried olive oil mill wastewaters in milk was illustrated in Chapter 4. This ingredient acts as a source of phenylethanoids, which can trap a-hydroxycarbonyls and a-dicarbonyls and can form adducts with amino groups after the oxidation of phenolic rings into quinone. The use of this functional ingredient before milk thermal treatment resulted in a reduction of off-flavor, reactive carbonyls species and bound MRPs.

    The possibilities offered by the location of MR reactants in microemulsion was investigated in Chapter 5. The oil/water partition coefficient of amino acids played a key role in the formation of Amadori compounds. The anchoring effect of tricaprylin and Tween 20 toward aliphatic amino acids in microemulsion systems was evaluated and compared to a control aqueous solution of amino acids and glucose. Results confirmed the hypothesis: the higher the partition coefficient the lower the formation of aliphatic amino acids Amadori compounds.

    All of the four proposed strategies involved location and interaction of reagents, reactants, intermediates and final products. As a result each strategy depicted a specific route for the control of the final extent of the MR. Many steps are still necessary to scale up these methodologies into the food production chain, however new ways for obtaining foods of superior quality have been paved.

    Protein redesign by learning from data
    Berg, B.A. van den; Reinders, M.J.T. ; Laan, J.M. van der; Roubos, J.A. ; Ridder, D. de - \ 2014
    Protein Engineering, Design & Selection 27 (2014)9. - ISSN 1741-0126 - p. 281 - 288.
    computational enzyme design - aspergillus - stabilization - optimization - generation - prediction - secretion - hydrolase - peptides - tools
    Protein redesign methods aim to improve a desired property by carefully selecting mutations in relevant regions guided by protein structure. However, often protein structural requirements underlying biological characteristics are not well understood. Here, we introduce a methodology that learns relevant mutations from a set of proteins that have the desired property and demonstrate it by successfully improving production levels of two enzymes by Aspergillus niger, a relevant host organism for industrial enzyme production. We validated our method on two enzymes, an esterase and an inulinase, creating four redesigns with 5-45 mutations. Up to 10-fold increase in production was obtained with preserved enzyme activity for small numbers of mutations, whereas production levels and activities dropped for too aggressive redesigns. Our results demonstrate the feasibility of protein redesign by learning. Such an approach has great potential for improving production levels of many industrial enzymes and could potentially be employed for other design goals.
    Introducing Chaetothyriothecium, a new genus of Microthyriales
    Hongsanan, S. ; Chomnunti, P. ; Crous, P.W. ; Chukeatirote, E. ; Hyde, K.D. - \ 2014
    Phytotaxa 161 (2014)2. - ISSN 1179-3155 - p. 157 - 164.
    probability - sequences - bootstrap - inference - alignment - genera - trees - tools
    The order Microthyriales comprises foliar biotrophs, epiphytes, pathogens or saprobes that occur on plant leaves and stems. The order is relatively poorly known due to limited sampling and few in-depth studies. There is also a lack of phylogenetic data for these fungi, which form small black spots on plant host surfaces, but rarely cause any damage to the host. A "Microthyriaceae"-like fungus collected in central Thailand is described as a new genus, Chaetothyriothecium (type species Chaetothyriothecium elegans sp. nov.). Phylogenetic analyses of LSU gene data showed this species to cluster with other members of Microthyriales, where it is related to Microthyrium microscopicum the type of the order. The description of the new species is supplemented by DNA sequence data, which resolves its placement in the order. Little molecular data is available for this order, stressing the need for further collections and molecular data.
    Protein Inference Using Peptide Quantification Patterns
    Lukasse, P.N.J. ; America, A.H.P. - \ 2014
    Journal of Proteome Research 13 (2014). - ISSN 1535-3893 - p. 3191 - 3199.
    spectrometry-based proteomics - quantitative proteomics - tools
    Determining the list of proteins present in a sample, based on the list of identified peptides, is a crucial step in the untargeted proteomics LC-MS/MS data-processing pipeline. This step, commonly referred to as protein inference, turns out to be a very challenging problem because many peptide sequences are found across multiple proteins. Current protein inference engines typically use peptide to spectrum match (PSM) quality measures and spectral count information to score protein identifications in LC-MS/MS data sets. This is, however, not enough to confidently validate or otherwise rule out many of the proteins. Here we introduce the basis for a new way of performing protein inference based on accurate quantification patterns of identified peptides using the correlation of these patterns to validate peptide to protein matches. For the first implementation of this new approach, we focused on (1) distinguishing between unambiguously and ambiguously identified proteins and (2) generating hypotheses for the discrimination of subsets of the ambiguously identified proteins. Our preprocessing pipelines support both labeled LC-MS/MS or label-free LC-MS followed by LC-MS/MS providing the peptide quantification. We apply our procedure to two published data sets and show that it is able to detect and infer proteins that would otherwise not be confidently inferred.
    Reproduction train : hulpmiddel bij inseminatie van zeugen
    Ellen, H.H. ; Classens, P.J.A.M. - \ 2014
    Lelystad : Wageningen UR Livestock Research
    inseminatie - zeugen - inseminatieplaats - dekstallen - medische materialen - gereedschappen - insemination - sows - deposition site - service crates - medical materials - tools
    De Reproduction Train is bedacht door een groep zeugenhouders en samen met hen ontwikkeld bij MS Schippers. Het is een ‘trein’ die op de boxen in de dekstal gemonteerd wordt. Op deze trein kunnen alle materialen die nodig zijn voor het insemineren van de zeugen geplaatst worden, zoals pipetten, koelbox, inseminatie gel, papier enzovoorts. Op deze manier zijn de materialen makkelijk te vervoeren door de stal en heeft men ze dicht bij de hand.
    Characterisation of the transcriptome of Aphelenchoides besseyi and identification of a GHF 45 cellulase
    Kikuchi, T. ; Cock, P.J.A. ; Helder, J. ; Jones, J.T. - \ 2014
    Nematology 16 (2014)1. - ISSN 1388-5545 - p. 99 - 107.
    expressed sequence tags - nematode bursaphelenchus-xylophilus - horizontal gene-transfer - root-lesion nematode - radopholus-similis - plant parasitism - signal peptides - family - technology - tools
    While the majority of Aphelenchoides species are fungivorous, some species are plant parasites that have retained the ability to feed on fungi. Aphelenchoides besseyi is an important and widespread pathogen that causes ‘white tip’ disease on rice. This migratory endoparasitic nematode makes a significant contribution to the estimated $US 16 billion worth of damage caused by nematodes to rice crops. Here we describe a small-scale analysis of the transcriptome of A. besseyi. After sequencing, QC and assembly, approximately 5000 contigs were analysed. Bioinformatic analysis allowed 375 secreted proteins to be identified, including orthologues of proteins known to be secreted by other nematodes. One contig could encode an A. besseyi orthologue of a GHF45 cellulase, similar to those present in Bursaphelenchus xylophilus. No transcripts similar to GHF5 cellulases were present in this dataset.
    Climate adaptation services for the Netherlands: An operational approach to support spatial adaptation planning
    Goosen, H. ; Groot, M.A.M. de; Masselink, L. ; Koekoek, A. ; Swart, R.J. ; Bessembinder, J. ; Witte, J.M.P. ; Stuyt, L.C.M. ; Blom-Zandstra, G. ; Immerzeel, W. - \ 2014
    Regional Environmental Change 14 (2014)3. - ISSN 1436-3798 - p. 1035 - 1048.
    landgebruik - klimaatverandering - landgebruiksplanning - stakeholders - kennisoverdracht - land use - climatic change - land use planning - stakeholders - knowledge transfer - decision-support - design - visualization - thinking - tools - maps - gap
    There is a growing availability of climate change information, offered to scientists and policy makers through climate services. However, climate services are not well taken up by the policy-making and planning community. Climate services focus on primary impacts of climate change, e.g., the disclosure of precipitation and temperature data, and this seems insufficient in meeting their needs. In this paper, we argue that, in order to reach the spatial planning community, climate services should take on a wider perspective by translating climate data to policy-relevant indicators and by offering support in the design of adaptation strategies. We argue there should be more focus on translating consequences of climate change to land-use claims and subsequently discuss the validity, consequences and implications of these claims with stakeholders, so they can play a role in spatial planning processes where much of the climate adaptation takes place. The term Climate Adaptation Services is introduced as being a stepwise approach supporting the assessment of vulnerability in a wider perspective and include the design and appraisal of adaptation strategies in a multi-stakeholder setting. We developed the Climate Adaptation Atlas and the Climate Ateliers as tools within the Climate Adaptation Services approach to support decision-making and planning processes. In this paper, we describe the different steps of our approach and report how some of the challenges were addressed
    Climate proofing of the Zuidplaspolder: a guiding model approach to climate adaptation
    Groot, M.A.M. de; Goosen, H. ; Steekelenburg, M.G.N. van - \ 2014
    Regional Environmental Change 14 (2014)3. - ISSN 1436-3798 - p. 909 - 918.
    polders - klimaatverandering - landgebruiksplanning - modellen - zuid-holland - polders - climatic change - land use planning - models - zuid-holland - vulnerability - sustainability - netherlands - landscape - knowledge - policies - tools - city
    Climate change will have an impact on various sectors, such as housing, infrastructure, recreation and agriculture. Climate change may change spatial demands. For example, rising temperatures will increase the need for recreation areas, and areas could be assigned for water storage. There is a growing sense that, especially at the local scale, spatial planning has a key role in addressing the causes and impacts of climate change. This paper promotes an approach to help translate information on climate change impacts into a guiding model for adaptive spatial planning. We describe how guiding models can be used in designing integrated adaptation strategies. The concept of guiding models has been developed in the 1990s by Tjallingii to translate the principles of integrated water management in urban planning. We have integrated information about the present and future climate change and set up a climate adaptation guiding model approach. Making use of climate adaptation guiding models, spatial planners should be able to better cope with complexities of climate change impacts and be able to translate these to implications for spatial planning. The climate adaptation guiding model approach was first applied in the Zuidplaspolder case study, one of the first major attempts in the Netherlands to develop and implement an integrated adaptation strategy. This paper demonstrates how the construction of climate adaptation guiding models requires a participatory approach and how the use of climate adaptation guiding models can contribute to the information needs of spatial planners at the local scale, leading to an increasing sense of urgency and integrated adaptation planning process
    Managing uncertainty in integrated environmental modelling: The UncertWeb framework.
    Bastin, L. ; Cornford, D. ; Jones, R. ; Heuvelink, G.B.M. ; Pebesma, E. ; Stasch, C. ; Nativi, S. ; Mazzetti, P. - \ 2013
    Environmental Modelling & Software 39 (2013). - ISSN 1364-8152 - p. 116 - 134.
    sensitivity-analysis - parameter-estimation - bayesian-approach - watershed model - climate-change - error - calibration - systems - design - tools
    Web-based distributed modelling architectures are gaining increasing recognition as potentially useful tools to build holistic environmental models, combining individual components in complex workflows. However, existing web-based modelling frameworks currently offer no support for managing uncertainty. On the other hand, the rich array of modelling frameworks and simulation tools which support uncertainty propagation in complex and chained models typically lack the benefits of web based solutions such as ready publication, discoverability and easy access. In this article we describe the developments within the UncertWeb project which are designed to provide uncertainty support in the context of the proposed ‘Model Web’. We give an overview of uncertainty in modelling, review uncertainty management in existing modelling frameworks and consider the semantic and interoperability issues raised by integrated modelling. We describe the scope and architecture required to support uncertainty management as developed in UncertWeb. This includes tools which support elicitation, aggregation/disaggregation, visualisation and uncertainty/sensitivity analysis. We conclude by highlighting areas that require further research and development in UncertWeb, such as model calibration and inference within complex environmental models.
    Scripting for construction of a transactive memory system in multidisciplinary CSCL environments
    Noroozi, O. ; Biemans, H.J.A. ; Weinberger, A. ; Mulder, M. ; Chizari, M. - \ 2013
    Learning and Instruction 25 (2013)1. - ISSN 0959-4752 - p. 1 - 12.
    argumentative knowledge construction - functional roles - group efficiency - convergence - performance - tools
    Establishing a Transactive Memory System (TMS) is essential for groups of learners, when they are multidisciplinary and collaborate online. Environments for Computer-Supported Collaborative Learning (CSCL) could be designed to facilitate the TMS. This study investigates how various aspects of a TMS (i.e., specialization, coordination, and trust) can be facilitated using a transactive memory script that spans three interdependent processes (i.e., encoding, storage, and retrieval) in multidisciplinary CSCL. Sixty university students were assigned to multidisciplinary pairs based on their disciplines (water management or international development). These pairs were randomly assigned to a scripted or non-scripted condition and asked to discuss and solve a problem case. The script facilitated construction of a TMS, fostered learners' knowledge transfer and convergence, and improved the quality of problem solution plans. Specialization and coordination aspects of the TMS were mediators for the impacts of the script on joint but not individual problem solution plans.
    Integrating three lake models into a Phytoplankton Prediction System for Lake Taihu (Taihu PPS) with Python
    Huang, J.C. ; Gao, J.F. ; Hormann, G. ; Mooij, W.M. - \ 2012
    Journal of Hydroinformatics 14 (2012)2. - ISSN 1464-7141 - p. 523 - 534.
    water-quality - framework - interface - ecosystem - issues - tools - china
    In the past decade, much work has been done on integrating different lake models using general frameworks to overcome model incompatibilities. However, a framework may not be flexible enough to support applications in different fields. To overcome this problem, we used Python to integrate three lake models into a Phytoplankton Prediction System for Lake Taihu (Taihu PPS). The system predicts the short-term (1-4 days) distribution of phytoplankton biomass in this large eutrophic lake in China. The object-oriented scripting language Python is used as the so-called 'glue language' (a programming language used for connecting software components). The distinguishing features of Python include rich extension libraries for spatial and temporal modelling, modular software architecture, free licensing and a high performance resulting in short execution time. These features facilitate efficient integration of the three models into Taihu PPS. Advanced tools (e. g. tools for statistics, 3D visualization and model calibration) could be developed in the future with the aid of the continuously updated Python libraries. Taihu PPS simulated phytoplankton biomass well and has already been applied to support decision making.
    Environmental decision support systems (EDSS) development - Challenges and best practices
    McIntosh, B.S. ; Ascough, J.C. ; Twery, M. ; Chew, J. ; Elmahdi, A. ; Haase, D. ; Harou, J.J. ; Hepting, D. ; Cuddy, S. ; Jakeman, A.J. ; Chen, S. ; Kassahun, A. ; Lautenbach, S. ; Matthews, K. ; Merritt, W. ; Quinn, N.W.T. ; Rodriguez-Roda, I. ; Sieber, S. ; Stavenga, M. ; Sulis, A. ; Ticehurst, J. ; Volk, M. ; Wrobel, M. ; Delden, H. ; El-Sawah, S. ; Rizzoli, A. ; Voinov, A. - \ 2011
    Environmental Modelling & Software 26 (2011)12. - ISSN 1364-8152 - p. 1389 - 1402.
    river-basin management - ecosystem management - resource management - united-states - integration - models - tools - information - policy - dss
    Despite the perceived value of DSS in informing environmental and natural resource management, DSS tools often fail to be adopted by intended end users. By drawing together the experience of a global group of EDSS developers, we have identified and assessed key challenges in EDSS development and offer recommendations to resolve them. Challenges related to engaging end users in EDSS development emphasise the need for a participatory process that embraces end users and stakeholders throughout the design and development process. Adoption challenges concerned with individual and organisational capacities to use EDSS and the match between EDSS and organisational goals can be overcome through the use of an internal champion to promote the EDSS at different levels of a target organisation; coordinate and build capacity within the organisation, and; ensure that developers maintain focus on developing EDSS which are relatively easy and inexpensive to use and update (and which are perceived as such by the target users). Significant challenges exist in relation to ensuring EDSS longevity and financial sustainability. Such business challenges may be met through planning and design that considers the long-term costs of training, support, and maintenance; revenue generation and licensing by instituting processes which support communication and interactions; and by employing software technology which enables easy model expansion and re use to gain an economy of scale and reduce development costs. A final group of perhaps more problematic challenges relate to how the success of EDSS ought to be evaluated. Whilst success can be framed relatively easily in terms of interactions with end users, difficulties of definition and measurability emerge in relation to the extent to which EDSS achieve intended outcomes. To tackle the challenges described, the authors provide a set of best practice recommendations concerned with promoting design for ease of use, design for usefulness, establishing trust and credibility, promoting EDSS acceptance, and starting simple and small in functionality terms. Following these recommendations should enhance the achievement of successful EDSS adoption, but more importantly, help facilitate the achievement of desirable social and environmental outcomes.
    Landscape Scenarios and Multifunctionality: Making Land Use Impact Assessment Operational
    Helming, K. ; Perez-Soba, M. - \ 2011
    Ecology and Society 16 (2011)1. - ISSN 1708-3087
    analytical framework - policies - stakeholders - tools - part
    Ex ante impact assessment can help in structuring the analysis of human-environment interactions thereby supporting land use decision making for sustainable development. The contributions to this special feature focus on some of the challenges of making land use impact assessment operational for policy making. A total of nine papers deal with the needs and uses of assessment tools for policy making at the European level, with the value-based influence in scenario development, and with ex ante impact assessment studies in different contexts, spatial systems, and for different purposes and user groups. The concept of landscape multifunctionality was implicitly or explicitly employed as an integrating entity between socioeconomic and biogeophysical features of a spatial system. Three major aspects were revealed that could improve the relevance of the policy of land use impact assessment: the involvement of decision makers early on in the design of the impact assessment study; the integration of quantitative analysis with participatory valuation methods; and the robust and transparent design of the analytical methods.
    Tool voor verdeling rivierwater
    Hellegers, P.J.G.J. - \ 2011
    Kennis Online 8 (2011)augustus. - p. 8 - 8.
    waterbeheer - waterbeschikbaarheid - watervoorziening - landgebruik - beslissingsondersteunende systemen - gereedschappen - gegevens verzamelen - multimedia - afrika - water management - water availability - water supply - land use - decision support systems - tools - data collection - multimedia - africa
    In het stroomgebied van de Inkomati-rivier in zuidelijk Afrika, maken partijen uit drie landen aanspraak op het rivierwater. LEI, Alterra en adviesbureau WaterWatch ontwikkelden met lokale partners een tool die betrokkenen laat zien wat ander landgebruik betekent voor de beschikbaarheid van dat water.
    Perceived effectiveness of environmental decision support systems in participatory planning: Evidence from small groups of end-users
    Inman, D. ; Blind, M. ; Ribarova, I. ; Krause, A. ; Roosenschoon, O.R. ; Kassahun, A. ; Scholten, H. ; Arampatzis, G. ; Abrami, G. ; McIntosh, B.S. ; Jeffrey, P. - \ 2011
    Environmental Modelling & Software 26 (2011)3. - ISSN 1364-8152 - p. 302 - 309.
    bayesian belief networks - management - acceptance - conflict - choice - information - difficulty - impact - tools
    The challenges associated with evaluating the effectiveness of environmental decision support systems (EDSS) based on the perceptions of only a small sample of end-users are well understood. Although methods adopted from Management Information Systems (MISs) evaluation research have benefited from relatively large (100+) sample sizes, permitting the use of multi-criteria analysis of users perceptions, there are few examples of methods for quantifying effectiveness based on smaller groups of end-users. Use of environmental decision support systems in Integrated Water Resources Management (IWRM) has become increasingly prevalent over the passed twenty years, where their potential for facilitating the participatory process has been recognised; however, few quantitative assessments have been reported. This paper reports the application of a quantitative approach to evaluating environmental decision support systems with small groups of end-users in two case studies where the objective was to facilitate the participatory decision-making process in water management projects. The first case study involved nine end-users applying and evaluating a Bayesian network-based tool to facilitate water demand management implementation in Sofia, the capital city of Bulgaria. The second involved eleven end-users applying and evaluating an integrated tool – the Integrated Solution Support System (I3S) - during a water stress mitigation project in a European context. End-users’ perceptions of effectiveness were elicited and compared using statistical analysis. The results of the two case studies suggest that end-user’s employment influences their perceptions of EDSS effectiveness. We also show how the applied evaluation method is flexible enough to assess different EDSS types from a range of dimensions.
    Ex Ante Impact Assessment of Policies Affecting Land Use, Part B: Application of the Analytical Framework
    Helming, K. ; Diehl, K. ; Kuhlman, J.W. ; Bakker, M.M. ; Perez-Soba, M. - \ 2011
    Ecology and Society 16 (2011)1. - ISSN 1708-3087 - 23 p.
    ecosystem services - europe - model - consequences - scenarios - tools
    The use of science-based tools for impact assessment has increasingly gained focus in addressing the complexity of interactions between environment, society, and economy. For integrated assessment of policies affecting land use, an analytical framework was developed. The aim of our work was to apply the analytical framework for specific scenario cases and in combination with quantitative and qualitative application methods. The analytical framework was tested for two cases involving the ex ante impact assessment of: (1) a European Common Agricultural Policy (CAP) financial reform scenario employing a modeling approach and combined with a comprehensive indicator analysis and valuation; and (2) a regional bioenergy policy scenario, employing a fully participatory approach. The results showed that European land use in general is less sensitive to changes in the Common Agricultural Policy, but in the context of regions there can be significant impacts on the functions of land use. In general, the implementation of the analytical framework for impact assessment proved to be doable with both methods, i.e., with the quantitative modeling and with the qualitative participatory approach. A key advantage of using the system of linked quantitative models is that it makes possible the simultaneous consideration of all relevant sectors of the economy without abstaining from a great level of detail for sectors of particular interest. Other advantages lie in the incontestable character of the results. Based on neutral, existing data with a fixed set of settings and regions, an absolute comparability and reproducibility throughout Europe can be maintained. Analyzing the pros and cons of both approaches showed that they could be used complementarily rather than be seen as competing alternatives.
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