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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    Onderzoek naar een kennisbasis voor natuurgedreven landbouw
    Dijk, J. van; Veer, G. van der; Woestenburg, M. ; Stoop, J. ; Wijdeven, M. ; Veluw, K. van; Schrijver, R. ; Akker, J. van den; Woudenberg, E. van; Kerkhoven, D. ; Slot, M. - \ 2020
    WINK - 52
    Klimaatschadeschatter Rapportage 2019
    Jacobs, C.M.J. ; Budding-Polo Ballinas, Monserrat ; Spijker, J.H. ; Kok, Sien ; Bel, Mark de; Jong, Dick de; Kluck, Jeroen ; Harten, Floris ; Stoop, Bianca ; Noome, Wilmer ; Slingerland, Erwin ; Bosch, Peter ; Leuken, Jeroen P.G. van; Goosen, H. ; Koekoek, Arjen ; Bijsterveldt, M.A.J.C. van; Hofland, Sandy - \ 2019
    Bussum : Stichting Climate Adaptation Services (CAS) - 52 p.
    De warme en droge zomers van 2018 en 2019 braken allerlei records, en we zullen er nog veel vaker mee te maken krijgen. Ook korte hevige regen- en hagelbuien komen steeds vaker voor. De effecten van klimaatverandering hebben verschillende gevolgen. Zo moeten er meer mensen naar het ziekenhuis in hete zomers, kan er vaker water het gebouw in stromen en verzakken wegen en panden door droogte. De Klimaatschadeschatter (KSS) helpt om inzicht te krijgen in de schade door klimaatverandering met de focus op de stedelijke omgeving.
    Artisanal or industrial conflict minerals? Evidence from Eastern Congo
    Stoop, Nik ; Verpoorten, Marijke ; Windt, Peter van der - \ 2019
    World Development 122 (2019). - ISSN 0305-750X - p. 660 - 674.
    Africa - Artisanal mining - Conflict - Democratic Republic of Congo - Industrial mining - Natural resources

    Existing research suggests a strong link between mining and local conflict but makes no distinction between artisanal and industrial mining. We exploit variation in mineral prices and the granting of industrial mining concessions to investigate how the mode of extraction affects conflict in Eastern Congo. Rising mineral prices increase battles over artisanal mines, indicating competition between armed groups. This effect is much less pronounced for industrial mining. Moreover, the expansion of industrial mining decreases battles, suggesting that companies can secure their concessions. Such expansion does, however, trigger riots, and, when it crowds out artisanal mining, also increases violence against civilians and looting. In line with case-study evidence, these negative effects only materialize when industrial mining companies expand their activities from the research to the production phase.

    Genomic Breeding Value Estimation in countries without large-scale genotyping: merging two training populations to increase genomic reliabilities
    Stoop, W.M. ; Calus, M.P.L. ; Schrooten, C. ; Gombacsi, P. ; Weller, J.I. ; Jong, G. de - \ 2018
    In: Proceedings of the 11th World Congress on Genetics Applied to Livestock Production. - WCGALP - 6 p.
    For countries without large-scale genotyping, it is a challenge to implement an effective genomic evaluation system. Breeding company CRV has merged its bull training population with two such countries to build a training population of significance, and provide genomic software. Results show 6-20 times increase in training population adding the CRV bulls. The b-factors of the model(s) improve for most traits for both countries, with an exception for Israeli calving traits. Finally, the added reliability of genomic information, measured as equivalent daughter contributions, is on average four times bigger in the training populations including the CRV bulls, as compared to using only bulls genotyped by the country itself. Validation success may depend on the heritability of the trait, the estimated between-country correlation for the trait, the kinship between the two populations, as well as between the training population and the validation population, and -implicit in that between-country kinship- the past selection criteria as reflected in the similarities in the total merit indices over time.
    More legislation, more violence? The impact of Dodd-Frank in the DRC
    Stoop, Nik ; Verpoorten, Marijke ; Windt, Peter van der - \ 2018
    PLoS ONE 13 (2018)8. - ISSN 1932-6203

    The Dodd Frank Act was passed by the US Congress in July 2010 and included a provision—Section 1502—that aimed to break the link between conflict and minerals in the Eastern Democratic Republic of Congo. To date there is only one rigorous quantitative analysis that investigates the impact of Dodd-Frank on local conflict events. Looking at the short-term impact (2011–2012), it finds that the policy backfired. This study builds on a larger, more representative, dataset of mining sites and extends the time horizon by three years (2013–2015). The results indicate that the policy also backfired in the longer run, especially in areas home to gold mines. For territories with the average number of gold mines, the introduction of Dodd-Frank increased the incidence of battles with 44%; looting with 51% and violence against civilians with 28%, compared to pre-Dodd Frank averages. Delving deeper into the impact of the conflict minerals legislation is important, as President Trump suspended the legislation in February 2017 for a two-year period, ordering his administration to replace it with another policy.

    Maatschappelijke participatie van mensen met dementie: de waarde van dagbesteding op zorgboerderijen
    Bruin, S.R. de; Stoop, H.J. ; Molema, C.C.M. ; Hop, P. ; Vaandrager, L. ; Baan, C.A. - \ 2016
    Supporting data of spatiotemporal proliferation of human stromal cells adjusts to nutrient availability and leads to stanniocalcin-1 expression in vitro and in vivo
    Higuera, Gustavo A. ; Fernandes, Hugo ; Spitters, Tim W.G.M. ; Peppel, Jeroen van de; Aufferman, Nils ; Truckenmueller, Roman ; Escalante, Maryana ; Stoop, Reinout ; Leeuwen, Johannes P. van; Boer, Jan de; Subramaniam, Vinod ; Karperien, Marcel ; Blitterswijk, Clemens van; Boxtel, Ton van; Moroni, Lorenzo - \ 2015
    Data in Brief 5 (2015). - ISSN 2352-3409 - p. 84 - 94.

    This data article contains seven figures and two tables supporting the research article entitled: spatiotemporal proliferation of human stromal cells adjusts to nutrient availability and leads to stanniocalcin-1 expression in vitro and in vivo [1]. The data explain the culture of stromal cells in vitro in three culture systems: discs, scaffolds and scaffolds in a perfusion bioreactor system. Also, quantification of extracellular matrix components (ECM) in vitro and staining of ECM components in vivo can be found here. Finally the quantification of blood vessels dimensions from CD31 signals and representative histograms of stanniocalcin-1 fluorescent signals in negative controls and experimental conditions in vivo are presented.

    Maatschappelijke participatie van mensen met dementie: de waarde van dagbesteding op zorgboerderijen
    Bruin, S.R. de; Stoop, A. ; Molema, C.C.M. ; Hop, P. ; Vaandrager, L. ; Baan, C.A. - \ 2015
    Green Care Farms: An Innovative Type of Adult Day Service to Stimulate Social Participation of People With Dementia
    Bruin, S.R. de; Stoop, A. ; Molema, C.C.M. ; Vaandrager, L. ; Hop, P.J.W.M. ; Baan, C.A. - \ 2015
    Gerontology & Geriatric Medicine 1 (2015). - ISSN 2333-7214 - 10 p.
    Objective: To explore the value of day services at green care farms (GCFs) in terms of social participation for people with dementia. Method: Semi-structured interviews were conducted with people with dementia who attended day services at a GCF (GCF group, n = 21), were on a waiting list (WL) for day services at a GCF (WL group, n = 12), or attended day services in a regular day care facility (RDCF group, n = 17) and with their family caregivers. Results: People with dementia in the GCF and WL group were primarily males, with an average age of 71 and 76 years, respectively, who almost all had a spousal caregiver. People with dementia in the RDCF group were mostly females with an average age of 85 years, most of whom had a non-spousal caregiver. For both the GCF and RDCF groups, it was indicated that day services made people with dementia feel part of society. The most important domains of social participation addressed by RDCFs were social interactions and recreational activities. GCFs additionally addressed the domains “paid employment” and “volunteer work.” Conclusion: GCFs are valuable in terms of social participation for a particular group of people with dementia. Matching characteristics of adult day services (ADS) centers to the preferences and capacities of people with dementia is of importance. Diversity in ADS centers is therefore desirable.
    Genetic correlation between composition of bovine milk fat in winter and summer, and DGAT1 and SCD1 by season interactions
    Duchemin, S.I. ; Bovenhuis, H. ; Stoop, W.M. ; Bouwman, A.C. ; Arendonk, J.A.M. van; Visker, M.H.P.W. - \ 2013
    Journal of Dairy Science 96 (2013)1. - ISSN 0022-0302 - p. 592 - 604.
    conjugated linoleic-acid - coa-diacylglycerol acyltransferase - dairy-cows - short communication - production traits - desaturase - parameters - enzyme - cla - biohydrogenation
    Milk fat composition shows substantial seasonal variation, most of which is probably caused by differences in the feeding of dairy cows. The present study aimed to know whether milk fat composition in winter is genetically the same trait as milk fat composition in summer. For this purpose, we estimated heritabilities, genetic correlations, effects of acyl-coenzyme A:diacylglycerol acyltransferase 1 (DGAT1) K232A, and stearoyl-coenzyme A desaturase 1 (SCD1) A293V polymorphisms for milk fat composition in winter and summer, and tested for genotype by season interactions of DGAT1 K232A and SCD1 A293V polymorphisms. Milk samples were obtained from 2,001 first-lactation Dutch Holstein-Friesian cows, most with records in both winter and summer. Summer milk contained higher amounts of unsaturated fatty acids (FA) and lower amounts of saturated FA compared with winter milk. Heritability estimates were comparable between seasons: moderate to high for short- and medium-chain FA (0.33 to 0.74) and moderate for long-chain FA (0.19 to 0.43) in both seasons. Genetic correlations between winter and summer milk were high, indicating that milk fat composition in winter and in summer can largely be considered as genetically the same trait. Effects of DGAT1 K232A and SCD1 A293V polymorphisms were similar across seasons for most FA. Allele DGAT1 232A in winter as well as in summer milk samples was negatively associated with most FA with less than 18 carbons, saturated FA, saturated FA to unsaturated FA ratio, and C10 to C16 unsaturation indices, and was positively associated with C14:0, unsaturated C18, unsaturated FA, and C18 and conjugated linoleic acid unsaturation indices. Allele SCD1 293V in winter as well as in summer milk samples was negatively associated with C18:0, C10:1 to cis-9 C14:1, trans-11 C18:1, and C10 to C14 unsaturation indices, and positively associated with C8:0 to C14:0, cis-9 C16:1, and C16 to conjugated linoleic acid unsaturation indices. In addition, significant DGAT1 K232A by season interaction was found for some FA and SCD1 A293V by season interaction was only found for trans-11 C18:1. These interactions were due to scaling of genotype effects.
    Ordered packing of elastic wires in a sphere
    Najafi, Javad ; Stoop, Norbert ; Wittel, Falk ; Habibi, Mehdi - \ 2012
    Physical Review. E, Statistical nonlinear, and soft matter physics 85 (2012)6. - ISSN 1539-3755

    In this paper we study the ordered packing of wires in a sphere. We propose an analytical model and compare the model predictions with the results of our experiments and simulations for the maximum packing fraction, the number of formed coils, the fractal dimension, and bending energy. We show that the relative system size [i.e., the ratio of the wire radius to the sphere radius (a/R)] is the most important control parameter for the maximum packing fraction. We find that the number of coils obeys a power-law relation of the form N∼ (R /a )1.5 and the fractal dimension of the structures is 2.5, independent of the system size. Our theoretical results are in good agreement with the experimental data and the predictions of the numerical simulations.

    Packing of elastic wires in spherical cavities
    Stoop, N. ; Najafi, J. ; Wittel, F.K. ; Habibi, M. ; Herrmann, H.J. - \ 2011
    Physical Review Letters 106 (2011)21. - ISSN 0031-9007

    We investigate the morphologies and maximum packing density of thin wires packed into spherical cavities. Using simulations and experiments, we find that ordered as well as disordered structures emerge, depending on the amount of internal torsion. We find that the highest packing densities are achieved in low torsion packings for large systems, but in high torsion packings for small systems. An analysis of both situations is given in terms of energetics and comparison is made to analytical models of DNA packing in viral capsids.

    The Effect of Preanalytical Factors on Stability of the Proteome and Selected Metabolites in Cerebrospinal Fluid (CSF)
    Rosenling, T. ; Slim, C.L. ; Christin, C. ; Coulier, L. ; Shi, S. ; Stoop, M.P. ; Bosman, J. ; Suits, F. ; Horvatovich, P.L. ; Stockhofe, N. ; Vreeken, R. ; Hankemeier, T. ; Gool, A.J. ; Luider, T.M. ; Bischoff, R. - \ 2009
    Journal of Proteome Research 8 (2009)12. - ISSN 1535-3893 - p. 5511 - 5522.
    chromatography-mass spectrometry - multiple-sclerosis - liquid-chromatography - biomarker discovery - cystatin-c - storage-conditions - sample collection - clinical-practice - lc-ms - serum
    To standardize the use of cerebrospinal fluid (CSF) for biomarker research, a set of stability studies have been performed on porcine samples to investigate the influence of common sample handling procedures on proteins, peptides, metabolites and free amino acids. This study focuses at the effect on proteins and peptides, analyzed by applying label-free quantitation using microfluidics nanoscale liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (chipLC-MS) as well as matrix-assisted laser desorption ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT-ICR-MS) and Orbitrap LC-MS/MS to trypsin-digested CSF samples, The factors assessed were a 30 or 120 min time delay at room temperature before storage at -80 degrees C after the collection of CSF in order to mimic potential delays in the clinic (delayed storage), storage at 4 degrees C after trypsin digestion to mimic the time that samples remain in the cooled autosampler of the analyzer, and repeated freeze-thaw cycles to mimic storage and handling procedures in the laboratory. The delayed storage factor was also analyzed by gas chromatography mass spectrometry (GC-MS) and liquid chromatography mass spectrometry (LC-MS) for changes of metabolites and free amino acids, respectively. Our results show that repeated freeze/thawing introduced changes in transthyretin peptide levels. The trypsin digested samples left at 4 degrees C in the autosampler showed a time-dependent decrease of peak areas for peptides from prostaglandin D-synthase and serotransferrin. Delayed storage of CSF led to changes in prostaglandin D-synthase derived peptides as well as to increased levels of certain amino acids and metabolites. The changes of metabolites, amino acids and proteins in the delayed storage study appear to be related to remaining white blood cells. Our recommendations are to centrifuge CSF samples immediately after collection to remove white blood cells, aliquot, and then snap-freeze the supernatant in liquid nitrogen for storage at -80 degrees C. Preferably samples should not be left in the autosampler for more than 24 h and freeze/thaw cycles should be avoided if at all possible.
    Milk genomics
    Mullaart, E. ; Heck, J.M.L. ; Stoop, W.M. ; Schennink, A. ; Schopen, G.C.B. ; Visker, M.H.P.W. ; Arendonk, J.A.M. van - \ 2009
    Short communication: Genome-wide scan for bovine milk-fat composition. II. Quantitative trait loci for long-chain fatty acids
    Schennink, A. ; Stoop, W.M. ; Visker, M.H.P.W. ; Poel, J.J. van der; Bovenhuis, H. ; Arendonk, J.A.M. van - \ 2009
    Journal of Dairy Science 92 (2009)9. - ISSN 0022-0302 - p. 4676 - 4682.
    dairy-cattle - genetic-parameters - f-2 population - rat-liver - fish-oil - dgat1 - polymorphism - trans - cows - qtl
    We present the results of a genome-wide scan to identify quantitative trait loci (QTL) that contribute to genetic variation in long-chain milk fatty acids. Milk-fat composition phenotypes were available on 1,905 Dutch Holstein-Friesian cows. A total of 849 cows and their 7 sires were genotyped for 1,341 single nucleotide polymorphisms across all Bos taurus autosomes (BTA). We detected significant QTL on BTA14, BTA15, and BTA16: for C18:1 cis-9, C18:1 cis-12, C18:2 cis-9,12, CLA cis-9,trans-11, C18:3 cis-9,12,15, the C18 index, the total index, total saturated fatty acids, total unsaturated fatty acids (UFA), and the ratio of saturated fatty acids:unsaturated fatty acids on BTA14; for C18:1 trans fatty acids on BTA15; and for the C18 and CLA indices on BTA16. The QTL explained 3 to 19% of the phenotypic variance. Suggestive QTL were found on 16 other chromosomes. The diacylglycerol acyltransferase 1 (DGAT1) K232A polymorphism on BTA14, which is known to influence fatty acid composition, most likely explains the QTL that was detected on BTA14
    Melkvet met meerwaarde
    Stoop, W.M. ; Arendonk, J.A.M. van; Bovenhuis, H. ; Heck, J. - \ 2009
    Veeteelt 26 (2009)6. - ISSN 0168-7565 - p. 12 - 14.
    melkveehouderij - melkvee - dierveredeling - melkvet - samenstelling - dairy farming - dairy cattle - animal breeding - milk fat - composition
    Fokken op melkvet richt zich vooralsnog alleen op de hoeveelheid vet. Onderzoekers van Wageningen Universiteit tonen aan dat niet alleen de hoeveelheid melkvet, maar ook de melkvetsamenstelling met behulp van fokkerij verbeterd kan worden
    Melk nog verder verbeteren door fokkerijmaatregelen : eerste drie promoties op basis van Milk Genomics Initiative (interview met Johan van Arendonk)
    Blom, J. ; Arendonk, J.A.M. van; Stoop, W.M. ; Schennink, A. ; Heck, J. - \ 2009
    VoedingsMagazine 22 (2009)3. - ISSN 0922-8012 - p. 4 - 10.
    melksamenstelling - dierveredeling - genetische variatie - melkvetpercentage - onverzadigde vetzuren - melkeiwit - genexpressieanalyse - milk composition - animal breeding - genetic variation - milk fat percentage - unsaturated fatty acids - milk protein - genomics
    In 2004, the Milk Genomics Initiative (NGI) was launched – an exploration of the possibility to change the composition of milk though breeding measures. Five years later, it has become a fact that it is possible indeed, through selection of the most suitable animals, to attune the composition of both dairy fat and dairy protein to specific wishes. In milk fat the content of saturated fatty acids can be raised while in milk protein the casein concentration can be increased. In March and April 2009, the first three MGI research assistants obtained their doctoral degree on the basis of MGI research. An interview with the MGI project manager, Prof. Johan van Arendonk
    Genome-wide scan for bovine milk-fat composition. I. Quantitative trait loci for short- and medium-chain fatty acids
    Stoop, W.M. ; Schennink, A. ; Visker, M.H.P.W. ; Mullaart, E. ; Arendonk, J.A.M. van; Bovenhuis, H. - \ 2009
    Journal of Dairy Science 92 (2009)9. - ISSN 0022-0302 - p. 4664 - 4675.
    stearoyl-coa desaturase - half-sib populations - growth-hormone - dairy-cattle - alternative transcript - genetic-parameters - carboxylase-alpha - mammary-gland - ppar-gamma - fasn gene
    A genome-wide scan was performed to identify quantitative trait loci (QTL) for short- and medium-chain fatty acids (expressed in wt/wt %). Milk samples were available from 1,905 cows from 398 commercial herds in the Netherlands, and milk-fat composition was measured by gas chromatography. DNA was available from 7 of the paternal half-sib families: 849 cows and their 7 sires. A genetic map was constructed comprising 1,341 SNP and 2,829 cM, with an average information content of 0.83. Multimarker interval mapping was used in an across-family regression on corrected phenotypes for the 7 half-sib families. Four QTL were found: on Bos taurus autosome (BTA) 6, a QTL was identified for C6:0 and C8:0; on BTA14, a QTL was identified for fat percentage, all odd-chain fatty acids, and C14:0, C16:0, C16:1, and their unsaturation indices; on BTA19, a QTL affected C14:0; and on BTA26, a QTL was identified for the monounsaturated fatty acids and their unsaturation indices. The QTL explained 3 to 19% of phenotypic variance. Furthermore, 49 traits with suggestive evidence for linkage were found on 21 chromosomes. Additional analyses revealed that the QTL on BTA14 was most likely caused by a mutation in DGAT1, whereas the QTL on BTA26 was most likely caused by a mutation in the SCD1 gene. Quantitative trait loci that affect specific fatty acids might increase the understanding of physiological processes regarding fat synthesis and the position of the causal genes
    Effect of lactation stage and energy status on milk fat composition of Holstein-Friesian cows
    Stoop, W.M. ; Bovenhuis, H. ; Heck, J.M.L. ; Arendonk, J.A.M. van - \ 2009
    Journal of Dairy Science 92 (2009)4. - ISSN 0022-0302 - p. 1469 - 1478.
    dairy-cows - genetic-parameters - acid-composition - balance - prediction - cattle - fertility - yield - model
    The effects of lactation stage, negative energy balance (NEB), and milk fat depression (MFD) were estimated on detailed milk fat composition in primiparous Holstein-Friesian cows. One morning milk sample was collected from each of 1,933 cows from 398 commercial Dutch herds in winter 2005. Milk fat composition was measured using gas chromatography, and fat and protein percentage were measured using infrared spectrometry. Each fatty acid changed 0.5 to 1 phenotypic standard deviation over lactation, except odd-chain C5:0 to C15:0, branched-chain fatty acids, and trans-10, cis-12 conjugated linoleic acid (CLA). The greatest change was an increase from 31.2 to 33.3% (wt/wt) for C16:0 from d 80 to 150 of lactation. Energy status was estimated for each cow as the deviation from each average lactation fat-to-protein ratio (FPdev). A high FPdev (>0.12) indicated NEB. Negative energy balance was associated with an increase in C16:0 (0.696 ± 0.178) and C18:0 (0.467 ± 0.093), which suggested mobilization of body fat reserves. Furthermore, NEB was associated with a decrease in odd-chain C5:0 to C15:0 (¿0.084 ± 0.020), which might reflect a reduced allocation of C3 components to milk fat synthesis. A low FPdev indicated MFD (
    Genetic variation in bovine milk fat composition
    Stoop, W.M. - \ 2009
    Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Henk Bovenhuis. - [S.l.] : S.n. - ISBN 9789085853558
    melk - melkvet - melksamenstelling - genetische variatie - selectie - dierveredeling - selectief fokken - vetzuren - milk - milk fat - milk composition - genetic variation - selection - animal breeding - selective breeding - fatty acids
    In her thesis, Stoop shows that there is considerable genetic variation in milk fat composition, which opens opportunities to improve milk fat composition by selective breeding. Short and medium chain fatty acids had high heritabilities, whereas variation due to herd (mainly feed effects) was moderate. Long chain fatty acids had moderate heritabilities, whereas variation due to herd was high. Several genomic regions (QTL) with effect on short and medium chain, long chain, or both types of fatty acids were identified. Differences in results could be explained by the origin of the fatty acids; short and medium chain fatty acids are predominantly synthesized by the cow in the mammary gland, whereas long chain fatty acid are mainly of dietary origin. Results show that milk fat composition can be improved by selective breeding, which offers opportunities to meet consumers’ demands regarding health and technological aspects.
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