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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    Addressing the Challenges Related to Transforming Qualitative Into Quantitative Data in Qualitative Comparative Analysis
    Block, Debora de; Vis, Barbara - \ 2019
    Journal of Mixed Methods Research 13 (2019)4. - ISSN 1558-6898 - p. 503 - 535.
    calibration - data presentation - mixed methods research - qualitative comparative analysis - qualitative data - quantitizing - sensitivity testing
    The use of qualitative data has so far received relatively little attention in methodological discussions on qualitative comparative analysis (QCA). This article addresses this lacuna by discussing the challenges researchers face when transforming qualitative data into quantitative data in QCA. By reviewing 29 empirical studies using qualitative data for QCA, we explore common practices related to data calibration, data presentation, and sensitivity testing. Based on these three issues, we provide considerations when using qualitative data for QCA, which are relevant both for QCA scholars working with qualitative data and the wider mixed methods research community involved in quantitizing.
    Kalibratie pH meter Inolab
    Bom, Jesse ; Dijksman, J.A. ; Lageschaar, Luuk ; Galen, Martijn van; Hoogendam, C.W. ; Wegh, R.A.J. - \ 2016
    Wageningen : Wageningen UR
    ph - zuurgraad - meetinstrumenten - instrumenten (meters) - kalibratie - ph - acidity - indicating instruments - instruments - calibration
    Instructievideo over de kalibratie van de InoLab pH meter
    Kalibratie pH meter Schott
    Bom, Jesse ; Dijksman, J.A. ; Lageschaar, Luuk ; Galen, Martijn van; Hoogendam, C.W. ; Wegh, R.A.J. - \ 2016
    Wageningen : Wageningen UR
    ph - zuurgraad - meetinstrumenten - instrumenten (meters) - kalibratie - ph - acidity - indicating instruments - instruments - calibration
    Instructievideo over de kalibratie van de Schott pH meter
    Statistical modelling for exposure measurement error with application to epidemiological data
    Agogo, G.O. - \ 2016
    Wageningen University. Promotor(en): Hendriek Boshuizen; Fred van Eeuwijk, co-promotor(en): Hilko van der Voet. - Wageningen : Wageningen University - ISBN 9789462576223 - 160
    calibration - regression analysis - exposure assessment - validity - simulation models - statistical bias - epidemiology - kalibratie - regressieanalyse - blootstellingsbepaling - geldigheid - simulatiemodellen - statistische vertekening - epidemiologie

    Background Measurement error in exposure variables is an important issue in epidemiological studies that relate exposures to health outcomes. Such studies, however, usually pay limited attention to the quantitative effects of exposure measurement error on estimated exposure-outcome associations. Therefore, the estimators for exposure-outcome associations are prone to bias. Existing methods to adjust for the bias in the associations require a validation study with multiple replicates of a reference measurement. Validation studies with multiple replicates are quite costly and therefore, in some cases only a single–replicate validation study is conducted besides the main study. For a study that does not include an internal validation study, the challenge in dealing with exposure measurement error is even bigger. The challenge is how to use external data from other similar validation studies to adjust for the bias in the exposure-outcome association. In accelerometry research, various accelerometer models have currently been developed. However, some of these new accelerometer models have not been properly validated in field situations. Despite the widely recognized measurement error in the accelerometer, some accelerometers have been used to validate other instruments, such as physical activity questionnaires, in measuring physical activity. Consequently, if an instrument is validated against the accelerometer, and the accelerometer itself has considerable measurement error, the observed validity in the instrument being validated will misrepresent the true validity.

    Methodology In this thesis, we adapted regression calibration to adjust for exposure measurement error for a single-replicate validation study with zero-inflated reference measurements and assessed the adequacy of the adapted method in a simulation study. For the case where there is no internal validation study, we showed how to combine external data on validity for self-report instruments with the observed questionnaire data to adjust for the bias in the associations caused by measurement error in correlated exposures. In the last part, we applied a measurement error model to assess the measurement error in physical activity as measured by an accelerometer in free-living individuals in a recently concluded validation study.

    Results The performance of the proposed two-part model was sensitive to the form of continuous independent variables and was minimally influenced by the correlation between the probability of a non-zero response and the actual non-zero response values. Reducing the number of covariates in the model seemed beneficial, but was not critical in large-sample studies. We showed that if the confounder is strongly linked with the outcome, measurement error in the confounder can be more influential than measurement error in the exposure in causing the bias in the exposure-outcome association, and that the bias can be in any direction. We further showed that when accelerometers are used to monitor the level of physical activity in free-living individuals, the mean level of physical activity would be underestimated, the associations between physical activity and health outcomes would be biased, and there would be loss of statistical power to detect associations.

    Conclusion The following remarks were made from the work in this thesis. First, when only a single-replicate validation study with zero-inflated reference measurements is available, a correctly specified regression calibration can be used to adjust for the bias in the exposure-outcome associations. The performance of the proposed calibration model is influenced more by the assumption made on the form of the continuous covariates than the form of the response distribution. Second, in the absence of an internal validation study, carefully extracted validation data that is transportable to the main study can be used to adjust for the bias in the associations. The proposed method is also useful in conducting sensitivity analyses on the effect of measurement errors. Lastly, when “reference” instruments are themselves marred by substantial bias, the effect of measurement error in an instrument being validated can be seriously underestimated.

    Kalibratie van het Landelijk KRW-Verkenner Model 2.0
    Mulder, H.M. ; Cleij, P. - \ 2015
    Deltares - 41
    kaderrichtlijn water - kalibratie - modelleren - stikstofretentie - voedingsstoffenretentie - fosfor - water framework directive - calibration - modeling - nitrogen retention - nutrient retention - phosphorus
    Bij de laatste validatie van het Landelijk KRW-Verkenner Model (Cleij et al. 2014) is gebleken dat de concentraties voor N-totaal en P-totaal vaak matig tot slecht voorspeld worden. Eén van de manieren om de voorspellende waarde van een model te verhogen is kalibratie. Het LKM is echter modelparameter-arm, en de enige 'knoppen', waaraan wat betreft modelparameters gedraaid kan worden zijn de parameters van het eerste-orde afbraak proces voor -totaal en -totaal de a raakconstante ij en de temperatuurco ici nt De tot nu toe gebruikte retentieparameters zijn afkomstig van een vertaling van de retentieparameters van het KRW-ECHO systeem naar de retentieparameters voor de KRWVerkenner (Roovaart et al. 2012). Het in dit rapport beschreven onderzoek is via kalibratie gezocht naar een nieuwe set retentieparameters voor N-totaal en P-totaal, uitgaande van de tot nu toe gehanteerde parameterwaarden met als doel het voorspellend vermogen van het LKM op dit punt te verbeteren.
    Spatially explicit fate modelling of nanomaterials in natural waters
    Quik, J.T.K. ; Klein, J.J.M. de; Koelmans, A.A. - \ 2015
    Water Research 80 (2015). - ISSN 0043-1354 - p. 200 - 208.
    engineered nanomaterials - aquatic environments - nanoparticles - aggregation - systems - exposure - sedimentation - calibration - matrices - silver
    Site specific exposure assessments for engineered nanoparticles (ENPs) require spatially explicit fate models, which however are not yet available. Here we present an ENP fate model (NanoDUFLOW) that links ENP specific process descriptions to a spatially explicit hydrological model. The link enables the realistic modelling of feedbacks between local flow conditions and ENP fate processes, such as homo- and heteroaggregation, resuspension and sedimentation. Spatially explicit simulations using five size classes of ENPs and five size classes of natural solids showed how ENP sediment contamination ‘hot spots’ and ENP speciation can be predicted as a function of place and time. For the catchment modelled, neglect of spatial heterogeneity caused relatively small differences in ENP retention. However, simplification of the number of size classes to one average class, resulted in up to 3.3 times lower values of retention compared to scenarios that used detailed size distributions. Local concentrations in sediment were underestimated up to 20 fold upon simplification of spatial heterogeneity or particle size distribution. We conclude that spatial heterogeneity should not be neglected when assessing the risks of ENPs.
    Plasma carotenoids, vitamin C, retinol and tocopherols levels and pancreatic cancer risk within the European Prospective Investigation into Cancer and Nutrition: A nested case-control study : Plasma micronutrients and pancreatic cancer risk
    Jeurnink, S.M. ; Ros, M.M. ; Leenders, M. ; Duijnhoven, F.J.B. van - \ 2015
    International Journal of Cancer 136 (2015)6. - ISSN 0020-7136 - p. E665 - E676.
    alpha-tocopherol - beta-carotene - serum - smoking - cohorts - antioxidants - consumption - calibration - population - metabolism
    Evidence of a protective effect of several antioxidants and other nutrients on pancreatic cancer risk is inconsistent. The aim of this study was to investigate the association for prediagnostic plasma levels of carotenoids, vitamin C, retinol and tocopherols with risk of pancreatic cancer in a case–control study nested within the European Prospective Investigation into Cancer and Nutrition (EPIC). 446 incident exocrine pancreatic cancer cases were matched to 446 controls by age at blood collection, study center, sex, date and time of blood collection, fasting status and hormone use. Plasma carotenoids (a- and ß-carotene, lycopene, ß-cryptoxanthin, canthaxanthin, zeaxanthin and lutein), a- and ¿-tocopherol and retinol were measured by reverse phase high-performance liquid chromatography and plasma vitamin C by a colorimetric assay. Incidence rate ratios (IRRs) with 95% confidence intervals (95%CIs) for pancreatic cancer risk were estimated using a conditional logistic regression analysis, adjusted for smoking status, smoking duration and intensity, waist circumference, cotinine levels and diabetes status. Inverse associations with pancreatic cancer risk were found for plasma ß-carotene (IRR highest vs. lowest quartile 0.52, 95%CI 0.31–0.88, p for trend¿=¿0.02), zeaxanthin (IRR highest vs. lowest quartile 0.53, 95%CI 0.30–0.94, p for trend¿=¿0.06) and a-tocopherol (IRR highest vs. lowest quartile 0.62, 95%CI 0.39–0.99, p for trend¿=¿0.08. For a- and ß-carotene, lutein, sum of carotenoids and ¿-tocopherol, heterogeneity between geographical regions was observed. In conclusion, our results show that higher plasma concentrations of ß-carotene, zeaxanthin and a-tocopherol may be inversely associated with risk of pancreatic cancer, but further studies are warranted.
    Preparing suitable climate scenario data to assess impacts on local food safety
    Liu, C. ; Hofstra, N. ; Leemans, R. - \ 2015
    Food Research International 68 (2015). - ISSN 0963-9969 - p. 31 - 40.
    stochastic weather generator - multimodel ensemble - change projections - model - precipitation - cmip5 - uncertainty - temperature - calibration - growth
    Quantification of climate change impacts on food safety requires food safety assessment with different past and future climate scenario data to compare current and future conditions. This study presents a tool to prepare climate and climate change data for local food safety scenario analysis and illustrates how this tool can be used with impact models, such as bacterial and mycotoxin growth and pesticide models. As an example, coarse gridded data from two global climate models (GCMs), HadGEM2-ES and CCSM4, are selected and downscaled using the “Delta method” with quantile-quantile correction for Ukkel, Belgium. Observational daily temperature and precipitation data from 1981 to 2000 are used as a reference for this downscaling. Data are provided for four future representative concentration pathways (RCPs) for the periods 2031–2050 and 2081–2100. These RCPs are radiative forcing scenarios for which future climate conditions are projected. The climate projections for these RCPs show that both temperature and precipitation will increase towards the end of the century in Ukkel. The climate change data are then used with Ratkowsky's bacterial growth model to illustrate how projected climate data can be used for projecting bacterial growth in the future. In this example, the growth rate of Lactobacillus plantarum in Ukkel is projected to increase in the future and the number of days that the bacteria are able to grow is also projected to increase. This example shows that this downscaling method can be applied to assess future food safety. However, we only used two GCMs. To obtain a more realistic uncertainty range, using many different GCM output datasets and working directly with climate modellers is recommended. Our approach helps food safety researchers to perform their own climate change scenario analysis. The actual algorithm of the downscaling method and its detailed manual is available in the supplementary material.
    Multimodel ensembles of wheat growth: Many models are better than one
    Martre, P. ; Wallach, D. ; Asseng, S. ; Ewert, F. ; Jones, J.W. ; Rötter, R.P. ; Boote, K.J. ; Ruane, A.C. ; Thorburn, P. ; Cammarano, D. ; Hatfield, J.L. ; Rosenzweig, C. ; Aggarwal, P.K. ; Angula, C. ; Basso, B. ; Bertuzzi, P. ; Biernath, C. ; Brisson, N. ; Challinor, A. ; Doltra, J. ; Gayler, S. ; Goldberg, R.A. ; Grant, R.F. ; Heng, L. ; Hooker, J. ; Hunt, L.A. ; Ingwersen, J. ; Izaurralde, C. ; Kersebaum, K.C. ; Mueller, C. ; Kumar, S. ; Nendel, C. ; O'Leary, G.J. ; Olesen, J.E. ; Osborne, T.M. ; Palosuo, T. ; Priesack, E. ; Ripoche, D. ; Semenov, M.A. ; Shcherbak, I. ; Steduto, P. ; Stöckle, C.O. ; Stratonovitch, P. ; Streck, T. ; Supit, I. ; Tao, Fulu ; Travasso, M. ; Waha, K. ; White, J.W. ; Wolf, J. - \ 2015
    Global Change Biology 21 (2015)2. - ISSN 1354-1013 - p. 911 - 925.
    climate-change - crop production - impacts - yield - simulations - calibration - australia - billion - europe - grain
    Crop models of crop growth are increasingly used to quantify the impact of global changes due to climate or crop management. Therefore, accuracy of simulation results is a major concern. Studies with ensembles of crop models can give valuable information about model accuracy and uncertainty, but such studies are difficult to organize and have only recently begun. We report on the largest ensemble study to date, of 27 wheat models tested in four contrasting locations for their accuracy in simulating multiple crop growth and yield variables. The relative error averaged over models was 24-38% for the different end-of-season variables including grain yield (GY) and grain protein concentration (GPC). There was little relation between error of a model for GY or GPC and error for in-season variables. Thus, most models did not arrive at accurate simulations of GY and GPC by accurately simulating preceding growth dynamics. Ensemble simulations, taking either the mean (e-mean) or median (e-median) of simulated values, gave better estimates than any individual model when all variables were considered. Compared to individual models, e-median ranked first in simulating measured GY and third in GPC. The error of e-mean and e-median declined with an increasing number of ensemble members, with little decrease beyond 10 models. We conclude that multimodel ensembles can be used to create new estimators with improved accuracy and consistency in simulating growth dynamics. We argue that these results are applicable to other crop species, and hypothesize that they apply more generally to ecological system models.
    The Wageningen Lowland Runoff Simulator (WALRUS): a lumped rainfall-runoff model for catchments with shallow groundwater
    Brauer, C.C. ; Teuling, A.J. ; Torfs, P.J.J.F. ; Uijlenhoet, R. - \ 2014
    Geoscientific Model Development 7 (2014)5. - ISSN 1991-959X - p. 2313 - 2332.
    flow route contributions - surface water interactions - soil-moisture - process conceptualization - hydrological models - root-growth - tile drain - scale - calibration - discharge
    We present the Wageningen Lowland Runoff Simulator (WALRUS), a novel rainfall-runoff model to fill the gap between complex, spatially distributed models which are often used in lowland catchments and simple, parametric (conceptual) models which have mostly been developed for sloping catchments. WALRUS explicitly accounts for processes that are important in lowland areas, notably (1) groundwater-unsaturated zone coupling, (2) wetness-dependent flow routes, (3) groundwater-surface water feedbacks and (4) seepage and surface water supply. WALRUS consists of a coupled groundwater-vadose zone reservoir, a quickflow reservoir and a surface water reservoir. WALRUS is suitable for operational use because it is computationally efficient and numerically stable (achieved with a flexible time step approach). In the open source model code default relations have been implemented, leaving only four parameters which require calibration. For research purposes, these defaults can easily be changed. Numerical experiments show that the implemented feedbacks have the desired effect on the system variables.
    Technical notes: A detailed study for the provision of measurement uncertainty and traceability for goniospectrometers
    Peltoniemi, J.I. ; Hakala, T. ; Suomalainen, J.M. ; Honkavaara, E. ; Markelin, L. ; Gritsevich, M. ; Eskelinen, J. ; Jaanson, P. ; Ikonen, E. - \ 2014
    Journal of Quantitative Spectroscopy and Radiative Transfer 146 (2014). - ISSN 0022-4073 - p. 376 - 390.
    reflectance distribution function - laboratory goniometer system - bidirectional reflectance - diffuse-reflectance - spectro-goniometer - test field - light - polarization - snow - calibration
    The measurement uncertainty and traceability of the Finnish Geodetic Institutes¿s field gonio-spectro-polarimeter FIGIFIGO have been assessed. First, the reference standard (Spectralon sample) was measured at the National Standard Laboratory of MIKES-Aalto. This standard was transferred to FGI¿s field reference standard (larger Spectralon sample), and from that to the unmanned aerial vehicle (UAV), reference standards (1 m2 plates). The reflectance measurement uncertainty of FIGIFIGO has been estimated to be 0.01 in ideal laboratory conditions, but about 0.02–0.05 in typical field conditions, larger at larger solar or observation zenith angles. Target specific uncertainties can increase total uncertainty even to 0.1–0.2. The angular reading uncertainty is between 1° and 3°, depending on user selection, and the polarisation uncertainty is around 0.01. For UAV, the transferred reflectance uncertainty is about 0.05–0.1, depending on, how ideal the measurement conditions are. The design concept of FIGIFIGO has been proved to have a number of advantages, such as a well-adopted user-friendly interface, a high level of automation and excellent suitability for the field measurements. It is a perfect instrument for collection of reference data on a given target in natural (and well-recorded) conditions. In addition to the strong points of FIGIFIGO, the current study reveals several issues that need further attention, such as the field of view, illumination quality, polarisation calibration, Spectralon reflectance and polarisation properties in the 1000–2400 nm range.
    Reactie op het artikel ‘Controle van kalibratiegegevens’
    Knotters, M. ; Hoogland, T. - \ 2013
    Stromingen : vakblad voor hydrologen 19 (2013)3/4. - ISSN 1382-6069 - p. 125 - 126.
    hydrologie - grondwaterstand - watervoorziening - informatiesystemen - kalibratie - hydrology - groundwater level - water supply - information systems - calibration
    Grondwaterstandsinformatie van goede kwaliteit vinden wij belangrijk. Iedere inspanning om deze kwaliteit vast te stellen en te verbeteren juichen wij toe, vooral als zo’n inspanning wetenschappelijk degelijk is onderbouwd. Wat betreft dat laatste willen wij graag twee opmerkingen plaatsen bij het artikel ‘Controle van kalibratiegegevens’ van Jaco van der Gaast in Stromingen 19(2), pag. 85-90
    Reduced carbon uptake during the 2010 Northern Hemisphere summer from GOSAT
    Guerlet, S. ; Basu, S. ; Butz, A. ; Krol, M.C. ; Hahne, P. ; Houweling, S. ; Hasekamp, O.P. ; Aben, I. - \ 2013
    Geophysical Research Letters 40 (2013)10. - ISSN 0094-8276 - p. 2378 - 2383.
    column observing network - calibration - transport - dioxide - europe
    Column-averaged dry air mole fractions of carbon dioxide (XCO2) measured by the Greenhouse Gases Observing Satellite (GOSAT) reveal significant interannual variation (IAV) of CO(2)uptake during the Northern Hemisphere summer between 2009 and 2010. The XCO(2)drawdown in 2010 is shallower than in 2009 by 2.4ppm and 3.0ppm over North America and Eurasia, respectively. Reduced carbon uptake in the summer of 2010 is most likely due to the heat wave in Eurasia driving biospheric fluxes and fire emissions. A joint inversion of GOSAT and surface data estimates an integrated biospheric and fire emission anomaly in April-September of 0.89 0.20 PgC over Eurasia. In contrast, inversions of surface measurements alone fail to replicate the observed XCO(2)IAV and underestimate emission IAV over Eurasia. This shows the value of GOSAT XCO(2)in constraining the response of land-atmosphere exchange of CO2 to climate events.
    Fruit and Vegetable Consumption and Mortality: European Prospective Investigation Into Cancer and Nutrition
    Leenders, M. ; Sluijs, I. van der; Ros, M.M. ; Boshuizen, H.C. ; Siersema, P.D. ; Ferrari, P. ; Weikert, C. ; Tjonneland, A. ; Olsen, A. ; Boutron-Ruault, M.C. ; Clavel-Chapelon, F. ; Nailler, L. ; Teucher, B. ; Li, K.R. ; Boeing, H. ; Bergmann, M.M. ; Trichopoulou, A. ; Lagiou, P. ; Trichopoulos, D. ; Palli, D. ; Pala, V. ; Panico, S. ; Tumino, R. ; Sacerdote, C. ; Peeters, P.H.M. ; Gils, C.H. van; Lund, E. ; Engeset, D. ; Redondo, M.L. ; Agudo, A. ; Sanchez, M.J. ; Navarro, C. ; Ardanaz, E. ; Sonestedt, E. ; Ericson, U. ; Nilsson, L.M. ; Khaw, K.T. ; Warcham, N.J. ; Key, T.J. ; Crowe, F.L. ; Romieu, I. ; Gunter, M.J. ; Gallo, V. ; Overvad, K. ; Riboli, E. ; Bueno-de-Mesquita, H.B. - \ 2013
    American Journal of Epidemiology 178 (2013)4. - ISSN 0002-9262 - p. 590 - 602.
    cardiovascular-disease - oxidative stress - heart-disease - dietary assessment - risk - population - impact - men - calibration - health
    In this study, the relation between fruit and vegetable consumption and mortality was investigated within the European Prospective Investigation Into Cancer and Nutrition. Survival analyses were performed, including 451,151 participants from 10 European countries, recruited between 1992 and 2000 and followed until 2010. Hazard ratios, rate advancement periods, and preventable proportions to respectively compare risk of death between quartiles of consumption, to estimate the period by which the risk of death was postponed among high consumers, and to estimate proportions of deaths that could be prevented if all participants would shift their consumption 1 quartile upward. Consumption of fruits and vegetables was inversely associated with all-cause mortality (for the highest quartile, hazard ratio = 0.90, 95% confidence interval (CI): 0.86, 0.94), with a rate advancement period of 1.12 years (95% CI: 0.70, 1.54), and with a preventable proportion of 2.95%. This association was driven mainly by cardiovascular disease mortality (for the highest quartile, hazard ratio = 0.85, 95% CI: 0.77, 0.93). Stronger inverse associations were observed for participants with high alcohol consumption or high body mass index and suggested in smokers. Inverse associations were stronger for raw than for cooked vegetable consumption. These results support the evidence that fruit and vegetable consumption is associated with a lower risk of death.
    Impact-based integrated real-time control for improvement of the Dommel River water quality
    Langeveld, J. ; Benedetti, L. ; Klein, J.J.M. de; Nopens, I. ; Amerlinck, Y. ; Nieuwenhuijzen, A.F. van; Flameling, T. ; Zanten, O. van; Weijers, S. - \ 2013
    Urban Water Journal 10 (2013)5. - ISSN 1573-062X - p. 312 - 329.
    drainage systems - treatment-plant - models - calibration - pollution - design
    The KALLISTO project aims at finding cost-efficient sets of measures to meet the Water Framework Directive (WFD) derived goals for the river Dommel. Within the project, both acute and long term impacts of the urban wastewater system on the chemical and ecological quality of the river are studied with an integral monitoring campaign in the urban wastewater system (WWTP and sewers) and in the river. Based on this monitoring campaign, detailed models were calibrated. These models are partly simplified and integrated in a single model, which is validated using the detailed submodels. The integrated model was used to study the potential for impact-based real-time control (RTC). Impact based RTC proved to be able to improve the quality of the receiving waters significantly, although additional measures remain necessary to be able to meet the WFD requirements
    Dietary intake of vitamin d and calcium and breast cancer risk in the European prospective investigation into cancer and nutrition
    Abbas, S. ; Linseisen, J. ; Rohrmann, S. ; Chang-Claude, J. ; Peeters, P.H. ; Engel, P. ; Brustad, M. ; Lund, E. ; Skeie, G. ; Duijnhoven, F.J.B. van - \ 2013
    Nutrition and Cancer 65 (2013)2. - ISSN 0163-5581 - p. 178 - 187.
    french e3n cohort - dairy-products - sunlight exposure - adolescent diet - women - micronutrients - calibration - metaanalysis - prevention
    Studies assessing the effects of vitamin D or calcium intake on breast cancer risk have been inconclusive. Furthermore, few studies have evaluated them jointly. This study is the largest so far examining the association of dietary vitamin D and calcium intake with breast cancer risk in the European Prospective Investigation into Cancer and Nutrition. During a mean follow-up of 8.8 yr, 7760 incident invasive breast cancer cases were identified among 319,985 women. Multivariable Cox proportional hazards regression was used to estimate hazard ratios (HR) and 95% confidence intervals (CI) for pre- and postmenopausal breast cancer risk. Comparing the highest with the lowest quintile of vitamin D intake, HR and 95% CI were 1.07 (0.87–1.32) and 1.02 (0.90–1.16) for pre- and postmenopausal women, respectively. The corresponding HR and 95% CIs for calcium intake were 0.98 (0.80–1.19) and 0.90 (0.79–1.02), respectively. For calcium intake in postmenopausal women, the test for trend was borderline statistically significant (Ptrend = 0.05). There was no significant interaction between vitamin D and calcium intake and cancer risk (Pinteraction = 0.57 and 0.22 in pre- and postmenopausal women, respectively). In this large prospective cohort, we found no evidence for an association between dietary vitamin D or calcium intake and breast cancer risk.
    On data requirements for calibration of integrated models for urban water systems
    Langeveld, J. ; Nopens, I. ; Schilperoort, R. ; Benedetti, L. ; Klein, J.J.M. de; Amerlinck, Y. ; Weijers, S. - \ 2013
    Water Science and Technology 68 (2013)3. - ISSN 0273-1223 - p. 728 - 736.
    afvalwaterbehandeling - afvalwaterbehandelingsinstallaties - riolering - watersystemen - stedelijke gebieden - monitoring - kalibratie - modellen - modelleren - oppervlaktewaterkwaliteit - noord-brabant - waste water treatment - waste water treatment plants - sewerage - water systems - urban areas - monitoring - calibration - models - modeling - surface water quality - noord-brabant - practical identifiability - simulation-models - optimization - uncertainty - quality
    Modeling of integrated urban water systems (IUWS) has seen a rapid development in recent years. Models and software are available that describe the process dynamics in sewers, wastewater treatment plants (WWTPs), receiving water systems as well as at the interfaces between the submodels. Successful applications of integrated modeling are, however, relatively scarce. One of the reasons for this is the lack of high-quality monitoring data with the required spatial and temporal resolution and accuracy to calibrate and validate the integrated models, even though the state of the art of monitoring itself is no longer the limiting factor. This paper discusses the efforts to be able to meet the data requirements associated with integrated modeling and describes the methods applied to validate the monitoring data and to use submodels as software sensor to provide the necessary input for other submodels
    Managing uncertainty in integrated environmental modelling: The UncertWeb framework.
    Bastin, L. ; Cornford, D. ; Jones, R. ; Heuvelink, G.B.M. ; Pebesma, E. ; Stasch, C. ; Nativi, S. ; Mazzetti, P. - \ 2013
    Environmental Modelling & Software 39 (2013). - ISSN 1364-8152 - p. 116 - 134.
    sensitivity-analysis - parameter-estimation - bayesian-approach - watershed model - climate-change - error - calibration - systems - design - tools
    Web-based distributed modelling architectures are gaining increasing recognition as potentially useful tools to build holistic environmental models, combining individual components in complex workflows. However, existing web-based modelling frameworks currently offer no support for managing uncertainty. On the other hand, the rich array of modelling frameworks and simulation tools which support uncertainty propagation in complex and chained models typically lack the benefits of web based solutions such as ready publication, discoverability and easy access. In this article we describe the developments within the UncertWeb project which are designed to provide uncertainty support in the context of the proposed ‘Model Web’. We give an overview of uncertainty in modelling, review uncertainty management in existing modelling frameworks and consider the semantic and interoperability issues raised by integrated modelling. We describe the scope and architecture required to support uncertainty management as developed in UncertWeb. This includes tools which support elicitation, aggregation/disaggregation, visualisation and uncertainty/sensitivity analysis. We conclude by highlighting areas that require further research and development in UncertWeb, such as model calibration and inference within complex environmental models.
    Adherence to the mediterranean diet and risk of breast cancer in the European prospective investigation into cancer and nutrition cohort study
    Buckland, G. ; Travier, N. ; Cottet, V. ; Gonzalez, C.A. ; Lujan-Barroso, L. ; Agudo, A. ; Trichopoulou, A. ; Lagiou, P. ; Trichopoulos, D. ; Duijnhoven, F.J.B. van - \ 2013
    International Journal of Cancer 132 (2013)12. - ISSN 0020-7136 - p. 2918 - 2927.
    postmenopausal women - fatty-acid - patterns - estrogen - population - metaanalysis - calibration - rationale - validity - disease
    Epidemiological evidence suggests that the Mediterranean diet (MD) could reduce the risk of breast cancer (BC). As evidence from the prospective studies remains scarce and conflicting, we investigated the association between adherence to the MD and risk of BC among 335,062 women recruited from 1992 to 2000, in ten European countries, and followed for 11 years on average. Adherence to the MD was estimated through an adapted relative Mediterranean diet (arMED) score excluding alcohol. Cox proportional hazards regression models were used while adjusting for BC risk factors. A total of 9,009 postmenopausal and 1,216 premenopausal first primary incident invasive BC were identified (5,862 estrogen or progesterone receptor positive [ER+/PR+] and 1,018 estrogen and progesterone receptor negative [ER-/PR-]). The arMED was inversely associated with the risk of BC overall and in postmenopausal women (high vs. low arMED score; hazard ratio [HR] = 0.94 [95% confidence interval [CI]: 0.88, 1.00] ptrend = 0.048, and HR = 0.93 [95% CI: 0.87, 0.99] ptrend = 0.037, respectively). The association was more pronounced in ER-/PR- tumors (HR = 0.80 [95% CI: 0.65, 0.99] ptrend = 0.043). The arMED score was not associated with BC in premenopausal women. Our findings show that adherence to a MD excluding alcohol was related to a modest reduced risk of BC in postmenopausal women, and this association was stronger in receptor-negative tumors. The results support the potential scope for BC prevention through dietary modification.
    Calibration and validation of land-use models
    Vliet, J. van - \ 2013
    Wageningen University. Promotor(en): Arnold Bregt. - S.l. : s.n. - ISBN 9789461734433 - 162
    landgebruik - modellen - kalibratie - verandering - beoordeling - stedelijke gebieden - modelleren - land use - models - calibration - change - assessment - urban areas - modeling

    Land use is constantly changing. For example, urban areas expand as a result of population growth, cropping patterns change to fulfil the demand for bioenergy and natural vegetation recovers in locations where farmers cease to farm. Understanding these changes is pivotal to explore future land-use scenarios and to design spatial policies. Land-use models are increasingly being used for these purposes. They function as virtual laboratories in which scientists or policy analysts can conduct experiments. In order to reliably apply models for these purposes, they need to be calibrated, where calibration is the adjustment of parameters to improve the model’s performance. Consequently, the value of modelled land-use scenarios and policy assessments depends on the quality of the calibration. Assessment of the quality of the calibration is termed validation, and is ideally performed independently in the sense that the data that is used for validation has not been used for calibration.

    The development of a land-use model can be described by four sequential phases: analysis and conceptual modelling, computer programming of the conceptual model, calibration of the computerized model, and experimentation with the calibrated model. The first three phases all have their own evaluation procedures: conceptual validation, code verification and operational validation, respectively. Operational validation provides insights into the strengths and weaknesses of a particular model application, and sometimes it can suggest directions for improvement. However, available assessment methods have limitations for their application in land-use modelling. Therefore, there is a demand to develop and apply more appropriate methods. The work presented in this thesis first considers the properties of land-use models that are important for their assessment, and subsequently presents and applies several methods that can be used for this assessment.

    Many land-use changes are directly or indirectly the result of human decisions. However, human decisions are inherently uncertain, and therefore land-use models cannot be expected to simulate these land-use changes exactly. This is acknowledged by many land-use models as they use a stochastic component to simulate land-use changes. Therefore, land-use models should not only be validated on their predictive accuracy, their capacity to accurately allocate land-use changes on the map, but also on their process accuracy, their capacity to realistically simulate land-use change processes. Moreover, many models start from an initial land-use map and simulate changes relative to this map. The amount of change for a simulation is typically small relative to the entire map, which means that a large part of the result is caused by persistence. For this reason, a benchmark, such as a naive predictor, is required to properly asses the accuracy of simulation results. This benchmark can be implicit to the assessment method itself, or explicit, i.e. another land-use model which serves as a reference model. Outperforming the benchmark can be considered a minimum threshold to pass; however, it cannot directly inform whether a model is acceptable as this depends on the purpose of the model, the requirements of the study and the application domain.

    The predictive accuracy of a land-use model is typically assessed by comparing a simulation result with the actual land-use map at the end of a simulation. A common method for this is the Kappa statistic, which expresses the agreement between two land-use maps corrected for the expected agreement from a random allocation given the distribution of class sizes. However, this is not an appropriate reference level to assess the predictive accuracy of land-use models, because it does not account for the amount of change. This thesis presents Kappa Simulation, a new map-comparison method that is identical in form to Kappa, but which instead applies a more appropriate reference model based on random allocation of class transitions relative to the initial map. This implicitly accounts for the amount of change, which truly allows gauging the predictive accuracy of changes in land-use models. However, Kappa Simulation cannot differentiate between near-hits and complete misses, while this distinction is often very relevant for land-use modellers. This thesis therefore presents Fuzzy Kappa Simulation. This statistic is an improvement of Kappa Simulation, as it applies a fuzzy interpretation of class transitions and their locations. This means that it can account for near-hits, which makes it arguably the most suitable map comparison method to assess the predictive accuracy of land-use models.

    Because of the intrinsic uncertainty underlying land-use change processes, a realistic land-use model does not necessarily generate a high predictive accuracy, which justifies a separate assessment of its process accuracy. Ideally, process accuracy is assessed directly from the values of model parameters. However, it is often impossible to observe real-world values for these parameters because drivers for land-use changes are correlated or they cannot be measured. Therefore, the process accuracy is typically assessed indirectly from the land-use patterns generated by the model. Two groups of methods exist to characterize land-use patterns: landscape metrics and fractal metrics. Landscape metrics are a collection of algorithms that have been applied in landscape ecology to characterize land-use patterns. In this thesis, landscape metrics have been used to compare the simulated land-use map with the observed land-use map instead. Fractal metrics, which have their origin in complexity science, are another type of measures to characterize regularities in (urban) land-use patterns. Examples are power-law distributions for urban clusters and fractal dimensions of patches of urban land. Moreover, fractal metrics can be interpreted in absolute terms since they represent general regularities in urban systems for which values are known from literature. Therefore, fractal metrics also allow evaluation of the process accuracy of a synthetic application for which no observed land-use pattern is available for comparison.

    Neighbourhood rules represent the influence of the existing land-use distribution on the location of land-use changes. This includes the persistence, conversion and attraction/repulsion of land uses in the neighbourhood of a location. Because neighbourhood rules cannot be estimated directly from data, they need to be set in a calibration procedure. The work in this thesis indicates that agents consider their neighbourhood at different spatial scales: the direct vicinity of a location has a strong influence on the allocation of new urban land, but neighbourhood rules over larger distance – typically the size of urban regions – also improve the model performance. This thesis also discusses a special type of neighbourhood rules: rules describing the influence of the existing activity distribution on the allocation of activity changes, where activities denote a quantity or density related to a land use, such as inhabitants for residential land use. This study shows that relatively simple rules can grow a realistic urban settlement structure, which confirms that neighbourhood rules improve the process accuracy of a land-use model.

    It should be noted that while the methods presented and applied in this thesis are objective, the selection of assessment methods remains subjective. Moreover, because no method is yet capable of describing land-use patterns satisfactorily, more subjective methods such as visual assessment of simulation results or interpretation of parameter values remain of added value in the calibration and validation of land-use models.

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