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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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.
An integrated risk-based assessment of the North Sea to guide ecosystem-based management
Piet, Gerjan ; Culhane, Fiona ; Jongbloed, Ruud ; Robinson, Leonie ; Rumes, Bob ; Tamis, Jacqueline - \ 2019
Science of the Total Environment 654 (2019). - ISSN 0048-9697 - p. 694 - 704.
This study provides an integrated perspective to ecosystem based management (EBM) by considering a diverse array of societal goals, i.e. sustainable food supply, clean energy and a healthy marine ecosystem, and a selection of management measures to achieve them. The primary aim of this exercise is to provide guidance for (more) integrated EBM in the North Sea based on an evaluation of the effectiveness of those management measures in contributing to the conservation of marine biodiversity. A secondary aim is to identify the requirements of the knowledge base to guide such future EBM initiatives.
Starting from the societal goals we performed a scoping exercise to identify a “focal social-ecological system” which is a subset of the full social-ecological system but considered adequate to guide EBM towards the achievement of those societal goals. A semi-quantitative risk assessment including all the relevant human activities, their pressures and the impacted ecosystem components was then applied to identify the main threats to the North Sea biodiversity and evaluate the effectiveness of the management measures to mitigate those threats.
This exercise revealed the need for such risk-based approaches in providing a more integrated perspective but also the trade-off between being comprehensive but qualitative versus quantitative but limited in terms of the “focal” part of the SES that can be covered. The findings in this paper provide direction to the (further) development of EBM and its knowledge base that should ultimately allow an integrated perspective while maintaining its capacity to deliver the accuracy and detail needed for decision-making.
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
Fatty acid biomarkers of dairy fat consumption and incidence of type 2 diabetes : A pooled analysis of prospective cohort studies
Imamura, Fumiaki ; Fretts, Amanda ; Marklund, Matti ; Ardisson Korat, Andres V. ; Yang, Wei Sin ; Lankinen, Maria ; Qureshi, Waqas ; Helmer, Catherine ; Chen, Tzu An ; Wong, Kerry ; Bassett, Julie K. ; Murphy, Rachel ; Tintle, Nathan ; Yu, Chaoyu Ian ; Brouwer, Ingeborg A. ; Chien, Kuo Liong ; Frazier-Wood, Alexis C. ; Gobbo, Liana C. Del; Djoussé, Luc ; Geleijnse, Johanna M. ; Giles, Graham G. ; Goede, Janette de; Gudnason, Vilmundur ; Harris, William S. ; Hodge, Allison ; Hu, Frank ; Koulman, Albert ; Laakso, Markku ; Lind, Lars ; Lin, Hung Ju ; McKnight, Barbara ; Rajaobelina, Kalina ; Risérus, Ulf ; Robinson, Jennifer G. ; Samieri, Cécilia ; Siscovick, David S. ; Soedamah-Muthu, Sabita S. ; Sotoodehnia, Nona ; Sun, Qi ; Tsai, Michael Y. ; Uusitupa, Matti ; Wagenknecht, Lynne E. ; Wareham, Nick J. ; Wu, Jason Hy ; Micha, Renata ; Forouhi, Nita G. ; Lemaitre, Rozenn N. ; Mozaffarian, Dariush - \ 2018
PLOS Medicine 15 (2018)10. - ISSN 1549-1676 - p. e1002670 - e1002670.

BACKGROUND: We aimed to investigate prospective associations of circulating or adipose tissue odd-chain fatty acids 15:0 and 17:0 and trans-palmitoleic acid, t16:1n-7, as potential biomarkers of dairy fat intake, with incident type 2 diabetes (T2D).

METHODS AND FINDINGS: Sixteen prospective cohorts from 12 countries (7 from the United States, 7 from Europe, 1 from Australia, 1 from Taiwan) performed new harmonised individual-level analysis for the prospective associations according to a standardised plan. In total, 63,682 participants with a broad range of baseline ages and BMIs and 15,180 incident cases of T2D over the average of 9 years of follow-up were evaluated. Study-specific results were pooled using inverse-variance-weighted meta-analysis. Prespecified interactions by age, sex, BMI, and race/ethnicity were explored in each cohort and were meta-analysed. Potential heterogeneity by cohort-specific characteristics (regions, lipid compartments used for fatty acid assays) was assessed with metaregression. After adjustment for potential confounders, including measures of adiposity (BMI, waist circumference) and lipogenesis (levels of palmitate, triglycerides), higher levels of 15:0, 17:0, and t16:1n-7 were associated with lower incidence of T2D. In the most adjusted model, the hazard ratio (95% CI) for incident T2D per cohort-specific 10th to 90th percentile range of 15:0 was 0.80 (0.73-0.87); of 17:0, 0.65 (0.59-0.72); of t16:1n7, 0.82 (0.70-0.96); and of their sum, 0.71 (0.63-0.79). In exploratory analyses, similar associations for 15:0, 17:0, and the sum of all three fatty acids were present in both genders but stronger in women than in men (pinteraction < 0.001). Whereas studying associations with biomarkers has several advantages, as limitations, the biomarkers do not distinguish between different food sources of dairy fat (e.g., cheese, yogurt, milk), and residual confounding by unmeasured or imprecisely measured confounders may exist.

CONCLUSIONS: In a large meta-analysis that pooled the findings from 16 prospective cohort studies, higher levels of 15:0, 17:0, and t16:1n-7 were associated with a lower risk of T2D.

A methodology to derive global maps of leaf traits using remote sensing and climate data
Moreno-Martínez, Álvaro ; Camps-Valls, Gustau ; Kattge, Jens ; Robinson, Nathaniel ; Reichstein, Markus ; Bodegom, Peter van; Kramer, Koen ; Cornelissen, J.H.C. ; Reich, Peter ; Bahn, Michael ; Niinemets, Ülo ; Peñuelas, Josep ; Craine, Joseph M. ; Cerabolini, Bruno E.L. ; Minden, Vanessa ; Laughlin, Daniel C. ; Sack, Lawren ; Allred, Brady ; Baraloto, Christopher ; Byun, Chaeho ; Soudzilovskaia, Nadejda A. ; Running, Steve W. - \ 2018
Remote Sensing of Environment 218 (2018). - ISSN 0034-4257 - p. 69 - 88.
Climate - Landsat - Machine learning - MODIS - Plant ecology - Plant traits - Random forests - Remote sensing

This paper introduces a modular processing chain to derive global high-resolution maps of leaf traits. In particular, we present global maps at 500 m resolution of specific leaf area, leaf dry matter content, leaf nitrogen and phosphorus content per dry mass, and leaf nitrogen/phosphorus ratio. The processing chain exploits machine learning techniques along with optical remote sensing data (MODIS/Landsat) and climate data for gap filling and up-scaling of in-situ measured leaf traits. The chain first uses random forests regression with surrogates to fill gaps in the database (> 45% of missing entries) and maximizes the global representativeness of the trait dataset. Plant species are then aggregated to Plant Functional Types (PFTs). Next, the spatial abundance of PFTs at MODIS resolution (500 m) is calculated using Landsat data (30 m). Based on these PFT abundances, representative trait values are calculated for MODIS pixels with nearby trait data. Finally, different regression algorithms are applied to globally predict trait estimates from these MODIS pixels using remote sensing and climate data. The methods were compared in terms of precision, robustness and efficiency. The best model (random forests regression) shows good precision (normalized RMSE≤ 20%) and goodness of fit (averaged Pearson's correlation R = 0.78) in any considered trait. Along with the estimated global maps of leaf traits, we provide associated uncertainty estimates derived from the regression models. The process chain is modular, and can easily accommodate new traits, data streams (traits databases and remote sensing data), and methods. The machine learning techniques applied allow attribution of information gain to data input and thus provide the opportunity to understand trait-environment relationships at the plant and ecosystem scales. The new data products – the gap-filled trait matrix, a global map of PFT abundance per MODIS gridcells and the high-resolution global leaf trait maps – are complementary to existing large-scale observations of the land surface and we therefore anticipate substantial contributions to advances in quantifying, understanding and prediction of the Earth system.

Environmental and taxonomic controls of carbon and oxygen stable isotope composition in Sphagnum across broad climatic and geographic ranges
Granath, Gustaf ; Rydin, Håkan ; Baltzer, Jennifer L. ; Bengtsson, Fia ; Boncek, Nicholas ; Bragazza, Luca ; Bu, Zhao Jun ; Caporn, Simon J.M. ; Dorrepaal, Ellen ; Galanina, Olga ; GaÅka, Mariusz ; Ganeva, Anna ; Gillikin, David P. ; Goia, Irina ; Goncharova, Nadezhda ; Hájek, Michal ; Haraguchi, Akira ; Harris, Lorna I. ; Humphreys, Elyn ; Jiroušek, Martin ; KajukaÅo, Katarzyna ; Karofeld, Edgar ; Koronatova, Natalia G. ; Kosykh, Natalia P. ; Lamentowicz, Mariusz ; Lapshina, Elena ; Limpens, Juul ; Linkosalmi, Maiju ; Ma, Jin Ze ; Mauritz, Marguerite ; Munir, Tariq M. ; Natali, Susan M. ; Natcheva, Rayna ; Noskova, Maria ; Payne, Richard J. ; Pilkington, Kyle ; Robinson, Sean ; Robroek, Bjorn J.M. ; Rochefort, Line ; Singer, David ; Stenøien, Hans K. ; Tuittila, Eeva Stiina ; Vellak, Kai ; Verheyden, Anouk ; Michael Waddington, James ; Rice, Steven K. - \ 2018
Biogeosciences 15 (2018)16. - ISSN 1726-4170 - p. 5189 - 5202.

Rain-fed peatlands are dominated by peat mosses (Sphagnum sp.), which for their growth depend on nutrients, water and CO2 uptake from the atmosphere. As the isotopic composition of carbon (12,13C) and oxygen (16,18O) of these Sphagnum mosses are affected by environmental conditions, Sphagnum tissue accumulated in peat constitutes a potential long-term archive that can be used for climate reconstruction. However, there is inadequate understanding of how isotope values are influenced by environmental conditions, which restricts their current use as environmental and palaeoenvironmental indicators. Here we tested (i) to what extent C and O isotopic variation in living tissue of Sphagnum is species-specific and associated with local hydrological gradients, climatic gradients (evapotranspiration, temperature, precipitation) and elevation; (ii) whether the C isotopic signature can be a proxy for net primary productivity (NPP) of Sphagnum; and (iii) to what extent Sphagnum tissue δ18O tracks the δ18O isotope signature of precipitation. In total, we analysed 337 samples from 93 sites across North America and Eurasia using two important peat-forming Sphagnum species (S. magellanicum, S. fuscum) common to the Holarctic realm. There were differences in δ13C values between species. For S. magellanicum δ13C decreased with increasing height above the water table (HWT, R2 =17%) and was positively correlated to productivity (R2 = 7%). Together these two variables explained 46% of the between-site variation in δ13C values. For S. fuscum, productivity was the only significant predictor of δ13C but had low explanatory power (total R2 = 6%). For δ18O values, approximately 90% of the variation was found between sites. Globally modelled annual δ18O values in precipitation explained 69% of the between-site variation in tissue δ18O. S. magellanicum showed lower δ18O enrichment than S. fuscum (-0.83 ‰ lower). Elevation and climatic variables were weak predictors of tissue δ18O values after controlling for δ18O values of the precipitation. To summarize, our study provides evidence for (a) good predictability of tissue δ18O values from modelled annual δ18O values in precipitation, and (b) the possibility of relating tissue δ13C values to HWT and NPP, but this appears to be species-dependent. These results suggest that isotope composition can be used on a large scale for climatic reconstructions but that such models should be species-specific.

Development and analysis of the Soil Water Infiltration Global database
Rahmati, Mehdi ; Weihermüller, Lutz ; Vanderborght, Jan ; Pachepsky, Yakov A. ; Mao, Lili ; Sadeghi, Seyed Hamidreza ; Moosavi, Niloofar ; Kheirfam, Hossein ; Montzka, Carsten ; Looy, Kris Van; Toth, Brigitta ; Hazbavi, Zeinab ; Yamani, Wafa Al; Albalasmeh, Ammar A. ; Alghzawi, M.Z. ; Angulo-Jaramillo, Rafael ; Antonino, Antônio Celso Dantas ; Arampatzis, George ; Armindo, Robson André ; Asadi, Hossein ; Bamutaze, Yazidhi ; Batlle-Aguilar, Jordi ; Béchet, Béatrice ; Becker, Fabian ; Blöschl, Günter ; Bohne, Klaus ; Braud, Isabelle ; Castellano, Clara ; Cerdà, Artemi ; Chalhoub, Maha ; Cichota, Rogerio ; Císlerová, Milena ; Clothier, Brent ; Coquet, Yves ; Cornelis, Wim ; Corradini, Corrado ; Coutinho, Artur Paiva ; Oliveira, Muriel Bastista De; Macedo, José Ronaldo De; Durães, Matheus Fonseca ; Emami, Hojat ; Eskandari, Iraj ; Farajnia, Asghar ; Flammini, Alessia ; Fodor, Nándor ; Gharaibeh, Mamoun ; Ghavimipanah, Mohamad Hossein ; Ghezzehei, Teamrat A. ; Giertz, Simone ; Hatzigiannakis, Evangelos G. ; Horn, Rainer ; Jiménez, Juan José ; Jacques, Diederik ; Keesstra, Saskia Deborah ; Kelishadi, Hamid ; Kiani-Harchegani, Mahboobeh ; Kouselou, Mehdi ; Jha, Madan Kumar ; Lassabatere, Laurent ; Li, Xiaoyan ; Liebig, Mark A. ; Lichner, Lubomír ; López, María Victoria ; Machiwal, Deepesh ; Mallants, Dirk ; Mallmann, Micael Stolben ; Oliveira Marques, Jean Dalmo De; Marshall, Miles R. ; Mertens, Jan ; Meunier, Félicien ; Mohammadi, Mohammad Hossein ; Mohanty, Binayak P. ; Pulido-Moncada, Mansonia ; Montenegro, Suzana ; Morbidelli, Renato ; Moret-Fernández, David ; Moosavi, Ali Akbar ; Mosaddeghi, Mohammad Reza ; Mousavi, Seyed Bahman ; Mozaffari, Hasan ; Nabiollahi, Kamal ; Neyshabouri, Mohammad Reza ; Ottoni, Marta Vasconcelos ; Ottoni Filho, Theophilo Benedicto ; Pahlavan-Rad, Mohammad Reza ; Panagopoulos, Andreas ; Peth, Stephan ; Peyneau, Pierre Emmanuel ; Picciafuoco, Tommaso ; Poesen, Jean ; Pulido, Manuel ; Reinert, Dalvan José ; Reinsch, Sabine ; Rezaei, Meisam ; Roberts, Francis Parry ; Robinson, David ; Rodrigo-Comino, Jesüs ; Rotunno Filho, Otto Corrêa ; Saito, Tadaomi ; Suganuma, Hideki ; Saltalippi, Carla ; Sándor, Renáta ; Schütt, Brigitta ; Seeger, Manuel ; Sepehrnia, Nasrollah ; Sharifi Moghaddam, Ehsan ; Shukla, Manoj ; Shutaro, Shiraki ; Sorando, Ricardo ; Stanley, Ajayi Asishana ; Strauss, Peter ; Su, Zhongbo ; Taghizadeh-Mehrjardi, Ruhollah ; Taguas, Encarnación ; Teixeira, Wenceslau Geraldes ; Vaezi, Ali Reza ; Vafakhah, Mehdi ; Vogel, Tomas ; Vogeler, Iris ; Votrubova, Jana ; Werner, Steffen ; Winarski, Thierry ; Yilmaz, Deniz ; Young, Michael H. ; Zacharias, Steffen ; Zeng, Yijian ; Zhao, Ying ; Zhao, Hong ; Vereecken, Harry - \ 2018
Earth System Science Data 10 (2018)3. - ISSN 1866-3508 - p. 1237 - 1263.

In this paper, we present and analyze a novel global database of soil infiltration measurements, the Soil Water Infiltration Global (SWIG) database. In total, 5023 infiltration curves were collected across all continents in the SWIG database. These data were either provided and quality checked by the scientists who performed the experiments or they were digitized from published articles. Data from 54 different countries were included in the database with major contributions from Iran, China, and the USA. In addition to its extensive geographical coverage, the collected infiltration curves cover research from 1976 to late 2017. Basic information on measurement location and method, soil properties, and land use was gathered along with the infiltration data, making the database valuable for the development of pedotransfer functions (PTFs) for estimating soil hydraulic properties, for the evaluation of infiltration measurement methods, and for developing and validating infiltration models. Soil textural information (clay, silt, and sand content) is available for 3842 out of 5023 infiltration measurements (∼76%) covering nearly all soil USDA textural classes except for the sandy clay and silt classes. Information on land use is available for 76ĝ€% of the experimental sites with agricultural land use as the dominant type (∼40%). We are convinced that the SWIG database will allow for a better parameterization of the infiltration process in land surface models and for testing infiltration models. All collected data and related soil characteristics are provided online in ∗.xlsx and ∗.csv formats for reference, and we add a disclaimer that the database is for public domain use only and can be copied freely by referencing it. Supplementary data are available at https://doi.org/10.1594/PANGAEA.885492 (Rahmati et al., 2018). Data quality assessment is strongly advised prior to any use of this database. Finally, we would like to encourage scientists to extend and update the SWIG database by uploading new data to it.

The legacy of 4,500 years of polyculture agroforestry in the eastern Amazon
Maezumi, S.Y. ; Alves, Daiana ; Robinson, Mark ; Souza, Jonas Gregorio de; Levis, Carolina ; Barnett, Robert L. ; Almeida de Oliveira, Edemar ; Urrego, Dunia ; Schaan, Denise ; Iriarte, José - \ 2018
Nature Plants 4 (2018)8. - ISSN 2055-026X - p. 540 - 547.

The legacy of pre-Columbian land use in the Amazonian rainforest is one of the most controversial topics in the social1–10 and natural sciences11,12. Until now, the debate has been limited to discipline-specific studies, based purely on archaeological data8, modern vegetation13, modern ethnographic data3 or a limited integration of archaeological and palaeoecological data12. The lack of integrated studies to connect past land use with modern vegetation has left questions about the legacy of pre-Columbian land use on the modern vegetation composition in the Amazon, unanswered11. Here, we show that persistent anthropogenic landscapes for the past 4,500 years have had an enduring legacy on the hyperdominance of edible plants in modern forests in the eastern Amazon. We found an abrupt enrichment of edible plant species in fossil lake and terrestrial records associated with pre-Columbian occupation. Our results demonstrate that, through closed-canopy forest enrichment, limited clearing for crop cultivation and low-severity fire management, long-term food security was attained despite climate and social changes. Our results suggest that, in the eastern Amazon, the subsistence basis for the development of complex societies began ~4,500 years ago with the adoption of polyculture agroforestry, combining the cultivation of multiple annual crops with the progressive enrichment of edible forest species and the exploitation of aquatic resources. This subsistence strategy intensified with the later development of Amazonian dark earths, enabling the expansion of maize cultivation to the Belterra Plateau, providing a food production system that sustained growing human populations in the eastern Amazon. Furthermore, these millennial-scale polyculture agroforestry systems have an enduring legacy on the hyperdominance of edible plants in modern forests in the eastern Amazon. Together, our data provide a long-term example of past anthropogenic land use that can inform management and conservation efforts in modern Amazonian ecosystems.

Assessing the Greenhouse Gas Mitigation effect of removing bovine trypanosomiasis in Eastern Africa
MacLeod, Michael ; Eory, Vera ; Wint, William ; Shaw, Alexandra ; Gerber, Pierre J. ; Cecchi, Giuliano ; Mattioli, Raffaele ; Sykes, Alasdair ; Robinson, Timothy - \ 2018
Sustainability 10 (2018)5. - ISSN 2071-1050
Cattle health - Climate change - GLEAM - Livestock modelling - Sustainable intensification

Increasing the production of meat and milk within sub-Saharan Africa should provide significant food security benefits. However, greenhouse gas (GHG) emissions represent a challenge, as cattle production in the region typically has high emissions intensity (EI), i.e., high rates of GHG emissions per unit of output. The high EI is caused by the relatively low production efficiencies in the region, which are in turn partly due to endemic cattle diseases. In theory, improved disease control should increase the efficiency and decrease the emissions intensity of livestock production; however quantitative analysis of the potential GHG mitigation effects of improved disease control in Africa is lacking. This paper seeks to respond to this by using a hybrid modelling approach to quantify the production and emissions effects of removing trypanosomiasis from East African cattle production systems. The emissions are quantified for each cattle production system using an excel version of GLEAM, the Food and Agriculture Organization's Global Livestock Environmental Assessment Model. The results indicate that removing trypanosomiasis leads to a reduction in the emissions intensity per unit of protein produced of between 0% and 8%, driven mainly by the increases in milk yields and cow fertility rates. Despite the limitations, it is argued that the approach provides considerable scope for modelling the GHG impacts of disease interventions.

Plasmodium-associated changes in human odor attract mosquitoes
Robinson, Ailie ; Busula, Annette O. ; Voets, Mirjam A. ; Beshir, Khalid B. ; Caulfield, John C. ; Powers, Stephen J. ; Verhulst, Niels O. ; Winskill, Peter ; Muwanguzi, Julian ; Birkett, Michael A. ; Smallegange, Renate C. ; Masiga, Daniel K. ; Mukabana, W.R. ; Sauerwein, Robert W. ; Sutherland, Colin J. ; Bousema, Teun ; Pickett, John A. ; Takken, Willem ; Logan, James G. ; Boer, Jetske G. De - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)18. - ISSN 0027-8424 - p. E4209 - E4218.
Aldehydes - Disease biomarkers - Host attractiveness - Malaria transmission - Parasite–vector–host interactions

Malaria parasites (Plasmodium) can change the attractiveness of their vertebrate hosts to Anopheles vectors, leading to a greater number of vector–host contacts and increased transmission. Indeed, naturally Plasmodium-infected children have been shown to attract more mosquitoes than parasite-free children. Here, we demonstrate Plasmodium-induced increases in the attractiveness of skin odor in Kenyan children and reveal quantitative differences in the production of specific odor components in infected vs. parasite-free individuals. We found the aldehydes heptanal, octanal, and nonanal to be produced in greater amounts by infected individuals and detected by mosquito antennae. In behavioral experiments, we demonstrated that these, and other, Plasmodium-induced aldehydes enhanced the attractiveness of a synthetic odor blend mimicking “healthy” human odor. Heptanal alone increased the attractiveness of “parasite-free” natural human odor. Should the increased production of these aldehydes by Plasmodium-infected humans lead to increased mosquito biting in a natural setting, this would likely affect the transmission of malaria.

Biophysical landscape interactions : Bridging disciplines and scale with connectivity
Ploeg, Martine J. van der; Baartman, Jantiene E.M. ; Robinson, David A. - \ 2018
Land Degradation and Development 29 (2018)4. - ISSN 1085-3278 - p. 1167 - 1175.
biophysical landscape processes - connectivity - interdisciplinary - scale
Landscape composition and land use impact the interactions between soil and vegetation. Differences in micro-behaviour, driven by the interplay of heterogeneous soil and vegetation dynamics, affect emergent characteristics across a landscape. Scaling approaches to understand the drivers of these emergent characteristics have been attempted, but the blueprint of interacting biophysical processes in landscapes is inherently messy and often still unknown. A complicating factor is single disciplinary focus in environmental sciences. Integrated knowledge is vital especially in view of future challenges posed by climate change, population growth, and soil threats. In this paper, we give examples of biophysical interactions that occur across various temporal and spatial scales and discuss how connectivity can be useful for bridging disciplines and scales to increase our understanding.
Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels
Jiang, Xia ; O'Reilly, Paul F. ; Aschard, Hugues ; Hsu, Yi Hsiang ; Richards, J.B. ; Dupuis, Josée ; Ingelsson, Erik ; Karasik, David ; Pilz, Stefan ; Berry, Diane ; Kestenbaum, Bryan ; Zheng, Jusheng ; Luan, Jianan ; Sofianopoulou, Eleni ; Streeten, Elizabeth A. ; Albanes, Demetrius ; Lutsey, Pamela L. ; Yao, Lu ; Tang, Weihong ; Econs, Michael J. ; Wallaschofski, Henri ; Völzke, Henry ; Zhou, Ang ; Power, Chris ; McCarthy, Mark I. ; Michos, Erin D. ; Boerwinkle, Eric ; Weinstein, Stephanie J. ; Freedman, Neal D. ; Huang, Wen Yi ; Schoor, Natasja M. van; Velde, Nathalie van der; Groot, Lisette C.P.G.M. de; Enneman, Anke ; Cupples, L.A. ; Booth, Sarah L. ; Vasan, Ramachandran S. ; Liu, Ching Ti ; Zhou, Yanhua ; Ripatti, Samuli ; Ohlsson, Claes ; Vandenput, Liesbeth ; Lorentzon, Mattias ; Eriksson, Johan G. ; Shea, M.K. ; Houston, Denise K. ; Kritchevsky, Stephen B. ; Liu, Yongmei ; Lohman, Kurt K. ; Ferrucci, Luigi ; Peacock, Munro ; Gieger, Christian ; Beekman, Marian ; Slagboom, Eline ; Deelen, Joris ; Deelen, Joris ; Heemst, Diana van; Kleber, Marcus E. ; März, Winfried ; Boer, Ian H. De; Wood, Alexis C. ; Rotter, Jerome I. ; Rich, Stephen S. ; Robinson-Cohen, Cassianne ; Heijer, Martin Den; Jarvelin, Marjo Riitta ; Jarvelin, Marjo Riitta ; Cavadino, Alana ; Cavadino, Alana ; Joshi, Peter K. ; Wilson, James F. ; Hayward, Caroline ; Lind, Lars ; Michaëlsson, Karl ; Trompet, Stella ; Zillikens, M.C. ; Uitterlinden, Andre G. ; Rivadeneira, Fernando - \ 2018
Nature Communications 9 (2018)1. - ISSN 2041-1723
Vitamin D is a steroid hormone precursor that is associated with a range of human traits and diseases. Previous GWAS of serum 25-hydroxyvitamin D concentrations have identified four genome-wide significant loci (GC, NADSYN1/DHCR7, CYP2R1, CYP24A1). In this study, we expand the previous SUNLIGHT Consortium GWAS discovery sample size from 16,125 to 79,366 (all European descent). This larger GWAS yields two additional loci harboring genome-wide significant variants (P = 4.7×10 -9 at rs8018720 in SEC23A, and P = 1.9×10 -14 at rs10745742 in AMDHD1). The overall estimate of heritability of 25-hydroxyvitamin D serum concentrations attributable to GWAS common SNPs is 7.5%, with statistically significant loci explaining 38% of this total. Further investigation identifies signal enrichment in immune and hematopoietic tissues, and clustering with autoimmune diseases in cell-type-specific analysis. Larger studies are required to identify additional common SNPs, and to explore the role of rare or structural variants and gene-gene interactions in the heritability of circulating 25-hydroxyvitamin D levels.
Invited review: A position on the Global Livestock Environmental Assessment Model (GLEAM)
MacLeod, M.J. ; Vellinga, T. ; Opio, C. ; Falcucci, A. ; Tempio, G. ; Henderson, B. ; Makkar, H. ; Mottet, A. ; Robinson, T. ; Steinfeld, H. ; Gerber, P.J. - \ 2018
Animal 12 (2018)2. - ISSN 1751-7311 - p. 383 - 397.
climate change - environmental assessment - life-cycle analysis - livestock - models
The livestock sector is one of the fastest growing subsectors of the agricultural economy and, while it makes a major contribution to global food supply and economic development, it also consumes significant amounts of natural resources and alters the environment. In order to improve our understanding of the global environmental impact of livestock supply chains, the Food and Agriculture Organization of the United Nations has developed the Global Livestock Environmental Assessment Model (GLEAM). The purpose of this paper is to provide a review of GLEAM. Specifically, it explains the model architecture, methods and functionality, that is the types of analysis that the model can perform. The model focuses primarily on the quantification of greenhouse gases emissions arising from the production of the 11 main livestock commodities. The model inputs and outputs are managed and produced as raster data sets, with spatial resolution of 0.05 decimal degrees. The Global Livestock Environmental Assessment Model v1.0 consists of five distinct modules: (a) the Herd Module; (b) the Manure Module; (c) the Feed Module; (d) the System Module; (e) the Allocation Module. In terms of the modelling approach, GLEAM has several advantages. For example spatial information on livestock distributions and crops yields enables rations to be derived that reflect the local availability of feed resources in developing countries. The Global Livestock Environmental Assessment Model also contains a herd model that enables livestock statistics to be disaggregated and variation in livestock performance and management to be captured. Priorities for future development of GLEAM include: improving data quality and the methods used to perform emissions calculations; extending the scope of the model to include selected additional environmental impacts and to enable predictive modelling; and improving the utility of GLEAM output.
Detecting macroecological patterns in bacterial communities across independent studies of global soils
Ramirez, Kelly S. ; Knight, Christopher G. ; Hollander, Mattias de; Brearley, Francis Q. ; Constantinides, Bede ; Cotton, Anne ; Creer, Si ; Crowther, Thomas W. ; Davison, John ; Delgado-Baquerizo, Manuel ; Dorrepaal, Ellen ; Elliott, David R. ; Fox, Graeme ; Griffiths, Robert I. ; Hale, Chris ; Hartman, Kyle ; Houlden, Ashley ; Jones, David L. ; Krab, Eveline J. ; Maestre, Fernando T. ; McGuire, Krista L. ; Monteux, Sylvain ; Orr, Caroline H. ; Putten, Wim H. van der; Roberts, Ian S. ; Robinson, David A. ; Rocca, Jennifer D. ; Rowntree, Jennifer ; Schlaeppi, Klaus ; Shepherd, Matthew ; Singh, Brajesh K. ; Straathof, Angela L. ; Bhatnagar, Jennifer M. ; Thion, Cécile ; Heijden, Marcel G.A. van der; Vries, Franciska T. de - \ 2018
Nature Microbiology 3 (2018). - ISSN 2058-5276 - p. 189 - 196.
The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential ‘indicator’ taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.
Plasmodium falciparum parasites with histidine-rich protein 2 (pfhrp2) and pfhrp3 gene deletions in two endemic regions of Kenya
Beshir, Khalid B. ; Sepúlveda, Nuno ; Bharmal, Jameel ; Robinson, Ailie ; Mwanguzi, Julian ; Busula, Annette Obukosia ; Boer, Jetske Gudrun De; Sutherland, Colin ; Cunningham, Jane ; Hopkins, Heidi - \ 2017
Scientific Reports 7 (2017)1. - ISSN 2045-2322
017-4052
Deletions of the Plasmodium falciparum hrp2 and hrp3 genes can affect the performance of HRP2-based malaria rapid diagnostic tests (RDTs). Such deletions have been reported from South America, India and Eritrea. Whether these parasites are widespread in East Africa is unknown. A total of 274 samples from asymptomatic children in Mbita, western Kenya, and 61 genomic data from Kilifi, eastern Kenya, were available for analysis. PCR-confirmed samples were investigated for the presence of pfhrp2 and pfhrp3 genes. In samples with evidence of deletion, parasite presence was confirmed by amplifying three independent genes. We failed to amplify pfhrp2 from 25 of 131 (19.1%) PCR-confirmed samples. Of these, only 8 (10%) samples were microscopic positive and were classified as pfhrp2-deleted. Eight microscopically-confirmed pfhrp2-deleted samples with intact pfhrp3 locus were positive by HRP2-based RDT. In addition, one PCR-confirmed infection showed a deletion at the pfhrp3 locus. One genomic sample lacked pfhrp2 and one lacked pfhrp3. No sample harbored parasites lacking both genes. Parasites lacking pfhrp2 are present in Kenya, but may be detectable by HRP-based RDT at higher parasitaemia, possibly due to the presence of intact pfhrp3. These findings warrant further systematic study to establish prevalence and diagnostic significance.
Open soil science: technology is helping us discover the mysteries under our feet
Hobley, E.U. ; Schultze, D.G. ; Robinson, D.A. ; Jahanshiri, E. ; Aitkenhead, M. ; Batjes, N.H. ; Hengl, T. - \ 2017
The Conversation
Odours of Plasmodium falciparum-infected participants influence mosquito-host interactions
Boer, Jetske G. De; Robinson, Ailie ; Powers, Stephen J. ; Burgers, Saskia L.G.E. ; Caulfield, John C. ; Birkett, Michael A. ; Smallegange, Renate C. ; Genderen, Perry J.J. Van; Bousema, Teun ; Sauerwein, Robert W. ; Pickett, John A. ; Takken, Willem ; Logan, James G. - \ 2017
Scientific Reports 7 (2017)1. - ISSN 2045-2322
017-4006
Malaria parasites are thought to influence mosquito attraction to human hosts, a phenomenon that may enhance parasite transmission. This is likely mediated by alterations in host odour because of its importance in mosquito host-searching behaviour. Here, we report that the human skin odour profile is affected by malaria infection. We compared the chemical composition and attractiveness to Anopheles coluzzii mosquitoes of skin odours from participants that were infected by Controlled Human Malaria Infection with Plasmodium falciparum. Skin odour composition differed between parasitologically negative and positive samples, with positive samples collected on average two days after parasites emerged from the liver into the blood, being associated with low densities of asexual parasites and the absence of gametocytes. We found a significant reduction in mosquito attraction to skin odour during infection for one experiment, but not in a second experiment, possibly due to differences in parasite strain. However, it does raise the possibility that infection can affect mosquito behaviour. Indeed, several volatile compounds were identified that can influence mosquito behaviour, including 2- and 3-methylbutanal, 3-hydroxy-2-butanone, and 6-methyl-5-hepten-2-one. To better understand the impact of our findings on Plasmodium transmission, controlled studies are needed in participants with gametocytes and higher parasite densities.
Land use change impacts on floods at the catchment scale : Challenges and opportunities for future research
Rogger, M. ; Agnoletti, M. ; Alaoui, A. ; Bathurst, J.C. ; Bodner, G. ; Borga, M. ; Chaplot, Vincent ; Gallart, F. ; Glatzel, G. ; Hall, J. ; Holden, J. ; Holko, L. ; Horn, R. ; Kiss, A. ; Kohnová, S. ; Leitinger, G. ; Lennartz, B. ; Parajka, J. ; Perdigão, R. ; Peth, S. ; Plavcová, L. ; Quinton, John N. ; Robinson, Matthew R. ; Salinas, J.L. ; Santoro, A. ; Szolgay, J. ; Tron, S. ; Akker, J.J.H. van den; Viglione, A. ; Blöschl, G. - \ 2017
Water Resources Research 53 (2017)7. - ISSN 0043-1397 - p. 5209 - 5219.
Catchment scale - Floods - Land use change
Research gaps in understanding flood changes at the catchment scale caused by changes in forest management, agricultural practices, artificial drainage, and terracing are identified. Potential strategies in addressing these gaps are proposed, such as complex systems approaches to link processes across time scales, long-term experiments on physical-chemical-biological process interactions, and a focus on connectivity and patterns across spatial scales. It is suggested that these strategies will stimulate new research that coherently addresses the issues across hydrology, soil and agricultural sciences, forest engineering, forest ecology, and geomorphology.
The effect of real-time vibrotactile feedback delivered through an augmented fork on eating rate, satiation, and food intake
Hermans, Roel C.J. ; Hermsen, Sander ; Robinson, Eric ; Higgs, Suzanne ; Mars, Monica ; Frost, Jeana H. - \ 2017
Appetite 113 (2017). - ISSN 0195-6663 - p. 7 - 13.
Digital technology - Eating rate - Food intake - Satiety - Vibrotactile feedback
Eating rate is a basic determinant of appetite regulation, as people who eat more slowly feel sated earlier and eat less. Without assistance, eating rate is difficult to modify due to its automatic nature. In the current study, participants used an augmented fork that aimed to decelerate their rate of eating. A total of 114 participants were randomly assigned to the Feedback Condition (FC), in which they received vibrotactile feedback from their fork when eating too fast (i.e., taking more than one bite per 10 s), or a Non-Feedback Condition (NFC). Participants in the FC took fewer bites per minute than did those in the NFC. Participants in the FC also had a higher success ratio, indicating that they had significantly more bites outside the designated time interval of 10 s than did participants in the NFC. A slower eating rate, however, did not lead to a significant reduction in the amount of food consumed or level of satiation. These findings indicate that real-time vibrotactile feedback delivered through an augmented fork is capable of reducing eating rate, but there is no evidence from this study that this reduction in eating rate is translated into an increase in satiation or reduction in food consumption. Overall, this study shows that real-time vibrotactile feedback may be a viable tool in interventions that aim to reduce eating rate. The long-term effectiveness of this form of feedback on satiation and food consumption, however, awaits further investigation.
Soil Functions in Earth's Critical Zone : Key Results and Conclusions
Banwart, S.A. ; Bernasconi, S.M. ; Blum, W.E.H. ; Souza, D.M. de; Chabaux, F. ; Duffy, C. ; Kercheva, M. ; Krám, P. ; Lair, G.J. ; Lundin, L. ; Menon, M. ; Nikolaidis, N. ; Novak, M. ; Panagos, P. ; Ragnarsdottir, K.V. ; Robinson, D.A. ; Rousseva, S. ; Ruiter, P. de; Gaans, P. van; Weng, L. ; White, T. ; Zhang, B. - \ 2017
Advances in Agronomy 142 (2017). - ISSN 0065-2113 - p. 1 - 27.
Critical zone - Ecosystem services - Soil - Soil functions - Water
This chapter summarizes the methods, results, and conclusions of a 5-year research project (SoilTrEC: Soil Transformations in European Catchments) on experimentation, process modeling, and computational simulation of soil functions and soil threats across a network of European, Chinese, and United States Critical Zone Observatories (CZOs). The study focused on the soil functions of biomass production, carbon storage, water storage and transmission, water filtration, transformation of nutrients, and maintaining habitat and genetic diversity.The principal results demonstrate that soil functions can be quantified as biophysical flows and transformations of material and energy. The functions can be simulated with mathematical models of soil processes within the soil profile and at the critical zone interfaces with vegetation and atmosphere, surface waters and the below-ground vadose zone and groundwater. A new dynamic model for soil structure development, together with data sets from the CZOs, demonstrate both seasonal fluctuations in soil structure dynamics related to vegetation dynamics and soil carbon inputs, and long-term trends (decadal) in soil carbon storage and soil structure development.Cross-site comparison for 20 soil profiles at seven field sites with variation in soil type, lithology, land cover, land use, and climate demonstrate that sites can be classified, using model parameter values for soil aggregation processes together with climatic conditions and soil physical properties, along a trajectory of soil structure development from incipient soil formation through productive land use to overly intensive land use with soil degradation.A new modeling code, the Integrated Critical Zone model, was applied with parameter sets developed from the CZO site data to simulate the biophysical flows and transformations that quantify multiple soil functions. Process simulations coupled the new model for soil structure dynamics with existing modeling approaches for soil carbon dynamics, nutrient transformations, vegetation dynamics, hydrological flow and transport, and geochemical equilibria and mineral weathering reactions. Successful calibration, testing, and application of the model with data sets from horticulture plot manipulation experiments demonstrate the potential to apply modeling and simulation to the scoping and design of new practices and policy options to enhance soil functions and reduce soil threats worldwide.
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