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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    Shifting the imbalance: Intentional reuse of Dutch sewage effluent in sub-surface irrigation
    Narain-Ford, Dominique M. ; Bartholomeus, Ruud P. ; Raterman, Bernard ; Zaanen, Ian van; Laak, Thomas T. ter; Wezel, Annemarie P. van; Dekker, Stefan C. - \ 2021
    Science of the Total Environment 752 (2021). - ISSN 0048-9697
    Worldwide, agricultural irrigation currently accounts for 69% of freshwater withdrawal. Countries with a temperate climate, such as the Netherlands, experience periodic freshwater shortages in agriculture. The pressure on available freshwater will increase due to climate change and a growing demand for freshwater by e.g. industrial activities. Possible alternative water resources are considered in order to meet the current and future water demand. In this study we explore where, and how much, sewage treatment plant (STP) effluent can directly be reused in agricultural sub-surface irrigation (SSI) during an average and a dry season scenario, for all active (335) Dutch STPs. SSI systems may have a higher water demand as part of the STP effluent is transported with groundwater flow, although aboveground irrigation has a loss of water due to interception. Furthermore, such aboveground irrigation systems provide direct contact of crops with irrigation water. SSI systems provide a soil barrier which may function as a filter and buffer zone. In the Dutch situation, direct intentional reuse of STP effluent can fulfill up to 25% of croplands SSI water demand present within a five-kilometer transport buffer from the STPs during an average season and 17% during a dry season. Hereto, respectively, 78% and 84% of the total available Dutch STP effluent would be used. Thus, the intentional direct STP effluent reuse in agricultural SSI has the potential to satisfy a significant amount of the agricultural water demand at a national scale, presuming responsible reuse: safe applications for humans and environment and no limiting effects on water availability for other actors.
    Commentaries on Top-Cited Boundary-Layer Meteorology Articles
    Garratt, John ; Wilczak, James ; Holtslag, Albert ; Schmid, Hans Peter ; Grachev, Andrey ; Beljaars, Anton ; Foken, Thomas ; Chen, Fei ; Fairall, Christopher ; Hicks, Bruce ; Kusaka, Hiroyuki ; Martilli, Alberto ; Masson, Valéry ; Mauder, Matthias ; Oncley, Steven ; Rotach, Mathias ; Tjernström, Michael - \ 2020
    Boundary-Layer Meteorology (2020). - ISSN 0006-8314
    Bending the curve of terrestrial biodiversity needs an integrated strategy
    Leclère, David ; Obersteiner, Michael ; Barrett, Mike ; Butchart, Stuart H.M. ; Chaudhary, Abhishek ; Palma, Adriana De; DeClerck, Fabrice A.J. ; Marco, Moreno Di; Doelman, Jonathan C. ; Dürauer, Martina ; Freeman, Robin ; Harfoot, Michael ; Hasegawa, Tomoko ; Hellweg, Stefanie ; Hilbers, Jelle P. ; Hill, Samantha L.L. ; Humpenöder, Florian ; Jennings, Nancy ; Krisztin, Tamás ; Mace, Georgina M. ; Ohashi, Haruka ; Popp, Alexander ; Purvis, Andy ; Schipper, Aafke M. ; Tabeau, Andrzej ; Valin, Hugo ; Meijl, Hans van; Zeist, Willem Jan van; Visconti, Piero ; Alkemade, Rob ; Almond, Rosamunde ; Bunting, Gill ; Burgess, Neil D. ; Cornell, Sarah E. ; Fulvio, Fulvio Di; Ferrier, Simon ; Fritz, Steffen ; Fujimori, Shinichiro ; Grooten, Monique ; Harwood, Thomas ; Havlík, Petr ; Herrero, Mario ; Hoskins, Andrew J. ; Jung, Martin ; Kram, Tom ; Lotze-Campen, Hermann ; Matsui, Tetsuya ; Meyer, Carsten ; Nel, Deon ; Newbold, Tim ; Schmidt-Traub, Guido ; Stehfest, Elke ; Strassburg, Bernardo B.N. ; Vuuren, Detlef P. van; Ware, Chris ; Watson, James E.M. ; Wu, Wenchao ; Young, Lucy - \ 2020
    Nature 585 (2020). - ISSN 0028-0836 - p. 551 - 556.

    Increased efforts are required to prevent further losses to terrestrial biodiversity and the ecosystem services that it provides1,2. Ambitious targets have been proposed, such as reversing the declining trends in biodiversity3; however, just feeding the growing human population will make this a challenge4. Here we use an ensemble of land-use and biodiversity models to assess whether—and how—humanity can reverse the declines in terrestrial biodiversity caused by habitat conversion, which is a major threat to biodiversity5. We show that immediate efforts, consistent with the broader sustainability agenda but of unprecedented ambition and coordination, could enable the provision of food for the growing human population while reversing the global terrestrial biodiversity trends caused by habitat conversion. If we decide to increase the extent of land under conservation management, restore degraded land and generalize landscape-level conservation planning, biodiversity trends from habitat conversion could become positive by the mid-twenty-first century on average across models (confidence interval, 2042–2061), but this was not the case for all models. Food prices could increase and, on average across models, almost half (confidence interval, 34–50%) of the future biodiversity losses could not be avoided. However, additionally tackling the drivers of land-use change could avoid conflict with affordable food provision and reduces the environmental effects of the food-provision system. Through further sustainable intensification and trade, reduced food waste and more plant-based human diets, more than two thirds of future biodiversity losses are avoided and the biodiversity trends from habitat conversion are reversed by 2050 for almost all of the models. Although limiting further loss will remain challenging in several biodiversity-rich regions, and other threats—such as climate change—must be addressed to truly reverse the declines in biodiversity, our results show that ambitious conservation efforts and food system transformation are central to an effective post-2020 biodiversity strategy.

    A benchmarking protocol for breath analysis: The peppermint experiment
    Henderson, Ben ; Ruszkiewicz, Dorota M. ; Wilkinson, Max ; Beauchamp, Jonathan D. ; Cristescu, Simona M. ; Fowler, Stephen J. ; Salman, Dahlia ; Francesco, Fabio Di; Koppen, Gudrun ; Langejürgen, Jens ; Holz, Olaf ; Hadjithekli, Andria ; Moreno, Sergi ; Pedrotti, Michele ; Sinues, Pablo ; Slingers, Gitte ; Wilde, Michael ; Lomonaco, Tommaso ; Zanella, Delphine ; Zenobi, Renato ; Focant, Jean François ; Grassin-Delyle, Stanislas ; Franchina, Flavio Antonio ; Malásková, Michaela ; Stefanuto, Pierre Hugues ; Pugliese, Giovanni ; Mayhew, Christopher ; Thomas, C.L.P. - \ 2020
    Journal of Breath Research 14 (2020)4. - ISSN 1752-7155
    benchmark - breathomics - peppermint - repeated sampling8pharmacokinetics - standardization

    Sampling of volatile organic compounds (VOCs) has shown promise for detection of a range of diseases but results have proved hard to replicate due to a lack of standardization. In this work we introduce the 'Peppermint Initiative'. The initiative seeks to disseminate a standardized experiment that allows comparison of breath sampling and data analysis methods. Further, it seeks to share a set of benchmark values for the measurement of VOCs in breath. Pilot data are presented to illustrate the standardized approach to the interpretation of results obtained from the Peppermint experiment. This pilot study was conducted to determine the washout profile of peppermint compounds in breath, identify appropriate sampling time points, and formalise the data analysis. Five and ten participants were recruited to undertake a standardized intervention by ingesting a peppermint oil capsule that engenders a predictable and controlled change in the VOC profile in exhaled breath. After collecting a pre-ingestion breath sample, five further samples are taken at 2, 4, 6, 8, and 10 h after ingestion. Samples were analysed using ion mobility spectrometry coupled to multi-capillary column and thermal desorption gas chromatography mass spectrometry. A regression analysis of the washout data was used to determine sampling times for the final peppermint protocol, and the time for the compound measurement to return to baseline levels was selected as a benchmark value. A measure of the quality of the data generated from a given technique is proposed by comparing data fidelity. This study protocol has been used for all subsequent measurements by the Peppermint Consortium (16 partners from seven countries). So far 1200 breath samples from 200 participants using a range of sampling and analytical techniques have been collected. The data from the consortium will be disseminated in subsequent technical notes focussing on results from individual platforms.

    Altered energy partitioning across terrestrial ecosystems in the European drought year 2018
    Graf, Alexander ; Klosterhalfen, Anne ; Arriga, Nicola ; Bernhofer, Christian ; Bogena, Heye ; Bornet, Frédéric ; Brüggemann, Nicolas ; Brümmer, Christian ; Buchmann, Nina ; Chi, Jinshu ; Chipeaux, Christophe ; Cremonese, Edoardo ; Cuntz, Matthias ; Dušek, Jiří ; El-Madany, Tarek S. ; Fares, Silvano ; Fischer, Milan ; Foltýnová, Lenka ; Gharun, Mana ; Ghiasi, Shiva ; Gielen, Bert ; Gottschalk, Pia ; Grünwald, Thomas ; Heinemann, Günther ; Heinesch, Bernard ; Heliasz, Michal ; Holst, Jutta ; Hörtnagl, Lukas ; Ibrom, Andreas ; Ingwersen, Joachim ; Jurasinski, Gerald ; Klatt, Janina ; Knohl, Alexander ; Koebsch, Franziska ; Konopka, Jan ; Korkiakoski, Mika ; Kowalska, Natalia ; Kremer, Pascal ; Kruijt, Bart ; Lafont, Sebastien ; Léonard, Joël ; Ligne, Anne De; Longdoz, Bernard ; Loustau, Denis ; Magliulo, Vincenzo ; Mammarella, Ivan ; Manca, Giovanni ; Mauder, Matthias ; Migliavacca, Mirco ; Mölder, Meelis ; Neirynck, Johan ; Ney, Patrizia ; Nilsson, Mats ; Paul-Limoges, Eugénie ; Peichl, Matthias ; Pitacco, Andrea ; Poyda, Arne ; Rebmann, Corinna ; Roland, Marilyn ; Sachs, Torsten ; Schmidt, Marius ; Schrader, Frederik ; Siebicke, Lukas ; Šigut, Ladislav ; Tuittila, Eeva Stiina ; Varlagin, Andrej ; Vendrame, Nadia ; Vincke, Caroline ; Völksch, Ingo ; Weber, Stephan ; Wille, Christian ; Wizemann, Hans Dieter ; Zeeman, Matthias ; Vereecken, Harry - \ 2020
    Philosophical Transactions of the Royal Society B. Biological sciences 375 (2020)1810. - ISSN 0962-8436 - 1 p.
    eddy covariance - energy balance - evapotranspiration - heat flux - net carbon uptake - water-use efficiency

    Drought and heat events, such as the 2018 European drought, interact with the exchange of energy between the land surface and the atmosphere, potentially affecting albedo, sensible and latent heat fluxes, as well as CO2 exchange. Each of these quantities may aggravate or mitigate the drought, heat, their side effects on productivity, water scarcity and global warming. We used measurements of 56 eddy covariance sites across Europe to examine the response of fluxes to extreme drought prevailing most of the year 2018 and how the response differed across various ecosystem types (forests, grasslands, croplands and peatlands). Each component of the surface radiation and energy balance observed in 2018 was compared to available data per site during a reference period 2004-2017. Based on anomalies in precipitation and reference evapotranspiration, we classified 46 sites as drought affected. These received on average 9% more solar radiation and released 32% more sensible heat to the atmosphere compared to the mean of the reference period. In general, drought decreased net CO2 uptake by 17.8%, but did not significantly change net evapotranspiration. The response of these fluxes differed characteristically between ecosystems; in particular, the general increase in the evaporative index was strongest in peatlands and weakest in croplands. This article is part of the theme issue 'Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale'.

    2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
    Kuhn, Jens H. ; Adkins, Scott ; Alioto, Daniela ; Alkhovsky, Sergey V. ; Amarasinghe, Gaya K. ; Anthony, Simon J. ; Avšič-Županc, Tatjana ; Ayllón, María A. ; Bahl, Justin ; Balkema-Buschmann, Anne ; Ballinger, Matthew J. ; Bartonička, Tomáš ; Basler, Christopher ; Bavari, Sina ; Beer, Martin ; Bente, Dennis A. ; Bergeron, Éric ; Bird, Brian H. ; Blair, Carol ; Blasdell, Kim R. ; Bradfute, Steven B. ; Breyta, Rachel ; Briese, Thomas ; Brown, Paul A. ; Buchholz, Ursula J. ; Buchmeier, Michael J. ; Bukreyev, Alexander ; Burt, Felicity ; Buzkan, Nihal ; Calisher, Charles H. ; Cao, Mengji ; Casas, Inmaculada ; Chamberlain, John ; Chandran, Kartik ; Charrel, Rémi N. ; Chen, Biao ; Chiumenti, Michela ; Choi, Ryong ; Clegg, J.C.S. ; Crozier, Ian ; Graça, John V. da; Bó, Elena Dal; Dávila, Alberto M.R. ; Torre, Juan Carlos de la; Lamballerie, Xavier de; Swart, Rik L. de; Bello, Patrick L. Di; Paola, Nicholas Di; Serio, Francesco Di; Dietzgen, Ralf G. ; Digiaro, Michele ; Dolja, Valerian V. ; Dolnik, Olga ; Drebot, Michael A. ; Drexler, Jan Felix ; Dürrwald, Ralf ; Dufkova, Lucie ; Dundon, William G. ; Duprex, W.P. ; Dye, John M. ; Easton, Andrew J. ; Ebihara, Hideki ; Elbeaino, Toufic ; Ergünay, Koray ; Fernandes, Jorlan ; Fooks, Anthony R. ; Formenty, Pierre B.H. ; Forth, Leonie F. ; Fouchier, Ron A.M. ; Freitas-Astúa, Juliana ; Gago-Zachert, Selma ; Gāo, George Fú ; García, María Laura ; García-Sastre, Adolfo ; Garrison, Aura R. ; Gbakima, Aiah ; Goldstein, Tracey ; Gonzalez, Jean Paul J. ; Griffiths, Anthony ; Groschup, Martin H. ; Günther, Stephan ; Guterres, Alexandro ; Hall, Roy A. ; Hammond, John ; Hassan, Mohamed ; Hepojoki, Jussi ; Hepojoki, Satu ; Hetzel, Udo ; Hewson, Roger ; Hoffmann, Bernd ; Hongo, Seiji ; Höper, Dirk ; Horie, Masayuki ; Hughes, Holly R. ; Hyndman, Timothy H. ; Jambai, Amara ; Jardim, Rodrigo ; Jiāng, Dàohóng ; Jin, Qi ; Jonson, Gilda B. ; Junglen, Sandra ; Karadağ, Serpil ; Keller, Karen E. ; Klempa, Boris ; Klingström, Jonas ; Kobinger, Gary ; Kondō, Hideki ; Koonin, Eugene V. ; Krupovic, Mart ; Kurath, Gael ; Kuzmin, Ivan V. ; Laenen, Lies ; Lamb, Robert A. ; Lambert, Amy J. ; Langevin, Stanley L. ; Lee, Benhur ; Lemos, Elba R.S. ; Leroy, Eric M. ; Li, Dexin ; Lǐ, Jiànróng ; Liang, Mifang ; Liú, Wénwén ; Liú, Yàn ; Lukashevich, Igor S. ; Maes, Piet ; Marciel de Souza, William ; Marklewitz, Marco ; Marshall, Sergio H. ; Martelli, Giovanni P. ; Martin, Robert R. ; Marzano, Shin Yi L. ; Massart, Sébastien ; McCauley, John W. ; Mielke-Ehret, Nicole ; Minafra, Angelantonio ; Minutolo, Maria ; Mirazimi, Ali ; Mühlbach, Hans Peter ; Mühlberger, Elke ; Naidu, Rayapati ; Natsuaki, Tomohide ; Navarro, Beatriz ; Navarro, José A. ; Netesov, Sergey V. ; Neumann, Gabriele ; Nowotny, Norbert ; Nunes, Márcio R.T. ; Nylund, Are ; Økland, Arnfinn L. ; Oliveira, Renata C. ; Palacios, Gustavo ; Pallas, Vicente ; Pályi, Bernadett ; Papa, Anna ; Parrish, Colin R. ; Pauvolid-Corrêa, Alex ; Pawęska, Janusz T. ; Payne, Susan ; Pérez, Daniel R. ; Pfaff, Florian ; Radoshitzky, Sheli R. ; ul Rahman, Aziz ; Ramos-González, Pedro L. ; Resende, Renato O. ; Reyes, Carina A. ; Rima, Bertus K. ; Romanowski, Víctor ; Robles Luna, Gabriel ; Rota, Paul ; Rubbenstroth, Dennis ; Runstadler, Jonathan A. ; Ruzek, Daniel ; Sabanadzovic, Sead ; Salát, Jiří ; Sall, Amadou Alpha ; Salvato, Maria S. ; Sarpkaya, Kamil ; Sasaya, Takahide ; Schwemmle, Martin ; Shabbir, Muhammad Z. ; Shí, Xiǎohóng ; Shí, Zhènglì ; Shirako, Yukio ; Simmonds, Peter ; Širmarová, Jana ; Sironi, Manuela ; Smither, Sophie ; Smura, Teemu ; Song, Jin Won ; Spann, Kirsten M. ; Spengler, Jessica R. ; Stenglein, Mark D. ; Stone, David M. ; Straková, Petra ; Takada, Ayato ; Tesh, Robert B. ; Thornburg, Natalie J. ; Tomonaga, Keizō ; Tordo, Noël ; Towner, Jonathan S. ; Turina, Massimo ; Tzanetakis, Ioannis ; Ulrich, Rainer G. ; Vaira, Anna Maria ; Hoogen, Bernadette van den; Varsani, Arvind ; Vasilakis, Nikos ; Verbeek, Martin ; Wahl, Victoria ; Walker, Peter J. ; Wang, Hui ; Wang, Jianwei ; Wang, Xifeng ; Wang, Lin Fa ; Wèi, Tàiyún ; Wells, Heather ; Whitfield, Anna E. ; Williams, John V. ; Wolf, Yuri I. ; Wú, Zhìqiáng ; Yang, Xin ; Yáng, Xīnglóu ; Yu, Xuejie ; Yutin, Natalya ; Zerbini, Murilo ; Zhang, Tong ; Zhang, Yong Zhen ; Zhou, Guohui ; Zhou, Xueping - \ 2020
    Archives of Virology (2020). - ISSN 0304-8608

    In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

    FEMA GRAS assessment of natural flavor complexes: Clove, cinnamon leaf and West Indian bay leaf-derived flavoring ingredients
    Gooderham, Nigel J. ; Cohen, Samuel M. ; Eisenbrand, Gerhard ; Fukushima, Shoji ; Guengerich, F.P. ; Hecht, Stephen S. ; Rietjens, Ivonne M.C.M. ; Rosol, Thomas J. ; Davidsen, Jeanne M. ; Harman, Christie L. ; Murray, Ian J. ; Taylor, Sean V. - \ 2020
    Food and Chemical Toxicology 145 (2020). - ISSN 0278-6915
    Cinnamon leaf oil - Clove essential oils, extract and oleoresin - GRAS - Natural flavor complex - Safety evaluation - West Indian bay leaf oil and oleoresin

    In 2015, the Expert Panel of the Flavor and Extract Manufacturers Association initiated the safety re-evaluation of over 250 natural flavor complexes (NFCs) used as flavor ingredients. This publication, 4th in a series focusing on the safety evaluation of NFCs, presents an evaluation of NFCs rich in hydroxyallylbenzene and hydroxypropenylbenzene constituents using a procedure initially published in 2005 and updated in 2018 that evaluates the safety of naturally occurring mixtures for their intended use as flavoring ingredients. The procedure requires the characterization of the chemical composition for each NFC and subsequent organization of the constituents into defined congeneric groups. The safety of each NFC is evaluated using the conservative threshold of toxicological concern (TTC) approach together with studies on absorption, metabolism and toxicology of the NFC and its constituent congeneric groups. By the application of this procedure, seven NFCs, derived from clove, cinnamon leaf and West Indian bay leaf were affirmed as “generally recognized as safe (GRAS)” under their conditions of intended use as flavor ingredients. An eighth NFC, an oleoresin of West Indian bay leaf, was affirmed based on its estimated intake, which is below the TTC of 0.15 μg/person per day for compounds with structural alerts for genotoxicity.

    Digital Twin helpt boer bij stikstofhuishouding
    Been, Thomas van; Kamphuis, Claudia ; Evert, Frits van; Bulens, Jan Dirk ; Athanasiadis, Ioannis ; Voort, Mariska van der - \ 2020
    Genome-wide Modeling of Polygenic Risk Score in Colorectal Cancer Risk
    Thomas, Minta ; Sakoda, Lori C. ; Hoffmeister, Michael ; Rosenthal, Elisabeth A. ; Lee, Jeffrey K. ; Duijnhoven, Franzel J.B. van; Platz, Elizabeth A. ; Wu, Anna H. ; Dampier, Christopher H. ; Chapelle, Albert de la; Wolk, Alicja ; Joshi, Amit D. ; Burnett-Hartman, Andrea ; Gsur, Andrea ; Lindblom, Annika ; Castells, Antoni ; Win, Aung Ko ; Namjou, Bahram ; Guelpen, Bethany Van; Tangen, Catherine M. ; He, Qianchuan ; Li, Christopher I. ; Schafmayer, Clemens ; Joshu, Corinne E. ; Ulrich, Cornelia M. ; Bishop, D.T. ; Buchanan, Daniel D. ; Schaid, Daniel ; Drew, David A. ; Muller, David C. ; Duggan, David ; Crosslin, David R. ; Albanes, Demetrius ; Giovannucci, Edward L. ; Larson, Eric ; Qu, Flora ; Mentch, Frank ; Giles, Graham G. ; Hakonarson, Hakon ; Hampel, Heather ; Stanaway, Ian B. ; Figueiredo, Jane C. ; Huyghe, Jeroen R. ; Minnier, Jessica ; Chang-Claude, Jenny ; Hampe, Jochen ; Harley, John B. ; Visvanathan, Kala ; Curtis, Keith R. ; Offit, Kenneth ; Li, Li ; Marchand, Loic Le; Vodickova, Ludmila ; Gunter, Marc J. ; Jenkins, Mark A. ; Slattery, Martha L. ; Lemire, Mathieu ; Woods, Michael O. ; Song, Mingyang ; Murphy, Neil ; Lindor, Noralane M. ; Dikilitas, Ozan ; Pharoah, Paul D.P. ; Campbell, Peter T. ; Newcomb, Polly A. ; Milne, Roger L. ; MacInnis, Robert J. ; Castellví-Bel, Sergi ; Ogino, Shuji ; Berndt, Sonja I. ; Bézieau, Stéphane ; Thibodeau, Stephen N. ; Gallinger, Steven J. ; Zaidi, Syed H. ; Harrison, Tabitha A. ; Keku, Temitope O. ; Hudson, Thomas J. ; Vymetalkova, Veronika ; Moreno, Victor ; Martín, Vicente ; Arndt, Volker ; Wei, Wei Qi ; Chung, Wendy ; Su, Yu Ru ; Hayes, Richard B. ; White, Emily ; Vodicka, Pavel ; Casey, Graham ; Gruber, Stephen B. ; Schoen, Robert E. ; Chan, Andrew T. ; Potter, John D. ; Brenner, Hermann ; Jarvik, Gail P. ; Corley, Douglas A. ; Peters, Ulrike ; Hsu, Li - \ 2020
    American Journal of Human Genetics 107 (2020)3. - ISSN 0002-9297 - p. 432 - 444.
    cancer risk prediction - colorectal cancer - machine learning - polygenic risk score

    Accurate colorectal cancer (CRC) risk prediction models are critical for identifying individuals at low and high risk of developing CRC, as they can then be offered targeted screening and interventions to address their risks of developing disease (if they are in a high-risk group) and avoid unnecessary screening and interventions (if they are in a low-risk group). As it is likely that thousands of genetic variants contribute to CRC risk, it is clinically important to investigate whether these genetic variants can be used jointly for CRC risk prediction. In this paper, we derived and compared different approaches to generating predictive polygenic risk scores (PRS) from genome-wide association studies (GWASs) including 55,105 CRC-affected case subjects and 65,079 control subjects of European ancestry. We built the PRS in three ways, using (1) 140 previously identified and validated CRC loci; (2) SNP selection based on linkage disequilibrium (LD) clumping followed by machine-learning approaches; and (3) LDpred, a Bayesian approach for genome-wide risk prediction. We tested the PRS in an independent cohort of 101,987 individuals with 1,699 CRC-affected case subjects. The discriminatory accuracy, calculated by the age- and sex-adjusted area under the receiver operating characteristics curve (AUC), was highest for the LDpred-derived PRS (AUC = 0.654) including nearly 1.2 M genetic variants (the proportion of causal genetic variants for CRC assumed to be 0.003), whereas the PRS of the 140 known variants identified from GWASs had the lowest AUC (AUC = 0.629). Based on the LDpred-derived PRS, we are able to identify 30% of individuals without a family history as having risk for CRC similar to those with a family history of CRC, whereas the PRS based on known GWAS variants identified only top 10% as having a similar relative risk. About 90% of these individuals have no family history and would have been considered average risk under current screening guidelines, but might benefit from earlier screening. The developed PRS offers a way for risk-stratified CRC screening and other targeted interventions.

    Arbuscular mycorrhizal symbiosis increases phosphorus uptake and productivity of mixtures of maize varieties compared to monocultures
    Wang, Xin Xin ; Hoffland, Ellis ; Feng, Gu ; Kuyper, Thomas W. - \ 2020
    Journal of Applied Ecology (2020). - ISSN 0021-8901
    complementarity effects - maize varieties - mixtures - monocultures - mycorrhizal networks - overyielding - phosphorus - relative yield total

    Ecological intensification seeks to achieve crop yield increases by intensifying complementary or facilitative interactions between plant species or varieties. Different species of arbuscular mycorrhizal fungi (AMF) exhibit niche differentiation and show selectivity towards certain plants, which can further enhance complementarity. It is not clear whether in the presence of one AMF species, where mycelial networks connect crop species, opportunities for complementarity effects may be reduced. We grew monocultures and mixtures of maize varieties in a greenhouse with one species of AMF, Funneliformis mosseae, during two consecutive years to investigate whether under such conditions the mycorrhizal symbiosis would affect complementarity and overyielding compared to non-mycorrhizal plants. Variety mixtures showed increased phosphatase activity and mycorrhizal colonization, enhanced phosphorus uptake and overyielding when plants were mycorrhizal. There was no overyielding when plants were non-mycorrhizal. The increase in relative yield total was due to complementarity effects. Synthesis and applications. Our study implies that appropriate agricultural management that enhances mycorrhizal fungal contribution to ecosystem services may result in overyielding in terms of yield or phosphorus uptake through mixing varieties within one crop species.

    Crop yield prediction using machine learning: A systematic literature review
    Klompenburg, Thomas van; Kassahun, Ayalew ; Catal, Cagatay - \ 2020
    Computers and Electronics in Agriculture 177 (2020). - ISSN 0168-1699
    Crop yield prediction - Decision support system - Deep learning - Machine learning - Systematic literature review

    Machine learning is an important decision support tool for crop yield prediction, including supporting decisions on what crops to grow and what to do during the growing season of the crops. Several machine learning algorithms have been applied to support crop yield prediction research. In this study, we performed a Systematic Literature Review (SLR) to extract and synthesize the algorithms and features that have been used in crop yield prediction studies. Based on our search criteria, we retrieved 567 relevant studies from six electronic databases, of which we have selected 50 studies for further analysis using inclusion and exclusion criteria. We investigated these selected studies carefully, analyzed the methods and features used, and provided suggestions for further research. According to our analysis, the most used features are temperature, rainfall, and soil type, and the most applied algorithm is Artificial Neural Networks in these models. After this observation based on the analysis of machine learning-based 50 papers, we performed an additional search in electronic databases to identify deep learning-based studies, reached 30 deep learning-based papers, and extracted the applied deep learning algorithms. According to this additional analysis, Convolutional Neural Networks (CNN) is the most widely used deep learning algorithm in these studies, and the other widely used deep learning algorithms are Long-Short Term Memory (LSTM) and Deep Neural Networks (DNN).

    Interactive governance for satisfaction measurements: Stakeholder involvement in design processes for flood risk management
    Nouzari, Ehsan ; Hartmann, Thomas ; Spit, Tejo - \ 2020
    Journal of Flood Risk Management (2020). - ISSN 1753-318X
    communication - consensus, stakeholder involvement, interactive governance - participation - procedural satisfaction

    The European Flood Directive (FD) shifted water management policy from flood protection to flood risk management. To facilitate the shift, a new instrument was introduced called the flood risk management plan. According to the FD, a flood risk management plan shall first take into account relevant aspects from water management, nature conservation, land use, spatial planning, navigation, and port infrastructure. Second, the flood risk management plan will be coordinated at the river basin level. This changes the spatial scope of water management compared to (old) flood protection approach and affects a broader group of stakeholder interests, namely landowners behind dikes. As a result, water management has to introduce a governance approach that facilitates stakeholder involvement in which different spatial interests are balanced, bargained and negotiated. Academic governance literature consists mostly of qualitative case studies, because of their complex nature. As a result, most governance literature operates on assumptions which make it difficult to formulate governance strategies that work based on general patterns. To contribute towards scientific methodologies for comparative research a quantitative method was developed to measure satisfaction in a stakeholder process. The method first provides new insights on the relation between interactive governance processes and the procedural satisfaction of stakeholders. Second, it provides insights that help to improve interactive governance in terms of managing a stakeholder process in such a way that greater procedural satisfaction can be achieved.

    Highly Stable Perovskite Supercrystals via Oil-in-Oil Templating
    Tang, Yingying ; Gomez, Leyre ; Lesage, Arnon ; Marino, Emanuele ; Kodger, Thomas E. ; Meijer, Janne Mieke ; Kolpakov, Paul ; Meng, Jie ; Zheng, Kaibo ; Gregorkiewicz, Tom ; Schall, Peter - \ 2020
    Nano Letters 20 (2020)8. - ISSN 1530-6984 - p. 5997 - 6004.
    assembly - emulsion-droplet templating - perovskite films - stability - supercrystals

    Inorganic perovskites display an enticing foreground for their wide range of optoelectronic applications. Recently, supercrystals (SCs) of inorganic perovskite nanocrystals (NCs) have been reported to possess highly ordered structure as well as novel collective optical properties, opening new opportunities for efficient films. Here, we report the large-scale assembly control of spherical, cubic, and hexagonal SCs of inorganic perovskite NCs through templating by oil-in-oil emulsions. We show that an interplay between the roundness of the cubic NCs and the tension of the confining droplet surface sets the superstructure morphology, and we exploit this interplay to design dense hyperlattices of SCs. The SC films show strongly enhanced stability for at least two months without obvious structural degradation and minor optical changes. Our results on the controlled large-scale assembly of perovskite NC superstructures provide new prospects for the bottom-up production of optoelectronic devices based on the microfluidic production of mesoscopic building blocks.

    Correcting course: the emission reduction potential of international cooperative initiatives
    Lui, Swithin ; Kuramochi, Takeshi ; Smit, Sybrig ; Roelfsema, Mark ; Hsu, Angel ; Weinfurter, Amy ; Chan, Sander ; Hale, Thomas ; Fekete, Hanna ; Lütkehermöller, Katharina ; Jose de Villafranca Casas, Maria ; Nascimento, Leonardo ; Sterl, Sebastian ; Höhne, Niklas - \ 2020
    Climate Policy (2020). - ISSN 1469-3062
    climate change mitigation - GHG reductions - international cooperation - mitigation scenarios - Non-state actors

    This article quantifies the aggregate potential of greenhouse gas (GHG) emissions reductions in 2030 from the assumed full implementation of major international cooperative initiatives (ICIs). To this end, a methodology is proposed to aggregate emission reduction goals of the most significant and potentially impactful global initiatives. We identified the extent to which reductions are additional to national policies, assuming these actions do not displace climate actions elsewhere, and accounted for overlap ranges between the ICIs. The analysis was conducted for 17 initiatives, selected from an original list of over 300 with a series of testing criteria, across eight sectors and ten major emitting economies. These initiatives include cities, regions, businesses, and other subnational and non-state actors, cooperating with each other and sometimes working in partnership with national governments or other international organizations. Our analysis shows that the combined achievement of initiatives’ reduction goals could reduce global emissions in 2030 by 18–21 GtCO2e/year in addition to current national policies (total of 60–63 GtCO2e/year), down to 39–44 GtCO2e/year. If delivered fully, reductions from these 17 initiatives would help move the global emissions trajectory within the range of a 2°C-consistent emission pathway by 2030, although a significant gap would remain to reduce emissions to a 1.5°C-consistent pathway. Key policy insights We propose a transparent and robust methodology to aggregate GHG mitigation potential of ICIs, accounting for overlaps between ICIs. If major initiatives meet their goals and do not change the course of other existing climate actions, they could make large contributions by 2030 towards global efforts to stay within the range of a below 2°C-consistent emission pathway by 2030. The full suite of existing initiatives beyond those in this analysis could further increase ambition towards achieving the Paris Agreement’s temperature goals. Cities and regions, businesses and forestry initiatives account for significantly more than half of all possible emission reductions from ICIs; implementation of their goals should be a key policy focus.

    Author Correction: Global status and conservation potential of reef sharks
    MacNeil, M.A. ; Chapman, Demian D. ; Heupel, Michelle ; Simpfendorfer, Colin A. ; Heithaus, Michael ; Meekan, Mark ; Harvey, Euan ; Goetze, Jordan ; Kiszka, Jeremy ; Bond, Mark E. ; Currey-Randall, Leanne M. ; Speed, Conrad W. ; Sherman, C.S. ; Rees, Matthew J. ; Udyawer, Vinay ; Flowers, Kathryn I. ; Clementi, Gina ; Valentin-Albanese, Jasmine ; Gorham, Taylor ; Adam, M.S. ; Ali, Khadeeja ; Pina-Amargós, Fabián ; Angulo-Valdés, Jorge A. ; Asher, Jacob ; Barcia, Laura García ; Beaufort, Océane ; Benjamin, Cecilie ; Bernard, Anthony T.F. ; Berumen, Michael L. ; Bierwagen, Stacy ; Bonnema, Erika ; Bown, Rosalind M.K. ; Bradley, Darcy ; Brooks, Edd ; Brown, J.J. ; Buddo, Dayne ; Burke, Patrick ; Cáceres, Camila ; Cardeñosa, Diego ; Carrier, Jeffrey C. ; Caselle, Jennifer E. ; Charloo, Venkatesh ; Claverie, Thomas ; Clua, Eric ; Cochran, Jesse E.M. ; Cook, Neil ; Cramp, Jessica ; D’Alberto, Brooke ; Graaf, Martin de; Dornhege, Mareike ; Estep, Andy ; Fanovich, Lanya ; Farabaugh, Naomi F. ; Fernando, Daniel ; Flam, Anna L. ; Floros, Camilla ; Fourqurean, Virginia ; Garla, Ricardo ; Gastrich, Kirk ; George, Lachlan ; Graham, Rory ; Guttridge, Tristan ; Hardenstine, Royale S. ; Heck, Stephen ; Henderson, Aaron C. ; Hertler, Heidi ; Hueter, Robert ; Johnson, Mohini ; Jupiter, Stacy ; Kasana, Devanshi ; Kessel, Steven T. ; Kiilu, Benedict ; Kirata, Taratu ; Kuguru, Baraka ; Kyne, Fabian ; Langlois, Tim ; Lédée, Elodie J.I. ; Lindfield, Steve ; Luna-Acosta, Andrea ; Maggs, Jade ; Manjaji-Matsumoto, B.M. ; Marshall, Andrea ; Matich, Philip ; McCombs, Erin ; McLean, Dianne ; Meggs, Llewelyn ; Moore, Stephen ; Mukherji, Sushmita ; Murray, Ryan ; Kaimuddin, Muslimin ; Newman, Stephen J. ; Nogués, Josep ; Obota, Clay ; O’Shea, Owen ; Osuka, Kennedy ; Papastamatiou, Yannis P. ; Perera, Nishan ; Peterson, Bradley ; Ponzo, Alessandro ; Prasetyo, Andhika ; Sjamsul Quamar, L.M. ; Quinlan, Jessica ; Ruiz-Abierno, Alexei ; Sala, Enric ; Samoilys, Melita ; Schärer-Umpierre, Michelle ; Schlaff, Audrey ; Simpson, Nikola ; Smith, Adam N.H. ; Sparks, Lauren ; Tanna, Akshay ; Torres, Rubén ; Travers, Michael J. ; Zinnicq Bergmann, Maurits van; Vigliola, Laurent ; Ward, Juney ; Watts, Alexandra M. ; Wen, Colin ; Whitman, Elizabeth ; Wirsing, Aaron J. ; Wothke, Aljoscha ; Zarza-Gonzâlez, Esteban ; Cinner, Joshua E. - \ 2020
    Nature (2020). - ISSN 0028-0836

    An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

    Strategic use of land policy instruments for affordable housing – Coping with social challenges under scarce land conditions in Swiss cities
    Debrunner, Gabriela ; Hartmann, Thomas - \ 2020
    Land Use Policy 99 (2020). - ISSN 0264-8377
    Affordable Housing - Densification - Gentrification - Land policy

    For decades, many cities have introduced densification policy objectives to stop urban sprawl or to promote efficient use of natural resources. In the urban housing sector, however, densification projects often intensify social challenges. Due to rising rents after modernization of existing housing stocks as a consequence of densification, low-income tenants are forced to leave their apartments. Risks of social exclusion and segregation increase simultaneously. In this article, we analyze how municipal planning authorities cope with affordable housing shortages in a context of urban densification. Specifically, we ask: How do municipal planning authorities promote affordable housing in densifying cities? To answer this research question, we apply a neoinstitutional analysis approach to better understand (1) the basic mechanisms of how land policy instruments impact affordability, and (2) why specific instruments are activated to defend affordable housing objectives. Through qualitative case study analysis of four Swiss urban municipalities, our results show that the mere availability of land policy instruments is not sufficient but that the strategic activation of specific instruments matters.

    Large-Scale Variability of Physical and Biological Sea-Ice Properties in Polar Oceans
    Castellani, Giulia ; Schaafsma, Fokje L. ; Arndt, Stefanie ; Lange, Benjamin A. ; Peeken, Ilka ; Ehrlich, Julia ; David, Carmen ; Ricker, Robert ; Krumpen, Thomas ; Hendricks, Stefan ; Schwegmann, Sandra ; Massicotte, Philippe ; Flores, Hauke - \ 2020
    Frontiers in Marine Science 7 (2020). - ISSN 2296-7745
    Antarctic - Arctic - ice algae - ice thickness - sea ice - spatial variability - under-ice light

    In this study, we present unique data collected with a Surface and Under-Ice Trawl (SUIT) during five campaigns between 2012 and 2017, covering the spring to summer and autumn transition in the Arctic Ocean, and the seasons of winter and summer in the Southern Ocean. The SUIT was equipped with a sensor array from which we retrieved: sea-ice thickness, the light field at the underside of sea ice, chlorophyll a concentration in the ice (in-ice chl a), and the salinity, temperature, and chl a concentration of the under-ice water. With an average trawl distance of about 2 km, and a global transect length of more than 117 km in both polar regions, the present work represents the first multi-seasonal habitat characterization based on kilometer-scale profiles. The present data highlight regional and seasonal patterns in sea-ice properties in the Polar Ocean. Light transmittance through Arctic sea ice reached almost 100% in summer, when the ice was thinner and melt ponds spread over the ice surface. However, the daily integrated amount of light under sea ice was maximum in spring. Compared to the Arctic, Antarctic sea-ice was thinner, snow depth was thicker, and sea-ice properties were more uniform between seasons. Light transmittance was low in winter with maximum transmittance of 73%. Despite thicker snow depth, the overall under-ice light was considerably higher during Antarctic summer than during Arctic summer. Spatial autocorrelation analysis shows that Arctic sea ice was characterized by larger floes compared to the Antarctic. In both Polar regions, the patch size of the transmittance followed the spatial variability of sea-ice thickness. In-ice chl a in the Arctic Ocean remained below 0.39 mg chl a m−2, whereas it exceeded 7 mg chl a m−2 during Antarctic winter, when water chl a concentrations remained below 1.5 mg chl a m−2, thus highlighting its potential as an important carbon source for overwintering organisms. The data analyzed in this study can improve large-scale physical and ecosystem models, habitat mapping studies and time series analyzed in the context of climate change effects and marine management.

    Proteins unbound – how ectomycorrhizal fungi can tap a vast reservoir of mineral-associated organic nitrogen
    Keiluweit, Marco ; Kuyper, Thomas W. - \ 2020
    New Phytologist (2020). - ISSN 0028-646X
    ectomycorrhizal fungi - enzyme-mediated mechanisms - forest soil - iron (Fe) oxyhydroxides - mineral-associated organic nitrogen - nitrogen (N) acquisition - soil organic matter
    Next-generation biological control: the need for integrating genetics and genomics
    Leung, Kelley ; Ras, Erica ; Ferguson, Kim B. ; Ariëns, Simone ; Babendreier, Dirk ; Bijma, Piter ; Bourtzis, Kostas ; Brodeur, Jacques ; Bruins, Margreet A. ; Centurión, Alejandra ; Chattington, Sophie R. ; Chinchilla-Ramírez, Milena ; Dicke, Marcel ; Fatouros, Nina E. ; González-Cabrera, Joel ; Groot, Thomas V.M. ; Haye, Tim ; Knapp, Markus ; Koskinioti, Panagiota ; Hesran, Sophie Le; Lyrakis, Manolis ; Paspati, Angeliki ; Pérez-Hedo, Meritxell ; Plouvier, Wouter N. ; Schlötterer, Christian ; Stahl, Judith M. ; Thiel, Andra ; Urbaneja, Alberto ; Zande, Louis van de; Verhulst, Eveline C. ; Vet, Louise E.M. ; Visser, Sander ; Werren, John H. ; Xia, Shuwen ; Zwaan, Bas J. ; Magalhães, Sara ; Beukeboom, Leo W. ; Pannebakker, Bart A. - \ 2020
    Biological Reviews (2020). - ISSN 1464-7931
    artificial selection - biological control - genetics - genome assembly - genomics - insect breeding - microbiome - modelling

    Biological control is widely successful at controlling pests, but effective biocontrol agents are now more difficult to import from countries of origin due to more restrictive international trade laws (the Nagoya Protocol). Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, application of genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined, including how to implement this information into a selective breeding program. Choosing a trait can be assisted by modelling to account for the proper agro-ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depend on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices includes marker-assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post-release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy.

    CloudRoots: integration of advanced instrumental techniques and process modelling of sub-hourly and sub-kilometre land–atmosphere interactions
    Vilà-Guerau de Arellano, Jordi ; Ney, Patrizia ; Hartogensis, Oscar ; Boer, Hugo De; Diepen, Kevin Van; Emin, Dzhaner ; Groot, Geiske De; Klosterhalfen, Anne ; Langensiepen, Matthias ; Matveeva, Maria ; Miranda-García, Gabriela ; Moene, Arnold F. ; Rascher, Uwe ; Röckmann, Thomas ; Adnew, Getachew ; Brüggemann, Nicolas ; Rothfuss, Youri ; Graf, Alexander - \ 2020
    Biogeosciences 17 (2020)17. - ISSN 1726-4170 - p. 4375 - 4404.
    The CloudRoots field experiment was designed to obtain a comprehensive observational dataset that includes soil, plant, and atmospheric variables to investigate the interaction between a heterogeneous land surface and its overlying atmospheric boundary layer at the sub-hourly and sub-kilometre scale. Our findings demonstrate the need to include measurements at leaf level to better understand the relations between stomatal aperture and evapotranspiration (ET) during the growing season at the diurnal scale. Based on these observations, we obtain accurate parameters for the mechanistic representation of photosynthesis and stomatal aperture. Once the new parameters are implemented, the model reproduces the stomatal leaf conductance and the leaf-level photosynthesis satisfactorily. At the canopy scale, we find a consistent diurnal pattern on the contributions of plant transpiration and soil evaporation using different measurement techniques. From highly resolved vertical profile measurements of carbon dioxide (CO2) and other state variables, we infer a profile of the CO2 assimilation in the canopy with non-linear variations with height. Observations taken with a laser scintillometer allow us to quantify the non-steadiness of the surface turbulent fluxes during the rapid changes driven by perturbation of photosynthetically active radiation by cloud flecks. More specifically, we find 2 min delays between the cloud radiation perturbation and ET. To study the relevance of advection and surface heterogeneity for the land–atmosphere interaction, we employ a coupled surface–atmospheric conceptual model that integrates the surface and upper-air observations made at different scales from leaf to the landscape. At the landscape scale, we calculate a composite sensible heat flux by weighting measured fluxes with two different land use categories, which is consistent with the diurnal evolution of the boundary layer depth. Using sun-induced fluorescence measurements, we also quantify the spatial variability of ET and find large variations at the sub-kilometre scale around the CloudRoots site. Our study shows that throughout the entire growing season, the wide variations in stomatal opening and photosynthesis lead to large diurnal variations of plant transpiration at the leaf, plant, canopy, and landscape scales. Integrating different advanced instrumental techniques with modelling also enables us to determine variations of ET that depend on the scale where the measurement were taken and on the plant growing stage
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