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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    Transforming, Genome Editing and Phenotyping the Nitrogen-fixing Tropical Cannabaceae Tree Parasponia andersonii
    Wardhani, Titis A.K. ; Roswanjaya, Yuda Purwana ; Dupin, Simon ; Li, Huchen ; Linders, Sidney ; Hartog, Marijke ; Geurts, Rene ; Zeijl, Arjan van - \ 2019
    Journal of Visualized Experiments (2019)150. - ISSN 1940-087X - 17 p.

    Parasponia andersonii is a fast-growing tropical tree that belongs to the Cannabis family (Cannabaceae). Together with 4 additional species, it forms the only known non-legume lineage able to establish a nitrogen-fixing nodule symbiosis with rhizobium. Comparative studies between legumes and P. andersonii could provide valuable insight into the genetic networks underlying root nodule formation. To facilitate comparative studies, we recently sequenced the P. andersonii genome and established Agrobacterium tumefaciens-mediated stable transformation and CRISPR/Cas9-based genome editing. Here, we provide a detailed description of the transformation and genome editing procedures developed for P. andersonii. In addition, we describe procedures for the seed germination and characterization of symbiotic phenotypes. Using this protocol, stable transgenic mutant lines can be generated in a period of 2-3 months. Vegetative in vitro propagation of T0 transgenic lines allows phenotyping experiments to be initiated at 4 months after A. tumefaciens co-cultivation. Therefore, this protocol takes only marginally longer than the transient Agrobacterium rhizogenes-based root transformation method available for P. andersonii, though offers several clear advantages. Together, the procedures described here permit P. andersonii to be used as a research model for studies aimed at understanding symbiotic associations as well as potentially other aspects of the biology of this tropical tree.

    Data from: Establishment of wildflower fields in poor quality landscapes enhances micro-parasite prevalence in wild bumble bees
    Piot, Niels ; Meeus, Ivan ; Kleijn, D. ; Scheper, J.A. ; Linders, Theo E.W. ; Smagghe, Guy - \ 2019
    Ghent University
    parasite - flower mix - conservation
    The current worldwide pollinator decline is caused by the interplay of different drivers. Several strategies have been undertaken to counteract or halt this decline, one of which is the implementation of wildflower fields. These supplementary flowers provide extra food resources and have proven their success in increasing pollinator biodiversity and abundance. Yet such landscape alterations could also alter the host–pathogen dynamics of pollinators, which could affect the populations. In this study, we investigated the influence of sown wildflower fields on the prevalence of micro-parasites and viruses in the wild bumble bee Bombus pascuorum, one of the most abundant bumble bee species in Europe and the Netherlands. We found that the effect of sown wildflower fields on micro-parasite prevalence is affected by the composition of the surrounding landscape and the size of the flower field. The prevalence of micro-parasites increases with increasing size of sown wildflower fields in landscapes with few semi-natural landscape elements. This effect was not observed in landscapes with a high amount of semi-natural landscape elements. We elaborate on two mechanisms which can support these findings: (1) “transmission hot spots” within the altered flower-networks, which could negatively impact hosts experiencing an increased exposure; (2) improved tolerance of the hosts, withstanding higher parasite populations.
    Bodem-, gewas-en ecologische kwaliteit Ilperveld : monitoringsresultaten 2015-2017
    Römkens, Paul ; Linders, Jim - \ 2019
    Wageningen : Wageningen Environmental Research (Wageningen Environmental Research report 2938) - 79
    In opdracht van de provincie Noord-Holland zijn een aantal voormalige stortplaatsen en een waterbodem in het Ilperveld gesaneerd in de periode 2003-2013. Daarbij zijn in het gebied zes verschillende deelsaneringen uitgevoerd. Daarbij is in een vooronderzoek vastgesteld dat de bodemkwaliteit, met name de gehalten aan koper, in een aantal deelgebieden mogelijk aanleiding geeft tot ecologische risico’s en gezondheidsrisico’s voor vee (schapen). Monitoring van bodem- en gewaskwaliteit gedurende drie opeenvolgende jaren (2015-2017) toont echter aan dat, ofschoon de bodemkwaliteit in een aantal deelgebieden niet aan de advieswaarde voor schapen voldoet, er geen sprake is van risico’s voor de diergezondheid. Ook de opname van koper door wormen wijkt niet af van die welke is aangetroffen in niet specifiek belaste gebieden. Wel toont het gewasonderzoek dat er sprake is van een grote jaarlijkse variatie in de gehalten aan koper in gras, met pieken in de winter en lage gehalten in de zomer. Dit onderzoek toont echter aan dat dit niet leidt tot een overschrijding van de toegestane dagelijkse inname – op jaarbasis – voor schapen. Bovendien is deze spreiding ook aangetoond in niet-belaste percelen. De gemeten verhoogde kopergehalten in gras zijn niet of slechts zeer beperkt het gevolg van de verhoogde bodemgehalten. Op basis van de huidige kwaliteit van de afdeklagen geven deze resultaten daarom geen aanleiding voor aanpassen van het beweidingsbeheer van het gebied met het oog op de diergezondheid.
    Establishment of wildflower fields in poor quality landscapes enhances micro-parasite prevalence in wild bumble bees
    Piot, Niels ; Meeus, Ivan ; Kleijn, David ; Scheper, Jeroen ; Linders, Theo ; Smagghe, Guy - \ 2019
    Oecologia 189 (2019)1. - ISSN 0029-8549 - p. 149 - 158.
    Bumble bee - Conservation - Flower mixes - Host–pathogen - Parasites

    The current worldwide pollinator decline is caused by the interplay of different drivers. Several strategies have been undertaken to counteract or halt this decline, one of which is the implementation of wildflower fields. These supplementary flowers provide extra food resources and have proven their success in increasing pollinator biodiversity and abundance. Yet such landscape alterations could also alter the host–pathogen dynamics of pollinators, which could affect the populations. In this study, we investigated the influence of sown wildflower fields on the prevalence of micro-parasites and viruses in the wild bumble bee Bombus pascuorum, one of the most abundant bumble bee species in Europe and the Netherlands. We found that the effect of sown wildflower fields on micro-parasite prevalence is affected by the composition of the surrounding landscape and the size of the flower field. The prevalence of micro-parasites increases with increasing size of sown wildflower fields in landscapes with few semi-natural landscape elements. This effect was not observed in landscapes with a high amount of semi-natural landscape elements. We elaborate on two mechanisms which can support these findings: (1) “transmission hot spots” within the altered flower-networks, which could negatively impact hosts experiencing an increased exposure; (2) improved tolerance of the hosts, withstanding higher parasite populations.

    Stakeholdersdialoog
    Groot, C.P.G.M. de - \ 2018

    De visies van... Drs. Irene Linders en Maike Blokhuis, adviseurs gezondheidsbevordering bij GGD Noord- en Oost-Gelderland en Prof. Lisette de Groot, hoogleraar Voeding van Oudere Mensen bij Wageningen Universiteit.

    Mobile Technology to Enable Tailor-Made Fertilizer Advice for Maize Smallholders in Western Kenya
    Jindo, Keiji ; Schut, A.G.T. ; Langeveld, Hans ; Linders, René ; Hermelink, Marleen ; Munikah, Lydia ; Ittersum, M.K. van - \ 2018
    In: ESA2018 XVe European Society for Agronomy Congress. - Schweizerische Eidgenossenschaft - ISBN 9782839925860 - p. 86 - 86.
    Data from: Scaling up effects of measures mitigating pollinator loss from local- to landscape-level population responses
    Kleijn, D. ; Linders, Theo E.W. ; Stip, Anthonie ; Biesmeijer, Jacobus C. ; Wäckers, Felix L. ; Bukovinszki, T. - \ 2018
    Wageningen University & Research
    1. Declining pollinator populations have caused concern about consequences for food production, and have initiated an increasing number of initiatives that aim to mitigate pollinator loss through enhancement of floral resources. Studies evaluating effects of mitigation measures generally demonstrate positive responses of pollinators to floral resource enhancement. However, it remains unclear whether this represents landscape-level population effects or results from a spatial redistribution of individuals from otherwise unaffected populations. 2. Here we present a method for estimating landscape-level population effects using data from commonly used standardized pollinator transect surveys. The approach links local density responses of pollinators in both mitigation sites and surrounding landscape elements to the area these habitats occupy in mitigation landscapes as well as control landscapes to obtain landscape-level population estimates. 3. We demonstrate the method using data from a two-year study examining the effects of experimental wildflower enhancements on wild bumble bees and solitary bees in Dutch agricultural landscapes. The results show that conclusions based on local responses may differ significantly from those based on landscape-level responses. 4. Wildflower enhancements significantly enhanced landscape-level abundance of both bumble bees and solitary bees. Bumble bees showed a pronounced positive local density response in mitigation sites and the surrounding landscape that was in line with significant landscape-level increases in abundance. However, solitary bees showed no local response to mitigation sites, and the landscape-level increases in abundance only became apparent when the area of bee habitat was taken into account. 5. Incorporating the area of both newly created and pre-existing pollinator habitats into effect estimates accounts for density-dependent processes such as dilution, spill-over and local concentration of individuals. It therefore results in more reliable estimates of the response to mitigation measures of pollinators, as well as other mobile arthropod groups that are often being surveyed using transect surveys.
    Scaling up effects of measures mitigating pollinator loss from local- to landscape-level population responses
    Kleijn, David ; Linders, Theo E.W. ; Stip, Anthonie ; Biesmeijer, Jacobus C. ; Wäckers, Felix L. ; Bukovinszky, Tibor - \ 2018
    Methods in Ecology and Evolution 9 (2018)7. - ISSN 2041-210X - p. 1727 - 1738.
    Agri-environment schemes - Bee abundance - Floral resources - Spatial scale - Transect surveys - Wildflower strips

    Declining pollinator populations have caused concern about consequences for food production, and have initiated an increasing number of initiatives that aim to mitigate pollinator loss through enhancement of floral resources. Studies evaluating effects of mitigation measures generally demonstrate positive responses of pollinators to floral resource enhancement. However, it remains unclear whether this represents landscape-level population effects or results from a spatial redistribution of individuals from otherwise unaffected populations. Here, we present a method for estimating landscape-level population effects using data from commonly used standardized pollinator transect surveys. The approach links local density responses of pollinators in both mitigation sites and surrounding landscape elements to the area these habitats occupy in mitigation landscapes as well as control landscapes to obtain landscape-level population estimates. We demonstrate the method using data from a 2-year study examining the effects of experimental wildflower enhancements on wild bumblebees and solitary bees in Dutch agricultural landscapes. The results show that conclusions based on local responses may differ significantly from those based on landscape-level responses. Wildflower enhancements significantly enhanced landscape-level abundance of both bumblebees and solitary bees. Bumblebees showed a pronounced positive local density response in mitigation sites and the surrounding landscape that was in line with significant landscape-level increases in abundance. However, solitary bees showed no local response to mitigation sites, and the landscape-level increases in abundance only became apparent when the area of bee habitat was taken into account. Incorporating the area of both newly created and pre-existing pollinator habitats into effect estimates accounts for density-dependent processes such as dilution, spillover and local concentration of individuals. It, therefore, results in more reliable estimates of the response to mitigation measures of pollinators, as well as other mobile arthropod groups that are often being surveyed using transect surveys.

    CRISPR/cas9-mediated mutagenesis of four putative symbiosis genes of the tropical tree parasponia andersonii reveals novel phenotypes
    Zeijl, Arjan Van; Wardhani, Titis A.K. ; Seifi Kalhor, Maryam ; Rutten, Luuk ; Bu, Fengjiao ; Hartog, Marijke ; Linders, Sidney ; Fedorova, Elena E. ; Bisseling, Ton ; Kohlen, Wouter ; Geurts, Rene - \ 2018
    Frontiers in Plant Science 9 (2018). - ISSN 1664-462X
    CRISPR/Cas9 - Nodule - Parasponia andersonii - Rhizobium - Stable transformation - Symbiosis
    Parasponia represents five fast-growing tropical tree species in the Cannabaceae and is the only plant lineage besides legumes that can establish nitrogen-fixing nodules with rhizobium. Comparative analyses between legumes and Parasponia allows identification of conserved genetic networks controlling this symbiosis. However, such studies are hampered due to the absence of powerful reverse genetic tools for Parasponia. Here, we present a fast and efficient protocol for Agrobacterium tumefaciens-mediated transformation and CRISPR/Cas9 mutagenesis of Parasponia andersonii. Using this protocol, knockout mutants are obtained within 3 months. Due to efficient micro-propagation, bi-allelic mutants can be studied in the T0 generation, allowing phenotypic evaluation within 6 months after transformation. We mutated four genes – PanHK4, PanEIN2, PanNSP1, and PanNSP2 – that control cytokinin, ethylene, or strigolactone hormonal networks and that in legumes commit essential symbiotic functions. Knockout mutants in Panhk4 and Panein2 displayed developmental phenotypes, namely reduced procambium activity in Panhk4 and disturbed sex differentiation in Panein2 mutants. The symbiotic phenotypes of Panhk4 and Panein2 mutant lines differ from those in legumes. In contrast, PanNSP1 and PanNSP2 are essential for nodule formation, a phenotype similar as reported for legumes. This indicates a conserved role for these GRAS-type transcriptional regulators in rhizobium symbiosis, illustrating the value of Parasponia trees as a research model for reverse genetic studies.
    The depth profile of buoyant microplastics: how much is overlooked with sea surface sampling?
    Kooi, Merel ; Reisser, J. ; Schmid, M. ; Ferrari, F. ; Cunsolo, S. ; Brambini, R. ; Noble, K. ; Sirks, L.A. ; Linders, Theo ; Slat, B. ; Koelmans, A.A. - \ 2016
    The effect of particle properties on the depth profile of buoyant plastics in the ocean
    Kooi, Merel ; Reisser, J. ; Slat, B. ; Ferrari, F. ; Schmid, M. ; Cunsolo, S. ; Brambini, R. ; Noble, K. ; Sirks, L.A. ; Linders, T.E.W. ; Schoeneich-Argent, R.I. ; Koelmans, A.A. - \ 2016
    Wageningen University, Wageningen UR
    Plastic pollution - Marine debris - Marine litter - Microplastics
    Most studies on buoyant microplastics in the marine environment rely on sea surface sampling. Consequently, microplastic amounts can be underestimated, as turbulence leads to vertical mixing. Models that correct for vertical mixing are based on limited data. In this study we report measurements of the depth profile of buoyant microplastics in the North Atlantic subtropical gyre, from 0 to 5 m depth. Microplastics were separated into size classes (0.5–1.5 and 1.5–5.0 mm) and types (‘fragments’ and ‘lines’), and associated with a sea state. Microplastic concentrations decreased exponentially with depth, with both sea state and particle properties affecting the steepness of the decrease. Concentrations approached zero within 5 m depth, indicating that most buoyant microplastics are present on or near the surface. Plastic rise velocities were also measured, and were found to differ significantly for different sizes and shapes. Our results suggest that (1) surface samplers such as manta trawls underestimate total buoyant microplastic amounts by a factor of 1.04–30.0 and (2) estimations of depth-integrated buoyant plastic concentrations should be done across different particle sizes and types. Our findings can assist with improving buoyant ocean plastic vertical mixing models, mass balance exercises, impact assessments and mitigation strategies.
    The effect of particle properties on the depth profile of buoyant plastics in the ocean
    Kooi, Merel ; Reisser, J. ; Slat, B. ; Ferrari, F. ; Schmid, M. ; Cunsolo, S. ; Brambini, R. ; Noble, K. ; Sirks, L.A. ; Linders, T.E.W. ; Schoeneich-Argent, R.I. ; Koelmans, A.A. - \ 2016
    Scientific Reports 6 (2016). - ISSN 2045-2322 - 10 p.
    Most studies on buoyant microplastics in the marine environment rely on sea surface sampling. Consequently, microplastic amounts can be underestimated, as turbulence leads to vertical mixing. Models that correct for vertical mixing are based on limited data. In this study we report measurements of the depth profile of buoyant microplastics in the North Atlantic subtropical gyre, from 0 to 5 m depth. Microplastics were separated into size classes (0.5–1.5 and 1.5–5.0 mm) and types (‘fragments’ and ‘lines’), and associated with a sea state. Microplastic concentrations decreased exponentially with depth, with both sea state and particle properties affecting the steepness of the decrease. Concentrations approached zero within 5 m depth, indicating that most buoyant microplastics are present on or near the surface. Plastic rise velocities were also measured, and were found to differ significantly for different sizes and shapes. Our results suggest that (1) surface samplers such as manta trawls underestimate total buoyant microplastic amounts by a factor of 1.04–30.0 and (2) estimations of depth-integrated buoyant plastic concentrations should be done across different particle sizes and types. Our findings can assist with improving buoyant ocean plastic vertical mixing models, mass balance exercises, impact assessments and mitigation strategies.
    Competitiveness Proofing - Fertilising Materials. Exante evaluation of competitiveness impacts of the European Commission's policy proposal Review of Regulation (EC) no 2003/2003 relating to fertilisers
    Wijnands, J.H.M. ; Linders, G.J. - \ 2013
    Rotterdam/The Hague : ECORYS Nederland BV - 92
    Scenarios for exposure of aquatic organisms to plant protection products in the Netherlands : part 1: Field crops and downward spraying
    Tiktak, A. ; Adriaanse, P.I. ; Boesten, J.J.T.I. ; Griethuysen, C. van; Horst, M.M.S. ter; Linders, J.B.H.J. ; Linden, A.M.A. van der; Zande, J.C. van de - \ 2012
    Bilthoven : National Institute for Public Health and the Environment (RIVM report ) - 129
    aquatische ecologie - waterorganismen - ecotoxicologie - pesticiden - waterverontreiniging - drift - modellen - aquatic ecology - aquatic organisms - ecotoxicology - pesticides - water pollution - drift - models
    In the current Dutch authorisation procedure for calculating the exposure of surface water organisms to plant protection products, drift deposition is considered to be the only source for exposure of surface water organisms. Although drift can still be considered the most important source, atmospheric deposition and drainage may constitute important sources as well. Therefore, RIVM, PBL, Wageningen UR and the Board for the authorisation of plant protection products and biocides have derived a new procedure in which these two potential sources are included. The new procedure, described in this report, is restricted to downward spray applications in field crops
    Agrochemicals
    Unsworth, J.B. ; Shakil, N.A. ; Kumar, J. ; Kleter, G.A. ; Linders, J.B.H.J. - \ 2012
    Chemistry International 34 (2012)jul-aug. - ISSN 0193-6484 - p. 34 - 36.
    Bioavailability of Xenobiotics in the Soil Environment
    Katayama, A. ; Bhula, R. ; Burns, G.R. ; Carazo, E. ; Felsot, A. ; Hamilton, D. ; Harris, C. ; Kim, Y.H. ; Kleter, G.A. ; Koedel, W. ; Linders, J. ; Peijnenburg, J.G.M.W. ; Sabljic, A. ; Stephenson, R.G. ; Racke, D.K. ; Rubin, B. ; Tanaka, K. ; Unsworth, J. ; Wauchope, R.D. - \ 2010
    In: Reviews of Environmental Contamination and Toxicology, Vol. 203 / Whitacre, D.M., New York : Springer - ISBN 9781441913517 - p. 1 - 86.
    polycyclic aromatic-hydrocarbons - supercritical-fluid extraction - bound pesticide-residues - field-moist soils - artificially contaminated soils - persistent organic pollutants - earthworms eisenia-foetida - carbon-dioxide extraction - bacterial outer-membrane
    When synthetic, xenobiotic compounds such as agrochemicals and industrial chemicals are utilized, they eventually reach the soil environment where they are subject to degradation, leaching, volatilization, sorption, and uptake by organisms. The simplest assumption is that such chemicals in soil are totally available to microorganisms, plant roots, and soil fauna via direct, contact exposure; subsequently these organisms are consumed as part of food web processes and bioaccumulation may occur, increasing exposures to higher organisms up the food chain. However, studies in the last two decades have revealed that chemical residues in the environment are not completely bioavailable, so that their uptake by biota is less than the total amount present in soil (Alexander 1995; Gevao et al. 2003; Paine et al. 1996). Therefore, the toxicity, biodegradability, and efficacy of xenobiotics are dependent on their soil bioavailability, rendering this concept profoundly important to chemical risk assessment and pesticide registration.
    Ex post evaluatie van het Plattelandsontwikkelingsprogramma 2000-2006 (POP1). Managementsamenvatting
    Staalduinen, L.C. van; Zee, F. van der; Venema, G.S. ; Bommel, K.H.M. van; Boonstra, F.G. ; Sanders, M.E. ; Linders, A.P.M. - \ 2008
    Den Haag : LEI (Samenvatting / LEI : Werkveld, Internationaal beleid ) - ISBN 9789086152780 - 35
    plattelandsontwikkeling - gemeenschappelijk landbouwbeleid - evaluatie - nederland - rural development - cap - evaluation - netherlands
    Het POP1 is de Nederlandse uitwerking van het EU plattelandsontwikkelingsbeleid in deze periode en is s opgebouwd rond zes prioritaire doelen op het gebied van duurzame landbouw, natuur en landschap, duurzaam waterbeheer, diversificatie economische dragers, recreatie en toerisme en leefbaarheid
    Ex post evaluatie van het Plattelandsontwikkelingsprogramma 2000-2006 (POP1). Deel 2: Bijlagen
    Venema, G.S. ; Staalduinen, L.C. van; Bommel, K.H.M. van; Boonstra, F.G. ; Sanders, M.E. ; Linders, A.P.M. - \ 2008
    Den Haag : LEI (Rapport / LEI : Werkveld, Internationaal beleid ) - ISBN 9789086152803 - 162
    plattelandsontwikkeling - gemeenschappelijk landbouwbeleid - evaluatie - nederland - rural development - cap - evaluation - netherlands
    Het eerste plattelandsontwikkelingsprogramma Nederland (POP1) vormde de invulling van de tweede pijler van het Gemeenschappelijk Landbouwbeleid van de EU
    Ex post evaluatie van het Plattelandsontwikkelingsprogramma 2000-2006 (POP1). Deel 1
    Venema, G.S. ; Staalduinen, L.C. van; Bommel, K.H.M. van; Boonstra, F.G. ; Sanders, M.E. ; Linders, A.P.M. - \ 2008
    Den Haag : LEI (Rapport / LEI : Werkveld Internationaal beleid ) - ISBN 9789086152797 - 306
    plattelandsontwikkeling - gemeenschappelijk landbouwbeleid - evaluatie - programma-evaluatie - nederland - financieren - rural development - cap - evaluation - program evaluation - netherlands - financing
    Het eerste plattelandsontwikkelingsprogramma Nederland (POP1) vormde de invulling van de tweede pijler van het Gemeenschappelijk Landbouwbeleid van de EU. Het programma liep van 2000 tot 2006 en heeft tot een forse investering geleid, ook van private partijen. Een consortium bestaande uit LEI en Alterra en adviesbureau ERAC, heeft het programma geëvalueerd
    Development of an assessment methodology to evaluate agricultural use of plant protection products for drinking water production from surface waters : a proposal for the registration procedure in the Netherlands
    Adriaanse, P.I. ; Linders, J.B.H.J. ; Berg, G.A. van den; Boesten, J.J.T.I. ; Bruggen, M.W.P. van der; Jilderda, K. ; Luttik, R. ; Merkens, W.S.W. ; Stienstra, Y.J. ; Teunissen, R.J.M. - \ 2008
    Wageningen : Alterra (Alterra-rapport 1635) - 245
    drinkwater - pesticiden - oppervlaktewater - waterkwaliteit - methodologie - normen - registratie - monitoring - landbouw - nederland - drinking water - pesticides - surface water - water quality - methodology - standards - registration - monitoring - agriculture - netherlands
    Two tiers were developed to assess the drinking water standard of 0.1 μg/L at nine locations where surface water is abstracted to produce drinking water in the Netherlands. Two tiers were developed to assess the drinking water standard of 0.1 μg/L at nine locations where surface water is abstracted to produce drinking water in the Netherlands. In Tier I, concentrations at the abstraction points are calculated on the basis of edge-of field surface water concentrations for all crops in the intake area on which the pesticide can be used. The edge-of-field concentrations are corrected to estimate the concentration at the abstraction point by factors accounting for e.g. the relative cropped area of the intake area, degradation and difference in timing of applications
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