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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    Response to commentary ‘towards more meaningful scenarios of biodiversity responses to land-use change in Central Asia
    Nunez, Sarahi ; Alkemade, Rob ; Kok, Kasper ; Leemans, Rik - \ 2020
    Regional Environmental Change 20 (2020)3. - ISSN 1436-3798
    Biodiversity change - Grasslands - Grazing intensification - Land-use scenarios

    With this letter, we respond to the commentary by Kamp et al. on our paper (Nunez et al. in Reg Environ Chang 20:39, 2020) that reports on potential biodiversity change in Central Asian grasslands using climate and land-use change scenarios. In their commentary, Kamp et al. criticize data and methods employed and discuss several shortfalls of our approach. In this response, we argue that in our paper projections of future biodiversity already acknowledge the issues indicated by Kamp et al. We elaborate on the reasons why. We maintain our main finding that, based on a number of contrasting scenarios (shared socioeconomic pathways and representative concentration pathways combinations), biodiversity in grasslands in Central Asia will potentially decline under each scenario. We conclude that while our data and methods conservatively estimate potential biodiversity changes in the Central Asian grasslands, they could be enriched with more elements. The results, however, are likely to confirm the vulnerability of these grasslands and the possible decline in their biodiversity.

    Data underlying the publication: Potato Virus Y Detection in Seed Potatoes Using Deep Learning on Hyperspectral Images
    Polder, Gerrit ; Marrewijk, Bart van; Blok, Pieter ; Villiers, Hendrik de; Wolf, Jan van der; Kamp, Jan - \ 2020
    Wageningen University & Research
    disease detection - Erwinia - hyperspectral imaging - imaging spectroscopy - potato plants - Potato Y virus
    Bacterial and virus diseases causes major damage in agriculture. Classifying those is an challenging but important task. This dataset contains +-274 000 spectral line images (512 pixels x 56 bands) of 6 different cultivars of healthy, bacterial (Erwinia) and virus (PVY) infected plants. The coordinates of each image is stored and can be compared with the stored position of individual plants labeled by crop experts
    Nieuw prototype ziekzoekrobot volop het veld in
    Kamp, Jan - \ 2020
    Whole Grain Wheat Consumption Affects Postprandial Inflammatory Response in a Randomized Controlled Trial in Overweight and Obese Adults with Mild Hypercholesterolemia in the Graandioos Study
    Hoevenaars, Femke P.M. ; Esser, Diederik ; Schutte, Sophie ; Priebe, Marion G. ; Vonk, Roel J. ; Brink, Willem J. van den; Kamp, Jan Willem van der; Stroeve, Johanna H.M. ; Afman, Lydia A. ; Wopereis, Suzan - \ 2019
    The Journal of Nutrition 149 (2019)12. - ISSN 0022-3166 - p. 2133 - 2144.
    (compromised) healthy subjects - challenge test - composite biomarkers - inflammation - liver - metabolic health - phenotypic flexibility - resilience - whole grain wheat

    BACKGROUND: Whole grain wheat (WGW) consumption is associated with health benefits in observational studies. However, WGW randomized controlled trial (RCT) studies show mixed effects. OBJECTIVES: The health impact of WGW consumption was investigated by quantification of the body's resilience, which was defined as the "ability to adapt to a standardized challenge." METHODS: A double-blind RCT was performed with overweight and obese (BMI: 25-35 kg/m2) men (n = 19) and postmenopausal women (n = 31) aged 45-70 y, with mildly elevated plasma total cholesterol (>5 mmol/L), who were randomly assigned to either 12-wk WGW (98 g/d) or refined wheat (RW). Before and after the intervention a standardized mixed-meal challenge was performed. Plasma samples were taken after overnight fasting and postprandially (30, 60, 120, and 240 min). Thirty-one biomarkers were quantified focusing on metabolism, liver, cardiovascular health, and inflammation. Linear mixed-models evaluated fasting compared with postprandial intervention effects. Health space models were used to evaluate intervention effects as composite markers representing resilience of inflammation, liver, and metabolism. RESULTS: Postprandial biomarker changes related to liver showed decreased alanine aminotransferase by WGW (P = 0.03) and increased β-hydroxybutyrate (P = 0.001) response in RW. Postprandial changes related to inflammation showed increased C-reactive protein (P = 0.001), IL-6 (P = 0.02), IL-8 (P = 0.007), and decreased IL-1B (P = 0.0002) in RW and decreased C-reactive protein (P < 0.0001), serum amyloid A (P < 0.0001), IL-8 (P = 0.02), and IL-10 (P < 0.0001) in WGW. Health space visualization demonstrated diminished inflammatory (P < 0.01) and liver resilience (P < 0.01) by RW, whereas liver resilience was rejuvenated by WGW (P < 0.05). CONCLUSIONS: Twelve-week 98 g/d WGW consumption can promote liver and inflammatory resilience in overweight and obese subjects with mildly elevated plasma cholesterol. The health space approach appeared appropriate to evaluate intervention effects as composite markers. This trial was registered at www.clinicaltrials.gov as NCT02385149.

    Object-Based Image Analysis Applied to Low Altitude Aerial Imagery for Potato Plant Trait Retrieval and Pathogen Detection
    Siebring, Jasper ; Valente, João ; Domingues Franceschini, Marston Heracles ; Kamp, Jan ; Kooistra, Lammert - \ 2019
    Sensors 19 (2019)24. - ISSN 1424-8220 - 15 p.
    There is a growing demand in both food quality and quantity, but as of now, one-third of all food produced for human consumption is lost due to pests and other pathogens accounting for roughly 40% of pre-harvest loss in potatoes. Pathogens in potato plants, like the Erwinia bacteria and the PVYNTN virus for example, exhibit symptoms of varying severity that are not easily captured by pixel-based classes (as these ignore shape, texture, and context in general). The aim of this research is to develop an object-based image analysis (OBIA) method for trait retrieval of individual potato plants that maximizes information output from Unmanned Aerial Vehicle (UAV) RGB very high resolution (VHR) imagery and its derivatives, to be used for disease detection of the Solanum tuberosum. The approach proposed can be split in two steps: (1) object-based mapping of potato plants using an optimized implementation of large scale mean-shift segmentation (LSMSS), and (2) classification of disease using a random forest (RF) model for a set of morphological traits computed from their associative objects. The approach was proven viable as the associative RF model detected presence of Erwinia and PVY pathogens with a maximum F1 score of 0.75 and an average Matthews Correlation Coefficient (MCC) score of 0.47. It also shows that low-altitude imagery acquired with a commercial UAV is a viable off-the-shelf tool for precision farming, and potato pathogen detection.
    Erwinia Detection in Potato Plants using Convolutional Neural Networks
    Afonso, M.V. ; Blok, P.M. ; Polder, G. ; Wolf, J.M. van der; Kamp, J.A.L.M. - \ 2019
    Smart disease detection seed potatoes 2015-2018. Detection of virus and bacterial diseases using vision and sensor technology
    Kamp, J.A.L.M. ; Blok, P.M. ; Polder, J.J. ; Wolf, J.M. van der; Jalink, H. - \ 2019
    Stichting Wageningen Research, Wageningen University & Research (Report WPR 793) - 57 p.
    Blackleg Detection in Potato Plants using Convolutional Neural Networks
    Afonso, M.V. ; Blok, P.M. ; Polder, G. ; Wolf, J.M. van der; Kamp, J.A.L.M. - \ 2019
    - 6 p.
    Potato blackleg is a tuber-borne bacterial disease caused by species within the genera Dickeya and Pectobacterium that can cause decay of plant tissue and wilting through the action of cell wall degrading enzymes released by the pathogen. In case of serious infections, tubers may rot before emergence. Management is largely based on the use of pathogen-free seed potato tubers. For this, fields are visually monitored both for certification and also to take out diseased plants to avoid spread to neighboring plants. Imaging potentially offers a quick and non-destructive way to inspect the health of potato plants in a field. Early detection of blackleg diseased plants with modern vision techniques can significantly reduce costs. In this paper, we studied the use of deep learning for detecting blackleg diseased potato plants. Two deep convolutional neural networks were trained on RGB images with healthy and diseased plants. One of these networks (ResNet18) was experimentally found to produce a precision of 95 % and recall of 91 % for the disease class. These results show that convolutional neural networks can be used to detect blackleg diseased potato plants.
    Op naar precisielandbouw 2.0 : eindrapport PPS PL2.0 2015-2019 topsectorproject AF-14275
    Kempenaar, Corné ; Dijk, Chris van; Hermans, Geert ; Steele-Dun, Susan ; Sande, Corné van de; Verschoore, Jeroen ; Wal, Tamme van der; Roerink, Gerbert ; Visser, Juriaan ; Kamp, Jan ; Blok, Pieter ; Polder, Gerrit ; Wolf, Jan van de; Jalink, Henk ; Bulle, Annette ; Meurs, Bert ; Michielsen, Jean-Marie ; Zande, Jan van de; Hoving, Idse ; Riel, Johan van; Holshof, Gertjan ; Boheemen, Koen van; Evert, Frits van; Riemens, Marleen ; Keizer, Paul ; Schnabel, Sabine ; Egmond, Fenny van; Walvoort, Dennis ; Janssen, Henk ; Riviėre, Inge La; Kocks, Corné ; Pot, Alfred - \ 2019
    Lelystad : Stichting Wageningen Research, Wageningen University & Research (Rapport WPR 921) - 138
    De publiek private samenwerking (PPS) ‘Op naar precisielandbouw 2.0’ (PL2.0) is een R&D project van de topsector AgriFood. Het project is gestart in 2015 met doorlooptijd van 4 jaar. Voor u ligt het eindrapport. In deze PPS werkten ruim 20 private bedrijven en organisaties, publieke kennisinstellingen en overheden samen aan strategische onderwerpen binnen precisielandbouw. Het project omvatte 13 deelprojecten verdeeld over vijf specifieke R&D thema’s, te weten slim satellietbeeldengebruik, sensorontwikkeling (ziektedetectie), slimme integratie van technologieën in toepassingen, perceelkarakteristieken voor schatten van opbrengstpotentie en ondersteunende ICT, en een generiek thema communicatie en kennisverspreiding.Met betrekking tot het thema satellietbeeldengebruik is uitgezocht hoe optische satellietbeelden in combinatie met radarbeelden of beelden verkregen via drone-camera’s beter gebruikt kunnen worden om de variatie en status van de bovengrondse hoeveelheid biomassa van gewassen in kaart te brengen en opbrengsten te voorspellen. Op het gebied van ziektedetectie is door middel van sensor fusion en artificial intelligence de detectie van virus- en bacterieziekten in aardappelplanten verbeterd. En werd een prototype sensorsysteem voor veldonderzoek ontwikkeld. Door slimme integratie van data, adviesmodellen en mechanisatie zijn er enkele variabel-doseertoepassingen ontwikkeld en gevalideerd. Het gaat hier om variabel doseren van Stikstof en herbiciden binnen teelten d.m.v. taakkaarten. In het verlengde hiervan is ook een ontwerp geleverd en als prototype gevalideerd voor een innovatieve beddenspuit in bloembollenteelt. Op grond van perceelkarakteristieken en ondersteunende ICT zijn inzichten en tools voor het inschatten van opbrengst(potentie) geleverd en wordt een doorkijk gegeven naar software voor verbeterde rijpadenplanning en perceelinformatie. De inzet op communicatie en kennisdeling heeft ca. 100 publicaties en presentaties in 4 jaar tijd opgeleverd. Voor meer details over resultaten wordt naar de rapportage met samenvatting per deelproject verwezen in de hoofdstukken 2 tot en met 7.Het grote succes van PL2.0 ligt vooral bij ruime aandacht voor integratie van componenten van precisielandbouwtoepassingen en de doorstroming daarvan naar de praktijk en onderwijs.Geconcludeerd mag worden dat PL2.0 een bijdrage leverde aan gewasmonitoringtoepassingen en diverse variabel-doseertoepassingen (variable rate applications, VRA). Die VRA-toepassingen zien we nu op de agenda in het in 2018 gestarte precisielandbouw-adoptie project ‘Nationale Proeftuin Precisielandbouw’ (NPPL). Meerdere bedrijven passen taakkaarten variabel doseren op een resolutie van 30-50 m2 op praktijkschaal toe en besparen zo’n 20 -30% op gewasbeschermingsmiddelen met behoud van goede werking. De basis hiervoor is een bodem- of gewaskaart die de relevante variatie binnen de bodem of gewas in kaart brengt. Ook zijn er via PL2.0 mooie resultaten met optimalisatie van plantdichtheid en vermindering van meststoffengebruik via deze kaarten. Doorstroming van kennis naar het groene onderwijs werd gerealiseerd via PL2.0 en een versterkend WURKS-traject. Negen lesmodules over gebruik software en inzet taakkaarten in precisielandbouw werden opgeleverd. Precisielandbouw is geen doel op zich, maar een manier om de duurzaamheid van landbouw te vergroten. Met PL2.0 toepassingen kan meer met minder en beter geproduceerd worden. De trend van precisielandbouw c.q. data-gedreven landbouw of smart farming, zal zich alleen maar doorzetten. Er zal gewerkt gaan worden met meer en hoog-resolutie data, complexere adviesmodellen en meer robotisering. Daarmee zullen de doelen van kringlooplandbouw beter en sneller gerealiseerd kunnen worden.
    HEVnet: A one health, collaborative, interdisciplinary network and sequence data repository for enhanced hepatitis e virus molecular typing, characterisation and epidemiological investigations
    Mulder, Annemieke Christine ; Kroneman, Annelies ; Franz, Eelco ; Vennema, Harry ; Tulen, Anna D. ; Takkinen, Johanna ; Hofhuis, Agnetha ; Adlhoch, Cornelia ; Aberle, Stephan ; Subissi, Lorenzo ; Suin, Vanessa ; Midgley, Sofie ; Kuznetsova, Tatiana ; Izopet, Jacques ; Pavio, Nicole ; Baechlein, Christine ; Baylisa, Sally A. ; Corman, Victor M. ; Fabera, Mirko ; Johne, Reimar ; Kamp, Christel ; Wenzel, Juergen J. ; Coughlan, Suzie ; Bartolo, Ilaria Di; Bruni, Roberto ; Ciccaglionea, Anna Rita ; Garbuglia, Anna Rosa ; Suffredini, Elisabetta ; Boxman, Ingeborg ; Hogema, Boris ; Poel, Wim van der; Zaaijera, Hans ; Sousaa, Rita de; Velebit, Branko ; Avellóna, Ana ; Buti, Maria ; Girones, Rosina ; Quer, Josep ; Widén, Frederik ; Norder, Heléne ; Nyström, Kristina ; Bachofen, Claudia ; Sahli, Roland ; Ijaza, Samreen ; Treagus, Samantha ; Kulka, Michael ; Rizzi, Valentina - \ 2019
    Eurosurveillance 24 (2019)10. - ISSN 1025-496X

    Hepatitis E virus (HEV) is a common cause of acute hepatitis worldwide. In Europe, HEV is a zoonosis transmitted via contaminated pork meat or other pork food products. Genotype 3 is the most prevalent HEV type in the animal reservoir, as well as in humans. Despite an increased incidence of hepatitis E across Europe, much remains unknown about its spread, sources and transmission routes. A One Health approach is crucial to better understand the (molecular) epidemiology of HEV. HEVnet was established in April 2017 as a network and database for sharing sequences and accompanying metadata collected from human, animal, food and environmental sources. HEVnet members working in the public health, veterinary health, food, environmental and blood safety sectors have submitted 1,615 HEV sequences from nine countries as at January 2019. Most are from humans (89%), and sequences of animal (5%), food (6%) or environmental (0.3%) origin are rare. Metadata for human sequences capture mostly sex (93%), year of birth (92%) and sampling (100%); data on region of sampling (37%) and clinical information (hospitalisation 27%, symptoms 20% or mortality 8%) are limited. HEVnet aims to expand into a global network capable of performing cross-sectoral and supranational studies, with a joint repository of molecular and epidemiological data on HEV.

    Veldrobot mist regie en samenwerking
    Booij, Johan ; Kamp, Jan ; Veldhuisen, Bram - \ 2019
    Potato Virus Y Detection in Seed Potatoes Using Deep Learning on Hyperspectral Images
    Polder, G. ; Blok, P.M. ; Villiers, H.A.C. de; Wolf, J.M. van der; Kamp, J.A.L.M. - \ 2019
    Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
    crop resistance - Phenotyping - hyperspectral imaging - classification - Convolutional neural network - Solanum tuberosum
    Virus diseases are of high concern in the cultivation of seed potatoes. Once found inthe field, virus diseased plants lead to declassification or even rejection of the seed lotsresulting in a financial loss. Farmers put in a lot of effort to detect diseased plants andremove virus-diseased plants from the field. Nevertheless, dependent on the cultivar,virus diseased plants can be missed during visual observations in particular in an earlystage of cultivation. Therefore, there is a need for fast and objective disease detection.Early detection of diseased plants with modern vision techniques can significantlyreduce costs. Laboratory experiments in previous years showed that hyperspectral imaging clearly could distinguish healthy from virus infected potato plants. This paper reports on our first real field experiment. A new imaging setup was designed, consisting of a hyperspectral line-scan camera. Hyperspectral images were taken in the field with a line interval of 5 mm. A fully convolutional neural network was adapted for hyperspectral images and trained on two experimental rows in the field. The trained network was validated on two other rows, with different potato cultivars. For three of the four row/date combinations the precision and recall compared to conventional disease assessment exceeded 0.78 and 0.88, respectively. This proves the suitability of this method for real world disease detection.
    Robot kan straks in kiemstadium onkruid herkennen
    Kamp, Jan - \ 2019
    Hydroplasticization of latex films with varying methacrylic acid content
    Voogt, Benjamin ; Huinink, Henk ; Kamp-Scheerder, Loes van der; Erich, Bart ; Scheerder, Jurgen ; Venema, P. ; Adana, Olaf - \ 2019
    Polymer 166 (2019). - ISSN 0032-3861 - p. 206 - 214.
    Hydroplasticization - Coating - Polymer mobility
    The hydroplasticization of coatings of acrylic copolymers with different amounts of methacrylic acid (MAA) was investigated to clarify the role of carboxylic acid functionalities on the change in polymer mobility due to water uptake. The coating Tg as a function of water uptake was studied using dynamic mechanical analysis. The Tg’s decreased with increasing water content, confirming the plasticizing effect of water on the coatings. At relative humidities between 0 and 60% the coating Tg shows a sharper decrease than at higher , an effect that increases with increasing MAA content. This behavior is attributed to the presence of dimers of carboxylic acid in the coatings, which is also observed with FTIR-ATR analyses. Due to water uptake, the dimers are disrupted and form “open” dimers where carboxylic acid groups remain in close proximity and are connected through water molecules. With 1H NMR relaxometry, two T2 relaxation times are found, representing two hydrogen pools with different mobilities. Both mobilities increase with increasing water content, indicating the presence of polymer domains with different hardness. Correlating the T2 relaxation times with the coating Tg’s shows that at higher MAA content the proton mobility as a function of Tg of the soft domains increases with increasing MAA content. Since the polymer proton mobility, and hence the polymer mobility, is expected to scale with the polymer Tg, it is hypothesized that harder domains are present in the coatings, which are not visible in the Ostroff-Waugh decays due to the fast relaxation behavior of these protons.
    Analysis of metabolome changes in the bile acid pool in feces and plasma of antibiotic-treated rats
    Behr, C. ; Slopianka, M. ; Haake, V. ; Strauss, V. ; Sperber, S. ; Kamp, H. ; Walk, T. ; Beekmann, K. ; Rietjens, I.M.C.M. ; Ravenzwaay, B. van - \ 2019
    Toxicology and Applied Pharmacology 363 (2019). - ISSN 0041-008X - p. 79 - 87.
    Antibiotics - Bile acid profiling - Gut microbiome - Metabolomics - Microbiome-related metabolites - Repeated dose oral toxicity study

    The bile acid-liver-gut microbiota axis plays an important role in the host's health. The gut microbiota has an impact on the bile acid pool, but also the bile acids themselves can influence the gut microbiota composition. In this study, six antibiotics from five different classes (i.e. lincosamides, glycopeptides, macrolides, fluoroquinolones, aminoglycosides) were used to modulate microbial communities of Wistar rats to elucidate changes in the bile acid metabolism and to identify key metabolites in the bile acid pool related to gut microbial changes. 20 primary and secondary bile acids were analyzed in plasma and feces of control and treated animals. Antibiotics treatment induced significant changes in primary and secondary bile acids in both matrices. Taurine-conjugated primary bile acids significantly increased in plasma and feces. Contrary, cholic acid and most of the analyzed secondary bile acids significantly decreased in plasma, and cholic acid accumulated in the feces after treatment with all antibiotics but roxithromycin. Despite the different activity spectra of the antibiotics applied against gut microbes, the overall effect on the bile acid pool tended to be similar in both matrices except for streptomycin. These results show that changes in the gut microbial community affect the bile acid pool in plasma and feces and that changes in the bile acid profile can be indicative of alterations of the gut microbiome. Due to the important role of bile acids for the host, changes in the bile acid pool can have severe consequences for the host.

    SMARAGD
    Schoorlemmer, H.B. ; Kamp, J.A.L.M. - \ 2018
    Slimme Mechanisatie, Automatisering en Robotisering voor een Akkerbouw met Groei en Duurzaamheid
    Towards a new way of farming
    Kamp, J.A.L.M. ; Schoorlemmer, H.B. - \ 2018
    Project SMARAGD - Farmtronics
    Microbiome-related metabolite changes in gut tissue, cecum content and feces of rats treated with antibiotics
    Behr, C. ; Sperber, S. ; Jiang, X. ; Strauss, V. ; Kamp, H. ; Walk, T. ; Herold, M. ; Beekmann, K. ; Rietjens, I.M.C.M. ; Ravenzwaay, B. van - \ 2018
    Toxicology and Applied Pharmacology 355 (2018). - ISSN 0041-008X - p. 198 - 210.
    Antibiotics - Gut content and tissue - Gut microbiome - Metabolite profiling - Metabolomics - Repeated dose oral toxicity study

    The metabolic functionality of the gut microbiota contributes to the metabolism and well-being of its host, although detailed insight in the microbiota's metabolism is lacking. Omics technologies could facilitate unraveling metabolism by the gut microbiota. In this study, we performed metabolite profiling of different matrices of the gut, after antibiotic treatment of rats in order to evaluate metabolite changes observed at different dose levels and in different sexes, and to identify the best tissue matrix for further investigations regarding an assessment of metabolic effects of new compounds with antibiotic activity. Three different antibiotics (vancomycin, streptomycin and roxithromycin) were administered orally to rats for 28 days according to the OECD 407 guideline with a subsequent metabolic profiling in feces, cecum content and gut tissue (jejunum, ileum, cecum, colon and rectum). The data were analyzed in the MetaMap®Tox database. Treatment-related effects could be observed in the metabolite profile of feces and cecum content, but not of the different gut tissues. The metabolite profile showed compound specific effects on the microbiome. In line with the activity spectra of the antibiotics tested, vancomycin showed the largest effects, followed by roxithromycin and then by streptomycin for which changes were modest. In general, for all antibiotics the largest changes were observed for the classes of lipids (increase up to 94-fold), bile acids (increase up to 33-fold), amino acids (increase up to 200-fold) and amino acid related (increase up to 348-fold). The most relevant changes in metabolite values were similar in feces and cecum content and among sexes. The results of this targeted analysis indicate that the metabolic profiles of male and female animals in the gut microbiome are comparable. Concluding, taking other samples than feces does not add any extra information. Thus, as a non-invasive sampling method, feces provide a suitable matrix for studies on metabolism by the gut microbiota.

    Bestrijding van aardappelopslag met robot, kappen en rollen
    Kamp, Jan - \ 2018
    'Smart Ziekzoeker is half klaar'
    Kamp, Jan - \ 2018
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