Staff Publications

Staff Publications

  • external user (warningwarning)
  • Log in as
  • language uk
  • About

    '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.

    We have a manual that explains all the features 

    Current refinement(s):

    Records 1 - 20 / 100

    • help
    • print

      Print search results

    • export

      Export search results

    Check title to add to marked list
    The emerging accountability regimes for the Sustainable Development Goals and policy integration : Friend or foe?
    Karlsson-Vinkhuyzen, Sylvia ; Dahl, Arthur L. ; Persson, Åsa - \ 2018
    Environment and Planning C: Politics and Space 36 (2018)8. - ISSN 2399-6544 - p. 1371 - 1390.
    Accountability - global - governance - integration - policy - sustainable development

    The 17 Sustainable Development Goals and the full Agenda 2030 in which they are embedded are aspirational and intended to be both transformational and integrative in a number of ways. The need for integration across policy domains is stressed throughout the agenda. The Sustainable Development Goals are also accompanied by an emerging system for follow-up and review centered on a long list of indicators that are intended to enable countries to be accountable towards their citizens. There is, however, in the accountability literature indication that some accountability mechanisms can be counterproductive for integrative policies. This paper is centered around the question whether an accountability regime, and if so how, is compatible with a high degree of policy integration both conceptually and in the context of the Sustainable Development Goals. We approach this question through looking both at the literature on integrative governance and some of the central concepts it covers such as (environmental) policy integration and mainstreaming, and the accountability literature. This enables us to provide an analytical framework for evaluating the potential of the emerging accountability regimes for the Sustainable Development Goals to enhance more integrated policy making and action. We conclude that there are little or no strong hierarchical elements of accountability relationships at the global level which can be good news for more integrative policies – but only if there is a strong sense of shared responsibility among actors at all levels, available information on the types of behavioural efforts that support integration, and accountholders that take an active interest in integration. At the national level, there may be hierarchical accountability mechanisms with sanction possibilities that may discourage integration. Here, those who hold actors to account can counteract this if they have deeper understanding of the underlying interlinkages among the goals and targets, and based on this, engage in accountability mechanisms.

    Framing and integration in the global forest, agriculture and climate change nexus
    Soto Golcher, Cinthia ; Visseren-Hamakers, Ingrid - \ 2018
    Environment and Planning C: Politics and Space 36 (2018)8. - ISSN 2399-6544 - p. 1415 - 1436.
    agriculture - climate change - climate smart agriculture - framing - integration - Integrative Governance - Interplay management - REDD+

    This article contributes to the debate on Integrative Governance by studying integration in the global forest–agriculture–climate change nexus. Since the 1990s, the role of the land-use sector, in particular forests and agriculture, has become increasingly prominent in climate change debates due to its vulnerability and its contribution to global greenhouse gas emissions. Addressing agriculture, climate change and forest policies in an integrated way could therefore create important synergies and reduce trade-offs. This article aims to analyse the extent of integration in current global governance in the nexus of agriculture, forests and climate change, and to explain this extent of integration. Based on the analysis of secondary data, participation in key events and semi-structured interviews, this article concludes that efforts to enhance integration have taken different forms for the different pairs of domains (climate change–agriculture, agriculture–forest, forest–climate change) as well as for the nexus of the three. Integration has been mainly enhanced through soft law, programmes and integrative approaches (e.g. landscape approach, climate smart agriculture, agroforestry). The analysis also shows that the extent of integration among the governance systems has differed. Interplay management efforts on forests and climate change have been relatively successful. Agriculture and forest, and agriculture and climate have low and modest levels of integration respectively, except adaptation in agriculture, which enjoys higher integration levels. Differences in integration can be explained by the medium to high degrees of legalization and the (in)compatibility of the dominant frames present in the different governance systems. Furthermore, our results show that integration in a governance system with a high degree of legalisation, and dominated by one regime, as is the case in climate change, presents important challenges. In such cases, integration might have greater potential outside the intergovernmental regime through soft law approaches.

    A process synthesis approach for isolation of isoflavones from okara
    Jankowiak, L. ; Mendez Sevillano, D. ; Boom, R.M. ; Ottens, M. ; Zondervan, E. ; Goot, A.J. van der - \ 2015
    Industrial & Engineering Chemistry Research 54 (2015)2. - ISSN 0888-5885 - p. 691 - 699.
    driven process synthesis - antioxidant activity - food - adsorption - extraction - separation - products - recovery - integration - components
    Owing to the complexity of food matrices, process synthesis methodologies have not been as widely applied in the food industry as in the chemical industry. Here, we describe the application of a process synthesis methodology to design a system to separate valuable components from a byproduct of the soymilk production. The method yielded a number of potential processing pathways and relevant mechanistic questions, which required experimental input. The combination of considering the overall system on the level of general transformations, heuristics, and additional insights through experiments resulted in a simplified conceptual process design for the separation of isoflavones from okara with a globally more sustainable choice. The holistic approach within process design as an implication of the methodology is discussed.
    Testing for disconnection and distance effects on physiological self-recognition within clonal fragments of Potentilla reptans
    Chen, B. ; Vermeulen, P.J. ; During, H.J. ; Anten, N.P.R. - \ 2015
    Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 9 p.
    herb glechoma-hederacea - fragaria-chiloensis - nutrient availability - kin recognition - rooting volume - pot size - plant - integration - ramets - discrimination
    Evidence suggests that belowground self-recognition in clonal plants can be disrupted between sister ramets by the loss of connections or long distances within a genet. However, these results may be confounded by severing connections between ramets in the setups. Using Potentilla reptans, we examined severance effects in a setup that grew ramet pairs with connections either intact or severed. We showed that severance generally reduced new stolon mass but had no effect on root allocation of ramets. However, it did reduce root mass of younger ramets of the pairs. We also explored evidence for physiological self-recognition with another setup that avoided severing connections by manipulating root interactions between closely connected ramets, between remotely connected ramets and between disconnected ramets within one genet. We found that ramets grown with disconnected neighbors had less new stolon mass, similar root mass but higher root allocation as compared to ramets grown with connected neighbors. There was no difference in ramet growth between closely connected- and remotely connected-neighbor treatments. We suggest that severing connections affects ramet interactions by disrupting their physiological integration. Using the second setup, we provide unbiased evidence for physiological self-recognition, while also suggesting that it can persist over long distances.
    Establishing Guidelines to Retain Viability of Probiotics during Spray Drying
    Perdana, J.A. ; Fox, M.B. ; Boom, R.M. ; Schutyser, M.A.I. - \ 2015
    Drying Technology 33 (2015)13. - ISSN 0737-3937 - p. 1560 - 1569.
    lactobacillus-plantarum wcfs1 - inactivation - integration - isotherms - products - sorption - storage - trends - foods - model
    We present the application of a model-based approach to map processing conditions suitable to spray dry probiotics with minimal viability loss. The approach combines the drying history and bacterial inactivation kinetics to predict the retention of viability after drying. The approach was used to systematically assess the influence of operational co-current spray drying conditions on residual viability. Moreover, two promising alternative drying strategies for probiotics were evaluated involving encapsulation in a hollow particle and using an ‘ideal-mixed’ dryer system. Finally, a graph was constructed with the model to provide visual guidelines to optimize spray dying for probiotics in terms of viability and drying efficiency.
    Prediction of in vivo developmental toxicity of all-trans-retinoic acid based on in vitro toxicity data and in silico physiologycally based kinetic modeling
    Louisse, J. ; Bosgra, S. ; Blaauboer, B.J. ; Rietjens, I. ; Verwei, M. - \ 2015
    Archives of Toxicology 89 (2015)7. - ISSN 0340-5761 - p. 1135 - 1148.
    dose-dependent kinetics - laboratory-animals - response curves - human liver - rat - metabolism - expression - integration - humans - glucuronidation
    The use of laboratory animals for toxicity testing in chemical safety assessment meets increasing ethical, economic and legislative constraints. The development, validation and application of reliable alternatives for in vivo toxicity testing are therefore urgently needed. In order to use toxicity data obtained from in vitro assays for risk assessment, in vitro concentration–response data need to be translated into in vivo dose–response data that are needed to obtain points of departure for risk assessment, like a benchmark dose (BMD). In the present study, we translated in vitro concentration–response data of the retinoid all-trans-retinoic acid (ATRA), obtained in the differentiation assay of the embryonic stem cell test, into in vivo dose–response data using a physiologically based kinetic model for rat and human that is mainly based on kinetic model parameter values derived using in vitro techniques. The predicted in vivo dose–response data were used for BMD modeling, and the obtained BMDL10 values [lower limit of the 95 % confidence interval on the BMD at which a benchmark response equivalent to a 10 % effect size (BMR10) is reached (BMD10)] for rat were compared with BMDL10 values derived from in vivo developmental toxicity data in rats reported in the literature. The results show that the BMDL10 values from predicted dose–response data differ about sixfold from the BMDL10 values obtained from in vivo data, pointing at the feasibility of using a combined in vitro–in silico approach for defining a point of departure for toxicological risk assessment.
    Governance capabilities for dealing wisely with wicked problems
    Termeer, C.J.A.M. ; Dewulf, A. ; Breeman, G.E. ; Stiller, S.J. - \ 2015
    Administration and Society 47 (2015)6. - ISSN 0095-3997 - p. 680 - 710.
    social-ecological systems - common agricultural policy - adaptive governance - framing theory - management - attention - netherlands - transitions - perspective - integration
    This article explores an integrative approach for dealing with wicked problems. Wicked problems not only require alternative action strategies but also alternative ways of observing and enabling. Four governance capabilities are essential: (a) reflexivity, or the capability to deal with multiple frames; (b) resilience, or the capability to adjust actions to uncertain changes; (c) responsiveness, or the capability to respond to changing agendas and expectations; (d) revitalization, or the capability to unblock stagnations. These capabilities form the basis for achieving small wins in wicked problems. We illustrate our argument with examples from sustainable food production of the Common Agricultural Policy.
    Harmonization and translation of crop modeling data to ensure interoperability
    Porter, C. ; Villalobos, C. ; Holzworth, D. ; Nelson, R. ; White, J.W. ; Athanasiadis, I.N. ; Janssen, S.J.C. ; Ripoche, D. ; Cufi, J. ; Raes, D. ; Zhang, M. ; Knapen, M.J.R. ; Sahajpal, R. ; Boote, K. ; Jones, J.W. - \ 2014
    Environmental Modelling & Software 62 (2014). - ISSN 1364-8152 - p. 495 - 508.
    simulate yield response - systems simulation - climate-change - integration - framework - protocols - seamless - nitrogen - openmi
    The Agricultural Model Intercomparison and Improvement Project (AgMIP) seeks to improve the capability of ecophysiological and economic models to describe the potential impacts of climate change on agricultural systems. AgMIP protocols emphasize the use of multiple models; consequently, data harmonization is essential. This interoperability was achieved by establishing a data exchange mechanism with variables defined in accordance with international standards; implementing a flexibly structured data schema to store experimental data; and designing a method to fill gaps in model-required input data. Researchers and modelers are able to use these tools to run an ensemble of models on a single, harmonized dataset. This allows them to compare models directly, leading ultimately to model improvements. An important outcome is the development of a platform that facilitates researcher collaboration from many organizations, across many countries. This would have been very difficult to achieve without the AgMIP data interoperability standards described in this paper.
    Adaptive developmental plasticity: Compartmentalized responses to environmental cues and corresponding internal signals provide phenotypic flexibility
    Mateus, A.R.A. ; Marques-Pita, M. ; Oostra, V. ; Lafuente, E. ; Brakefield, P.M. ; Zwaan, B.J. ; Beldade, P. - \ 2014
    BMC Biology 12 (2014). - ISSN 1741-7007 - 15 p.
    butterfly bicyclus-anynana - color pattern - wing patterns - distal-less - evo-devo - evolution - size - lepidoptera - integration - eyespots
    Background The environmental regulation of development can result in the production of distinct phenotypes from the same genotype and provide the means for organisms to cope with environmental heterogeneity. The effect of the environment on developmental outcomes is typically mediated by hormonal signals which convey information about external cues to the developing tissues. While such plasticity is a wide-spread property of development, not all developing tissues are equally plastic. To understand how organisms integrate environmental input into coherent adult phenotypes, we must know how different body parts respond, independently or in concert, to external cues and to the corresponding internal signals. Results We quantified the effect of temperature and ecdysone hormone manipulations on post-growth tissue patterning in an experimental model of adaptive developmental plasticity, the butterfly Bicyclus anynana. Following a suite of traits evolving by natural or sexual selection, we found that different groups of cells within the same tissue have sensitivities and patterns of response that are surprisingly distinct for the external environmental cue and for the internal hormonal signal. All but those wing traits presumably involved in mate choice responded to developmental temperature and, of those, all but the wing traits not exposed to predators responded to hormone manipulations. On the other hand, while patterns of significant response to temperature contrasted traits on autonomously-developing wings, significant response to hormone manipulations contrasted neighboring groups of cells with distinct color fates. We also showed that the spatial compartmentalization of these responses cannot be explained by the spatial or temporal compartmentalization of the hormone receptor protein. Conclusions Our results unravel the integration of different aspects of the adult phenotype into developmental and functional units which both reflect and impact evolutionary change. Importantly, our findings underscore the complexity of the interactions between environment and physiology in shaping the development of different body parts.
    Fuzzy Cognitive Maps for futures studies : a methodological assessment of concepts and methods
    Jetter, J.J. ; Kok, K. - \ 2014
    Futures 61 (2014). - ISSN 0016-3287 - p. 45 - 57.
    mapping approach - mental models - knowledge - scenarios - stakeholders - integration - management - policy - tool
    Fuzzy Cognitive Map (FCM) modelling is highly suitable for the demands of future studies: it uses a mix of qualitative and quantitative approaches, it enables the inclusion of multiple and diverse sources to overcome the limitations of expert opinions, it considers multivariate interactions that lead to nonlinearities, and it aims to make implicit assumptions (or mental models) explicit. Despite these properties, the field of future studies is slow to adopt FCM and to apply the increasingly solid theoretical foundations and rigorous practices for FCM applications that are evolving in other fields. This paper therefore discusses theoretical and practical aspects of constructing and applying FCMs within the context of future studies: based on an extensive literature review and the authors’ experience with FCM projects, it provides an introduction of fundamental concepts of FCM modelling, a step-wise description and discussion of practical methods and their pitfalls, and an overview over future research directions for FCM in future studies.
    Improving internal communication between marketing and technology functions for successful new food product development
    Jacobsen, L.F. ; Grunert, K.G. ; Søndergaard, H.A. ; Steenbekkers, B. ; Dekker, M. ; Lähteenmäki, L. - \ 2014
    Trends in Food Science and Technology 37 (2014)2. - ISSN 0924-2244 - p. 106 - 114.
    r-and-d - knowledge management - innovation - performance - integration - perspective - industry - projects - flows - teams
    In order to increase the new product development (NPD) success for novel food products, it is crucial to understand how information can be optimally disseminated within companies. This systematic literature review concentrates on factors influencing internal communication between market and technology experts within the NPD process from a food industry point of view. The review provides practical implications for improving internal communication in food companies and identifies knowledge gaps. By focussing on optimising organisational structure, team composition, management support, and knowledge management, food companies can enhance internal communication between market and technology functions during the NPD process.
    Power Europe: EU and the illegal, unreported and unregulated tuna fisheries regulation in the West and Central Pacific Ocean
    Miller, A.M.M. ; Bush, S.R. ; Mol, A.P.J. - \ 2014
    Marine Policy 45 (2014). - ISSN 0308-597X - p. 138 - 145.
    political-economy - integration - policy
    Illegal, unreported and unregulated (IUU) fishing activities are widely considered a main cause of unsustainable fisheries across the globe. The EU has taken a leading role in the fight against IUU fishing, using both its market and normative power to advance its EU IUU Regulation (no. 1005/2008) and wider fisheries sustainability agenda outside its territory. This paper examines how successful the EU has been in using its market and normative power to influence regulatory strategies and frameworks governing tuna fisheries in the Pacific Islands region of the Western Pacific Ocean. The results indicate that while the market power of the EU remains an influential factor, the diminishing normative power of the EU in WCPO is weakening any attempts to implement its IUU fishing regulation and Pacific Island nations have promoted their own regulatory agenda. We conclude that the changing asymmetries between market and normative power has led to a differentiated geography of regulatory uptake, and while market power will remain a dominant strategy for the EU, normative power, when exercised should focus on cooperation rather than ‘teaching’ the benefits of an EU regulatory approach.
    Combinatory Effects of Texture and Aroma Modification on Taste Perception of Model Gels
    Knoop, J.E. ; Sala, G. ; Smit, G. ; Stieger, M.A. - \ 2013
    Chemosensory Perception 6 (2013)2. - ISSN 1936-5802 - p. 60 - 69.
    sensory perception - flavor release - solution viscosity - sugar - fat - integration - odor - hydrocolloids - enhancement - preferences
    In this study, the effects of texture modification and aroma-induced sweetness enhancement were systematically investigated in apple-flavored semi-solid Na-caseinate gels. Gels containing apple juice as a basic flavor were developed differing in stiffness, brittleness and serum release (texture modification), aroma, and sugar concentration (flavor modification). In a full factorial design (2 x 2 x 2), eight samples were evaluated by a sensory panel on ten attributes (five texture, five flavor). Sweetness was enhanced significantly by modification of texture, aroma, and sugar concentration. Texture modification was found to be by far the greatest contributor to overall sweetness. In comparison to texture modifications, aroma modification and changes of sugar concentration resulted only in small sweetness enhancement. When texture and aroma modifications are combined, a small additive effect of aroma modification on sweetness enhancement was found in addition to the sweetness enhancement caused by texture modification. This suggests that the relationship between texture (modification) and flavor (modification) and sweetness is additive in a nonlinear manner. It can be concluded that texture modification is a valid tool to enhance taste intensity. Hence, texture modification can compensate for a loss of sweet taste intensity induced by sugar reduction, while aroma-induced sweetness enhancement can contribute to further taste enhancement in order to develop healthier products.
    Forest inventory stand height estimates from very high spatial resolution satellite imagery calibrated with lidar plots
    Mora, B. ; Wulder, M.A. ; Hobart, G.W. ; White, J.C. ; Bater, C.W. ; Gougeon, F.A. ; Varhola, A. ; Coops, N.C. - \ 2013
    International Journal of Remote Sensing 34 (2013)12. - ISSN 0143-1161 - p. 4406 - 4424.
    airborne scanning laser - tree height - canopy height - stem volume - large-area - integration - landsat - canada - segmentation - update
    Many areas of forest across northern Canada are challenging to monitor on a regular basis as a result of their large extent and remoteness. Although no forest inventory data typically exist for these northern areas, detailed and timely forest information for these areas is required to support national and international reporting obligations. We developed and tested a sample-based approach that could be used to estimate forest stand height in these remote forests using panchromatic Very High Spatial Resolution (VHSR, <1 m) optical imagery and light detection and ranging (lidar) data. Using a study area in central British Columbia, Canada, to test our approach, we compared four different methods for estimating stand height using stand-level and crown-level metrics generated from the VHSR imagery. 'Lidar plots' (voxel-based samples of lidar data) are used for calibration and validation of the VHSR-based stand height estimates, similar to the way that field plots are used to calibrate photogrammetric estimates of stand height in a conventional forest inventory or to make empirical attribute estimates from multispectral digital remotely sensed data. A k-nearest neighbours (k-NN) method provided the best estimate of mean stand height (R-2 = 0.69; RMSE = 2.3 m, RMSE normalized by the mean value of the estimates (RMSE-%) = 21) compared with linear regression, random forests, and regression tree methods. The approach presented herein demonstrates the potential of VHSR panchromatic imagery and lidar to provide robust and representative estimates of stand height in remote forest areas where conventional forest inventory approaches are either too costly or are not logistically feasible. While further evaluation of the methods is required to generalize these results over Canada to provide robust and representative estimation, VHSR and lidar data provide an opportunity for monitoring in areas for which there is no detailed forest inventory information available.
    Improving dryer energy efficiency and controllability simultaneously by process modification
    Atuonwu, J.C. ; Straten, G. van; Deventer, H.C. van; Boxtel, A.J.B. van - \ 2013
    Computers and Chemical Engineering 59 (2013). - ISSN 0098-1354 - p. 138 - 144.
    desiccant adsorption - optimization - design - integration - model - bed
    This work establishes a relationship between dryer energy performance and controllability using energy balances and process resiliency analysis. It is shown that using the process gain matrix, the dryer energy efficiency can be reliably calculated with conditions for simultaneous controllability improvement established. By incorporating a drying rate modifying system such as a desiccant dehumidifier as an add-on, these conditions are shown to be achievable due to the extra dehumidification which can be manipulated using the additional degrees of freedom introduced by the sorption system. Due to the adsorbent regulation properties which are enhanced by high-temperature regeneration, the resilience of energy performance to disturbances is significantly improved compared to conventional dryers. Also, a desiccant system performance indicator, the “adsorber–regenerator net energy efficiency ARNEE” is introduced and it is shown that energy efficiency improvement is possible only if the ARNEE is greater than the energy efficiency of the stand-alone dryer.
    Constraints on agricultural production in the Northern Uplands of Vietnam
    Bui Tan, Y. ; Visser, S.M. ; Hoanh, C.T. ; Stroosnijder, L. - \ 2013
    Mountain Research and Development 33 (2013)4. - ISSN 0276-4741 - p. 404 - 415.
    natural-resource management - land evaluation - fertility - system - suitability - integration - simulation - options
    The Northern Uplands of Vietnam form one of the largest ecological regions in the country, characterized by complex biophysical conditions and a high diversity in ethnic minorities, cultures, and farming systems. The Doi moi (“renovation”) program has, since the early 1980s, resulted in significant changes in agriculture production and related economic trends. However, poverty, low agricultural productivity, and land degradation are still major problems. This article illustrates the factors that drive these problems by analyzing agricultural land use in Suoi Con, a small agroforestry watershed in the Northern Uplands. We first identified the current land-use systems and analyzed constraints on agricultural production. The results indicate that although low soil fertility and land degradation are considerable problems, availability of household capital, low technology levels, and land fragmentation are major constraints on agricultural development. These constraints were analyzed from different points of view to identify mismatches between the implementation of top-down government policies and specific conditions that may explain why actual land-use change in the Northern Uplands deviates from the government's development plans. Results of land-use analysis in the Suoi Con watershed suggest that participatory and bottom-up approaches are needed to better understand problems and opportunities in household agricultural production in order to develop appropriate land-use plans and policies.
    Comparative genomic analysis of twelve Streptococcus suis (pro)phages
    Tang, F. ; Bossers, A. ; Harders, F.L. ; Lu, C. ; Smith, H.E. - \ 2013
    Genomics 101 (2013)6. - ISSN 0888-7543 - p. 336 - 344.
    listeria-monocytogenes - serotype 14 - bacteriophage - phage - protein - sequence - strains - integration - virulence - system
    Streptococcus suis (S. suis) is an important pathogen that can carry prophages. Here we present a comparative genomic analysis of twelve (pro)phages identified in the genomes of S. suis isolates. According to the putative functions of the open reading frames predicted, all genomes could be organized into five major functionally gene clusters involved in lysogeny, replication, packaging, morphogenesis and lysis. Phylogenetic analyses of the prophage sequences revealed that the prophages could be divided into five main groups. Whereas the genome content of the prophages in groups 1, 2 and 3 showed quite some similarity, the genome structures of prophages in groups 4 and 5 were quite distinct. Interestingly, several genes homologous to known virulence factors, including virulence associated protein E, a toxin-antitoxin system, a Clp protease and a DNA methyltransferase were found to be associated with various (pro)phages. This clearly indicates that these (pro)phages can contribute to the virulence of their hosts.
    Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes
    Kourmpetis, Y.A.I. ; Dijk, A.D.J. van; Braak, C.J.F. ter - \ 2013
    Algorithms for Molecular Biology 8 (2013)1. - ISSN 1748-7188
    arabidopsis-thaliana - integration - annotation - regression - network - classification - association - terms - tool
    Gene Ontology (GO) is a hierarchical vocabulary for the description of biological functions and locations, often employed by computational methods for protein function prediction. Due to the structure of GO, function predictions can be self- contradictory. For example, a protein may be predicted to belong to a detailed functional class, but not in a broader class that, due to the vocabulary structure, includes the predicted one.We present a novel discrete optimization algorithm called Functional Annotation with Labeling CONsistency (FALCON) that resolves such contradictions. The GO is modeled as a discrete Bayesian Network. For any given input of GO term membership probabilities, the algorithm returns the most probable GO term assignments that are in accordance with the Gene Ontology structure. The optimization is done using the Differential Evolution algorithm. Performance is evaluated on simulated and also real data from Arabidopsis thaliana showing improvement compared to related approaches. We finally applied the FALCON algorithm to obtain genome-wide function predictions for six eukaryotic species based on data provided by the CAFA (Critical Assessment of Function Annotation) project
    A systematic approach for re-assembly of crop models: An example to simulate pea growth from wheat growth
    Adam, M.Y.O. ; Wery, J. ; Leffelaar, P.A. ; Ewert, F. ; Corbeels, M. ; Keulen, H. van - \ 2013
    Ecological Modelling 250 (2013). - ISSN 0304-3800 - p. 258 - 268.
    nitrogen nutrition - expert knowledge - use efficiency - water-deficit - legume - apsim - integration - parameters - frameworks - selection
    The process of crop modelling to develop operational software requires different skills, from conceptualization of the biophysical system to computer programming, involving three main scientific disciplines: agronomy, mathematics, and software engineering. Model building implies transforming a conceptual model into sets of mathematical equations and then translating these equations into a computer program. Although recent crop modelling frameworks can technically support model building, the modelling process is not always well documented and difficult to repeat. The focus of this paper is therefore on developing and documenting an approach to re-assemble crop models, i.e. develop a new model from an existing one, using a crop modelling framework and crop physiological knowledge. Modifications to an initial crop model were classified according to three categories: (i) changes in parameter values, (ii) changes in equations, and (iii) changes in overall model structure. We illustrate the approach with a case study transforming a wheat crop model into a pea crop model. We discuss the role of each actor in the process to document diverse uncertainties related to the model (i.e. contextual situation, data, structure), and the general applicability of the approach for different crop modelling frameworks. We conclude that the use of our approach to re-assemble a crop model within a modelling framework facilitates integration of different disciplines around a modelling objective, and facilitates creating transparent and reproducible models
    Care Farms in the Netherlands: An Underexplored Example of Multifunctional Agriculture—Toward an Empirically Grounded, Organization-Theory-Based Typology
    Hassink, J. ; Hulsink, W. ; Grin, J. - \ 2012
    Rural Sociology 77 (2012)4. - ISSN 0036-0112 - p. 569 - 600.
    rural-development - diversification - configurations - pluriactivity - strategy - arrangements - integration - management - resources - pathways
    For agricultural and rural development in Europe, multifunctionality is a leading concept that raises many questions. Care farming is a promising example of multifunctional agriculture that has so far received little attention. An issue that has not been examined thoroughly is the strategic mapping of different care farm organizations in this emerging field. The objective of this article is to develop a typology for care farms in the Netherlands and provide insight into the diversity of care farms. We have used different concepts from organization theory and information from regional organizations of care farmers to identify key dimensions and develop a typology of care farms. Key dimensions are the ratio between agriculture and care, the background of the initiators, and the degree of collaboration with formal care institutions. We found six main types of care farms with different identities, four of which were initiated by the farmers' families (mainly female partners). The other two types were started by new entrants in agriculture. On the basis of our findings, we confirmed, disputed, and supplemented insights to multifunctional farming literature. As a further contribution to that field, drawing from the organization theories underlying our typology, we have sought to understand how different types of care farms could emerge.
    Check title to add to marked list
    << previous | next >>

    Show 20 50 100 records per page

    Please log in to use this service. Login as Wageningen University & Research user or guest user in upper right hand corner of this page.