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.
    Image-based particle filtering for navigation in a semi-structured agricultural environment.
    Hiremath, S. ; Evert, F.K. van; Braak, C.J.F. ter; Stein, A. ; Heijden, G.W.A.M. van der - \ 2014
    Biosystems Engineering 121 (2014). - ISSN 1537-5110 - p. 85 - 95.
    automatic guidance - weed-control - robot - vision - segmentation - localization - vehicles - system - detect
    Autonomous navigation of field robots in an agricultural environment is a difficult task due to the inherent uncertainty in the environment. The drawback of existing systems is the lack of robustness to these uncertainties. In this study we propose a vision-based navigation method to address these problems. The focus is on navigation through a maize field in an outdoor environment where the robot has to navigate through a corridor formed by two plant rows, detect the end of the rows, navigate the headland and turn into another corridor under natural conditions. The method is based on a Particle Filter (PF) using a novel measurement model, where we construct a model image from the particle and compare it directly with the measurement image after elementary processing, such as down-sampling, excessive-green filtering and thresholding. The new measurement model does not extract features from the image and thus does not suffer from errors associated with the feature extraction process. We show how PF can be used for robust navigation of a robot in a semi-structured agricultural environment such as maize fields with inherent uncertainty. We demonstrate the robustness of the algorithm through experiments in several maize fields with different row patterns, varying plant sizes and diverse lighting conditions. To date we have logged over 5 km of successful test runs in which the robot navigates through the corridor without touching the plant stems, accurately detects the end of the rows and traverses the headland. (C) 2014 IAgrE. Published by Elsevier Ltd. All rights reserved.
    A Unimodal Species Response Model Relating Traits to Environment with Application to Phytoplankton Communities.
    Jamil, T. ; Kruk, C. ; Braak, C.J.F. ter - \ 2014
    PLoS ONE 9 (2014)5. - ISSN 1932-6203 - 14 p.
    bayesian variable selection - climate-change - ecology - lake - variability - strategies - diversity - habitat - classification - regression
    In this paper we attempt to explain observed niche differences among species (i.e. differences in their distribution along environmental gradients) by differences in trait values (e.g. volume) in phytoplankton communities. For this, we propose the trait-modulated Gaussian logistic model in which the niche parameters (optimum, tolerance and maximum) are made linearly dependent on species traits. The model is fitted to data in the Bayesian framework using OpenBUGS (Bayesian inference Using Gibbs Sampling) to identify according to which environmental variables there is niche differentiation among species and traits. We illustrate the method with phytoplankton community data of 203 lakes located within four climate zones and associated measurements on 11 environmental variables and six morphological species traits of 60 species. Temperature and chlorophyll-a (with opposite signs) described well the niche structure of all species. Results showed that about 25% of the variance in the niche centres with respect to chlorophyll-a were accounted for by traits, whereas niche width and maximum could not be predicted by traits. Volume, mucilage, flagella and siliceous exoskeleton are found to be the most important traits to explain the niche centres. Species were clustered in two groups with different niches structures, group 1 high temperature-low chlorophyll-a species and group 2 low temperature-high chlorophyll-a species. Compared to group 2, species in group 1 had larger volume but lower surface area, had more often flagella but neither mucilage nor siliceous exoskeleton. These results might help in understanding the effect of environmental changes on phytoplankton community. The proposed method, therefore, can also apply to other aquatic or terrestrial communities for which individual traits and environmental conditioning factors are available.
    History of canonical correspondence analysis
    Braak, C.J.F. ter - \ 2014
    In: Visualization and verbalization of Data / Blasius, J., Greenacre, M., Londen : Chapman and Hall/CRC (Chapman & Hall/CRC Computer Science & Data Analysis ) - ISBN 9781466589803 - p. 61 - 75.
    Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection
    Fuentes Enriquez de Salamanca, S. ; Nood, E. van; Tims, S. ; Heikamp-de Jong, I. ; Braak, C.J.F. ter; Keller, J.J. ; Zoetendal, E.G. ; Vos, W.M. de - \ 2014
    ISME Journal 8 (2014). - ISSN 1751-7362 - p. 1621 - 1633.
    intestinal microbiota - gut microbiota - bacterial - disease - bacteriotherapy - enterotypes - diversity - diarrhea - therapy - article
    Recurrent Clostridium difficile infection (CDI) can be effectively treated by infusion of a healthy donor faeces suspension. However, it is unclear what factors determine treatment efficacy. By using a phylogenetic microarray platform, we assessed composition, diversity and dynamics of faecal microbiota before, after and during follow-up of the transplantation from a healthy donor to different patients, to elucidate the mechanism of action of faecal infusion. Global composition and network analysis of the microbiota was performed in faecal samples from nine patients with recurrent CDI. Analyses were performed before and after duodenal donor faeces infusion, and during a follow-up of 10 weeks. The microbiota data were compared with that of the healthy donors. All patients successfully recovered. Their intestinal microbiota changed from a low-diversity diseased state, dominated by Proteobacteria and Bacilli, to a more diverse ecosystem resembling that of healthy donors, dominated by Bacteroidetes and Clostridium groups, including butyrate-producing bacteria. We identified specific multi-species networks and signature microbial groups that were either depleted or restored as a result of the treatment. The changes persisted over time. Comprehensive and deep analyses of the microbiota of patients before and after treatment exposed a therapeutic reset from a diseased state towards a healthy profile. The identification of microbial groups that constitute a niche for C. difficile overgrowth, as well as those driving the reinstallation of a healthy intestinal microbiota, could contribute to the development of biomarkers predicting recurrence and treatment outcome, identifying an optimal microbiota composition that could lead to targeted treatment strategies.
    Sclerotium rolfsii dynamics in soil as affected by crop sequences
    Leoni, C. ; Braak, C.J.F. ter; Gilsanz, J.C. ; Dogliotti, S. ; Rossing, W.A.H. ; Bruggen, A.H.C. van - \ 2014
    Applied Soil Ecology 75 (2014). - ISSN 0929-1393 - p. 95 - 105.
    southern blight - vegetable farms - soilborne pathogens - population-dynamics - organic amendments - north-carolina - management - rotations - survival - residues
    Crop rotation has been used for the management of soilborne diseases for centuries, but has not often been planned based on scientific knowledge. Our objective was to generate information on Sclerotium rolfsii dynamics under different crop or intercrop activities, and design and test a research approach where simple experiments and the use of models are combined to explore crop sequences that minimize Southern blight incidence. The effect of seventeen green manure (GM) amendments on sclerotia dynamics was analyzed in greenhouse and field plot experiments during two years. The relative densities of viable sclerotia 90 days after winter GM (WGM) incorporation were generally lower than after summer GM (SGM) incorporation, with average recovery values of 60% and 61% for WGM in the field, 66% and 43% for WGM in the greenhouse, and 162% to 91% for SGM in the greenhouse, in 2009 and 2010, respectively. Sclerotia survival on day d after GM amendment was described by the model Sf = Si × exp(-b × d), relating initial (Si) and final (Sf) sclerotia densities. Relative decay rates of the sclerotia (b) in SGM amended soil were largest for alfalfa (0.0077 ± 0.0031 day-1) and sudangrass (0.0072 ± 0.0030 day-1). In WGM amended soil, the largest b values were for oat (0.0096 ± 0.0024 day-1), wheat (0.0090 ± 0.0024 day-1) and alfalfa (0.0087 ± 0.0023 day-1). The effect of three cropping sequences (sweet pepper–fallow, sweet pepper–black oat and sweet pepper–onion) on sclerotia dynamics was analyzed in microplot experiments, and the data were used to calibrate the model Pf = Pi/(a + ßPi), relating initial (Pi) and final (Pf) sclerotia densities. Median values for the relative rate of population increase at low Pi (1/a, dimension less) and the asymptote (1/ß, number of viable sclerotia in 100 g of dry soil) were 8.22 and 4.17 for black oat (BO), 1.13 and 8.64 for onion (O), and 6.26 and 17.93 for sweet pepper (SwP). By concatenating the two models, sclerotia population dynamics under several crop sequences were simulated. At steady state, the sequence SwP–O–Fallow–BO resulted in the lowest long-term sclerotia density (7.09 sclerotia/100 g soil), and SwP–Fallow in the highest (17.89 sclerotia/100 g soil). The developed methodology facilitates the selection of a limited number of rotation options to be tested in farmers’ fields.
    Laser range finder model for autonomous navigation of a robot in a maize field using a particle filter
    Hiremath, S.A. ; Heijden, G.W.A.M. van der; Evert, F.K. van; Stein, A. ; Braak, C.J.F. ter - \ 2014
    Computers and Electronics in Agriculture 100 (2014). - ISSN 0168-1699 - p. 41 - 50.
    guidance - systems
    Autonomous navigation of robots in an agricultural environment is a difficult task due to the inherent uncertainty in the environment. Many existing agricultural robots use computer vision and other sensors to supplement Global Positioning System (GPS) data when navigating. Vision based methods are sensitive to ambient lighting conditions. This is a major disadvantage in an outdoor environment. The current study presents a novel probabilistic sensor model for a 2D range finder (LIDAR) from first principles. Using this sensor model, a particle filter based navigation algorithm (PF) for autonomous navigation in a maize field was developed. The algorithm was tested in various field conditions with varying plant sizes, different row patterns and at several scanning frequencies. Results showed that the Root Mean Squared Error of the robot heading and lateral deviation were equal to 2.4 degrees and 0.04 m, respectively. It was concluded that the performance of the proposed navigation method is robust in a semi-structured agricultural environment.
    Combining the fourth-corner and the RLQ methods for assessing trait responses to environmental variation
    Dray, S. ; Choler, P. ; Dolédec, S. ; Peres-Neto, P.R. ; Thuiller, W. ; Pavoine, S. ; Braak, C.J.F. ter - \ 2014
    Ecology 95 (2014). - ISSN 0012-9658 - p. 14 - 21.
    co-inertia analysis - species traits - community ecology - plant - variables - linking
    Assessing trait responses to environmental gradients requires the simultaneous analysis of the information contained in three tables: L (species distribution across samples), R (environmental characteristics of samples) and Q (species traits). Among the available methods, the so-called fourth-corner and RLQ methods are two appealing alternatives that provide a direct way to test and estimate trait-environment relationships. Both methods are based on the analysis of the fourth-corner matrix which crosses traits and environmental variables weighted by species abundances. However, they greatly differ in their outputs: RLQ is a multivariate technique that provides ordination scores to summarize the joint structure among the three tables, whereas the fourth-corner method mainly tests for individual trait-environment relationships (i.e. one trait and one environmental variable at a time). Here, we illustrate how the complementarity between these two methods can be exploited to promote new ecological knowledge and to improve the study of trait-environment relationships. After a short description of each method, we apply them to real ecological data to present their different outputs and provide hints about the gain resulting from their combined use. Read More: http://www.esajournals.org/doi/abs/10.1890/13-0196.1
    Predicting changes in ecosystem functioning from shifts in plant traits
    Ozinga, W.A. ; Schaminee, J.H.J. ; Hennekens, S.M. ; Prinzing, A. ; Braak, C.J.F. ter; Groenendael, J.M. van - \ 2013
    NWO newsletter december (2013). - p. 24 - 25.
    Biologische grondontsmetting met Herbie (‘Bodemresetten’) als alternatief voor stomen 2011-2012
    Ludeking, D.J.W. ; Termorshuizen, A. ; Wubben, J. ; Wurff, A.W.G. van der; Streminska, M.A. ; Helm, F.P.M. van der - \ 2013
    Bleiswijk : Wageningen UR Glastuinbouw (Rapport / Wageningen UR Glastuinbouw 1272) - 120
    biologische grondontsmetting - bodemtemperatuur - stimulatie - alternatieve methoden - snijbloemen - chrysanthemum - landbouwkundig onderzoek - effecten - biological soil sterilization - soil temperature - stimulation - alternative methods - cut flowers - chrysanthemum - agricultural research - effects
    In een meerjarig onderzoek gefinancierd door het Productschap Tuinbouw en het Ministerie van Economische zaken in het kader van het programma Kas als Energiebron, hebben Wageningen UR Glastuinbouw en BLGG gekeken naar ‘Bodemresetten met Herbie’ als alternatief voor stomen. Gebleken is dat een hoge bodemtemperatuur het proces stimuleert. Zonder anaerobe omstandigheden is er geen effect. Er is positief (dus bestrijdend) effect gevonden op: Verticillium dahliae , wortelknobbel aaltjes, S clerotinia sclerotiorum, wortelduizendpoot, tripslarven, slakken en ook andere bodemorganismen zoals bodemmijten en springstaarten. Er kon geen effect van Bodemresetten aangetoond worden op verhoogde weerbaarheid tegen Pythium . Het proces kan worden gemonitord aan de hand van gasmetingen van O 2 en H 2 S. In een uitgedroogde grond en een bodem die lang braak gelegen heeft verloopt het proces niet goed. De hoeveelheid broeikasgas die vrijkomt bij Bodemresetten wordt als verwaarloosbaar ingeschat in vergelijking met stomen. In een gangbare chrysantenteelt is Bodemresetten zonder extra kosten ten opzichte van stomen toe te passen als dit maximaal twee weken duurt en uitgevoerd wordt rond periode 5 zodat het opbrengstverlies valt in periode 7-8.
    Crop rotation design in view of soilborne pathogen dynamics : a methodological approach illustrated with Sclerotium rolfsii and Fusarium oxysporum f.sp. cepae
    Leoni, C. - \ 2013
    Wageningen University. Promotor(en): Ariena van Bruggen; Cajo ter Braak, co-promotor(en): Walter Rossing. - Wageningen : Wageningen University - ISBN 9789461738028 - 173
    gewassen - rotaties - bodempathogenen - bodemschimmels - plantenziekteverwekkende schimmels - athelia rolfsii - fusarium oxysporum f.sp. cepae - populatiedynamica - modellen - crops - rotations - soilborne pathogens - soil fungi - plant pathogenic fungi - athelia rolfsii - fusarium oxysporum f.sp. cepae - population dynamics - models

    Key words: Sclerotium rolfsii, Fusarium oxysporum f.sp. cepae, soilborne pathogens, crop rotation, population dynamic models, simulation.

    During the last decades, agriculture went through an intensification process associated with an increased use of fossil fuel energy, which despite temporarily increasing yields often resulted in decreased overall sustainability. Crop rotation is considered a cornerstone of sustainable farming systems. The design of crop rotations is a complex process where several objectives should be combined.Models can support the design of crop sequences and help to reveal synergies and trade-offs among objectives.Despite their importance, pathogen dynamics are rarely taken into account in cropping system models, not in the least because quantitative information from classical crop rotation experiments to calibrate and evaluate the models is resource demanding, and therefore scarce.

    The aim of this thesis was to develop a research approach where data (greenhouse pot experiments, microplot experiments, surveys on commercial farm fields) and model simulations were combined to identify crop sequences that minimize soilborne pathogen inoculum build up, and to subsequently include this information into models for designing sustainable crop rotations. The study was carried out based on two ecologically distinct and relevant pathogens in vegetable production systems: Sclerotium rolfsiiand Fusarium oxysporum f.sp.cepae(Foc).

    Two aspects of the dynamics of S. rolfsiisclerotia were studied: survival after soil incorporation of green manures, and population changes under three cropping sequences. In pot experiments, sclerotia survival in soil after incorporation of a winter green manure and its decomposition during summer was generally lower than after summer green manure incorporation and decomposition during winter. The incorporation of various legume crops (black beans, cowpea, hairy vetch and lupines) allowed multiplication of sclerotia while various grasses (sudangrass, foxtail millet, oats and wheat) as well as sunhemp resulted in a reduction of sclerotia in the soil. The build-up of sclerotia populations in the microplots was dependent on the crop sequence. Multiplication in sweet pepper was greater after black oat than after onion or fallow.

    The dynamics of Focwas studied at two different levels: multiplication in individual plants and population changes in different crop sequences.Foccolonized and multiplied in the root systems of 13 non-Allium plant species without inducing disease symptoms or growth retardation. These species thus constituted “reservoir-hosts” for Foc. The lowest Foclevels per g of dry weight of root were found in wheat, sunflower, cowpea and millet whereas the highest Foclevel was found in black bean.Fusariumpathogen dynamics was strongly affected by the cropping history in a particular field. Fusariumpopulations increased from transplant to harvest of onion when another onion crop had been planted in the same field during the previous winter, whereas Fusariumpopulations decreased when a winter green manure had been planted.

    Pathogen dynamics in crop sequences was simulated by concatenating two simple models, the first one describing the build-up of the pathogen within a crop, and the second one describing the dynamic of the pathogen during the intercrop period. The simulations described differences among crop sequences and alternating cycles of increasing and decreasing soil pathogen populations, as well as differences at equilibrium populations related to host frequency and cropping history.

    This thesis provides a methodological approach to the design of crop rotations and their effects on soil borne pathogen dynamics. The combination of data from controlled experiments, novel analytical tools (Bayesian analysis, modelling and simulation) and on-farm observations can lead to the identification of optimal crop rotations without extensive field experiments that require a lot of time, space and economic resources.

    Fusarium oxysporum f.sp. cepae dynamics: in-plant multiplication and crop sequence simulations
    Leoni, C. ; Vries, M. de; Braak, C.J.F. ter; Bruggen, A.H.C. van; Rossing, W.A.H. - \ 2013
    European Journal of Plant Pathology 137 (2013)3. - ISSN 0929-1873 - p. 545 - 561.
    f-sp melonis - ecological intensification - verticillium-dahliae - disease suppression - population-dynamics - organic amendments - soilborne diseases - farming systems - root diseases - wilt pathogen
    To reduce Fusarium Basal Rot caused by Fusarium oxysporum f.sp. cepae (Foc) through crop rotation, plant species should be selected based on Foc multiplication in their roots. Foc multiplication rates in 13 plant species were tested in a greenhouse. All plant species enabled Foc multiplication. The lowest Foc levels (cfu g-1 dry root) were found for wheat, sunflower, cowpea and millet, the highest for black bean. The highest Foc levels per plant were calculated for sudan grass. These data were used to calibrate the model Pf¿=¿Pi/(a¿+¿ßPi) relating final (Pf) and initial (Pi) Foc levels in the soil. The rate of population increase at low Pi (1/a) was highest for onion and black oat and smallest for sunflower. The pathogen carrying capacity (1/ß) was highest for black oat and black bean, and lowest for wheat, cowpea and foxtail millet. Foc soil population dynamics was simulated for crop sequences by concatenating Pi-Pf values, considering instantaneous or gradual pathogen release after harvest. Different soil Foc populations were attained after reaching steady states. Foc populations in the sequence onion –foxtail millet - wheat – cowpea were 67 % lower than in the sequence onion – sudan grass - black oat - black beans. In this work, by combining detailed greenhouse experiments with modelling, we were able to screen crops for their ability to increase Foc population and to explore potential crop sequences that may limit pathogen build-up
    Preservation of the gut by preoperative carbohydrate loading improves postoperative food intake
    Luttikhold, J. ; Oosting, A. ; Braak, C.C.M. van den; Norren, K. van; Rijna, H. ; Leeuwen, P.A.M. ; Bouritius, H. - \ 2013
    Clinical Nutrition 32 (2013)4. - ISSN 0261-5614 - p. 556 - 561.
    randomized controlled-trial - insulin-resistance - colorectal surgery - abdominal-surgery - barrier function - supplementation - citrulline - rats - 3-methylhistidine - nutrition
    Background & aims A carbohydrate (CHO) drink given preoperatively changes the fasted state into a fed state. The ESPEN guidelines for perioperative care include preoperative CHO loading and re-establishment of oral feeding as early as possible after surgery. An intestinal ischaemia reperfusion (IR) animal model was used to investigate whether preoperative CHO loading increases spontaneous postoperative food intake, intestinal barrier function and the catabolic response. Methods Male Wistar rats (n = 65) were subjected to 16 h fasting with ad libitum water and: A) sham laparotomy (Sham fasted, n = 24); B) intestinal ischaemia (IR fasted, n = 27); and C) intestinal ischaemia with preoperatively access to a CHO drink (IR CHO, n = 14). Spontaneous food intake, intestinal barrier function, insulin sensitivity, intestinal motility and plasma amino acids were measured after surgery. Results The IR CHO animals started eating significantly earlier and also ate significantly more than the IR fasted animals. Furthermore, preoperative CHO loading improved the intestinal barrier function, functional enterocyte metabolic mass measured by citrulline and reduced muscle protein catabolism, as indicated by normalization of the biomarker 3-methylhistidine. Conclusions Preoperative CHO loading improves food intake, preserves the GI function and reduces the catabolic response in an IR animal model. These findings suggest that preoperative CHO loading preserves the intestinal function in order to accelerate recovery and food intake. If this effect is caused by overcoming the fasted state or CHO loading remains unclear
    Biofumigatie kan belofte nog niet waarmaken
    Hoek, H. ; Visser, J.H.M. - \ 2013
    Akker magazine augustus (2013)7. - ISSN 1875-9688 - p. 24 - 25.
    plagenbestrijding - biologische bestrijding - nematodenbestrijding - biofumigatie - akkerbouw - landbouwkundig onderzoek - veldproeven - pest control - biological control - nematode control - biofumigation - arable farming - agricultural research - field tests
    Biofumigatiegewassen kunnen hun belofte als effectieve aaltjesbestrijder vooralsnog niet waarmaken. De inzet van Afrikaantjes tegen wortellesieaaltjes blijkt aanmerkelijk effectiever en ook zwarte braak scoort beter. Dit blijkt uit onderzoek van PPO naar gewassen die worden ingezet bij biofumigatie: de bestrijding van een schadelijk organisme door een damp of gas met natuurlijke stoffen.
    Probabilistic methods for robotics in agriculture
    Hiremath, S. - \ 2013
    Wageningen University. Promotor(en): A. Stein; Cajo ter Braak, co-promotor(en): Gerie van der Heijden. - S.l. : s.n. - ISBN 9789461736413 - 109
    automatisering - robots - landbouw - beeldanalyse - bayesiaanse theorie - navigatie - modelleren - automation - robots - agriculture - image analysis - bayesian theory - navigation - modeling

    Autonomous operation of robotic systems in an agricultural environment is a difficult task due to the inherent uncertainty in the environment. The robot is in a dynamic, non-deterministic and semi-structured environment with many sources of noise and a high degree of uncertainty. A novel approach dealing with uncertainty is by means of probabilistic methods. This PhD thesis studies the efficacy of probabilistic methods for autonomous robot applications in agriculture focusing on two agricultural tasks namely automatic detection of weed in a grassland and autonomous navigation of a robot in a Maize field. In automatic weed detection we look at the detection of a common weed called Rumex obtusifolius (Rumex). The suitability of image analysis for the task is examined, various existing methods are scrutinized and new probabilistic methods are proposed for robust detection of Rumex using a monocular camera in real-time. For autonomous navigation in a Maize field, probabilistic methods are developed for row following using a camera as well as a laser scanner. New sensor models are proposed to characterize the noisy measurements which are used in the navigation method for tracking the position of the robot and the plant rows. Through extensive field experiments we show that the proposed probabilistic methods are robust to varying operating conditions and conclude that probabilistic methods are essential for autonomous operation of robotic systems in an agricultural environment.

    Generalized linear mixed models can detect unimodal species-environment relationships
    Jamil, Tahira ; Braak, C.J.F. ter - \ 2013
    PeerJ 1 (2013). - ISSN 2167-8359 - 14 p.
    Niche theory predicts that species occurrence and abundance show non-linear, unimodal relationships with respect to environmental gradients. Unimodal models, such as the Gaussian (logistic) model, are however more difficult to fit to data than linear ones, particularly in a multi-species context in ordination, with trait modulated response and when species phylogeny and species traits must be taken into account. Adding squared terms to a linear model is a possibility but gives uninterpretable parameters. This paper explains why and when generalized linear mixed models, even without squared terms, can effectively analyse unimodal data and also presents a graphical tool and statistical test to test for unimodal response while fitting just the generalized linear mixed model. The R-code for this is supplied in Supplemental Information 1
    An automated system for the recognition of various specific rat behaviours
    Dam, E.A. van; Harst, J.E. van der; Braak, C.J.F. ter; Tegelenbosch, R.A.J. ; Spruijt, B.M. ; Noldus, L.P.J.J. - \ 2013
    Journal of Neuroscience Methods 218 (2013)2. - ISSN 0165-0270 - p. 214 - 224.
    induced circling behavior - anticipatory behavior - free exploration - sensitization - amphetamine - mice - environment - expression
    The automated measurement of rodent behaviour is crucial to advance research in neuroscience and pharmacology. Rats and mice are used as models for human diseases; their behaviour is studied to discover and develop new drugs for psychiatric and neurological disorders and to establish the effect of genetic variation on behavioural changes. Such behaviour is primarily labelled by humans. Manual annotation is labour intensive, error-prone and subject to individual interpretation. We present a system for automated behaviour recognition (ABR) that recognises the rat behaviours ‘drink’, ‘eat’, ‘sniff’, ‘groom’, ‘jump’, ‘rear unsupported’, ‘rear wall’, ‘rest’, ‘twitch’ and ‘walk’. The ABR system needs no on-site training; the only inputs needed are the sizes of the cage and the animal. This is a major advantage over other systems that need to be trained with hand-labelled data before they can be used in a new experimental setup. Furthermore, ABR uses an overhead camera view, which is more practical in lab situations and facilitates high-throughput testing more easily than a side-view setup. ABR has been validated by comparison with manual behavioural scoring by an expert. For this, animals were treated with two types of psychopharmaca: a stimulant drug (Amphetamine) and a sedative drug (Diazepam). The effects of drug treatment on certain behavioural categories were measured and compared for both analysis methods. Statistical analysis showed that ABR found similar behavioural effects as the human observer. We conclude that our ABR system represents a significant step forward in the automated observation of rodent behaviour.
    A 3D Analysis of Flight Behavior of Anopheles gambiae sensu stricto Malaria Mosquitoes in Response to Human Odor and Heat
    Spitzen, J. ; Spoor, C.W. ; Grieco, F. ; Braak, C.J.F. ter; Beeuwkes, J. ; Brugge, S.P. van; Kranenbarg, S. ; Noldus, L. ; Leeuwen, J.L. van; Takken, W. - \ 2013
    PLoS ONE 8 (2013)5. - ISSN 1932-6203
    female culex-quinquefasciatus - fine-scale structure - mm-x traps - carbon-dioxide - upwind flight - host odor - diptera-culicidae - pheromone plumes - aedes-aegypti - tsetse-flies
    Female mosquitoes use odor and heat as cues to navigate to a suitable landing site on their blood host. The way these cues affect flight behavior and modulate anemotactic responses, however, is poorly understood. We studied in-flight behavioral responses of females of the nocturnal malaria mosquito Anopheles gambiae sensu stricto to human odor and heat. Flight-path characteristics in a wind tunnel (flow 20 cm/s) were quantified in three dimensions. With wind as the only stimulus (control), short and close to straight upwind flights were recorded. With heat alone, flights were similarly short and direct. The presence of human odor, in contrast, caused prolonged and highly convoluted flight patterns. The combination of odor+heat resulted in longer flights with more landings on the source than to either cue alone. Flight speed was greatest (mean groundspeed 27.2 cm/s) for odor+heat. Odor alone resulted in decreased flight speed when mosquitoes arrived within 30 cm of the source whereas mosquitoes exposed to odor+heat maintained a high flight speed while flying in the odor plume, until they arrived within 15 cm of the source. Human odor evoked an increase in crosswind flights with an additive effect of heat at close range (
    A novel protein mixture containing vegetable proteins renders enteral nutrition products non-coagulating after in vitro gastric digestion
    Braak, C.C.M. van den; Klebach, M. ; Abrahamse, E. ; Minor, M. ; Knol, J. ; Hofman, Z. ; Ludwig, T. - \ 2013
    Clinical Nutrition 32 (2013)5. - ISSN 0261-5614 - p. 765 - 771.
    critically-ill patients - upper gastrointestinal-tract - stress-ulcer prophylaxis - critical-care medicine - risk-factors - milk-proteins - american society - support therapy - patient society - intensive-care
    Background & aims: Non-coagulation of protein from enteral nutrition (EN) in the stomach is considered to improve gastric emptying and may result in reduced upper gastrointestinal complications such as reflux and aspiration pneumonia. For the development of a new EN protein mixture with reduced gastric coagulation, the coagulating properties of individual proteins, a novel blend of four proteins (P4 protein blend) and commercial EN products were investigated. Methods: A semi-dynamic, computer controlled setup was developed to mimic gastric digestion. The coagulation behaviour of 150 ml protein solutions and EN products was investigated. These were heattreated calcium caseinate, sodium caseinate, whey, soy and pea protein, and the P4 protein blend comprising of the latter four (all solutions 6% w/v protein), four new enteral nutrition product varieties (New Nutrison 1.0 or 1.5 kcal/ml, with and without MultiFibre MF6) based on the P4 protein blend and two other commercially available casein dominant EN products (T1 and T2). Results: Calcium caseinate and sodium caseinate yielded a total wet coagulate of 43.5 0.7 g and 52.7 6.2 g, respectively. Whey, soy, pea and the P4 protein blend did not produce any measurable coagulate. T1 and T2 resulted in a total wet coagulate of 37.5 0.8 g and 57.3 0.8 g, respectively, while all new EN product varieties based on the P4 protein blend did not produce any measurable coagulate. Conclusions: The P4 protein blend renders EN product varieties non-coagulating after in vitro gastric digestion.
    No Predictive Power without Knowing Parameter Uncertainty
    Mourik, S. van; Stigter, J.D. ; Braak, C.J.F. ter; Molenaar, J. - \ 2013
    No Predictive Power without Knowing Parameter Uncertainty
    Mourik, S. van; Stigter, J.D. ; Braak, C.J.F. ter; Molenaar, J. - \ 2013
    In: Proceedings of the 32nd Benelux Meeting on Systems and Control, 26-28 March 2013, Houffalize Belgium. - - p. 148 - 148.
    Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes
    Kourmpetis, Y.A.I. ; Dijk, A.D.J. van; Braak, C.J.F. ter - \ 2013
    Algorithms for Molecular Biology 8 (2013)1. - ISSN 1748-7188
    arabidopsis-thaliana - integration - annotation - regression - network - classification - association - terms - tool
    Gene Ontology (GO) is a hierarchical vocabulary for the description of biological functions and locations, often employed by computational methods for protein function prediction. Due to the structure of GO, function predictions can be self- contradictory. For example, a protein may be predicted to belong to a detailed functional class, but not in a broader class that, due to the vocabulary structure, includes the predicted one.We present a novel discrete optimization algorithm called Functional Annotation with Labeling CONsistency (FALCON) that resolves such contradictions. The GO is modeled as a discrete Bayesian Network. For any given input of GO term membership probabilities, the algorithm returns the most probable GO term assignments that are in accordance with the Gene Ontology structure. The optimization is done using the Differential Evolution algorithm. Performance is evaluated on simulated and also real data from Arabidopsis thaliana showing improvement compared to related approaches. We finally applied the FALCON algorithm to obtain genome-wide function predictions for six eukaryotic species based on data provided by the CAFA (Critical Assessment of Function Annotation) project
    Complex contexts and dynamic drivers: Understanding four decades of forest loss and recovery in an East African protected area
    Sassen, M. ; Sheil, D. ; Giller, K.E. ; Braak, C.J.F. ter - \ 2013
    Biological Conservation 159 (2013). - ISSN 0006-3207 - p. 257 - 268.
    land-cover change - accuracy assessment - tropical forest - mount-elgon - uganda - parks - conservation - people - deforestation - biodiversity
    Protected forests are sometimes encroached by surrounding communities. But patterns of cover change can vary even within one given setting – understanding these complexities can offer insights into the effective maintenance of forest cover. Using satellite image analyses together with historical information, population census data and interviews with local informants, we analysed the drivers of forest cover change in three periods between 1973 and 2009 on Mt Elgon, Uganda. More than 25% of the forest cover of the Mt Elgon Forest Reserve/National Park was lost in 35 years. In periods when law enforcement was weaker, forest clearing was greatest in areas combining a dense population and people who had become relatively wealthy from coffee production. Once stronger law enforcement was re-established forest recovered in most places. Collaborative management agreements between communities and the park authorities were associated with better forest recovery, but deforestation continued in other areas with persistent conflicts about park boundaries. These conflicts were associated with profitability of annual crops and political interference. The interplay of factors originating at larger scales (government policy, market demand, political agendas and community engagement) resulted in a “back-and-forth” of clearing and regrowth. Our study reveals that the context (e.g. law enforcement, collaborative management, political interference) under which drivers such as population, wealth, market access and commodity prices operate, rather than the drivers per se, determines impacts on forest cover. Conservation and development interventions need to recognize and address local factors within the context and conditionalities generated by larger scale external influences.
    Selecting traits that explain species–environment relationships: a generalized linear mixed model approach
    Jamil, T. ; Ozinga, W.A. ; Kleyer, M. ; Braak, C.J.F. ter - \ 2013
    Journal of Vegetation Science 24 (2013)6. - ISSN 1100-9233 - p. 988 - 1000.
    plant-communities - 4th-corner problem - functional diversity - logistic-regression - resource selection - habitat templet - distributions - dispersal - gradients - ecology
    Question: Quantification of the effect of species traits on the assembly of communities is challenging from a statistical point of view. A key question is how species occurrence and abundance can be explained by the traits values of the species and the environmental values at the sites. Methods: Using a sites x species abundance table, a site x environment data table and a species x trait data table, we address this question by a novel Generalized linear mixed model (GLMM) approach. The GLMM overcomes the problem of pseudoreplication and heteroscedastic variance by including sites and species as random factors. The method is equally well applicable to presence-absence data as to count and multinomial data. We present a tiered forward selection approach for obtaining a parsimonious model and compare the results with the fourth corner method and RLQ ordination. Results: We illustrate the approach on a presence-absence version on two well-known data sets. In the Dune Meadow data species presence is parsimoniously explained by moisture and manure of the meadows in combination with seed mass and specific leaf area, respectively. In the Grazed Grassland data species presence is parsimoniously explained by the grazing intensity and soil phosphorous in combination with the C:N ratio and flowering mode, respectively. Conclusions: Our GLMM approach can be used to identify which species traits and environmental variables best explain the species distribution, and which traits are significantly correlated with environmental variables. The method is better suited for providing an interpretable and predictive model than the fourth corner method and RLQ.
    Hydrologic data assimilation using particle Markov chain Monte Carlo simulation: Theory, concepts and applications
    Vrugt, J.A. ; Braak, C.J.F. ter; Diks, C.G.H. - \ 2013
    Advances in Water Resources 51 (2013). - ISSN 0309-1708 - p. 457 - 478.
    rainfall-runoff models - stochastic parameter-estimation - ensemble kalman filter - global optimization - differential evolution - streamflow simulation - automatic calibration - metropolis algorithm - genetic algorithm - input uncertainty
    During the past decades much progress has been made in the development of computer based methods for parameter and predictive uncertainty estimation of hydrologic models. The goal of this paper is twofold. As part of this special anniversary issue we first shortly review the most important historical developments in hydrologic model calibration and uncertainty analysis that has led to current perspectives. Then, we introduce theory, concepts and simulation results of a novel data assimilation scheme for joint inference of model parameters and state variables. This Particle-DREAM method combines the strengths of sequential Monte Carlo sampling and Markov chain Monte Carlo simulation and is especially designed for treatment of forcing, parameter, model structural and calibration data error. Two different variants of Particle-DREAM are presented to satisfy assumptions regarding the temporal behavior of the model parameters. Simulation results using a 40-dimensional atmospheric “toy” model, the Lorenz attractor and a rainfall–runoff model show that Particle-DREAM, P-DREAM(VP) and P-DREAM(IP) require far fewer particles than current state-of-the-art filters to closely track the evolving target distribution of interest, and provide important insights into the information content of discharge data and non-stationarity of model parameters. Our development follows formal Bayes, yet Particle-DREAM and its variants readily accommodate hydrologic signatures, informal likelihood functions or other (in)sufficient statistics if those better represent the salient features of the calibration data and simulation model used.
    Groenbemesters in de strijd tegen gewone wortellesieaaltjes (Pratylenchus penetrans) : eindrapportage
    Elberse, I.A.M. ; Hoek, H. - \ 2012
    Lisse : PPO Bloembollen en Bomen - 51
    houtachtige planten als sierplanten - rosa - veldgewassen - wintertarwe - pratylenchus penetrans - groenbemesters - tagetes - dekgewassen - proeven - alternatieve methoden - ornamental woody plants - rosa - field crops - winter wheat - pratylenchus penetrans - green manures - tagetes - cover crops - trials - alternative methods
    Wortellesieaaltjes (Pratylenchus penetrans) kunnen in vele gewassen grote schade aanrichten. Bestrijding kan chemisch gebeuren, met natte grondontsmetting, maar een goed alternatief is het bestrijden door het telen van Tagetes patula (afrikaantjes). Een geslaagde teelt van deze groenbemester zorgt zelfs voor een betere bestrijding dan chemische grondontsmetting. Een Tagetesteelt heeft echter ook nadelen. Het bestrijdt alleen Pratulenchus penetrans en P. crenatus. Voor andere Pratylenchussoorten is de werking niet duidelijk. Voor een aantal andere belangrijke aaltjessoorten (aardappelcystenaaltjes, bietencystenaaltjes, wortelknobbelaaltjes) is Tagetes patula geen waardplant. Voor deze aaltjes is het effect van de teelt van T. patula gelijk aan het braak laten liggen van het land (zie ook www.aaltjesschema.nl). Voor vrijlevende wortelaaltjes, die behoren tot de groep van de trichodoriden is de waardplantstatus van Tagetes momenteel niet duidelijk, omdat er tegenstrijdige informatie over is. Verder groeit er gemakkelijk onkruid in Tagetes door de trage beginontwikkeling van het gewas. Als er onkruid tussen de Tagetes groeit, is de bestrijding van P. penetrans niet meer optimaal, omdat deze aaltjes zich op diverse onkruidsoorten vaak in meer of mindere mate kunnen vermeerderen. Telers ervaren het ook als een groot nadeel dat de teelt van Tagetes een heel groeiseizoen kost, doordat het gewas tussen half mei en half juli gezaaid moet worden en dan drie maanden moet groeien. Bovendien is in een eerdere proef de werking van Tagetes wel eens tegen gevallen in diepere bodemlagen, na voorteelt van het houtige gewas roos.
    Grondontsmetting en braak effectief
    Lamers, J.G. ; Postma, J. ; Scholten, O.E. - \ 2012
    Boerderij/Akkerbouw 98 (2012)10. - ISSN 0169-0116 - p. A16 - A17.
    uien - fusarium oxysporum - plantenziektebestrijding - plantenziekten - plantenziekteverwekkende schimmels - bestrijdingsmethoden - landbouwkundig onderzoek - biologische grondontsmetting - fungiciden - akkerbouw - onions - fusarium oxysporum - plant disease control - plant diseases - plant pathogenic fungi - control methods - agricultural research - biological soil sterilization - fungicides - arable farming
    Naast witrot of stengelalen is in uien ook fusarium een probleem geworden. PPO onderzocht bestrijdingsopties en ziet heil in biologische grondontsmetting
    Oplossingen voor bodemmoeheid in de fruitteelt
    Wenneker, M. ; Visser, J.H.M. ; Vercammen, J. ; Gomand, A. - \ 2012
    BioKennis Fruit 3 (2012). - 4
    bodempathogenen - fruitteelt - biologische landbouw - gewasbescherming - grondsterilisatie - biologische grondontsmetting - biologische bestrijding - bestrijdingsmethoden - soilborne pathogens - fruit growing - organic farming - plant protection - soil sterilization - biological soil sterilization - biological control - control methods
    De herinplant in de fruitteelt is alleen mogelijk als de bodemmoeheid wordt aangepakt. Alternatieve methoden van grondontsmetting waren tot nu toe in de meeste gevallen minder effectief of in vergelijking met chemische grondontsmetting veel duurder. In de biologische fruitteelt is chemische ontsmetting geen optie. Uit recent onderzoek blijken een aantal biologische behandelingen geschikt om bodemmoeheid te bestrijden: zwarte braak, Tagetes (Afrikaantjes) en biologische grondontsmetting (BGO). Biofumigatie en compost bleken minder effectief of geschikt.
    Canoco reference manual and user's guide: software for ordination, version 5.0
    Braak, C.J.F. ter; Smilauer, P. - \ 2012
    Ithaca USA : Microcomputer Power - 496
    computer software - gegevensanalyse - statistische analyse - multivariate analyse - ecologie - biologie - handleidingen - computer software - data analysis - statistical analysis - multivariate analysis - ecology - biology - guide books
    Canoco is a software package for multivariate data analysis, with an emphasis on dimesional reduction (ordination), regression analysis, and the combination of the two, constrained ordination. Canoco makes effective and powerful ordination methods easilyt accessible for scientists wanting to infer and visualize pattern and structure in complex multivariate data, e.g. biologists researching the relations between plant and animal communities and their environment. Canoco contains linear and unimodal ordination methods, with the possibility to account for background variation specified by covariates. In combination with extensive facilities for permutation tests, these methods have proven to be remarkably effective in solving applied research problems.
    Image-Based Particle Filtering For Robot Navigation In A Maize Field
    Hiremath, S. ; Evert, F.K. van; Heijden, G.W.A.M. van der; Braak, C.J.F. ter; Stein, A. - \ 2012
    Autonomous navigation of a robot in an agricultural field is a challenge as the robot is in an environment with many sources of noise. This includes noise due to uneven terrain, varying shapes, sizes and colors of the plants, imprecise sensor measurements and effects due to wheel-slippage. The drawback of current navigation systems in use in agriculture is the lack of robustness against such noise. In this study we present a robust vision-based navigation method based on probabilistic methods. The focus is on navigation through a corn field. Here the robot has to navigate along the rows of the crops, detect the end of the rows, navigate in the headland and return in another row. A Particle Filter based navigation method is used based on a novel measurement model. This model results in an image from the particle state vector that allows the user to compare the observed image with the actual field conditions. In this way the noise is incorporated into the posterior distribution of the particle filter. The study shows that the new method accurately estimates the robot-environment state by means of a field experiment in which the robot navigates through the field using the particle filter.
    Nanoparticle risk assessment: a probabilistic approach
    Jacobs, R. ; Braak, C.J.F. ter; Voet, H. van der - \ 2012
    Legumes affect alpine tundra community composition via multiple biotic interactions
    Soudzilovskaia, N.A. ; Aksenova, A.A. ; Makarov, M.I. ; Onipchenko, V.G. ; Logvinenko, O.A. ; Braak, C.J.F. ter; Cornelissen, J.H.C. - \ 2012
    Ecosphere 3 (2012)4. - ISSN 2150-8925 - 15 p.
    arbuscular mycorrhizal fungi - biological nitrogen-fixation - n-2 fixation - northwestern caucasus - grassland ecosystems - acetylene-reduction - inorganic nitrogen - biomass production - natural-abundance - plant community
    The soil engineering function of legumes in natural ecosystems is paramount but associated solely with soil nitrogen (N) subsidies, ignoring concomitant biotic interactions such as competitive or inhibitory effects and exchange between mycorrhizas and rhizobia. We aim to (1) disentangle legume effects on plant community composition, and plant and soil N and phosphorus (P) concentrations, separating the effects of N subsidies from other legume effects; (2) estimate effects of mycorrhizal-rhizobial interactions on nutrient acquisition modes of plants co-existing with legumes. We compared plant community structure and plant nutrition modes in micro-sites in a Caucasian alpine tundra ecosystem that were either: (1) dominated by legumes in symbiosis with N-fixing rhizobia (‘N-fixing legumes'), (2) dominated by legumes without symbiosis with rhizobia (‘not N-fixing legumes'), or dominated by non-legumes and either (3) unfertilized (‘controls') or (4) experimentally fertilized. Fertilization and the presence of N-fixing legumes affected the ecosystem similarly: soil was enriched with plant-available N compared to controls and sites dominated by a not N-fixing legume. Also, N turnover pathways and plant nutrition modes were strongly affected by the latter site types, as indicated by 5–10% higher plant tissue N concentration, altered soil and plant d15N, more than 4-fold reduced lichen amounts, 2.5-fold increased litter accumulation and doubling of aboveground biomass of non-legume plants. Vascular plant community composition was affected by the presence of legumes in a similar way regardless of whether they fixed N, suggesting that other factors overrode the N subsidy effects. Shading and microclimate changes in sites dominated by both types of legumes are possible explanatory factors. Both tissue N and d15N of non-legume plants near legumes were affected by interactions of mycorrhizal type and site type (without legumes, dominated by N-fixing, or not N-fixing legume), suggesting an important role of plant mycorrhizal status for adjusting nutrition mode to the legume presence. We conclude that N-fixing legumes play an engineering role in natural plant communities, but their role goes much beyond N fixation. Plant mycorrhizal status defines the way plants adjust their nutrition mode to the presence of legumes
    Estimating the prediction uncertainty of biological models
    Mourik, S. van; Stigter, J.D. ; Braak, C.J.F. ter; Molenaar, J. - \ 2012
    In: Book of abstracts of the 31st Benelux Meeting on Systems and Control, 27-29 March 2012, Heijen, the Netherlands. - Wageningen : Wageningen UR - p. 136 - 136.
    Trait-Environment Relationships and Tiered Forward Model Selection in Linear Mixed Models
    Jamil, T. ; Opdekamp, W. ; Diggelen, R. ; Braak, C.J.F. ter - \ 2012
    International Journal of Ecology (2012). - ISSN 1687-9708 - 12 p.
    To understand patterns of variation in species biomass in terms of species traits and environmental variables a one-to-one approach might not be sufficient, and a multitrait multienvironment approach will be necessary. A multitrait multienvironment approach is proposed, based on a mixed model for species biomass. In the model, environmental variables are species-dependent random terms, whereas traits are fixed terms, and trait-environment relationships are fixed interaction terms. In this approach, identifying the important trait-environment relationship becomes a model selection problem. Because of the mix of fixed and random terms, we propose a novel tiered forward selection approach for this. In the first tier, the random factors are selected; in the second, the fixed effects; in the final tier, nonsignificant terms are removed using a modified Akaike information criterion. We complement this tiered selection with an alternative selection method, namely, type II maximum likelihood. A mesocosm experiment on early community assembly in wetlands with three two-level environmental factors is analyzed by the new approach. The results are compared with the fourth corner problem and the linear trait-environment method. Traits related to germination and seedling establishment are selected as being most important in the community assembly in these wetland mesocosms.
    Biowisselkas: bredere vruchtwisseling voor een gezondere bodem
    Cuijpers, W.J.M. ; Janmaat, L. - \ 2012
    Driebergen : Louis Bolk Instituut (Publicatie / Louis Bolk Instituut nr. 2012-007 LbP) - 42 p.
    glastuinbouw - glasgroenten - rotaties - biologische landbouw - plantenparasitaire nematoden - meloidogyne incognita - nematodenbestrijding - braak - teeltsystemen - paprika's - tomaten - greenhouse horticulture - greenhouse vegetables - rotations - organic farming - plant parasitic nematodes - meloidogyne incognita - nematode control - fallow - cropping systems - sweet peppers - tomatoes
    In 2009 and 2010 a field experiment was conducted with an alternative cultivation system in organic greenhouse production. The aim of the alternative system is to improve soil health, by broadening crop rotation. A precondition is the economic viability of the alternative system. In the so-called Köver system, planting beds are below-ground divided in compartments by means of a plastic sheet. On one half of the planting bed, greenhouse crops are grown, while on the other half antagonistic crops can be grown or the soil can be left fallow. Sweet pepper suffered from the antagonistic crops, which capture a lot of light. The rich soil stimulated the abundant growth of antagonistic crops (Tagetes patula c.v. Single Gold (Ground Control) and Capsicum annuum c.v. Snooker). This resulted in a production loss of 25% in sweet pepper. Although we didn’t measure a decline of production in combination with fallow, many stems of sweet pepper wilted. Future investigation should point out if the combination sweet pepper and fallow is viable. When cultivated in the alternative system, tomato reaches the same level of production as normal. The number of pathogenic root-knot nematodes (Meloidogyne incognita) drops sharply during fallow. Two years of fallow had no additional effect on the decline of the nematode population. At the end of the tomato crop, the number of nematodes had increased again, independent from the previous conditions (sweet pepper or fallow). Tomato roots were a little healthier after the fallow period. However, the improvement of plant health was too small to result in higher production levels. The system needs a different fertilization approach.
    Improved testing of species traits-environment relationships in the fourth corner problem
    Braak, C.J.F. ter; Cormont, A. ; Dray, S. - \ 2012
    Ecology 93 (2012)7. - ISSN 0012-9658 - p. 1525 - 1526.
    The fourth corner problem entails estimation and statistical testing of the relationship between species traits and environmental variables from the analysis of three data tables. Dray and Legendre (2008, Ecology, 89, 3400-34) proposed and evaluated five permutation methods for statistical significance testing, including a new two-step testing procedure. However, none of these attained the correct type I error in all cases of interest. We solve this problem by showing that a small modification of their two-step procedure controls the type I error in all cases. The modification consists of adjusting the significance level from va to a or, equivalently, of reporting the maximum of the individual P-values as the final one. The test is also applicable to the three table ordination method RLQ
    Response to "traits and stress: keys to identify community effects of low levels of toxicants in test systems" by Liess and Beketov (2011)
    Brink, P.J. van den; Braak, C.J.F. ter - \ 2012
    Ecotoxicology 21 (2012)2. - ISSN 0963-9292 - p. 297 - 299.
    aquatic invertebrates - sensitivity - carbendazim
    QTL linkage analysis of connected populations using ancestral marker and pedigree information
    Bink, M.C.A.M. ; Radu Totir, L. ; Braak, C.J.F. ter; Winkler, C.R. ; Boer, M.P. ; Smith, O.S. - \ 2012
    Theoretical and Applied Genetics 124 (2012)6. - ISSN 0040-5752 - p. 1097 - 1113.
    quantitative trait loci - plant-populations - kernel hardness - dough strength - model - maize - selection - families - wheat - identity
    The common assumption in quantitative trait locus (QTL) linkage mapping studies that parents of multiple connected populations are unrelated is unrealistic for many plant breeding programs. We remove this assumption and propose a Bayesian approach that clusters the alleles of the parents of the current mapping populations from locus-specific identity by descent (IBD) matrices that capture ancestral marker and pedigree information. Moreover, we demonstrate how the parental IBD data can be incorporated into a QTL linkage analysis framework by using two approaches: a Threshold IBD model (TIBD) and a Latent Ancestral Allele Model (LAAM). The TIBD and LAAM models are empirically tested via numerical simulation based on the structure of a commercial maize breeding program. The simulations included a pilot dataset with closely linked QTL on a single linkage group and 100 replicated datasets with five linkage groups harboring four unlinked QTL. The simulation results show that including parental IBD data (similarly for TIBD and LAAM) significantly improves the power and particularly accuracy of QTL mapping, e.g., position, effect size and individuals’ genotype probability without significantly increasing computational demand.
    Selection properties of Type II maximum likelihood (empirical bayes) linear models with individual variance components for predictors
    Jamil, T. ; Braak, C.J.F. ter - \ 2012
    Pattern Recognition Letters 33 (2012)9. - ISSN 0167-8655 - p. 1205 - 1212.
    gene-expression data - variable selection - elastic net - regression - regularization - shrinkage - chemometrics - networks - genome - lasso
    Maximum Likelihood (ML) in the linear model overfits when the number of predictors (M) exceeds the number of objects (N). One of the possible solution is the Relevance vector machine (RVM) which is a form of automatic relevance detection and has gained popularity in the pattern recognition machine learning community by the famous textbook of Bishop (2006). RVM assigns individual precisions to weights of predictors which are then estimated by maximizing the marginal likelihood (type II ML or empirical Bayes). We investigated the selection properties of RVM both analytically and by experiments in a regression setting. We show analytically that RVM selects predictors when the absolute z-ratio (|least squares estimate|/standard error) exceeds 1 in the case of orthogonal predictors and, for M = 2, that this still holds true for correlated predictors when the other z-ratio is large. RVM selects the stronger of two highly correlated predictors. In experiments with real and simulated data, RVM is outcompeted by other popular regularization methods (LASSO and/or PLS) in terms of the prediction performance. We conclude that Type II ML is not the general answer in high dimensional prediction problems. In extensions of RVM to obtain stronger selection, improper priors (based on the inverse gamma family) have been assigned to the inverse precisions (variances) with parameters estimated by penalized marginal likelihood. We critically assess this approach and suggest a proper variance prior related to the Beta distribution which gives similar selection and shrinkage properties and allows a fully Bayesian treatment.
    Models to relate species to environment: a hierarchical statistical approac
    Jamil, T. - \ 2012
    Wageningen University. Promotor(en): Cajo ter Braak. - S.l. : s.n. - ISBN 9789461731395 - 146
    statistiek - lineaire modellen - interacties - kenmerken - bayesiaanse theorie - plantenecologie - biostatistiek - statistics - linear models - interactions - traits - bayesian theory - plant ecology - biostatistics

    In the last two decades, the interest of community ecologists in trait-based approaches has grown dramatically and these approaches have been increasingly applied to explain and predict response of species to environmental conditions. A variety of modelling techniques are available. The dominant technique is tocluster the species based on their functional traits and then summarize the response of the clusters to environmental change. In general, fitting explicit models to data is always more informative and powerful than more informal approaches. The central theme of the thesis is how to quantify the relation of traits with the environment using three data tables, data on species occurrence and abundance in sites, data on traits of species and data on the environmental characteristics of sites. In this thesis, we place the challenge of quantifying trait-environment relationships in the context of species distribution modelling, so in the context of species-environment relationships. We present a hierarchal statistical approach to species distribution modelling that efficiently utilize the trait information and that is able to automatically select the relevant traits and environmental characteristics. This model-based approach, coupled with recent statistical developments and increased computing power, opens up possibilities that were unimaginable before.

    In the present study a hierarchical statistical approach is introduced for modeling and explaining species response along environmental gradients by species traits. The model is an extension of the generalized linear model with random terms that express the between-species variation in response to the environment. This so-called generalized linear mixed model (GLMM)is derived byintegrating a two-step procedure into one. As the basic GLMM we take the random intercept and random slope model. To introduce traits, the regression parameters (intercept and slope) are made linearly dependent on the species traits. As a consequence the trait-environment relationship is represented as an interaction term in the model. The method is illustrated using the famous Dune Meadow Data using Ellenberg indicator values as species traits.

    Niche theory proclaims that species response to environmental gradients is nonlinear. Each species has preferred an environmental condition in which it can survive and reproduce optimally. Thus each species tends to be most abundant around a specific environmental optimum and the distribution of species along any environmental gradient is usually unimodal, with the maximum at some ecological optimum.For presence-absence data, the simplest unimodal (non-negative) species response curve is the Gaussian logistic response curve with three parameters that characterize the niche: optimum (niche centre), tolerance (niche width) and maximum (expected occurrence at the centre). Niches of species differ between species and species are assumed to be evolutionary adapted. It is difficult to fit the Gaussian logistic model with linear trait submodels for the parameters with the available (generalized) nonlinear mixed model software.

    We develop the trait-modulated Gaussian logistic model in which the niche parameters are made linearly dependent on species traits. The model is fitted to data in the Bayesian frameworkusing OpenBUGS (Bayesian inference Using Gibbs Sampling).A Bayesian variable selection method is used to identify which species traits and environmental variables best explain the species data through this model. We extended the approach to find the best linear combination of environmental variables.

    We explained why and when (generalized) linear mixed models can effectively analyse unimodal data and presented a graphical tool and statistical test to test for unimodality while fitting just a generalized linear mixed model without any squared or other polynomial term. A GLMM is, of course, a linear model. Despite this fact, it can be used to detect unimodality and to fit unimodal data, with the provision that the differences in niche widthsamongspecies are not too large. As graphical tool we suggested to plot the random site effects against the environmental variable. There is an indication for unimodality, when this graph shows a quadratic relationship. The efficacy of GLMM to analyse unimodal data is illustrated by comparing the GLMM approach with an explicit unimodal model approach on simulated data and real data that show unimodality.

    When a system is described by a statistical model, model complexity leads to a very large computing time and poor estimation, especially if the number of predictors is large relative to the data size. As an alternative to and improvement over stepwise methods, shrinkage methods have been proposed. One of these is the Relevance vector machine (RVM). RVM assigns individual precisions to weights of predictors which are then estimated by maximizing the marginal likelihood (Type-II ML or empirical Bayes). We also investigated the selection properties of RVM both analytically and by experiments. We found that RVM is rather tolerant for predictors to stay in the model and concluded that RVM is not a real solution in high-dimensional data problems.

    By further study the multi-trait and multi-environmental variablemodel selection method developed that used our previous study in a linear mixed model context. The method is called tiered forward selection. In the first tier, the random factors are selected, in the second, the fixed effects are selected and in the final tier non-significant terms are removed based on a modified Akaike information criterion. The linear mixed model with the tiered forward selection is compared with Type-II ML and existing methods for detecting trait-environment relationships that are not based on mixed models, namely the fourth corner method and the linear trait-environment method (LTE).

    Arctic warming on two continents has consistent negativ effects on lichen diversity and mixed effects on bryophyte diversity
    Lang, S.I. ; Cornelissen, J.H.C. ; Shaver, G.R. ; Ahrens, M. ; Callaghan, T.V. ; Molau, U. ; Braak, C.J.F. ter; Hölzer, A. ; Aerts, R. - \ 2012
    Global Change Biology 18 (2012)3. - ISSN 1354-1013 - p. 1096 - 1107.
    simulated environmental-change - plant community responses - dwarf shrub heath - nitrogen mineralization - climate-change - tundra - vegetation - biomass - growth - ecosystems
    Little is known about the impact of changing temperature regimes on composition and diversity of cryptogam communities in the Arctic and Subarctic, despite the well-known importance of lichens and bryophytes to the functioning and climate feedbacks of northern ecosystems. We investigated changes in diversity and abundance of lichens and bryophytes within long-term (9–16 years) warming experiments and along natural climatic gradients, ranging from Swedish subarctic birch forest and subarctic/subalpine tundra to Alaskan arctic tussock tundra. In both Sweden and Alaska, lichen diversity responded negatively to experimental warming (with the exception of a birch forest) and to higher temperatures along climatic gradients. Bryophytes were less sensitive to experimental warming than lichens, but depending on the length of the gradient, bryophyte diversity decreased both with increasing temperatures and at extremely low temperatures. Among bryophytes, Sphagnum mosses were particularly resistant to experimental warming in terms of both abundance and diversity. Temperature, on both continents, was the main driver of species composition within experiments and along gradients, with the exception of the Swedish subarctic birch forest where amount of litter constituted the best explanatory variable. In a warming experiment in moist acidic tussock tundra in Alaska, temperature together with soil ammonium availability were the most important factors influencing species composition. Overall, dwarf shrub abundance (deciduous and evergreen) was positively related to warming but so were the bryophytes Sphagnum girgensohnii, Hylocomium splendens and Pleurozium schreberi; the majority of other cryptogams showed a negative relationship to warming. This unique combination of intercontinental comparison, natural gradient studies and experimental studies shows that cryptogam diversity and abundance, especially within lichens, is likely to decrease under arctic climate warming. Given the many ecosystem processes affected by cryptogams in high latitudes (e.g. carbon sequestration, N2-fixation, trophic interactions), these changes will have important feedback consequences for ecosystem functions and climate
    Waard- en niet waard planten van stengelaaltjes uit bloembolgewassen
    Doorn, J. van; Dees, R.H.L. ; Vreeburg, P.J.M. - \ 2011
    BloembollenVisie 2011 (2011)235. - ISSN 1571-5558 - p. 24 - 25.
    bloembollen - waardplanten - plantenziekteverwekkers - gewasbescherming - ziektepreventie - ditylenchus dipsaci - rotaties - teeltsystemen - landbouwkundig onderzoek - ornamental bulbs - host plants - plant pathogens - plant protection - disease prevention - ditylenchus dipsaci - rotations - cropping systems - agricultural research
    Als in een partij bloembollen stengelaaltjes wordt vastgesteld, zorgt dit voor veel problemen. Partijen tulpen moeten worden vernietigd, narcissenbollen moeten vernietigd of gekookt worden, en het perceel waarop geteelt werd moet worden ontsmet of anders braak liggen. Dit kost veel geld. Door gewassen in rotarie te nemen die geen waard zijn voor stengelaaltjes kan het economische probleem van stengelaaltjes minder groot worden. Dit is onderzocht door vier jaar twintig bloembolgewassen, groenbemesters, akkerbouwgewassen en vaste planten op met stengenaaltjes besmette gronden te telen. Naast lelie en dahlia bleek een aantal vaste planten, groenbemesters en akkerbouwgewassen geen waardplant te zijn.
    DREAM(D): an adaptive Markov Chain Monte Carlo simulation algorithm to solve discrete, noncontinuous, and combinatorial posterior parameter estimation problems.
    Vrugt, J.A. ; Braak, C.J.F. ter - \ 2011
    Hydrology and Earth System Sciences 15 (2011)12. - ISSN 1027-5606 - p. 3701 - 3713.
    rainfall-runoff models - metropolis algorithm - differential evolution - global optimization - uncertainty - spaces - mcmc
    Formal and informal Bayesian approaches have found widespread implementation and use in environmental modeling to summarize parameter and predictive uncertainty. Successful implementation of these methods relies heavily on the availability of efficient sampling methods that approximate, as closely and consistently as possible the (evolving) posterior target distribution. Much of this work has focused on continuous variables that can take on any value within their prior defined ranges. Here, we introduce theory and concepts of a discrete sampling method that resolves the parameter space at fixed points. This new code, entitled DREAM(D) uses the recently developed DREAM algorithm (Vrugt et al., 2008, 2009a, b) as its main building block but implements two novel proposal distributions to help solve discrete and combinatorial optimization problems. This novel MCMC sampler maintains detailed balance and ergodicity, and is especially designed to resolve the emerging class of optimal experimental design problems. Three different case studies involving a Sudoku puzzle, soil water retention curve, and rainfall – runoff model calibration problem are used to benchmark the performance of DREAM(D). The theory and concepts developed herein can be easily integrated into other (adaptive) MCMC algorithms.
    Correlated mutations via regularized multinomial regression
    Sreekumar, J. ; Braak, C.J.F. ter; Ham, R.C.H.J. van; Dijk, A.D.J. van - \ 2011
    BMC Bioinformatics 12 (2011). - ISSN 1471-2105 - 13 p.
    multiple sequence alignments - protein-protein interaction - mutual information - graphical models - prediction - families - identification - specificity - dimension - selection
    Background In addition to sequence conservation, protein multiple sequence alignments contain evolutionary signal in the form of correlated variation among amino acid positions. This signal indicates positions in the sequence that influence each other, and can be applied for the prediction of intra- or intermolecular contacts. Although various approaches exist for the detection of such correlated mutations, in general these methods utilize only pairwise correlations. Hence, they tend to conflate direct and indirect dependencies. Results We propose RMRCM, a method for Regularized Multinomial Regression in order to obtain Correlated Mutations from protein multiple sequence alignments. Importantly, our method is not restricted to pairwise (column-column) comparisons only, but takes into account the network nature of relationships between protein residues in order to predict residue-residue contacts. The use of regularization ensures that the number of predicted links between columns in the multiple sequence alignment remains limited, preventing overprediction. Using simulated datasets we analyzed the performance of our approach in predicting residue-residue contacts, and studied how it is influenced by various types of noise. For various biological datasets, validation with protein structure data indicates a good performance of the proposed algorithm for the prediction of residue-residue contacts, in comparison to previous results. RMRCM can also be applied to predict interactions (in addition to only predicting interaction sites or contact sites), as demonstrated by predicting PDZ-peptide interactions. Conclusions A novel method is presented, which uses regularized multinomial regression in order to obtain correlated mutations from protein multiple sequence alignments.
    The Predictability of Phytophagous Insect Communities: Host Specialists as Habitat Specialists
    Müller, J. ; Stadler, J. ; Jarzabek-Müller, A. ; Hacker, H. ; Braak, C.J.F. ter; Brandl, R. - \ 2011
    PLoS ONE 6 (2011)10. - ISSN 1932-6203 - 10 p.
    ecological specialization - arthropod assemblages - fragmented landscapes - herbivorous insects - species composition - pierid butterflies - geometrid moths - tropical forest - beta-diversity - niche breadth
    The difficulties specialized phytophagous insects face in finding habitats with an appropriate host should constrain their dispersal. Within the concept of metacommunities, this leads to the prediction that host-plant specialists should sort into local assemblages according to the local environmental conditions, i.e. habitat conditions, whereas assemblages of host-plant generalists should depend also on regional processes. Our study aimed at ranking the importance of local environmental factors and species composition of the vegetation for predicting the species composition of phytophagous moth assemblages with either a narrow or a broad host range. Our database consists of 351,506 specimens representing 820 species of nocturnal Macrolepidoptera sampled between 1980 and 2006 using light traps in 96 strict forest reserves in southern Germany. Species were grouped as specialists or generalists according to the food plants of the larvae; specialists use host plants belonging to one genus. We used predictive canonical correspondence and co-correspondence analyses to rank the importance of local environmental factors, the species composition of the vegetation and the role of host plants for predicting the species composition of host-plant specialists and generalists. The cross-validatory fit for predicting the species composition of phytophagous moths was higher for host-plant specialists than for host-plant generalists using environmental factors as well as the composition of the vegetation. As expected for host-plant specialists, the species composition of the vegetation was a better predictor of the composition of these assemblages than the environmental variables. But surprisingly, this difference for specialized insects was not due to the occurrence of their host plants. Overall, our study supports the idea that owing to evolutionary constraints in finding a host, host-plant specialists and host-plant generalists follow two different models of metacommunities: the species-sorting and the mass-effect model
    Using life-history traits to explain bird population responses to changing weather variability
    Cormont, A. ; Vos, C.C. ; Turnhout, C.A.M. van; Foppen, R.P.B. ; Braak, C.J.F. ter - \ 2011
    Climate Research 49 (2011)1. - ISSN 0936-577X - p. 59 - 71.
    climate-change - 4th-corner problem - species traits - migratory bird - consequences - netherlands - temperatures - adaptations - resilience - habitats
    Bird population dynamics are expected to change in response to increased weather variability, an expression of climate change. The extent to which species are sensitive to effects of weather on survival and reproduction depends on their life-history traits. We investigated how breeding bird species can be grouped, based on their life-history traits and according to weather-correlated population dynamics. We developed and applied the linear trait–environment method (LTE), which is a modified version of the fourth-corner method. Despite our focus on single traits, 2 strategies—combinations of several traits—stand out. As expected, breeding populations of waterfowl species are negatively impacted by severe winters directly preceding territory monitoring, probably because of increased adult mortality. Waterfowl species combine several traits: they often breed at ground or water level, feed on plant material, are precocial and are generally short-distance or partial migrants. Furthermore, we found a decline in population growth rates of insectivorous long-distance migrants due to mild winters and warm springs in the year before territory monitoring, which may be caused by reduced reproduction due to trophic mismatches. We identify species that are expected to show the most significant responses to changing weather variability, assuming that our conclusions are based on causal relationships and that the way species, weather variables and habitat interact will not alter. Species expected to respond positively can again be roughly categorized as waterfowl species, while insectivorous long-distance migrants are mostly expected to respond negatively. As species traits play an important role in constructing functional groups that are relevant to the provisioning of ecosystem services, our study enables the incorporation of ecosystem vulnerability to climate change into such functional approaches
    Bayesian Markov random field analysis for integrated network-based protein function prediction
    Kourmpetis, Y.I.A. - \ 2011
    Wageningen University. Promotor(en): Cajo ter Braak, co-promotor(en): Roeland van Ham. - [S.l.] : S.n. - ISBN 9789085859598 - 113
    statistiek - bayesiaanse theorie - markov-processen - netwerkanalyse - biostatistiek - toegepaste statistiek - bio-informatica - eiwitten - genen - moleculaire biologie - statistics - bayesian theory - markov processes - network analysis - biostatistics - applied statistics - bioinformatics - proteins - genes - molecular biology

    Unravelling the functions of proteins is one of the most important aims of modern biology. Experimental inference of protein function is expensive and not scalable to large datasets. In this thesis a probabilistic method for protein function prediction is presented that integrates different types of data such as sequences and networks. The method is based on Bayesian Markov Random Field (BMRF) analysis. BMRF was initially applied to genome wide protein function prediction using network data in yeast and in also in Arabidopsis by integrating protein domains (i.e InterPro signatures), expressions and protein protein interactions. Several of the predictions were confirmed by experimental evidence. Further, an evolutionary discrete optimization algorithm is presented that integrates function predictions from different Gene Ontology (GO) terms to a single prediction that is consistent to the True Path Rule as imposed by the GO Directed Acyclic Graph. This integration leads to predictions that are easy to be interpreted. Evaluation of of this algorithm using Arabidopsis data showed that the prediction performance is improved, compared to single GO term predictions.

    Effecten van Crotalaria juncea (Bengaalse hennep) op wortelknobbelaaltjes
    Thoden, T.C. ; Korthals, G.W. - \ 2011
    Lelystad : Praktijkonderzoek Plant en Omgeving Business unit Akkerbouw, Groene ruimte en Vollegrondsgroenten - 17
    nematodenbestrijding - ziektebestrijdende teeltmaatregelen - crotalaria juncea - akkerbouw - plantenparasitaire nematoden - bengaalse hennep - meloidogyne - nematode control - cultural control - crotalaria juncea - arable farming - plant parasitic nematodes - sunn hemp - meloidogyne
    Bengaalse hennep (Crotalaria juncea) is een vlinderbloemachtige “multipurpose” plant die in de tropen en subtropen vaak gebruikt wordt om wortelknobbelaaltjes te bestrijden. Deze deskstudie laat zien dat er veel onderzoek is gedaan waaruit blijkt, dat de juveniele van wortelknobbelaaltjes en andere sedentaire aaltjes vaak het wortelstelsel van desbetreffende planten infecteren, maar zich vervolgens niet tot volwassenen kunnen doorontwikkelen. Dit leidde vaak tot een directe afname van aaltjes die sterker was dan de afname bij een zwarte braak. Daarnaast werd gevonden dat dit soort onderzoek tot nu toe alleen met tropische soorten van wortelknobbelaaltjes is uitgevoerd. Verder zijn er tot nu toe geen proeven te vinden waarin Bengaalse hennep onder het Midden-Europees klimaat geteeld is. Omdat de nematicide werking van Crotalaria soorten vermoedelijk met een soort planteninhoudstof (pyrrolizidine alkaloïden, PA) te maken heeft zal ook de mogelijkheid bestaan om andere planten, die dezelfde stof bevatten, voor de bestrijding van wortelknobbelaaltjes in te zetten.
    Testing the significance of canonical axes in redundancy analysis
    Legendre, P. ; Oksanen, J. ; Braak, C.J.F. ter - \ 2011
    Methods in Ecology and Evolution 2 (2011)3. - ISSN 2041-210X - p. 269 - 277.
    ecological data - bimultivariate redundancy - environment relationships - neighbor matrices - monte-carlo - regression
    1. Tests of significance of the individual canonical axes in redundancy analysis allow researchers to determine which of the axes represent variation that can be distinguished from random. Variation along the significant axes can be mapped, used to draw biplots or interpreted through subsequent analyses, whilst the nonsignificant axes may be dropped from further consideration. 2. Three methods have been implemented in computer programs to test the significance of the canonical axes; they are compared in this paper. The simultaneous test of all individual canonical axes, which is appealing because of its simplicity, produced incorrect (highly inflated) levels of type I error for the axes following those corresponding to true relationships in the data, so it is invalid. The ‘marginal’ testing method implemented in the ‘vegan’ R package and the ‘forward’ testing method implemented in the program CANOCO were found to have correct levels of type I error and comparable power. Permutation of the residuals achieved greater power than permutation of the raw data. 3. R functions found in a Supplement to this paper provide the first formal description of the ‘marginal’ and ‘forward’ testing methods
    Genome-wide computational function prediction of Arabidopsis thaliana proteins by integration of multiple data sources
    Kourmpetis, Y.I.A. ; Dijk, A.D.J. van; Ham, R.C.H.J. van; Braak, C.J.F. ter - \ 2011
    Plant Physiology 155 (2011). - ISSN 0032-0889 - p. 271 - 281.
    generalized linear-models - transcription factor - flowering time - cell-death - thaliana - gene - algorithm - networks - biology - family
    Although Arabidopsis thaliana is the best studied plant species, the biological role of one third of its proteins is still unknown. We developed a probabilistic protein function prediction method that integrates information from sequences, protein-protein interactions and gene expression. The method was applied to proteins from Arabidopsis thaliana. Evaluation of prediction performance showed that our method has improved performance compared to single source-based prediction approaches and two existing integration approaches. An innovative feature of our method is that enables transfer of functional information between proteins that are not directly associated with each other. We provide novel function predictions for 5,807 proteins. Recent experimental studies confirmed several of the predictions. We highlight these in detail for proteins predicted to be involved in flowering and floral organ development.
    Gene Regulatory Networks from Multifactorial Perturbations Using Graphical Lasso: Application to the DREAM4 Challenge
    Menéndez, P. ; Kourmpetis, Y.I.A. ; Braak, C.J.F. ter; Eeuwijk, F.A. van - \ 2010
    PLoS ONE 5 (2010)12. - ISSN 1932-6203
    model - selection - likelihood - regression - inference
    A major challenge in the field of systems biology consists of predicting gene regulatory networks based on different training data. Within the DREAM4 initiative, we took part in the multifactorial sub-challenge that aimed to predict gene regulatory networks of size 100 from training data consisting of steady-state levels obtained after applying multifactorial perturbations to the original in silico network. Due to the static character of the challenge data, we tackled the problem via a sparse Gaussian Markov Random Field, which relates network topology with the covariance inverse generated by the gene measurements. As for the computations, we used the Graphical Lasso algorithm which provided a large range of candidate network topologies. The main task was to select the optimal network topology and for that, different model selection criteria were explored. The selected networks were compared with the golden standards and the results ranked using the scoring metrics applied in the challenge, giving a better insight in our submission and the way to improve it.Our approach provides an easy statistical and computational framework to infer gene regulatory networks that is suitable for large networks, even if the number of the observations (perturbations) is greater than the number of variables (genes)
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