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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    Nestelmogelijkheden voor solitaire bijen in bodems van bloemrijke bermen : Een vergelijkend onderzoek tussen ingezaaide en niet-ingezaaide bermen in de gemeente Sint Anthonis
    Sanders, Dianne ; Groot, Arjen de; Goedhart, Paul W. ; Dimmers, Wim J. ; Kats, Ruud van; Scheper, Jeroen A. ; Roessink, Ivo - \ 2020
    Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 3019) - 35
    Er zijn sterke aanwijzingen dat zowel de aantallen als de soortendiversiteit van bestuivers de laatste decennia sterk achteruit zijn gegaan. Een speerpunt van de Nationale Bijenstrategie is het verbeteren van het leefgebied van wilde bijen en andere bestuivers. De meeste initiatieven om leefgebied voor wilde bijen te creëren, richten zich op het aanleggen van een bloemrijke vegetatie. Belangrijk voor wilde bijen is echter dat naast voldoende voedsel ook voldoende geschikte nestlocaties aanwezig zijn. De bekende bijenhotels helpen daarbij, maar het overgrote deel van de Nederlandse wilde bijensoorten nestelt ondergronds. Nestgelegenheid voor deze bodemnestelende bijen kan o.a. worden gecreëerd door zogenaamde nestelhoopjes of nesteldijkjes vorm te geven, maar dergelijke maatregelen zijn lang niet overal mogelijk. Een voorbeeld zijn de wegbermen, waar relatief makkelijk meer bloemaanbod te genereren is, maar gezien de verkeersveiligheid minder ruimte is voor het creëren van kale bodem of taluds. Onduidelijk is in hoeverre bloemrijke grasstroken, zoals deze wegbermen, al functioneren als nestlocatie voor wilde bijen en hoe deze potentiële functie verder kan worden bevorderd. In het voorliggende onderzoek is die vraag nader onderzocht door gedurende twee jaren in wegbermen met en zonder ingezaaide bloemranden de aanwezigheid van bodemnestelende bijen te inventariseren.
    Correction to: Lack of adverse effects in subchronic and chronic toxicity/carcinogenicity studies on the glyphosate-resistant genetically modified maize NK603 in Wistar Han RCC rats
    Steinberg, Pablo ; Voet, Hilko van der; Goedhart, Paul W. ; Kleter, Gijs ; Kok, Esther J. ; Pla, Maria ; Nadal, Anna ; Zeljenková, Dagmar ; Aláčová, Radka ; Babincová, Júlia ; Rollerová, Eva ; Jaďuďová, Soňa ; Kebis, Anton ; Szabova, Elena ; Tulinská, Jana ; Líšková, Aurélia ; Takácsová, Melinda ; Mikušová, Miroslava Lehotská ; Krivošíková, Zora ; Spök, Armin ; Racovita, Monica ; Vriend, Huib de; Alison, Roger ; Alison, Clare ; Baumgärtner, Wolfgang ; Becker, Kathrin ; Lempp, Charlotte ; Schmicke, Marion ; Schrenk, Dieter ; Pöting, Annette ; Schiemann, Joachim ; Wilhelm, Ralf - \ 2020
    Archives of Toxicology 94 (2020). - ISSN 0340-5761 - p. 1779 - 1781.

    In the original publication, the starting point in time for the three feeding trials.

    Threshold effects of air pollution and climate change on understory plant communities at forested sites in the eastern United States
    McDonnell, T.C. ; Reinds, G.J. ; Wamelink, G.W.W. ; Goedhart, P.W. ; Posch, M. ; Sullivan, T.J. ; Clark, C.M. - \ 2020
    Environmental Pollution 262 (2020). - ISSN 0269-7491
    Biodiversity - Climate change - Critical load - Forest understory - Nitrogen

    Forest understory plant communities in the eastern United States are often diverse and are potentially sensitive to changes in climate and atmospheric inputs of nitrogen caused by air pollution. In recent years, empirical and processed-based mathematical models have been developed to investigate such changes in plant communities. In the study reported here, a robust set of understory vegetation response functions (expressed as version 2 of the Probability of Occurrence of Plant Species model for the United States [US-PROPS v2]) was developed based on observations of forest understory and grassland plant species presence/absence and associated abiotic characteristics derived from spatial datasets. Improvements to the US-PROPS model, relative to version 1, were mostly focused on inclusion of additional input data, development of custom species-level input datasets, and implementation of methods to address uncertainty. We investigated the application of US-PROPS v2 to evaluate the potential impacts of atmospheric nitrogen (N) and sulfur (S) deposition, and climate change on forest ecosystems at three forested sites located in New Hampshire, Virginia, and Tennessee in the eastern United States. Species-level N and S critical loads (CLs) were determined under ambient deposition at all three modeled sites. The lowest species-level CLs of N deposition at each site were between 2 and 11 kg N/ha/yr. Similarly, the lowest CLs of S deposition, based on the predicted soil pH response, were less than 2 kg S/ha/yr among the three sites. Critical load exceedance was found at all three model sites. The New Hampshire site included the largest percentage of species in exceedance. Simulated warming air temperature typically resulted in lower maximum occurrence probability, which contributed to lower CLs of N and S deposition. The US-PROPS v2 model, together with the PROPS-CLF model to derive CL functions, can be used to develop site-specific CLs for understory plants within broad regions of the United States. This study demonstrates that species-level CLs of N and S deposition are spatially variable according to the climate, light availability, and soil characteristics at a given location. Although the species niche models generally performed well in predicting occurrence probability, there remains uncertainty with respect to the accuracy of reported CLs. As such, the specific CLs reported here should be considered as preliminary estimates. Critical loads of atmospheric nitrogen and sulfur deposition were determined for maintaining understory vegetation diversity. Critical load exceedance was found at all model application sites.

    Estimating ammonia emission after field application of manure by the integrated horizontal flux method: a comparison of concentration and wind speed profiles
    Goedhart, Paul W. ; Mosquera, Julio ; Huijsmans, Jan F.M. - \ 2020
    Soil Use and Management 36 (2020)2. - ISSN 0266-0032 - p. 338 - 350.
    displacement height - exponential concentration model - gamma measurement errors - grassland - log wind profile - statistics

    The integrated horizontal flux method is commonly used to estimate ammonia emission from field-applied manure. The method involves measuring the wind speed and ammonia concentration at various heights on a post in the middle of a manured plot. Wind speed and concentration profiles are subsequently fitted to these measurements. The product of the profiles represents the amount of ammonia displaced by the wind, and the calculated ammonia emission is based on integrating the product of the profiles along the height. A crucial step is the functional form of the profiles, and linear relationships employing the logarithm of the height are generally used. In this study, 160 Dutch emission experiments on grassland were re-analysed to evaluate alternative profiles for the concentration and wind speed. It is shown that an exponential concentration model usually provides a better fit than the commonly used profile and that the measurement error for the concentration should be modelled by means of a gamma distribution. Based on the re-analysis, this new model reduces the calculated ammonia emission by around 10%. It is further shown that adding a displacement parameter to the wind speed model only has a minor effect on the calculated emission. Finally, a simulation study reveals that misspecification of the concentration profile may lead to a relative bias of up to 27%, that the precision of the estimated emission can be improved by increasing the number of concentration measurements near the ground and that wind speed measurements at three heights could suffice.

    Agricultural ammonia emissions 10 per cent less in fields: new model for calculating emissions
    Goedhart, Paul ; Mosquera Losada, Julio ; Huijsmans, Jan - \ 2020
    Herkennen habitatkwaliteit graslanden o.b.v. NDVI
    Visser, Tim ; Kuiper, Mark ; Melman, Dick ; Meijninger, W.M.L. ; Goedhart, P.W. - \ 2019
    Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2977) - 29
    De kern van weidevogelbeheer betreft in Nederland het op orde krijgen van de habitatkwaliteit in de graslanden. Eerdere ervaringen laten zien dat NDVI-satellietbeelden een belangrijke rol kunnen spelen om hier gebiedsdekkend inzicht in te krijgen. In dit onderzoek is op een aantal onderdelen getoetst in hoeverre deze beelden inzicht geven in de feitelijke situatie en in hoeverre ze een betrouwbaar hulpmiddel kunnen zijn bij het plannen en evalueren van weidevogelbeheer. In een eerste analyse is vastgesteld in hoeverre NDVI specifiek is voor het type grasland. Daarnaast is onderzocht in hoeverre NDVI indicerend is voor zwaarte (biomassa) en structuur van de vegetatie, de kruidenrijkdom en de doorwaadbaarheid van de vegetatie (als maat voor verplaatsingsweerstand voor kuikens). Ten slotte is in beeld gebracht hoe de verspreiding van weidevogels gedurende het broed- en opgroeiseizoen samenhangt met de NDVI-waarden. Voor alle aspecten is een (vrij) sterke, vaak significante samenhang gevonden. Daarmee lijken NDVI-beelden bruikbaar om een gebiedsdekkend, realistisch beeld van de feitelijke situatie te geven.
    Hoe een statistische fout het amoniakdebat op een dwaalspoor zet
    Goedhart, P.W. - \ 2019
    STAtOR 20 (2019)2. - ISSN 1567-3383 - p. 30 - 34.
    Effects of abiotic variables on the survival of discarded bycatches in North Sea pulse-trawl fisheries
    Schram, Edward ; Goedhart, Paul W. ; Molenaar, Pieke - \ 2019
    IJmuiden : Wageningen Marine Research (Wageningen Marine Research rapport C040/19) - 32
    Statistical models discriminating between complex samples measured with microfluidic receptor-cell arrays
    Wehrens, H.R.M.J. ; Roelse, M. ; Henquet, M.G.L. ; Lenthe, M.S. van; Goedhart, Paul ; Jongsma, M.A. - \ 2019
    PLoS ONE 14 (2019)4. - ISSN 1932-6203
    Data analysis for flow-based in-vitro receptomics array, like a tongue-on-a-chip, is complicated by the relatively large variability within and between arrays, transfected DNA types, spots, and cells within spots. Simply averaging responses of spots of the same type would lead to high variances and low statistical power. This paper presents an approach based on linear mixed models, allowing a quantitative and robust comparison of complex samples and indicating which receptors are responsible for any differences. These models are easily extended to take into account additional effects such as the build-up of cell stress and to combine data from replicated experiments. The increased analytical power this brings to receptomics research is discussed.
    Lack of adverse effects in subchronic and chronic toxicity/carcinogenicity studies on the glyphosate-resistant genetically modified maize NK603 in Wistar Han RCC rats
    Steinberg, Pablo ; Voet, Hilko van der; Goedhart, Paul W. ; Kleter, Gijs ; Kok, Esther J. ; Pla, Maria ; Nadal, Anna ; Zeljenková, Dagmar ; Aláčová, Radka ; Babincová, Júlia ; Rollerová, Eva ; Jaďuďová, Soňa ; Kebis, Anton ; Szabova, Elena ; Tulinská, Jana ; Líšková, Aurélia ; Takácsová, Melinda ; Mikušová, Miroslava Lehotská ; Krivošíková, Zora ; Spök, Armin ; Racovita, Monica ; Vriend, Huib de; Alison, Roger ; Alison, Clare ; Baumgärtner, Wolfgang ; Becker, Kathrin ; Lempp, Charlotte ; Schmicke, Marion ; Schrenk, Dieter ; Pöting, Annette ; Schiemann, Joachim ; Wilhelm, Ralf - \ 2019
    Archives of Toxicology 93 (2019)4. - ISSN 0340-5761 - p. 1095 - 1139.
    Biosafety - Combined chronic toxicity/carcinogenicity study - G-TwYST - Genetically modified maize NK603 - GMO risk assessment - OECD Test Guideline No. 408 - OECD Test Guideline No. 453 - Rat feeding trial - Subchronic oral toxicity study

    In 2012, a controversial study on the long-term toxicity of a Roundup herbicide and the glyphosate-tolerant genetically modified (GM) maize NK603 was published. The EC-funded G-TwYST research consortium tested the potential subchronic and chronic toxicity as well as the carcinogenicity of the glyphosate-resistant genetically modified maize NK603 by performing two 90-day feeding trials, one with GM maize inclusion rates of 11 and 33% and one with inclusion rates of up to 50%, as well as a 2-year feeding trial with inclusion rates of 11 and 33% in male and female Wistar Han RCC rats by taking into account OECD Guidelines for the testing of chemicals and EFSA recommendations on the safety testing of whole-food/feed in laboratory animals. In all three trials, the NK603 maize, untreated and treated once with Roundup during its cultivation, and the conventional counterpart were tested. Differences between each test group and the control group were evaluated. Equivalence was assessed by comparing the observed difference to differences between non-GM reference groups in previous studies. In case of significant differences, whether the effects were dose-related and/or accompanied by changes in related parameters including histopathological findings was evaluated. It is concluded that no adverse effects related to the feeding of the NK603 maize cultivated with or without Roundup for up to 2 years were observed. Based on the outcome of the subchronic and combined chronic toxicity/carcinogenicity studies, recommendations on the scientific justification and added value of long-term feeding trials in the GM plant risk assessment process are presented.

    Equivalence limit scaled differences for untargeted safety assessments : Comparative analyses to guard against unintended effects on the environment or human health of genetically modified maize
    Voet, Hilko van der; Goedhart, Paul W. ; García-Ruiz, Esteban ; Escorial, Concepción ; Tulinská, Jana - \ 2019
    Food and Chemical Toxicology 125 (2019). - ISSN 0278-6915 - p. 540 - 548.
    Arthropods - Equivalence test - Rat feeding study - Risk assessment - Standardised effect size - Unintended effects

    Safety assessments guard against unintended effects for human health and the environment. When new products are compared with accepted reference products by broad arrays of measurements, statistical analyses are usually summarised by significance tests or confidence intervals per endpoint. The traditional approach is to test for statistical significance of differences. However, absence or presence of significant differences is not a statement about safety. Equivalence limits are essential for safety assessment. We propose graphs to present the results of equivalence tests over the array of endpoints. It is argued that plots of the equivalence limit scaled difference (ELSD) are preferable over plots of the standardised effect size (SES) used previously for similar assessments. The ELSD method can be used either with externally specified equivalence limits or with equivalence limits estimated from (historical) data. The method is illustrated with two examples: first, environmental safety of MON810 Bt maize was assessed using field trial count data of arthropods; second, human safety of herbicide tolerant NK603 maize was assessed using haematological, biochemical and organ weight data from a 90-day rat feeding study. All assessed endpoints were classified in EFSA equivalence categories I or II, implying full equivalence or equivalence more likely than not.

    Data from: Equivalence analysis to support environmental safety assessment: using nontarget organism count data from field trials with cisgenically modified potato
    Voet, H. van der; Goedhart, P.W. ; Lazebnik, E. ; Kessel, G.J.T. ; Mullins, Ewen ; Loon, J.J.A. van; Arpaia, Salvatore - \ 2019
    Wageningen University & Research
    This paper considers the statistical analysis of entomological count data from field experiments with genetically modified (GM) plants. Such trials are carried out to assess environmental safety. Potential effects on nontarget organisms (NTOs), as indicators of biodiversity, are investigated. The European Food Safety Authority (EFSA) gives broad guidance on the environmental risk assessment (ERA) of GM plants. Field experiments must contain suitable comparator crops as a benchmark for the assessment of designated endpoints. In this paper, a detailed protocol is proposed to perform data analysis for the purpose of assessing environmental safety. The protocol includes the specification of a list of endpoints and their hierarchical relations, the specification of intended levels of data analysis, and the specification of provisional limits of concern to decide on the need for further investigation. The protocol emphasizes a graphical representation of estimates and confidence intervals for the ratio of mean abundances for the GM plant and its comparator crop. Interpretation relies mainly on equivalence testing in which confidence intervals are compared with the limits of concern. The proposed methodology is illustrated with entomological count data resulting from multiyear, multilocation field trials. A cisgenically modified potato line (with enhanced resistance to late blight disease) was compared to the original conventional potato variety in the Netherlands and Ireland in two successive years (2013, 2014). It is shown that the protocol encompasses alternative schemes for safety assessment resulting from different research questions and/or expert choices. Graphical displays of equivalence testing at several hierarchical levels and their interpretation are presented for one of these schemes. The proposed approaches should be of help in the ERA of GM or other novel plants.
    Equivalence analysis to support environmental safety assessment: Using nontarget organism count data from field trials with cisgenically modified potato
    Voet, Hilko van der; Goedhart, Paul W. ; Lazebnik, Jenny ; Kessel, Geert J.T. ; Mullins, Ewen ; Loon, Joop J.A. van; Arpaia, Salvatore - \ 2019
    Ecology and Evolution 9 (2019)5. - ISSN 2045-7758 - p. 2863 - 2882.
    This paper considers the statistical analysis of entomological count data from field experiments with genetically modified (GM) plants. Such trials are carried out to assess environmental safety. Potential effects on nontarget organisms (NTOs), as indicators of biodiversity, are investigated. The European Food Safety Authority (EFSA) gives broad guidance on the environmental risk assessment (ERA) of GM plants. Field experiments must contain suitable comparator crops as a benchmark for the assessment of designated endpoints. In this paper, a detailed protocol is proposed to perform data analysis for the purpose of assessing environmental safety. The protocol includes the specification of a list of endpoints and their hierarchical relations, the specification of intended levels of data analysis, and the specification of provisional limits of concern to decide on the need for further investigation. The protocol emphasizes a graphical representation of estimates and confidence intervals for the ratio of mean abundances for the GM plant and its comparator crop. Interpretation relies mainly on equivalence testing in which confidence intervals are compared with the limits of concern. The proposed methodology is illustrated with entomological count data resulting from multiyear, multilocation field trials. A cisgenically modified potato line (with enhanced resistance to late blight disease) was compared to the original conventional potato variety in the Netherlands and Ireland in two successive years (2013, 2014). It is shown that the protocol encompasses alternative schemes for safety assessment resulting from different research questions and/or expert choices. Graphical displays of equivalence testing at several hierarchical levels and their interpretation are presented for one of these schemes. The proposed approaches should be of help in the ERA of GM or other novel plants.
    An Integrated System for the Automated Recording and Analysis of Insect Behavior in T-maze Arrays
    Jongsma, M.A. ; Thoen, H. ; Poleij, L.M. ; Wiegers, G.L. ; Goedhart, P.W. ; Dicke, M. ; Noldus, Lucas P.J.J. ; Kruisselbrink, J.W. - \ 2019
    Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
    Host-plant resistance to insects like thrips and aphids is a complex trait that is difficult to phenotype quickly and reliably. Here, we introduce novel hardware and software to facilitate insect choice assays and automate the acquisition and analysis of movement tracks. The hardware consists of an array of individual T-mazes allowing simultaneous release of up to 90 insect individuals from their individual cage below each T-maze with choice of two leaf disks under a video camera. Insect movement tracks are acquired with computer vision software (EthoVision) and analyzed with EthoAnalysis, a novel software package that allows for automated reporting of highly detailed behavior parameters and
    statistical analysis. To validate the benefits of the system we contrasted two Arabidopsis accessions that were previously analyzed for differential resistance to western flower thrips. Results of two trials with 40 T-mazes are reported and we show how we arrived at optimized settings for the different filters and statistics. The statistics are reported in terms of frequency, duration, distance and speed of behavior events, both as sum totals and event averages, and both for the total trial period and in time bins of 1 h. Also included are higher level analyses with subcategories like short-medium-long events and slow-medium-fast events. The time bins showed how some behavior elements are more descriptive of differences between the genotypes during the first hours, whereas
    others are constant or become more relevant at the end of an 8 h recording. The three overarching behavior categories, i.e., choice, movement, and halting, were automatically corrected for the percentage of time thrips were detected and 24 out of 38 statistics of behavior parameters differed by a factor 2–6 between the accessions. The analysis resulted in much larger contrasts in behavior traits than reported previously. Compared to leaf damage assays on whole plants or detached leaves that take a week or more to complete, results were obtained in 8 h, with more detail, fewer individuals and higher significance. The potential value of the new integrated system, named EntoLab, for discovery of genetic traits in plants and insects by high throughput screening of large populations is discussed.
    The Role of Abiotic Soil Parameters as a Factor in the Success of Invasive Plant Species
    Wamelink, Wieger ; Dobben, H.F. Van; Goedhart, P.W. ; Jones-Walters, L.M. - \ 2018
    Emerging Science Journal 2 (2018)6. - ISSN 2610-9182 - p. 308 - 365.
    Plant species dispersal has been strongly enhanced by human activities. Introduced species have to cope with indigenous species and local conditions. They may avoid indigenous species by occupying new (abiotic) territory. Once a species is established it may become a pest, and may seriously threaten other species and ecosystems. In this paper we focus on invasive plant species of the Dutch flora. We make two comparisons: (1) Dutch neophytes (i.e. arrived in The Netherlands after 1825) vs. indigenous Dutch flora; and (2) species of the Dutch flora that have become invasive outside Europe vs. non-invasive species of the Dutch flora. We hypothesize that at least part of the success of the invasive or neophyte species is due to their ability to grow under a wider range of abiotic soil circumstances than other species. We regard an invasive species as successful if it is able to disperse from the introduction site(s) and remain present in the invaded vegetation.For ten out of the sixteen abiotic factors there isa wider range for the neophytes: chlorine, potassium, mean highest and lowest groundwater level, phosphorus (and total content) and pH H2O. We hypothesized that part of the success of invasive species may be the adaptation to a variety of abiotic soil parameters. This is indeed the case for a number of the examined parameters, mostly related to nutrient availability and soil pH. This indicates that the success of invasive species is at least partly caused by their ability to grow under a wide range of nutrient availability and soil pH. Their success may therefore be stimulated by the increasing pollution of natural areas by excessive nitrogen
    G-TwYST study B a 90-day toxicity study in rats fed GM maize NK603 : statistical report
    Goedhart, Paul W. ; Voet, Hilko van der - \ 2018
    Wageningen : Biometris, Wageningen University & Research (Biometris report 31.10.17) - 81
    G-TwYST study A combined chronic toxicity and carcinogenicity study in rats fed GM maize NK603 : main statistical report
    Goedhart, Paul W. ; Voet, Hilko van der - \ 2018
    Wageningen : Biometris, Wageningen University & Research (Biometris report 30.02.18) - 78
    G-TwYST study A combined chronic toxicity and carcinogenicity study in rats fed GM maize NK603 : statistical report, 3 months data
    Goedhart, Paul W. ; Voet, Hilko van der - \ 2018
    Wageningen : Biometris, Wageningen University & Research (Biometris report 33.10.17) - 155
    G-TwYST study A combined chronic toxicity and carcinogenicity study in rats fed GM maize NK603 : statistical report, 6 months data
    Goedhart, Paul W. ; Voet, Hilko van der - \ 2018
    Wageningen : Biometris, Wageningen University & Research (Biometris report 34.02.18) - 159
    G-TwYST study A combined chronic toxicity and carcinogenicity study in rats fed GM maize NK603 : statistical report, 12 months data
    Goedhart, Paul W. ; Voet, Hilko van der - \ 2018
    Wageningen : Biometris, Wageningen University & Research (Biometris report 35.02.18) - 172
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