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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Global distribution of earthworm diversity
Phillips, Helen R.P. ; Guerra, Carlos A. ; Bartz, Marie L.C. ; Briones, Maria J.I. ; Brown, George ; Crowther, Thomas W. ; Ferlian, Olga ; Gongalsky, Konstantin B. ; Hoogen, Johan Van Den; Krebs, Julia ; Orgiazzi, Alberto ; Routh, Devin ; Schwarz, Benjamin ; Bach, Elizabeth M. ; Bennett, Joanne ; Brose, Ulrich ; Decaëns, Thibaud ; König-Ries, Birgitta ; Loreau, Michel ; Mathieu, Jérôme ; Mulder, Christian ; Putten, Wim H. Van Der; Ramirez, Kelly S. ; Rillig, Matthias C. ; Russell, David ; Rutgers, Michiel ; Thakur, Madhav P. ; Vries, Franciska T. De; Wall, Diana H. ; Wardle, David A. ; Arai, Miwa ; Ayuke, Fredrick O. ; Baker, Geoff H. ; Beauséjour, Robin ; Bedano, José C. ; Birkhofer, Klaus ; Blanchart, Eric ; Blossey, Bernd ; Bolger, Thomas ; Bradley, Robert L. ; Callaham, Mac A. ; Capowiez, Yvan ; Caulfield, Mark E. ; Choi, Amy ; Crotty, Felicity V. ; Dávalos, Andrea ; Diaz Cosin, Darío J. ; Dominguez, Anahí ; Duhour, Andrés Esteban ; Eekeren, Nick Van; Emmerling, Christoph ; Falco, Liliana B. ; Fernández, Rosa ; Fonte, Steven J. ; Fragoso, Carlos ; Franco, André L.C. ; Fugère, Martine ; Fusilero, Abegail T. ; Gholami, Shaieste ; Gundale, Michael J. ; Gutiérrez Lopez, Monica ; Hackenberger, Davorka K. ; Hernández, Luis M. ; Hishi, Takuo ; Holdsworth, Andrew R. ; Holmstrup, Martin ; Hopfensperger, Kristine N. ; Lwanga, Esperanza Huerta ; Huhta, Veikko ; Hurisso, Tunsisa T. ; Iannone, Basil V. ; Iordache, Madalina ; Joschko, Monika ; Kaneko, Nobuhiro ; Kanianska, Radoslava ; Keith, Aidan M. ; Kelly, Courtland A. ; Kernecker, Maria L. ; Klaminder, Jonatan ; Koné, Armand W. ; Kooch, Yahya ; Kukkonen, Sanna T. ; Lalthanzara, H. ; Lammel, Daniel R. ; Lebedev, Iurii M. ; Li, Yiqing ; Jesus Lidon, Juan B. ; Lincoln, Noa K. ; Loss, Scott R. ; Marichal, Raphael ; Matula, Radim ; Moos, Jan Hendrik ; Moreno, Gerardo ; Mor n-Ríos, Alejandro ; Muys, Bart ; Neirynck, Johan ; Norgrove, Lindsey ; Novo, Marta ; Nuutinen, Visa ; Nuzzo, Victoria ; Mujeeb Rahman, P. ; Pansu, Johan ; Paudel, Shishir ; Pérès, Guénola ; Pérez-Camacho, Lorenzo ; Piñeiro, Raúl ; Ponge, Jean François ; Rashid, Muhammad Imtiaz ; Rebollo, Salvador ; Rodeiro-Iglesias, Javier ; Rodríguez, Miguel ; Roth, Alexander M. ; Rousseau, Guillaume X. ; Rozen, Anna ; Sayad, Ehsan ; Schaik, Loes Van; Scharenbroch, Bryant C. ; Schirrmann, Michael ; Schmidt, Olaf ; Schröder, Boris ; Seeber, Julia ; Shashkov, Maxim P. ; Singh, Jaswinder ; Smith, Sandy M. ; Steinwandter, Michael ; Talavera, José A. ; Trigo, Dolores ; Tsukamoto, Jiro ; Valença, Anne W. De; Vanek, Steven J. ; Virto, Iñigo ; Wackett, Adrian A. ; Warren, Matthew W. ; Wehr, Nathaniel H. ; Whalen, Joann K. ; Wironen, Michael B. ; Wolters, Volkmar ; Zenkova, Irina V. ; Zhang, Weixin ; Cameron, Erin K. ; Eisenhauer, Nico - \ 2019
Science 366 (2019)6464. - ISSN 0036-8075 - p. 480 - 485.

Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.

The value of using hydrological datasets for water allocation decisions: earth observations, hydrological models, and seasonal forecasts
Kaune Schmidt, Alexander José - \ 2019
Wageningen University. Promotor(en): C.M.S. de Fraiture, co-promotor(en): M.G.F. Werner. - Leiden : CRC Press/Balkema - ISBN 9780367429553 - 166
Macrophage-Specific NF-κB Activation Dynamics Can Segregate Inflammatory Bowel Disease Patients
Papoutsopoulou, Stamatia ; Burkitt, Michael D. ; Bergey, François ; England, Hazel ; Hough, Rachael ; Schmidt, Lorraine ; Spiller, David G. ; White, Michael H.R. ; Paszek, Pawel ; Jackson, Dean A. ; Martins Dos Santos, Vitor A.P. ; Sellge, Gernot ; Pritchard, D.M. ; Campbell, Barry J. ; Müller, Werner ; Probert, Chris S. - \ 2019
Frontiers in Immunology 10 (2019). - ISSN 1664-3224 - 11 p.
The heterogeneous nature of inflammatory bowel disease (IBD) presents challenges, particularly when choosing therapy. Activation of the NF-κB transcription factor is a highly regulated, dynamic event in IBD pathogenesis. Using a lentivirus approach, NF-κB-regulated luciferase was expressed in patient macrophages, isolated from frozen peripheral blood mononuclear cell samples. Following activation, samples could be segregated into three clusters based on the NF-κB-regulated luciferase response. The ulcerative colitis (UC) samples appeared only in the hypo-responsive Cluster 1, and in Cluster 2. Conversely, Crohn's disease (CD) patients appeared in all Clusters with their percentage being higher in the hyper-responsive Cluster 3. A positive correlation was seen between NF-κB-induced luciferase activity and the concentrations of cytokines released into medium from stimulated macrophages, but not with serum or biopsy cytokine levels. Confocal imaging of lentivirally-expressed p65 activation revealed that a higher proportion of macrophages from CD patients responded to endotoxin lipid A compared to controls. In contrast, cells from UC patients exhibited a shorter duration of NF-κB p65 subunit nuclear localization compared to healthy controls, and CD donors. Analysis of macrophage cytokine responses and patient metadata revealed a strong correlation between CD patients who smoked and hyper-activation of p65. These in vitro dynamic assays of NF-κB activation in blood-derived macrophages have the potential to segregate IBD patients into groups with different phenotypes and may therefore help determine response to therapy.
Climate change adaptation and the role of fuel subsidies: An empirical bio-economic modeling study for an artisanal open-access fishery
Lancker, Kira ; Deppenmeier, Anna Lena ; Demissie, Teferi ; Schmidt, Jörn O. - \ 2019
PLoS ONE 14 (2019)8. - ISSN 1932-6203

Climate change can severely impact artisanal fisheries and affect the role they play in food security. We study climate change effects on the triple bottom line of ecological productivity, fishers’ incomes, and fish consumption for an artisanal open-access fishery. We develop and apply an empirical, stochastic bio-economic model for the Senegalese artisanal purse seine fishery on small pelagic fish and compare the simulated fishery’s development using four climate projections and two policy scenarios. We find that economic processes of adaptation may amplify the effects of climate variations. The regions’ catch potential increases with climate change, induced by stock distribution changes. However, this outcome escalates over-fishing, whose effects outpace the incipiently favorable climate change effects under three of the four climate projections. Without policy action, the fishery is estimated to collapse in 2030–2035 on average over 1000 runs. We propose an easily implementable and overall welfare-increasing intervention: reduction of fuel subsidies. If fuel subsidies were abolished, ecological sustainability as well as the fishery’s welfare contribution would increase regardless of the climate projection.

Seasonal drivers of understorey temperature buffering in temperate deciduous forests across Europe
Zellweger, Florian ; Coomes, David ; Lenoir, Jonathan ; Depauw, Leen ; Maes, Sybryn L. ; Wulf, Monika ; Kirby, Keith J. ; Brunet, Jörg ; Kopecký, Martin ; Máliš, František ; Schmidt, Wolfgang ; Heinrichs, Steffi ; Ouden, Jan den; Jaroszewicz, Bogdan ; Buyse, Gauthier ; Spicher, Fabien ; Verheyen, Kris ; Frenne, Pieter De - \ 2019
Global Ecology and Biogeography 28 (2019)12. - ISSN 1466-822X - p. 1774 - 1786.
canopy density - climate change - forest composition - forest structure - global warming - macroclimate - microclimate - temperature buffering - understorey

Aim: Forest understorey microclimates are often buffered against extreme heat or cold, with important implications for the organisms living in these environments. We quantified seasonal effects of understorey microclimate predictors describing canopy structure, canopy composition and topography (i.e., local factors) and the forest patch size and distance to the coast (i.e., landscape factors). Location: Temperate forests in Europe. Time period: 2017–2018. Major taxa studied: Woody plants. Methods: We combined data from a microclimate sensor network with weather-station records to calculate the difference, or offset, between temperatures measured inside and outside forests. We used regression analysis to study the effects of local and landscape factors on the seasonal offset of minimum, mean and maximum temperatures. Results: The maximum temperature during the summer was on average cooler by 2.1 °C inside than outside forests, and the minimum temperatures during the winter and spring were 0.4 and 0.9 °C warmer. The local canopy cover was a strong nonlinear driver of the maximum temperature offset during summer, and we found increased cooling beneath tree species that cast the deepest shade. Seasonal offsets of minimum temperature were mainly regulated by landscape and topographic features, such as the distance to the coast and topographic position. Main conclusions: Forest organisms experience less severe temperature extremes than suggested by currently available macroclimate data; therefore, climate–species relationships and the responses of species to anthropogenic global warming cannot be modelled accurately in forests using macroclimate data alone. Changes in canopy cover and composition will strongly modulate the warming of maximum temperatures in forest understories, with important implications for understanding the responses of forest biodiversity and functioning to the combined threats of land-use change and climate change. Our predictive models are generally applicable across lowland temperate deciduous forests, providing ecologically important microclimate data for forest understories.

De variatie aan insecten in laagveenmoerassen : Het spectrum aan soortgroepen in verschillende habitattypen in Nederlandse laagveenmoerassen
Stam, Jeltje M. ; Kleijn, Davis ; Beest, Dennis te; Ozinga, Wim A. ; Schmidt, Anne M. ; Noordam, A.P. ; Burgers, J. ; Kats, R.J.M. van; Aukema, B. ; Lammertsma, D.R. ; Siepel, H. - \ 2019
Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2961) - 41
Recently, the alarming decrease of insect populations has received much attention, especially since the publication of a German study that showed strong decline of insects in nature reserves. Similar declines may be expected in the Netherlands, but many knowledge gaps exist about what we already know about the current situation and what influences the species composition of insects. This report aims to use information from an existing dataset to explore the species composition of insects in Dutch peat marchlands. The influence of habitat types and other environmental factors such as land use on the species composition was analyzed. Furthermore, the three different trapping methods used in this study were evaluated. This report thereby contributes to filling some of the existing knowledge gaps about Dutch insect populations and provides a number of recommendations for future monitoring of insects.
Co-designing a data platform to impact nature policy and management: experiences from the Dutch Caribbean
Verweij, P. ; Cormont, A. ; Hoetjes, P. ; Meyer, K. de; Bussel, T. van; Roosenschoon, O. ; Henkens, R. ; Schmidt, A. ; Janssen, S. - \ 2019
Environmental Science & Policy 100 (2019). - ISSN 1462-9011 - p. 13 - 20.
biodiversity - clearinghouse - indicators - reporting obligations - stakeholders

To secure the sustainable use of nature, governments track nature's health and develop regulations and policies. Although there is a seeming abundance in observation-recordings, decision- and policy-makers are constrained by the lack of data and indicators, mostly as a result of barriers preventing existing data from being found, accessed, made suitable for (automated) processing and reused, but also due to missing visualisations targeted at answering questions asked by policy makers. This paper explores the process and principles for developing a biodiversity web-platform that informs policy and management on the state and trends of nature, based on experiences with the Dutch Caribbean Biodiversity Database (DCBD). The DCBD supports the assessment of the state of nature and guarantees long-term data availability in an environment that experiences a high turnover in project funds and personnel. Three principles made DCBD's uptake and growth possible: The platform is funded, promoted and used by national and regional policy makers, it simplifies tasks of local management and rapporteurs, and it is continuously being adapted to changing needs and insights. Stronger dissemination of DCBD's narratives in social arenas (e.g. newspapers, social media) may make Caribbean nature and biodiversity more politically and societally relevant.

Science-based wildlife disease response
Vicente, Joaquín ; Apollonio, Marco ; Blanco-Aguiar, Jose A. ; Borowik, Tomasz ; Brivio, Francesca ; Casaer, Jim ; Croft, Simon ; Ericsson, Göran ; Ferroglio, Ezio ; Gavier-Widen, Dolores ; Gortázar, Christian ; Jansen, Patrick A. ; Keuling, Oliver ; Kowalczyk, Rafał ; Petrovic, Karolina ; Plhal, Radim ; Podgórski, Tomasz ; Sange, Marie ; Scandura, Massimo ; Schmidt, Krzysztof ; Smith, Graham C. ; Soriguer, Ramon ; Thulke, Hans Hermann ; Zanet, Stefania ; Acevedo, Pelayo - \ 2019
Science 364 (2019)6444. - ISSN 0036-8075 - p. 943 - 944.
Measuring chain performance beyond supplier–buyer relationships in agri-food chains
Kataike, Joanita ; Aramyan, Lusine H. ; Schmidt, Oliver ; Molnár, Adrienn ; Gellynck, Xavier - \ 2019
Supply Chain Management : an International Journal 24 (2019)4. - ISSN 1359-8546
Food industry - Performance - Performance measurement

Purpose: Measuring chain performance which extends beyond supplier–buyer interface is of paramount importance in tracking and tracing the ineffectiveness and inefficiency of the entire chain. In response to chain inefficiencies, key performance indicators need to be assessed at different chain levels. Knowledge amongst chain members and evident research on the chain members’ assessment of the chain partners’ contribution to their individual chain performance is equivocal. The purpose of this study is to investigate perceived performance contribution of bilateral relationships of each chain member to its chain partners’ performance across the dairy sector. Design/methodology/approach: The research was conducted in a dairy agri-food sector in Uganda. A total of 115 triad chains (three matching chain members) were obtained during the period of January to April 2016. Using simple random sampling, the dairy farmers (first suppliers), the cooperative supply managers (second suppliers) and the processors (buyers) were surveyed. Means and standard deviations presented descriptive findings. Furthermore, Kruskal–Wallis and Mann–Whitney U tests were used to assess the differences and similarities of the perceived performance contribution of the individual chain partners. Findings: The results revealed that each chain members’ perception of chain performance contribution toward the individual chain performance is relatively high. Further, it was found that there were significant differences between the chain members about the perceived chain performance contributions. However, within the internal chain analysis, no significant differences were observed. Research limitations/implications: Although limited to a single agri-food sector within the Ugandan dairy sector, the findings support evidence from similar agri-food chains worldwide. Originality/value: Literature shows shortcomings in measuring chain performance at three chain levels. Therefore, this shift from single or dyad to triad chain analysis provides new insights into the field of agri-food chains and supply chain performance in particular. It also provides important empirical results on how each chain member contributes to the chain partners’ performance.

sPlot – A new tool for global vegetation analyses
Bruelheide, Helge ; Dengler, Jürgen ; Jiménez-Alfaro, Borja ; Purschke, Oliver ; Hennekens, Stephan M. ; Chytrý, Milan ; Pillar, Valério D. ; Jansen, Florian ; Kattge, Jens ; Sandel, Brody ; Aubin, Isabelle ; Biurrun, Idoia ; Field, Richard ; Haider, Sylvia ; Jandt, Ute ; Lenoir, Jonathan ; Peet, Robert K. ; Peyre, Gwendolyn ; Sabatini, Francesco Maria ; Schmidt, Marco ; Schrodt, Franziska ; Winter, Marten ; Aćić, Svetlana ; Agrillo, Emiliano ; Alvarez, Miguel ; Ambarlı, Didem ; Angelini, Pierangela ; Apostolova, Iva ; Arfin Khan, Mohammed A.S. ; Arnst, Elise ; Attorre, Fabio ; Baraloto, Christopher ; Beckmann, Michael ; Berg, Christian ; Bergeron, Yves ; Bergmeier, Erwin ; Bjorkman, Anne D. ; Bondareva, Viktoria ; Borchardt, Peter ; Botta-Dukát, Zoltán ; Boyle, Brad ; Breen, Amy ; Brisse, Henry ; Byun, Chaeho ; Cabido, Marcelo R. ; Casella, Laura ; Cayuela, Luis ; Černý, Tomáš ; Chepinoga, Victor ; Csiky, János ; Curran, Michael ; Ćušterevska, Renata ; Dajić Stevanović, Zora ; Bie, Els De; Ruffray, Patrice de; Sanctis, Michele De; Dimopoulos, Panayotis ; Dressler, Stefan ; Ejrnæs, Rasmus ; El-Sheikh, Mohamed A.E.R.M. ; Enquist, Brian ; Ewald, Jörg ; Fagúndez, Jaime ; Finckh, Manfred ; Font, Xavier ; Forey, Estelle ; Fotiadis, Georgios ; García-Mijangos, Itziar ; Gasper, André Luis de; Golub, Valentin ; Gutierrez, Alvaro G. ; Hatim, Mohamed Z. ; He, Tianhua ; Higuchi, Pedro ; Holubová, Dana ; Hölzel, Norbert ; Homeier, Jürgen ; Indreica, Adrian ; Işık Gürsoy, Deniz ; Jansen, Steven ; Janssen, John ; Jedrzejek, Birgit ; Jiroušek, Martin ; Jürgens, Norbert ; Kącki, Zygmunt ; Kavgacı, Ali ; Kearsley, Elizabeth ; Kessler, Michael ; Knollová, Ilona ; Kolomiychuk, Vitaliy ; Korolyuk, Andrey ; Kozhevnikova, Maria ; Kozub, Łukasz ; Krstonošić, Daniel ; Kühl, Hjalmar ; Kühn, Ingolf ; Kuzemko, Anna ; Küzmič, Filip ; Landucci, Flavia ; Lee, Michael T. ; Levesley, Aurora ; Li, Ching Feng ; Liu, Hongyan ; Lopez-Gonzalez, Gabriela ; Lysenko, Tatiana ; Macanović, Armin ; Mahdavi, Parastoo ; Manning, Peter ; Marcenò, Corrado ; Martynenko, Vassiliy ; Mencuccini, Maurizio ; Minden, Vanessa ; Moeslund, Jesper Erenskjold ; Moretti, Marco ; Müller, Jonas V. ; Munzinger, Jérôme ; Niinemets, Ülo ; Nobis, Marcin ; Noroozi, Jalil ; Nowak, Arkadiusz ; Onyshchenko, Viktor ; Overbeck, Gerhard E. ; Ozinga, Wim A. ; Pauchard, Anibal ; Pedashenko, Hristo ; Peñuelas, Josep ; Pérez-Haase, Aaron ; Peterka, Tomáš ; Petřík, Petr ; Phillips, Oliver L. ; Prokhorov, Vadim ; Rašomavičius, Valerijus ; Revermann, Rasmus ; Rodwell, John ; Ruprecht, Eszter ; Rūsiņa, Solvita ; Samimi, Cyrus ; Schaminée, Joop H.J. ; Schmiedel, Ute ; Šibík, Jozef ; Šilc, Urban ; Škvorc, Željko ; Smyth, Anita ; Sop, Tenekwetche ; Sopotlieva, Desislava ; Sparrow, Ben ; Stančić, Zvjezdana ; Svenning, Jens Christian ; Swacha, Grzegorz ; Tang, Zhiyao ; Tsiripidis, Ioannis ; Turtureanu, Pavel Dan ; Uğurlu, Emin ; Uogintas, Domas ; Valachovič, Milan ; Vanselow, Kim André ; Vashenyak, Yulia ; Vassilev, Kiril ; Vélez-Martin, Eduardo ; Venanzoni, Roberto ; Vibrans, Alexander Christian ; Violle, Cyrille ; Virtanen, Risto ; Wehrden, Henrik von; Wagner, Viktoria ; Walker, Donald A. ; Wana, Desalegn ; Weiher, Evan ; Wesche, Karsten ; Whitfeld, Timothy ; Willner, Wolfgang ; Wiser, Susan ; Wohlgemuth, Thomas ; Yamalov, Sergey ; Zizka, Georg ; Zverev, Andrei - \ 2019
Journal of Vegetation Science 30 (2019)2. - ISSN 1100-9233 - p. 161 - 186.
biodiversity - community ecology - ecoinformatics - functional diversity - global scale - macroecology - phylogenetic diversity - plot database - sPlot - taxonomic diversity - vascular plant - vegetation relevé

Aims: Vegetation-plot records provide information on the presence and cover or abundance of plants co-occurring in the same community. Vegetation-plot data are spread across research groups, environmental agencies and biodiversity research centers and, thus, are rarely accessible at continental or global scales. Here we present the sPlot database, which collates vegetation plots worldwide to allow for the exploration of global patterns in taxonomic, functional and phylogenetic diversity at the plant community level. Results: sPlot version 2.1 contains records from 1,121,244 vegetation plots, which comprise 23,586,216 records of plant species and their relative cover or abundance in plots collected worldwide between 1885 and 2015. We complemented the information for each plot by retrieving climate and soil conditions and the biogeographic context (e.g., biomes) from external sources, and by calculating community-weighted means and variances of traits using gap-filled data from the global plant trait database TRY. Moreover, we created a phylogenetic tree for 50,167 out of the 54,519 species identified in the plots. We present the first maps of global patterns of community richness and community-weighted means of key traits. Conclusions: The availability of vegetation plot data in sPlot offers new avenues for vegetation analysis at the global scale.

Source partitioning of H 2 O and CO 2 fluxes based on high-frequency eddy covariance data : A comparison between study sites
Klosterhalfen, Anne ; Graf, Alexander ; Brüggemann, Nicolas ; Drüe, Clemens ; Esser, Odilia ; González-Dugo, María P. ; Heinemann, Günther ; Jacobs, Cor M.J. ; Mauder, Matthias ; Moene, Arnold F. ; Ney, Patrizia ; Pütz, Thomas ; Rebmann, Corinna ; Rodríguez, Mario Ramos ; Scanlon, Todd M. ; Schmidt, Marius ; Steinbrecher, Rainer ; Thomas, Christoph K. ; Valler, Veronika ; Zeeman, Matthias J. ; Vereecken, Harry - \ 2019
Biogeosciences 16 (2019)6. - ISSN 1726-4170 - p. 1111 - 1132.

For an assessment of the roles of soil and vegetation in the climate system, a further understanding of the flux components of H 2 O and CO 2 (e.g., transpiration, soil respiration) and their interaction with physical conditions and physiological functioning of plants and ecosystems is necessary. To obtain magnitudes of these flux components, we applied source partitioning approaches after Scanlon and Kustas (2010; SK10) and after Thomas et al. (2008; TH08) to high-frequency eddy covariance measurements of 12 study sites covering different ecosystems (croplands, grasslands, and forests) in different climatic regions. Both partitioning methods are based on higher-order statistics of the H 2 O and CO 2 fluctuations, but proceed differently to estimate transpiration, evaporation, net primary production, and soil respiration. We compared and evaluated the partitioning results obtained with SK10 and TH08, including slight modifications of both approaches. Further, we analyzed the interrelations among the performance of the partitioning methods, turbulence characteristics, and site characteristics (such as plant cover type, canopy height, canopy density, and measurement height). We were able to identify characteristics of a data set that are prerequisites for adequate performance of the partitioning methods. SK10 had the tendency to overestimate and TH08 to underestimate soil flux components. For both methods, the partitioning of CO 2 fluxes was less robust than for H 2 O fluxes. Results derived with SK10 showed relatively large dependencies on estimated water use efficiency (WUE) at the leaf level, which is a required input. Measurements of outgoing longwave radiation used for the estimation of foliage temperature (used in WUE) could slightly increase the quality of the partitioning results. A modification of the TH08 approach, by applying a cluster analysis for the conditional sampling of respiration-evaporation events, performed satisfactorily, but did not result in significant advantages compared to the original method versions developed by Thomas et al. (2008). The performance of each partitioning approach was dependent on meteorological conditions, plant development, canopy height, canopy density, and measurement height. Foremost, the performance of SK10 correlated page1112 negatively with the ratio between measurement height and canopy height. The performance of TH08 was more dependent on canopy height and leaf area index. In general, all site characteristics that increase dissimilarities between scalars appeared to enhance partitioning performance for SK10 and TH08.

Comparison of soil physical quality indicators using direct and indirect data inputs derived from a combination of in-situ and ex-situ methods
Bacher, M.G. ; Schmidt, O. ; Bondi, G. ; Creamer, R. ; Fenton, O. - \ 2019
Soil Science Society of America Journal 83 (2019)1. - ISSN 0361-5995 - p. 5 - 17.
AW - Integral air-water energy; PAWC - Particle size distribution; SPQ - Plant available water capacity; PSD - Soil physical quality; SQI - Soil quality indicator; SWRC - Soil water retention curve
The quality of a soil is its ability to deliver functions providing ecosystem services, human health and well-being. Soil physical quality (SPQ) values use different parts of the soil water retention curve (SWRC) to calculate SPQ. For example, the plant available water capacity (PAWC) method is the difference in water content between permanent wilting point and field capacity. The S-index uses the slope of the SWRC at its inflection point and the relative air-water energy (AWr) is the integral of “dry” divided by the “wet” area of the SWRC. Increasing demand for soil monitoring policies calls for reliable and sensitive soil quality indicators (SQIs). The objectives of the study were to assess the sensitivity and applicability of SPQ indicators using direct and indirect data inputs. The indirect approach provided sufficient data complexity for the PAWC and S-index values, but the more complex AWr required the direct approach. PAWC and S-index values were identified as static SPQ indicators. The values obtained from these approaches should be used to form baseline static datasets and therefore have an indicative role only. The AWr value was identified as a dynamic SPQ indicator and provided required sensitivity to pick up temporal changes in SPQ. This indicator could be used at multiple scales and could even guide grassland management in terms of SPQ. Higher SWRC data resolution will require more complex hydraulic models to fit and will ultimately improve the accuracy of soil hydraulic data and improve the sensitivity of AWr as a SPQ indicator.
The Basophil Activation Test reduces the need for a food challenge test in children suspected of IgE-mediated cow's milk allergy
Ruinemans-Koerts, Janneke ; Schmidt-Hieltjes, Yvonne ; Jansen, Ad ; Savelkoul, Huub F.J. ; Plaisier, Annejet ; Setten, Petra van - \ 2019
Clinical and Experimental Allergy 49 (2019)3. - ISSN 0954-7894 - p. 350 - 356.

Background: The gold standard for the diagnosis of cow's milk allergy is the Double-Blind Placebo-Controlled Food Challenge (DBPCFC) test. However, disadvantages of the DBPCFC are the potential risk of anaphylactic reactions, the time-consuming procedure and high costs. Objective: The aim of this study was to determine the reliability of the Basophil Activation Test (BAT) both for the initial diagnosis of cow's milk allergy in children and for the determination of tolerance in children with cow's milk allergy. Methods: Ninety-seven BATs and cow's milk-specific IgE (sIgE) tests were performed in 86 infants/young children, suspected of (persistent) cow's milk allergy, who were qualified for an in-hospital DBPCFC. The BAT was performed with cow's milk extract and the purified major allergens casein, α-lactalbumin, β-lactoglubulin. Basophil activation was determined by CD63 upregulation measured by flow cytometry. The BAT results were compared to the DBPCFC outcomes. Results: Based on unequivocal DBPCFC and BAT result combinations (80%), the BAT had a sensitivity and specificity of 100% (CI: 86%-100% and 68%-100%, respectively) in IgE-sensitized children (41% of the tested children). All non-IgE-sensitized children (59%) had a negative DBPCFC and BAT, except for five patients. These latter showed delayed and relatively mild symptoms in the DBPCFC with a negative BAT, supporting a non-IgE-mediated allergy in these children. Conclusions and Clinical Relevance: The BAT seems reliable and cost-effective to diagnose patients with an IgE-mediated cow's milk allergy. In IgE-sensitized patients, a BAT might replace a DBPCFC. For non-IgE-sensitized patients presenting with mild symptoms, we propose to consider a (double-blind) extended (time) challenge test at home.

Sensitivity analysis of a source partitioning method for H2O and CO2 fluxes based on high frequency eddy covariance data : Findings from field data and large eddy simulations
Klosterhalfen, A. ; Moene, A.F. ; Schmidt, M. ; Scanlon, T.M. ; Vereecken, H. ; Graf, A. - \ 2019
Agricultural and Forest Meteorology 265 (2019). - ISSN 0168-1923 - p. 152 - 170.
Flux partitioning - Latent heat flux - LES - Net ecosystem exchange - Sensitivity analysis - Water use efficiency

Scanlon and Sahu (2008) and Scanlon and Kustas (2010) proposed a source partitioning method (SK10 in the following) to estimate contributions of transpiration, evaporation, photosynthesis, and respiration to H2O and CO2 fluxes obtained by the eddy covariance method. High frequency eddy covariance raw data time series are needed, and the source partitioning is estimated based on separate application of the flux-variance similarity theory to stomatal and non-stomatal components of the regarded fluxes, as well as on additional assumptions on leaf-level water use efficiency (WUE). We applied SK10 to data from two test sites (forest and cropland) and analyzed partitioning results depending on various ways to estimate WUE from available data. Also, we conducted large eddy simulations (LES), simulating the turbulent transport of H2O and CO2 for contrasting vertical distributions of the canopy sinks/sources, as well as for varying relative magnitudes of soil sources and canopy sinks/sources. SK10 was applied to the synthetic high frequency data generated by LES and the effects of canopy type, measurement height, given sink-source-distributions, and input of varying WUEs were tested regarding the partitioning performance. SK10 requires that the correlation coefficient between stomatal and non-stomatal scalar fluctuations is determined by the ratio of the transfer efficiencies of these scalar components, an assumption (transfer assumption in the following) that could be tested with the generated LES data. The partitioning results of the field sites yielded satisfactory flux fractions, when fair-weather conditions (no precipitation) and a high productive state of the vegetation were present. Further, partitioning performance with regard to soil fluxes increased with crop maturity. Results also showed relatively large dependencies on WUE, where the partitioning factors (median) changed by around -57% and +36%. Measurements of outgoing longwave radiation used for the estimation of foliage temperature and WUE could slightly increase the plausibility of the partitioning results in comparison to soil respiration measurements by decreasing the partitioning factor by up to 42%. The LES-based analysis revealed that for a satisfying performance of SK10, a certain degree of decorrelation of the H2O and CO2 fluctuations (here, |ρq'c’| < 0.975) was needed. This decorrelation is enhanced by a clear separation between soil sources and canopy sinks/sources, and for observations within the roughness sublayer. The expected dependence of the partitioning results on the WUE input could be observed. However, due to violation of the abovementioned transfer assumption, the known true input WUE did not yield the known true input partitioning. This could only be achieved after introducing correction factors for the transfer assumption, which were known however only in the special case of the LES experiments.

The impact of cattle dung pats on earthworm distribution in grazed pastures
Bacher, M.G. ; Fenton, O. ; Bondi, G. ; Creamer, R.E. ; Karmarkar, M. ; Schmidt, O. - \ 2018
BMC Ecology 18 (2018)1. - ISSN 1472-6785
Earthworms - Grassland - Lumbricidae - Population aggregation - Populations - Sampling - Soil biodiversity - Soil fauna - Spatial distribution

Background: Grazed grassland management regimes can have various effects on soil fauna. For example, effects on earthworms can be negative through compaction induced by grazing animals, or positive mediated by increases in sward productivity and cattle dung pats providing a food source. Knowledge gaps exist in relation to the behaviour of different earthworm species i.e. their movement towards and aggregation under dung pats, the legacy effects of pats and the spatial area of recruitment. The present study addressed these knowledge gaps in field experiments, over 2 years, using natural and simulated dung pats on two permanent, intensively grazed pastures in Ireland. Results: Dung pats strongly affected spatial earthworm distribution, with up to four times more earthworms aggregating beneath pats, than in the control locations away from pats. In these earthworm communities comprising 11 species, temporally different aggregation and dispersal patterns were observed, including absence of individual species from control locations, but no clear successional responses. Epigeic species in general, but also certain species of the anecic and endogeic groups were aggregating under dung. Sampling after complete dung pat disappearance (27 weeks after application) suggested an absence of a dung pat legacy effect on earthworm communities. Based on species distributions, the maximum size of the recruitment area from which earthworms moved to pats was estimated to be 3.8 m2 per dung pat. Since actual grazing over 6 weeks would result in the deposition of about 300 dung pats per ha, it is estimated that a surface area of 1140 m2 or about 11% of the total grazing area can be influenced by dung pats in a given grazing period. Conclusions: This study showed that the presence of dung pats in pastures creates temporary hot spots in spatial earthworm species distribution, which changes over time. The findings highlight the importance of considering dung pats, temporally and spatially, when sampling earthworms in grazed pastures. Published comparisons of grazed and cut grasslands probably reached incorrect conclusions by ignoring or deliberately avoiding dung pats. Furthermore, the observed intense aggregation of earthworms beneath dung pats suggests that earthworm functions need to be assessed separately at these hot spots.

FEM growth and yield data Monocultures - Poplar (2nd revised version)
Mohren, G.M.J. ; Goudzwaard, L. ; Jansen, J.J. ; Schmidt, P. ; Oosterbaan, A. ; Oldenburger, J.F. ; Ouden, J. den; Copini, P. - \ 2018
growth and yield - even-aged monoculture forest - tree diameter - tree height - crown class - coordinates stem positions - age - mean height - spacing - without thinning - systematic thinning - monitoring - Poplar - Aspen - Populus species - Populus x canadensis - Populus x interamericana - Populus alba - Populus tremula
In this new version, the data of 227 test plots of the former Stichting Industriehout were added. Also the location information of the test plots of the Dorschkamp/IBN were added. This database is part of the FEM growth and yield database, a collection of growth and yield data from even-aged monocultures.
Opbrengsttabellen Nederland 2018
Jansen, Hans ; Oosterbaan, Anne ; Mohren, G.M.J. ; Goudzwaard, L. ; Ouden, J. den; Schoonderwoerd, H. ; Thomassen, E.A.H. ; Schmidt, P. ; Copini, P. - \ 2018
Wageningen : Wageningen Academic Publishers - ISBN 9789086868766 - 172
In deze bundel zijn opbrengsttabellen van 15 boomsoorten opgenomen. In vergelijking met de tot nu toe geldende opbrengsttabellen uit 1996, bevat deze bundel meer soorten, meer dunningregimes, en zijn alle tabellen gebaseerd op Nederlandse meetgegevens. Voor 10 soorten zijn tabellen met zowel een matige als sterke dunning opgenomen. Voor de Japanse Lariks zijn twee regionale tabellen opgenomen. De populier heeft in deze bundel een tabel voor bomen in lijnbeplanting, naast de tabellen voor bos met diverse plantverbanden. Per soort is het rapport van de onderliggende studie weergegeven. Al deze studies volgden in grote lijnen de studie Groei en productie van douglas in Nederland. Becking's dunningproeven ontsloten. In vergelijking met de studies uit 1996, blijkt enerzijds de hoogtegroei per boniteit te verschillen (slechte boniteiten starten lager dan goede boniteiten, maar halen de groei later deels in). Anderzijds blijk de range tussen de beste en slechtste boniteit vaak ruimer dan in de eerdere studies.
Crop pests and predators exhibit inconsistent responses to surrounding landscape composition
Karp, Daniel S. ; Chaplin-Kramer, Rebecca ; Meehan, Timothy D. ; Martin, Emily A. ; Declerck, Fabrice ; Grab, Heather ; Gratton, Claudio ; Hunt, Lauren ; Larsen, Ashley E. ; Martínez-Salinas, Alejandra ; O’Rourke, Megan E. ; Rusch, Adrien ; Poveda, Katja ; Jonsson, Mattias ; Rosenheim, Jay A. ; Schellhorn, Nancy A. ; Tscharntke, Teja ; Wratten, Stephen D. ; Zhang, Wei ; Iverson, Aaron L. ; Adler, Lynn S. ; Albrecht, Matthias ; Alignier, Audrey ; Angelella, Gina M. ; Zubair Anjum, Muhammad ; Avelino, Jacques ; Batáry, Péter ; Baveco, Johannes M. ; Bianchi, Felix J.J.A. ; Birkhofer, Klaus ; Bohnenblust, Eric W. ; Bommarco, Riccardo ; Brewer, Michael J. ; Caballero-López, Berta ; Carrière, Yves ; Carvalheiro, Luísa G. ; Cayuela, Luis ; Centrella, Mary ; Ćetković, Aleksandar ; Henri, Dominic Charles ; Chabert, Ariane ; Costamagna, Alejandro C. ; La Mora, Aldo De; Kraker, Joop De; Desneux, Nicolas ; Diehl, Eva ; Diekötter, Tim ; Dormann, Carsten F. ; Eckberg, James O. ; Entling, Martin H. ; Fiedler, Daniela ; Franck, Pierre ; Veen, F.J.F. van; Frank, Thomas ; Gagic, Vesna ; Garratt, Michael P.D. ; Getachew, Awraris ; Gonthier, David J. ; Goodell, Peter B. ; Graziosi, Ignazio ; Groves, Russell L. ; Gurr, Geoff M. ; Hajian-Forooshani, Zachary ; Heimpel, George E. ; Herrmann, John D. ; Huseth, Anders S. ; Inclán, Diego J. ; Ingrao, Adam J. ; Iv, Phirun ; Jacot, Katja ; Johnson, Gregg A. ; Jones, Laura ; Kaiser, Marina ; Kaser, Joe M. ; Keasar, Tamar ; Kim, Tania N. ; Kishinevsky, Miriam ; Landis, Douglas A. ; Lavandero, Blas ; Lavigne, Claire ; Ralec, Anne Le; Lemessa, Debissa ; Letourneau, Deborah K. ; Liere, Heidi ; Lu, Yanhui ; Lubin, Yael ; Luttermoser, Tim ; Maas, Bea ; Mace, Kevi ; Madeira, Filipe ; Mader, Viktoria ; Cortesero, Anne Marie ; Marini, Lorenzo ; Martinez, Eliana ; Martinson, Holly M. ; Menozzi, Philippe ; Mitchell, Matthew G.E. ; Miyashita, Tadashi ; Molina, Gonzalo A.R. ; Molina-Montenegro, Marco A. ; O’Neal, Matthew E. ; Opatovsky, Itai ; Ortiz-Martinez, Sebaastian ; Nash, Michael ; Östman, Örjan ; Ouin, Annie ; Pak, Damie ; Paredes, Daniel ; Parsa, Soroush ; Parry, Hazel ; Perez-Alvarez, Ricardo ; Perović, David J. ; Peterson, Julie A. ; Petit, Sandrine ; Philpott, Stacy M. ; Plantegenest, Manuel ; Plećaš, Milan ; Pluess, Therese ; Pons, Xavier ; Potts, Simon G. ; Pywell, Richard F. ; Ragsdale, David W. ; Rand, Tatyana A. ; Raymond, Lucie ; Ricci, Benoît ; Sargent, Chris ; Sarthou, Jean-Pierre ; Saulais, Julia ; Schäckermann, Jessica ; Schmidt, Nick P. ; Schneider, Gudrun ; Schüepp, Christof ; Sivakoff, Frances S. ; Smith, Henrik G. ; Stack Whitney, Kaitlin ; Stutz, Sonja ; Szendrei, Zsofia ; Takada, Mayura B. ; Taki, Hisatomo ; Tamburini, Giovanni ; Thomson, Linda J. ; Tricault, Yann ; Tsafack, Noelline ; Tschumi, Matthias ; Valantin-Morison, Muriel ; Trinh, Mai Van; Werf, Wopke Van Der; Vierling, Kerri T. ; Werling, Ben P. ; Wickens, Jennifer B. ; Wickens, Victoria J. ; Woodcock, Ben A. ; Wyckhuys, Kris ; Xiao, Haijun ; Yasuda, Mika ; Yoshioka, Akira - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)33. - ISSN 0027-8424 - p. E7863 - E7870.
The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are measured. Here, we use a pest-control database encompassing 132 studies and 6,759 sites worldwide to model natural enemy and pest abundances, predation rates, and crop damage as a function of landscape composition. Our results showed that although landscape composition explained significant variation within studies, pest and enemy abundances, predation rates, crop damage, and yields each exhibited different responses across studies, sometimes increasing and sometimes decreasing in landscapes with more noncrop habitat but overall showing no consistent trend. Thus, models that used landscape-composition variables to predict pest-control dynamics demonstrated little potential to explain variation across studies, though prediction did improve when comparing studies with similar crop and landscape features. Overall, our work shows that surrounding noncrop habitat does not consistently improve pest management, meaning habitat conservation may bolster production in some systems and depress yields in others. Future efforts to develop tools that inform farmers when habitat conservation truly represents a win–win would benefit from increased understanding of how landscape effects are modulated by local farm management and the biology of pests and their enemies.
Scholarly Metrics Recommendations for Research Libraries: Deciphering the trees in the forest
Coombs, S. ; Peters, I. ; Schmidt, B. ; Princic, A. ; Martinez, M. ; Kraker, P. ; Jahn, N. ; Haustein, S. ; Cornée, N. ; Abcouwer, K. ; Gorraiz, J. ; Fest, P.M.J. ; Tsakonas, G. - \ 2018
Liber - 17 p.
The digital era has brought new and exciting changes to scholarly communication. Modern scientific libraries and information infrastructures are obliged to face these new challenges in a professional way sooner rather than later.The monitoring and execution of policies, the facilitation of Open Access publishing, and support for research data management are but a few examples of adaptation to the digital era. The use of scholarly metrics is also an emerging field for academic libraries, brought on by digital change. To foster this vision, LIBER's Innovative Metrics Working Group has set out recommendations on how academic libraries and information infrastructures can deal with scholarly metrics, and how to get started with the development of services to support this.

The recommendations are grouped into four sections:
- Discovery and Discoverability
- Showcasing Achievements
- Service Development
- Research Assessment

Each section covers a set of activities, and makes suggestions for libraries which want to promote the transparent, standardized and responsible use of scholarly metrics. As part of LIBER’s focus on Open Science, the Working Group has placed a special emphasis on recommendations addressing open scholarly metrics. Throughout this report, we have organised our recommendations into three levels. Which recommendations a library adopts will depend on their current level of engagement with scholarly metrics. The levels are as follows:
- Initial Steps (circular bullet)
- Intermediate Steps (square bullet)
- Advanced Steps (triangular bullet)

The order in which the recommendations appear are in correlation with the potential importance they can have for an institution. These two indications of use were developed during the Working Group’s workshop during LIBER’s 2017 Annual Conference. They are there to assist in prioritizing, but are not mandatory to follow and are not dependent on each other.
Fifty Percent Human – how art brings us in touch with our microbial cohabitants
Bäumel, Sonja ; Tytgat, Hanne L.P. ; Nemec, Birgit ; Schmidt, Ruth ; Chia, Loo W. ; Smidt, Hauke - \ 2018
Microbial Biotechnology 11 (2018)4. - ISSN 1751-7907 - p. 571 - 574.

The Human Microbiome, as well as the exploration of the microorganisms inhabiting the human body, are not only integral to the field of microbiology but represent an intrinsic part of all human beings. Consequently, along with scientists, artists have been inspired by the microbiome: transforming it in to tangible artefacts in order to critically question, reflect on and break down the barrier between humans and their microcohabitants. By artistic means, artists help us to understand how microbial research topics are inevitably affected by societal influences, including (health) politics, economics and the arts. Fifty Percent Human is a multidisciplinary artistic research project that aims to reshape our understanding of the human body and its environment as well as to explore possibilities for conscious coexistence in order to bridge the gap between science and society.

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