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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Hepcidin-guided screen-and-treat interventions against iron-deficiency anaemia in pregnancy: a randomised controlled trial in The Gambia
Bah, Amat ; Muhammad, Abdul Khalie ; Wegmuller, Rita ; Verhoef, Hans ; Goheen, Morgan M. ; Sanyang, Saikou ; Danso, Ebrima ; Sise, Ebrima A. ; Pasricha, Sant Rayn ; Armitage, Andrew E. ; Drakesmith, Hal ; Cross, James H. ; Moore, Sophie E. ; Cerami, Carla ; Prentice, Andrew M. - \ 2019
The Lancet Global Health 7 (2019)11. - ISSN 2214-109X - p. e1564 - e1574.

Background: WHO recommends daily iron supplementation for pregnant women, but adherence is poor because of side-effects, effectiveness is low, and there are concerns about possible harm. The iron-regulatory hormone hepcidin can signal when an individual is ready-and-safe to receive iron. We tested whether a hepcidin-guided screen-and-treat approach to combat iron-deficiency anaemia could achieve equivalent efficacy to universal administration, but with lower exposure to iron. Methods: We did a three-arm, randomised, double-blind, non-inferiority trial in 19 rural communities in the Jarra West and Kiang East districts of The Gambia. Eligible participants were pregnant women aged 18–45 years at between 14 weeks and 22 weeks of gestation. We randomly allocated women to either WHO's recommended regimen (ie, a daily UN University, UNICEF, and WHO international multiple-micronutrient preparation [UNIMMAP] containing 60 mg iron), a 60 mg screen-and-treat approach (ie, daily UNIMMAP containing 60 mg iron for 7 days if weekly hepcidin was <2·5 μg/L or UNIMMAP without iron if hepcidin was ≥2·5 μg/L), or a 30 mg screen-and-treat approach (ie, daily UNIMMAP containing 30 mg iron for 7 days if weekly hepcidin was <2·5 μg/L or UNIMMAP without iron if hepcidin was ≥2·5 μg/L). We used a block design stratified by amount of haemoglobin at enrolment (above and below the median amount of haemoglobin on every enrolment day) and stage of gestation (14–18 weeks vs 19–22 weeks). Participants and investigators were unaware of the random allocation. The primary outcome was the amount of haemoglobin at day 84 and was measured as the difference in haemoglobin in each screen-and-treat group compared with WHO's recommended regimen; the non-inferiority margin was set at −5·0 g/L. The primary outcome was assessed in the per-protocol population, which comprised all women who completed the study. This trial is registered with the ISRCTN registry, number ISRCTN21955180. Findings: Between June 16, 2014, and March 3, 2016, 498 participants were randomised, of whom 167 were allocated to WHO's recommended regimen, 166 were allocated to the 60 mg per day screen-and-treat approach, and 165 were allocated to the 30 mg per day screen-and-treat approach. 78 participants were withdrawn or lost to follow-up during the study; thus, the per-protocol population comprised 140 women assigned to WHO's recommended regimen, 133 allocated to the 60 mg screen-and-treat approach, and 147 allocated to the 30 mg screen-and-treat approach. The screen-and-treat approaches did not exceed the non-inferiority margin. Compared with WHO's recommended regimen, the difference in the amount of haemoglobin at day 84 was −2·2 g/L (95% CI −4·6 to 0·1) with the 60 mg screen-and-treat approach and −2·7 g/L (–5·0 to −0·5) with the 30 mg screen-and-treat approach. Adherence, reported side-effects, and adverse events were similar between the three groups. The most frequent side-effect was stomachache, which was similar in the 60 mg screen-and-treat group (82 cases per 1906 person-weeks) and with WHO's recommended regimen (81 cases per 1974 person-weeks; effect 1·0, 95% CI 0·7 to 1·6); in the 30 mg screen-and-treat group the frequency of stomachache was slightly lower than with WHO's recommended regimen (58 cases per 2009 person-weeks; effect 0·7, 95% CI 0·5 to 1·1). No participants died during the study. Interpretation: The hepcidin-guided screen-and-treat approaches had no advantages over WHO's recommended regimen in terms of adherence, side-effects, or safety outcomes. Our results suggest that the current WHO policy for iron administration to pregnant women should remain unchanged while more effective approaches continue to be sought. Funding: Bill & Melinda Gates Foundation and the UK Medical Research Council.

Recept voor plastic soep
Verburg, Charlotte - \ 2019
In: Plastic: Van zegen tot vloek / van Everdingen, Jannes, van Donk, Ellen, Poolen, Daniël, Buiter, Rob, Den Haag : Stichting Biowetenschappen en Maatschappij (Cahier Biowetenschappen en Maatschappij 2) - ISBN 9789073196957 - p. 36 - 47.
Twintig jaar terug ontdekte de Amerikaanse oceanograaf en kapitein Charles Moore in de StilleOceaan de eerste zogenoemde ‘plastic soep’: een enorme plek met een relatief hoge concentratieronddrijvend plastic. Inmiddels is die soep een iconisch begrip bij het grote publiek. Om tebegrijpen wat er aan de plastic soep kan worden gedaan – opruimen bij de bron of de uitgang? –zul je het moeten terugvolgen naar de bron. Waar komt al dat plastic vandaan?
Review of the evidence regarding the use of antenatal multiple micronutrient supplementation in low- and middle-income countries
Bourassa, Megan W. ; Osendarp, Saskia J.M. ; Adu-Afarwuah, Seth ; Ahmed, Saima ; Ajello, Clayton ; Bergeron, Gilles ; Black, Robert ; Christian, Parul ; Cousens, Simon ; Pee, Saskia de; Dewey, Kathryn G. ; Arifeen, Shams El ; Engle-Stone, Reina ; Fleet, Alison ; Gernand, Alison D. ; Hoddinott, John ; Klemm, Rolf ; Kraemer, Klaus ; Kupka, Roland ; McLean, Erin ; Moore, Sophie E. ; Neufeld, Lynnette M. ; Persson, Lars Åke ; Rasmussen, Kathleen M. ; Shankar, Anuraj H. ; Smith, Emily ; Sudfeld, Christopher R. ; Udomkesmalee, Emorn ; Vosti, Stephen A. - \ 2019
Annals of the New York Academy Of Sciences 1444 (2019)1. - ISSN 0077-8923 - p. 6 - 21.
LMICs - micronutrient - pregnancy - supplements

Inadequate micronutrient intakes are relatively common in low- and middle-income countries (LMICs), especially among pregnant women, who have increased micronutrient requirements. This can lead to an increase in adverse pregnancy and birth outcomes. This review presents the conclusions of a task force that set out to assess the prevalence of inadequate micronutrient intakes and adverse birth outcomes in LMICs; the data from trials comparing multiple micronutrient supplements (MMS) that contain iron and folic acid (IFA) with IFA supplements alone; the risks of reaching the upper intake levels with MMS; and the cost-effectiveness of MMS compared with IFA. Recent meta-analyses demonstrate that MMS can reduce the risks of preterm birth, low birth weight, and small for gestational age in comparison with IFA alone. An individual-participant data meta-analysis also revealed even greater benefits for anemic and underweight women and female infants. Importantly, there was no increased risk of harm for the pregnant women or their infants with MMS. These data suggest that countries with inadequate micronutrient intakes should consider supplementing pregnant women with MMS as a cost-effective method to reduce the risk of adverse birth outcomes.

An architectural understanding of natural sway frequencies in trees
Jackson, T. ; Shenkin, A. ; Moore, J. ; Bunce, A. ; Emmerik, T. Van; Kane, B. ; Burcham, D. ; James, K. ; Selker, J. ; Calders, K. ; Origo, N. ; Disney, M. ; Burt, A. ; Wilkes, P. ; Raumonen, P. ; Gonzalez De Tanago Menaca, J. ; Lau, A. ; Herold, M. ; Goodman, R.C. ; Fourcaud, T. ; Malhi, Y. - \ 2019
Journal of the Royal Society, Interface 16 (2019)155. - ISSN 1742-5689 - 9 p.
The relationship between form and function in trees is the subject of a longstanding debate in forest ecology and provides the basis for theories concerning forest ecosystem structure and metabolism. Trees interact with the wind in a dynamic manner and exhibit natural sway frequencies and damping processes that are important in understanding wind damage. Tree-wind dynamics are related to tree architecture, but this relationship is not well understood. We present a comprehensive view of natural sway frequencies in trees by compiling a dataset of field measurement spanning conifers and broadleaves, tropical and temperate forests. The field data show that a cantilever beam approximation adequately predicts the fundamental frequency of conifers, but not that of broadleaf trees. We also use structurally detailed tree dynamics simulations to test fundamental assumptions underpinning models of natural frequencies in trees. We model the dynamic properties of greater than 1000 trees using a finite-element approach based on accurate three-dimensional model trees derived from terrestrial laser scanning data. We show that (1) residual variation, the variation not explained by the cantilever beam approximation, in fundamental frequencies of broadleaf trees is driven by their architecture; (2) slender trees behave like a simple pendulum, with a single natural frequency dominating their motion, which makes them vulnerable to wind damage and (3) the presence of leaves decreases both the fundamental frequency and the damping ratio. These findings demonstrate the value of new three-dimensional measurements for understanding wind impacts on trees and suggest new directions for improving our understanding of tree dynamics from conifer plantations to natural forests.
Toll-like receptor agonists as adjuvants for inactivated porcine reproductive and respiratory syndrome virus (PRRSV) vaccine
Vreman, Sandra ; McCaffrey, Joanne ; Popma-de Graaf, Ditta J. ; Nauwynck, Hans ; Savelkoul, Huub F.J. ; Moore, Anne ; Rebel, Johanna M.J. ; Stockhofe-Zurwieden, Norbert - \ 2019
Veterinary Immunology and Immunopathology 212 (2019). - ISSN 0165-2427 - p. 27 - 37.
Adjuvant - PRRSV - Skin vaccination - Toll-like receptor agonist - Vaccine

Toll-like receptor (TLR) agonists can effectively stimulate antigen-presenting cells (APCs) and are anticipated to be promising adjuvants in combination with inactivated vaccines. In this study, the adjuvant potential of three different TLR-agonists were compared with an oil-in-water (O/W) adjuvant in combination with inactivated porcine reproductive and respiratory syndrome virus (iPRRSV) applied by different administration routes: intramuscular (i.m.) or into the skin using dissolving microneedle (DMN) patches. Pigs received a prime vaccination followed by a booster vaccination four weeks later. TLR1/2 (Pam3Cys), TLR7/8 (R848) or TLR9 (CpG ODN) agonists were used as adjuvant in combination with iPRRSV strain 07V063. O/W adjuvant (Montanide™) was used as reference control adjuvant and one group received a placebo vaccination containing diluent only. All animals received a homologous challenge with PRRSV three weeks after the booster vaccination. Antibody and IFN-γ production, serum cytokines and viremia were measured at several time-points after vaccination and/or challenge, and lung pathology at necropsy. Our results indicate that a TLR 1/2, 7/8 or 9 agonist as adjuvant with iPRRSV does not induce a detectable PRRSV-specific immune response, independent of the administration route. However, the i.m. TLR9 agonist group showed reduction of viremia upon challenge compared to the non-vaccinated animals, supported by a non-antigen-specific IFN-γ level after booster vaccination and an anamnestic antibody response after challenge. Montanide™-adjuvanted iPRRSV induced antigen-specific immunity after booster combined with reduction of vireamia. Skin application of TLR7/8 agonist, but not the other agonists, induced a local skin reaction. Further research is needed to explore the potential of TLR agonists as adjuvants for inactivated porcine vaccines with a preference for TLR9 agonists.

Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight
Küpers, Leanne K. ; Monnereau, Claire ; Sharp, Gemma C. ; Yousefi, Paul ; Salas, Lucas A. ; Ghantous, Akram ; Page, Christian M. ; Reese, Sarah E. ; Wilcox, Allen J. ; Czamara, Darina ; Starling, Anne P. ; Novoloaca, Alexei ; Lent, Samantha ; Roy, Ritu ; Hoyo, Cathrine ; Breton, Carrie V. ; Allard, Catherine ; Just, Allan C. ; Bakulski, Kelly M. ; Holloway, John W. ; Everson, Todd M. ; Xu, Cheng Jian ; Huang, Rae Chi ; Plaat, Diana A. van der; Wielscher, Matthias ; Merid, Simon Kebede ; Ullemar, Vilhelmina ; Rezwan, Faisal I. ; Lahti, Jari ; Dongen, Jenny van; Langie, Sabine A.S. ; Richardson, Tom G. ; Magnus, Maria C. ; Nohr, Ellen A. ; Xu, Zongli ; Duijts, Liesbeth ; Zhao, Shanshan ; Zhang, Weiming ; Plusquin, Michelle ; DeMeo, Dawn L. ; Solomon, Olivia ; Heimovaara, Joosje H. ; Jima, Dereje D. ; Gao, Lu ; Bustamante, Mariona ; Perron, Patrice ; Wright, Robert O. ; Hertz-Picciotto, Irva ; Zhang, Hongmei ; Karagas, Margaret R. ; Gehring, Ulrike ; Marsit, Carmen J. ; Beilin, Lawrence J. ; Vonk, Judith M. ; Jarvelin, Marjo Riitta ; Bergström, Anna ; Örtqvist, Anne K. ; Ewart, Susan ; Villa, Pia M. ; Moore, Sophie E. ; Willemsen, Gonneke ; Standaert, Arnout R.L. ; Håberg, Siri E. ; Sørensen, Thorkild I.A. ; Taylor, Jack A. ; Räikkönen, Katri ; Yang, Ivana V. ; Kechris, Katerina ; Nawrot, Tim S. ; Silver, Matt J. ; Gong, Yun Yun ; Richiardi, Lorenzo ; Kogevinas, Manolis ; Litonjua, Augusto A. ; Eskenazi, Brenda ; Huen, Karen ; Mbarek, Hamdi ; Maguire, Rachel L. ; Dwyer, Terence ; Vrijheid, Martine ; Bouchard, Luigi ; Baccarelli, Andrea A. ; Croen, Lisa A. ; Karmaus, Wilfried ; Anderson, Denise ; Vries, Maaike de; Sebert, Sylvain ; Kere, Juha ; Karlsson, Robert ; Arshad, Syed Hasan ; Hämäläinen, Esa ; Routledge, Michael N. ; Boomsma, Dorret I. ; Feinberg, Andrew P. ; Newschaffer, Craig J. ; Govarts, Eva ; Moisse, Matthieu ; Fallin, M.D. ; Melén, Erik ; Prentice, Andrew M. ; Kajantie, Eero ; Almqvist, Catarina ; Oken, Emily ; Dabelea, Dana ; Boezen, H.M. ; Melton, Phillip E. ; Wright, Rosalind J. ; Koppelman, Gerard H. ; Trevisi, Letizia ; Hivert, Marie France ; Sunyer, Jordi ; Munthe-Kaas, Monica C. ; Murphy, Susan K. ; Corpeleijn, Eva ; Wiemels, Joseph ; Holland, Nina ; Herceg, Zdenko ; Binder, Elisabeth B. ; Davey Smith, George ; Jaddoe, Vincent W.V. ; Lie, Rolv T. ; Nystad, Wenche ; London, Stephanie J. ; Lawlor, Debbie A. ; Relton, Caroline L. ; Snieder, Harold ; Felix, Janine F. - \ 2019
Nature Communications 10 (2019)1. - ISSN 2041-1723

Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, we find that DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from −183 to 178 grams per 10% increase in methylation (P Bonferroni < 1.06 x 10 −7 ). In additional analyses in 7,278 participants, <1.3% of birthweight-associated differential methylation is also observed in childhood and adolescence, but not adulthood. Birthweight-related CpGs overlap with some Bonferroni-significant CpGs that were previously reported to be related to maternal smoking (55/914, p = 6.12 x 10 −74 ) and BMI in pregnancy (3/914, p = 1.13x10 −3 ), but not with those related to folate levels in pregnancy. Whether the associations that we observe are causal or explained by confounding or fetal growth influencing DNA methylation (i.e. reverse causality) requires further research.

Large-scale flow patterns associated with extreme precipitation and atmospheric rivers over Norway
Benedict, Imme ; Ødemark, Karianne ; Nipen, Thomas ; Moore, Richard - \ 2019
Monthly Weather Review 147 (2019)4. - ISSN 0027-0644 - p. 1415 - 1428.
Atmosphere - Empirical orthogonal functions - Precipitation - Reanalysis data - Topographic effects - Water vapor

A climatology of extreme cold season precipitation events in Norway from 1979 to 2014 is presented, based on the 99th percentile of the 24-h accumulated precipitation. Three regions, termed north, west, and south are identified, each exhibiting a unique seasonal distribution. There is a proclivity for events to occur during the positive phase of the NAO. The result is statistically significant at the 95th percentile for the north and west regions. An overarching hypothesis of this work is that anomalous moisture flux, or so-called atmospheric rivers (ARs), are integral to extreme precipitation events during the Norwegian cold season. An objective analysis of the integrated vapor transport illustrates that more than 85% of the events are associated with ARs. An empirical orthogonal function and fuzzy cluster technique is used to identify the large-scale weather patterns conducive to the moisture flux and extreme precipitation. Five days before the event and for each of the three regions, two patterns are found. The first represents an intense, southward-shifted jet with a southwest-northeast orientation. The second identifies a weak, northward-shifted, zonal jet. As the event approaches, regional differences become more apparent. The distinctive flow pattern conducive to orographically enhanced precipitation emerges in the two clusters for each region. For the north and west regions, this entails primarily zonal flow impinging upon the south-north-orientated topography, the difference being the latitude of the strong flow. In contrast, the south region exhibits a significant southerly component to the flow.

What agricultural practices are most likely to deliver “sustainable intensification” in the UK?
Dicks, Lynn V. ; Rose, David C. ; Ang, Frederic ; Aston, Stephen ; Birch, A.N.E. ; Boatman, Nigel ; Bowles, Elizabeth L. ; Chadwick, David ; Dinsdale, Alex ; Durham, Sam ; Elliott, John ; Firbank, Les ; Humphreys, Stephen ; Jarvis, Phil ; Jones, Dewi ; Kindred, Daniel ; Knight, Stuart M. ; Lee, Michael R.F. ; Leifert, Carlo ; Lobley, Matt ; Matthews, Kim ; Midmer, Alice ; Moore, Mark ; Morris, Carol ; Mortimer, Simon ; Murray, T.C. ; Norman, Keith ; Ramsden, Stephen ; Roberts, Dave ; Smith, Laurence G. ; Soffe, Richard ; Stoate, Chris ; Taylor, Bryony ; Tinker, David ; Topliff, Mark ; Wallace, John ; Williams, Prysor ; Wilson, Paul ; Winter, Michael ; Sutherland, William J. - \ 2019
Food and Energy Security 8 (2019)1. - ISSN 2048-3694

Sustainable intensification is a process by which agricultural productivity is enhanced whilst also creating environmental and social benefits. We aimed to identify practices likely to deliver sustainable intensification, currently available for UK farms but not yet widely adopted. We compiled a list of 18 farm management practices with the greatest potential to deliver sustainable intensification in the UK, following a well-developed stepwise methodology for identifying priority solutions, using a group decision-making technique with key agricultural experts. The list of priority management practices can provide the focal point of efforts to achieve sustainable intensification of agriculture, as the UK develops post-Brexit agricultural policy, and pursues the second Sustainable Development Goal, which aims to end hunger and promote sustainable agriculture. The practices largely reflect a technological, production-focused view of sustainable intensification, including for example, precision farming and animal health diagnostics, with less emphasis on the social and environmental aspects of sustainability. However, they do reflect an integrated approach to farming, covering many different aspects, from business organization and planning, to soil and crop management, to landscape and nature conservation. For a subset of 10 of the priority practices, we gathered data on the level of existing uptake in English and Welsh farms through a stratified survey in seven focal regions. We find substantial existing uptake of most of the priority practices, indicating that UK farming is an innovative sector. The data identify two specific practices for which uptake is relatively low, but which some UK farmers find appealing and would consider adopting. These practices are: prediction of pest and disease outbreaks, especially for livestock farms; staff training on environmental issues, especially on arable farms.

Inactivated porcine reproductive and respiratory syndrome virus adjuvanted with single Toll like receptor 2, 7 and 9 agonists induces low antibody responses and limited protection
Vreman, S. ; McCaffrey, Joanne ; Trus, I. ; Rebel, J.M.J. ; Nauwynck, H. ; Moore, A. ; Stockhofe, Norbert - \ 2018
- 1 p.
Post-thaw variability in litter decomposition best explained by microtopography at an ice-rich permafrost peatland
Malhotra, Avni ; Moore, Tim R. ; Limpens, Juul ; Roulet, Nigel T. - \ 2018
Arctic, Antarctic and Alpine Research 50 (2018)1. - ISSN 1523-0430
Discontinuous permafrost zone - litter decomposition - microtopography - peatland - permafrost thaw

Litter decomposition, a key process by which recently fixed carbon is lost from ecosystems, is a function of environmental conditions and plant community characteristics. In ice-rich peatlands, permafrost thaw introduces high variability in both abiotic and biotic factors, both of which may affect litter decomposition rates in different ways. Can the existing conceptual frameworks of litter decomposition and its controls be applied across a structurally heterogeneous thaw gradient? We investigated the variability in litter decomposition and its predictors at the Stordalen subarctic peatland in northern Sweden. We measured in situ decomposition of representative litter and environments using litter bags throughout two years. We found highly variable litter decomposition rates with turnover times ranging from five months to four years. Surface elevation was a strong correlate of litter decomposition across the landscape, likely as it integrates multiple environmental and plant community changes brought about by thaw. There was faster decomposition but also more mass remaining after two years in thawed areas relative to permafrost areas, suggesting faster initial loss of carbon but more storage into the slow-decomposing carbon pool. Our results highlight mechanisms and predictors of carbon cycle changes in ice-rich peatlands following permafrost thaw.

Field methods for sampling tree height for tropical forest biomass estimation
Sullivan, Martin J.P. ; Lewis, Simon L. ; Hubau, Wannes ; Qie, Lan ; Baker, Timothy R. ; Banin, Lindsay F. ; Chave, Jerôme ; Cuni-Sanchez, Aida ; Feldpausch, Ted R. ; Lopez-Gonzalez, Gabriela ; Arets, Eric ; Ashton, Peter ; Bastin, Jean François ; Berry, Nicholas J. ; Bogaert, Jan ; Boot, Rene ; Brearley, Francis Q. ; Brienen, Roel ; Burslem, David F.R.P. ; Canniere, Charles de; Chudomelová, Markéta ; Dančák, Martin ; Ewango, Corneille ; Hédl, Radim ; Lloyd, Jon ; Makana, Jean Remy ; Malhi, Yadvinder ; Marimon, Beatriz S. ; Junior, Ben Hur Marimon ; Metali, Faizah ; Moore, Sam ; Nagy, Laszlo ; Vargas, Percy Nuñez ; Pendry, Colin A. ; Ramírez-Angulo, Hirma ; Reitsma, Jan ; Rutishauser, Ervan ; Salim, Kamariah Abu ; Sonké, Bonaventure ; Sukri, Rahayu S. ; Sunderland, Terry ; Svátek, Martin ; Umunay, Peter M. ; Martinez, Rodolfo Vasquez ; Vernimmen, Ronald R.E. ; Torre, Emilio Vilanova ; Vleminckx, Jason ; Vos, Vincent ; Phillips, Oliver L. - \ 2018
Methods in Ecology and Evolution 9 (2018)5. - ISSN 2041-210X - p. 1179 - 1189.
Above-ground biomass estimation - Allometry - Carbon stocks - Forest inventory - Forest structure - Sample size
Quantifying the relationship between tree diameter and height is a key component of efforts to estimate biomass and carbon stocks in tropical forests. Although substantial site-to-site variation in height-diameter allometries has been documented, the time consuming nature of measuring all tree heights in an inventory plot means that most studies do not include height, or else use generic pan-tropical or regional allometric equations to estimate height. Using a pan-tropical dataset of 73 plots where at least 150 trees had in-field ground-based height measurements, we examined how the number of trees sampled affects the performance of locally derived height-diameter allometries, and evaluated the performance of different methods for sampling trees for height measurement. Using cross-validation, we found that allometries constructed with just 20 locally measured values could often predict tree height with lower error than regional or climate-based allometries (mean reduction in prediction error = 0.46 m). The predictive performance of locally derived allometries improved with sample size, but with diminishing returns in performance gains when more than 40 trees were sampled. Estimates of stand-level biomass produced using local allometries to estimate tree height show no over- or under-estimation bias when compared with biomass estimates using field measured heights. We evaluated five strategies to sample trees for height measurement, and found that sampling strategies that included measuring the heights of the ten largest diameter trees in a plot outperformed (in terms of resulting in local height-diameter models with low height prediction error) entirely random or diameter size-class stratified approaches. Our results indicate that even limited sampling of heights can be used to refine height-diameter allometries. We recommend aiming for a conservative threshold of sampling 50 trees per location for height measurement, and including the ten trees with the largest diameter in this sample.
Linking ecology and epidemiology: The case of infected resource
Selakovic, Sanja ; Ruiter, Peter C. de; Heesterbeek, Hans - \ 2017
In: Adaptive Food Webs / Moore, J.C., de Ruiter, P.C., McCann, K.S., Wolters, V., Cambridge University Press - ISBN 9781107182110 - p. 384 - 405.

Introduction Interspecific interactions in ecological communities are the main mechanisms that determine structure, functioning, and stability of ecosystems (May, 1972, 1973; Neutel et al., 2002; Alessina and Tang, 2012; Mougi and Kondoh, 2012, 2014). These interactions can be qualitatively positive, negative, or neutral, and pairs of these interactions between two species may be of opposite sign (e.g., trophic, parasitic) or of equivalent sign (e.g., mutualistic, competitive). Most of the research on ecological interactions has focused on feeding relations (Odum, 1971; Pimm, 1982; Levin et al., 2009; McCann, 2011; Moore and de Ruiter, 2012), but in recent studies of ecological communities this was extended to parasitic (Huxham et al., 1995; Thompson et al., 2004; Lafferty et al., 2006; Kuris et al., 2008) and non-parasitic non-trophic relations (Thebault and Fountaine, 2010; Fontaine et al., 2011; Kéfi et al., 2012; Mougi and Kondoh, 2012; Sauve et al., 2014). In this chapter, we focus on parasitic relations and notably on the question of how trophic interactions and infectious agents mutually influence each other. Here we will refer to the combined classes of infectious species as parasites (see next section for details). The impact of parasites in an ecological community can be quantified through their direct influence on the food-web structure, as well as more indirectly through the way they influence physiological traits of host species and trophic relations of the host and non-host species (Kéfi et al., 2012; Selakovic et al., 2014). In this chapter we first briefly discuss the diversity of parasitic interactions, their relationships with host and non-host species, as well as their effects on a simple consumer–resource relationship consisting of one host and one non-host species. The largest part of the chapter is devoted to exploring a basic model, to show how intricately ecological and epidemiological effects are interwoven, even in the simplest possible ecosystem consisting of two species. Even though this model is basic in the sense that it is low dimensional and not meant to realistically represent any particular system, the analysis does hint at broader ecological insight, for example into possible differences between terrestrial and aquatic ecosystems based on parasitic interaction. The simple analysis highlights the need to study the link between ecology and infectious disease epidemiology in more realistic models.

Adaptive food webs: stability and transitions of real and model ecosystems
Moore, John C. ; Ruiter, Peter C. de; McCann, Kevin S. ; Wolters, Volkmar - \ 2017
Cambridge University Press - ISBN 9781107182110 - 416 p.

Presenting new approaches to studying food webs, this book uses practical management and policy examples to demonstrate the theory behind ecosystem management decisions and the broader issue of sustainability. All the information that readers need to use food web analyses as a tool for understanding and quantifying transition processes is provided. Advancing the idea of food webs as complex adaptive systems, readers are challenged to rethink how changes in environmental conditions affect these systems. Beginning with the current state of thinking about community organisation, complexity and stability, the book moves on to focus on the traits of organisms, the adaptive nature of communities and their impacts on ecosystem function. The final section of the book addresses the applications to management and sustainability. By helping to understand the complexities of multispecies networks, this book provides insights into the evolution of organisms and the fate of ecosystems in a changing world.

Introduction
Moore, John C. ; Ruiter, Peter C. de; McCann, Kevin S. ; Wolters, Volkmar - \ 2017
In: Adaptive Food Webs Cambridge University Press - ISBN 9781107182110 - p. 1 - 6.

Many systems being studied today are dynamic, large and complex: traffic at an airport with 100 planes, slum areas with 10 4 persons or the human brain with 10 10 neuron(e)s. In such systems, stability is of central importance, for instability usually appears as a self-generating catastrophe. Unfortunately, present theoretical knowledge of stability in large systems is meager: the work described here was intended to add to it. Gardner and Ashby (1970) A variety of ecologically interesting interpretations can be, and have been, attached to the term “stability.” May (1973) Climate change, eutrophication, land-use practices, deforestation, intensification of agriculture, and harvesting from fisheries are changing ecosystems across the globe. The study of food webs provides a framework to address these environmental challenges. Food webs are descriptions of the trophic interactions among consumers and resources. The information contained within these descriptions includes aspects of ecosystem structure (i.e., species richness, network architecture), ecosystem function (i.e., primary production, decomposition, biogeochemical cycles), and dynamics (i.e., population and process rates and change, stability and persistence) that all ecosystems share. Understanding how food webs respond to natural and anthropogenic disturbances, be they gradual or abrupt, is important to our basic knowledge of systems, to the formulation of environmental policies, and the implementation of management practices. Ecologists have long understood the observed patterns in distribution of species and their biomass resulted in part from offsetting processes of births and death, immigration and emigration, competition for resources, production and predation, and basic energetic properties, and that they were in some way related to their stability or ability to persist (Elton, 1927; Lotka, 1956; Hutchison, 1959; Hairston et al., 1960; Paine, 1966). In the past 50 years, there have been several attempts to tie structural, functional, and dynamic aspects of ecosystems together in a unifying way. Two contemporary works: one from the community ecology perspective provided by MacArthur and Wilson (1967) – The Theory of Island Biogeography – and one from the ecosystem ecology perspective provided by Odum (1969) – “The strategy of ecosystem development” – summarized the thinking at that time. The Theory of Island Biogeography offered a fresh perspective that blended nearly a century of empirical data on the distribution of species across the globe collected by naturalists with mathematical representations of the processes of colonization and extinction to explain these observations.

Ecological networks in managed ecosystems: Connecting structure to services
Mulder, Christian ; Sechi, Valentina ; Woodward, Guy ; Bohan, David Andrew - \ 2017
In: Adaptive Food Webs Cambridge University Press - ISBN 9781107182110 - p. 214 - 227.

Introduction Ecological networks represent a cornerstone of ecology: they describe and evaluate the links between form and function in multispecies systems, such as food-web structure and dynamics, and they connect different scales and levels of biological organization (Moore and de Ruiter, 2012; Wall et al., 2015). These properties of being able to elucidate both the structure within complex systems and their scaling indicate that ecological networks and network theory could be widely applied to practical problems, including management decision-making processes such as the design of nature reserves and the preservation of ecosystem services. While the study of networks – initially food-web compartments, then community assemblages, and more recently mutualistic networks – is now firmly embedded in ecology (Levins, 1974; Cohen, 1978; Hunt et al., 1987; Beare et al., 1992; Solé and Montoya, 2001; Berlow et al., 2004; Moore et al., 2004; Cohen and Carpenter, 2005; Thébault and Fontaine, 2010; Moore and de Ruiter, 2012; Pocock et al., 2012; Neutel and Thorne, 2014), the application of such approaches to managed ecosystems has lagged far behind. There are many explanations for this disconnection between agro-ecology and ecology, not least the pervasive view that because they are human managed and disturbed agro-systems are fundamentally “unnatural” and different from natural ecosystems: most ecologists prefer to study so-called natural ecosystems, even though most of these have in fact been heavily influenced by mankind for centuries either directly by local activity or indirectly by long-distance pollution. Network approaches have rarely been applied to agriculture and forestry, which is perhaps surprising given that much of the early, integrated management research (e.g., from the seminal works by Von Carlowitz, 1713, and Von Liebig, 1840, onwards) and the study of networks that stimulated major advances in ecological theory was grounded in attempts to improve agricultural and timber production (Wardle, 2002; Schröter et al., 2003; Coleman et al., 2004; Moore and de Ruiter, 2012, and the references therein). The last two decades have seen a hiatus in advances in agro-ecology in this area, while new network theory and empirical studies have elucidated the roles of body size in ecosystems and the study of plant–pollinator networks and other mutualistic webs have redefined our understanding of general ecology.

Plant Cytokinesis : Terminology for Structures and Processes
Smertenko, Andrei ; Assaad, Farhah ; Baluška, František ; Bezanilla, Magdalena ; Buschmann, Henrik ; Drakakaki, Georgia ; Hauser, Marie Theres ; Janson, Marcel ; Mineyuki, Yoshinobu ; Moore, Ian ; Müller, Sabine ; Murata, Takashi ; Otegui, Marisa S. ; Panteris, Emmanuel ; Rasmussen, Carolyn ; Schmit, Anne Catherine ; Šamaj, Jozef ; Samuels, Lacey ; Staehelin, L.A. ; Damme, Daniel Van; Wasteneys, Geoffrey ; Žárský, Viktor - \ 2017
Trends in Cell Biology 27 (2017)12. - ISSN 0962-8924 - p. 885 - 894.
Cell plate - Cytokinesis - Division plane - Phragmoplast - Preprophase band

Plant cytokinesis is orchestrated by a specialized structure, the phragmoplast. The phragmoplast first occurred in representatives of Charophyte algae and then became the main division apparatus in land plants. Major cellular activities, including cytoskeletal dynamics, vesicle trafficking, membrane assembly, and cell wall biosynthesis, cooperate in the phragmoplast under the guidance of a complex signaling network. Furthermore, the phragmoplast combines plant-specific features with the conserved cytokinetic processes of animals, fungi, and protists. As such, the phragmoplast represents a useful system for understanding both plant cell dynamics and the evolution of cytokinesis. We recognize that future research and knowledge transfer into other fields would benefit from standardized terminology. Here, we propose such a lexicon of terminology for specific structures and processes associated with plant cytokinesis. A large number of phragmoplast proteins have been identified.Electron microscopy/tomography studies have produced nanoscale information about the architecture of phragmoplast and cell plate assembly stages in cryofixed cells.Novel components of the cortical division zone and cell plate fusion site have been discovered. This information lays a foundation for understanding how plant cells memorize the division plane throughout mitosis and how the cell plate is guided to its predetermined attachment site.MAP65 and plus end-directed kinesins contribute to the maintenance of the antiparallel overlap of phragmoplast microtubules. In addition, the MAP65-TRAPPII interaction plays a key role in cell plate assembly.Actin filaments align parallel to microtubules in the phragmoplast, while some microfilaments extend from cell plate margin to guide its expansion towards the fusion site.

Addressing complex challenges using a co-innovation approach : Lessons from five case studies in the New Zealand primary sector
Vereijssen, Jessica ; Srinivasan, M.S. ; Dirks, Sarah ; Fielke, Simon ; Jongmans, C.T. ; Agnew, Natasha ; Klerkx, Laurens ; Pinxterhuis, Ina ; Moore, John ; Edwards, Paul ; Brazendale, Rob ; Botha, Neels ; Turner, James A. - \ 2017
Outlook on Agriculture 46 (2017)2. - ISSN 0030-7270 - p. 108 - 116.
Agricultural innovation systems - Co-innovation principles - Innovation projects - Primary industries - Transdisciplinary research

Co-innovation can be effective for complex challenges – involving interactions amongst multiple stakeholders, viewpoints, perceptions, practices and interests across programmes, sectors and national systems. Approaches to challenges in the primary sector have tended to be linear, where tools and outputs are developed by a few, mostly scientists/researchers, and then extended to stakeholders. A co-innovation approach first deciphers and delineates the biophysical, societal, regulatory, policy, economic and environmental drivers, constraints and controls influencing these challenges at multiple levels. Second, stakeholder interactions and perspectives can inform and change the focus as well as help in co-developing solutions to deliver agreed outcomes. However, there is limited systematic and comparative research on how co-innovation works out in different projects. Here we analyse the results of applying a co-innovation approach to five research projects in the New Zealand primary sector. The projects varied in depth and breadth of stakeholder engagement, availability of ready-made solutions and prevalence of interests and conflicts. The projects show how and why co-innovation approaches in some cases contributed to a shared understanding of complex problems. Our results confirm the context specificity of co-innovation practices.

Metagenomic analysis of the complex microbial consortium associated with cultures of the oil-rich alga Botryococcus braunii
Sambles, Christine ; Moore, Karen ; Lux, Thomas M. ; Jones, Katy ; Littlejohn, George R. ; Gouveia, João D. ; Aves, Stephen J. ; Studholme, David J. ; Lee, Rob ; Love, John - \ 2017
MicrobiologyOpen 6 (2017)4. - ISSN 2045-8827
Botryococcus braunii - Biofuel - Consortium - Metagenomics - Microcosm
Microalgae are widely viewed as a promising and sustainable source of renewable chemicals and biofuels. Botryococcus braunii synthesizes and secretes significant amounts of long-chain (C30-C40) hydrocarbons that can be subsequently converted into gasoline, diesel, and aviation fuel. B. braunii cultures are not axenic and the effects of co-cultured microorganisms on B. braunii growth and hydrocarbon yield are important, but sometimes contradictory. To understand the composition of the B. braunii microbial consortium, we used high throughput Illumina sequencing of metagenomic DNA to profile the microbiota within a well established, stable B. braunii culture and characterized the demographic changes in the microcosm following modification to the culture conditions. DNA sequences attributed to B. braunii were present in equal quantities in all treatments, whereas sequences assigned to the associated microbial community were dramatically altered. Bacterial species least affected by treatments, and more robustly associated with the algal cells, included members of Rhizobiales, comprising Bradyrhizobium and Methylobacterium, and representatives of Dyadobacter, Achromobacter and Asticcacaulis. The presence of bacterial species identified by metagenomics was confirmed by additional 16S rDNA analysis of bacterial isolates. Our study demonstrates the advantages of high throughput sequencing and robust metagenomic analyses to define microcosms and further our understanding of microbial ecology.
Denial of long-term issues with agriculture on tropical peatlands will have devastating consequences
Wijedasa, Lahiru S. ; Jauhiainen, Jyrki ; Könönen, Mari ; Lampela, Maija ; Vasander, Harri ; Leblanc, Marie-Claire ; Evers, Stephanie ; Smith, Thomas E.L. ; Yule, Catherine M. ; Varkkey, Helena ; Lupascu, Massimo ; Parish, Faizal ; Singleton, Ian ; Clements, Gopalasamy R. ; Aziz, Sheema Abdul ; Harrison, Mark E. ; Cheyne, Susan ; Anshari, Gusti Z. ; Meijaard, Erik ; Goldstein, Jenny E. ; Waldron, Susan ; Hergoualc'h, Kristell ; Dommain, Rene ; Frolking, Steve ; Evans, Christopher D. ; Posa, Mary Rose C. ; Glaser, Paul H. ; Suryadiputra, Nyoman ; Lubis, Reza ; Santika, Truly ; Padfield, Rory ; Kurnianto, Sofyan ; Hadisiswoyo, Panut ; Lim, Teck Wyn ; Page, Susan E. ; Gauci, Vincent ; Meer, Peter J. Van Der; Buckland, Helen ; Garnier, Fabien ; Samuel, Marshall K. ; Choo, Liza Nuriati Lim Kim ; O'reilly, Patrick ; Warren, Matthew ; Suksuwan, Surin ; Sumarga, Elham ; Jain, Anuj ; Laurance, William F. ; Couwenberg, John ; Joosten, Hans ; Vernimmen, Ronald ; Hooijer, Aljosja ; Malins, Chris ; Cochrane, Mark A. ; Perumal, Balu ; Siegert, Florian ; Peh, Kelvin S.H. ; Comeau, Louis-Pierre ; Verchot, Louis ; Harvey, Charles F. ; Cobb, Alex ; Jaafar, Zeehan ; Wösten, Henk ; Manuri, Solichin ; Müller, Moritz ; Giesen, Wim ; Phelps, Jacob ; Yong, Ding Li ; Silvius, Marcel ; Wedeux, Béatrice M.M. ; Hoyt, Alison ; Osaki, Mitsuru ; Hirano, Takashi ; Takahashi, Hidenori ; Kohyama, Takashi S. ; Haraguchi, Akira ; Nugroho, Nunung P. ; Coomes, David A. ; Quoi, Le Phat ; Dohong, Alue ; Gunawan, Haris ; Gaveau, David L.A. ; Langner, Andreas ; Lim, Felix K.S. ; Edwards, David P. ; Giam, Xingli ; Werf, Guido Van Der; Carmenta, Rachel ; Verwer, Caspar C. ; Gibson, Luke ; Gandois, Laure ; Graham, Laura Linda Bozena ; Regalino, Jhanson ; Wich, Serge A. ; Rieley, Jack ; Kettridge, Nicholas ; Brown, Chloe ; Pirard, Romain ; Moore, Sam ; Capilla, B.R. ; Ballhorn, Uwe ; Ho, Hua Chew ; Hoscilo, Agata ; Lohberger, Sandra ; Evans, Theodore A. ; Yulianti, Nina ; Blackham, Grace ; Onrizal, O. ; Husson, Simon ; Murdiyarso, Daniel ; Pangala, Sunita ; Cole, Lydia E.S. ; Tacconi, Luca ; Segah, Hendrik ; Tonoto, Prayoto ; Lee, Janice S.H. ; Schmilewski, Gerald ; Wulffraat, Stephan ; Putra, Erianto Indra ; Cattau, Megan E. ; Clymo, R.S. ; Morrison, Ross ; Mujahid, Aazani ; Miettinen, Jukka ; Liew, Soo Chin ; Valpola, Samu ; Wilson, David ; Arcy, Laura D'; Gerding, Michiel ; Sundari, Siti ; Thornton, Sara A. ; Kalisz, Barbara ; Chapman, Stephen J. ; Su, Ahmad Suhaizi Mat ; Basuki, Imam ; Itoh, Masayuki ; Traeholt, Carl ; Sloan, Sean ; Sayok, Alexander K. ; Andersen, Roxane - \ 2017
Global Change Biology 23 (2017)3. - ISSN 1354-1013 - p. 977 - 982.
The first International Peat Congress (IPC) held in the tropics – in Kuching (Malaysia) – brought together over 1000 international peatland scientists and industrial partners from across the world (“International Peat Congress with over 1000 participants!,” 2016). The congress covered all aspects of peatland ecosystems and their management, with a strong focus on the environmental, societal and economic challenges associated with contemporary large-scale agricultural conversion of tropical peat.
Towards a new generation of agricultural system data, models and knowledge products : Information and communication technology
Janssen, Sander J.C. ; Porter, Cheryl H. ; Moore, Andrew D. ; Athanasiadis, Ioannis N. ; Foster, Ian ; Jones, James W. ; Antle, John M. - \ 2017
Agricultural Systems 155 (2017). - ISSN 0308-521X - p. 200 - 212.
Agricultural models - Big data - ICT - Linked data - Open science - Sensing - Visualization

Agricultural modeling has long suffered from fragmentation in model implementation. Many models are developed, there is much redundancy, models are often poorly coupled, model component re-use is rare, and it is frequently difficult to apply models to generate real solutions for the agricultural sector. To improve this situation, we argue that an open, self-sustained, and committed community is required to co-develop agricultural models and associated data and tools as a common resource. Such a community can benefit from recent developments in information and communications technology (ICT). We examine how such developments can be leveraged to design and implement the next generation of data, models, and decision support tools for agricultural production systems. Our objective is to assess relevant technologies for their maturity, expected development, and potential to benefit the agricultural modeling community. The technologies considered encompass methods for collaborative development and for involving stakeholders and users in development in a transdisciplinary manner.Our qualitative evaluation suggests that as an overall research challenge, the interoperability of data sources, modular granular open models, reference data sets for applications and specific user requirements analysis methodologies need to be addressed to allow agricultural modeling to enter in the big data era. This will enable much higher analytical capacities and the integrated use of new data sources + . Overall agricultural systems modeling needs to rapidly adopt and absorb state-of-the-art data and ICT technologies with a focus on the needs of beneficiaries and on facilitating those who develop applications of their models. This adoption requires the widespread uptake of a set of best practices as standard operating procedures.

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