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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    Relative Validity of the HELIUS Food Frequency Questionnaire for Measuring Dietary Intake in Older Adult Participants of the Longitudinal Aging Study Amsterdam
    Visser, Marjolein ; Elstgeest, Liset E.M. ; Winkens, Laura H.H. ; Brouwer, Ingeborg A. ; Nicolaou, Mary - \ 2020
    Nutrients 12 (2020)7. - ISSN 2072-6643
    24-hour recall - diet assessment - elderly - FFQ - validation

    The aim of this study was to determine the relative validity of the HEalthy LIfe in an Urban Setting (HELIUS) food frequency questionnaire (FFQ) in assessing the dietary intake of energy, nutrients, and food groups of Dutch older men and women. In 2014-2015, 88 participants of the Longitudinal Aging Study Amsterdam aged 71.9 (SD 8.6) years completed the 238-item HELIUS FFQ and three 24-hour dietary recalls. The mean group-level bias in the intakes of energy, nutrients, and food groups between the two methods was assessed, as well as Pearson's correlation coefficients and level of agreement using quintile distribution. For the intakes of energy and macronutrients, the group-level bias was ≤5%, Pearson's correlation coefficients were moderate to good (ranging from 0.26 for total fat to 0.72 for alcohol), and agreement was moderate to high (classification in same or adjacent quintile ranging from 63% for energy, protein, and carbohydrate to 91% for alcohol). For most micronutrients and food groups, the relative validity was moderate (Pearson's correlation coefficients between 0.3 and 0.5), with the lowest correlations for β-carotene (0.08), vitamin B1 (0.19), fish (0.14), and grains (0.24). In conclusion, for energy and macronutrients, most micronutrients, and most food groups, the relative validity of the HELIUS FFQ to assess dietary intake in Dutch older adults was acceptable to good.

    How to compare sampling designs for mapping?
    Wadoux, Alexandre M.J.C. ; Brus, Dick J. - \ 2020
    European Journal of Soil Science (2020). - ISSN 1351-0754
    Kriging - machine learning - pedometrics - random forest - soil sampling - validation

    If a map is constructed through prediction with a statistical or non-statistical model, the sampling design used for selecting the sample on which the model is fitted plays a key role in the final map accuracy. Several sampling designs are available for selecting these calibration samples. Commonly, sampling designs for mapping are compared in real-world case studies by selecting just one sample for each of the sampling designs under study. In this study, we show that sampling designs for mapping are better compared on the basis of the distribution of the map quality indices over repeated selection of the calibration sample. In practice this is only feasible by subsampling a large dataset representing the population of interest, or by selecting calibration samples from a map depicting the study variable. This is illustrated with two real-world case studies. In the first case study a quantitative variable, soil organic carbon, is mapped by kriging with an external drift in France, whereas in the second case a categorical variable, land cover, is mapped by random forest in a region in France. The performance of two sampling designs for mapping are compared: simple random sampling and conditioned Latin hypercube sampling, at various sample sizes. We show that in both case studies the sampling distributions of map quality indices obtained with the two sampling design types, for a given sample size, show large variation and largely overlap. This shows that when comparing sampling designs for mapping on the basis of a single sample selected per design, there is a serious risk of an incidental result. Highlights: We provide a method to compare sampling designs for mapping. Random designs for selecting calibration samples should be compared on the basis of the sampling distribution of the map quality indices.

    Simultaneous Analysis of Glucosinolates and Isothiocyanates by Reversed-Phase Ultra-High-Performance Liquid Chromatography-Electron Spray Ionization-Tandem Mass Spectrometry
    Andini, Silvia ; Araya-Cloutier, Carla ; Sanders, Mark ; Vincken, Jean Paul - \ 2020
    Journal of Agricultural and Food Chemistry 68 (2020)10. - ISSN 0021-8561 - p. 3121 - 3131.
    dithiocarbamate - glucosinolate breakdown product - LC-MS analysis - mustard - thioglucosidase - validation

    A new method to simultaneously analyze various glucosinolates (GSLs) and isothiocyanates (ITCs) by reversed-phase ultra-high-performance liquid chromatography-electron spray ionization-tandem mass spectrometry has been developed and validated for 14 GSLs and 15 ITCs. It involved derivatization of ITCs with N-acetyl-l-cysteine (NAC). The limits of detection were 0.4-1.6 μM for GSLs and 0.9-2.6 μM for NAC-ITCs. The analysis of Sinapis alba, Brassica napus, and Brassica juncea extracts spiked with 14 GSLs and 15 ITCs indicated that the method generally had good intraday (≤10% RSD) and interday precisions (≤16% RSD). Recovery of the method was unaffected by the extracts and within 71-110% for GSLs and 66-122% for NAC-ITCs. The method was able to monitor the enzymatic hydrolysis of standard GSLs to ITCs in mixtures. Furthermore, GSLs and ITCs were simultaneously determined in Brassicaceae plant extracts before and after myrosinase treatment. This method can be applied to further investigate the enzymatic conversion of GSLs to ITCs in complex mixtures.

    Field data of "Monitoring forest phenology and leaf area index with the autonomous, low-cost transmittance sensor PASTiS-57"
    Brede, Benjamin ; Gastellu-Etchegorry, Jean Philippe ; Lauret, Nicolas ; Baret, Frederic ; Clevers, Jan ; Verbesselt, Jan ; Herold, Martin - \ 2020
    Wageningen University & Research
    forest - ground-based - Land Surface Phenology - Leaf Area Index - validation
    Land Surface Phenology (LSP) and Leaf Area Index (LAI) are important variables that describe the photosynthetically active phase and capacity of vegetation. Both are derived on the global scale from optical satellite sensors and require robust validation based on in situ sensors at high temporal resolution. This study assesses the PAI Autonomous System from Transmittance Sensors at 57? (PASTiS-57) instrument as a low-cost transmittance sensor for simultaneous monitoring of LSP and LAI in forest ecosystems. In a field experiment, spring leaf flush and autumn senescence in a Dutch beech forest were observed with PASTiS-57 and illumination independent, multi-temporal Terrestrial Laser Scanning (TLS) measurements in five plots. Both time series agreed to less than a day in Start Of Season (SOS) and End Of Season (EOS). LAI magnitude was strongly correlated with a Pearson correlation coefficient of 0.98. PASTiS-57 summer and winter LAI were on average 0.41m2m-2 and 1.43m2m-2 lower than TLS. This can be explained by previously reported overestimation of TLS. Additionally, PASTiS-57 was implemented in the Discrete Anisotropic Radiative Transfer (DART) Radiative Transfer Model (RTM) model for sensitivity analysis. This confirmed the robustness of the retrieval with respect to non-structural canopy properties and illumination conditions. Generally, PASTiS-57 fulfilled the CEOS LPV requirement of 20% accuracy in LAI for a wide range of biochemical and illumination conditions for turbid medium canopies. However, canopy non-randomness in discrete tree models led to strong biases. Overall, PASTiS-57 demonstrated the potential of autonomous devices for monitoring of phenology and LAI at daily temporal resolution as required for validation of satellite products that can be derived from ESA Copernicus’ optical missions, Sentinel-2 and -3.
    Evaluating the ecological realism of plant species distribution models with ecological indicator values
    Hellegers, Marjon ; Ozinga, Wim A. ; Hinsberg, Arjen ; Huijbregts, Mark A.J. ; Hennekens, Stephan M. ; Schaminée, Joop H.J. ; Dengler, Jürgen ; Schipper, Aafke M. - \ 2020
    Ecography 43 (2020)1. - ISSN 0906-7590 - p. 161 - 170.
    BioScore - ecological niche model - Ellenberg indicator values - model selection - scale dependency - validation

    Species distribution models (SDMs) are routinely applied to assess current as well as future species distributions, for example to assess impacts of future environmental change on biodiversity or to underpin conservation planning. It has been repeatedly emphasized that SDMs should be evaluated based not only on their goodness of fit to the data, but also on the realism of the modeled ecological responses. However, possibilities for the latter are hampered by limited knowledge on the true responses as well as a lack of quantitative evaluation methods. Here we compared modeled niche optima obtained from European-scale SDMs of 1476 terrestrial vascular plant species with empirical ecological indicator values indicating the preferences of plant species for key environmental conditions. For each plant species we first fitted an ensemble SDM including three modeling techniques (GLM, GAM and BRT) and extracted niche optima for climate, soil, land use and nitrogen deposition variables with a large explanatory power for the occurrence of that species. We then compared these SDM-derived niche optima with the ecological indicator values by means of bivariate correlation analysis. We found weak to moderate correlations in the expected direction between the SDM-derived niche optima and ecological indicator values. The strongest correlation occurred between the modeled optima for growing degree days and the ecological indicator values for temperature. Correlations were weaker for SDM-derived niche optima with a more distal relationship to ecological indicator values (notably precipitation and soil moisture). Further, correlations were consistently highest for BRT, followed by GLM and GAM. Our method gives insight into the ecological realism of modeled niche optima and projected core habitats and can be used to improve SDMs by making a more informed selection of environmental variables and modeling techniques.

    Risk assessment of exotic disease incursion and spread
    Cabral, M. ; Taylor, R. ; Vos, C.J. de - \ 2019
    EFSA Journal 17 (2019)S2. - ISSN 1831-4732
    generic model - Import risk assessment - introduction risk - livestock disease - validation

    This Technical Report describes the activities developed in the scope of the EU-FORA Fellowship, within the work programme of risk assessment (RA) of exotic disease incursion and spread, developed at Wageningen Bioveterinary Research (WBVR). The programme focused on the work carried out in the Generic risk assessment for introduction of animal diseases (G-RAID) project, which brings together a number of different generic RA tools from multiple European partners. The aim of the fellowship was to gain understanding of veterinary import risk assessment by using different RA tools and to learn how different algorithms can be used to calculate disease incursion risks. G-RAID's tools cover a wide range of RA methodologies; from purely qualitative, to semi-quantitative and fully stochastic quantitative methods, which allowed the fellow to understand a variety of algorithms used to produce the final risk estimate. The fellowship programme provided the fellow with the chance to learn in detail about how generic RAs are performed across Europe, understanding how to deal with the uncertainty and variability involved in RAs and the potential problems of data availability and reliability. The fellow made an inventory of publicly available databases on disease occurrence and international trade that could be used for import RA and assessed their quality and usefulness for the different generic RA tools. The programme also provided the fellow the opportunity to perform several import risk assessments using the RA tools of G-RAID. She completed a RA on African swine fever using the MINTRISK model developed by WBVR. Furthermore, she assessed the risk of foot and mouth disease introduction using the Rapid Risk Assessment Tool (RRAT) model developed by WBVR and the COMPARE model developed by the Animal and Plant Health Agency (APHA). To this end, the fellow completed a short-term visit to APHA, enabling her to have additional training in quantitative RA and to expand her professional network in this area.

    Evaluation of Mycotoxin Screening Tests in a Verification Study Involving First Time Users
    Lattanzio, Veronica M.T. ; Holst, Christoph von; Lippolis, Vincenzo ; Girolamo, Annalisa De; Logrieco, Antonio F. ; Mol, Hans G.J. ; Pascale, Michelangelo - \ 2019
    Toxins 11 (2019)2. - ISSN 2072-6651 - 18 p.
    cereals - immunoassay - mass spectrometry - mycotoxins - screening - validation

    (AFB₁) in maize and wheat using LFD and LC-HRMS, respectively. The results of analyses were used to calculate intermediate precision (RSDip, covering the inter-analyst variability in preparing the analytical samples and the precision under repeatability conditions) cut-off values and false suspect rates. RSDip ranged from 6.5% to 30% for DON, and from 16% to 33% for AFB₁. The highest obtained variances were associated with the AFB₁ analyses due to working with much lower mass fractions. The rate of false suspect results were lower than 0.1% for all tested methods. All methods showed a fit-for-purpose method performance profile, which allowed a clear distinction of samples containing the analytes at the screening target concentration (STC) from negative control samples. Moreover, the first time users obtained method performances similar to those obtained for validation studies previously performed on the screening methods included in the training course.

    Pooling of genital swabs for detection by PCR of Taylorella equigenitalis, the cause of contagious equine metritis
    Mawhinney, I. ; Errington, J. ; Stamper, N. ; Torrens, N. ; Engelsma, M.Y. ; Roest, H.I.J. - \ 2019
    Equine Veterinary Journal 51 (2019)2. - ISSN 0425-1644 - p. 227 - 230.
    diagnosis - horse - infection - validation

    Background: Sets of genital swabs are routinely taken from horses to screen for the presence of Taylorella equigenitalis, the cause of contagious equine metritis. Typically, two to four different sites are swabbed at a time and tested by culture or PCR. Objectives: This study explored the feasibility of pooling these swabs for a single PCR test per animal instead of testing each swab individually. Study design: In vitro. Methods: PCR signal strengths (Ct values) from 149 historical PCR positive genital swabs, together with historical data on the number of swabs in a set expected to be positive, were used to assess the suitability of pooling for screening horses for T. equigenitalis infection in the population at large. Twenty-four sets of four equine genital swabs were tested. The sets were prepared in the laboratory using one or more swabs positive for T. equigenitalis from naturally infected cases. Positive and negative swabs were selected to reflect a typical range of PCR Ct values expected in field cases of T. equigenitalis infection. These pools were tested by an established PCR to assess the impact and suitability of a PCR test on pooled swabs compared to individual swab testing, by comparing the Ct values. Results: Pooling one positive swab with three negative swabs produced a small drop in Ct value but all pools were still clearly positive. Main limitations: Large numbers of field positive horses are not available, but the proof of concept approach with laboratory prepared pools shows the method is applicable to field cases. Conclusions: It was concluded that pooling of swabs would confer no appreciable drop in the ability to detect a positive animal compared to individual swab testing; pooling is therefore a suitable alternative to individual swab testing with reduced costs. The Summary is available in Spanish – see Supporting Information.

    Validation of a mathematical model of the bovine estrous cycle for cows with different estrous cycle characteristics
    Boer, H.M.T. ; Butler, S.T. ; Stötzel, C. ; Pas, M.F.W. te; Veerkamp, R.F. ; Woelders, H. - \ 2017
    Animal 11 (2017)11. - ISSN 1751-7311 - p. 1991 - 2001.
    bovine - estrous cycle - mathematical model - parameter identification - validation

    A recently developed mechanistic mathematical model of the bovine estrous cycle was parameterized to fit empirical data sets collected during one estrous cycle of 31 individual cows, with the main objective to further validate the model. The a priori criteria for validation were (1) the resulting model can simulate the measured data correctly (i.e. goodness of fit), and (2) this is achieved without needing extreme, probably non-physiological parameter values. We used a least squares optimization procedure to identify parameter configurations for the mathematical model to fit the empirical in vivo measurements of follicle and corpus luteum sizes, and the plasma concentrations of progesterone, estradiol, FSH and LH for each cow. The model was capable of accommodating normal variation in estrous cycle characteristics of individual cows. With the parameter sets estimated for the individual cows, the model behavior changed for 21 cows, with improved fit of the simulated output curves for 18 of these 21 cows. Moreover, the number of follicular waves was predicted correctly for 18 of the 25 two-wave and three-wave cows, without extreme parameter value changes. Estimation of specific parameters confirmed results of previous model simulations indicating that parameters involved in luteolytic signaling are very important for regulation of general estrous cycle characteristics, and are likely responsible for differences in estrous cycle characteristics between cows.

    Development and validation of the Axiom®Apple480K SNP genotyping array
    Bianco, Luca ; Cestaro, Alessandro ; Linsmith, Gareth ; Muranty, Hélène ; Denancé, Caroline ; Théron, Anthony ; Poncet, Charles ; Micheletti, Diego ; Kerschbamer, Emanuela ; Pierro, Erica A. Di; Larger, Simone ; Pindo, Massimo ; De Weg, Eric Van; Davassi, Alessandro ; Laurens, François ; Velasco, Riccardo ; Durel, Charles Eric ; Troggio, Michela - \ 2016
    The Plant Journal 86 (2016)1. - ISSN 0960-7412 - p. 62 - 74.
    genome-wide association study - genotyping - linkage mapping - Malus × domestica Borkh. - SNP chip - validation

    Cultivated apple (Malus × domestica Borkh.) is one of the most important fruit crops in temperate regions, and has great economic and cultural value. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid linkage disequilibrium decay, makes it difficult to perform genome-wide association (GWA) studies. Single nucleotide polymorphism arrays offer highly multiplexed assays at a relatively low cost per data point and can be a valid tool for the identification of the markers associated with traits of interest. Here, we describe the development and validation of a 487K SNP Affymetrix Axiom® genotyping array for apple and discuss its potential applications. The array has been built from the high-depth resequencing of 63 different cultivars covering most of the genetic diversity in cultivated apple. The SNPs were chosen by applying a focal points approach to enrich genic regions, but also to reach a uniform coverage of non-genic regions. A total of 1324 apple accessions, including the 92 progenies of two mapping populations, have been genotyped with the Axiom®Apple480K to assess the effectiveness of the array. A large majority of SNPs (359 994 or 74%) fell in the stringent class of poly high resolution polymorphisms. We also devised a filtering procedure to identify a subset of 275K very robust markers that can be safely used for germplasm surveys in apple. The Axiom®Apple480K has now been commercially released both for public and proprietary use and will likely be a reference tool for GWA studies in apple.

    Monitoring forest cover loss using multiple data streams, a case study of a tropical dry forest in Bolivia
    Dutrieux, L.P. ; Verbesselt, J. ; Kooistra, L. ; Herold, M. - \ 2015
    ISPRS Journal of Photogrammetry and Remote Sensing 107 (2015). - ISSN 0924-2716 - p. 112 - 125.
    landsat time-series - structural-change - vegetation indexes - rainfall products - detecting trends - east-africa - amazon - disturbance - validation - modis
    Automatically detecting forest disturbances as they occur can be extremely challenging for certain types of environments, particularly those presenting strong natural variations. Here, we use a generic structural break detection framework (BFAST) to improve the monitoring of forest cover loss by combining multiple data streams. Forest change monitoring is performed using Landsat data in combination with MODIS or rainfall data to further improve the modelling and monitoring. We tested the use of the Normalized Difference Vegetation Index (NDVI) from the Moderate Resolution Imaging Spectroradiometer (MODIS) with varying spatial aggregation window sizes as well as a rainfall derived index as external regressors. The method was evaluated on a dry tropical forest area in lowland Bolivia where forest cover loss is known to occur, and we validated the results against a set of ground truth samples manually interpreted using the TimeSync environment. We found that the addition of an external regressor allows to take advantage of the difference in spatial extent between human induced and naturally induced variations and only detect the processes of interest. Of all configurations, we found the 13 by 13 km MODIS NDVI window to be the most successful, with an overall accuracy of 87%. Compared with a single pixel approach, the proposed method produced better time-series model fits resulting in increases of overall accuracy (from 82% to 87%), and decrease in omission and commission errors (from 33% to 24% and from 3% to 0% respectively). The presented approach seems particularly relevant for areas with high inter-annual natural variability, such as forests regularly experiencing exceptional drought events.
    Evaluation of Satellite Rainfall Estimates for Drought and Flood Monitoring in Mozambique
    Tote, C. ; Patricio, D. ; Boogaard, H.L. ; Wijngaart, R. van der; Tarnavsky, E. ; Funk, C. - \ 2015
    Remote Sensing 7 (2015)2. - ISSN 2072-4292 - p. 1758 - 1776.
    west-africa - precipitation - validation - products - microwave - climate - dataset - gages - sahel - trmm
    Satellite derived rainfall products are useful for drought and flood early warning and overcome the problem of sparse, unevenly distributed and erratic rain gauge observations, provided their accuracy is well known. Mozambique is highly vulnerable to extreme weather events such as major droughts and floods and thus, an understanding of the strengths and weaknesses of different rainfall products is valuable. Three dekadal (10-day) gridded satellite rainfall products (TAMSAT African Rainfall Climatology And Time-series (TARCAT) v2.0, Famine Early Warning System NETwork (FEWS NET) Rainfall Estimate (RFE) v2.0, and Climate Hazards Group InfraRed Precipitation with Stations (CHIRPS)) are compared to independent gauge data (2001–2012). This is done using pairwise comparison statistics to evaluate the performance in estimating rainfall amounts and categorical statistics to assess rain-detection capabilities. The analysis was performed for different rainfall categories, over the seasonal cycle and for regions dominated by different weather systems. Overall, satellite products overestimate low and underestimate high dekadal rainfall values. The RFE and CHIRPS products perform as good, generally outperforming TARCAT on the majority of statistical measures of skill. TARCAT detects best the relative frequency of rainfall events, while RFE underestimates and CHIRPS overestimates the rainfall events frequency. Differences in products performance disappear with higher rainfall and all products achieve better results during the wet season. During the cyclone season, CHIRPS shows the best results, while RFE outperforms the other products for lower dekadal rainfall. Products blending thermal infrared and passive microwave imagery perform better than infrared only products and particularly when meteorological patterns are more complex, such as over the coastal, central and south regions of Mozambique, where precipitation is influenced by frontal systems.
    Loss of Olfactory Function and Nutritional Status in Vital Older Adults and Geriatric Patients
    Toussaint, N. ; Roon, M. de; Campen, J.P.C.M. van; Kremer, S. ; Boesveldt, S. - \ 2015
    Chemical Senses 40 (2015)3. - ISSN 0379-864X - p. 197 - 203.
    mild cognitive impairment - odor identification - normative data - taste - malnutrition - smell - discrimination - dysfunction - prevalence - validation
    The aim of this cross-sectional study was to assess the association of olfactory function and nutritional status in vital older adults and geriatric patients. Three hundred forty-five vital (mean age 67.1 years) and 138 geriatric older adults (mean age 80.9 years) were included. Nutritional status was assessed using the mini nutritional assessment-short form. The Sniffin’ Sticks was used to measure olfactory function. Eleven percentage of the vital older adults were at risk of malnutrition, whereas 60% of the geriatric participants were malnourished or at risk. Only 2% of the vital older adults were anosmic, compared with 46% of the geriatric participants. Linear regression demonstrated a significant association (P = 0.015) between olfactory function and nutritional status in the geriatric subjects. However, this association became insignificant after adjustment for confounders. Both crude and adjusted analysis in the vital older adults did not show a significant association. The results indicate that, in both groups of elderly, there is no direct relation between olfactory function and nutritional status. We suggest that a decline in olfactory function may still be considered as one of the risk-factors for malnutrition in geriatric patients—once co-occurring with other mental and/or physical problems that are more likely to occur in those patients experience.
    Surface water risk assessment of pesticides in Ethiopia
    Teklu, B.M. ; Adriaanse, P.I. ; Horst, M.M.S. ter; Deneer, J.W. ; Brink, P.J. van den - \ 2015
    Science of the Total Environment 508 (2015). - ISSN 0048-9697 - p. 566 - 574.
    predict insecticide concentrations - models fail - field - validation - exposure
    Scenarios for future use in the pesticide registration procedure in Ethiopia were designed for 3 separate Ethiopian locations, which are aimed to be protective for the whole of Ethiopia. The scenarios estimate concentrations in surface water resulting from agricultural use of pesticides for a small stream and for two types of small ponds. Seven selected pesticides were selected since they were estimated to bear the highest risk to humans on the basis of volume of use, application rate and acute and chronic human toxicity, assuming exposure as a result of the consumption of surface water. Potential ecotoxicological risks were not considered as a selection criterion at this stage. Estimates of exposure concentrations in surface water were established using modelling software also applied in the EU registration procedure (PRZM and TOXSWA). Input variables included physico-chemical properties, and data such as crop calendars, irrigation schedules, meteorological information and detailed application data which were specifically tailored to the Ethiopian situation. The results indicate that for all the pesticides investigated the acute human risk resulting from the consumption of surface water is low to negligible, whereas agricultural use of chlorothalonil, deltamethrin, endosulfan and malathion in some crops may result in medium to high risk to aquatic species. The predicted environmental concentration estimates are based on procedures similar to procedures used at the EU level and in the USA. Addition of aquatic macrophytes as an ecotoxicological endpoint may constitute a welcome future addition to the risk assessment procedure. Implementation of the methods used for risk characterization constitutes a good step forward in the pesticide registration procedure in Ethiopia. KEYWORDS: Aquatic ecosystems; Drinking water; Ecological risk assessment; Ethiopia; Exposure modelling; Pesticides; Tropics
    Probabilistic networks of blood metabolites in healthy subjects as indicators of latent cardiovascular risk
    Saccenti, E. ; Suarez Diez, M. ; Luchinat, C. ; Santucci, C. ; Tenori, L. - \ 2015
    Journal of Proteome Research 14 (2015)2. - ISSN 1535-3893 - p. 1101 - 1111.
    l-arginine supplementation - gene-coexpression network - insulin-resistance - metabolomic networks - disease - obesity - expression - cholesterol - association - validation
    The complex nature of the mechanisms behind cardiovascular diseases prevents the detection of latent early risk conditions. Network representations are ideally suited to investigate the complex interconnections between the individual components of a biological system underlying complex diseases. Here we investigate the patterns of correlations of an array of 29 metabolites identified and quantified in the plasma of 864 healthy blood donors and use a systems biology approach to define metabolite probabilistic networks specific for low and high latent cardiovascular risk. We adapted methods based on the likelihood of correlation and methods from information theory and combined them with resampling techniques. Our results show that plasma metabolite networks can be defined that associate with latent cardiovascular disease risk. The analysis of the networks supports our previous finding of a possible association between cardiovascular risk and impaired mitochondrial activity and highlights post-translational modifications (glycosilation and oxidation) of lipoproteins as a possible target-mechanism for early detection of latent cardiovascular risk.
    Multi-model radiometric slope correction of SAR images of complex terrain using a two-stage semi-empirical approach
    Hoekman, D.H. ; Reiche, J. - \ 2015
    Remote Sensing of Environment 156 (2015). - ISSN 0034-4257 - p. 1 - 10.
    radar imagery - topography - forest - classification - backscatter - validation
    Practical approaches for the implementation of terrain type dependent radiometric slope correction for SAR data are introduced. Radiometric slope effects are modelled as the products of two models. The first is a simple physical model based on the assumption of a uniform opaque layer of isotropic scatterers, which is independent of terrain type, frequency and polarization. It accounts for the slope-induced variation in the number of scatterers per resolution cell. The second is a semi-empirical model, which accounts for the variation in scattering mechanisms, dependent on terrain type, frequency and polarization. PALSAR FBD (L-band, HH- and HV-polarization) data are used at two test sites in Brazil and Fiji. Results for the Brazilian area, which has slopes up to 25°, show that remaining slope effects for the multi-model case are much smaller than 0.1 dB, for all land cover types. This is much better than the best single-model approach where remaining slope effects can be very small for forests but be as large as 1.77 dB for woodland in HH-polarization. Results for the Fiji area, which has different vegetation types, are very similar. The potential large improvement, using this multi-model approach, in the accuracy of biomass estimation for transparent or open canopies is discussed. It is also shown that biomass change on slopes can be systematically under- or overestimated because of associated change in scattering mechanism.
    Comparison of approaches to correct intake-health association for FFQ measurement eroor using a duplicate recovery biomarker and a duplicate 24h dietary recall as reference method
    Geelen, A. ; Souverein, O.W. ; Busstra, M.C. ; Vries, J.H.M. de; Veer, P. van 't - \ 2015
    Public Health Nutrition 18 (2015)2. - ISSN 1368-9800 - p. 226 - 233.
    episodically consumed foods - european centers - urinary nitrogen - potassium intake - validation - cancer - nutrition - protein - questionnaires - individuals
    Objective To illustrate the impact of intake-related bias in FFQ and 24 h recall (24hR), and correlated errors between these methods, on intake–health associations. Design Dietary intake was assessed by a 180-item semi-quantitative FFQ and two 24hR. Urinary N and urinary K were estimated from two 24 h urine samples. We compared four scenarios to correct associations for errors in an FFQ estimating protein and K intakes. Setting Wageningen, The Netherlands. Subjects Fifty-nine men and fifty-eight women aged 45–65 years. Results For this FFQ, measurement error weakened a true relative risk of 2·0 to 1·4 for protein and 1·5 for K. As compared with calibration to duplicate recovery biomarkers (i.e. the preferred scenario 1), estimating a validity coefficient using this duplicate biomarker resulted in overcorrected associations, caused by intake-related bias in the FFQ (scenario 2). The correction factor based on a triad using biomarkers and 24hR was hampered by this intake-related bias and by correlated errors between FFQ and 24hR, and in this population resulted in a nearly perfect correction for protein but an overcorrection for K (scenario 3). When the 24hR was used for calibration, only a small correction was done, due to correlated errors between the methods and intake-related bias in the 24hR (scenario 4). Conclusions Calibration to a gold standard reference method is the preferred approach to correct intake–health associations for FFQ measurement error. If it is not possible to do so, using the 24hR as reference method only partly removes the errors, but may result in improved intake–health associations.
    Moisture transport in swelling media modelled with a Lattice Boltzmann scheme having a deforming lattice
    Sman, R.G.M. van der - \ 2014
    Journal of Food Engineering 124 (2014). - ISSN 0260-8774 - p. 54 - 63.
    non-brownian suspensions - diffusion lattice - water transport - flow - simulations - profiles - kinetics - food - gels - validation
    In this paper we present a novel numerical scheme for simulating the one-dimensional deformation of hydrogel material due to drying or rehydration. The scheme is based on the versatile Lattice Boltzmann method, which has been extended such that the computational grid (lattice) deforms due to shrinkage or swelling. This property of a deforming grid is new to the lattice Boltzmann method, and a detailed description of this new method is given. Via simulations we show that self-similar moisture concentration profiles occur in two periods in both drying and swelling processes: the penetration period and the regular regime. Given the property of self-similarity, we have been able to formulate a reduced-order model for the regular regime of swelling.
    The Wageningen Lowland Runoff Simulator (WALRUS): application to the Hupsel Brook catchement and Cabauw polder
    Brauer, C.C. ; Torfs, P.J.J.F. ; Teuling, A.J. ; Uijlenhoet, R. - \ 2014
    Hydrology and Earth System Sciences 18 (2014). - ISSN 1027-5606 - p. 4007 - 4028.
    surface parameterization schemes - distributed hydrological model - flow route contributions - land-surface - groundwater interactions - spatial variability - rainfall - scale - netherlands - validation
    The Wageningen Lowland Runoff Simulator (WALRUS) is a new parametric (conceptual) rainfall–runoff model which accounts explicitly for processes that are important in lowland areas, such as groundwater-unsaturated zone coupling, wetness-dependent flowroutes, groundwater–surface water feedbacks, and seepage and surface water supply (see companion paper by Brauer et al., 2014). Lowland catchments can be divided into slightly sloping, freely draining catchments and flat polders with controlled water levels. Here, we apply WALRUS to two contrasting Dutch catchments: the Hupsel Brook catchment and the Cabauw polder. In both catchments, WALRUS performs well: Nash–Sutcliffe efficiencies obtained after calibration on 1 year of discharge observations are 0.87 for the Hupsel Brook catchment and 0.83 for the Cabauw polder, with values of 0.74 and 0.76 for validation. The model also performs well during floods and droughts and can forecast the effect of control operations. Through the dynamic division between quick and slow flowroutes controlled by a wetness index, temporal and spatial variability in groundwater depths can be accounted for, which results in adequate simulation of discharge peaks as well as low flows. The performance of WALRUS is most sensitive to the parameter controlling the wetness index and the groundwater reservoir constant, and to a lesser extent to the quickflow reservoir constant. The effects of these three parameters can be identified in the discharge time series, which indicates that the model is not overparameterised (parsimonious). Forcing uncertainty was found to have a larger effect on modelled discharge than parameter uncertainty and uncertainty in initial conditions.
    Status quo and future research challenges on organic food quality determination with focus on laboratory methods
    Kahl, J. ; Bodroza-Solarov, M. ; Busscher, N. ; Hajslova, J. ; Kneifel, W. ; Kokornaczyk, M.O. ; Ruth, S.M. van; Schulzova, V. ; Stolz, P. - \ 2014
    Journal of the Science of Food and Agriculture 94 (2014)13. - ISSN 0022-5142 - p. 2595 - 2599.
    wheat-grain leakages - grown winter-wheat - nutritional quality - crystallization patterns - samples - standardization - authentication - definition - validation - products
    Organic food quality determination needs multi-dimensional evaluation tools. The main focus is on the authentication as an analytical verification of the certification process. New fingerprinting approaches such as ultra-performance liquid chromatography–mass spectrometry, gas chromatography–mass spectrometry, direct analysis in real time–high-resolution mass spectrometry as well as crystallization with and without the presence of additives seem to be promising methods in terms of time of analysis and detecting organic system-related parameters. For further methodological development, a system approach is recommended, which also takes into account food structure aspects. Furthermore, the authentication of processed organic samples needs more consciousness, hence most of organic food is complex and processed.
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