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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Long-term effects of wild ungulates on the structure, composition and succession of temperate forests
Ramirez Chiriboga, J.I. ; Jansen, P.A. ; Ouden, J. den; Goudzwaard, L. ; Poorter, L. - \ 2019
Forest Ecology and Management 432 (2019). - ISSN 0378-1127 - p. 478 - 488.
Ungulates in temperate regions are increasing in range and abundance, leading to concerns that browsing and trampling reach levels that hamper tree recruitment and forest regeneration. However, studies that actually quantify the long-term effects of ungulates on forest succession are scarce. Here, we use a chronosequence of ungulate exclosures (fenced) and control (unfenced) plots to assess the long-term effects of ungulates on forest structure, diversity and litter depth in forests on poor sandy soils at the Veluwe, the Netherlands, which have moderate ungulate densities ( = 13.6 ungulates km−2). We surveyed the vegetation in 27 paired fenced and unfenced plots that ranged from 1 to 33 years old, and measured seven variables to characterize forest structure (stem density, canopy cover and understory vegetation cover), composition (Shannon diversity, species richness and conifer proportion) and leaf litter depth. We found on average that fencing compared to unfencing reduced understory vegetation cover (fenced = 64.3 ± 20.2%, unfenced = 80.3 ± 19.4%), increased canopy cover (fenced = 47.4 ± 30.1%, unfenced = 29.3 ± 21.1%), tree species richness (fenced = 4.5 ± 1.3 spp., unfenced = 2.7 ± 1.2 spp.), tree Shannon diversity (fenced = 1.1 ± 0.3 index, unfenced = 0.7 ± 0.3 index) and litter layer depth (fenced = 4.4 ± 1.4 cm, unfenced = 2.4 ± 1.1 cm). While fenced plots developed woody vegetation with palatable broadleaved species such as Betula pendula, Betula pubescens, Prunus serotina, and Quercus robur, unfenced plots were not associated with any particular tree species. Our results show that current ungulate densities in this system have pronounced long-term effects on forest structure, composition and litter depth, implying that ungulates can slow down natural succession of temperate forest, from light demanding to shade tolerant species, by keeping the system in an arrested state consisting of light demanding species.
Similarities and differences of the volatile profiles of six spices explored by Proton Transfer Reaction Mass Spectrometry
Silvis, I.C.J. ; Luning, P.A. ; Klose, N. ; Jansen, M. ; Ruth, S.M. van - \ 2019
Food Chemistry 271 (2019). - ISSN 0308-8146 - p. 318 - 327.
2-Butanone (PubChem CID: 6569) - Acetic acid (PubChem CID: 176) - Aroma - Cinnamaldehyde (PubChem CID: 637511) - Estragole (PubChem CID: 8815) - Fingerprints - Methanol (PubChem CID: 887) - Non-destructive - P-cymene (PubChem CID: 7463) - PTR-TOFMS - Safranal (PubChem CID: 61041) - Volatile compounds

Aroma properties of spices are related to the volatile organic compounds (VOCs) present, which can provide distinct analytical signatures. The aim of the study was to examine similarity and diversity of VOC profiles of six common market spices (black/white pepper, chili paprika, cinnamon, nutmeg and saffron). The key volatiles were identified by PTR-TOFMS. Twelve samples per spice were subjected to PTR-Quadrupole MS (PTR-QMS) and Principal Component Analysis to compare the groups and examine diversity. With PTR-TOFMS, 101 volatile compounds were identified as total sum across all samples by mass and comparing them with literature data. Some spices comprised key character aroma compounds, e.g. cinnamaldehyde in cinnamon. For others, VOC groups, such as terpenes, acids and aldehydes topped the list. The PTR-QMS in combination with variables selection resulted in distinct PCA patterns for each spice. Variation within the spice groups was observed, but varied with the kind of spice. The results are valuable for future authentication studies.

Zeewier, niet alleen maar lekker bij vis: WMR Regiocentrum Yerseke
Tonk, Linda ; Jansen, H.M. - \ 2018
Visserijnieuws 38 (2018)35. - ISSN 1380-5061 - p. 4 - 4.
Comparative institutional analysis for public health: governing voluntary collaborative agreements for public health in England and the Netherlands
Bekker, Marleen ; Mays, N. ; Helderman, J.K. ; Petticrew, M. ; Jansen, M.W.J. ; Knai, C. ; Ruwaard, D. - \ 2018
European Journal of Public Health 28 (2018)suppl. 3. - ISSN 1101-1262 - p. 19 - 25.
Democratic institutions and state-society relations shape governance arrangements and expectations between public and private stakeholders about public health impact. We illustrate this with a comparison between the English Public Health Responsibility Deal (RD) and the Dutch ‘All About Health…’ (AaH) programme. As manifestations of a Whole-of-Society approach, in which governments, civil society and business take responsibility for the co-production of economic utility and good health, these programmes are two recent collaborative platforms based on voluntary agreements to improve public health. Using a ‘most similar cases’ design, we conducted a comparative secondary analysis of data from the evaluations of the two programmes. The underlying rationale of both programmes was that voluntary agreements would be better suited than regulation to encourage business and civil society to take more responsibility for improving health. Differences between the two included: expectations of an enforcing versus facilitative role for government; hierarchical versus horizontal coordination; big business versus civil society participants; top-down versus bottom-up formulation of voluntary pledges and progress monitoring for accountability versus for learning and adaptation. Despite the attempt in both programmes to base voluntary commitments on trust, the English ‘shadow of hierarchy’ and adversarial state-society relationships conditioned non-governmental parties to see the pledges as controlling, quasi-contractual agreements that were only partially lived up to. The Dutch consensual political tradition enabled a civil society-based understanding and gradual acceptance of the pledges as the internalization by partner organizations of public health values within their operations. We conclude that there are institutional limitations to the implementation of generic trust-building and learning-based models of change ‘Whole-of-Society’ approaches.
Zorgen voor ontheemden : migratie en ontwikkeling
Jansen, Bram ; Stuiver, Marian ; Voors, Maarten ; Boas, Ingrid ; Pittore, Katherine ; Rooij, Bertram de - \ 2018
Looking after displaced people : migration and development
Jansen, Bram ; Stuiver, Marian ; Voors, Maarten ; Boas, Ingrid ; Pittore, Katherine ; Rooij, Bertram de - \ 2018
polymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids
Bourke, Peter M. ; Geest, Geert van; Voorrips, Roeland E. ; Jansen, Johannes ; Kranenburg, Twan ; Shahin, Arwa ; Visser, Richard G.F. ; Arens, Paul ; Smulders, Marinus J.M. ; Maliepaard, Chris - \ 2018
Bioinformatics 34 (2018)20. - ISSN 1367-4803 - p. 3496 - 3502.

Motivation: Polyploid species carry more than two copies of each chromosome, a condition found in many of the world's most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realize all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops.

Results: polymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops.

Availability and implementation: polymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at

Supplementary information: Supplementary data are available at Bioinformatics online.

Nest defensibility decreases home-range size in central place foragers
Lameris, Thomas K. ; Brown, Joel S. ; Kleyheeg, Erik ; Jansen, Patrick A. ; Langevelde, Frank van - \ 2018
Behavioral Ecology 29 (2018)5. - ISSN 1045-2249 - p. 1038 - 1045.
Central place foraging - defensibility - movement behavior - nest predation - theoretical model

Variation in the home-range size of nesting animals is thought to be driven by nutritional requirements, food availability, and predation risk of the animals during foraging. Only few studies have considered that the risk of nest predation may also affect home-range size because nests become more difficult to defend as animals move further away. We used a theoretical model to explore the combined effects of nest defensibility, nest predation risk, and food availability on foraging distance from the nest, and hence home-range size. In our model, foragers adjust the foraging distance around the central place such that the required amount of food is collected within the available time with the lowest predation risk for the nest. We found that foraging distance decreased with food availability and the risk of nest predation during absence, but also with nest defensibility. When food was abundant, both nest predation risk and defensibility hardly influenced foraging distance. When food was scarce, animals able to deter predators foraged close-by, whereas animals less able to deter predators foraged further away. Likewise, animals that were themselves vulnerable to predation stayed closer to their nest if the nest provided safety, as is typical for central place foragers. This study is the first to assess the importance of nest defense and nest predation risk for foraging distance of central place foragers and provides a better understanding of the drivers of home-range size.

ASCA: The Implementation of Design of Experiments Into Multivariate Modelling in Chemometrics
Jansen, Jeroen ; Engel, Jasper - \ 2018
Comprehensive Analytical Chemistry 82 (2018). - ISSN 0166-526X - p. 301 - 335.
Chemometrics - Multivariate modelling

The untargeted metabolomics paradigm may be very helpful to reveal biochemical patterns in the multifactorial experiments in environmental analysis. Specific combinations between metabolites may be highly specific biomarkers for environmental and/or ecological change. However, such patterns need to be recovered from a background of many unrelated metabolites within a wealth of cooccurring environmental processes. The range of methods we present here, based around Analysis-of-Variance-Simultaneous Component Analysis (ASCA), have been specifically developed retrieve such patterns. They combine the merits of quantitatively describing the Design-of-Experiments that underlies an environmental study with the multivariate nature of metabolomics data. The ASCA toolbox has by now extended into a comprehensive and generic approach that allows analysis of, e.g., unbalanced data, quantitative significance of effects and of relevant biomarkers. The same approach can also be taken to analyse specific effects with respect to positive and negative controls, to reveal specific experimentally relevant deviations in metabolism. We show the ASCA results of a specific plant chemical ecology dataset, in which all glucosinolates within a wild cabbage were profiled upon induction of an ecological defence response. ASCA provides direct insight in the variability associated with different aspects of this response, and relatively recent extensions in data preprocessing reveal very clearly the metabolites that are most relevant to the response.

The relationship between job demands, job resources and teachers’ professional learning : is it explained by self-determination theory?
Jansen in de Wal, Joost ; Beemt, Antoine van den; Martens, Rob L. ; Brok, Perry J. den - \ 2018
Studies in Continuing Education (2018). - ISSN 0158-037X
Job demands - job resources - motivation - self-determination theory - teacher professional learning

Although teachers’ commitment to continuous professional learning is crucial for high quality education, research shows that this learning cannot be taken for granted. To better understand how teachers’ learning at work can be supported, this study investigates how effects of job demands (i.e. work pressure and emotional pressure) and job resources (i.e. task autonomy, transformational leadership, and collegial support) on teachers’ learning commitment (i.e. learning frequency and engagement) can be explained by basic psychological need satisfaction and autonomous motivation, as posited by self-determination theory. At two occasions, approximately one year apart, data was collected in a sample of 678 (T1) and 536 (T2) Dutch secondary school teachers. Structural equation models showed the consecutive positive longitudinal relationships between teachers’ experience of job resources, basic psychological need satisfaction, autonomous motivation, and commitment to professional learning. Job demands were not related to basic need satisfaction over and above the effects of job resources. Implications for how self-determination theory and the job demands resources model can mutually inform each other are discussed. In addition, implications for stimulating teachers’ professional learning in practice are provided.

Opbrengsttabellen Nederland 2018
Jansen, Hans ; Oosterbaan, Anne ; Mohren, G.M.J. ; Goudzwaard, L. ; Ouden, J. den; Schoonderwoerd, H. ; Thomassen, E.A.H. ; Schmidt, P. ; Copini, P. - \ 2018
Wageningen : Wageningen Academic Publishers - ISBN 9789086868766 - 172
In deze bundel zijn opbrengsttabellen van 15 boomsoorten opgenomen. In vergelijking met de tot nu toe geldende opbrengsttabellen uit 1996, bevat deze bundel meer soorten, meer dunningregimes, en zijn alle tabellen gebaseerd op Nederlandse meetgegevens. Voor 10 soorten zijn tabellen met zowel een matige als sterke dunning opgenomen. Voor de Japanse Lariks zijn twee regionale tabellen opgenomen. De populier heeft in deze bundel een tabel voor bomen in lijnbeplanting, naast de tabellen voor bos met diverse plantverbanden. Per soort is het rapport van de onderliggende studie weergegeven. Al deze studies volgden in grote lijnen de studie Groei en productie van douglas in Nederland. Becking's dunningproeven ontsloten. In vergelijking met de studies uit 1996, blijkt enerzijds de hoogtegroei per boniteit te verschillen (slechte boniteiten starten lager dan goede boniteiten, maar halen de groei later deels in). Anderzijds blijk de range tussen de beste en slechtste boniteit vaak ruimer dan in de eerdere studies.
Humanitarianism As Buffer : Displacement, aid and the politics of belonging in Abyei, Sudan/South Sudan
Jansen, Bram J. - \ 2018
African Affairs 117 (2018)468. - ISSN 0001-9909 - p. 370 - 391.

This article explores how the humanitarian presence and programs in the disputed border area of Abyei between Sudan and South Sudan can be understood as a buffer between conflicting parties, rather than as mere assistance to a displaced population. It aims to contribute to debates about the spatial impact of humanitarian governance and the politicization of aid in protracted crisis contexts, and specifically in relation to territorial disputes and border struggles. It is based on ethnographic fieldwork in South Sudan between 2011 and 2013. The article argues that the humanitarian response became part of the politics of belonging that lies at the heart of the dispute. The very acts of labelling, categorizing, and maintaining the subjects of aid are highly political, such as the creation of the category of the 'people of Abyei' in contrast to refugees or Internally Displaced People. As a result, the interventions have sustained governance over the territory and can be understood as a humanitarian buffer that may shape the border area of Abyei for many years to come.

Omics analyses of potato plant materials using an improved one-class classification tool to identify aberrant compositional profiles in risk assessment procedures
Kok, Esther ; Dijk, Jeroen van; Voorhuijzen, Marleen ; Staats, Martijn ; Slot, Martijn ; Lommen, Arjen ; Venema, Dini ; Pla, Maria ; Corujo, Maria ; Barros, Eugenia ; Hutten, Ronald ; Jansen, Jeroen ; Voet, Hilko van der - \ 2018
Food Chemistry (2018). - ISSN 0308-8146
Compositional analysis - Genetically modified organism - GMO - Omics profiling - Risk assessment

The objective of this study was to quantitatively assess potato omics profiles of new varieties for meaningful differences from analogous profiles of commercial varieties through the SIMCA one-class classification model. Analytical profiles of nine commercial potato varieties, eleven experimental potato varieties, one GM potato variety that had acquired Phytophtora resistance based on a single insert with potato-derived DNA sequences, and its non-GM commercial counterpart were generated. The ten conventional varieties were used to construct the one-class model. Omics profiles from experimental non-GM and GM varieties were assessed using the one-class SIMCA models. No potential unintended effects were identified in the case of the GM variety. The model showed that varieties that were genetically more distant from the commercial varieties were recognized as aberrant, highlighting its potential in determining whether additional evaluation is required for the risk assessment of materials produced from any breeding technique, including genetic modification.

Heruitgave Opbrengsttabellen Becking & de Vries Nederland 1959
Jansen, J.J. - \ 2018
Wageningen : Wageningen University & Research - 39 p.
Effecten van mosselkweek op sediment-dynamiek in de Waddenzee : uitgebreide samenvatting van het rapport “The effect of mussel farming on sedimentdynamics in the Wadden Sea - case studies evaluating the local effects of mussel seedfisheries and mussel harvest on turbidity and sedimentation”
Jansen, Henrice M. ; Capelle, Jacob J. - \ 2018
IJmuiden : Wageningen Marine Research (Wageningen Marine Research report C047/18) - 67
The effect of mussel farming on sediment dynamics in the Wadden Sea : case studies evaluating the local effects of mussel seed fisheries and mussel harvest on turbidity and sedimentation
Jansen, Henrice M. ; Capelle, Jacob J. - \ 2018
IJmuiden : Wageningen Marine Research (Wageningen Marine Research report C046/18) - 67
Data from: Towards smarter harvesting from natural palm populations by sparing the individuals that contribute most to population growth or productivity
Jansen, M. ; Anten, N.P.R. ; Bongers, F. ; Martínez-Ramos, Miguel ; Zuidema, P.A. - \ 2018
Chamaedorea - forest management - harvest simulations - individual heterogenity - Integral Project Model - leaf harvesting - NFTP - sustainability - Chamaedorea elegans
1. Natural populations deliver a wide range of products that provide income for millions of people and need to be exploited sustainably. Large heterogeneity in individual performance within these exploited populations has the potential to improve population recovery after exploitation and thus help sustaining yields over time. 2. We explored the potential of using individual heterogeneity to design smarter harvest schemes, by sparing individuals that contribute most to future productivity and population growth, using the understorey palm Chamaedorea elegans as a model system. Leaves of this palm are an important non-timber forest product and long-term inter-individual growth variability can be evaluated from internode lengths. 3. We studied a population of 830 individuals, half of which was subjected to a 67 % defoliation treatment for three years. We measured effects of defoliation on vital rates and leaf size – a trait that determines marketability. We constructed integral projection models in which vital rates depended on stem length, past growth rate, and defoliation, and evaluated transient population dynamics to quantify population development and leaf yield. We then simulated scenarios in which we spared individuals that were either most important for population growth or had leaves smaller than marketable size. 4. Individuals varying in size or past growth rate responded similarly to leaf harvesting in terms of growth and reproduction. By contrast, defoliation-induced reduction in survival chance was smaller in large individuals than in small ones. Simulations showed that harvest-induced population decline was much reduced when individuals from size and past growth classes that contributed most to population growth were spared. Under this scenario cumulative leaf harvest over 20 years was somewhat reduced, but long-term leaf production was sustained. A three-fold increase in leaf yield was generated when individuals with small leaves are spared. 5. Synthesis and applications This study demonstrates the potential to create smarter systems of palm leaf harvest by accounting for individual heterogeneity within exploited populations. Sparing individuals that contribute most to population growth ensured sustained leaf production over time. The concepts and methods presented here are generally applicable to exploited plant and animal species which exhibit considerable individual heterogeneity.
Thought for urban food planning : The Oosterwold (NL) experiment to normalise agriculture in urban planning
Jansma, J.E. ; Janssen-Jansen, L. ; Valk, A.J.J. van der; Wertheim-Heck, S.C.O. - \ 2018
In: Proceedings of Annual AESOP congress 10-14 July 2018, Gothenburg - p. 10 - 13.
Proceedings of Annual AESOP congress 10-14 Juli 2018, Gothenburg
Increasing quality of life in pulmonary arterial hypertension : is there a role for nutrition?
Vinke, Paulien ; Jansen, Suzanne M. ; Witkamp, Renger F. ; Norren, Klaske van - \ 2018
Heart Failure Reviews 23 (2018)5. - ISSN 1382-4147 - p. 711 - 722.
Deficiencies - Exercise - Lifestyle - Nutrition - Pulmonary arterial hypertension - Review

Pulmonary arterial hypertension (PAH) is a progressive disease primarily affecting the pulmonary vasculature and heart. PAH patients suffer from exercise intolerance and fatigue, negatively affecting their quality of life. This review summarizes current insights in the pathophysiological mechanisms underlying PAH. It zooms in on the potential involvement of nutritional status and micronutrient deficiencies on PAH exercise intolerance and fatigue, also summarizing the potential benefits of exercise and nutritional interventions. Pubmed/Medline, Scopus, and Web of Science were searched for publications on pathophysiological mechanisms of PAH negatively affecting physical activity potential and nutritional status, and for potential effects of interventions involving exercise or nutritional measures known to improve exercise intolerance. Pathophysiological processes that contribute to exercise intolerance and impaired quality of life of PAH patients include right ventricular dysfunction, inflammation, skeletal muscle alterations, and dysfunctional energy metabolism. PAH-related nutritional deficiencies and metabolic alterations have been linked to fatigue, exercise intolerance, and endothelial dysfunction. Available evidence suggests that exercise interventions can be effective in PAH patients to improve exercise tolerance and decrease fatigue. By contrast, knowledge on the prevalence of micronutrient deficiencies and the possible effects of nutritional interventions in PAH patients is limited. Although data on nutritional status and micronutrient deficiencies in PAH are scarce, the available knowledge, including that from adjacent fields, suggests that nutritional intervention to correct deficiencies and metabolic alterations may contribute to a reduction of disease burden.

Groei en productie van zwarte els in Nederland
Jansen, J.J. ; Oosterbaan, A. ; Mohren, G.M.J. ; Copini, P. ; Ouden, J. den - \ 2018
Wageningen : Wageningen University & Research (FEM Groei en Productie rapport 2018-10) - 47
In the Netherlands growth and yield research on black alder was done on a limited scale from 1965 to 1990. This regards two studies by the Dorschkamp/IBN research institute; together with the permanent sample plots from the timber prognosis system HOSP, this comprises a dataset of 14 plots with 59 recordings. In addition, the information from 518 stands of the Fourth National Forest Inventory was used. For the development of top height htop with age t Jansen’s et al. polymorphic model with site index h50 and four additional parameters fitted best. The diameter at a height of 7 m (d7) was estimated from data of the Fourth National Forest Inven-tory. The diameter development up to stand height of 7 m was described with a model of Jansen et al., a power function in htop and the estimated value for d7. From a stand height of 7 m upwards, the basal area increment (iG) was also described by Jansen’s et al. model based on a power function with t, year of recording (yor), and the stand density of Hart (S %). For S% > 15.7 the basal area increment decreases non-linear with increasing S %. The model contains a correction factor for yor, although this was not significant, as the year of recording (yor), turned out to be not significant. The effect of thinning on the diameter after thinning was modelled with the La Bastide-Faber model. The models were used to construct a yield table with five site classes and one thinning intensity.
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