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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    Drivers of groundwater utilization in water-limited rice production systems in Nepal
    Urfels, Anton ; McDonald, Andrew J. ; Krupnik, Timothy J. ; Oel, Pieter R. van - \ 2020
    Water International 45 (2020)1. - ISSN 0250-8060 - p. 39 - 59.
    decision processes - Eastern Gangetic Plains - Groundwater irrigation - Nepal - resilience - smallholders

    Most rice farmers in Nepal’s Terai region do not fully utilize irrigation during breaks in monsoon rainfall. This leads to yield losses despite abundant groundwater resources and ongoing expansion of diesel pumps and tubewell infrastructure. We investigate this puzzle by characterizing delay factors governing tubewell irrigation across wealth and precipitation gradients. After the decision to irrigate, different factors delay irrigation by roughly one week. While more sustainable and inexpensive energy for pumping may eventually catalyze transformative change, we identify near-term interventions that may increase rice farmers’ resilience to water stress in smallholder-dominated farming communities based on prevailing types of irrigation infrastructure.

    Operationalizing the concept of robustness of nitrogen networks in mixed smallholder systems: A pilot study in the mid-hills and lowlands of Nepal
    Alomia-Hinojosa, Victoria ; Groot, Jeroen C.J. ; Speelman, Erika N. ; Bettinelli, Carlo ; Mcdonald, Andrew J. ; Alvarez, Stephanie ; Tittonell, Pablo - \ 2020
    Ecological Indicators 110 (2020). - ISSN 1470-160X
    Nitrogen (N) is often the most limiting nutrient to productivity in smallholder mixed crop-livestock systems such as commonly found in the mid-hills and lowland (Terai) of Nepal. Identifying current bottlenecks constraining agroecosystem functioning in terms of N flows and associated improvement options in these systems is paramount. Here, we explore variations in robustness, a concept from ecological network analysis (ENA) which represents the balance of system’s degree of order between organization (order/constraint) and adaptive flexibility (freedom/resilience) of N flows. Robustness can provide a detailed assessment of N flows and assist in evaluation of measures to reduce nutrient losses. In this study, the FarmDESIGN model was employed to quantify nitrogen flows, generate ENA indicators of integration, diversity and robustness, and to explore the impact of crop intensification options on N networks across farm types in the mid-hills and lowland (Terai) of Nepal. Results revealed that the farms in the different agroecosystems recycled only a small portion of the total N inputs (<15%), and had therefore high rates of N losses (63–1135 kg N per ha per year) and high dependency on N imports in the form of fodder (feed self-reliance 11–43%). The farm N networks were organised (high productivity) but inflexible (poorly resilient) and consequently unbalanced (low robustness). Scenarios of improved management (improved seed, intercropping, use of fertilizers, better timing of activities) resulted in improved crop production, leading to reduced fodder imports and less N losses. Consequently, the N networks increased in flexibility which resulted in greater robustness of the N flow network in the farm systems. Increasing on-farm biomass production by improved farm management could be an important element on the way to sustainably intensify smallholder farms, especially when dependency on external resources can be reduced. We conclude that a detailed analysis of nutrient flows and their robustness is a suitable instrument for targeted improvement of nutrient use in smallholder crop-livestock systems.
    First international descriptive and interventional survey for cholesterol and non-cholesterol sterol determination by gas- and liquid-chromatography–Urgent need for harmonisation of analytical methods
    Lütjohann, Dieter ; Björkhem, Ingemar ; Friedrichs, Silvia ; Kerksiek, Anja ; Lövgren-Sandblom, Anita ; Geilenkeuser, Wolf Jochen ; Ahrends, Robert ; Andrade, Isabel ; Ansorena, Diana ; Astiasarán, Iciar ; Baila-Rueda, Lucía ; Barriuso, Bianca ; Becker, Susen ; Bretillon, Lionel ; Browne, Richard W. ; Caccia, Claudio ; Ceglarek, Uta ; Cenarro, Ana ; Crick, Peter J. ; Fauler, Günter ; Garcia-Llatas, Guadalupe ; Gray, Robert ; Griffiths, William J. ; Gylling, Helena ; Harding, Scott ; Helmschrodt, Christin ; Iuliano, Luigi ; Janssen, Hans Gerd ; Jones, Peter ; Kaipiainen, Leena ; Kannenberg, Frank ; Lagarda, María Jesús ; Leoni, Valerio ; Lottenberg, Ana Maria ; MacKay, Dylan S. ; Matysik, Silke ; McDonald, Jeff ; Menendez-Carreño, Maria ; Myrie, Semone B. ; Sutti Nunes, Valéria ; Ostlund, Richard E. ; Polisecki, Eliana ; Ramos, Fernando ; Rideout, Todd C. ; Schaefer, Ernst J. ; Schmitz, Gerd ; Wang, Yuqin ; Zerbinati, Chiara ; Diczfalusy, Ulf ; Schött, Hans Frieder - \ 2019
    Journal of Steroid Biochemistry and Molecular Biology 190 (2019). - ISSN 0960-0760 - p. 115 - 125.
    Atherosclerosis - Cholesterol absorption - Cholesterol balance - Cholesterol synthesis - Phytosterols - Surrogate marker

    Serum concentrations of lathosterol, the plant sterols campesterol and sitosterol and the cholesterol metabolite 5α-cholestanol are widely used as surrogate markers of cholesterol synthesis and absorption, respectively. Increasing numbers of laboratories utilize a broad spectrum of well-established and recently developed methods for the determination of cholesterol and non-cholesterol sterols (NCS). In order to evaluate the quality of these measurements and to identify possible sources of analytical errors our group initiated the first international survey for cholesterol and NCS. The cholesterol and NCS survey was structured as a two-part survey which took place in the years 2013 and 2014. The first survey part was designed as descriptive, providing information about the variation of reported results from different laboratories. A set of two lyophilized pooled sera (A and B) was sent to twenty laboratories specialized in chromatographic lipid analysis. The different sterols were quantified either by gas chromatography-flame ionization detection, gas chromatography- or liquid chromatography-mass selective detection. The participants were requested to determine cholesterol and NCS concentrations in the provided samples as part of their normal laboratory routine. The second part was designed as interventional survey. Twenty-two laboratories agreed to participate and received again two different lyophilized pooled sera (C and D). In contrast to the first international survey, each participant received standard stock solutions with defined concentrations of cholesterol and NCS. The participants were requested to use diluted calibration solutions from the provided standard stock solutions for quantification of cholesterol and NCS. In both surveys, each laboratory used its own internal standard (5α-cholestane, epicoprostanol or deuterium labelled sterols). Main outcome of the survey was, that unacceptably high interlaboratory variations for cholesterol and NCS concentrations are reported, even when the individual laboratories used the same calibration material. We discuss different sources of errors and recommend all laboratories analysing cholesterol and NCS to participate in regular quality control programs.

    Farmer perspectives on sustainable crop-livestock integration in cereal based farm systems of Nepal
    Alomia-Hinojosa, Victoria - \ 2019
    Wageningen University. Promotor(en): P.A. Tittonell, co-promotor(en): J. Groot; A. McDonald. - Wageningen : Wageningen University - ISBN 9789463952125 - 190

    Small-scale farms play an important role in feeding rural communities in low and low middle-income countries through the contribution of staple commodities. However, the production of crop and livestock of small-scale farms are commonly at low to medium level of intensity. As a result, these farm systems are often affected by food-insecurity. Moreover, the demand for animal protein is estimated to grow rapidly as a result of a fast population growth. Therefore, there is a need to increase food productivity in a sustainable manner. In Nepal, most of the farm systems are characterized as small-scale. These farm systems are mixed, combining cereals (maize, wheat and rice) and livestock production. Nevertheless, Nepalese crop-livestock systems are low productive. In addition, farms are continuously decreasing in size due to land fragmentation caused by cultural reasons. Thus integrated crop-livestock systems may contribute to an efficient design of a sustainable farm system, as they aim at achieving synergism between soil, plant, animal and atmosphere.

    This thesis explores and evaluates crop-livestock integration as a pathway to achieve sustainable intensification in cereal-based farming systems in Nepal from a farmer’s perspective. This thesis employs a diversity of methods from hard and soft sciences with quantitative methods: intercrop field experiments, Ecological Network Analysis, biophysical-socioeconomic modelling; and semi-quantitative methods: Fuzzy Cognitive Mapping, interviews, and on farm-discussion groups with farmers.

    Chapter 2 explores the concept of robustness for nutrient flows. The main results show that the farms in the different agro-ecosystems recycle only a small portion of the total Nitrogen (N) inputs and have therefore high rates of N losses. Moreover, they display a high dependency on N imports in the form of fodder. Furthermore, farm N networks are organised (high productivity) but inflexible (poorly resilient) and consequently unbalanced (low robustness). However, scenarios of improved management demonstrate that crop production can be improved, leading to reduced fodder imports and less N losses. Consequently, the N networks increase the flexibility, which results in higher level of robustness of the N flow network.

    In Chapter 3, it is shown that 1) substantial productivity improvements can be achieved through intensification methods, 2) the active involvement of farmers in on-farm trials increases understanding of underlying decision-making factors to adopt or non-adopt improved practices, and 3) engaging farmers positively influence farmer perceptions towards the adoption of innovative practices. Even though it is shown that productivity increases significantly by the explored improved methods, social and cultural factors still limit its fast adoption.

    Chapter 4 shows how farmers identify trade-offs between the benefits of increased cash income and farmyard manure production from intensified livestock production versus increases in labour requirements for fodder imports. It is shown that farmers are not willing to make additional investments in on-farm feed production, as they perceive these as insufficient to bridge the widening feed gap resulting from additional livestock. Furthermore, a sensitivity analysis shows that, given the farmers’ perceptions, an increase in milk market demand could have enhanced positive effects on livestock production and on-farm income.

    Chapter 5 identifies the main drivers associated with agricultural intensification that occurred in the farming systems in the mid-hills since 1985. These drivers are based on the access to agricultural inputs such as improved varieties of seeds and livestock. This has been a consequence of improved connectivity and access to markets, which have been stimulated by agricultural policies and developmental projects. Furthermore, the trade-off analysis of two contrasting scenarios: 1) dairy cattle specialized vs. 2) average mixed farm systems showed that there is space for improving farm configurations by minimizing trade-offs between livestock intensification (profit) on the one hand and N losses and leisure time in the specialized farm on the other hand. This is associated to the farm larger landholding size.

    Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
    Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, C.T. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo Da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
    Nature Biotechnology (2019). - ISSN 1087-0156

    In the version of this article initially published, some reference citations were incorrect. The three references to Jupyter Notebooks should have cited Kluyver et al. instead of Gonzalez et al. The reference to Qiita should have cited Gonzalez et al. instead of Schloss et al. The reference to mothur should have cited Schloss et al. instead of McMurdie & Holmes. The reference to phyloseq should have cited McMurdie & Holmes instead of Huber et al. The reference to Bioconductor should have cited Huber et al. instead of Franzosa et al. And the reference to the biobakery suite should have cited Franzosa et al. instead of Kluyver et al. The errors have been corrected in the HTML and PDF versions of the article.

    Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
    Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, Titus C. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
    Nature Biotechnology 37 (2019)8. - ISSN 1087-0156 - p. 852 - 857.
    Impact of maternal body mass index and gestational weight gain on pregnancy complications: an individual participant data meta-analysis of European, North American and Australian cohorts
    Santos, S. ; Voerman, E. ; Amiano, P. ; Barros, H. ; Beilin, L.J. ; Bergström, A. ; Charles, M.A. ; Chatzi, L. ; Chevrier, C. ; Chrousos, G.P. ; Corpeleijn, E. ; Costa, O. ; Costet, N. ; Crozier, S. ; Devereux, G. ; Doyon, M. ; Eggesbø, M. ; Fantini, M.P. ; Farchi, S. ; Forastiere, F. ; Georgiu, V. ; Godfrey, K.M. ; Gori, D. ; Grote, V. ; Hanke, W. ; Hertz-Picciotto, I. ; Heude, B. ; Hivert, M.F. ; Hryhorczuk, D. ; Huang, R.C. ; Inskip, H. ; Karvonen, A.M. ; Kenny, L.C. ; Koletzko, B. ; Küpers, L.K. ; Lagström, H. ; Lehmann, I. ; Magnus, P. ; Majewska, R. ; Mäkelä, J. ; Manios, Y. ; McAuliffe, F.M. ; McDonald, S.W. ; Mehegan, J. ; Melén, E. ; Mommers, M. ; Morgen, C.S. ; Moschonis, G. ; Murray, D. ; Ní Chaoimh, C. ; Nohr, E.A. ; Nybo Andersen, A.M. ; Oken, E. ; Oostvogels, A.J.J.M. ; Pac, A. ; Papadopoulou, E. ; Pekkanen, J. ; Pizzi, C. ; Polanska, K. ; Porta, D. ; Richiardi, L. ; Rifas-Shiman, S.L. ; Roeleveld, N. ; Ronfani, L. ; Santos, A.C. ; Standl, M. ; Stigum, H. ; Stoltenberg, C. ; Thiering, E. ; Thijs, C. ; Torrent, M. ; Tough, S.C. ; Trnovec, T. ; Turner, S. ; Gelder, M.M.H.J. van; Rossem, L. van; Berg, A. von; Vrijheid, M. ; Vrijkotte, T.G.M. ; West, J. ; Wijga, A.H. ; Wright, J. ; Zvinchuk, O. ; Sørensen, T.I.A. ; Lawlor, D.A. ; Gaillard, R. ; Jaddoe, V.W.V. - \ 2019
    BJOG : an international journal of obstetrics and gynaecology 126 (2019)8. - ISSN 1470-0328 - p. 984 - 995.
    Birthweight - body mass index - pregnancy complications - preterm birth - weight gain

    Objective: To assess the separate and combined associations of maternal pre-pregnancy body mass index (BMI) and gestational weight gain with the risks of pregnancy complications and their population impact. Design: Individual participant data meta-analysis of 39 cohorts. Setting: Europe, North America, and Oceania. Population: 265 270 births. Methods: Information on maternal pre-pregnancy BMI, gestational weight gain, and pregnancy complications was obtained. Multilevel binary logistic regression models were used. Main outcome measures: Gestational hypertension, pre-eclampsia, gestational diabetes, preterm birth, small and large for gestational age at birth. Results: Higher maternal pre-pregnancy BMI and gestational weight gain were, across their full ranges, associated with higher risks of gestational hypertensive disorders, gestational diabetes, and large for gestational age at birth. Preterm birth risk was higher at lower and higher BMI and weight gain. Compared with normal weight mothers with medium gestational weight gain, obese mothers with high gestational weight gain had the highest risk of any pregnancy complication (odds ratio 2.51, 95% CI 2.31– 2.74). We estimated that 23.9% of any pregnancy complication was attributable to maternal overweight/obesity and 31.6% of large for gestational age infants was attributable to excessive gestational weight gain. Conclusions: Maternal pre-pregnancy BMI and gestational weight gain are, across their full ranges, associated with risks of pregnancy complications. Obese mothers with high gestational weight gain are at the highest risk of pregnancy complications. Promoting a healthy pre-pregnancy BMI and gestational weight gain may reduce the burden of pregnancy complications and ultimately the risk of maternal and neonatal morbidity. Tweetable abstract: Promoting a healthy body mass index and gestational weight gain might reduce the population burden of pregnancy complications.

    Maternal body mass index, gestational weight gain, and the risk of overweight and obesity across childhood : An individual participant data meta-analysis
    Voerman, Ellis ; Santos, Susana ; Patro Golab, Bernadeta ; Amiano, Pilar ; Ballester, Ferran ; Barros, Henrique ; Bergström, Anna ; Charles, Marie Aline ; Chatzi, Leda ; Chevrier, Cécile ; Chrousos, George P. ; Corpeleijn, Eva ; Costet, Nathalie ; Crozier, Sarah ; Devereux, Graham ; Eggesbø, Merete ; Ekström, Sandra ; Fantini, Maria Pia ; Farchi, Sara ; Forastiere, Francesco ; Georgiu, Vagelis ; Godfrey, Keith M. ; Gori, Davide ; Grote, Veit ; Hanke, Wojciech ; Hertz-Picciotto, Irva ; Heude, Barbara ; Hryhorczuk, Daniel ; Huang, Rae Chi ; Inskip, Hazel ; Iszatt, Nina ; Karvonen, Anne M. ; Kenny, Louise C. ; Koletzko, Berthold ; Küpers, Leanne K. ; Lagström, Hanna ; Lehmann, Irina ; Magnus, Per ; Majewska, Renata ; Mäkelä, Johanna ; Manios, Yannis ; McAuliffe, Fionnuala M. ; McDonald, Sheila W. ; Mehegan, John ; Mommers, Monique ; Morgen, Camilla S. ; Mori, Trevor A. ; Moschonis, George ; Murray, Deirdre ; Chaoimh, Carol Ní ; Nohr, Ellen A. ; Nybo Andersen, Anne Marie ; Oken, Emily ; Oostvogels, Adriëtte J.J.M. ; Pac, Agnieszka ; Papadopoulou, Eleni ; Pekkanen, Juha ; Pizzi, Costanza ; Polanska, Kinga ; Porta, Daniela ; Richiardi, Lorenzo ; Rifas-Shiman, Sheryl L. ; Ronfani, Luca ; Santos, Ana C. ; Standl, Marie ; Stoltenberg, Camilla ; Thiering, Elisabeth ; Thijs, Carel ; Torrent, Maties ; Tough, Suzanne C. ; Trnovec, Tomas ; Turner, Steve ; Rossem, Lenie van; Berg, Andrea von; Vrijheid, Martine ; Vrijkotte, Tanja G.M. ; West, Jane ; Wijga, Alet ; Wright, John ; Zvinchuk, Oleksandr ; Sørensen, Thorkild I.A. ; Lawlor, Debbie A. ; Gaillard, Romy ; Jaddoe, Vincent W.V. - \ 2019
    PLOS Medicine 16 (2019)2. - ISSN 1549-1676 - p. e1002744 - e1002744.

    BACKGROUND: Maternal obesity and excessive gestational weight gain may have persistent effects on offspring fat development. However, it remains unclear whether these effects differ by severity of obesity, and whether these effects are restricted to the extremes of maternal body mass index (BMI) and gestational weight gain. We aimed to assess the separate and combined associations of maternal BMI and gestational weight gain with the risk of overweight/obesity throughout childhood, and their population impact. METHODS AND FINDINGS: We conducted an individual participant data meta-analysis of data from 162,129 mothers and their children from 37 pregnancy and birth cohort studies from Europe, North America, and Australia. We assessed the individual and combined associations of maternal pre-pregnancy BMI and gestational weight gain, both in clinical categories and across their full ranges, with the risks of overweight/obesity in early (2.0-5.0 years), mid (5.0-10.0 years) and late childhood (10.0-18.0 years), using multilevel binary logistic regression models with a random intercept at cohort level adjusted for maternal sociodemographic and lifestyle-related characteristics. We observed that higher maternal pre-pregnancy BMI and gestational weight gain both in clinical categories and across their full ranges were associated with higher risks of childhood overweight/obesity, with the strongest effects in late childhood (odds ratios [ORs] for overweight/obesity in early, mid, and late childhood, respectively: OR 1.66 [95% CI: 1.56, 1.78], OR 1.91 [95% CI: 1.85, 1.98], and OR 2.28 [95% CI: 2.08, 2.50] for maternal overweight; OR 2.43 [95% CI: 2.24, 2.64], OR 3.12 [95% CI: 2.98, 3.27], and OR 4.47 [95% CI: 3.99, 5.23] for maternal obesity; and OR 1.39 [95% CI: 1.30, 1.49], OR 1.55 [95% CI: 1.49, 1.60], and OR 1.72 [95% CI: 1.56, 1.91] for excessive gestational weight gain). The proportions of childhood overweight/obesity prevalence attributable to maternal overweight, maternal obesity, and excessive gestational weight gain ranged from 10.2% to 21.6%. Relative to the effect of maternal BMI, excessive gestational weight gain only slightly increased the risk of childhood overweight/obesity within each clinical BMI category (p-values for interactions of maternal BMI with gestational weight gain: p = 0.038, p < 0.001, and p = 0.637 in early, mid, and late childhood, respectively). Limitations of this study include the self-report of maternal BMI and gestational weight gain for some of the cohorts, and the potential of residual confounding. Also, as this study only included participants from Europe, North America, and Australia, results need to be interpreted with caution with respect to other populations. CONCLUSIONS: In this study, higher maternal pre-pregnancy BMI and gestational weight gain were associated with an increased risk of childhood overweight/obesity, with the strongest effects at later ages. The additional effect of gestational weight gain in women who are overweight or obese before pregnancy is small. Given the large population impact, future intervention trials aiming to reduce the prevalence of childhood overweight and obesity should focus on maternal weight status before pregnancy, in addition to weight gain during pregnancy.

    Risk to the supply of ecosystem services across aquatic ecosystems
    Culhane, Fiona ; Teixeira, Heliana ; Nogueira, Antonio J.A. ; Borgwardt, Florian ; Trauner, Daniel ; Lillebø, Ana ; Piet, Gerjan ; Kuemmerlen, Mathias ; McDonald, Hugh ; O'Higgins, Tim ; Barbosa, Ana Luisa ; Wal, Jan Tjalling Van Der; Iglesias-Campos, Alejandro ; Arevalo-Torres, Juan ; Barbière, Julian ; Robinson, Leonie A. - \ 2019
    Science of the Total Environment 660 (2019). - ISSN 0048-9697 - p. 611 - 621.
    Sustainability - Biodiversity
    The capacity of ecosystems to supply ecosystem services is decreasing. Sustaining this supply requires an under- standing of the links between the impacts of pressures introduced by human activities and how this can lead to
    changes in the supply of services. Here, we apply a novel approach, assessing‘
    risk to ecosystem service supply’ (RESS), across a range of aquatic ecosystems in seven case studies. We link aggregate impact risk from human activities on ecosystem components, with a relative score of their potential to supply services. The greatest RESS is found where an ecosystem component with a high potential to supply services is subject to high impact risk. In this context, we explore variability in RESS across 99 types of aquatic ecosystem component from 11 realms, ranging from oceanic to wetlands. We explore some causes of variability in the RESS observed, including assessment area, Gross Domestic Product (GDP) and population density. We found that Lakes, Rivers, Inlets and
    Coastal realms had some of the highest RESS, though this was highly dependent on location. We found a positive relationship between impact risk and service supply potential, indicating the ecosystem components we rely on mostfor services, are also those most at risk. However, variability in this relationship indicates that protecting the supply of ecosystem services alone will not protect all parts of the ecosystem at high risk. Broad socio-economic factors explained some of the variability found in RESS. For example, RESS was positively associated with GDP and artificial and agricultural land use in most realms, highlighting the need to achieve balance between increasing GDP and sustaining ecosystem health and human wellbeing more broadly. This approach can be used for sustainablemanagement of ecosystemservice use, to highlight the ecosystemcomponents mostcriticalto supplying services, and those most at risk

    Linking biodiversity to ecosystem services supply: Patterns across aquatic ecosystems
    Teixeira, Heliana ; Lillebø, Ana I. ; Culhane, Fiona ; Robinson, Leonie ; Trauner, Daniel ; Borgwardt, Florian ; Kummerlen, Mathias ; Barbosa, Ana ; McDonald, Hugh ; Funk, Andrea ; O'Higgins, Tim ; Wal, Jan Tjalling Van Der; Piet, Gerjan ; Hein, Thomas ; Arévalo-Torres, Juan ; Iglesias-Campos, Alejandro ; Barbière, Julian ; Nogueira, António J.A. - \ 2019
    Science of the Total Environment 657 (2019). - ISSN 0048-9697 - p. 517 - 534.
    Global initiatives have been increasingly focusing on mainstreaming the values of biodiversity and ecosystem services into decision-making at all levels. Due to the accelerated rate at which biodiversity is declining and its consequences for the functioning of ecosystems and subsequently, the services they provide, there is need to develop comprehensive assessments of the services and the benefits nature delivers to society. Based on expertevaluation, we identified relevant flow linkages in the supply-side of the socio-ecological system, i.e. from biodiversity to ecosystem services supply for eight case studies across European aquatic ecosystems covering freshwater, transitional, coastal and marine waters realms. Biological mediated services were considered, as well as those reliant on purely physical aspects of the ecosystem, i.e. abiotic outputs, since both have implications for spatial planning, management and decision-making. Due to the multidimensional nature of ecosystems and their biodiversity, our approach used ecosystem components such as habitats and biota as proxies for biodiversity and as the focal point for linkage identification. Statistical analysis revealed the importance of considering mobile biota in the spatial assessment of habitats. Contrary to literature evidences so far, our results showed significantly different and complementary ecosystem services supply patterns across the continuum of aquatic realms. The implemented score of ecosystem services supply has a high potential for integrated aquatic ecosystem service supply assessments in the context of ecosystem-based management.
    Introducing the H2020 AQUACROSS project: Knowledge, Assessment, and Management for AQUAtic Biodiversity and Ecosystem Services aCROSS EU policies
    Lago, M. ; Boteler, B. ; Rouillard, J. ; Abhold, K. ; Jähnig, S.C. ; Iglesias-Campos, A. ; Delacámara, G. ; Piet, G.J. ; Hein, T. ; Nogueira, A.J.A. ; Lillebø, A.I. ; Strosser, P. ; Robinson, L.A. ; Wever, A. De; O'Higgins, T. ; Schlüter, M. ; Török, L. ; Reichert, P. ; Ham, C. Van; Villa, F. ; Hugh, Mcdonald - \ 2019
    Science of the Total Environment 652 (2019). - ISSN 0048-9697 - p. 320 - 329.
    Freshwater - Coastal - Marine ecosystems - Resilience - Social-ecological modelling - EU 2020 Biodiversity Strategy - Social learning - stakeholder engagement
    The AQUACROSS project was an unprecedented effort to unify policy concepts, knowledge, and management of freshwater, coastal, and marine ecosystems to support the cost-effective achievement of the targets set by the EU Biodiversity Strategy to 2020. AQUACROSS aimed to support EU efforts to enhance the resilience and stop the loss of biodiversity of aquatic ecosystems as well as to ensure the ongoing and future provision of aquatic ecosystem services. The project focused on advancing the knowledge base and application of Ecosystem-Based Management. Through elaboration of eight diverse case studies in freshwater and marine and estuarine aquatic ecosystem across Europe covering a range of environmental management problems including, eutrophication, sustainable fisheries as well as invasive alien species AQUACROSS demonstrated the application of a common framework to establish cost-effective measures and integrated Ecosystem-Based Management practices. AQUACROSS analysed the EU policy framework (i.e. goals, concepts, time frames) for aquatic ecosystems and built on knowledge stemming from different sources (i.e. WISE, BISE, Member State reporting within different policy processes, modelling) to develop innovative management tools, concepts, and business models (i.e. indicators, maps, ecosystem assessments, participatory approaches, mechanisms for promoting the delivery of ecosystem services) for aquatic ecosystems at various scales of space and time and relevant to different ecosystem types.
    Exploring variability in environmental impact risk from human activities across aquatic ecosystems
    Borgwardt, Florian ; Robinson, Leonie ; Trauner, Daniel ; Teixeira, Heliana ; Nogueira, Antonio J.A. ; Lillebø, Ana I. ; Piet, Gerjan ; Kuemmerlen, Mathias ; O'Higgins, Tim ; McDonald, Hugh ; Arevalo-Torres, Juan ; Barbosa, Ana Luisa ; Iglesias-Campos, Alejandro ; Hein, Thomas ; Culhane, Fiona - \ 2019
    Science of the Total Environment 652 (2019). - ISSN 0048-9697 - p. 1396 - 1408.
    Aquatic ecosystem - Freshwater - Marine - Coastal - Biodiversity - Drivers
    Aquatic ecosystems are under severe pressure. Human activities introduce an array of pressures that impact ecosystems and their components. In this study we focus on the aquatic domains of fresh, coastal and marine waters, including rivers, lakes and riparian habitats to transitional, coastal as well as shelf and oceanic habitats. In an environmental risk assessment approach, we identified impact chains that link 45 human activities through 31 pressures to 82 ecosystem components. In this linkage framework >22,000 activity-pressure-ecosystem component interactions were found across seven European case studies. We identified the environmental impact risk posed by each impact chain by first categorically weighting the interactions according to five criteria: spatial extent, dispersal potential, frequency of interaction, persistence of pressure and severity of the interaction, where extent, dispersal, frequency and persistence account for the exposure to risk (spatial and temporal), and the severity accounts for the consequence of the risk. After assigning a numerical score to each risk criterion, we came up with an overall environmental impact risk score for each impact chain. This risk score was analysed in terms of (1) the activities and pressures that introduce the greatest risk to European aquatic domains, and (2) the aquatic ecosystem components and realms that are at greatest risk from human activities. Activities related to energy production were relevant across the aquatic domains. Fishing was highly relevant in marine and environmental engineering in fresh waters. Chemical and physical pressures introduced the greatest risk to the aquatic realms. Ecosystem components that can be seen as ecotones between different ecosystems had high impact risk. We show how this information can be used in informing management on trade-offs in freshwater, coastal and marine resource use and aid decision-making
    Social engagement and the elderly in rural Indonesia
    Utomo, Ariane ; Mcdonald, Peter ; Utomo, Iwu ; Cahyadi, Nur ; Sparrow, Robert - \ 2019
    Social Science and Medicine 229 (2019). - ISSN 0277-9536 - p. 22 - 31.
    Ageing - Demography - Indonesia - Rural - Social engagement

    Rural areas in Indonesia are older relative to urban areas. This paper questions how levels of social engagement vary across among the elderly in rural Indonesia. A sample of 2750 respondents aged 60 and over was drawn from 10 purposely-selected relatively “old” villages. Our three measures of social engagement are: participation in income-generating activities, in communal activities, and in care work. While there are notable village-level differences in patterns of social engagement, the majority of our respondents are actively engaged in productive activities in their old age until they can no longer be so. A negative educational gradient in the likelihood of work participation suggests that needs for income security is a driver of the elderly's work participation. The notion of promoting active ageing, as typically understood in the Western and/or urban contexts, is of secondary importance to health care provision and managing old-age disability in these ageing rural communities.

    Unexpected slowdown of US pollutant emission reduction in the past decade
    Jiang, Zhe ; McDonald, Brian C. ; Worden, Helen ; Worden, John R. ; Miyazaki, Kazuyuki ; Qu, Zhen ; Henze, Daven K. ; Jones, Dylan B.A. ; Arellano, Avelino F. ; Fischer, Emily V. ; Zhu, Liye ; Folkert Boersma, K. - \ 2018
    Proceedings of the National Academy of Sciences of the United States of America 115 (2018)20. - ISSN 0027-8424 - p. 5099 - 5104.
    Decadal scale variation - Emission regulations - Nitrogen oxides

    Ground and satellite observations show that air pollution regulations in the United States (US) have resulted in substantial reductions in emissions and corresponding improvements in air quality over the last several decades. However, large uncertainties remain in evaluating how recent regulations affect different emission sectors and pollutant trends. Here we show a significant slowdown in decreasing US emissions of nitrogen oxides (NOx) and carbon monoxide (CO) for 2011–2015 using satellite and surface measurements. This observed slowdown in emission reductions is significantly different from the trend expected using US Environmental Protection Agency (EPA) bottom-up inventories and impedes compliance with local and federal agency air-quality goals. We find that the difference between observations and EPA’s NOx emission estimates could be explained by: (i) growing relative contributions of industrial, area, and off-road sources, (ii) decreasing relative contributions of on-road gasoline, and (iii) slower than expected decreases in on-road diesel emissions.

    Exploring farmer perceptions of agricultural innovations for maize-legume intensification in the mid-hills region of Nepal
    Alomía Hinojosa, M.V. ; Speelman, Erika N. ; Thapa, Arun ; Wei, Hisiang-En ; Mcdonald, Andrew J. ; Tittonell, Pablo ; Groot, Jeroen C.J. - \ 2018
    International Journal of Agricultural Sustainability 16 (2018)1. - ISSN 1473-5903 - p. 74 - 93.
    Maize-legume intercropping is a fundamental component of mixed farming systems in the mid-hills of Nepal. However, its productivity is constrained by several biophysical and social factors, and limited adoption of proven agricultural innovations. In this study, we assessed the productivity impact of a selection of relevant agricultural innovations and changes in the associated perceptions of farmers through a series of two-year participatory on-farm trials. The evaluated innovations resulted in higher yields as compared to farmers' current practices. The active involvement of farmers enlarged our understanding of underlying decision-making factors to adopt or non-adopt agricultural innovations. Additionally, the in-depth farmer engagement in our onfarm trials positively influenced farmer perceptions of the innovations and their interest to adopt the agricultural innovations. Yet, farmers final decisions to adopt some of the evaluated innovations were limited by a host of factors including labour scarcity, the availability of inputs, and by cultural preferences despite the increased yields. This was particularly true for low and medium resource-endowed farmers. This study shows the importance of active farmer participation and context-specific design of research and development projects aiming for local impact.
    A communal catalogue reveals Earth's multiscale microbial diversity
    Thompson, Luke R. ; Sanders, Jon G. ; Mcdonald, D. ; Fogliano, V. ; Jurburg, S.D. ; Larsen, Peter - \ 2017
    Nature 551 (2017)7681. - ISSN 0028-0836 - p. 457 - 463.
    Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.
    Enhanced methane emissions from tropical wetlands during the 2011 la Niña
    Pandey, Sudhanshu ; Houweling, Sander ; Krol, Maarten ; Aben, Ilse ; Monteil, Guillaume ; Nechita-Banda, Narcisa ; Dlugokencky, Edward J. ; Detmers, Rob ; Hasekamp, Otto ; Xu, Xiyan ; Riley, William J. ; Poulter, Benjamin ; Zhang, Zhen ; McDonald, Kyle C. ; White, James W.C. ; Bousquet, Philippe ; Röckmann, Thomas - \ 2017
    Scientific Reports 7 (2017). - ISSN 2045-2322
    Year-to-year variations in the atmospheric methane (CH4) growth rate show significant correlation with climatic drivers. The second half of 2010 and the first half of 2011 experienced the strongest La Niña since the early 1980s, when global surface networks started monitoring atmospheric CH4 mole fractions. We use these surface measurements, retrievals of column-averaged CH4 mole fractions from GOSAT, new wetland inundation estimates, and atmospheric δ13C-CH4 measurements to estimate the impact of this strong La Niña on the global atmospheric CH4 budget. By performing atmospheric inversions, we find evidence of an increase in tropical CH4 emissions of ∼6-9 TgCH4 yr-1 during this event. Stable isotope data suggest that biogenic sources are the cause of this emission increase. We find a simultaneous expansion of wetland area, driven by the excess precipitation over the Tropical continents during the La Niña. Two process-based wetland models predict increases in wetland area consistent with observationally-constrained values, but substantially smaller per-area CH4 emissions, highlighting the need for improvements in such models. Overall, tropical wetland emissions during the strong La Niña were at least by 5% larger than the long-term mean.
    A framework for determining unsaturated zone water quality time lags at catchment scale
    Vero, Sara E. ; Healy, Mark G. ; Henry, Tiernan ; Creamer, Rachel E. ; Ibrahim, Tristan G. ; Richards, Karl G. ; Mellander, Per Erik ; McDonald, Noeleen T. ; Fenton, Owen - \ 2017
    Agriculture, Ecosystems and Environment 236 (2017). - ISSN 0167-8809 - p. 234 - 242.
    Nitrate - Soil - Time lag - Unsaturated - Water framework directive
    The responses of waterbodies to agricultural programmes of measures are frequently delayed by hydrological time lags through the unsaturated zone and groundwater. Time lag may therefore, impede the achievement of remediation deadlines such as those described in the EU Water Framework Directive (WFD). Omitting time lag from catchment characterisation renders evaluation of management practices impossible. Time lag aside, regulators at national scale can only manage the expectations of policy-makers at larger scales (e.g. European Union) by demonstrating positive nutrient trajectories in catchments failing to achieve at least ‘good’ status. Presently, a flexible tool for developing spatial and temporal estimates of trends in water quality/nutrient transport and time lags is not available. The objectives of the present study were first to develop such a flexible, parsimonious framework incorporating existing soil maps, meteorological data and a structured modelling approach, and to secondly, to demonstrate its use in a grassland and an arable catchment (∼10 km2) in Ireland, assuming full implementation of measures in 2012. Data pertaining to solute transport (meteorology, soil hydraulics, depth of profile and boundary conditions) were collected for both catchments. Low complexity textural data alone gave comparable estimates of nutrient trajectories and time lags but with no spatial or soil series information. Taking a high complexity approach, coupling high resolution soil mapping (1:10,000) with national scale (1:25,000) representative profile datasets to <5 m depth, indicated trends in nutrient transport of 10–12 months and 13–17 months throughout the grassland and arable catchments, respectively. For the same conditions, regulators relying on data from groundwater sampling to test the efficacy of the present measures would be delayed by 61–76 months and 46–79 months, respectively. Variation in meteorological datasets enabled temporal analysis of the trends in nutrient transport and time lag estimates. Such a tool could help catchment scientists to better characterise and manage catchments, determine locations for monitoring or mitigation, assess the efficacy of current measures, and ultimately, advise policy makers and regulators.
    Improving the identification of hydrologically sensitive areas using LiDAR DEMs for the delineation and mitigation of critical source areas of diffuse pollution
    Thomas, I.A. ; Jordan, P. ; Mellander, P.E. ; Fenton, O. ; Shine, O. ; Ó hUallacháin, D. ; Creamer, R. ; McDonald, N.T. ; Dunlop, P. ; Murphy, P.N.C. - \ 2016
    Science of the Total Environment 556 (2016). - ISSN 0048-9697 - p. 276 - 290.
    Agriculture - Critical source area - Diffuse pollution - Hydrologically sensitive area - LiDAR DEM - Mitigation

    Identifying critical source areas (CSAs) of diffuse pollution in agricultural catchments requires the accurate identification of hydrologically sensitive areas (HSAs) at highest propensity for generating surface runoff and transporting pollutants. A new GIS-based HSA Index is presented that improves the identification of HSAs at the sub-field scale by accounting for microtopographic controls. The Index is based on high resolution LiDAR data and a soil topographic index (STI) and also considers the hydrological disconnection of overland flow via topographic impediment from flow sinks. The HSA Index was applied to four intensive agricultural catchments (~7.5-12 km2) with contrasting topography and soil types, and validated using rainfall-quickflow measurements during saturated winter storm events in 2009-2014. Total flow sink volume capacities ranged from 8298 to 59,584 m3 and caused 8.5-24.2% of overland-flow-generating-areas and 16.8-33.4% of catchment areas to become hydrologically disconnected from the open drainage channel network. HSA maps identified 'breakthrough points' and 'delivery points' along surface runoff pathways as vulnerable points where diffuse pollutants could be transported between fields or delivered to the open drainage network, respectively. Using these as proposed locations for targeting mitigation measures such as riparian buffer strips reduced potential costs compared to blanket implementation within an example agri-environment scheme by 66% and 91% over 1 and 5 years respectively, which included LiDAR DEM acquisition costs. The HSA Index can be used as a hydrologically realistic transport component within a fully evolved sub-field scale CSA model, and can also be used to guide the implementation of 'treatment-train' mitigation strategies concurrent with sustainable agricultural intensification.

    Participatory Maize-Legume Experimental Trials as a Tool to Explore Social-Ecological Niches for Innovation Adoption in Small Scale Farming Systems
    Alomía Hinojosa, M.V. ; Speelman, E.N. ; Thapa, Arun ; Wei, Hsiang-En ; McDonald, Andrew ; Tittonell, P.A. ; Groot, J.C.J. - \ 2016
    Maize-legume mixed cropping is essential part of the farming systems in the mid-hills of Nepal. However, its productivity remains low. The low adoption of innovations are among the causes that condition the yield improvement of the systems. Therefore, we performed two years participatory on-farm trials with maize-legume crop combinations under best-bet management to determine their productivity, and the farmers' reasons of low innovation adoption. We also tested whether providing more information about innovations would influence farmer perceptions. Maize yielded on average 7 Mg/ha in the intercrop, in comparison to 2 Mg/ha under farmer practice. The intercrop under best-bet management showed higher land use efficiency and economy return. We involved farmers on field discussions during the duration of trials. In addition we assessed, by using a board impact tool, their perceptions about 1) technologies tested (mini-tiller, hybrid seeds and chemical fertilisers), and 2) improved cropping practices (optimal plant population in row arrangement). Farmers initially expected a high demand of labour for both row seeding and mini-tiller use before the trials, but this was adjusted to lower anticipated labour demand after the participatory trials. In contrast, the perception of high investment costs for both innovations persisted. By the second year of trials there was a relatively large percentage (17%) of farmers that partially adopted the improved seeds and row seeding, the reasons for the non-adopters were the preference to consume local varieties and high labour at planting time for the row arrangement. The use of a mini-tiller was low (3%) due to the low availability and the difficulty to take it to remote fields. The adoption rate of chemical fertilisers was low, because most of the households perceived the quantity of FYM they produced as sufficient, and perceived a risk of damaging soil if using chemical fertilisers without proper rainfall. Most of the early adopter farmers belonged to a medium to high resource endowment type and high caste. Our study shows that the participatory on-farm trials were effective to explore perceptions and preferences of farmers, and it increased understanding on targeting of innovations to achieve sustainable intensification in the mid-hills agroecosystems.
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