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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    An economic approach to non-animal toxicity testing for skin sensitisation
    Leontaridou, Maria - \ 2017
    Wageningen University. Promotor(en): E.C. van Ierland, co-promotor(en): S.G.M. Gabbert; R. Landsiedel. - Wageningen : Wageningen University - ISBN 9789463431361 - 151
    animal testing alternatives - toxicity - testing - sensitivity - sensitivity analysis - bayesian theory - alternatieven voor dierproeven - toxiciteit - testen - gevoeligheid - gevoeligheidsanalyse - bayesiaanse theorie

    Chemicals applied in products, such as food products, pharmaceuticals or cosmetics, create great benefits in society while posing risks to human health and the quality of the environment. To control those risks, it is mandatory to perform risk assessments of chemicals which require information on their hazardous properties. To meet these information requirements without sacrificing large numbers of animal tests, many non-animal testing methods and strategies have become available. Given the increasing needs for assessing chemicals’ risks, toxicity testing has become costly in terms of testing costs, time and animal welfare.

    Focusing on skin sensitisation as a case study, this thesis aims at introducing an economic approach towards the optimisation of toxicity testing strategies. Chapter 2 surveys the current status of non-animal toxicity testing strategies assessing skin sensitisation and compares criteria suggested in the toxicological literature with the conceptual and informational criteria introduced in this chapter for increasing resource-efficiency in the development of testing strategies. Chapter 3 extends to the development of a Bayesian Value-of-Information model for the optimisation of non-animal toxicity testing strategies. This optimisation model is applied to construct optimal non-animal toxicity testing strategies for the assessment of skin sensitisation potential.

    Chapter 4 focuses on the precision of testing methods and the impact of limited precision on the evaluation of test results. The borderline range of testing methods is quantified and applied as an additional evaluation measure in the prediction models of testing methods to identify substances as positive and negative (for substances yielding clear-cut test results), or as discordant (for substances yielding test results within the borderline range). Chapter 5 addresses the uncertainties underlying the predictive accuracy metrics for non-animal testing methods due to their limited precision, the sample size and composition of the samples of chemicals used to estimate the predictive capacity of testing methods. Chapters 4 and 5 focus on non-animal testing methods for the assessment of skin sensitisation potential.

    This thesis concludes that introducing the economic perspective into the construction of toxicity testing strategies is necessary to develop the means by which resource-efficiency in toxicity testing is achieved. Furthermore, the evaluation of testing methods should consider both predictivity and precision limitations such that decision makers can draw robust conclusions on the hazardous properties of chemicals.

    The origin, versatility and distribution of azole fungicide resistance in the banana black Sigatoka pathogen Pseudocercospora fijiensis
    Chong Aguirre, Pablo A. - \ 2016
    Wageningen University. Promotor(en): Gert Kema; Pedro Crous. - Wageningen : Wageningen University - ISBN 9789462578791 - 289
    pseudocercospora - plant pathogenic fungi - fungicides - pesticide resistance - defence mechanisms - genetic diversity - genetic mapping - sensitivity - musa - bananas - fungal diseases - disease control - pseudocercospora - plantenziekteverwekkende schimmels - fungiciden - resistentie tegen pesticiden - verdedigingsmechanismen - genetische diversiteit - genetische kartering - gevoeligheid - musa - bananen - schimmelziekten - ziektebestrijding

    Pseudocercospora fijiensis causes black Sigatoka disease of banana. It is one of the most damaging threats of the crop requiring excessive fungicide applications for disease control as the major export “Cavendish” clones are highly susceptible. The consequence of this practice is the reduced efficacy of disease management strategies due to increasing levels of fungicide resistance. In this thesis the history and current practices of black Sigatoka disease management as well as the underlying mechanisms of fungicide resistance to a major group of fungicides are described. We discovered that both target site mutations and promotor insertions are crucial for modulating sensitivity. The more insertions, the higher the expression of the gene and the more resistant the strain. Using this information, we advocate modern monitoring techniques and improved disease control strategies as well as the urgent need for innovative banana breeding to develop resistant varieties for a sustainable global banana production.

    Koudeschade afhankelijk van samenstelling celmembraan : groot verschil in gevoeligheid tussen gewassen
    Heuvelink, E. ; Kierkels, T. - \ 2014
    Onder Glas 11 (2014)6/7. - p. 24 - 25.
    glastuinbouw - kasgewassen - potplanten - koudebeschadiging - temperatuur - celmembranen - samenstelling - gevoeligheid - greenhouse horticulture - greenhouse crops - pot plants - chilling injury - temperature - cell membranes - composition - sensitivity
    De kassen staan vol met sub-tropische en soms tropische gewassen. Die houden niet zo van kou. Of er daadwerkelijk schade optreedt, hangt niet alleen af van de temperatuur maar ook van de duur van de kouval. De verschillen tussen gewassen in vatbaarheid voor kou zijn groot; die blijkt af te hangen van de samenstelling van de celmembranen.
    The sensitivity of tropical forests to climate variability and change in Bolivia
    Seiler, C. - \ 2014
    Wageningen University. Promotor(en): Pavel Kabat, co-promotor(en): Ronald Hutjes; Bart Kruijt. - Wageningen : Wageningen University - ISBN 9789461739230 - 157
    tropische bossen - klimaatverandering - gevoeligheid - klimaat - remote sensing - koolstof - bolivia - tropical forests - climatic change - sensitivity - climate - remote sensing - carbon - bolivia
    Breeding for quality of button mushrooms: genetically dissecting bruising sensitivity and quality-related traits of Agaricus bisporus
    Gao, W. - \ 2014
    Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Anton Sonnenberg; Johan Baars. - Wageningen : Wageningen University - ISBN 9789461739018 - 174
    agaricus bisporus - eetbare paddestoelen - plantenveredeling - kneuzen - gevoeligheid - loci voor kwantitatief kenmerk - kwaliteit - kenmerken - genetische analyse - agaricus bisporus - edible fungi - plant breeding - bruising - sensitivity - quantitative trait loci - quality - traits - genetic analysis

    The present-day cultivars of button mushroom are too sensitive to mechanical damage. Consequently, mushrooms for the fresh market are still handpicked, which is a main cost factor for the Dutch mushroom industry. The main objective of this thesis is to use the phenotypic variation and segregation to study the genetic determinants explaining the differences in bruising sensitivity and generate breeding stocks that can be used to construct commercial varieties that are suitable for mechanical harvest. In addition, the genetic basis of other quality-related traits was investigated. For this, segregating populations were generated and used to study in more detail the life cycle of the bisporicvariety. The availability of the whole genome sequence allowsa more detailed study of recombination frequencies generating knowledge invaluable for further mushroom breeding.

    Snow shoes and sandals? : genetic aspects of heat stress sensitivity and sow reproduction
    Bloemhof, S. - \ 2013
    Wageningen University. Promotor(en): Johan van Arendonk; I. Misztal, co-promotor(en): E.F. Knol; Liesbeth van der Waaij. - S.l. : s.n. - ISBN 9789461735881 - 173
    zeugen - warmtestress - diergenetica - gevoeligheid - geslachtelijke voortplanting - voortplantingsvermogen - kritische temperatuur - hittetolerantie - selectief fokken - genetische correlatie - veredelingsprogramma's - varkensfokkerij - sows - heat stress - animal genetics - sensitivity - sexual reproduction - reproductive performance - critical temperature - heat tolerance - selective breeding - genetic correlation - breeding programmes - pig breeding

    Globally the average size of pig herds are increasing and amount of labour spent per sow / finisher pig is decreasing. These changes require sows which need less management interventions. In addition to easier manageable sows modern genotypes will also need to be more adaptable considering that global temperatures are expected to increase and pork production is partially moving to warmer climates. The end result is that commercial pigs nowadays will potentially face more heat stress challenges during their productive lives.

    In this thesis, a model was developed which was used to estimate upper critical temperatures for sows’ reproductive performance. Additionally the possibility to breed for reduced heat tolerance of sows was investigated. Therefore heritability for the random regression slope of farrowing rate against increasing temperature at day of insemination (= heat tolerance) and the genetic correlation between farrowing rate and heat tolerance was estimated.Commercial production pigs are crossbreds farmed all over the world. In contrast, selection is practiced mainly in temperate climates, in nucleus herds using purebred pigs. The success of genetic selection depends on how much genetic progress is realized in crossbred pigs. Within this thesis these genetic correlations for farrowing rate between purebreds and crossbreds were estimated.

    Sow productivity depends on a number of related traits, such as ovulation rate, the number of litters per sow per year, the number of weaned piglets per sow per year, and the length of productive live. Traditionally pig breeding programs have improved sow productivity by increasing number weaned piglets per sow per year. To improve herd-level litters per sow per year a new trait was proposed called problem free sow production by parity, which incorporates the traits interval weaning first insemination, non-return rate, farrowing rate, and selection for next parity. Heritability of problem free sow production and genetic correlations with other sow production traits were estimated.

    The main conclusion of this thesis was that it is possible to select for improved heat resistance in addition to improved commercial production levels in commercial pigs. However, genetic correlation between production in temperate and hot climates is high. This high correlation implies that, within-line, pigs with the best performance in a hot climate will be the best in temperate climate too. Most important for the success of a pig breeding program is to define appropriate breeding goals which are based on the environment(s) that market pigs are expected to perform in. The overall data collection for the genetic evaluation needs to be done in those specific environments and this will favour pigs which are able to produce over more than one specific environment.

    Natuurdoelen en klimaatverandering : "State-of-the-Art"
    Lototskaya, A.A. ; Geertsema, W. ; Griffioen, A.J. ; Veen, M. van der; Verdonschot, P.F.M. - \ 2011
    Wageningen : Alterra (Alterra-rapport 2135) - 156
    natuurbescherming - klimaatverandering - natuurbeleid - aquatische ecosystemen - terrestrische ecosystemen - adaptatie - veerkracht van de natuur - gevoeligheid - nederland - nature conservation - climatic change - nature conservation policy - aquatic ecosystems - terrestrial ecosystems - adaptation - resilience of nature - sensitivity - netherlands
    Er bestaat geen twijfel meer over dat klimaatverandering belangrijke gevolgen zal hebben voor de Nederlandse natuur. Enerzijds is veel bekend over de directe mechanismen van klimaatverandering en anderzijds over de ecologische eigenschappen van organismen, maar het Nederlandse beleid vraagt kennis over de specifieke gevolgen van klimaatverandering op de natuurdoelen. Wat zijn de achterliggende mechanismen van klimaatverandering in relatie tot aquatische en terrestrische ecosystemen? Dit rapport biedt een gestructureerd overzicht van directe gevolgen van klimaatverandering voor natuurdoelen en adaptatiemaatregelen voor aquatische en terrestrische natuur. Het rapport beschrijft landschapsecologische processen en functionele relaties in aquatische en terrestrische ecosystemen onder invloed van klimaatverandering, de invloed van nieuwe soortgroepen daarin, analyseert de kwetsbaarheid van natuurdoelen voor klimaatverandering en geeft een overzicht van adaptatie-maatregelen.
    Zuur in tulp : optimaal pelmoment afhankelijk van ethyleen
    Dam, M.F.N. van; Kreuk, Frank - \ 2011
    bloembollen - ethyleen - gevoeligheid - zuurbehandeling - informatieontsluiting - ornamental bulbs - ethylene - sensitivity - acid treatment - information retrieval
    Informatieposter over zuur in tulp; optimaal pelmoment afhankelijk van ethyleen
    Achter ‘hooikoortsplant’schuilt gezondheidsgevaar; doortesten op specifiek IgE tegen ambrosia blijkt noodzakelijk
    Vliet, A.J.H. van - \ 2010
    News Reporter / Siemens Diagnostics 6 (2010). - p. 14 - 15.
    ambrosia - onkruiden - invasie - geïntroduceerde soorten - allergieën - volksgezondheid - gevoeligheid - hooikoorts - groeiplaatsen - klimaatverandering - ambrosia - weeds - invasion - introduced species - allergies - public health - sensitivity - pollen allergy - sites - climatic change
    Is sensibilisatie voor ambrosiapollen een kruisreactie met de inheemse bijvoet, of zorgt de opkomst van de exoot wel degelijk voor een verlenging van het hooikoortsseizoen? Klinisch chemicus Cees Beijer van het Rijnland Ziekenhuis in Leiderdorp en het Diaconessenhuis in Leiden onderzocht de kruisreactiviteit van de allergenen. Conclusie: sensibilisatie voor specifieke allergenen van ambrosia kan ook in Nederland een probleem worden.
    Functional aspects of baculovirus DNA photolyases
    Xu, F. - \ 2010
    Wageningen University. Promotor(en): Just Vlak, co-promotor(en): Monique van Oers. - [S.l. : S.n. - ISBN 9789085857730 - 112
    baculoviridae - organismen ingezet bij biologische bestrijding - insectenplagen - fotolyse - chrysodeixis chalcites - kernpolyedervirussen - lyasen - genen - genexpressie - fylogenetica - lokalisatie - ultraviolette straling - eiwitexpressieanalyse - gevoeligheid - baculoviridae - biological control agents - insect pests - photolysis - chrysodeixis chalcites - nuclear polyhedrosis viruses - lyases - genes - gene expression - phylogenetics - localization - ultraviolet radiation - proteomics - sensitivity
    Keywords: baculovirus, ChchNPV, CPD photolyase, phylogeny, UV resistance, DNA binding, localization, proteomics

    Baculoviruses are insect viruses that are applied as biological control agents due to adequate virulence, host specificity and safety for the environment. Solar light negatively affects field performance of baculoviruses by reducing their infectivity, most likely as a consequence of the formation of cyclobutane pyrimidine dimers (CPDs) in the viral DNA upon ultraviolet (UV) irradiation. CPDs can be repaired by CPD photolyases when exposed to blue light photons, a process called photoreactivation. From previous work it was known that the Cc-phr2 gene of the baculovirus Chrysodeixis chalcites nucleopolyhedrovirus (ChchNPV) encodes a biochemically active photolyase. The research in this thesis focuses on (i) the degree of conservation of CPD photolyase (phr) genes in a subgroup of baculoviruses, (ii) the localization of baculovirus photolyase proteins in insect cells and occlusion derived virus (ODV), and (iii) the in vivo effect of phr genes on the UV sensitivity of baculoviruses. Homologues of the Cc-phr genes were found in all studied group II NPVs in the genus Alphabaculovirus that infect insects in the subfamily Plusiinae insects. Phylogenetic analysis suggested that these phr-like genes have a common ancestor. Intracellular localization of the two ChchNPV encoded PHR proteins in insect cells was studied using enhanced GFP fusion. Both PHR1 and PHR2 localized in the nucleus and associated with chromosomes, spindle, aster and midbody structures during host cell mitosis. Moreover, Cc-PHR2 co-localized with virogenic stroma, when PHR2-EGFP-transfected cells were infected with Autographa californica (Ac) MNPV. Neither of the two Cc-PHR proteins was identified by LC/MS-MS in the ODVs of ChchNPV. To evaluate the potential of the Cc-PHR2 protein to reduce the UV sensitivity of a baculovirus, the Cc-phr2 gene was incorporated in the genome of Helicoverpa armigera (Hear) NPV, which does not have a UV damage repair system. This resulted in a decreased sensitivity to UV-light compared to wild type HearNPV. A cell line was established from embryos of the insect C. chalcites. This cell line was shown to be permissive for both ChchNPV and the related Trichoplusia ni NPV (TnSNPV). This novel cell line will be a useful tool for making ChchNPV phr mutant viruses to study the impact of DNA repair mediated by photolyases on baculovirus ecology. The collected data support the hypothesis that the Cc- phr2 gene provides a baculovirus with an ecological benefit by increasing the resistance to UV.

    Predicting the response of aquatic invertebrates to stress using species traits and stressor mode of action
    Rubach, M.N. - \ 2010
    Wageningen University. Promotor(en): Paul van den Brink, co-promotor(en): D.J. Baird; S.J. Maund. - [S.l. : S.n. - ISBN 9789085857679 - 194
    waterarthropoden - waterinvertebraten - insecticiden - chloorpyrifos - kenmerken - toxiciteit - ecotoxicologie - ecologische risicoschatting - gevoeligheid - aquatic arthropods - aquatic invertebrates - insecticides - chlorpyrifos - traits - toxicity - ecotoxicology - ecological risk assessment - sensitivity
    How much stress can one take? It depends, on the combination of your mental and physical characteristics (traits), but it’s hard to predict. Chemicals can have devastating effects on ecosystems and they can cause stress in animals and plants. Thus, their risk for ecosystem health needs to be assessed, before use. Species show very different tolerances to the diversity of chemicals due to the combination of both their traits and the molecular mechanism of causing damage in the cell. The challenge lies in finding the relevant species traits and their link to the chemical. In this project an insecticide and 15 freshwater species were used to develop and test a framework for the prediction of responses to stress using traits. Time dependent processes, such as exposure patterns, uptake and excretion of the chemical, but also compensation, detoxification and thresholds were investigated and modelled. These processes were successfully linked to several traits such as size, lipid content, breathing strategy, exoskeleton thickness and evolutionary descent.
    Gebruikswaardeonderzoek onderstammen
    Janse, J. - \ 2009
    Oude Leede : Wageningen UR Glastuinbouw - 5
    wortelknobbel - nematoda - onderstammen - vatbaarheid - meloidogyne - onderzoek - gevoeligheid - gebruikswaarde - nederland - crown gall - nematoda - rootstocks - susceptibility - meloidogyne - research - sensitivity - use value - netherlands
    Op basis van onderzoek in 2008 naar de gevoeligheid van onderstammen voor wortelknobbelaaltjes (onderzoek in voor- en najaar) bij Wageningen UR Glastuinbouw, zijn er een aantal onderstammen uitgelicht die relatief weinig wortelknobbels vertoonden. Deze zijn in 2009 op enkele biologische bedrijven getoetst op hun gebruikswaarde. Het doel was om na te gaan wat de productie en kwaliteit is van enkele onderstammen die zich positief onderscheiden voor wat betreft gevoeligheid voor wortelknobbelaaltjes ofwel die relatief weinig wortelknobbels vertonen
    Snijbloemen versterken positieve gevoelens en stemmingen : wetenschappelijk onderzoek naar het effect van snijbloemen op de gemoedstoestand van de mens
    Vermeer, F. ; Mojet, J. ; Veggel, R.J.F.M. van; Koster, A.C. - \ 2009
    Zoetermeer : Produktschap Tuinbouw, afdeling Markt & Innovatie
    snijbloemen - visuele prikkels - stimulatie - emoties - plezier - kleur - welriekendheid - verkoopbevordering - consumentengedrag - marketing - belevingswaarde - gevoeligheid - cut flowers - visual stimuli - stimulation - emotions - enjoyment - colour - fragrance - sales promotion - consumer behaviour - marketing - experiential value - sensitivity
    Onderzoek van Wageningen UR naar de invloed van snijbloemen op gevoelens en stemmingen toont postieve resultaten. Dit biedt veel kansen voor reclame- en voorlichtingscampagnes, maar ook voor verkoopgesprekken en toepassingsmogelijkheden in bijvoorbeeld restaurants
    Habitataspecten en drukfactoren voor soorten : rapport in het kader van het WOT programma Informatievoorziening Natuur i.o. (WOT IN)
    Kleunen, A. van; Dobben, H.F. van; Schmidt, A.M. - \ 2007
    Wageningen : Alterra (WOT IN serie nr. 6) - 41
    habitats - soorten - milieueffect - vegetatie - monitoring - dieren - planten - vogels - insecten - habitatrichtlijn - gevoeligheid - habitats - species - environmental impact - vegetation - monitoring - animals - plants - birds - insects - habitats directive - sensitivity
    Het belang van 'habitataspecten' en 'drukfactoren' voor alle individuele soorten van de Vogel- en Habitatrichtlijn is geschat door deskundigen. Dit rapport heeft het resultaat in tabelvorm. Er wordt een globaal overzicht gegeven van de wijze van meten en de beschikbaarheid van metingen voor alle habitataspecten en drukfactoren, en er wordt een vergelijking gemaakt van de hier gebruikte indeling met de classificatie van 'impacts' in het rapportageformaat van de EU. Dit rapport is tot stand gekomen dankzij samenwerking met VOFF, via SOVON, Vlinderstichting en met RAVON, VZZ, Floron, EIS en BLWG
    Parameter sensitivity of climate models and climate driven ecological systems
    Moolenaar, H.E. - \ 2006
    Wageningen University. Promotor(en): Johan Grasman, co-promotor(en): F.M. Selten. - [S.l. ] : S.n. - ISBN 9789085044529 - 133
    klimatologie - klimaat - ecologie - wiskundige modellen - betrouwbaarheid - gevoeligheid - verstoring - climatology - climate - ecology - mathematical models - reliability - sensitivity - disturbance
    Uncertainty in the outcome of numerical models of physical and biological processes, such as the climate and ecological systems, is widely recognized. One contributing factor is uncertainty in model parameters. Because of this uncertainty, a range of model outcomes is usually given. This might obstruct policy making for topics such as the reduction of climate change and nature conservation management. Part of the estimation of uncertainty is a parameter sensitivity analysis. It is important to verify how small changes in parameters can affect the model outcome. Especially extreme deviations are of interest to gain an understanding of the variability of the result. We therefore need to identify the parameter perturbations the model is most sensitive to. 

    Since the atmospheric circulation behaves as a chaotic system quantities that characterise the climate have to be computed froman integrationover a large time interval. Perturbing a large set of parameters to analyse the variability of the outcome would require an enormous computing time. It would therefore be advantageous to select effective parameters a priori. In this thesis a method is described that selects these parameters in an efficient way. The short term behaviour of a nonlinear model is used to select parameter perturbations that are likely to cause a large change in the dynamics of the long term behaviour of the model. A short section of a reference orbit is calculated. Next the error growth from the parameter perturbation can be computed with the use of tangent linear equations. The adjoint of the model acts as a backward integration and can then be used to calculate the parameter perturbation that causes the largest error growth over this interval. This perturbation vector is more likely to be also an effective parameter perturbation for a long time integration simulating the climate than a randomly chosen one. More precisely, it turns out that not exactly at a point of the chaotic attractor with a large error growth but just a moment later when this growth has fallen back has to be selected. These points are found by analysing a succession of many short time intervals over each of which the tangent linear approximation holds.

    We apply this adjoint method to two climate models; the Lorenz 63 model and the atmospheric T21QG model, and a climate driven metapopulation model; the Rosenzweig-McArthur model coupled to the Lorenz 84 model. The success rate of drawing a parameter perturbation causing a large change should for the adjoint method be considerably higher than for a random search method. Climate change is defined in terms of changes in the occurrence and strength of different preferred atmospheric circulation patterns. In the contextof metapopulationmodels and conservation management, the goal is to find perturbations in the biological parameters that lower the risk of extinction of herbivore subpopulations. 

    It is found that in the simple models, where only 5 parameters are varied (Lorenz 63 and the Rosenzweig-McArthur model forced by Lorenz 84), the adjoint method has a significantly higher success rate in drawing effective parameter perturbations than a random search method does. In the more complex T21QG model drawing an effective parameter perturbation appears to be a much more strenuous task due to the large number of 1449 parameters that are varied. However, although hampered by this large parameter set and the required long time integrationof thissystem with many degrees of freedom, the adjoint method comes much closer to selecting the parameter perturbation causing the largest climate change than the random method
    Borium belangrijk bij vatensysteem en de celstrekking van wortels
    Heuvelink, E. ; Kierkels, T. - \ 2006
    Onder Glas 3 (2006)3. - p. 20 - 21.
    voedingsstoffentekorten - sporenelementen - borium - toepassing - afwijkingen, planten - symptomen - gevoeligheid - bemesting - glastuinbouw - nutrient deficiencies - trace elements - boron - application - plant disorders - symptoms - sensitivity - fertilizer application - greenhouse horticulture
    Er is weinig bekend over de rol van het sporenelement borium in planten. Duidelijk is wel dat een tekort de celstrekking en de celdeling van de wortels remt. Het element is ook belangrijk bij de opbouw van de vaten, het transportsysteem voor water en mineralen in de plant. Een overmaat aan borium geeft verkleuring en vlekken die papierachtig indrogen in de oudste bladeren. Daarom is van belang met regelmaat analyses te laten uitvoeren
    Automatic differentiation algorithms in model analysis
    Huiskes, M.J. - \ 2002
    Wageningen University. Promotor(en): J. Grasman; A. Stein; M. de Gee. - S.l. : S.n. - ISBN 9789058086013 - 152
    wiskunde - wiskundige modellen - differentiatie - algoritmen - computeranalyse - statistische inferentie - statistische analyse - gevoeligheid - mathematics - mathematical models - differentiation - algorithms - computer analysis - statistical inference - statistical analysis - sensitivity
    Title: Automatic differentiation algorithms in model analysis
    Author: M.J. Huiskes
    Date: 19 March, 2002

    In this thesis automatic differentiation algorithms and derivative-based methods are combined to develop efficient tools for model analysis. Automatic differentiation algorithms comprise a class of algorithms aimed at the derivative computation of functions that are represented as computer code. Derivative-based methods that may be implemented using these algorithms are presented for sensitivity analysis and statistical inference, particularly in the context of nonlinear parameter estimation.

    Local methods of sensitivity analysis are discussed for both explicit and implicit relations between variables. Particular attention is paid to propagation of uncertainty, and to the subsequent uncertainty decomposition of output uncertainty in the various sources of input uncertainty.

    Statistical methods are presented for the computation of accurate inferential information for nonlinear parameter estimation problems by means of higher-order derivatives of the model functions. Methods are also discussed for the assessment of the appropriateness of model structure complexity in relation to quality of data.

    To realize and demonstrate the potential of routines for model analysis based on automatic differentiation a software library is developed: a C++ library for the analysis of nonlinear models that can be represented by differentiable functions in which the methods for parameter estimation, statistical inference, model selection and sensitivity analysis are implemented. Several experiments are performed to assess the performance of the library. The application of the derivative-based methods and the routines of the library is further demonstrated by means of a number of case studies in ecological assessment. In two studies, large parameter estimation procedures for fish stock assessment are analyzed: for the Pacific halibut and North Sea herring species. The derivative-based methods of sensitivity analysis are applied in a study on the contribution of Russian forests to the global carbon cycle.

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