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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The significance of meaning. Why IPBES needs the social sciences and humanities
Jetzkowitz, Jens ; Koppen, C.S.A. van; Lidskog, Rolf ; Ott, Konrad ; Voget-Kleschin, Lieske ; Wong, Catherine Mei Ling - \ 2018
Innovation: The European Journal of Social Science Research 31 (2018)sup1. - ISSN 1351-1610 - p. S38 - S60.
biodiversity - ethics - foundations of biodiversity research - IPBES - methodology - science–policy interface - social sciences

The term “biodiversity” is often used to describe phenomena of nature, which can be studied without a reference to the socially constructed, evaluative, or indeed normative contexts. In our paper, we challenge this conception by focusing particularly on methodological aspects of biodiversity research. We thereby engage with the idea of interdisciplinary biodiversity research as a scientific approach directed at the recognition and management of contemporary society in its ecological embedding. By doing this, we explore how research on and assessments of biodiversity can be enhanced if meaning, aspiration, desires, and related aspects of agency are methodically taken into account. In six sections, we substantiate our claim that the discourse on biodiversity (including the IPBES (Intergovernmental science-policy Platform on Biodiversity and Ecosystem Services) debate) is incomplete without contributions from the social sciences and humanities. In the introduction, a brief overview of biodiversity’s conceptual history is provided showing that “biodiversity” is a lexical invention intended to create a strong political momentum. However, that does not impede its usability as a research concept. Section 2 examines the origins of the Convention on Biological Diversity (CBD) by way of sociological discourse analysis. Subsequently, it proposes a matrix as a means to structure the ambiguities and tensions inherent in the CBD. The matrix reemphasizes our main thesis regarding the need to bring social and ethical expertise to the biodiversity discourse. In Section 3, we offer a brief sketch of the different methods of the natural and social sciences as well as ethics. This lays the groundwork for our Section 4, which explains and illustrates what social sciences and ethics can contribute to biodiversity research. Section 5 turns from research to politics and argues that biodiversity governance necessitates deliberative discourses in which participation of lay people plays an important role. Section 6 provides our conclusions.

Sensitivity analysis methodologies for analysing emergence using agent-based models
Broeke, Guus ten - \ 2017
University. Promotor(en): Jaap Molenaar, co-promotor(en): George van Voorn; Arend Ligtenberg. - Wageningen : Wageningen University - ISBN 9789463436991 - 211
mathematics - computational mathematics - mathematical models - dynamic modeling - sensitivity analysis - adaptation - methodology - simulation - wiskunde - computerwiskunde - wiskundige modellen - dynamisch modelleren - gevoeligheidsanalyse - adaptatie - methodologie - simulatie

Many human and natural systems are highly complex, because they consist of many interacting parts. Such systems are known as complex adaptive systems (CAS). Understanding CAS is possible only by studying the interactions between constituent parts, rather than focussing only on the properties of the parts in isolation. Often, the possibilities for systematically studying these interactions in real-life systems are limited. Simulation models can then be an important tool for testing what properties may emerge, given various assumptions on the interactions in the system. Agent-based models (ABMs) are particularly useful for studying CAS, because ABMs explicitly model interactions between autonomous agents and their environment.

Currently, the utility of ABMs is limited by a lack of available methodologies for analysing their results. The main tool for analysing CAS models is sensitivity analysis. Yet, standard methods of sensitivity analysis are not well-suited to deal with the complexity of ABMs. Thus, there is a need for sensitivity analysis methodologies that are specifically developed for analysing ABMs. The objective of this thesis is to contribute such methodologies. Specifically, we propose methodologies for (1) detecting tipping points, (2) analysing the effects of agent adaptation, and (3) analysing resilience of ABMs.

Chapter 2 introduces traditional methods of sensitivity analysis. These methods are demonstrated by applying them to rank the most influential parameters of an ODE model of predator-prey interaction. Furthermore, the role of sensitivity analysis in model validation is discussed.

In Chapter 3 we investigate the use of sensitivity analysis for detecting tipping points. Whereas bifurcation analysis methods are available for detecting tipping points in ODE models, these methods are not applicable to ABMs. Therefore, we use an ODE model to verify the results from sensitivity analysis against those of bifurcation analysis. We conclude that one-factor-at-a-time sensitivity analysis (OFAT) is a helpful method for detecting tipping points. However, OFAT is a local method that considers only changes in individual parameters. It is therefore recommended to supplement OFAT with a global method to investigate interaction effects. For this purpose, we recommend all-but-one-at-a-time sensitivity analysis (ABOS) as a graphical sensitivity analysis method that takes into account parameter interactions and can help with the detection of tipping points.

In Chapter 4 we introduce a basic ABM model of agents competing in a spatial environment for a renewable resource. This basic model will be extended in the subsequent chapters, and will serve as a testing case for various sensitivity analysis methods. In Chapter 4, it is used to assess the utility of existing sensitivity analysis methods for ABMs. The results show that traditional methods of sensitivity are not sufficient to analyse the ABM, due to the presence of tipping points and other strong non-linearities in the model output. In contrast, OFAT is found to be helpful for detecting tipping points, as was suggested in Chapter 3. Based on these outcomes, OFAT is recommended as a starting point for sensitivity analysis of ABMs, preferably supplemented by a global method to investigate interaction effects.

In Chapter 5 we extend the ABM of Chapter 4 by adding agent adaptation in the form of a mechanism of natural selection. On short time-scales, the model behaviour appears to be similar to the non-adaptive model version. On longer time-scales, the agent adaptation causes the state of the model to gradually change as agents continue to adapt to their surroundings. We propose a sensitivity analysis method to measure the effects of this adaptation. This method is based on a quantification of the difference between probability density functions of model version with and without adaptation. Using this method, we show that this adaptation increases the resilience of the system by giving it the flexibility needed to respond to pressures.

In Chapter 6 we further extend the test-case by giving agents the option to harvest either cooperatively or individually. Cooperation increases the potential yields, but introduces the risk of defection of the interaction partner. It is shown that ecological factors, which are usually not considered in models on cooperation, strongly affect the level of cooperation in the system. For example, low levels of cooperation lead to a decreased population size, and causes the formation of small groups of agents with a higher level of cooperation. As a result, cooperation persists even without any mechanisms to promote it. Nevertheless, the inclusion of such mechanisms in the form of indirect reciprocity does further increase the level of cooperation. Furthermore, we show that the resulting high levels of cooperation, depending on the circumstances, can increase the resilience of the agent population against shocks.

To conclude, in this thesis several methodologies have been proposed to help with ABM analysis. Specifically, OFAT and ABOS are recommended for detecting tipping points in ABMs, and in Chapter 5 a protocol is introduced for quantifying the effects of adaptation. By suggesting these methodologies, this thesis aims to contribute to the utility of ABMs, especially for studying CAS.

Greenhouse gas reporting for the LULUCF sector in the Netherlands : methodological background, update 2016
Arets, E.J.M.M. ; Kolk, J.W.H. van der; Hengeveld, G.M. ; Lesschen, J.P. ; Kramer, H. ; Kuikman, P.J. ; Schelhaas, M.J. - \ 2017
Wageningen : Statutory Research Tasks Unit for Nature & the Environment (WOt-technical report 89) - 90
greenhouse gases - methodology - emission - netherlands - broeikasgassen - methodologie - emissie - nederland
This report provides a complete methodological description and background information of the DutchNational System for Greenhouse gas Reporting of the LULUCF sector. It provides detailed description of themethodologies, activity data and emission factors that were used. Additionally it gives a table-by-tableelaboration of the choices and motivations for filling the CRF tables for KP-LULUCF
Bacteriophage: from exploration to exploitation
Nobrega, Franklin L. - \ 2017
University. Promotor(en): John van der Oost, co-promotor(en): J. Azeredo; Stan Brouns. - Wageningen : Wageningen University - ISBN 9789463430524 - 338
bacteriophages - hosts - interactions - genetic engineering - methodology - screening - bacteriofagen - gastheren (dieren, mensen, planten) - interacties - genetische modificatie - methodologie - screenen

Over the past decades, bacteriophage research has revealed the abundance of phages in nature, their morphological and genomic diversity, their influence in the regulation of microbial balance in the ecosystem and their impact on the evolution of microbial diversity. Since the 1950s, phages have also played a central role in some of the most significant fundamental discoveries in biological sciences that have been crucial for the development of molecular biology. More recently, phage research has resulted in the development of genome editing tools, and it has generated the renewed interest of using phages and phage-related products as therapeutic agents. Although major progress has been made, basic understanding on phage biology is still lacking. The number of phage genes with unknown function still largely outnumber those with established roles. Therefore, further progress depends on a deeper understanding on phage biology.

The present thesis aims at developing tools to support phage research, explores the use of phages for therapeutic purposes, and expands our insights into the biology of phages. A literature review on the molecular, structural and evolutionary determinants of phage-host interaction (Chapters 1 and 2) underlines the relatively poor understanding of the subject. A great variety of structures and mechanisms of infection are being revealed, but no correlations have yet been established between these and host interaction. Furthermore, so far no evolutionary model accurately describes the coevolution of phages and bacteria. A particular interest of evolutionary studies concerns the understanding of the prevalence of broad-host range phages in natural environments, since these are rarely isolated using standard laboratory isolation procedures. Indeed, we have tried to isolate broad host range phages targeting the Escherichia coli reference collection (Chapter 3), but found narrow-host range phages to be more prevalent. Only one phage of relatively broad host range was found (S2-36s), being able to infect 14 of the 72 strains. Proteins of interest for further exploration were found, such as depolymerases and colanic acid-degrading proteins, both with potential anti-biofilm activity.

The isolation procedures against the ECOR collection proved to be challenging due to the amount of strains and samples to be evaluated. Consequently, a high-throughput methodology was developed to simplify these isolation procedures (Chapter 4). By automated monitoring of cell growth in 96-well plates it is possible to use differences in optical densities (plotted as heatmaps) between cells subjected to the samples and in control conditions to screen for the presence of phages. The method revealed an accuracy of 98% and reduced the workload by 90%. The method developed can also be used to screen for broad-host range phages or to screen collections of phages for variants or cocktails that are suitable for treating bacterial infections. A discussion is provided of the advantages and limitations of phages for therapeutic applications (Chapter 5). It is suggested that phages in their natural state cannot be used in therapeutic applications. The future of phage therapy may possibly be genome engineering for tailoring of phage properties. Subsequently, the genetic modification of phage T7 was shown to improve (2-log) the capacity of the phage to resist to the strongly acidic conditions and enzymatic challenges of the gastrointestinal tract (Chapter 6). This was achieved by modifying the phage to express a signal peptide on its capsid to which phospholipids attach forming a protective coating. The removal of the phospholipid coating using phospholipase caused reversion to the pH-sensitive phenotype of the wild-type phage. In case of orally-delivered phages, this may improve the efficacy of phage therapy.

Engineering of phage genomes can also support evolutionary studies and basic phage research, e.g. analyzing if a certain gene is essential. A strategy developed for the random recombination of phage genomes (Chapter 7) demonstrated that it is possible to create novel productive phages by combining elements of different phage families. The findings reveal an unexpected level of flexibility and adaptability of phage genomes to accommodate and re-arrange genetic information, reflecting the pre-existing evolutionary compatibility of genes from different phages. The method is further expected to serve as a platform for improving our understanding of phage gene function and importance, where the random recombination of a single phage genome may be the preferred approach.

A different approach for the therapeutic application of phages was explored. Using phage display it was possible to identify peptides targeting claudin-low breast cancer cells (Chapter 8) and osteoarthritis cells (Chapter 9) with high levels of specificity. The peptides identified may contribute to an early detection of claudin-low breast carcinomas, and to develop more individualized therapies for both breast cancer and osteoarthritis.

In summary, the work developed in this thesis has resulted in new methodologies and biological data, thereby contributing to an increased understanding of phage biology and of the opportunities for the use of phages for diagnosis and therapy.

Nanostructured imaging surface plasmon resonance biosensing
Joshi, Sweccha - \ 2017
University. Promotor(en): Michel Nielen; Han Zuilhof, co-promotor(en): Teris van Beek. - Wageningen : Wageningen University - ISBN 9789463430203 - 164
methodology - techniques - biosensors - resonance - mass spectrometry - organic chemistry - physics - methodologie - technieken - biosensoren - resonantie - massaspectrometrie - organische scheikunde - fysica

The testing and further development of a prototype nanostructured imaging surface plasmon resonance (iSPR) biosensor, with a focus on surface modification and detailed characterization of the biosensor chip and in-field and at-line applicability in the food industry is described. Furthermore, a simplified coupling of SPR and MS is described that allows identification of the mycotoxins of interest along with any other cross-reacting analytes. Chapter 1 describes general information about SPR, SPR instruments along with their components, development of a multiplex SPR biosensor and coupling of SPR to mass spectrometry.

In Chapter 2, the surface modification, in-depth characterization and the antifouling performance of the nanostructured iSPR chip is described. Different types of polyethylene glycol (PEG) and zwitterionic polymers were chosen as antifouling chemistries. Various surface characterization techniques such as atomic force microscopy, scanning electron microscopy, water contact angle, X-ray photoelectron spectroscopy and direct analysis in real time high resolution mass spectrometry provided complementary information about the chip before and after the modification. Antifouling chemistry, an essential first step in the development of an SPR biosensor, prevents false positive results arising from non-specific binding of sample components to the SPR chip. Upon comparison of the surface modification and antifouling behavior with conventional flat SPR chips, the latter were only slightly better. Zwitterionic polymers and long chain PEG had the best antifouling performance. A proof-of-principle experiment was done to demonstrate the selective detection of streptavidin binding to a surface partially modified with biotin.

A 6-plex SPR assay for the detection of mycotoxins in barley was developed in Chapter 3. A benchmark double 3-plex assay was developed for the detection of deoxynivalenol (DON), zearalenone (ZEA), T-2 toxin (T-2), ochratoxin A (OTA), fumonisin B1 (FB1) and aflatoxin B1 (AFB1) using benchtop SPR instrument (Biacore). Preliminary in-house validation of the competitive inhibition assay developed using ovalbumin conjugates of the mycotoxins showed that the method is suitable for detection of DON, ZEA, T-2 and FB1 whereas further improvement is required for OTA and AFB1. The method was then transferred to the nanostructured iSPR, which although less sensitive than the benchtop SPR, was able to detect DON, T-2, ZEA and FB1 at the relevant levels.

In Chapter 4, the assay developed in Chapter 3 was further optimized and an entire assay along with in-house validation and measurement of naturally contaminated was developed using the nanostructured iSPR. The antifouling chemistry used in Chapter 3, PEG, was replaced by carboxymethylated dextran (CMD) that not only allowed direct immobilization of toxins but also helped to improve the stability of the chip whereby the chip could be used for more than 450 cycles. DON could be detected at the relevant levels in beer with minimal sample preparation whereas for OTA an enrichment step using solid phase extraction was required.

As demonstrated in Chapter 3 and 4, the nanostructured iSPR instrument can be used for screening of different mycotoxins in beer and related ingredients. However, SPR is not able to provide chemical information of the binding analyte especially in cases where the antibodies have cross-reactivity towards conjugates of the analyte. Therefore, a simplified coupling for SPR with ambient mass spectrometry was developed in Chapter 5. The method allowed identification of DON as well as its cross-reacting conjugates such as deoxynivalenol-3-glucoside and 3-acetyl DON.

The research presented in this thesis is an important step towards the use of the nanostructured iSPR instrument for label free in-field and at-line detection of various analytes. In Chapter 6, discussion of the main achievements of this thesis, challenges and future perspectives of the technology is described.

Probing the power of Apollo : methodological challenges and opportunities of the Delphi methods for developing rankings
Meijering, Jurian V. - \ 2016
University. Promotor(en): Adri van den Brink, co-promotor(en): Hilde Tobi. - Wageningen : Wageningen University - ISBN 9789462579187 - 184
delphi method - methodology - ranking - landscape architecture - delphimethode - methodologie - rangordening - landschapsarchitectuur

The Delphi method is a structured data-collection process aimed at facilitating experts to achieve a certain level of agreement on a complex problem. In several subsequent rounds experts give their opinion on the problem of interest, usually by means of a standardized questionnaire. After each round experts receive controlled opinion feedback in the form of a summary of the findings. Based on this feedback experts are allowed to reconsider their opinion in the next round.

Although the Delphi method seems to provide opportunities for developing rankings, research into its application to the development of rankings seems to be non-existent. Furthermore, the Delphi method has several unresolved methodological issues, in particular regarding the measurement of agreement and the provision of controlled opinion feedback. Therefore, the general objective of this PhD project was to find out what the methodological challenges and opportunities are of the Delphi method for developing rankings.

To achieve this objective, four studies were conducted. In the first study, simulations were performed to find out how various agreement indices behave within and across the rounds of a Delphi study. In the second study, the Delphi method was applied to develop a ranking of research domains in landscape architecture. An experiment within the study investigated the effect of two types of controlled opinion feedback on the drop-out rate, experts’ degree of opinion change, and the level of agreement among experts. The third study investigated the methodological characteristics of six urban sustainability rankings, which resulted in a recommendation to define and operationalize the concept ‘urban sustainability’ using the Delphi method. Therefore, in the fourth and final study the Delphi method was applied to find out which components experts find most relevant for defining and measuring urban sustainability. An experiment within this study provided insight into the effect of feeding back experts’ initial ratings on the degree of opinion change and the level of agreement.

Overall, this PhD project showed how the Delphi method may be used to: (1) obtain a ranking of objects on a ranking attribute and (2) obtain a definition and operationalization of a complex ranking attribute. It was also shown that these applications of the Delphi method do not come without challenges. First, selection criteria and search strategies need to be developed by which sufficient numbers of different types of experts may be found. Second, for the first Delphi questionnaire a parsimonious list of items (e.g. ranking objects or components of a ranking attribute) needs to be drawn up that largely covers the potentially great diversity of existing items. Third, careful considerations need to be made about which types of information (i.e. summary statistics, rationales, experts’ own initial ratings) to feed back to experts after every round as this may influence various Delphi outcome measures. Fourth, the choice for a particular consensus, agreement, or association index needs to be carefully made and justified as it determines the level of agreement among experts that is obtained. Finally, this project showed that by means of a simulation study and two real-world Delphi experiments new knowledge about the functioning of the Delphi method could be acquired. More of these studies are needed to establish evidence-based guidelines and to uncover the full potential of the Delphi method for developing rankings.

Toetsontwikkeling PSTVd in Dahlia
Leeuwen, P.J. van; Trompert, J.P.T. ; Lemmers, M.E.C. ; Verbeek, M. ; Meekes, E.T. - \ 2016
Lisse : Praktijkonderzoek Plant & Omgeving, onderdeel van Wageningen UR Business Unit Bloembollen, Boomkwekerij en Fruit - 23 p.
dahlia - plantenvirussen - aardappelspindelknolviroïde - detectie - extractie - experimenteel veldonderzoek - methodologie - diagnostische technieken - nederland - plant viruses - potato spindle tuber viroid - detection - extraction - field experimentation - methodology - diagnostic techniques - netherlands
Effectiviteit wildschadepreventie : beoordelingsmethodiek en literatuurreview
Buij, R. ; Lammertsma, D.R. ; Melman, T.C.P. - \ 2016
Wageningen : Alterra, Wageningen-UR (Alterra-rapport 2740) - 41 p.
schade - beweidingsschade - wilde dieren - methodologie - schadepreventie - damage - browsing damage - wild animals - methodology - loss prevention
Er is een methodiek opgesteld om studies naar middelen voor wildschadepreventie te kunnen beoordelen. De methodiek betreft enerzijds de wetenschappelijke kwaliteit van het onderzoek en anderzijds de effectiviteit van de middelen. Naast effectiviteit van de middelen wordt ook aandacht geschonken aan aspecten als ontwikkelingsfase van het middel, aanschaf- en gebruikskosten, neveneffecten e.d. Aan de hand van deze methodiek is voor de tien belangrijkste schadesoorten in Nederland een literatuurreview gemaakt van onderzoeken naar de effectiviteit van verjagingsmiddelen. Wat betreft internationale literatuur hebben we ons beperkt tot peer-reviewed publicaties, voor Nederlands onderzoek is ook gekeken naar grijze literatuur.
Onafhankelijke bemonstering vaste mest : globale indicatie van de kosten en administratieve lasten
Koeijer, T.J. de; Luesink, H.H. - \ 2016
Wageningen : LEI Wageningen UR (Rapport / LEI Wageningen UR 2016-050) - 35 p.
dierlijke meststoffen - rundvee - varkens - bemonsteren - kosten - methodologie - animal manures - cattle - pigs - sampling - costs - methodology
Bij invoering van de nieuwe systematiek van onafhankelijke bemonstering van de dikke fractie van rundvee- en varkensdrijfmest nemen de kosten voor de sector naar schatting toe met circa 2 mln. euro per jaar. Daarbij is aangenomen dat ondernemers kiezen voor de goedkoopste methode op basis van de gegeven inschatting van de kosten van de verschillende opties voor bemonstering en de logistieke situatie en aantallen transporten van dikke fractie van 2015. In dat geval zullen de ondernemers kiezen voor een variant waarin zo veel mogelijk met geautomatiseerde vrachtbemonstering wordt gewerkt, in combinatie met ‘handmatige bemonstering per partij vlak voor afvoer.
Niet-chemische aanpak mineermot in tomaat en trips in chrysant en paprika
Qiu, Yutong - \ 2016
greenhouse horticulture - vegetables - plant pests - tuta absoluta - thrips - cut flowers - controlled atmospheres - temperature - atmosphere - methodology - quarantine organisms - agricultural research
Nanoscale force sensors to study supramolecular systems
Cingil, E.H. - \ 2016
University. Promotor(en): Martien Cohen Stuart, co-promotor(en): Joris Sprakel. - Wageningen : Wageningen University - ISBN 9789462576971 - 136 p.
sensors - supramolecular chemistry - molecules - biopolymers - polymers - methodology - rheology - supramoleculaire chemie - moleculen - biopolymeren - polymeren - methodologie - reologie

Supramolecular systems are solutions, suspensions or solids, formed by physical and non-covalent interactions. These weak and dynamic bonds drive molecular self-assembly in nature, leading to formation of complex ordered structures in high precision. Understanding self-assembly and co-assembly is crucial to unravel and mimic many processes occurring in nature. However, the challenge cannot be easily addressed especially in biological systems as it involves many dynamic interactions which may cooperatively, noncooperatively or competitively generate a complex manifold of interaction pathways. In this thesis, we employed two techniques to understand these complex interactions in various supramolecular systems at the nanoscale 1) multiple particle tracking microrheology to study thermoreversible assembly of triple helices in a collagen-inspired recombinant polypeptide in the form of a triblock copolymer gel former; and 2) polyfluorene-based conjugated polyelctrolyte mechosensors to monitor electrostatic co-assembly dynamics of (i) a recombinant diblock copolypeptide which encapsulates the conjugated polyelectrolyte like a protein capsid and (ii) various synthetic diblock copolymers which forms complex coacervate micelles; and finally the orthogonal self-assembly dynamics of (iii) a recombinant viral coat protein which mimics natural rod-like viruses. These novel polymeric mechanosensors work as versatile, non-invasive tools to detect even low degrees of analyte binding or complex formation due to the stress applied on their conjugated backbone. This mechanical stress causes the polymeric backbone to stretch which can be detected by a shift in its fluorescence spectra.

Measurement errors in dietary assessment using duplicate portions as reference method
Trijsburg, L.E. - \ 2016
University. Promotor(en): Pieter van 't Veer; Anouk Geelen; Jeanne de Vries. - Wageningen : Wageningen University - ISBN 9789462576421 - 128 p.
diet studies - nutritional assessment - questionnaires - reference standards - correction factors - validity - body mass index - regression analysis - food intake - food - protein - potassium - sodium - energy intake - methodology - dieetstudies - voedingstoestandbepaling - vragenlijsten - referentienormen - correctiefactoren - geldigheid - quetelet index - regressieanalyse - voedselopname - voedsel - eiwit - kalium - natrium - energieopname - methodologie

Measurement errors in dietary assessment using duplicate portions as reference method

Laura Trijsburg

Background: As Food Frequency Questionnaires (FFQs) are subject to measurement error, associations between self-reported intake by FFQ and outcome measures should be corrected for measurement error with data from a reference method. Whether the correction is adequate depends on the characteristics of the reference method used in the validation study. The duplicate portion method (DP), compared to the often used 24h recall (24hR), seems a promising reference method as correlated errors between FFQ and DP, such as memory bias, errors in portion size estimations and food composition databases, are not expected.

Aim: This thesis aimed to determine the validity of the DP compared to the 24hR as a reference method for FFQ validation. The second aim was to explore the validity of nutrient densities for DP, 24hR and FFQ. The third aim was to determine the factors associated with misreporting of energy, protein and potassium as estimated by DP, 24hR and FFQ.

Methods: Within the DuPLO-study, a Dutch validation study which is part of the NQplus study, two DPs, two FFQs, two blood and urinary biomarkers and one to fifteen 24hRs (web-based and/or telephone-based) were collected in 198 subjects, within 1.5 years. Also, one or two doubly labelled water measurements were available for 69 participants. Multivariate measurement error models were used to assess proportional scaling bias, error correlations with the FFQ, validity coefficients and attenuation factors. Furthermore linear regression analysis was used to determine the association between misreporting and various factors.

Results: The DP was less influenced by proportional scaling bias, had lower correlated errors with the FFQ and showed higher attenuation factors than the 24hR for potassium, sodium and protein. Also, the DP seemed a better reference method than the 24hR for the assessment of validity coefficients for the FFQ for various fatty acids. The attenuation factors for the FFQ, using either the DP or 24hR as reference method, agreed reasonably well. Furthermore, the DP showed, when using plasma fatty acids as reference, slightly better ranking of participants according to their intake of n-3 fatty acids (0.33) and the n‑3/LA ratio (0.34) than the 24hR (0.22 and 0.24, respectively). Less group level bias was observed for protein and sodium densities compared to their absolute intakes for FFQ, 24hR and DP, but not for potassium. Overall the validity coefficients and attenuation factors for DP, 24hR and FFQ did not improve for nutrient densities compared to absolute intakes, except for the attenuation factor for sodium density. Lastly, BMI proved to be the most consistent determinant associated with misreporting (group level bias) of energy, protein and potassium for DP, 24hR and FFQ. Men tended to underreport protein by the DP, FFQ and 24hR and persons of older age underreported potassium but only by the 24hR and FFQ. Other explorative determinants did not show a consistent association with misreporting of energy or nutrients by the different dietary assessment methods.

Conclusion: With respect to error correlations and attenuation factors the DP performed slightly better than the 24hR as a reference method for validating FFQs in epidemiological research. Furthermore, the use of nutrient densities does not necessarily improve the validity of the dietary intake estimates from DP, 24hR and FFQ. Moreover, it was shown that BMI is an important determinant of misreporting of energy, protein and potassium for these three assessment methods.

Eerste resultaten CATT-behandeling positief
Vreeburg, P.J.M. - \ 2015
BloembollenVisie (2015)325. - ISSN 1571-5558 - p. 20 - 21.
bloembollen - hyacinthus - thrips - methodologie - gecontroleerde omgeving - nematoda - landbouwkundig onderzoek - bestrijdingsmethoden - ornamental bulbs - methodology - controlled atmospheres - agricultural research - control methods
Het eerste jaar onderzoek naar de bestrijding van trips in hyacint door een CATT-behandeling geeft veel hoop op een effectieve bestrijding van trips bij holbollen en leverbaar. Een afdoende bestrijding van stengelaaltjes in bollen is nog niet behaald, maar de behandeling kan mogelijk wel de standaard lichtere warmwaterbehandeling bij narcis vervangen. In 2015 worden de behandelingen verder geoptimaliseerd.
Protocol Energiemonitor Glastuinbouw : vernieuwde versie tot en met 2014
Velden, N.J.A. van der - \ 2015
Den Haag : LEI, onderdeel van Wageningen UR (LEI-nota 2015-122a) - 42 p.
kassen - glastuinbouw - energie - duurzaamheid (sustainability) - duurzame energie - energiegebruik - protocollen - methodologie - bedrijfsvoering - kastechniek - klimaatregeling - energiebesparing - greenhouses - greenhouse horticulture - energy - sustainability - sustainable energy - energy consumption - protocols - methodology - management - greenhouse technology - air conditioning - energy saving
Het LEI voert de Energiemonitor Glastuinbouw uit in opdracht van de Stichting Programmafonds Glastuinbouw/LTO Glaskracht Nederland en het ministerie van Economische Zaken (EZ). In de Energiemonitor Glastuinbouw wordt jaarlijks als eerste de energie-input en -output en de fysieke productie van glastuinbouwproducten gekwantificeerd. Vervolgens wordt de ontwikkeling van de energie-indicatoren bepaald. Ook wordt een jaarlijkse elektriciteitsbalans van de glastuinbouw opgesteld. Naast de elektriciteitsinput en -output wordt hierbij ook de elektriciteitsproductie en -consumptie in kaart gebracht. In de Energiemonitor Glastuinbouw word ook het effect op het primaire brandstofverbruik c.q. de energie-efficiëntie en op het fossiel brandstofverbruik c.q. de CO2-emissie door wk-installaties in gebruik door de glastuinbouw bepaald. Dit geldt ook voor de inkoop van efficiënter geproduceerde energie (restwarmte en wk-warmte van energiebedrijven) en duurzame energie.
Greenhouse gas reporting for the LULUCF sector in the Netherlands : methodological background
Arets, E.J.M.M. ; Kolk, J.W.H. van der; Hengeveld, G.M. ; Lesschen, J.P. ; Kramer, H. ; Kuikman, P.J. ; Schelhaas, M. - \ 2015
Wageningen : Statutory Research Tasks Unit for Nature & the Environment (WOT Natuur & Milieu) (WOt-technical report 52) - 78 p.
greenhouse gases - air pollutants - greenhouse effect - climatic change - emission - methodology - netherlands - broeikasgassen - luchtverontreinigende stoffen - broeikaseffect - klimaatverandering - emissie - methodologie - nederland
This report provides a complete methodological description of the Dutch National System for Greenhouse gas Reporting of the LULUCF sector for the UN Framework Convention on Climate Change (UNFCCC). The methodologies follow the IPCC 2006 guidelines for Agriculture, Forestry and Other Land-Uses (AFOLU).
Based on these guidelines, this report provides detailed descriptions and motivations of the used methods, activity data, and emission factors for calculation of the emissions and removals as reported in the National Inventory Report (NIR). The structure of the report follows the structure for national inventory reports as
laid out in the appendix to Decision 24/CP.19 of the UNFCCC.
Openheid van het landschap : berekeningen met het model ViewScape
Meeuwsen, H.A.M. ; Jochem, R. - \ 2015
Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-technical report 44) - 89
landschap - open ruimten - modellen - zichtbaarheid - berekening - methodologie - landscape - open spaces - models - visibility - calculation - methodology
Op verzoek van het Planbureau voor de Leefomgeving (PBL) heeft Alterra de methode om de openheid van het landschap te berekenen vernieuwd. Het model Viewscape dat op basis van zichtlijnen de oppervlakte zichtbaar landschap berekent, is daartoe aangepast, getest en gevalideerd. Er is een methode ontwikkeld die topografische informatie bewerkt tot een basiskaart voor het model dat rekening houdt met reliëf. In de basiskaart worden bomenrijen als ondoorzichtige elementen meegenomen, maar een toekomstige nuancering op dit punt is wenselijk. Bij het reliëf lag de uitdaging in het negeren van flauwe hellingen. Uit de validatie bleek dat de oppervlaktes van grotere open ruimten goed konden worden berekend, maar structureel iets worden onderschat. De oppervlakte van het zichtbare deel van het landschap blijkt een goede maat te zijn voor de openheid ervan. De verbeterde versie van ViewScape is gebruikt om met een resolutie van 100 meter die oppervlakte landsdekkend te berekenen. Het resultaat voldoet aan de verwachtingen van het PBL. Het is nog wel de vraag of de topografische informatie betrouwbaar genoeg is om de openheid te kunnen monitoren aangezien een onbekend deel van de veranderingen op de kaart niet voortkomt uit veranderingen in het veld, maar uit verbeterde kartering.
Boomkronen afleiden uit het Actueel Hoogtebestand Nederland : kwaliteitsaspecten rondom het geautomatiseerd in kaart brengen van bomen op basis van het AHN2-bestand
Meijer, M. ; Rip, Frans ; Benthem, R. van; Clement, J. ; Sande, C. van der - \ 2015
Wageningen : Alterra, Wageningen-UR (Alterra-rapport 2671) - 85
bomen - kroondak - kroon - gegevensanalyse - gegevens verzamelen - methodologie - remote sensing - hoogteligging - cartografie - nederland - trees - canopy - crown - data analysis - data collection - methodology - altitude - mapping - netherlands
Alom wordt erkend dat bomen belangrijk zijn. Zowel voor de mens, de natuur als het klimaat. Recentelijk is een procedure ontwikkeld om op basis van het nationale Nederlandse hoogtebestand AHN2 een bestand te genereren met alle boomkronen in Nederland, genaamd ‘CP’. Een dergelijk bestand kan onder andere het groenbeheer van de gemeenten in Nederland vereenvoudigen en helpen bij het inventariseren van landschapselementen. De vraag is echter: hoe goed is dit bestand? In dit rapport wordt voor een drietal verschillende gebieden onderzocht wat de kwaliteit is van CP. Verder wordt mede op basis van de ervaringen die tijdens het kwaliteitsonderzoek zijn gedaan een standaard kwaliteitsraamwerk opgezet voor het controleren van nieuwe versies van het boomkronenbestand. Daarnaast is dit document er ook op gericht om de potentiële gebruiker een beter beeld van de kwaliteit te geven.
Interpreting plant-sampled ¿14CO2 to study regional anthropogenic CO2 signals in Europe
Bozhinova, D.N. - \ 2015
University. Promotor(en): Maarten Krol; Wouter Peters, co-promotor(en): Michiel van der Molen. - Wageningen : Wageningen University - ISBN 9789462574946 - 155
kooldioxide - emissie - planten - atmosfeer - gewassen - plantensamenstelling - koolstofcyclus - methodologie - luchtkwaliteit - carbon dioxide - emission - plants - atmosphere - crops - plant composition - carbon cycle - methodology - air quality

"Interpreting plant-sampled Δ14CO2 to study regional anthropogenic CO2 signals in Europe"

Author: Denica Bozhinova

This thesis investigates the quantitative interpretation of plant-sampled ∆14CO2 as an indicator of fossil fuel CO2 recently added to the atmosphere. We present a methodology to calculate the ∆14CO2 that has accumulated in a plant over its growing period, based on a modeling framework consisting of a plant growth model (SUCROS) and an atmospheric transport model (WRF-Chem). We verify our framework against available atmospheric observations and use it to evaluate the ∆14CO2 budget of Europe, which is influenced by both fossil fuel CO2 and nuclear 14CO2 anthropogenic emissions. Finally, we present the results of the 14C analysis of samples of maize leaves that were obtained from the Netherlands, Germany and France in an experimental campaign conducted during 2010-2012. We use our modeling framework to interpret the ∆14CO2 signals of the samples and evaluate the different type of emission sources that have contributed for their final signatures.

Integrale aanpak enige optie beheersing Leucocoprinus : plooipaddestoel remt potplanten in groei
Velden, P. van; Hofland-Zijlstra, J.D. - \ 2015
Onder Glas 12 (2015)1. - p. 28 - 29.
glastuinbouw - potplanten - plantenziekteverwekkende schimmels - agaricaceae - ziektepreventie - groeivertraging - bedrijfshygiëne - in groei belemmeren - proeven - methodologie - greenhouse horticulture - pot plants - plant pathogenic fungi - disease prevention - growth retardation - industrial hygiene - dwarfing - trials - methodology
Leucocoprinus is een hardnekkige schimmel die niet alleen het eindproduct ontsiert, maar indirect ook groeiremming geeft. Eigenlijk hebben potplantentelers maar één schimmelbestrijdingsmiddel dat nog werkt. Meer toekomst bieden plantversterkende middelen op basis van schimmels en bacteriën, gecombineerd met een streng hygiëneprotocol.
What happens in the bag? : development and evaluation of a modified in situ protocol to estimate degradation of nitrogen and starch in the rumen
Jonge, L.H. de - \ 2015
University. Promotor(en): Wouter Hendriks, co-promotor(en): Jan Dijkstra; H. van Laar. - Wageningen : Wageningen University - ISBN 9789462574519 - 175
herkauwers - pensfermentatie - stikstof - zetmeelvertering - pensvertering - protocollen - evaluatie - methodologie - schatting - voedingsfysiologie - ruminants - rumen fermentation - nitrogen - starch digestion - rumen digestion - protocols - evaluation - methodology - estimation - nutrition physiology

The most widely used method to estimate the rumen degradation of dietary components in feedstuffs is the in situ or in sacco method. This method is based on rumen incubation of substrate (feed) in nylon or dacron bags followed by rinsing and analysis of the residue. Small pores in the bag allow microbes to enter the bag whilst a variable portion of the feed is retained in the bag. The results are used to estimate the ruminal effective degradation (ED) that is used in several protein evaluation systems. The weaknesses of the in situ method are its low precision, the lack of standardization, and its inaccuracy. The accuracy can be divided in a bias with respect to the in situ method itself, and the difference between the in situ and in vivo degradation. The bias of the in situ method itself is related to several assumptions regarding the size and degradation rate of the washable fraction, secondary particle loss, and microbial contamination. The aim of this thesis was to examine possibilities to reduce this bias by modification of the in situ methodology.

The bias related to the assumptions regarding the washout fraction was successfully reduced by developing and using a modified rinsing method that involves less vigorously shaking conditions and a solvent which mimics the rumen pH and osmolality. This modified rinsing method markedly reduced the soluble (S) fraction of N, especially for legume seeds, and the non-soluble washout (W-S) fraction, especially for starch, compared to the conventional method. Consequently, the estimation of the ED became less dependent on the assumptions regarding the degradation of the S and W-S fraction. In vitro results did not support the assumption of a much faster degradation of the W-S fraction of starch than that of the non-washout fraction of starch. The modified rinsing method also allowed measuring the in situ degradation of products that contain mainly small particles such as wheat yeast concentrates.

The bias related to the breakdown of particles was also successfully reduced by development and application of a combination of the modified rinsing method and an in vitro method that simulates particulate matter loss during incubation. This in vitro method was based on in situ results obtained with an inert marker (i.e., silica gel) which showed that particulate matter loss during incubation was moderate and limited to particles smaller than approximately 40 μm. Correction for these losses decreased the estimated ED of feed ingredients used. This study also showed that the fractional degradation rate of starch in grains was strongly affected by the process of secondary particulate loss when using the conventional method, and applying the modified rinsing method markedly reduced the error due to secondary particulate loss.

In comparison to the conventional method, the modified method resulted in an increase of the bias related to microbial contamination of the residues. The ratio between diaminopimelic acid (DAPA), a marker for bacterial protein, and N in the residues was higher when using the modified method than that in the conventional method. The results obtained for the modified method also indicated lysis of bacterial cells during rinsing. This bias led to a lower ED when using the modified method with the impact greatly depending on the degree of lysis of bacterial cells.

In summary, the modified method increased the non-washout fraction of N and starch of various feed ingredients, which offers the possibility to use it for a larger range of feed ingredients, and reduced the bias related to assumptions on the washout fraction and the breakdown of particles compared to the conventional method. On the other hand, the modified method increased the bias related to microbial contamination and enlarged the difference between the in situ and in vivo degradation.

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