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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    Welfare of Farmed Fish in Different Production Systems and Operations
    Vis, J.W. van de; Kolarevic, Jelena ; Stien, L.H. ; Kristiansen, T.S. ; Gerritzen, M.A. ; Braak, Karin van de; Abbink, W. ; Saether, B.S. ; Noble, C. - \ 2020
    In: The welfare of fish / Kristiansen, T.S., Fernö, A., Pavlidis, M.A., van de Vis, H., Cham : Springer (Animal Welfare ) - ISBN 9783030416744 - p. 323 - 361.
    When fish are reared for food production in aquaculture, they can be held in different types of rearing systems and subjected to various husbandry routines and operations. Each of these systems or operations can present different welfare risks to the fish, which in turn are dependent upon both the species and its life stage. In this chapter, we address and outline potential welfare hazards the fish may encounter in a wide range of existing and emerging rearing systems used for on-growing. These systems include: (1) pond-based aquaculture, (2) flow-through systems, (3) semi-closed containment systems, (4) RAS, (5) net cages and (6) farming offshore using sea cages in exposed conditions. We also outline potential welfare hazards for two key farming operations: transport and slaughter. We present the tools the farmer can use to assess fish welfare during on-growing and also outline relevant welfare actions that can be taken to militate against welfare hazards.
    De noodzaak van een nieuwe landbouwbenadering
    Zanten, H.H.E. van; Ittersum, M.K. van; Boer, I.J.M. de - \ 2020
    In: Beter weten over eten / van der Aalsvoort, J., Coebergh van den Braak, M., Domis-Hoos, M., Lever-de Vries, C., Nederlandse Vereniging voor het Onderwijs in de Natuurwetenschappen (NVON) (NVON-reeks 16) - ISBN 9789087970161 - p. 192 - 200.
    De gevolgen van het gevoerde landbouwbeleid; een circulair voedselsysteem; plantaardige biomassa, de basis van een circulair voedselsysteem; landbouwhuisdieren en hun rol in het circulaire voedselsysteem; hoe verder?
    Impact of Gut Bacteria on the Infection and Transmission of Pathogenic Arboviruses by Biting Midges and Mosquitoes
    Möhlmann, Tim W.R. ; Vogels, Chantal B.F. ; Göertz, Giel P. ; Pijlman, Gorben P. ; Braak, Cajo J.F. ter; Beest, Dennis E. te; Hendriks, Marc ; Nijhuis, Els H. ; Warris, Sven ; Drolet, Barbara S. ; Overbeek, Leo van; Koenraadt, Constantianus J.M. - \ 2020
    Microbial Ecology 80 (2020)3. - ISSN 0095-3628 - p. 703 - 717.
    Arbovirus - Biting midge - Microbiome - Mosquito - Transmission

    Tripartite interactions among insect vectors, midgut bacteria, and viruses may determine the ability of insects to transmit pathogenic arboviruses. Here, we investigated the impact of gut bacteria on the susceptibility of Culicoides nubeculosus and Culicoides sonorensis biting midges for Schmallenberg virus, and of Aedes aegypti mosquitoes for Zika and chikungunya viruses. Gut bacteria were manipulated by treating the adult insects with antibiotics. The gut bacterial communities were investigated using Illumina MiSeq sequencing of 16S rRNA, and susceptibility to arbovirus infection was tested by feeding insects with an infectious blood meal. Antibiotic treatment led to changes in gut bacteria for all insects. Interestingly, the gut bacterial composition of untreated Ae. aegypti and C. nubeculosus showed Asaia as the dominant genus, which was drastically reduced after antibiotic treatment. Furthermore, antibiotic treatment resulted in relatively more Delftia bacteria in both biting midge species, but not in mosquitoes. Antibiotic treatment and subsequent changes in gut bacterial communities were associated with a significant, 1.8-fold increased infection rate of C. nubeculosus with Schmallenberg virus, but not for C. sonorensis. We did not find any changes in infection rates for Ae. aegypti mosquitoes with Zika or chikungunya virus. We conclude that resident gut bacteria may dampen arbovirus transmission in biting midges, but not so in mosquitoes. Use of antimicrobial compounds at livestock farms might therefore have an unexpected contradictory effect on the health of animals, by increasing the transmission of viral pathogens by biting midges.

    Author Correction: A global database for metacommunity ecology, integrating species, traits, environment and space
    Jeliazkov, Alienor ; Mijatovic, Darko ; Chantepie, Stéphane ; Andrew, Nigel ; Arlettaz, Raphaël ; Barbaro, Luc ; Barsoum, Nadia ; Bartonova, Alena ; Belskaya, Elena ; Bonada, Núria ; Brind’Amour, Anik ; Carvalho, Rodrigo ; Castro, Helena ; Chmura, Damian ; Choler, Philippe ; Chong-Seng, Karen ; Cleary, Daniel ; Cormont, Anouk ; Cornwell, William ; Campos, Ramiro de; Voogd, Nicole de; Doledec, Sylvain ; Drew, Joshua ; Dziock, Frank ; Eallonardo, Anthony ; Edgar, Melanie J. ; Farneda, Fábio ; Hernandez, Domingo Flores ; Frenette-Dussault, Cédric ; Fried, Guillaume ; Gallardo, Belinda ; Gibb, Heloise ; Gonçalves-Souza, Thiago ; Higuti, Janet ; Humbert, Jean Yves ; Krasnov, Boris R. ; Saux, Eric Le ; Lindo, Zoe ; Lopez-Baucells, Adria ; Lowe, Elizabeth ; Marteinsdottir, Bryndis ; Martens, Koen ; Meffert, Peter ; Mellado-Díaz, Andres ; Menz, Myles H.M. ; Meyer, Christoph F.J. ; Miranda, Julia Ramos ; Mouillot, David ; Ossola, Alessandro ; Pakeman, Robin ; Pavoine, Sandrine ; Pekin, Burak ; Pino, Joan ; Pocheville, Arnaud ; Pomati, Francesco ; Poschlod, Peter ; Prentice, Honor C. ; Purschke, Oliver ; Raevel, Valerie ; Reitalu, Triin ; Renema, Willem ; Ribera, Ignacio ; Robinson, Natalie ; Robroek, Bjorn ; Rocha, Ricardo ; Shieh, Sen Her ; Spake, Rebecca ; Staniaszek-Kik, Monika ; Stanko, Michal ; Tejerina-Garro, Francisco Leonardo ; Braak, Cajo ter; Urban, Mark C. ; Klink, Roel van; Villéger, Sébastien ; Wegman, Ruut ; Westgate, Martin J. ; Wolff, Jonas ; Żarnowiec, Jan ; Zolotarev, Maxim ; Chase, Jonathan M. - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463

    Following publication of this Data Descriptor it was found that the affiliation of Oliver Purschke was stated incorrectly. The correct affiliations are stated below: Department of Physical Geography and Ecosystem Science, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden Biodiversity, Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden This has been corrected in both the HTML and PDF versions.

    Benthic invertebrate and microbial biodiversity in sub-tropical urban rivers: Correlations with environmental variables and emerging chemicals
    Peng, Feng Jiao ; Pan, Chang Gui ; Zhang, Nai Sheng ; Braak, Cajo J.F. ter; Salvito, Daniel ; Selck, Henriette ; Ying, Guang Guo ; Brink, Paul J. Van den - \ 2020
    Science of the Total Environment 709 (2020). - ISSN 0048-9697
    Benthic bacterial community - Benthic macroinvertebrates - Double constrained ordination - Traits - Urban rivers - WWTP effluents

    Urban rivers often function as sinks for various contaminants potentially placing the benthic communities at risk of exposure. We performed a comprehensive biological survey of the benthic macroinvertebrate and bacterial community compositions in six rivers from the suburb to the central urban area of Guangzhou city (South China), and evaluated their correlations with emerging organic contaminants, heavy metals and nutrients. Overall, the benthic macroinvertebrate community shifted from molluscs to oligochaete from the suburban to the central urban rivers that receive treated and untreated sewage. An exception was the site in the Sha River where chironomids were most abundant. The differences in macroinvertebrate community assemblages were significantly associated with chromium, total phosphorus, galaxolide, triclosan and sand content in the sediment. There was no significant difference in benthic macroinvertebrate composition between the dry and wet season. As assessed by double constrained ordination, sexual reproduction was the only trait of benthic macroinvertebrates that showed a significant correlation with pollution variables, as it was significantly positively correlated with chromium and total phosphorus. This suggests that r-strategist occurs in polluted sampling sites. The benthic bacterial community composition showed a significant difference between seasons and among the Liuxi River, Zhujiang River and central urban rivers. The differences in community composition of the benthic bacteria were significantly correlated with galaxolide, total phosphorus, lead and triclosan. These results suggest that input of treated and untreated sewage significantly altered the benthic macroinvertebrate and bacterial community compositions in urban rivers.

    Investigating microbial associations from sequencing survey data with co-correspondence analysis
    Alric, Benjamin ; Braak, Cajo J.F. ter; Desdevises, Yves ; Lebredonchel, Hugo ; Dray, Stéphane - \ 2020
    Molecular Ecology Resources 20 (2020)2. - ISSN 1755-098X - p. 468 - 480.
    co-correspondence analysis - co-occurrence network - Mamiellophyceae - microbial eukaryotes - next-generation sequencing - Prasinovirus

    Microbial communities, which drive major ecosystem functions, consist of a wide range of interacting species. Understanding how microbial communities are structured and the processes underlying this is crucial to interpreting ecosystem responses to global change but is challenging as microbial interactions cannot usually be directly observed. Multiple efforts are currently focused to combine next-generation sequencing (NGS) techniques with refined statistical analysis (e.g., network analysis, multivariate analysis) to characterize the structures of microbial communities. However, most of these approaches consider a single table of sequencing data measured for several samples. Technological advances now make it possible to collect NGS data on different taxonomic groups simultaneously for the same samples, allowing us to analyse a pair of tables. Here, an analytical framework based on co-correspondence analysis (CoCA) is proposed to study the distributions, assemblages and interactions between two microbial communities. We show the ability of this approach to highlight the relationships between two microbial communities, using two data sets exhibiting various types of interactions. CoCA identified strong association patterns between autotrophic and heterotrophic microbial eukaryote assemblages, on the one hand, and between microalgae and viruses, on the other. We demonstrate also how CoCA can be used, complementary to network analysis, to reorder co-occurrence networks and thus investigate the presence of patterns in ecological networks.

    A global database for metacommunity ecology, integrating species, traits, environment and space
    Jeliazkov, Alienor ; Mijatovic, Darko ; Chantepie, Stéphane ; Andrew, Nigel ; Arlettaz, Raphaël ; Barbaro, Luc ; Barsoum, Nadia ; Bartonova, Alena ; Belskaya, Elena ; Bonada, Núria ; Brind’Amour, Anik ; Carvalho, Rodrigo ; Castro, Helena ; Chmura, Damian ; Choler, Philippe ; Chong-Seng, Karen ; Cleary, Daniel ; Cormont, Anouk ; Cornwell, William ; Campos, Ramiro de; Voogd, Nicole de; Doledec, Sylvain ; Drew, Joshua ; Dziock, Frank ; Eallonardo, Anthony ; Edgar, Melanie J. ; Farneda, Fábio ; Hernandez, Domingo Flores ; Frenette-Dussault, Cédric ; Fried, Guillaume ; Gallardo, Belinda ; Gibb, Heloise ; Gonçalves-Souza, Thiago ; Higuti, Janet ; Humbert, Jean Yves ; Krasnov, Boris R. ; Saux, Eric Le ; Lindo, Zoe ; Lopez-Baucells, Adria ; Lowe, Elizabeth ; Marteinsdottir, Bryndis ; Martens, Koen ; Meffert, Peter ; Mellado-Díaz, Andres ; Menz, Myles H.M. ; Meyer, Christoph F.J. ; Miranda, Julia Ramos ; Mouillot, David ; Ossola, Alessandro ; Pakeman, Robin ; Pavoine, Sandrine ; Pekin, Burak ; Pino, Joan ; Pocheville, Arnaud ; Pomati, Francesco ; Poschlod, Peter ; Prentice, Honor C. ; Purschke, Oliver ; Raevel, Valerie ; Reitalu, Triin ; Renema, Willem ; Ribera, Ignacio ; Robinson, Natalie ; Robroek, Bjorn ; Rocha, Ricardo ; Shieh, Sen Her ; Spake, Rebecca ; Staniaszek-Kik, Monika ; Stanko, Michal ; Tejerina-Garro, Francisco Leonardo ; Braak, Cajo ter; Urban, Mark C. ; Klink, Roel van; Villéger, Sébastien ; Wegman, Ruut ; Westgate, Martin J. ; Wolff, Jonas ; Żarnowiec, Jan ; Zolotarev, Maxim ; Chase, Jonathan M. - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463

    The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology.

    Compositional turnover and variation in Eemian pollen sequences in Europe
    Felde, Vivian A. ; Flantua, Suzette G.A. ; Jenks, Cathy R. ; Benito, Blas M. ; Beaulieu, Jacques Louis de; Kuneš, Petr ; Magri, Donatella ; Nalepka, Dorota ; Risebrobakken, Bjørg ; Braak, Cajo J.F. ter; Allen, Judy R.M. ; Granoszewski, Wojciech ; Helmens, Karin F. ; Huntley, Brian ; Kondratienė, Ona ; Kalniņa, Laimdota ; Kupryjanowicz, Mirosława ; Malkiewicz, Małgorzata ; Milner, Alice M. ; Nita, Małgorzata ; Noryśkiewicz, Bożena ; Pidek, Irena A. ; Reille, Maurice ; Salonen, Sakari ; Šeirienė, Vaida ; Winter, Hanna ; Tzedakis, Polychronis C. ; Birks, John B. - \ 2020
    Vegetation History and Archaeobotany 29 (2020)1. - ISSN 0939-6314 - p. 101 - 109.
    Detrended canonical correspondence analysis - Extrinsic and intrinsic processes - Inertia - Last interglacial dataset - Multivariate regression trees - Neutral processes - Principal curves

    The Eemian interglacial represents a natural experiment on how past vegetation with negligible human impact responded to amplified temperature changes compared to the Holocene. Here, we assemble 47 carefully selected Eemian pollen sequences from Europe to explore geographical patterns of (1) total compositional turnover and total variation for each sequence and (2) stratigraphical turnover between samples within each sequence using detrended canonical correspondence analysis, multivariate regression trees, and principal curves. Our synthesis shows that turnover and variation are highest in central Europe (47–55°N), low in southern Europe (south of 45°N), and lowest in the north (above 60°N). These results provide a basis for developing hypotheses about causes of vegetation change during the Eemian and their possible drivers.

    Differently Pre-treated Alfalfa Silages Affect the in vitro Ruminal Microbiota Composition
    Hartinger, Thomas ; Edwards, Joan E. ; Gómez Expósito, Ruth ; Smidt, Hauke ; Braak, Cajo J.F. ter; Gresner, Nina ; Südekum, Karl Heinz - \ 2019
    Frontiers in Microbiology 10 (2019). - ISSN 1664-302X
    16S rRNA gene sequencing - anaerobic fungi - archaea - bacteria - lucerne silage - qPCR - rumen microbiota - Rusitec

    Alfalfa (Medicago sativa L.) silage (AS) is an important feedstuff in ruminant nutrition. However, its high non-protein nitrogen content often leads to poor ruminal nitrogen retention. Various pre-ensiling treatments differing with respect to dry matter concentrations, wilting intensities and sucrose addition have been previously shown to improve the quality and true protein preservation of AS, and have substantial effects on in vitro ruminal fermentation of the resulting silages. However, it is unknown how these pre-ensiling treatments affect the ruminal microbiota composition, and whether alterations in the microbiota explain previously observed differences in ruminal fermentation. Therefore, during AS incubation in a rumen simulation system, liquid and solid phases were sampled 2 and 7 days after first incubating AS, representing an early (ET) and late (LT) time point, respectively. Subsequently, DNA was extracted and qPCR (bacteria, archaea, and anaerobic fungi) and prokaryotic 16S rRNA gene amplicon sequence analyses were performed. At the ET, high dry matter concentration and sucrose addition increased concentrations of archaea in the liquid phase (P = 0.001) and anaerobic fungi in the solid phase (P < 0.001). At the LT, only sucrose addition increased archaeal concentration in the liquid phase (P = 0.014) and anaerobic fungal concentration in the solid phase (P < 0.001). Bacterial concentrations were not affected by pre-ensiling treatments. The prokaryotic phylogenetic diversity index decreased in the liquid phase from ET to LT (P = 0.034), whereas the solid phase was not affected (P = 0.060). This is suggestive of a general adaption of the microbiota to the soluble metabolites released from the incubated AS, particularly regarding the sucrose-treated AS. Redundancy analysis of the sequence data at the genus level indicated that sucrose addition (P = 0.001), time point (P = 0.001), and their interaction (P = 0.001) affected microbial community composition in both phases. In summary, of the pre-ensiling treatments tested sucrose addition had the largest effect on the microbiota, and together with sampling time point affected microbiota composition in both phases of the rumen simulation system. Thus, microbiota composition analysis helped to understand the ruminal fermentation patterns, but could not fully explain them.

    Biomarker Research in ADHD: The Impact of Nutrition (BRAIN) - Study protocol of an open-label trial to investigate the mechanisms underlying the effects of a few-foods diet on ADHD symptoms in children
    Stobernack, Tim ; Vries, Stefan P.W. De; Rodrigues Pereira, Rob ; Pelsser, Lidy M. ; Braak, Cajo J.F. Ter; Aarts, Esther ; Baarlen, Peter Van; Kleerebezem, Michiel ; Frankena, Klaas ; Hontelez, Saartje - \ 2019
    BMJ Open 9 (2019)11. - ISSN 2044-6055
    ADHD - biomarker - brain activity - few-foods diet - fMRI - microbiota

    Introduction Attention deficit hyperactivity disorder (ADHD) is the most common childhood behavioural disorder, causing significant impediment to a child's development. It is a complex disorder with numerous contributing (epi)genetic and environmental factors. Currently, treatment consists of behavioural and pharmacological therapy. However, ADHD medication is associated with several side effects, and concerns about long-term effects and efficacy exist. Therefore, there is considerable interest in the development of alternative treatment options. Double-blind research investigating the effects of a few-foods diet (FFD) has demonstrated a significant decrease in ADHD symptoms following an FFD. However, an FFD requires a considerable effort of both child and parents, limiting its applicability as a general ADHD treatment. To make FFD intervention less challenging or potentially obsolete, we need to understand how, and in which children, an FFD affects ADHD behaviour and, consequently, the child's well-being. We hypothesise that an FFD affects brain function, and that the nutritional impact on ADHD is effectuated by a complex interplay between the microbiota, gut and brain, that is, the microbiota-gut-brain axis. Methods and analysis The Biomarker Research in ADHD: the Impact of Nutrition (BRAIN) study is an open-label trial with researchers blinded to changes in ADHD symptoms during sample processing and initial data analyses. Ethics and dissemination The Medical Research and Ethics Committee of Wageningen University has approved this study (NL63851.081.17, application 17/24). Results will be disseminated through peer-reviewed journal publications, conference presentations, (social) media and the BRAIN study website. A summary of the findings will be provided to the participants. Trial registration number NCT03440346. Study dates Collection of primary outcome data started in March 2018 and will be ongoing until 100 children have participated in the study. Sample data analysis will start after all samples have been collected.

    New robust weighted averaging- and model-based methods for assessing trait–environment relationships
    Braak, Cajo J.F. ter - \ 2019
    Methods in Ecology and Evolution 10 (2019)11. - ISSN 2041-210X - p. 1962 - 1971.
    community assembly - community-weighted means - fourth-corner approach - generalized linear mixed models - species niche centroid - trait-based ecology - weighted averaging - Whittaker Siskiyou Mountains data

    Statistical analysis of trait–environment association is challenging owing to the lack of a common observation unit: Community-weighted mean regression (CWMr) uses site points, multilevel models focus on species points, and the fourth-corner correlation uses all species-site combinations. This situation invites the development of new methods capable of using all observation levels. To this end, new multilevel and weighted averaging-based regression methods are proposed. Compared to existing methods, the new multilevel method, called MLM3, has additional site-related random effects; they represent the unknowns in the environment that interact with the trait. The new weighted averaging method combines site-level CWMr with a species-level regression of Species Niche Centroids on to the trait. Because species can vary enormously in frequency and abundance giving diversity variation among sites, the regressions are weighted by Hill's effective number (N2) of occurrences of each species and the N2-diversity of a site, and are subsequently combined in a sequential test procedure known as the max test. Using the test statistics of these new methods, the permutation-based max test provides strong statistical evidence for trait–environment association in a plant community dataset, where existing methods show weak evidence. In simulations, the existing multilevel model showed bias and type I error inflation, whereas MLM3 did not. Out of the weighted averaging-based regression methods, the N2-weighted version best controlled the type I error rate. MLM3 was superior to the weighted averaging-based methods with up to 30% more power. Both methods can be extended (a) to account for phylogeny and spatial autocorrelation and (b) to select functional traits and environmental variables from a greater set of variables.

    Kosten van zwarte braak voor aaltjesbestrijding : Saldoverliezen en bewerkingskosten van zwarte braak bij sanering van Melodogyne soorten
    Smit, A.B. ; Jager, J.H. - \ 2019
    Wageningen : Wageningen Economic Research - 2 p.
    Relating ultrasonic vocalizations from a pair of rats to individual behavior : A composite link model approach
    Vendrig, Nadia J. ; Hemerik, Lia ; Pinter, Ilona J. ; Braak, Cajo J.F. ter - \ 2019
    Statistica Neerlandica 73 (2019)1. - ISSN 0039-0402 - p. 139 - 156.
    automated home cage - composite link model - model identification - social behavior - ultrasonic vocalization

    Ultrasonic vocalizations (USVs) are crucial in the social behavior of rats. We aim to relate USV rates of pairs of rats to individual activity in an automated home cage (PhenoTyper®) where USVs are recorded per pair and not per individual. We propose a composite link model approach to parametrize a mechanistic “sum-of-rates” model in which the pair's USV rate is the sum of the USV rates of individuals depending on their own behavior. In generalized linear models (GLMs), the individual's USV rates are multiplied. We verified through simulation that composite link model gave lower Poisson deviance than GLM. We analyzed the data from an experiment in which half of the cages did allow the pairs to interact (Pair Housing) and the other half did not (Individual Housing). The “sum-of-rates” model fits best for Individual Housing and GLM for Pair Housing. An additional simulation study strongly suggests that interaction between rats changes the underlying mechanism for vocalization behavior.

    Integrating spatial and phylogenetic information in the fourth-corner analysis to test trait–environment relationships
    Braga, João ; Braak, Cajo J.F. ter; Thuiller, Wilfried ; Dray, Stéphane - \ 2018
    Ecology 99 (2018)12. - ISSN 0012-9658 - p. 2667 - 26764.
    community ecology - fourth-corner analysis - functional ecology - Moran's spectral randomization - null models - type I error

    The fourth-corner analysis aims to quantify and test for relationships between species traits and site-specific environmental variables, mediated by site-specific species abundances. Since there is no common unit of observation, the significance of the relationships is tested using a double permutation procedure (site based and species based). This method implies that all species and sites are independent of each other. However, this fundamental hypothesis might be flawed because of phylogenetic relatedness between species and spatial autocorrelation in the environmental data. Here, using a simulation-based experiment, we demonstrate how the presence of spatial and phylogenetic autocorrelations can, in some circumstances, lead to inflated type I error rates, suggesting that significant associations can be misidentified. As an alternative, we propose a new randomization approach designed to avoid this issue, based on Moran's spectral randomization. In this approach, standard permutations are replaced by constrained randomizations so that the distribution of the statistic under the null hypothesis is built with additional constraints to preserve the phylogenetic and spatial structures of the observed data. The inclusion of this new randomization approach provides total control over type I error rates and should be used in real studies where spatial and phylogenetic autocorrelations often occur.

    Meer aardappels met minder water dankzij slimme irrigatie en andere rassen
    Blom-Zandstra, M. - \ 2018
    Simple parametric tests for trait–environment association
    Braak, Cajo J.F. ter; Peres-Neto, Pedro R. ; Dray, Stéphane - \ 2018
    Journal of Vegetation Science 29 (2018)5. - ISSN 1100-9233 - p. 801 - 811.
    community ecology - community-level test - CWM of traits - environmental gradients - fourth-corner - functional traits - modified test - species niche centroid - species-level test - statistical ecology - trait–environment relationship

    Question: The CWM approach is an easy way of analysing trait–environment association by regressing (or correlating) the mean trait per plot against an environmental variable and assessing the statistical significance of the slope or the associated correlation coefficient. However, the CWM approach does not yield valid tests, as random traits (or random indicator values) are far too often judged significantly related to the environmental variable, even when the trait and environmental variable are extrinsic to (not derived from) the community data. Existing solutions are the ZS-modified test (Zelený & Schaffers,) and the max (or sequential) test based on the fourth-corner correlation. Both tests are based on permutations which become cumbersome when many tests need to be carried out and many permutations are required, as in methods that correct for multiple testing. The main goal of this study was to compare these existing permutation-based solutions and to develop a quick and easy parametric test that can replace them. Methods: This study decomposes the fourth-corner correlation in two ways, which suggests a simple parametric approach consisting of assessing the significances of two linear regressions, one plot-level test as in the CWM approach and one species-level test, the reverse of the CWM approach, that regresses the environmental mean per species (i.e. the species niche centroid) on to the trait. The tests are combined by taking the maximum p-value. The type I error rates and power of this parametric max test are examined by simulation of one- and two-dimensional Gaussian models and log-linear models. Results: The ZS-modified test and the fourth-corner max test are conservative in different scenarios, the ZS-modified test being even more conservative than the fourth-corner. The new parametric max test is shown to control the type I error and has equal or even higher power than permutation tests based on the fourth-corner, the ZS-modified test and variants thereof. A weighted version of the new test showed inflated type I error. Conclusion: The combination of two simple regressions is a good alternative to the fourth-corner and the ZS-modified test. This combination is also applicable when multiple trait measurements are made per plot.

    Een eureka-moment dat nog een beetje natrilt : over zwaartekrachtgolven en Bayesiaans rekenen
    Braak, C.J.F. ter - \ 2018
    Stator, periodiek van VVS 19 (2018)2. - ISSN 1567-3383 - p. 14 - 17.
    Out of the box : Statistical methods for the analysis of automated home cage experiments
    Vendrig, Nadia J. - \ 2018
    Wageningen University. Promotor(en): C.J.F. ter Braak, co-promotor(en): L. Hemerik. - Wageningen : Wageningen University - ISBN 9789463432627 - 181

    Automated home cage experiments have been proposed as an alternative to the classical tests used for behavioural phenotyping. As the name implies, automated home cage experiments are conducted in home cage environments and the behaviour is recorded automatically. The experiments can thus be conducted without human interference and can last for several days.

    All data incorporated in this thesis is collected using a PhenoTyper® system (Noldus Information Technology, Wageningen, The Netherlands). The Pheno- Typer is a home cage environment with an integrated top-view camera. The ex- act location of the rat or mouse is determined for every frame in the video. Be- havioural response variables such as Distance Moved or Duration Progressing are extracted from the location.

    Data from automated home cage experiments typically consists of multiple re- sponse variables that can be highly correlated. In addition to the location-based activity response variables, automated home cage environments have the poten- tial to incorporate data from other sources such as biometric parameters.

    The aim of this thesis is to expand the methodology available to analyse these data.

    In Chapter 2, the use of multivariate statistics for data from automated home cage experiments is demonstrated in two case studies. Data from automated home cage experiments is pre-dominantly analysed using univariate statistics in which the significance and magnitude of the effect of a treatment on a single response variable is tested. By analysing single response variables the benefit that au- tomated home cage experiments allow for the collection of numerous response variables simultaneously is not fully utilized. The use of multivariate statistics allows for simultaneous analysis of multiple response variables. The multivari- ate methods described in Chapter 2 are Redundancy Analysis (RDA) and Principal Response Curves (PRC). Both of these methods are frequently used in (aquatic) ecology, toxicology, and microbiology. RDA is a constrained form of Principal Components Analysis (PCA). RDA describes the underlying structure of a data set in terms of the explanatory variables (such as experimental treatment). It quan- tifies the proportion of variance in the data set that can be described using these explanatory variables. PRC is a special case of RDA used to describe experimen- tal multivariate longitudinal data. It estimates differences among treatments on a collection of response variables over time and the extent to which the response of those individual response variables resembles the overall response. In both case studies, the multivariate analyses were able to draw the same main conclusions as the contrasting univariate analyses. The advantages of using a multivariate analysis rather than a univariate analysis on a single response variable is that the multivariate methods provide a graphical representation of the data set, are easy to interpret, and allow for estimation of the relation between response variables.

    In Chapter 3, a novel extension to PRC is presented that allows for response variable selection using permutation testing. Often, not all of the response vari- ables included in PRC are affected by the treatment which can make response vari- able selection desirable. One approach is to use a straightforward cut-off value for coefficient size. Because coefficient size of response variables are affected by more factors than effect-size alone, results of this approach can be variable between data sets. A backward selection approach was expected to give a more robust result. Four backward selection approaches based on permutation testing were presented. The approaches differ in whether coefficient size is used or not in ranking the response variables to test. The performance of these approaches was demonstrated in a simulation study using a well known data set in the field of aquatic ecology. The permutation testing approach that uses information on coefficient size of RVs sped up the algorithm without affecting its performance. This most successful permutation testing approach removed roughly 95% of the response variables that are unaffected by the treatment irrespective of the char- acteristics of the data set (which is a desirable property of a statistical test) and, in the simulations, correctly identified up to 97% of response variables affected by the treatment.

    In Chapter 4, a case study is used to illustrate the power of combining mecha- nistic and statistical modelling, and the benefits of simulation studies. In this case study, an integrated analysis of two streams of information: activity response variables per rat and Ultrasonic Vocalisations (USVs) per cage (containing a pair of rats). USVs are crucial in the social behaviour of rats. The aim of the first part of the chapter was to develop methodology to predict the USV-rate of the pair of rats as a function of the activity of the individuals. A mechanistic model is that the USV-rate of the pair of rats is the sum of the USV-rates of the two individuals depending on their own behaviour (“sum-of-rates” model). It turns out that this “sum-of-rates” model can be fitted to data using a Composite Link Model (CLM) approach. In generalized linear models (GLM) the individual’s USV-rates are mul- tiplied rather than summed. A simulation study verified that CLM gave a better fit (lower Poisson Deviance) than GLM. In the second part of the chapter, data from an experiment in which half of the cages did allow the rats of the pair to interact (Pair Housing) and the other half did not (Individual Housing). A num- ber of models was fitted to investigate whether there is evidence that interaction between rats affects their behaviour. The “sum-of-rates” model fit best for In- dividual Housing and GLM for Pair Housing. This difference in fit supports the hypothesis that interaction between rats affects their behaviour. An additional simulation study strongly suggested that this difference was not due to chance and that the underlying mechanism that links activity and USVs structurally dif- fered between Pair Housing and Individual Housing.

    In Chapter 5, a simulation study is described that evaluates the performance of a new and promising statistical learning method under circumstances relevant for automated home cage experiments. Targeted Maximum Likelihood Estima- tion (TMLE) is a new and promising statistical method for causal effect estima- tion, even in observational studies, that can use machine learning methods to increase performance. The intended role of TMLE in the analysis of home cage ex- periments was to account for inter-individual variation in behaviour when test- ing specific treatment effects. TMLE is a doubly robust method, which means that it is robust to misspecification of either the treatment outcome model or the treatment assignment model. A treatment outcome model predicts the effect of a treatment on the response variable given the covariates. A treatment assignment model predicts the probability that an individual is in a treatment group given the covariates. In theory, when all assumptions are correct, TMLE should thus pro- vide unbiased causal effect estimators even when either the treatment outcome or treatment assignment model is misspecified. When TMLE is applied in prac- tice however, it is possible that these required theoretical assumptions such as the positivity assumption and no unobserved confounders are violated. The sim- ulation study in Chapter 5 illustrates the effects of unobserved (non-)confounding covariates and noise covariates on bias, mean square error, and coverage of TMLE on near-balanced data sets (with low risk of positivity violations) and unbalanced data sets (with higher risks of positivity violations). The conclusion was that TMLE is able to estimate average causal effects with low bias and mean square error, compared to the golden standard linear regression, given that the sample size is large, the data set is near-balanced, and the assignment model is specified cor- rectly. In unbalanced data sets TMLE did not live up to expectations, also in data sets in which the positivity assumption was not violated. The conclusion from the simulation study is that TMLE is as yet not suited for the intended use in home cage experiments.

    In Chapter 6, the General Discussion, the main findings of the thesis are sum- marised and discussed in relation to the aim of the thesis. In addition, several hot topics in biostatistics for automated home cage experiments are discussed.

    Achteruitgang insectenpopulaties in Nederland: trends, oorzaken en kennislacunes
    Kleijn, David ; Bink, Ruud J. ; Braak, Cajo J.F. ter; Grunsven, Roy van; Ozinga, Wim A. ; Roessink, Ivo ; Scheper, Jeroen A. ; Schmidt, Anne M. ; Wallis de Vries, Michiel F. ; Wegman, Ruut ; Zee, Friso F. van der; Zeegers, Th. - \ 2018
    Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2871) - 85
    Canoco reference manual and user's guide : software for ordination (version 5.10)
    Braak, Cajo J.F. ter; Šmilauer, Petr - \ 2018
    Wageningen : Biometris, Wageningen University & Research - 536
    Algorithms and biplots for double constrained correspondence analysis
    Braak, Cajo J.F. Ter; Šmilauer, Petr ; Dray, Stéphane - \ 2018
    Environmental and Ecological Statistics 25 (2018)2. - ISSN 1352-8505 - p. 171 - 197.
    Biplot - Canonical correlation analysis - Canonical correspondence analysis - Community ecology - Fourth-corner correlation - Multivariate analysis - Trait-environment relations
    Correspondence analysis with linear external constraints on both the rows and the columns has been mentioned in the ecological literature, but lacks full mathematical treatment and easily available algorithms and software. This paper fills this gap by defining the method as maximizing the fourth-corner correlation between linear combinations, by providing novel algorithms, which demonstrate relationships with related methods, and by making a detailed study of possible biplots and associated approximations. The method is illustrated using ecological data on the abundances of species in sites and where the species are characterized by traits and sites by environmental variables. The trait data and environment data form the external constraints and the question is which traits and environmental variables are associated, how these associations drive species abundances and how they can be displayed in biplots. With microbiome data becoming widely available, these and related multivariate methods deserve more study as they might be routinely used in the future.
    Flow thresholds for leaf retention in hydrodynamic wakes downstream of obstacles
    Brouwer, J.H.F. de; Eekhout, J.P.C. ; Besse-Lototskaya, A.A. ; Hoitink, A.J.F. ; Braak, C.J.F. ter; Verdonschot, P.F.M. - \ 2017
    Ecohydrology 10 (2017)7. - ISSN 1936-0584 - 10 p.
    current velocity - flow velocity - leaves entrainment - leaves transport - lowland streams - wake

    Leaves are the major component of terrestrial litter input into aquatic systems. Leaves are distributed by the flow, accumulate in low flow areas, and form patches. In natural streams, stable leaf patches form around complex structures, such as large woody debris. Until now, little is known about flow conditions under which leaf patches persist. This study aims to quantify flow conditions for stable leaf patches and entrainment of leaf patches. We hypothesize that entraining flow processes, such as turbulence, Reynolds stress, or lift forcing (vertical flow velocity), best explain local leaf retention. This study was performed in an unscaled flume experiment, which conditions coincide with conditions found in low-energetic lowland streams. We positioned a wooden obstacle perpendicular to the flow on the bed of the flume. A leaf patch was positioned downstream from the wooden obstacle. The experiment was performed under 5 flow conditions. We monitored leaf patch cover and near-bed flow conditions in the area downstream of the wooden obstacle. We showed that near-bed flow velocities explain leaf retention better than more complex flow velocity derivatives such as turbulence, Reynolds stress, and vertical flow velocity. The entrainment near-bed flow velocity for leaves ranges from 0.037 to 0.050 m/s. Flow velocities frequently exceed those values, even in low-energetic lowland streams. Therefore, complex structures, such as woody debris, create flow conditions to support stable leaf patches. Thus, adding instead of removing obstacles may be a key strategy in restoring biodiversity in deteriorated streams.

    Biodiversity analyses for risk assessment of genetically modified potato
    Lazebnik, Jenny ; Dicke, Marcel ; Braak, Cajo J.F. ter; Loon, Joop J.A. van - \ 2017
    Agriculture, Ecosystems and Environment 249 (2017). - ISSN 0167-8809 - p. 196 - 205.
    Biodiversity - Biodiversity index - Environmental risk assessment - Functional groups - Genetically modified crops - Multivariate analysis
    An environmental risk assessment for the introduction of genetically modified crops includes assessing the consequences for biodiversity. In this study arthropod biodiversity was measured using pitfall traps in potato agro-ecosystems in Ireland and The Netherlands over two years. We tested the impact of site, year, potato genotype, and fungicide management regime on arthropod community composition. Three potato genotypes were compared: the cultivar Désirée, susceptible to the late blight pathogen Phytophthora infestans, a genetically modified cisgenic clone of Désirée resistant to P. infestans and the cultivar Sarpo Mira, also resistant to late blight. We aimed to test several ways to measure biodiversity in the context of risk assessment by using both univariate biodiversity indices and multivariate ordination methods, categorizing the pitfall trap catch by taxonomic or functional category. The Shannon-Wiener and Simpson biodiversity indices both showed strong differences between sites, years and potato genotypes, but showed no effects of the fungicide management regime. The effect of genotype was due to cultivar differences between Désirée and Sarpo Mira rather than between the GM-event (A15-31) and its isogenic comparator Désirée. Multivariate permutation analyses and RDA ordination confirmed these findings and also showed interactions between year, site and either genotype or treatment. The added value of the multivariate analysis was that it provided information on the specific arthropod groups or taxa that contributed to community structure. Multivariate analyses are recommended for use as a sensitive method to compare functionally important arthropod groups driving community structure within the framework of environmental risk assessments, or for the process of indicator species selection.
    Linking trait variation to the environment : Critical issues with community-weighted mean correlation resolved by the fourth-corner approach
    Peres-Neto, Pedro R. ; Dray, Stéphane ; Braak, Cajo ter - \ 2017
    Ecography 40 (2017)7. - ISSN 0906-7590 - p. 806 - 816.

    Establishing trait-environment relationships has become routine in community ecology. Here, we demonstrate that the community weighted means correlation (CWM) and its parallel approach in linking trait variation to the environment, the species niche centroid correlation (SNC), have important shortcomings, arguing against their continuing application. Using mathematical derivations and simulations, we show that the two major issues are inconsistent parameter estimation and unacceptable significance rates when only the environment or only traits are structuring species distributions, but they themselves are not linked. We show how both CWM and SNC are related to the fourth-corner correlation and propose to replace all by the Chessel fourth-corner correlation, which is the fourth-corner correlation divided by its maximum attainable value. We propose an appropriate hypothesis testing procedure that is not only unbiased but also has much greater statistical power in detecting trait-environmental relationships. We derive an additive framework in which trait variation is partitioned among and within communities, which can be then modeled against the environment. We finish by presenting a contrast between methods and an application of our proposed framework across 85 lake-fish metacommunities.

    Fourth-corner correlation is a score test statistic in a log-linear trait–environment model that is useful in permutation testing
    Braak, Cajo J.F. ter - \ 2017
    Environmental and Ecological Statistics 24 (2017)2. - ISSN 1352-8505 - p. 219 - 242.
    Community ecology - Correspondence analysis - Fourth-corner - Permutation test - Score test statistic - Trait–environment association

    Ecologists wish to understand the role of traits of species in determining where each species occurs in the environment. For this, they wish to detect associations between species traits and environmental variables from three data tables, species count data from sites with associated environmental data and species trait data from data bases. These three tables leave a missing part, the fourth-corner. The fourth-corner correlations between quantitative traits and environmental variables, heuristically proposed 20 years ago, fill this corner. Generalized linear (mixed) models have been proposed more recently as a model-based alternative. This paper shows that the squared fourth-corner correlation times the total count is precisely the score test statistic for testing the linear-by-linear interaction in a Poisson log-linear model that also contains species and sites as main effects. For multiple traits and environmental variables, the score test statistic is proportional to the total inertia of a doubly constrained correspondence analysis. When the count data are over-dispersed compared to the Poisson or when there are other deviations from the model such as unobserved traits or environmental variables that interact with the observed ones, the score test statistic does not have the usual chi-square distribution. For these types of deviations, row- and column-based permutation methods (and their sequential combination) are proposed to control the type I error without undue loss of power (unless no deviation is present), as illustrated in a small simulation study. The issues for valid statistical testing are illustrated using the well-known Dutch Dune Meadow data set.

    A critical issue in model-based inference for studying trait-based community assembly and a solution
    Braak, Cajo J.F. ter; Peres-Neto, Pedro ; Dray, Stéphane - \ 2017
    PeerJ 5 (2017). - ISSN 2167-8359
    Community composition - Compositional count data - Fourthcorner problem - Generalized linear models - Log-linear model - Negative-binomial response - Poisson regression - Trait-environment association

    Statistical testing of trait-environment association from data is a challenge as there is no common unit of observation: the trait is observed on species, the environment on sites and the mediating abundance on species-site combinations. A number of correlation-based methods, such as the community weighted trait means method (CWM), the fourth-corner correlation method and the multivariate method RLQ, have been proposed to estimate such trait-environment associations. In these methods, valid statistical testing proceeds by performing two separate resampling tests, one sitebased and the other species-based and by assessing significance by the largest of the two p-values (the pmax test). Recently, regression-based methods using generalized linear models (GLM) have been proposed as a promising alternative with statistical inference via site-based resampling. We investigated the performance of this new approach along with approaches that mimicked the pmax test using GLM instead of fourth-corner. By simulation using models with additional random variation in the species response to the environment, the site-based resampling tests using GLM are shown to have severely inflated type I error, of up to 90%, when the nominal level is set as 5%. In addition, predictive modelling of such data using site-based cross-validation very often identified trait-environment interactions that had no predictive value. The problem that we identify is not an ``omitted variable bias'' problem as it occurs even when the additional random variation is independent of the observed trait and environment data. Instead, it is a problem of ignoring a random effect. In the same simulations, the GLM-based pmax test controlled the type I error in all models proposed so far in this context, but still gave slightly inflated error in more complex models that included both missing (but important) traits and missing (but important) environmental variables. For screening the importance of single trait-environment combinations, the fourth-corner test is shown to give almost the same results as the GLM-based tests in far less computing time.

    Response variable selection in principal response curves using permutation testing
    Vendrig, Nadia J. ; Hemerik, Lia ; Braak, Cajo J.F. Ter - \ 2017
    Aquatic Ecology 51 (2017)1. - ISSN 1386-2588 - p. 131 - 143.
    longitudinal data - multivariate analysis - multivariate time series - permutation testing - Principal response curves - variable selection
    Principal response curves analysis (PRC) is widely applied to experimental multivariate longitudinal data for the study of time-dependent treatment effects on the multiple outcomes or response variables (RVs). Often, not all of the RVs included in such a study are affected by the treatment and RV-selection can be used to identify those RVs and so give a better estimate of the principal response. We propose four backward selection approaches, based on permutation testing, that differ in whether coefficient size is used or not in ranking the RVs. These methods are expected to give a more robust result than the use of a straightforward cut-off value for coefficient size. Performance of all methods is demonstrated in a simulation study using realistic data. The permutation testing approach that uses information on coefficient size of RVs speeds up the algorithm without affecting its performance. This most successful permutation testing approach removes roughly 95 % of the RVs that are unaffected by the treatment irrespective of the characteristics of the data set and, in the simulations, correctly identifies up to 97 % of RVs affected by the treatment.
    Flow velocity tolerance of lowland stream caddisfly larvae (Trichoptera)
    Brouwer, J.H.F. de; Besse-Lototskaya, A.A. ; Braak, C.J.F. Ter; Kraak, M.H.S. ; Verdonschot, P.F.M. - \ 2017
    Aquatic Sciences 79 (2017)3. - ISSN 1015-1621 - p. 419 - 425.
    Drift - Flow velocity - Lowland streams - Return rates - Trichoptera
    The process of macroinvertebrate drift in streams is characterized by dislodgement, drift distance and subsequent return to the bottom. While dislodgement is well studied, the fate of drifting organisms is poorly understood, especially concerning Trichoptera. Therefore, the aim of the present study was to determine the ability of six case-building Trichoptera species to return to the stream bottom under different flow velocity conditions in a laboratory flume. The selected species occur in North-West European sandy lowland streams along a gradient from lentic to lotic environments. We determined species specific probability curves for both living and dead (control) specimens to return to the bottom from drift at different flow velocities and established species specific return rates. Species on the lotic end of the gradient had highest return rates at high flow velocity and used active behaviour most efficiently to return to the bottom from drift. The observed gradient of flow velocity tolerance and species specific abilities to settle from drift indicate that, in addition to dislodgement, the process of returning to the bottom is of equal importance in determining flow velocity tolerance of Trichoptera species.
    A risk assessment-driven quantitative comparison of gene expression profiles in PBMCs and white adipose tissue of humans and rats after isoflavone supplementation
    Velpen, V. van der; Veer, P. van 't; Islam, M.A. ; Braak, C.J.F. ter; Leeuwen, F.X.R. ; Afman, L.A. ; Hollman, P.C.H. ; Schouten, A. ; Geelen, M.M.E.E. - \ 2016
    Food and Chemical Toxicology 95 (2016). - ISSN 0278-6915 - p. 203 - 210.
    Risk assessment - Gene expression - Species and tissue differences - Quantitative evaluation - Isoflavones - Multivariate model
    Quantitative insight into species differences in risk assessment is expected to reduce uncertainty and variability related to extrapolation from animals to humans. This paper explores quantification and comparison of gene expression data between tissues and species from intervention studies with isoflavones.

    Gene expression data from peripheral blood mononuclear cells (PBMCs) and white adipose tissue (WAT) after 8wk isoflavone interventions in postmenopausal women and ovariectomized F344 rats were used. A multivariate model was applied to quantify gene expression effects, which showed 3–5-fold larger effect sizes in rats compared to humans. For estrogen responsive genes, a 5-fold greater effect size was found in rats than in humans. For these genes, intertissue correlations (r = 0.23 in humans, r = 0.22 in rats) and interspecies correlation in WAT (r = 0.31) were statistically significant. Effect sizes, intertissue and interspecies correlations for some groups of genes within energy metabolism, inflammation and cell cycle processes were significant, but weak.

    Quantification of gene expression data reveals differences between rats and women in effect magnitude after isoflavone supplementation. For risk assessment, quantification of gene expression data and subsequent calculation of intertissue and interspecies correlations within biological pathways will further strengthen knowledge on comparability between tissues and species.
    Networking Our Way to Better Ecosystem Service Provision
    Braak, C.J.F. ter - \ 2016
    Trends in Ecology and Evolution 31 (2016)2. - ISSN 0169-5347 - p. 105 - 115.
    The ecosystem services (EcoS) concept is being used increasingly to attach values to natural systems and the multiple benefits they provide to human societies. Ecosystem processes or functions only become EcoS if they are shown to have social and/or economic value. This should assure an explicit connection between the natural and social sciences, but EcoS approaches have been criticized for retaining little natural science. Preserving the natural, ecological science context within EcoS research is challenging because the multiple disciplines involved have very different traditions and vocabularies (common-language challenge) and span many organizational levels and temporal and spatial scales (scale challenge) that define the relevant interacting entities (interaction challenge). We propose a network-based approach to transcend these discipline challenges and place the natural science context at the heart of EcoS research
    Combining exposure and effect modeling into an integrated probabilistic environmental risk assessment for nanoparticles
    Jacobs, Rianne ; Meesters, Johannes A.J. ; Braak, Cajo J.F. ter; Meent, Dik van de; Voet, Hilko van der - \ 2016
    Environmental Toxicology and Chemistry 35 (2016)12. - ISSN 0730-7268 - p. 2958 - 2967.
    2-dimensional Monte Carlo - Biostatistics - Hazard/risk assessment - Nanoparticle - Species sensitivity distribution - Uncertainty/variability

    There is a growing need for good environmental risk assessment of engineered nanoparticles (ENPs). Environmental risk assessment of ENPs has been hampered by lack of data and knowledge about ENPs, their environmental fate, and their toxicity. This leads to uncertainty in the risk assessment. To deal with uncertainty in the risk assessment effectively, probabilistic methods are advantageous. In the present study, the authors developed a method to model both the variability and the uncertainty in environmental risk assessment of ENPs. This method is based on the concentration ratio and the ratio of the exposure concentration to the critical effect concentration, both considered to be random. In this method, variability and uncertainty are modeled separately so as to allow the user to see which part of the total variation in the concentration ratio is attributable to uncertainty and which part is attributable to variability. The authors illustrate the use of the method with a simplified aquatic risk assessment of nano-titanium dioxide. The authors' method allows a more transparent risk assessment and can also direct further environmental and toxicological research to the areas in which it is most needed.

    Statistical modelling of variability and uncertainty in risk assessment of nanoparticles
    Jacobs, R. - \ 2016
    Wageningen University. Promotor(en): Cajo ter Braak, co-promotor(en): Hilko van der Voet. - Wageningen : Wageningen University - ISBN 9789462578197 - 205
    modeling - statistics - particles - risk assessment - uncertainty - uncertainty analysis - nanotechnology - probabilistic models - modelleren - statistiek - deeltjes - risicoschatting - onzekerheid - onzekerheidsanalyse - nanotechnologie - waarschijnlijkheidsmodellen

    Engineered nanoparticles (ENPs) are used everywhere and have large technological and economic potential. Like all novel materials, however, ENPs have no history of safe use. Insight into risks of nanotechnology and the use of nanoparticles is an essential condition for the societal acceptance and safe use of nanotechnology.

    Risk assessment of ENPs has been hampered by lack of knowledge about ENPs, their environmental fate, toxicity, testing considerations, characterisation of nanoparticles and human and environmental exposures and routes. This lack of knowledge results in uncertainty in the risk assessment. Moreover, due to the novelty of nanotechnology, risk assessors are often confronted with small samples of data on which to perform a risk assessment. Dealing with this uncertainty and the small sample sizes are main challenges when it comes to risk assessment of ENPs. The objectives of this thesis are (i) to perform a transparent risk assessment of nanoparticles in the face of large uncertainty in such a way that it can guide future research to reduce the uncertainty and (ii) to evaluate empirical and parametric methods to estimate the risk probability in the case of small sample sizes.

    To address the first objective, I adapted an existing Integrated Probabilistic Risk Assessment (IPRA) method for use in nanoparticle risk assessment. In IPRA, statistical distributions and bootstrap methods are used to quantify uncertainty and variability in the risk assessment in a two-dimensional Monte Carlo algorithm. This method was applied in a human health (nanosilica in food) and an environmental (nanoTiO2 in water) risk context. I showed that IPRA leads to a more transparent risk assessment and can direct further environmental and toxicological research to the areas in which it is most needed.

    For the second objective, I addressed the problem of small sample size of the critical effect concentration (CEC) in the estimation of R = P(ExpC > CEC), where ExpC is the exposure concentration. First I assumed normality and investigated various parametric and non-parametric estimators. I found that, compared to the non-parametric estimators, the parametric estimators enable us to better estimate and bound the risk when sample sizes and/or small risks are small. Moreover, the Bayesian estimator outperformed the maximum likelihood estimators in terms of coverage and interval lengths. Second, I relaxed the normality assumption for the tails of the exposure and effect distributions. I developed a mixture model to estimate the risk, R = P(ExpC > CEC), with the assumption of a normal distribution for the bulk data and generalised Pareto distributions for the tails. A sensitivity analysis showed significant influence of the tail heaviness on the risk probability, R, especially for low risks.

    In conclusion, to really be able to focus the research into the risks of ENPs to the most needed areas, probabilistic methods as used and developed in this thesis need to be implemented on a larger scale. With these methods, it is possible to identify the greatest sources of uncertainty. Based on such identification, research can be focused on those areas that need it most, thereby making large leaps in reducing the uncertainty that is currently hampering risk assessment of ENPs.

    Consumer segmentation based on taste preference of tomatoes : methodological approach
    Snoek, H.M. ; Sijtsema, S.J. ; Labrie, C.W. ; Braak, C.J.F. ter - \ 2015
    - 1 p.
    Dispersal versus environmental filtering in a dynamic system: drivers of vegetation patterns and diversity along stream riparian gradients
    Fraaije, R.G.A. ; Braak, C.J.F. ter; Verduyn, B. ; Verhoeven, Jos T.A. ; Soons, M.B. - \ 2015
    Wageningen UR
    community assembly - determinants of plant commiunity diversity and structure - directed dispersal - hydrological gradients - lowland streams - neutral versus niche - plant diversity - riparian vegetation - riparian zone - wetland restoration
    1. Both environmental filtering and dispersal filtering are known to influence plant species distribution patterns and biodiversity. Particularly in dynamic habitats, however, it remains unclear whether environmental filtering (stimulated by stressful conditions) or dispersal filtering (during re-colonization events) dominates in community assembly, or how they interact. Such a fundamental understanding of community assembly is critical to the design of biodiversity conservation and restoration strategies. 2. Stream riparian zones are species-rich dynamic habitats. They are characterized by steep hydrological gradients likely to promote environmental filtering, and by spatiotemporal variation in the arrival of propagules likely to promote dispersal filtering. We quantified the contributions of both filters by monitoring natural seed arrival (dispersal filter) and experimentally assessing germination, seedling survival and growth of 17 riparian plant species (environmental filter) along riparian gradients of three lowland streams that were excavated to bare substrate for restoration. Subsequently, we related spatial patterns in each process to species distribution and diversity patterns after 1 and 2 years of succession. 3. Patterns in initial seed arrival were very clearly reflected in species distribution patterns in the developing vegetation and were more significant than environmental filtering. However, environmental filtering intensified towards the wet end of the riparian gradient, particularly through effects of flooding on survival and growth, which strongly affected community diversity and generated a gradient in the vegetation. Strikingly, patterns in seed arrival foreshadowed the gradient that developed in the vegetation; seeds of species with adult optima at wetter conditions dominated seed arrival at low elevations along the riparian gradient while seeds of species with drier optima arrived higher up. Despite previous assertions suggesting a dominance of environmental filtering, our results demonstrate that nonrandom dispersal may be an important driver of early successional riparian vegetation zonation and biodiversity patterns as well. 4. Synthesis: Our results demonstrate (and quantify) the strong roles of both environmental and dispersal filtering in determining plant community assemblies in early successional dynamic habitats. Furthermore, we demonstrate that dispersal filtering can already initiate vegetation gradients, a mechanism that may have been overlooked along many environmental gradients where interspecific interactions are (temporarily) reduced.
    Early plant recruitment stages set the template for the development of vegetation patterns along a hydrological gradient
    Fraaije, R.G.A. ; Braak, C.J.F. ter; Verduyn, B. ; Breeman, L.B.S. ; Verhoeven, J.T.A. ; Soons, M.B. - \ 2015
    Wageningen UR
    biodiversity - colonization - environmental filtering - lowland streams - niche segregation - plant community assembly - riparian zones - wetland restoration
    1. Recruitment processes are critical components of a plant's life cycle. However, in comparison with later stages in the plant life cycle (e.g. competition among adults), relatively little is known about their contribution to the regulation of plant species distribution. Particularly little is known about the individual contributions of the three main recruitment processes—germination, seedling survival, and seedling growth—to community assembly, while quantitative information on these contributions is essential for a more mechanistic understanding of the regulation of plant species distribution and biodiversity. 2. Riparian zones along streams provide a globally-relevant case study for evaluating the importance of the different stages of plant recruitment. The natural hydrological gradients of stream riparian zones are currently being restored after a period of worldwide habitat degradation. To identify how recruitment contributes to vegetation patterns and biodiversity in riparian zones, we carried out field experiments at restored lowland streams. We quantified the germination of introduced seeds, and survival and growth of introduced seedlings of 17 riparian plant species across a gradient from the stream channel to upland. 3. The hydrological gradient of riparian zones acted as a strong environmental filter on all three recruitment processes, through imposing an abiotic limitation (excess water) at low elevations and a resource limitation (water shortage) at higher elevations. Other variables, such as soil organic matter content and nutrient availability, only affected recruitment marginally. 4. Species-specific patterns of environmental filtering initiated niche segregation along the riparian gradient during all three recruitment processes, but particularly during germination and seedling growth. These recruitment niches appeared strongly related to indicator values for adult distribution optima, suggesting that at least some riparian plant species may have evolutionary adaptations that promote recruitment under favourable hydrological conditions for adult growth and reproduction. 5. Our results suggest that strong environmental filtering during germination and seedling growth plays an important role in determining later adult distributions, by forming the spatial template on which all subsequent processes operate. In addition to well-known mechanisms, such as competitive exclusion at the adult stage, environmental filtering during early recruitment stages already strongly affect plant distribution and diversity.
    Early plant recruitment stages set the template for the development of vegetation patterns along a hydrological gradient
    Fraaije, Rob G.A. ; Braak, C.J.F. ter; Verduyn, Betty ; Breeman, Leonieke B.S. ; Verhoeven, Jos T.A. ; Soons, Merel B. - \ 2015
    Functional Ecology 29 (2015)7. - ISSN 0269-8463 - p. 971 - 980.
    Biodiversity - Colonization - Environmental filtering - Lowland streams - Niche segregation - Plant community assembly - Riparian zones - Wetland restoration

    Recruitment processes are critical components of a plant's life cycle. However, in comparison with later stages in the plant life cycle (e.g. competition among adults), relatively little is known about their contribution to the regulation of plant species distribution. Particularly, little is known about the individual contributions of the three main recruitment processes - germination, seedling survival and seedling growth - to community assembly, while quantitative information on these contributions is essential for a more mechanistic understanding of the regulation of plant species distribution and biodiversity. Riparian zones along streams provide a globally-relevant case study for evaluating the importance of the different stages of plant recruitment. The natural hydrological gradients of stream riparian zones are currently being restored after a period of world-wide habitat degradation. To identify how recruitment contributes to vegetation patterns and biodiversity in riparian zones, we carried out field experiments at restored lowland streams. We quantified the germination of introduced seeds, and survival and growth of introduced seedlings of 17 riparian plant species across a gradient from the stream channel to upland. The hydrological gradient of riparian zones acted as a strong environmental filter on all three recruitment processes, through imposing an abiotic limitation (excess water) at low elevations and a resource limitation (water shortage) at higher elevations. Other variables, such as soil organic matter content and nutrient availability, only affected recruitment marginally. Species-specific patterns of environmental filtering initiated niche segregation along the riparian gradient during all three recruitment processes, but particularly during germination and seedling growth. These recruitment niches appeared strongly related to indicator values for adult distribution optima, suggesting that at least some riparian plant species may have evolutionary adaptations that promote recruitment under favourable hydrological conditions for adult growth and reproduction. Our results suggest that strong environmental filtering during germination and seedling growth plays an important role in determining later adult distributions, by forming the spatial template on which all subsequent processes operate. In addition to well-known mechanisms, such as competitive exclusion at the adult stage, environmental filtering during early recruitment stages already strongly affect plant distribution and diversity.

    Dispersal versus environmental filtering in a dynamic system : Drivers of vegetation patterns and diversity along stream riparian gradients
    Fraaije, R.G.A. ; Braak, C.J.F. ter; Verduyn, Betty ; Verhoeven, J.T.A. ; Soons, M.B. - \ 2015
    Journal of Ecology 103 (2015)6. - ISSN 0022-0477 - p. 1634 - 1646.
    Community assembly - Determinants of plant community diversity and structure - Directed dispersal - Hydrological gradients - Lowland streams - Neutral versus niche - Plant diversity - Riparian vegetation - Riparian zone - Wetland restoration

    Both environmental filtering and dispersal filtering are known to influence plant species distribution patterns and biodiversity. Particularly in dynamic habitats, however, it remains unclear whether environmental filtering (stimulated by stressful conditions) or dispersal filtering (during recolonization events) dominates in community assembly, or how they interact. Such a fundamental understanding of community assembly is critical to the design of biodiversity conservation and restoration strategies. Stream riparian zones are species-rich dynamic habitats. They are characterized by steep hydrological gradients likely to promote environmental filtering, and by spatiotemporal variation in the arrival of propagules likely to promote dispersal filtering. We quantified the contributions of both filters by monitoring natural seed arrival (dispersal filter) and experimentally assessing germination, seedling survival and growth of 17 riparian plant species (environmental filter) along riparian gradients of three lowland streams that were excavated to bare substrate for restoration. Subsequently, we related spatial patterns in each process to species distribution and diversity patterns after 1 and 2 years of succession. Patterns in initial seed arrival were very clearly reflected in species distribution patterns in the developing vegetation and were more significant than environmental filtering. However, environmental filtering intensified towards the wet end of the riparian gradient, particularly through effects of flooding on survival and growth, which strongly affected community diversity and generated a gradient in the vegetation. Strikingly, patterns in seed arrival foreshadowed the gradient that developed in the vegetation; seeds of species with adult optima at wetter conditions dominated seed arrival at low elevations along the riparian gradient, while seeds of species with drier optima arrived higher up. Despite previous assertions suggesting a dominance of environmental filtering, our results demonstrate that non-random dispersal may be an important driver of early successional riparian vegetation zonation and biodiversity patterns as well. Synthesis. Our results demonstrate (and quantify) the strong roles of both environmental and dispersal filtering in determining plant community assemblies in early successional dynamic habitats. Furthermore, we demonstrate that dispersal filtering can already initiate vegetation gradients, a mechanism that may have been overlooked along many environmental gradients where interspecific interactions are (temporarily) reduced. Our results demonstrate and quantify the strong roles of both environmental and dispersal filtering in determining plant community assemblies in early successional dynamic habitats. Furthermore, we demonstrate that dispersal filtering can already initiate vegetation gradients, a mechanism that may have been overlooked along many environmental gradients where interspecific interactions are (temporarily) reduced.

    Inventarisatie potentiële locaties Tijdelijke Natuur in Nederland
    Gies, T.J.A. ; Agricola, H.J. ; Beun, N.J. - \ 2015
    Utrecht : InnovatieNetwerk (Rapport / InnovatieNetwerk nr. 15.2.335) - ISBN 9789050595254
    natuurbeheer - braak - verlaten grond - bestemmingsplannen - inventarisaties - landgebruiksplanning - natuurontwikkeling - natuurgebieden - nature management - fallow - abandoned land - zoning plans - inventories - land use planning - nature development - natural areas
    InnovatieNetwerk heeft in samenwerking met partijen uit de samenleving het concept ‘Tijdelijke Natuur’ ontwikkeld. Dit heeft ertoe geleid dat tot op heden dertig grondeigenaren op 2.000 ha tijdelijke natuur hebben laten ontstaan. Het concept houdt in dat op gronden die wachten op realisatie van bestemmingen zoals bedrijvigheid of wonen, natuur voor een beperkt aantal jaren een kans krijgt zich te ontwikkelen. Dit levert winst op voor mens én natuur. Het doel van het project is om inzichtelijk te maken wat de aard en omvang zijn van de locaties die potentieel geschikt zijn voor het concept ‘Tijdelijke Natuur’ in Nederland. Deze inventarisatie geeft een zo goed mogelijk landsdekkend beeld (gespecificeerd naar provincies en gemeenten) van potentiële locaties Tijdelijke Natuur.
    Parametric estimation of P(X >Y) for normal distributions in the context of probabilistic environmental risk assessment.
    Jacobs, R. ; Bekker, A.A. ; Voet, H. van der; Braak, C.J.F. ter - \ 2015
    PeerJ 3 (2015). - ISSN 2167-8359
    species sensitivity distributions - stress-strength model - confidence-intervals - reliability - less - inference
    Estimating the risk, P(X > Y), in probabilistic environmental risk assessment of nanoparticles is a problem when confronted by potentially small risks and small sample sizes of the exposure concentration X and/or the effect concentration Y. This is illustrated in the motivating case study of aquatic risk assessment of nano-Ag. A non-parametric estimator based on data alone is not sufficient as it is limited by sample size. In this paper, we investigate the maximum gain possible when making strong parametric assumptions as opposed to making no parametric assumptions at all. We compare maximum likelihood and Bayesian estimators with the non-parametric estimator and study the influence of sample size and risk on the (interval) estimators via simulation. We found that the parametric estimators enable us to estimate and bound the risk for smaller sample sizes and small risks. Also, the Bayesian estimator outperforms the maximum likelihood estimators in terms of coverage and interval lengths and is, therefore, preferred in our motivating case study.
    Integrated probabilistic risk assessment for nanoparticles: the case of nanosilica in food
    Jacobs, R. ; Voet, H. van der; Braak, C.J.F. ter - \ 2015
    Journal of Nanoparticle Research : an Interdisciplinary Forum for Nanoscale Science and Technology 17 (2015). - ISSN 1388-0764 - 14 p.
    Insight into risks of nanotechnology and the use of nanoparticles is an essential condition for the social acceptance and safe use of nanotechnology. One of the problems with which the risk assessment of nanoparticles is faced is the lack of data, resulting in uncertainty in the risk assessment. We attempt to quantify some of this uncertainty by expanding a previous deterministic study on nanosilica (5–200 nm) in food into a fully integrated probabilistic risk assessment. We use the integrated probabilistic risk assessment method in which statistical distributions and bootstrap methods are used to quantify uncertainty and variability in the risk assessment. Due to the large amount of uncertainty present, this probabilistic method, which separates variability from uncertainty, contributed to a better understandable risk assessment. We found that quantifying the uncertainties did not increase the perceived risk relative to the outcome of the deterministic study. We pinpointed particular aspects of the hazard characterization that contributed most to the total uncertainty in the risk assessment, suggesting that further research would benefit most from obtaining more reliable data on those aspects.
    Bangladesh - The Netherlands : 50 years of water cooperation
    Braak, B. ter; Staveren, M.F. van - \ 2015
    Netherlands Water Partnership (NWP) - 23
    hoogwaterbeheersing - waterverontreiniging - verziltingsbestrijding - internationale samenwerking - nederland - bangladesh - flood control - water pollution - salinity control - international cooperation - netherlands
    Cooperation between Bangladesh and the Netherlands in the water sector goes back over half a century. We have worked together on flood management, drainage, river basin management and coastal zone management – creating safe polders and making land available for the landless. And together with NGOs and the private sector we have improved access to safe water and sanitation for millions of people in Bangladesh. Bangladesh has an impressive track record for growth and development, and aspires to be a middle-income country within the next ten years. So over the past few years our relationship has gradually evolved from a single focus on development cooperation to a stronger emphasis on trade and investment, creating opportunities for Dutch and Bangladeshi companies to do business.
    Tijdelijk gebruik als antwoord op braakligging
    Kruit, J. ; Jagt, P.D. van der - \ 2015
    Wageningen : Wageningen UR, Wetenschapswinkel (Rapport / Wageningen UR, Wetenschapswinkel 310) - ISBN 9789461738813 - 48
    stedelijke terreinen - braak - tijdigheid - buurtactie - stedelijke samenleving - urban sites - fallow - timeliness - community action - urban society
    Een tijdelijke vrije ruimte midden in de wijk is een schatkamer voor een buurt. Met dit beeld voor ogen gingen actieve buurtbewoners en ouders van een aangrenzende school in 2012 aan de slag met plannen en ideeën om iets te doen met een tijdelijk braakliggend terrein. Doel van dit rapport: achterhalen hoe de buurt het tijdelijk gebruik heeft ervaren, met als achterliggend idee anderen onderbouwd te kunnen ondersteunen ook zoiets te doen. Een aanvullende vraag is wat tijdelijk gebruik nu interessant maakt en voor wie.
    Macroinvertebrate survival during cessation of flow and streambed drying in a lowland stream
    Verdonschot, R.C.M. ; Oosten-Siedlecka, A.M. van; Braak, C.J.F. ter; Verdonschot, P.F.M. - \ 2015
    Freshwater Biology 60 (2015)2. - ISSN 0046-5070 - p. 282 - 296.
    invertebrate communities - prairie stream - desert stream - drought - intermittent - assemblages - responses - rivers - recolonization - resilience
    1.The number of perennial low-order lowland streams likely to experience intermittent flow is predicted to increase in north-western Europe. To understand the effects of such a change on macroinvertebrates, a field experiment was carried out in a currently perennial sandy lowland stream. 2.Using a before–after control–impact design, the flow regime was manipulated to yield two distinct treatments: stagnation (although with little water loss) and drying of the stream (although artificial remnant pools remained in the bed). There was also an unmanipulated control reach. The two treatments were applied simultaneously in separate, consecutive reaches, resulting in 29 days of stagnation and 25 days of streambed drying with surface water only present in the remnant pools. Changes in macroinvertebrate richness, abundance and community composition were recorded, and we assessed whether these changes could be explained by ecological preferences for flow of the various taxa. 3.Stagnation resulted in only minor changes in community composition. A small number of rheophilic taxa disappeared, while taxa preferring standing waters complemented those already present, increasing total biodiversity. In remnant pools in the otherwise dry reach, richness and abundance peaked after they became isolated, indicating a concentration of invertebrates. A subsequent steep decline in richness coincided with hypoxia and increasing conductivity. Culex pipiens/torrentium colonised the pools and was then dominant. Only a small subset of the assemblage successfully used the dry streambed as a refuge. 4.The effect of a shift from perennial to intermittent flow evidently depends on the degree of habitat change. Environmental conditions after cessation of flow are crucial in determining lowland stream macroinvertebrate persistence during water drawdown.
    Analysing chemical-induced changes in macroinvertebrate communities in aquatic mesocosm experiments: a comparison of methods
    Szöcs, E. ; Brink, P.J. van den; Lagadic, L. ; Caquet, T. ; Roucaute, M. ; Auber, A. ; Bayona, Y. ; Liess, M. ; Ebke, P. ; Ippolito, A. ; Braak, C.J.F. ter; Brock, T.C.M. ; Schäfer, R.B. - \ 2015
    Ecotoxicology 24 (2015)4. - ISSN 0963-9292 - p. 760 - 769.
    fresh-water microcosms - fungicide carbendazim - pond mesocosms - responses - insecticide - models - impact - chlorpyrifos - zooplankton - conclusions
    Mesocosm experiments that study the ecological impact of chemicals are often analysed using the multivariate method ‘Principal Response Curves’ (PRCs). Recently, the extension of generalised linear models (GLMs) to multivariate data was introduced as a tool to analyse community data in ecology. Moreover, data aggregation techniques that can be analysed with univariate statistics have been proposed. The aim of this study was to compare their performance. We compiled macroinvertebrate abundance datasets of mesocosm experiments designed for studying the effect of various organic chemicals, mainly pesticides, and re-analysed them. GLMs for multivariate data and selected aggregated endpoints were compared to PRCs regarding their performance and potential to identify affected taxa. In addition, we analysed the inter-replicate variability encountered in the studies. Mesocosm experiments characterised by a higher taxa richness of the community and/or lower taxonomic resolution showed a greater inter-replicate variability, whereas variability decreased the more zero counts were encountered in the samples. GLMs for multivariate data performed equally well as PRCs regarding the community response. However, compared to first axis PRCs, GLMs provided a better indication of individual taxa responding to treatments, as separate models are fitted to each taxon. Data aggregation methods performed considerably poorer compared to PRCs. Multivariate community data, which are generated during mesocosm experiments, should be analysed using multivariate methods to reveal treatment-related community-level responses. GLMs for multivariate data are an alternative to the widely used PRCs
    Topics in constrained and unconstrained ordination
    Braak, C.J.F. ter; Smilauer, P. - \ 2015
    Plant Ecology 216 (2015)5. - ISSN 1385-0237 - p. 683 - 696.
    canonical correspondence-analysis - detrended correspondence-analysis - linear mixed models - putting things - environment relationships - gaussian ordination - redundancy analysis - zero inflation - response model - abundance data
    In this paper, we reflect on a number of aspects of ordination methods: how should absences be treated in ordination and how do model-based methods, including Gaussian ordination and methods using generalized linear models, relate to the usual least-squares (eigenvector) methods based on (log-) transformed data. We defend detrended correspondence analysis by theoretical arguments and by reanalyzing data that previously gave bad results. We show by examples that constrained ordination can yield more informative views on effects of interest compared to unconstrained ordination (where such effects can be invisible) and show how constrained axes can be interpreted. Constrained ordination uses an ANOVA/regression approach to enable the user to focus on particular aspects of species community data, in particular the effects of qualitative and quantitative environmental variables. We close with an analysis examining the interaction effects between two factors, and we demonstrate how principal response curves can help in their visualisation. Example data and Canoco 5 projects are provided as Supplementary Material.
    Corrigendum to "An automated system for the recognition of various specific rat behaviors"
    Dam, Elsbeth A. Van; Harst, Johanneke E. van der; Braak, Cajo J.F. ter; Tegelenbosch, Ruud A.J. ; Spruijt, Berry M. ; Noldus, Lucas P.J.J. - \ 2014
    Journal of Neuroscience Methods 221 (2014). - ISSN 0165-0270 - 1 p.
    Integrated probabilistic risk assessment: the case of nano-silica in food
    Jacobs, R. ; Voet, H. van der; Braak, C.J.F. ter - \ 2014
    The effect of fibers on coagulation of casein-based enteral nutrition in an artificial gastric digestion model
    Luttikhold, J. ; Norren, K. van; Minor, M. ; Buijs, N. ; Braak, C.C.M. van den; Ludwig, T. ; Abrahamse, E. ; Rijna, H. ; Leeuwen, P.A.M. - \ 2014
    Food & Function 5 (2014). - ISSN 2042-6496 - p. 1866 - 1871.
    critically-ill patients - thermodynamic incompatibility - intestinal-obstruction - in-vitro - motility - proteins - absorption - guidelines - mixtures - feedings
    A serious complication seen in critically ill patients is the solidification of enteral nutrition causing gastrointestinal obstruction. It has been suggested that enteral nutrition enriched with insoluble fibers may increase the risk of this complication. Therefore, we investigate the effect of soluble and insoluble dietary fibers on the coagulation of a casein-based enteral nutrition in an artificial gastric digestion model. A 100% casein-based enteral nutrition was enriched with increasing concentrations of soluble fibers (acacia fiber, oligofructose and inulin) and insoluble fibers (soy polysaccharide, resistant starch and alpha cellulose). After digestion in an artificial gastric model, the chyme was poured over sequentially placed sieves, separating the coagulate into size fractions of larger than 2 mm, between 1 and 2 mm, and between 0.25 and 1 mm. Of these fractions we measured wet weight, dry weight and protein content. A significant effect on the fraction larger than 2 mm was considered to be clinically relevant. Addition of high concentrations soy polysaccharide and resistant starch to a casein-based enteral nutrition, did not alter the wet weight, whereas dry weight and protein content of the coagulate was significantly reduced. When high concentrations of soy polysaccharide and resistant starch are added to a 100% casein-based enteral nutrition, the coagulate consist of more water and less proteins, which may lead to an increased protein digestion and absorption in a clinical setting. The suggestion that insoluble fibers increase the risk of gastrointestinal obstruction in critically ill patients is not supported by these data.
    Alternatieve methoden voor chemische bodemontsmetting voor de appelteelt op zandgrond
    Wenneker, M. ; Steeg, P.A.H. van der; Visser, J.H.M. ; Korthals, G.W. - \ 2014
    Randwijk : Praktijkonderzoek Plant en Omgeving, Bloembollen, Boomkwekerij & Fruitteelt - 21
    malus domestica - appels - bodemmoeheid - plantenparasitaire nematoden - pratylenchus penetrans - grondsterilisatie - biologische grondontsmetting - tagetes patula - biologische bestrijding - biofumigatie - ziektebestrijdende teeltmaatregelen - compost - grondverbeteraars - geïntegreerde plagenbestrijding - veldproeven - nederland - malus domestica - apples - soil sickness - plant parasitic nematodes - pratylenchus penetrans - soil sterilization - biological soil sterilization - tagetes patula - biological control - biofumigation - cultural control - composts - soil amendments - integrated pest management - field tests - netherlands
    Met name op zandgronden speelt de problematiek van herinplantziekte. Zonder grondontsmetting lijkt herinplant van fruitbomen niet rendabel. Een van de veroorzakers van herinplantziekte is het wortellesieaaltje (Pratylenchus penetrans). Op een appelperceel met een vrij hoge bodembesmetting van het wortellesieaaltje Pratylenchus penetrans (één van de veroorzakers van bodemmoeheid) zijn na het rooien van de bomen in het voor en najaar van 2007 zeven verschillende behandelingen toegepast: Tagetes (‘Afrikaantje’), Tagetes + biologische grondontsmetting, Japanse haver (Avena strigosa) + late biologische grondontsmetting, biofumigatie met Sarepta mosterd, compost, zwarte braak en natte grondontsmetting (controle behandelingen). De methode met Afrikaantjes en die met Afrikaantjes gecombineerd met Biologische grondontsmetting (BGO) bleken de populaties van Pratylenchus aanzienlijk te reduceren, bijna net zo goed als natte grondontsmetting. Afrikaantjes bestrijden de aaltjes en door de combinatie met BGO worden ook andere (bodemmoeheid veroorzakende) ziekteverwekkers bestreden. Compost en late BGO hadden een vergelijkbaar effect als onbehandelde grond. Na biofumigatie was de aaltjespopulatie toegenomen.
    Prediction uncertainty assessment of a systems biology model requires a sample of the full probability distribution of its parameters
    Mourik, S. van; Braak, C.J.F. ter; Stigter, J.D. ; Molenaar, J. - \ 2014
    PeerJ 2 (2014). - ISSN 2167-8359 - 17 p.
    identifiability analysis - regulatory networks - experimental-design - profile likelihood - sloppy models - oscillations - proteins - cyclin - kinase - cdc2
    Multi-parameter models in systems biology are typically ‘sloppy’: some parameters or combinations of parameters may be hard to estimate from data, whereas others are not. One might expect that parameter uncertainty automatically leads to uncertain predictions, but this is not the case. We illustrate this by showing that the prediction uncertainty of each of six sloppy models varies enormously among different predictions. Statistical approximations of parameter uncertainty may lead to dramatic errors in prediction uncertainty estimation. We argue that prediction uncertainty assessment must therefore be performed on a per-prediction basis using a full computational uncertainty analysis. In practice this is feasible by providing a model with a sample or ensemble representing the distribution of its parameters. Within a Bayesian framework, such a sample may be generated by a Markov Chain Monte Carlo (MCMC) algorithm that infers the parameter distribution based on experimental data. Matlab code for generating the sample (with the Differential Evolution Markov Chain sampler) and the subsequent uncertainty analysis using such a sample, is supplied as Supplemental Information.
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