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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Characterisation of friction behaviour of intact soft solid foods and food boli
Fuhrmann, Philipp L. ; Aguayo-Mendoza, Monica ; Jansen, Bas ; Stieger, Markus ; Scholten, Elke - \ 2020
Food Hydrocolloids 100 (2020). - ISSN 0268-005X

Methodologies to quantify friction forces between soft solid foods or food boli and (model) oral surfaces are desired to better understand how changes in food properties during oral processing affect sensory perception. In this short communication, friction forces (FF) occurring between polydimethylsiloxane (PDMS) surfaces and intact soft solid foods/boli were quantified. As models for intact foods, we used gelatine gels varying in composition and particle size, and sausages were used as an example for real foods. Friction forces measured during the relative motion of intact foods against a rough PDMS surface (“oral surface”), strongly depended on the composition of the food. Friction forces were significantly lower for PDMS against emulsion-filled gels, than for PDMS against unfilled gels, likely due to the lubricating effect of released oil from the gel. Moreover, sausages, displayed significantly higher friction forces than gelatine gels when moving against the PDMS probe, presumably linked to differences in the surface of the foods. The friction forces observed for the PDMS probe moving against food boli were dependent on particle size and saliva quantity; boli with larger particle sizes showed significantly lower friction forces, whereas the addition of saliva to food boli first increased friction forces, but with increasing amount decreased the friction forces significantly. We conclude that the presented methodology is able to quantify the friction behaviour of intact soft solid foods and boli directly, taking into account (i) the effect of composition and added fillers, (ii) serum or oil release and (iii) bolus particle size.

Bos vernielen voor het klimaat
Jansen, P.A. - \ 2019
Trouw 2019 (2019). - p. 11 - 11.
The impact of sensitivity and uncertainty of soil physical parameters on the terms of the water balance: Some case studies with default R packages. Part I: Theory, methods and case descriptions
Wesseling, Jan ; Kroes, Joop ; Campos Oliveira, Thalita ; Damiano, Francisco - \ 2019
Computers and Electronics in Agriculture (2019). - ISSN 0168-1699
HPC - IRS - LHS - Numerical model - R - Sensitivity - Sobol - SWAP - Uncertainty

These papers (part I and part II) emphasize the need for sensitivity and uncertainty analyses. A number of techniques are applied, e.g. latin hypercube sampling, impact response surfaces and Sobol-analyses. Five examples are presented, four of them concerning the numerical model SWAP. The data generation and analysis is performed with standard R packages. Although the computations can be made on any computer, the most time-consuming examples in this paper have been run on a High Performance Computer Cluster. With the relatively simple Impact Response Surface technique it is shown that variation of the saturated hydraulic conductivity has far less impact than changing the moisture content at saturation. Analyses according to the Sobol-Jansen method show that when the soil physical relationships are described according to Damiano, then the parameter b has a very large influence on the results. If the well-known Mualem - Van Genuchten equations are applied, most variation can be explained by the parameter n.

The impact of sensitivity and uncertainty of soil physical parameters on the terms of the water balance: Some case studies with default R packages. Part II: Results and discussion
Wesseling, Jan ; Kroes, Joop ; Campos Oliveira, Thalita ; Damiano, Francisco - \ 2019
Computers and Electronics in Agriculture (2019). - ISSN 0168-1699
HPC - IRS - LHS - Numerical model - R - Sensitivity - Sobol - Swap - Uncertainty

These papers (part I and part II) emphasize the need for sensitivity and uncertainty analyses. A number of techniques are applied, e.g. latin hypercube sampling, impact response surfaces and Sobol-analyses. Five examples are presented, four of them concerning the numerical model Swap. The data generation and analysis is performed with standard R packages. Although the computations can be made on any computer, the most time-consuming examples in this paper have been run on a High Performance Computer Cluster. With the relatively simple Impact Response Surface technique it is shown that variation of the saturated hydraulic conductivity has far less impact than changing the moisture content at saturation. Analyses according to the Sobol-Jansen method show that when the soil physical relationships are described according to Damiano, then the parameter b has a very large influence on the results. If the well-known Mualem - Van Genuchten equations are applied, most variation can be explained by the parameter n.

Prognose van de prijzen van varkensrechten in de concentratiegebieden Zuid en Oost per 25 november 2019
Hoste, R. ; Puister-Jansen, L.F. ; Bens, Paul ; Verstegen, Loes - \ 2019
Wageningen Economic Research (Factsheet Wageningen Economic Research 2019-118) - 5 p.
Maatregel op de Kaart (Fase 1) : Identificeren van kansrijke landbouwmaatregelen per perceel voor schoner grond- en oppervlaktewater
Gerven, L.P.A. van; Jansen, Stefan ; Groenendijk, P. - \ 2019
Wageningen : Wageningen Environmental Research - 16 p.
In dit project ‘Maatregel op de Kaart (Fase 1)’ is voor elk landbouwperceel in Nederland aangegeven welke DAW-maatregelen kansrijk zijn om de grond- en oppervlaktewater kwaliteit te verbeteren. Dit is gedaan door het koppelen van expert kennis over de toepasbaarheid en effectiviteit van de maatregelen aan perceelskenmerken zoals gewas, bodem, hydrologie en morfologie. Dit resulteert perperceel in een ‘inspiratielijst’ van kansrijke maatregelen. Voor de gebruiker is zo de groslijst aan DAW maatregelen uitgedund tot een op zijn situatie gerichte selectie van maatregelen.
Gesnapt! Intelligente camera’s leren welke dieren voorbijlopen
Jansen, Patrick - \ 2019
Camera trapping reveals trends in forest duiker populations in African National Parks
O'Brien, Timothy G. ; Ahumada, Jorge ; Akampurila, Emmanuel ; Beaudrot, Lydia ; Boekee, Kelly ; Brncic, Terry ; Hickey, Jena ; Jansen, Patrick A. ; Kayijamahe, Charles ; Moore, Jennifer ; Mugerwa, Badru ; Mulindahabi, Felix ; Ndoundou-Hockemba, Mireille ; Niyigaba, Protais ; Nyiratuza, Madeleine ; Opepa, Cisquet K. ; Rovero, Francesco ; Uzabaho, Eustrate ; Strindberg, Samantha - \ 2019
Remote Sensing in Ecology and Conservation (2019). - ISSN 2056-3485
Abundance - Africa - bushmeat - camera trapping - Forest duikers - occupancy - protected areas - Royle-Nichols models

Bushmeat hunting is widely cited as cause for declines of wildlife populations throughout Africa. Forest duikers (Bovidae, Cephalophinae) are among the most exploited species. Whether current harvest rates imperil duikers is debated because of the difficulty of accurately assessing population trends. To assess population trends, we first reviewed literature for historical duiker population estimates. Second, we used systematic camera-trap monitoring to assess population trends for 15 populations of nine duiker species in six national parks in Central and East Africa. We analysed annual monitoring data using Royle-Nichols heterogeneity-induced occupancy models to estimate abundance/sample point and derive occupancy estimates. Published density estimates indicate that duiker populations declined significantly throughout Africa between 1973 and 2013. There was a wide range of densities depending on species ((Formula presented.) range: 0.26–20.6 km−1) and whether populations were hunted ((Formula presented.) =6.3 km−1) or unhunted ((Formula presented.) = 16.3 km−1). More recent analysis of camera-trap monitoring produced different results. Estimated mean point abundance over time was between 0 and 0.99 individuals/point for four populations, between 1.0 and 1.99 for six populations, and greater than 2.0 for five populations. We observed five populations of duikers with negative trends in point abundances, although only one trend was significant and point abundance estimates for three populations were above 2.0 in the final survey year. Six populations showed positive trends in point abundance (three significant), and the remaining populations displayed no trends. Average occupancy was high (Ψ > 0.60) except for three populations. While literature indicates that historical population declines have occurred, most duiker populations appear relatively healthy in monitored parks. Our results indicate that these parks are effective in protecting most duikers despite hunting pressure. We recommend that systematic, standardized camera-trap monitoring be initiated in other African parks in combination with point-abundance models to objectively assess forest ungulate population trends.

Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan
Rougeot, Julien ; Chrispijn, Naomi D. ; Aben, Marco ; Elurbe, Dei M. ; Andralojc, Karolina M. ; Murphy, Patrick J. ; Jansen, Pascal W.T.C. ; Vermeulen, Michiel ; Cairns, Bradley R. ; Kamminga, Leonie M. - \ 2019
Development 146 (2019)19. - ISSN 0950-1991
ChIP-seq - Ezh2 - Polycomb - Proteomics - Transcriptomics - Zebrafish

Polycomb group (PcG) proteins are transcriptional repressors that are important regulators of cell fate during embryonic development. Among them, Ezh2 is responsible for catalyzing the epigenetic repressive mark H3K27me3 and is essential for animal development. The ability of zebrafish embryos lacking both maternal and zygotic ezh2 to form a normal body plan provides a unique model for comprehensively studying Ezh2 function during early development in vertebrates. By using a multi-omics approach, we found that Ezh2 is required for the deposition of H3K27me3 and is essential for proper recruitment of Polycomb group protein Rnf2. However, despite the complete absence of PcG-associated epigenetic mark and proteins, only minor changes in H3K4me3 deposition and gene and protein expression occur. These changes were mainly due to local dysregulation of transcription factors outside their normal expression boundaries. Altogether, our results in zebrafish show that Polycomb-mediated gene repression is important immediately after the body plan is formed to maintain spatially restricted expression profiles of transcription factors, and we highlight the differences that exist in the timing of PcG protein action between vertebrate species.

Tick Burdens in a Small-Mammal Community in Virginia
Card, Leah R. ; McShea, William J. ; Fleischer, Robert C. ; Maldonado, Jesús E. ; Stewardson, Kristin ; Campana, Michael G. ; Jansen, Patrick A. ; Calabrese, Justin M. - \ 2019
Northeastern Naturalist 26 (2019)3. - ISSN 1092-6194 - p. 641 - 655.

Virginia has seen dramatic increases in reported cases of Lyme disease and Rocky Mountain spotted fever, but basic knowledge on the community ecology of these tick-borne diseases is poor. We examined the tick burdens of 5 small-mammal species in northwest Virginia from October 2011 to December 2012. We live-trapped individuals, quantified the tick burdens, assessed the burden structure, and tested a subset of the ticks for tick-borne pathogens. We found the tick burdens to be composed predominantly of Ixodes scapularis (Black-Legged Tick), and Ixodes sp. ticks, with Amblyomma americanum (Lone Star Tick) and Dermacentor variabilis (American Dog Tick) also present at lower densities. We detected Borrelia burgdorferi (prevalence 15%), Rickettsia spp. (4%), Anaplasma phagocytophilum (4%), and Hepatozoon spp. (1%). Black-Legged Ticks, a species which has shown range expansion in recent decades, tested positive for B. burgdorferi (17%) and for multiple pathogens in individual ticks. For better predictions of tick-borne disease risk across the Mid-Atlantic region, we recommend tracking changes in tick communities by continuous monitoring of tick burdens, densities of questing ticks, and prevalence of tick-borne pathogens.

Cost-effectiveness of the SLIMMER diabetes prevention intervention in Dutch primary health care: economic evaluation from a randomised controlled trial
Duijzer, Geerke ; Bukman, Andrea J. ; Meints-Groenveld, Aafke ; Haveman-Nies, Annemien ; Jansen, Sophia C. ; Heinrich, Judith ; Hiddink, Gerrit J. ; Feskens, Edith J.M. ; Wit, G.A. de - \ 2019
BMC Health services research 19 (2019)1. - ISSN 1472-6963 - 1 p.
Cost-effectiveness - Diabetes - Economic evaluation - Lifestyle intervention - Prevention

BACKGROUND: Although evidence is accumulating that lifestyle modification may be cost-effective in patients with prediabetes, information is limited on the cost-effectiveness of interventions implemented in public health and primary health care settings. Evidence from well-conducted pragmatic trials is needed to gain insight into the realistic cost-effectiveness of diabetes prevention interventions in real-world settings. The aim of this study is to assess the cost-effectiveness of the SLIMMER lifestyle intervention targeted at patients at high risk of developing type 2 diabetes compared with usual health care in a primary care setting in the Netherlands. METHODS: Three hundred and sixteen high-risk subjects were randomly assigned to the SLIMMER lifestyle intervention or to usual health care. Costs and outcome assessments were performed at the end of the intervention (12 months) and six months thereafter (18 months). Costs were assessed from a societal perspective. Patients completed questionnaires to assess health care utilisation, participant out-of-pocket costs, and productivity losses. Quality Adjusted Life Years (QALY) were calculated based on the SF-36 questionnaire. Cost-effectiveness planes and acceptability curves were generated using bootstrap analyses. RESULTS: The cost-effectiveness analysis showed that the incremental costs of the SLIMMER lifestyle intervention were €547 and that the incremental effect was 0.02 QALY, resulting in an incremental cost-effectiveness ratio (ICER) of €28,094/QALY. When cost-effectiveness was calculated from a health care perspective, the ICER decreased to €13,605/QALY, with a moderate probability of being cost-effective (56% at a willingness to pay, WTP, of €20,000/QALY and 81% at a WTP of €80,000/QALY). CONCLUSIONS: The SLIMMER lifestyle intervention to prevent type 2 diabetes had a low to moderate probability of being cost-effective, depending on the perspective taken. TRIAL REGISTRATION: The SLIMMER study is retrospectively registered with ClinicalTrials.gov (Identifier NCT02094911) since March 19, 2014.

Plantaardige ketens in beeld
Bremmer, Johan ; Janssens, Bas ; Ruijs, Marc ; Benninga, Jan ; Stokkers, Robert ; Splinter, Gerben ; Smit, Pepijn ; Puister-Jansen, Linda ; Lakner, Dóra - \ 2019
Wageningen : Wageningen Economic Research (Wageningen Economic Research 2019-069) - 148
Data from: A standardized assessment of forest mammal communities reveals consistent functional composition and vulnerability across the tropics
Rovero, Francesco ; Ahumada, Jorge ; Jansen, Patrick ; Sheil, Douglas ; Alvarez, Patricia ; Boekee, Kelly ; Espinosa, Santiago ; Lima, Marcela Guimarães Moreira ; Martin, Emanuel H. ; O'Brien, Timothy G. ; Salvador, Julia ; Santos, Fernanda ; Rosa, Melissa ; Sutherland, Chris ; Tenan, Simone - \ 2019
University of Florence
community structure - conservation - functional traits - mammals - trophic guild - tropical forest - camera traps
Understanding global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110-200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g., habitat features and anthropogenic activities) and biotic interactions occur. Here, we used standardized camera trapping data and a novel analytical method that accounts for imperfect detection to assess how the functional composition of terrestrial mammal communities for two traits – trophic guild and body mass – varies across 16 protected areas in tropical forests and three continents, in relation to the extent of protected habitat and anthropogenic pressures. We found that despite their taxonomic differences, communities generally have a consistent trophic guild composition, and respond similarly to these factors. Insectivores were found to be sensitive to the size of protected habitat and surrounding human population density. Body mass distribution varied little among communities both in terms of central tendency and spread, and interestingly, community average body mass declined with proximity to human settlements. Results indicate predicted trait convergence among assemblages at the coarse scale reflects consistent functional composition among communities at the local scale, suggesting that broadly similar habitats and selective pressures shaped communities with similar trophic strategies and responses to drivers of change. These similarities provide a foundation for assessing assemblages under anthropogenic threats and sharing conservation measures.Understanding global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110-200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g., habitat features and anthropogenic activities) and biotic interactions occur. Here, we used standardized camera trapping data and a novel analytical method that accounts for imperfect detection to assess how the functional composition of terrestrial mammal communities for two traits – trophic guild and body mass – varies across 16 protected areas in tropical forests and three continents, in relation to the extent of protected habitat and anthropogenic pressures. We found that despite their taxonomic differences, communities generally have a consistent trophic guild composition, and respond similarly to these factors. Insectivores were found to be sensitive to the size of protected habitat and surrounding human population density. Body mass distribution varied little among communities both in terms of central tendency and spread, and interestingly, community average body mass declined with proximity to human settlements. Results indicate predicted trait convergence among assemblages at the coarse scale reflects consistent functional composition among communities at the local scale, suggesting that broadly similar habitats and selective pressures shaped communities with similar trophic strategies and responses to drivers of change. These similarities provide a foundation for assessing assemblages under anthropogenic threats and sharing conservation measures.
A standardized assessment of forest mammal communities reveals consistent functional composition and vulnerability across the tropics
Rovero, Francesco ; Ahumada, Jorge ; Jansen, Patrick A. ; Sheil, Douglas ; Alvarez, Patricia ; Boekee, Kelly ; Espinosa, Santiago ; Lima, Marcela Guimarães Moreira ; Martin, Emanuel H. ; O'Brien, Timothy G. ; Salvador, Julia ; Santos, Fernanda ; Rosa, Melissa ; Zvoleff, Alexander ; Sutherland, Chris ; Tenan, Simone - \ 2019
Ecography (2019). - ISSN 0906-7590
The understanding of global diversity patterns has benefitted from a focus on functional traits and how they relate to variation in environmental conditions among assemblages. Distant communities in similar environments often share characteristics, and for tropical forest mammals, this functional trait convergence has been demonstrated at coarse scales (110–200 km resolution), but less is known about how these patterns manifest at fine scales, where local processes (e.g. habitat features and anthropogenic activities) and biotic interactions occur. Here, we used standardized camera trapping data and a novel analytical method that accounts for imperfect detection to assess how the functional composition of terrestrial mammal communities for two traits – trophic guild and body mass – varies across 16 protected areas in tropical forests and three continents, in relation to the extent of protected habitat and anthropogenic pressures. We found that despite their taxonomic differences, communities generally have a consistent trophic guild composition, and respond similarly to these factors. Insectivores were found to be sensitive to the size of protected habitat and surrounding human population density. Body mass distribution varied little among communities both in terms of central tendency and spread, and interestingly, community average body mass declined with proximity to human settlements. Results indicate predicted trait convergence among assemblages at the coarse scale reflects consistent functional composition among communities at the local scale, suggesting that broadly similar habitats and selective pressures shaped communities with similar trophic strategies and responses to drivers of change. These similarities provide a foundation for assessing assemblages under anthropogenic threats and sharing conservation measures.
Te veel natuur kan haast niet
Jansen, P.A. - \ 2019
Trouw (2019). - p. 11 - 11.
Comparing diel activity patterns of wildlife across latitudes and seasons: Time transformations using day length
Vazquez, Carmen ; Rowcliffe, Marcus ; Spoelstra, Kamiel ; Jansen, Patrick A. - \ 2019
Methods in Ecology and Evolution (2019). - ISSN 2041-210X
activity level - activity pattern - camera trapping - day length - diel activity - double anchoring - equinoctial anchoring - mouflon - red deer - seasonal variation

Camera trapping allows scientists to study activity patterns of animals under natural conditions. However, comparisons of activity patterns across seasons or latitudes can be biased, because activity is often attuned to sunrise and sunset, the timing of which varies with latitude and season. Existing transformation methods to solve this problem have limitations. Here, we explore whether and how activity patterns can be transformed more accurately using two alternative ‘double anchoring’ transformations – equinoctial and average anchoring – that anchor activity time to two chosen anchor points during the study period. Using simulated noisy datasets mimicking species with either crepuscular, diurnal or cathemeral activity patterns, we compared the ability of different transformation methods to extract the latent pattern and activity levels under different study conditions. We found that average anchoring best retrieved the original diel activity pattern and yielded accurate estimates of activity level. Two alternative transformation methods – single anchoring and equinoctial anchoring – performed less well. Bias in estimates from using untransformed clock times was most marked (up to 2.5-fold overestimation) for longer studies covering 4–5 months either side of an equinox at high latitude, and focusing on crepuscular species. We applied the average anchoring method to 9 months of data on Red deer Cervus elaphus, Wild boar Sus scrofa and Mouflon Ovis amon musimon activity as captured by camera traps in National Park Hoge Veluwe, the Netherlands. Average anchoring revealed more pronounced peaks of activity after sunset than was apparent from untransformed data in red deer and wild boar, but not for mouflon, a cathemeral species. Similarly, activity level was lower when calculated using average anchored time for red deer and wild boar, but no difference was observed for mouflon. We conclude that transformation of time might not be necessary at latitudes below 20°, or in studies with a duration of less than a month (below 40° latitude). For longer study periods and/or higher latitudes, average anchoring resolves the problem of variable day length. Code is provided. The transformation functions are incorporated in the r-package ‘activity’.

Chicken lines divergently selected on feather pecking differ in immune characteristics
Eijk, Jerine A.J. van der; Verwoolde, Michel B. ; Vries Reilingh, Ger de; Jansen, Christine A. ; Rodenburg, Bas ; Lammers, Aart - \ 2019
Physiology and Behavior 212 (2019). - ISSN 0031-9384
Feather pecking - Immune system - Natural (auto)antibodies - Nitric oxide production - Specific antibodies

It is crucial to identify whether relations between immune characteristics and damaging behaviors in production animals exist, as these behaviors reduce animal welfare and productivity. Feather pecking (FP) is a damaging behavior in chickens, which involves hens pecking and pulling at feathers of conspecifics. To further identify relationships between the immune system and FP we characterized high FP (HFP) and low FP (LFP) selection lines with regard to nitric oxide (NO) production by monocytes, specific antibody (SpAb) titers, natural (auto)antibody (N(A)Ab) titers and immune cell subsets. NO production by monocytes was measured as indicator for innate pro-inflammatory immune functioning, SpAb titers were measured as part of the adaptive immune system and N(A)Ab titers were measured as they play an essential role in both innate and adaptive immunity. Immune cell subsets were measured to identify whether differences in immune characteristics were reflected by differences in the relative abundance of immune cell subsets. Divergent selection on FP affected NO production by monocytes, SpAb and N(A)Ab titers, but did not affect immune cell subsets. The HFP line showed higher NO production by monocytes and higher IgG N(A)Ab titers compared to the LFP line. Furthermore the HFP line tended to have lower IgM NAAb titers, but higher IgM and IgG SpAb titers compared to the LFP line. Thus, divergent selection on FP affects the innate and adaptive immune system, where the HFP line seems to have a more responsive immune system compared to the LFP line. Although causation cannot be established in the present study, it is clear that relationships between the immune system and FP exist. Therefore, it is important to take these relationships into account when selecting on behavioral or immunological traits.

Draagkracht van de Oosterschelde en westelijke Waddenzee voor schelpdieren : evaluatie van veranderingen in de voedselcondities en schelpdierbestanden in relatie tot de mosselkweek in de periode 1990-2016
Jansen, Henrice ; Kamermans, Pauline ; Glorius, Sander ; Asch, Margriet van - \ 2019
Yerseke : Wageningen Marine Research (Wageningen Marine Research rapport C096/19) - 46
Diergeneesmiddelen in het milieu - een synthese van de huidige kennis
Moermond, Caroline ; Lahr, Joost ; Montforts, Mark ; Derksen, Anja ; Bondt, Nico ; Puister-Jansen, Linda ; Koeijer, Tanja de; Hoeksma, Paul - \ 2019
Bilthoven : Rijksinstituut voor Volksgezondheid en Milieu (RIVM) - 15
Diergeneesmiddelen in het milieu : een synthese van de huidige kennis
Lahr, Joost ; Moermond, Caroline ; Montforts, Mark ; Derksen, Anja ; Bondt, Nico ; Puister-Jansen, Linda ; Koeijer, Tanja de; Hoeksma, Paul - \ 2019
Amersfoort : Stowa (Stowa rapport 2019-26) - ISBN 9789057738616 - 117
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