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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    Cow and herd-level risk factors associated with mobility scores in pasture-based dairy cows
    O'Connor, A.H. ; Bokkers, E.A.M. ; Boer, I.J.M. de; Hogeveen, H. ; Sayers, R. ; Byrne, N. ; Ruelle, E. ; Engel, B. ; Shalloo, L. - \ 2020
    Preventive Veterinary Medicine 181 (2020). - ISSN 0167-5877
    Animal-health - Grass-based - Lameness - Locomotion - Risk-factors

    Lameness in dairy cows is an area of concern from an economic, environmental and animal welfare point of view. While the potential risk factors associated with suboptimal mobility in non-pasture-based systems are evident throughout the literature, the same information is less abundant for pasture-based systems specifically those coupled with seasonal calving, like those in Ireland. Therefore, the objective of this study was to determine the potential risk factors associated with specific mobility scores (0 = good, 1 = imperfect, 2 = impaired, and 3 = severely impaired mobility) for pasture-based dairy cows. Various cow and herd-level potential risk factors from Irish pasture-based systems were collected and analyzed for their association with suboptimal mobility, whereby a mobility score of 0 refers to cows with optimal mobility and a mobility score ≥ 1 refers to a cow with some form of suboptimal mobility. Combined cow and herd-level statistical models were used to determine the increased or decreased risk for mobility score 1, 2, and 3 (any form of suboptimal mobility) compared to the risk for mobility score 0 (optimal mobility), as the outcome variable and the various potential risk factors at both the cow and herd-level were included as predictor type variables. Cow-level variables included body condition score, milk yield, genetic predicted transmitting ability for ‘lameness’, somatic cell score, calving month and cow breed. Herd-level variables included various environmental and management practices on farm. These analyses have identified several cow-level potential risk factors (including low body condition score, high milk yield, elevated somatic cell count, stage of lactation, calving month, and certain breed types), as well as various herd-level potential risk factors (including the amount of time taken to complete the milking process, claw trimmer training, farm layout factors and foot bathing practices) which are associated with suboptimal mobility. The results of this study should be considered by farm advisors when advising and implementing a cow/herd health program for dairy cows in pasture-based systems.

    The Disruptive 4IR in the Life Sciences: Metabolomics
    Tugizimana, Fidele ; Engel, Jasper ; Salek, Reza ; Dubery, Ian ; Piater, Lizelle ; Burgess, Karl - \ 2020
    In: Lecture Notes in Electrical Engineering Springer (Lecture Notes in Electrical Engineering ) - p. 227 - 256.
    Artificial intelligence (AI) - Big data - Cloud computing - Cloud metabolomics - Fourth industrial revolution—4IR - Machine learning - Metabolomics

    A new era of systems biology is disruptively emerging, holistically describing biochemical events at both organismal and cellular level. In this new era, emerging ‘-omics’ technologies have brought about a paradigm shift in biological sciences and research. Metabolomics, the youngest of the omics trilogy and defined as the qualitative and quantitative investigation of the entire metabolome of a biological system, has positioned itself as an indispensable methodology to investigate global biochemistry phenomena at a cellular level. Metabolomics is a multidisciplinary research field, involving a convergence of biology, chemistry, chemometrics, statistics and computer science. Metabolomics accordingly can provide unprecedented in-depth explanations and insights of the mechanisms responsible for various physiological conditions, given the innovative developments in analytical technologies (integrating artificial intelligence and machine learning), advancement in chemometric and statistical methods (big data analytics and management), and the integration of orthogonal biological approaches. Thus, the objective of this Chapter is to provide an overview of 4IR in life sciences, illustratively pointing to some aspects in the metabolomics field. The latter, in its ontology, applies different 4IR technologies including big data analytics, machine learning, cloud computing, and artificial intelligence, amongst others. The momentum and maturation of metabolomics is undeniably evident, positively disruptive, and the field has visibly revolutionised the life sciences. The application of metabolomics spans a wide spectrum of the afore-said sciences, including biomedical technology, natural products, and plant biochemistry and—biotechnology research to name a few.

    Mimicry of emergent traits amplifies coastal restoration success
    Temmink, Ralph J.M. ; Christianen, Marjolijn J.A. ; Fivash, Gregory S. ; Angelini, Christine ; Boström, Christoffer ; Didderen, Karin ; Engel, Sabine M. ; Esteban, Nicole ; Gaeckle, Jeffrey L. ; Gagnon, Karine ; Govers, Laura L. ; Infantes, Eduardo ; Katwijk, Marieke M. van; Kipson, Silvija ; Lamers, Leon P.M. ; Lengkeek, Wouter ; Silliman, Brian R. ; Tussenbroek, Brigitta I. van; Unsworth, Richard K.F. ; Yaakub, Siti Maryam ; Bouma, Tjeerd J. ; Heide, Tjisse van der - \ 2020
    Nature Communications 11 (2020)1. - ISSN 2041-1723

    Restoration is becoming a vital tool to counteract coastal ecosystem degradation. Modifying transplant designs of habitat-forming organisms from dispersed to clumped can amplify coastal restoration yields as it generates self-facilitation from emergent traits, i.e. traits not expressed by individuals or small clones, but that emerge in clumped individuals or large clones. Here, we advance restoration science by mimicking key emergent traits that locally suppress physical stress using biodegradable establishment structures. Experiments across (sub)tropical and temperate seagrass and salt marsh systems demonstrate greatly enhanced yields when individuals are transplanted within structures mimicking emergent traits that suppress waves or sediment mobility. Specifically, belowground mimics of dense root mats most facilitate seagrasses via sediment stabilization, while mimics of aboveground plant structures most facilitate marsh grasses by reducing stem movement. Mimicking key emergent traits may allow upscaling of restoration in many ecosystems that depend on self-facilitation for persistence, by constraining biological material requirements and implementation costs.

    Biased-corrected richness estimates for the Amazonian tree flora
    Steege, Hans ter; Prado, Paulo I. ; Lima, Renato A.F. de; Pos, Edwin ; Souza Coelho, Luiz de; Andrade Lima Filho, Diogenes de; Salomão, Rafael P. ; Amaral, Iêda Leão ; Almeida Matos, Francisca Dionízia de; Castilho, Carolina V. ; Phillips, Oliver L. ; Guevara, Juan Ernesto ; Jesus Veiga Carim, Marcelo de; Cárdenas López, Dairon ; Magnusson, William E. ; Wittmann, Florian ; Martins, Maria Pires ; Sabatier, Daniel ; Irume, Mariana Victória ; Silva Guimarães, José Renan da; Molino, Jean François ; Bánki, Olaf S. ; Piedade, Maria Teresa Fernandez ; Pitman, Nigel C.A. ; Ramos, José Ferreira ; Monteagudo Mendoza, Abel ; Venticinque, Eduardo Martins ; Luize, Bruno Garcia ; Núñez Vargas, Percy ; Silva, Thiago Sanna Freire ; Leão Novo, Evlyn Márcia Moraes de; Reis, Neidiane Farias Costa ; Terborgh, John ; Manzatto, Angelo Gilberto ; Casula, Katia Regina ; Honorio Coronado, Euridice N. ; Montero, Juan Carlos ; Duque, Alvaro ; Costa, Flávia R.C. ; Castaño Arboleda, Nicolás ; Schöngart, Jochen ; Zartman, Charles Eugene ; Killeen, Timothy J. ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Vasquez, Rodolfo ; Mostacedo, Bonifacio ; Demarchi, Layon O. ; Feldpausch, Ted R. ; Engel, Julien ; Petronelli, Pascal ; Baraloto, Chris ; Assis, Rafael L. ; Castellanos, Hernán ; Simon, Marcelo Fragomeni ; Medeiros, Marcelo Brilhante de; Quaresma, Adriano ; Laurance, Susan G.W. ; Rincón, Lorena M. ; Andrade, Ana ; Sousa, Thaiane R. ; Camargo, José Luís ; Schietti, Juliana ; Laurance, William F. ; Queiroz, Helder Lima de; Nascimento, Henrique Eduardo Mendonça ; Lopes, Maria Aparecida ; Sousa Farias, Emanuelle de; Magalhães, José Leonardo Lima ; Brienen, Roel ; Aymard C, Gerardo A. ; Revilla, Juan David Cardenas ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Stevenson, Pablo R. ; Feitosa, Yuri Oliveira ; Duivenvoorden, Joost F. ; Mogollón, Hugo F. ; Araujo-Murakami, Alejandro ; Ferreira, Leandro Valle ; Lozada, José Rafael ; Comiskey, James A. ; Toledo, José Julio de; Damasco, Gabriel ; Dávila, Nállarett ; Lopes, Aline ; García-Villacorta, Roosevelt ; Draper, Freddie ; Vicentini, Alberto ; Cornejo Valverde, Fernando ; Lloyd, Jon ; Gomes, Vitor H.F. ; Neill, David ; Alonso, Alfonso ; Dallmeier, Francisco ; Souza, Fernanda Coelho de; Maas, Paul ; Baker, Tim R. ; Andel, Tinde R. van; Noronha, Janaína Costa ; Barbosa, Edelcilio Marques ; Malhi, Yadvinder ; Tirado, Milton ; Wang, Ophelia ; Nascimento, Marcelo Trindade ; Flores, Bernardo Monteiro - \ 2020
    Scientific Reports 10 (2020)1. - ISSN 2045-2322

    Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia is best approximated by a logseries with aggregated individuals, where aggregation increases with rarity. By averaging several methods to estimate total richness, we confirm that over 15,000 tree species are expected to occur in Amazonia. We also show that using ten times the number of plots would result in an increase to just ~50% of those 15,000 estimated species. To get a more complete sample of all tree species, rigorous field campaigns may be needed but the number of trees in Amazonia will remain an estimate for years to come.

    Regularized Multivariate Analysis of Variance
    Engel, J. ; Houthuijs, Kas J. ; Vasiliou, Vasilis ; Charkoftaki, Georgia - \ 2020
    In: Comprehensive Chemometrics / Brown, Steven, Tauler, Romà, Walczak, Beata, Elsevier - ISBN 9780444641663 - p. 479 - 494.
    Experimental designs in modern experiments in the life sciences often comprise multiple factors. Usually, the number of response variables vastly exceeds the sample size and well-established methods for analysis of multifactor data such as multivariate analysis of variance (MANOVA) cannot be applied. This issue can be circumvented by combining MANOVA with a shrinkage estimator of the correlation matrix. This chapter discusses the principles of this regularized MANOVA (rMANOVA) approach. Two examples from untargeted metabolomics studies are used to demonstrate application of rMANOVA in practice. Focus lies on identification of significant main and interaction effects and the variables associated to them
    A comparison of high‑throughput plasma NMR protocols for comparative untargeted metabolomics (Metabolomics
    Bliziotis, Nikolaos G. ; Engelke, Udo F.H. ; Aspers, Ruud L.E.G. ; Engel, Jasper ; Deinum, Jaap ; Timmers, Henri J.L.M. ; Wevers, Ron A. ; Kluijtmans, Leo A.J. - \ 2020
    Metabolomics 16 (2020)6. - ISSN 1573-3882

    Following publication of the original article, the authors would like to correct a sentence in the paragraph “1H-NMR spectra were recorded at 298 K…” under the heading “NMR experiments”. The sentence currently reads: “The LED pulse sequence had the form -RD-901-G1- 1801-G1-901-G2-T-901-G1-1801-G1-901-G2-t-901-acquire FID, where RD is a relaxation delay, 901 is a 901 RF pulse, G1 is the pulsed-field gradient that is applied to allow editing, 1801 is a 1801 RF pulse, G2 is a spoil gradient applied to remove unwanted magnetization components. The diffusion delay Δ is the time during which the molecules are allowed to diffuse—this is the period (901-G1-1801-G1- 901-G2-T-); and t is a delay to allow the longitudinal eddy currents caused within the sample to decay (Beckonert et al. 2007).” The sentence should read: “The LED pulse sequence had the form -RD-90°-G1- 180°-G1-90°-G2-T-90°-G1-180°-G1-90°-G2-t-90°-acquire FID, where RD is a relaxation delay, 90° is a 90° RF pulse, G1 is the pulsed-field gradient that is applied to allow editing, 180° is a 180° RF pulse, G2 is a spoil gradient applied to remove unwanted magnetization components. The diffusion delay ? is the time during which the molecules are allowed to diffuse—this is the period (90°-G1-180°-G1-90°-G2 T-); and t is a delay to allow the longitudinal eddy currents caused within the sample to decay (Beckonert et al. 2007).” This has been corrected with this erratum.

    A comparison of high-throughput plasma NMR protocols for comparative untargeted metabolomics
    Bliziotis, Nikolaos G. ; Engelke, Udo F.H. ; Aspers, Ruud L.E.G. ; Engel, Jasper ; Deinum, Jaap ; Timmers, Henri J.L.M. ; Wevers, Ron A. ; Kluijtmans, Leo A.J. - \ 2020
    Metabolomics 16 (2020)5. - ISSN 1573-3882
    Classification - High-throughput - Large scale - LED - Metabolomics - NMR

    Introduction: When analyzing the human plasma metabolome with Nuclear Magnetic Resonance (NMR) spectroscopy, the Carr–Purcell–Meiboom–Gill (CPMG) experiment is commonly employed for large studies. However, this process can lead to compromised statistical analyses due to residual macromolecule signals. In addition, the utilization of Trimethylsilylpropanoic acid (TSP) as an internal standard often leads to quantification issues, and binning, as a spectral summarization step, can result in features not clearly assignable to metabolites. Objectives: Our aim was to establish a new complete protocol for large plasma cohorts collected with the purpose of describing the comparative metabolic profile of groups of samples. Methods: We compared the conventional CPMG approach to a novel procedure that involves diffusion NMR, using the Longitudinal Eddy-Current Delay (LED) experiment, maleic acid (MA) as the quantification reference and peak picking for spectral reduction. This comparison was carried out using the ultrafiltration method as a gold standard in a simple sample classification experiment, with Partial Least Squares–Discriminant Analysis (PLS-DA) and the resulting metabolic signatures for multivariate data analysis. In addition, the quantification capabilities of the method were evaluated. Results: We found that the LED method applied was able to detect more metabolites than CPMG and suppress macromolecule signals more efficiently. The complete protocol was able to yield PLS-DA models with enhanced classification accuracy as well as a more reliable set of important features than the conventional CPMG approach. Assessment of the quantitative capabilities of the method resulted in good linearity, recovery and agreement with an established amino acid assay for the majority of the metabolites tested. Regarding repeatability, ~ 85% of all peaks had an adequately low coefficient of variation (< 30%) in replicate samples. Conclusion: Overall, our comparison yielded a high-throughput untargeted plasma NMR protocol for optimized data acquisition and processing that is expected to be a valuable contribution in the field of metabolic biomarker discovery.

    Prevalence of coeliac disease in Northwest China: heterogeneity across Northern Silk road ethnic populations
    Zhou, Chunyan ; Gao, Feng ; Gao, Jinyan ; Yuan, Juanli ; Lu, Jiajie ; Sun, Zhenzhu ; Xu, Mengyu ; Engel, J. ; Hui, Wenjia ; Gilissen, L.J.W.J. ; Chen, Hongbing - \ 2020
    Alimentary Pharmacology and Therapeutics 51 (2020)11. - ISSN 0269-2813 - p. 1116 - 1129.
    Background: Epidemiological data of coeliac disease are lacking from the central Asian region. Aims: To verify the occurrence of coeliac disease amongst four major ethnic groups of Xinjiang Uyghur Autonomus Region, China. Methods: 2277 in-patients with gastrointestinal symptoms (1391 Han, 608 Uyghur, 146 Kazakh and 132 Hui; mean age: 54 ± 12.8 years) were included. Total IgA, anti-deamidated gliadin peptide (DGP)-IgG, and anti-tissue transglutaminase (anti-tTG)-IgA were analysed. All antibody-positive subjects were further tested for endomysial (EMA) antibodies and were HLA genotyped. All subjects with antibody positivity were asked to undergo intestinal biopsy. In addition, a subset of antibody-negative subjects were tested for HLA-DQA1and DQB1. Results: Among the 2277 subjects, 29 subjects were defined as coeliac disease au-toimmune (positive results for anti-tTG IgA and EMA-IgA) (1.27%; 95% confidence interval, 0.81%-1.73%), eight of them underwent biopsy and all showed coeliac dis-ease histology (0.35%; 95% Cl, 0.11%-0.59%). The frequency of coeliac disease au-toimmunity was lowest among the Han (0.79%), followed by the Uyghur (1.81%), the Kazakh (2.05%) and the Hui (3.03%). The frequency of the HLA-DQ2 and/or DQ8 haplotype was highest in the Uyghur (52.1%), followed by the Hui (44.4%), the Kazakh (40.0%) and the Han (39.4%). Besides, a three times higher frequency of coeliac dis-ease autoimmunity was found among rural living subjects with significantly higher wheat consumption compared to urban living subjects (3.16% vs 0.97%, P < 0.01). Conclusions: In Xinjiang, coeliac disease does occur, especially in the rural area. The HLA haplotype and environment play key roles in the development of coeliac disease.
    Transport of young veal calves: effects of pre-transport diet, transport duration and condition on clinical health, behaviour and antibiotic treatments
    Marcato, F. ; Brand, H. van den; Engel, B. ; Kemp, B. ; Wolthuis-Fillerup, M. ; Reenen, C.G. van - \ 2020
    In: WIAS Annual Conference 2020. - Wageningen : Wageningen University & Research - p. 20 - 20.
    Large expert-curated database for benchmarking document similarity detection in biomedical literature search
    Brown, Peter ; Zhou, Yaoqi ; Tan, Aik Choon ; El-Esawi, Mohamed A. ; Liehr, Thomas ; Blanck, Oliver ; Gladue, Douglas P. ; Almeida, Gabriel M.F. ; Cernava, Tomislav ; Sorzano, Carlos O. ; Yeung, Andy W.K. ; Engel, Michael S. ; Chandrasekaran, Arun R. ; Muth, Thilo ; Staege, Martin S. ; Daulatabad, Swapna V. ; Widera, Darius ; Zhang, Junpeng ; Meule, Adrian ; Honjo, Ken ; Pourret, Olivier ; Yin, Cong Cong ; Zhang, Zhongheng ; Cascella, Marco ; Flegel, Willy A. ; Goodyear, Carl S. ; Raaij, Mark J. van; Bukowy-Bieryllo, Zuzanna ; Campana, Luca G. ; Kurniawan, Nicholas A. ; Lalaouna, David ; Hüttner, Felix J. ; Ammerman, Brooke A. ; Ehret, Felix ; Cobine, Paul A. ; Tan, Ene Choo ; Han, Hyemin ; Xia, Wenfeng ; McCrum, Christopher ; Dings, Ruud P.M. ; Marinello, Francesco ; Nilsson, Henrik ; Nixon, Brett ; Voskarides, Konstantinos ; Yang, Long ; Costa, Vincent D. ; Bengtsson-Palme, Johan ; Bradshaw, William ; Smeets, Paul A.M. ; Heijne, Marloes - \ 2019
    Database : the Journal of Biological Databases and Curation 2019 (2019). - ISSN 1758-0463 - p. 1 - 67.

    Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science.

    Critical comparison of methods for fault diagnosis in metabolomics data
    Koeman, M. ; Engel, J. ; Jansen, J. ; Buydens, L. - \ 2019
    Scientific Reports 9 (2019)1. - ISSN 2045-2322
    Platforms like metabolomics provide an unprecedented view on the chemical versatility in biomedical samples. Many diseases reflect themselves as perturbations in specific metabolite combinations. Multivariate analyses are essential to detect such combinations and associate them to specific diseases. For this, usually targeted discriminations of samples associated to a specific disease from non-diseased control samples are used. Such targeted data interpretation may not respect the heterogeneity of metabolic responses, both between diseases and within diseases. Here we show that multivariate methods that find any set of perturbed metabolites in a single patient, may be employed in combination with data collected with a single metabolomics technology to simultaneously investigate a large array of diseases. Several such untargeted data analysis approaches have been already proposed in other fields to find both expected and unexpected perturbations, e.g. in Statistical Process Control. We have critically compared several of these approaches for their sensitivity and their correct identification of the specifically perturbed metabolites. Also a new approach is introduced for this purpose. The newly introduced Sparse Mean approach, which we find here as most sensitive and best able to identify the specifically perturbed metabolites, turns metabolomics into an untargeted diagnostic platform. Aside from metabolomics, the proposed approach may greatly benefit fault diagnosis with untargeted analyses in many other fields, such as Industrial Process Control, food Adulteration Detection, and Intrusion Detection.
    Scientific opinion on the proposed amendment of the EU specifications for titanium dioxide (E 171) with respect to the inclusion of additional parameters related to its particle size distribution
    Younes, Maged ; Aquilina, Gabriele ; Castle, Laurence ; Engel, Karl Heinz ; Fowler, Paul ; Frutos Fernandez, Maria Jose ; Gürtler, Rainer ; Gundert-Remy, Ursula ; Husøy, Trine ; Mennes, Wim ; Agneta Oskarsson, Peter Moldeus ; Rainieri, Sandra ; Shah, Romina ; Waalkens-Berendsen, Ine ; Wölfle, Detlef ; Gaffet, Eric ; Mast, Jan ; Peters, Ruud ; Rincon, Ana Maria ; Fürst, Peter - \ 2019
    EFSA Journal 17 (2019)7. - ISSN 1831-4732
    E 171 - food additive - particle size - specifications - Titanium dioxide

    The present opinion deals with the assessment of the data provided by interested business operators in support of an amendment of the EU specifications for titanium dioxide (E 171) with respect to the inclusion of additional parameters related to its particle size distribution. Titanium dioxide which is used as a food additive E 171 in food undergoes no surface treatment and is not coated. It consists of anatase or rutile generally containing small amounts of the other phase (rutile or anatase, < 2% m/m) and it may also contain small quantities (< 0.5%) of constituent particle growth and crystal phase control agents (alumina, sodium or potassium in combination with phosphate). Particle size analyses, by TEM, SEM, XDC or DC, have been carried out on five commercial brands of anatase E 171 and one of rutile E 171 manufactured by the only three EU manufacturers that, according to information submitted by interested business operators, produce food-grade titanium dioxide. Interested business operators proposed to introduce in the EU specifications for E 171 a specification of more than 100 nm for median Feret min diameter and less than 50% of the number of constituent particles below 100 nm; measured by EM in both cases. The Panel, after reviewing the data, concluded that a specification of more than 100 nm for median minimal external dimension, equivalent to less than 50% of the number of constituent particles with a median minimal external dimension below 100 nm, should be inserted in the current EU specifications. The Panel considered that the conclusions made, and the uncertainties identified, in the previous EFSA assessments on E 171 remain valid. The Panel reiterates the need for the further research as recommended in the previous opinions in order to decrease the level of uncertainty and acknowledged that additional studies with characterised E 171 are being carried out by interested business operators.

    Coupling DAD and MS data in untargeted metabolomics
    Wehrens, H.R.M.J. ; Engel, J. ; Treuren, R. van; Vos, R. de; Haug, Kenneth ; Rocca-Serra, Philippe - \ 2019
    Resilience in Talcahuano, Chile: appraising local disaster response
    Engel, Karen Elisabeth ; Warner, Jeroen Frank - \ 2019
    Disaster Prevention and Management 28 (2019)5. - ISSN 0965-3562 - p. 585 - 602.
    Community response - Disaster

    Purpose: The purpose of this paper is to present the findings of a qualitative and exploratory study aimed at learning more about the local forms of resilience that emerged in two localities (one rural and one urban locality) in Talcahuano, Chile, in response to the major earthquake and devastating tsunami that hit them on February 27, 2010. Design/methodology/approach: To ensure that people’s experiences remained leading throughout the study, data were collected in the field by the first author over a period of 13 months using a variety of qualitative methods. The primary methods were observation, participation and semi-structured interviews with a variety of actors, ranging from community members to local leaders and emergency professionals. For the analysis, a scheme was used that categorizes manifested resilience using two dimensions: damage and responsiveness. Since this scheme has been mostly used to evaluate tree populations, it was adapted to fit the appraisal of a social system. Findings: The findings suggest that damage levels in the two communities were similar, but that the responsiveness was not. One locality revealed high levels of resilience, while the other exposed increased susceptibility to future similar events. Originality/value: This research initiative was relevant because it exposed actual resilience. Also, the specificities of the findings enable insights about prevalent vulnerability, in particular the local capacity of response, and that can be used to elaborate concrete earthquake/tsunami disaster scenarios and design local disaster risk reduction interventions.

    Rarity of monodominance in hyperdiverse Amazonian forests
    Steege, Hans Ter; Henkel, Terry W. ; Helal, Nora ; Marimon, Beatriz S. ; Marimon-Junior, Ben Hur ; Huth, Andreas ; Groeneveld, Jürgen ; Sabatier, Daniel ; Souza Coelho, Luiz de; Andrade Lima Filho, Diogenes de; Salomão, Rafael P. ; Amaral, Iêda Leão ; Almeida Matos, Francisca Dionízia de; Castilho, Carolina V. ; Phillips, Oliver L. ; Guevara, Juan Ernesto ; Jesus Veiga Carim, Marcelo de; Cárdenas López, Dairon ; Magnusson, William E. ; Wittmann, Florian ; Irume, Mariana Victória ; Martins, Maria Pires ; Silva Guimarães, José Renan da; Molino, Jean François ; Bánki, Olaf S. ; Piedade, Maria Teresa Fernandez ; Pitman, Nigel C.A. ; Mendoza, Abel Monteagudo ; Ramos, José Ferreira ; Luize, Bruno Garcia ; Moraes de Leão Novo, Evlyn Márcia ; Núñez Vargas, Percy ; Silva, Thiago Sanna Freire ; Venticinque, Eduardo Martins ; Manzatto, Angelo Gilberto ; Reis, Neidiane Farias Costa ; Terborgh, John ; Casula, Katia Regina ; Honorio Coronado, Euridice N. ; Montero, Juan Carlos ; Feldpausch, Ted R. ; Duque, Alvaro ; Costa, Flávia R.C. ; Arboleda, Nicolás Castaño ; Schöngart, Jochen ; Killeen, Timothy J. ; Vasquez, Rodolfo ; Mostacedo, Bonifacio ; Demarchi, Layon O. ; Assis, Rafael L. ; Baraloto, Chris ; Engel, Julien ; Petronelli, Pascal ; Castellanos, Hernán ; Medeiros, Marcelo Brilhante de; Quaresma, Adriano ; Simon, Marcelo Fragomeni ; Andrade, Ana ; Camargo, José Luís ; Laurance, Susan G.W. ; Laurance, William F. ; Rincón, Lorena M. ; Schietti, Juliana ; Sousa, Thaiane R. ; Sousa Farias, Emanuelle de; Lopes, Maria Aparecida ; Magalhães, José Leonardo Lima ; Mendonça Nascimento, Henrique Eduardo ; Lima de Queiroz, Helder ; Aymard C, Gerardo A. ; Brienen, Roel ; Revilla, Juan David Cardenas ; Vieira, Ima Célia Guimarães ; Cintra, Bruno Barçante Ladvocat ; Stevenson, Pablo R. ; Feitosa, Yuri Oliveira ; Duivenvoorden, Joost F. ; Mogollón, Hugo F. ; Araujo-Murakami, Alejandro ; Ferreira, Leandro Valle ; Lozada, José Rafael ; Comiskey, James A. ; Toledo, José Julio de; Damasco, Gabriel ; Dávila, Nállarett ; Draper, Freddie ; García-Villacorta, Roosevelt ; Lopes, Aline ; Vicentini, Alberto ; Alonso, Alfonso ; Dallmeier, Francisco ; Gomes, Vitor H.F. ; Lloyd, Jon ; Neill, David ; Aguiar, Daniel Praia Portela de; Arroyo, Luzmila ; Carvalho, Fernanda Antunes ; Souza, Fernanda Coelho de; Amaral, Dário Dantas do; Feeley, Kenneth J. ; Gribel, Rogerio ; Pansonato, Marcelo Petratti ; Barlow, Jos ; Berenguer, Erika ; Ferreira, Joice ; Fine, Paul V.A. ; Guedes, Marcelino Carneiro ; Jimenez, Eliana M. ; Licona, Juan Carlos ; Peñuela Mora, Maria Cristina ; Villa, Boris ; Cerón, Carlos ; Maas, Paul ; Silveira, Marcos ; Stropp, Juliana ; Thomas, Raquel ; Baker, Tim R. ; Daly, Doug ; Dexter, Kyle G. ; Huamantupa-Chuquimaco, Isau ; Milliken, William ; Pennington, Toby ; Ríos Paredes, Marcos ; Fuentes, Alfredo ; Klitgaard, Bente ; Pena, José Luis Marcelo ; Peres, Carlos A. ; Silman, Miles R. ; Tello, J.S. ; Chave, Jerome ; Cornejo Valverde, Fernando ; Fiore, Anthony Di; Hilário, Renato Richard ; Phillips, Juan Fernando ; Rivas-Torres, Gonzalo ; Andel, Tinde R. van; Hildebrand, Patricio von; Noronha, Janaína Costa ; Barbosa, Edelcilio Marques ; Barbosa, Flávia Rodrigues ; Matos Bonates, Luiz Carlos de; Sá Carpanedo, Rainiellen de; Dávila Doza, Hilda Paulette ; Fonty, Émile ; GómeZárate Z, Ricardo ; Gonzales, Therany ; Gallardo Gonzales, George Pepe ; Hoffman, Bruce ; Junqueira, André Braga ; Malhi, Yadvinder ; Andrade Miranda, Ires Paula de; Pinto, Linder Felipe Mozombite ; Prieto, Adriana ; Jesus Rodrigues, Domingos de; Rudas, Agustín ; Ruschel, Ademir R. ; Silva, Natalino ; Vela, César I.A. ; Vos, Vincent Antoine ; Zent, Egleé L. ; Zent, Stanford ; Weiss Albuquerque, Bianca ; Cano, Angela ; Carrero Márquez, Yrma Andreina ; Correa, Diego F. ; Costa, Janaina Barbosa Pedrosa ; Flores, Bernardo Monteiro ; Galbraith, David ; Holmgren, Milena ; Kalamandeen, Michelle ; Nascimento, Marcelo Trindade ; Oliveira, Alexandre A. ; Ramirez-Angulo, Hirma ; Rocha, Maira ; Scudeller, Veridiana Vizoni ; Sierra, Rodrigo ; Tirado, Milton ; Umaña Medina, Maria Natalia ; Heijden, Geertje van der; Vilanova Torre, Emilio ; Vriesendorp, Corine ; Wang, Ophelia ; Young, Kenneth R. ; Ahuite Reategui, Manuel Augusto ; Baider, Cláudia ; Balslev, Henrik ; Cárdenas, Sasha ; Casas, Luisa Fernanda ; Farfan-Rios, William ; Ferreira, Cid ; Linares-Palomino, Reynaldo ; Mendoza, Casimiro ; Mesones, Italo ; Torres-Lezama, Armando ; Giraldo, Ligia Estela Urrego ; Villarroel, Daniel ; Zagt, Roderick ; Alexiades, Miguel N. ; Oliveira, Edmar Almeida de; Garcia-Cabrera, Karina ; Hernandez, Lionel ; Palacios Cuenca, Walter ; Pansini, Susamar ; Pauletto, Daniela ; Ramirez Arevalo, Freddy ; Sampaio, Adeilza Felipe ; Valderrama Sandoval, Elvis H. ; Valenzuela Gamarra, Luis ; Levesley, Aurora ; Pickavance, Georgia ; Melgaço, Karina - \ 2019
    Scientific Reports 9 (2019). - ISSN 2045-2322

    Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors.

    Developing a stronger and better - tasting mushroom with unique features : An innovative multi-disciplinary approach
    Baars, Johan ; Mumm, Roland ; Stijger, Ineke ; Engel, Jasper ; Wehrens, Ron - \ 2019
    Wageningen : Stichting Wageningen Research, Wageningen Plant Research, Business unit Plant Breeding (Rapport / Stichting Wageningen Research, Wageningen Plant Research, Business unit Plant Breeding 2019-1) - 36
    Nederland is een van de grootste producenten van champignons in de wereld. Er zijn echter de laatste decennia slechts weinig nieuwe champignon-gebaseerde producten op de markt gekomen. Dit project beoogt een aanzet te leveren tot de ontwikkeling van champignonrassen die zich onderscheiden in smaak en die zich daarnaast zichtbaar onderscheiden van de huidige commercieel verkrijgbare champignons. Als eerste stap voor dergelijk toekomstig veredelingsonderzoek moeten metabolieten in champignons worden geïdentificeerd die voorspellende waarde hebben voor de smaak. Als dergelijke merker-moleculen betrouwbaar zijn geïdentificeerd, kan in een vervolgproject daadwerkelijk een veredelingstraject worden opgestart. Uit een collectie van ongeveer 250 wildisolaten van de champignons is een selectie gemaakt van 43 isolaten die de gehele genetische variatie van de collectie min of meer omvatten. Deze isolaten zijn opgekweekt in 6 verschillende teeltproeven en aangeboden aan een sensorisch panel dat verschillende aspecten van de smaak heeft beoordeeld. Statistische analyse van de resultaten laat zien dat hoewel voor de meeste isolaten de smaak erg lijkt op de commercieel beschikbare witte champignons, er een aantal isolaten zijn die anders smaken. Dezelfde champignons die zijn aangeboden aan het sensorisch panel zijn daarnaast onderzocht op metaboliet samenstelling. Het is nog niet mogelijk gebleken om de verschillen in smaak te koppelen aan specifieke metaboliet samenstellingen in de champignons. Een van de oorzaken is de grote variatie in beoordeling van smaakaspecten door het sensorisch panel. Daarnaast bleek bij vergelijking van de verschillende batches van controle ras A15, ook batch tot batch variatie op te treden in metabolietgehalten. Vervolgens is geprobeerd om de variatie in beoordeling door het sensorisch smaakpanel te verminderen door: • Veel minder rassen aanbieden aan het sensorisch panel • Rassen met grootst mogelijk verschil in smaak aanbieden • Interne herhalingen aanbieden als extra controle. Helaas bleek ook bij deze opzet het niet mogelijk om de beoordeling van de verschillende aspecten van champignonsmaak te koppelen aan merkermoleculen.
    Correcting fresh grass allowance for rejected patches due to excreta in intensive grazing systems for dairy cows
    Klootwijk, Cindy W. ; Holshof, Gertjan ; Boer, Imke J.M. de; Pol-Van Dasselaar, Agnes Van den; Engel, Bas ; Middelaar, Corina E. Van - \ 2019
    Journal of Dairy Science 102 (2019)11. - ISSN 0022-0302 - p. 10451 - 10459.
    fresh grass allowance - intensive grazing - rejected patches - rising plate meter

    Dairy farms with intensive grazing systems combine grazing with supplemental feeding, which can be challenging because an incorrect balance between fresh grass allowance and feed supplementation results in inefficient use of the pasture, lower feed efficiency, and potential decreases in animal production. When estimating fresh grass allowance, we currently do not correct for the formation of rejected patches (RP) surrounding excreta, which can lead to overestimation of the potential fresh grass intake and hampers optimal grazing. In this study, therefore, we aim to quantify the formation of RP in intensive grazing systems and improve the quantification of fresh grass allowance. To do so, we studied 2 grazing systems (i.e., compartmented continuous grazing and strip grazing) that differ in key grazing characteristics, such as pre- and post-grazing heights and period of regrowth. The experiment was performed from April to October in 2016 and 2017 with 60 dairy cows at a fixed stocking rate of 7.5 cows/ha. Average pre-grazing grass height was measured with a rising plate meter. To quantify the formation of RP after grazing, individual grass height measurements were conducted after grazing and classified as RP or not, based on visual assessment. Our analysis showed that the average percentage of grassland covered with RP increased from around 22% at the end of May to around 43% at the end of July/beginning of August, and these percentages do not differ across grazing systems. The percentage of grassland covered with RP should be subtracted from the total grazed area to better estimate true fresh grass allowance.

    The effect of intensive grazing systems on the rising plate meter calibration for perennial ryegrass pastures
    Klootwijk, Cindy W. ; Holshof, Gertjan ; Pol-van Dasselaar, Agnes van den; Helvoort, Koen L.M. van; Engel, Bas ; Boer, Imke J.M. de; Middelaar, Corina E. van - \ 2019
    Journal of Dairy Science 102 (2019)11. - ISSN 0022-0302 - p. 10439 - 10450.
    forage management - herbage mass - intensive grazing - rising plate meter

    The rising plate meter (RPM) is used to measure grass height, which subsequently is used in a calibration equation to estimate herbage mass (HM), an important parameter for optimization of feed management in grazing systems. The RPM is placed on the sward and measures the resistance of the sward toward the plate, which depends not only on grass length, but also on sward structure. The accuracy of the calibration equation for the RPM to estimate HM across grazing systems, however, has not yet been evaluated. Therefore, our aim was to analyze the effect of intensive grazing systems on RPM calibration for perennial ryegrass pastures. To do so, we studied 2 grazing systems: compartmented continuous grazing (CCG) and strip grazing (SG), which differ in key grazing characteristics, such as pre- and post-grazing heights and period of regrowth, that may influence tiller density and vertical flexibility of the sward. The experiment was performed from April until October in 2016 and 2017 with 60 dairy cows, at a fixed stocking rate of 7.5 cows per hectare. To calibrate the RPM, 256 direct measurements of HM >4 cm (i.e., above stubble) were collected by cutting and weighing plots of grass for CCG and SG. Our main interest was in the HM above stubble because this is consumed by cows. Herbage mass <4 cm represents the stubble left after grazing. Differences in HM <4 cm may (partially) explain differences in HM >4 cm between the grazing systems. Therefore, HM <4 cm was additionally measured on 4 out of every 8 plots per grazing system by cutting out quadrats to 0 cm with an electric grass trimmer. Our results showed an average error margin in our calibration equations of 25 to 31%, expressed as the root mean square error of prediction (RMSEP) as a percentage of the observed HM >4 cm. Differences between grazing systems were relatively small, and including grazing system as a factor in the regression model to explain the increase in HM per centimeter of grass did not reduce the RMSEP of the model to any relevant extent. On the other hand, HM <4 cm was significantly greater on CCG compared with SG, with 2,042 kg of DM per hectare for CCG and 1,676 kg of DM per hectare for SG. The HM <4 cm, however, is not used for grazing, and this difference was not reflected in the HM >4 cm. Our results indicate that we can use one region-specific calibration equation for perennial ryegrass pastures across intensive grazing systems, despite relatively large differences in pre- and post-grazing heights and period of regrowth.

    Patterns of distribution and drivers of change in shallow seagrass and algal assemblages of a non-estuarine Southern Caribbean mangrove lagoon
    Debrot, A.O. ; Hylkema, A. ; Vogelaar, W. ; Prud'homme van Reine, W.F. ; Engel, M.S. ; Hateren, J.A. van; Meesters, E.H. - \ 2019
    Aquatic Botany 159 (2019). - ISSN 0304-3770
    Drivers of assemblage structure - Mangrove land reclamation - Non-estuarine mangrove system model - Tropical seagrass

    Shallow marine macrophyte communities serve key roles in the tropical coastal ecosystem but are undergoing large and rapid deterioration worldwide, as is also the case in the non-estuarine mangrove lagoon of Lac Bay, Bonaire, in the Southern Caribbean. To help better understand both the drivers of assemblage structure and potential consequences of the changes taking place in the bay, we here quantify and describe the distribution of algal and seagrass assemblages along the environmental gradient from the turbid, inner mangrove pools to the clear, open bay conditions, based on 98 randomly-chosen, 4 m2 survey plots. Seven assemblages were described along this land-to-sea gradient, five of which were dominated by marine macrophytes, one by sponges and one by a polychaete. With exception of the hypersaline backwaters which were devoid of benthic macrophyte vegetation, isolated mangrove pools showed the lowest total benthic cover, species richness and biodiversity of all habitats. Salinity and substrate particle-size composition accounted for most variation between the different assemblages and appear to be the key known determinants of assemblage composition. We developed a conceptual model to help disentangle the relationship between and the relative roles of the two principal drivers, as part of a cascade of effects which ultimately result from terrestrial run-off into the bay as mediated by mangrove encroachment into the bay. The model links spatial patterns to ongoing processes and implies that the assemblage patterns described are not only a reflection of, but also allow prediction of how the assemblages develop through time.

    Effects of pre-transport diet, transport duration and type of vehicle on metabolism and immunity of young veal calves
    Marcato, F. ; Brand, H. van den; Kemp, B. ; Engel, B. ; Wolthuis-Fillerup, M. ; Reenen, C.G. van - \ 2019
    In: Proceedings of the 17th International Conference on Production Diseases in Farm Animals. - Bern, Switserland : University of Bern - ISBN 9783906813936 - p. 97 - 97.
    Transport is one of the largest challenges faced by veal calves. The first transport occurs when calves are transported from the dairy farms to a collection center at 14-20 days of age. Then, with a second transport, calves are brought to the veal farms. During transport and at the collection center, calves are mixed and exposed to new environmental conditions and microorganisms. Consequently, transport is associated with a high level of stress and an increase in infectious disease incidence. As a consequence of stress, the metabolism, immunity and health of calves might be compromised. Previous studies explored effects of transport on hematological, metabolic and immunological variables of calves. However, these studies focused just on one single factor (e.g. transport duration or pre-transport nutrition) and not on a combination of multiple factors associated with transport. The current research aimed to investigate effects of a pre-transport diet, transport duration and type of vehicle on metabolic and immunological variables of young calves upon arrival at the veal farm.
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