Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Global patterns and drivers of ecosystem functioning in rivers and riparian zones
    Tiegs, Scott D. ; Costello, David M. ; Isken, Mark W. ; Woodward, Guy ; McIntyre, Peter B. ; Gessner, Mark O. ; Chauvet, Eric ; Griffiths, Natalie A. ; Flecker, Alex S. ; Acuña, Vicenç ; Albariño, Ricardo ; Allen, Daniel C. ; Alonso, Cecilia ; Andino, Patricio ; Arango, Clay ; Aroviita, Jukka ; Barbosa, Marcus V.M. ; Barmuta, Leon A. ; Baxter, Colden V. ; Bell, Thomas D.C. ; Bellinger, Brent ; Boyero, Luz ; Brown, Lee E. ; Bruder, Andreas ; Bruesewitz, Denise A. ; Burdon, Francis J. ; Callisto, Marcos ; Canhoto, Cristina ; Capps, Krista A. ; Castillo, María M. ; Clapcott, Joanne ; Colas, Fanny ; Colón-Gaud, Checo ; Cornut, Julien ; Crespo-Pérez, Verónica ; Cross, Wyatt F. ; Culp, Joseph M. ; Danger, Michael ; Dangles, Olivier ; Eyto, Elvira De; Derry, Alison M. ; Villanueva, Veronica Díaz ; Douglas, Michael M. ; Elosegi, Arturo ; Encalada, Andrea C. ; Entrekin, Sally ; Espinosa, Rodrigo ; Ethaiya, Diana ; Ferreira, Verónica ; Ferriol, Carmen ; Flanagan, Kyla M. ; Fleituch, Tadeusz ; Follstad Shah, Jennifer J. ; Barbosa, André Frainer ; Friberg, Nikolai ; Frost, Paul C. ; Garcia, Erica A. ; Lago, Liliana García ; Soto, Pavel Ernesto García ; Ghate, Sudeep ; Giling, Darren P. ; Gilmer, Alan ; Gonçalves, José Francisco ; Gonzales, Rosario Karina ; Graça, Manuel A.S. ; Grace, Mike ; Grossart, Hans Peter ; Guérold, François ; Gulis, Vlad ; Hepp, Luiz U. ; Higgins, Scott ; Hishi, Takuo ; Huddart, Joseph ; Hudson, John ; Imberger, Samantha ; Iñiguez-Armijos, Carlos ; Iwata, Tomoya ; Janetski, David J. ; Jennings, Eleanor ; Kirkwood, Andrea E. ; Koning, Aaron A. ; Kosten, Sarian ; Kuehn, Kevin A. ; Laudon, Hjalmar ; Leavitt, Peter R. ; Lemes Da Silva, Aurea L. ; Leroux, Shawn J. ; LeRoy, Carri J. ; Lisi, Peter J. ; MacKenzie, Richard ; Marcarelli, Amy M. ; Masese, Frank O. ; McKie, Brendan G. ; Medeiros, Adriana Oliveira ; Meissner, Kristian ; Miliša, Marko ; Mishra, Shailendra ; Miyake, Yo ; Moerke, Ashley ; Mombrikotb, Shorok ; Mooney, Rob ; Moulton, Tim ; Muotka, Timo ; Negishi, Junjiro N. ; Neres-Lima, Vinicius ; Nieminen, Mika L. ; Nimptsch, Jorge ; Ondruch, Jakub ; Paavola, Riku ; Pardo, Isabel ; Patrick, Christopher J. ; Peeters, Edwin T.H.M. ; Pozo, Jesus ; Pringle, Catherine ; Prussian, Aaron ; Quenta, Estefania ; Quesada, Antonio ; Reid, Brian ; Richardson, John S. ; Rigosi, Anna ; Rincón, José ; Rîşnoveanu, Geta ; Robinson, Christopher T. ; Rodríguez-Gallego, Lorena ; Royer, Todd V. ; Rusak, James A. ; Santamans, Anna C. ; Selmeczy, Géza B. ; Simiyu, Gelas ; Skuja, Agnija ; Smykla, Jerzy ; Sridhar, Kandikere R. ; Sponseller, Ryan ; Stoler, Aaron ; Swan, Christopher M. ; Szlag, David ; Teixeira-De Mello, Franco ; Tonkin, Jonathan D. ; Uusheimo, Sari ; Veach, Allison M. ; Vilbaste, Sirje ; Vought, Lena B.M. ; Wang, Chiao Ping ; Webster, Jackson R. ; Wilson, Paul B. ; Woelfl, Stefan ; Xenopoulos, Marguerite A. ; Yates, Adam G. ; Yoshimura, Chihiro ; Yule, Catherine M. ; Zhang, Yixin X. ; Zwart, Jacob A. - \ 2019
    Science Advances 5 (2019)1. - ISSN 2375-2548 - p. 14966 - 14973.

    River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.

    Biomarkers of Dietary Omega-6 Fatty Acids and Incident Cardiovascular Disease and Mortality: An Individual-Level Pooled Analysis of 30 Cohort Studies
    Marklund, Matti ; Wu, Jason H.Y. ; Imamura, Fumiaki ; Gobbo, Liana C. Del; Fretts, Amanda ; Goede, Janette De; Shi, Peilin ; Tintle, Nathan ; Wennberg, Maria ; Aslibekyan, Stella ; Chen, Tzu An ; Oliveira Otto, Marcia C. De; Hirakawa, Yoichiro ; Eriksen, Helle Højmark ; Kröger, Janine ; Laguzzi, Federica ; Lankinen, Maria ; Murphy, Rachel A. ; Prem, Kiesha ; Samieri, Cécilia ; Virtanen, Jyrki ; Wood, Alexis C. ; Wong, Kerry ; Yang, Wei Sin ; Zhou, Xia ; Baylin, Ana ; Boer, Jolanda M.A. ; Brouwer, Ingeborg A. ; Campos, Hannia ; Chaves, Paulo H.M. ; Chien, Kuo Liong ; Faire, Ulf De; Djoussé, Luc ; Eiriksdottir, Gudny ; El-Abbadi, Naglaa ; Forouhi, Nita G. ; Michael Gaziano, J. ; Geleijnse, Johanna M. ; Gigante, Bruna ; Giles, Graham ; Guallar, Eliseo ; Gudnason, Vilmundur ; Harris, Tamara ; Harris, William S. ; Helmer, Catherine ; Hellenius, Mai Lis ; Hodge, Allison ; Hu, Frank B. ; Jacques, Paul F. ; Jansson, Jan Håkan ; Kalsbeek, Anya ; Khaw, Kay Tee ; Koh, Woon Puay ; Laakso, Markku ; Leander, Karin ; Lin, Hung Ju ; Lind, Lars ; Luben, Robert ; Luo, Juhua ; Mcknight, Barbara ; Mursu, Jaakko ; Ninomiya, Toshiharu ; Overvad, Kim ; Psaty, Bruce M. ; Rimm, Eric ; Schulze, Matthias B. ; Siscovick, David ; Skjelbo Nielsen, Michael ; Smith, Albert V. ; Steffen, Brian T. ; Steffen, Lyn ; Sun, Qi ; Sundström, Johan ; Tsai, Michael Y. ; Tunstall-Pedoe, Hugh ; Uusitupa, Matti I.J. ; Dam, Rob M. van; Veenstra, Jenna ; Verschuren, Monique ; Wareham, Nick ; Willett, Walter ; Woodward, Mark ; Yuan, Jian Min ; Micha, Renata ; Lemaitre, Rozenn N. ; Mozaffarian, Dariush ; Risérus, Ulf - \ 2019
    Circulation 139 (2019)21. - ISSN 0009-7322 - p. 2422 - 2436.
    arachidonic acid - biomarkers - cardiovascular diseases - diet - epidemiology - linoleic acid - primary prevention

    Background: Global dietary recommendations for and cardiovascular effects of linoleic acid, the major dietary omega-6 fatty acid, and its major metabolite, arachidonic acid, remain controversial. To address this uncertainty and inform international recommendations, we evaluated how in vivo circulating and tissue levels of linoleic acid (LA) and arachidonic acid (AA) relate to incident cardiovascular disease (CVD) across multiple international studies. Methods: We performed harmonized, de novo, individual-level analyses in a global consortium of 30 prospective observational studies from 13 countries. Multivariable-adjusted associations of circulating and adipose tissue LA and AA biomarkers with incident total CVD and subtypes (coronary heart disease, ischemic stroke, cardiovascular mortality) were investigated according to a prespecified analytic plan. Levels of LA and AA, measured as the percentage of total fatty acids, were evaluated linearly according to their interquintile range (ie, the range between the midpoint of the first and fifth quintiles), and categorically by quintiles. Study-specific results were pooled using inverse-variance-weighted meta-analysis. Heterogeneity was explored by age, sex, race, diabetes mellitus, statin use, aspirin use, omega-3 levels, and fatty acid desaturase 1 genotype (when available). Results: In 30 prospective studies with medians of follow-up ranging 2.5 to 31.9 years, 15 198 incident cardiovascular events occurred among 68 659 participants. Higher levels of LA were significantly associated with lower risks of total CVD, cardiovascular mortality, and ischemic stroke, with hazard ratios per interquintile range of 0.93 (95% CI, 0.88-0.99), 0.78 (0.70-0.85), and 0.88 (0.79-0.98), respectively, and nonsignificantly with lower coronary heart disease risk (0.94; 0.88-1.00). Relationships were similar for LA evaluated across quintiles. AA levels were not associated with higher risk of cardiovascular outcomes; in a comparison of extreme quintiles, higher levels were associated with lower risk of total CVD (0.92; 0.86-0.99). No consistent heterogeneity by population subgroups was identified in the observed relationships. Conclusions: In pooled global analyses, higher in vivo circulating and tissue levels of LA and possibly AA were associated with lower risk of major cardiovascular events. These results support a favorable role for LA in CVD prevention.

    A perspective on water quality in connected systems: modelling feedback between upstream and downstream transport and local ecological processes
    Teurlincx, Sven ; Wijk, Dianneke van; Mooij, Wolf M. ; Kuiper, Jan J. ; Huttunen, Inese ; Brederveld, Robert J. ; Chang, Manqi ; Janse, Jan H. ; Woodward, Ben ; Hu, Fenjuan ; Janssen, Annette B.G. - \ 2019
    Current Opinion in Environmental Sustainability 40 (2019). - ISSN 1877-3435 - p. 21 - 29.

    Food production for a growing world population relies on application of fertilisers and pesticides on agricultural lands. However, these substances threaten surface water quality and thereby endanger valued ecosystem services such as drinking water supply, food production and recreational water use. Such deleterious effects do not merely arise on the local scale, but also on the regional scale through transport of substances as well as energy and biota across the catchment. Here we argue that aquatic ecosystem models can provide a process-based understanding of how these transports by water and organisms as vectors affect – and are affected by – ecosystem state and functioning in networks of connected lakes. Such a catchment scale approach is key to setting critical limits for the release of substances by agricultural practices and other human pressures on aquatic ecosystems. Thereby, water and food production and the trade-offs between them may be managed more sustainably.

    Natural variation in tolerance to sub-zero temperatures among populations of Arabidopsis lyrata ssp. petraea
    Davey, Matthew P. ; Palmer, Ben G. ; Armitage, Emily ; Vergeer, Philippine ; Kunin, William E. ; Woodward, F.I. ; Quick, W.P. - \ 2018
    BMC Plant Biology 18 (2018)1. - ISSN 1471-2229
    Acclimation - Arabidopsis lyrata ssp. petraea - Chlorophyll fluorescence - Marginal populations - Survival

    BACKGROUND: Temperature is one of the most important abiotic factors limiting plant growth and productivity. Many plants exhibit cold acclimation to prepare for the likelihood of freezing as temperatures decrease towards 0 °C. The physiological mechanisms associated with enabling increased tolerance to sub-zero temperatures vary between species and genotypes. Geographically and climatically diverse populations of Arabidopsis lyrata ssp. petraea were examined for their ability to survive, maintain functional photosynthetic parameters and cellular electrolyte leakage integrity after being exposed to sub-zero temperatures. The duration of cold acclimation prior to sub-zero temperatures was also manipulated (2 and 14 days). RESULTS: We found that there was significant natural variation in tolerances to sub-zero temperatures among populations of A. petraea. The origin of the population affected the acclimation response and survival after exposure to sub-zero temperatures. Cold acclimation of plants prior to sub-zero temperatures affected the maximum quantum efficiency of photosystem II (PSII) (Fv/Fm) in that plants that were cold acclimated for longer periods had higher values of Fv/Fm as a result of sub-zero temperatures. The inner immature leaves were better able to recover Fv/Fm from sub-zero temperatures than mature outer leaves. The Irish population (Leitrim) acclimated faster, in terms of survival and electrolyte leakage than the Norwegian population (Helin). CONCLUSION: The ability to survive, recover photosynthetic processes and cellular electrolyte leakage after exposure to sub-zero temperatures is highly dependent on the duration of cold acclimation.

    Contributions of mean and shape of blood pressure distribution to worldwide trends and variations in raised blood pressure : A pooled analysis of 1018 population-based measurement studies with 88.6 million participants
    Ezzati, Majid ; Zhou, Bin ; Bentham, James ; Cesare, Mariachiara di; Bixby, Honor ; Danaei, Goodarz ; Hajifathalian, Kaveh ; Taddei, Cristina ; Carrillo-Larco, Rodrigo M. ; Djalalinia, Shirin ; Khatibzadeh, Shahab ; Lugero, Charles ; Peykari, Niloofar ; Zhang, Wan Zhu ; Bennett, James ; Bilano, Ver ; Stevens, Gretchen A. ; Cowan, Melanie J. ; Riley, Leanne M. ; Chen, Zhengming ; Hambleton, Ian R. ; Jackson, Rod T. ; Kengne, Andre Pascal ; Khang, Young Ho ; Laxmaiah, Avula ; Liu, Jing ; Malekzadeh, Reza ; Neuhauser, Hannelore K. ; Sorić, Maroje ; Starc, Gregor ; Sundström, Johan ; Woodward, Mark ; Abarca-Gómez, Leandra ; Abdeen, Ziad A. ; Abu-Rmeileh, Niveen M. ; Acosta-Cazares, Benjamin ; Adams, Robert J. ; Aekplakorn, Wichai ; Afsana, Kaosar ; Aguilar-Salinas, Carlos A. ; Geleijnse, Johanna M. - \ 2018
    International Journal of Epidemiology 47 (2018)3. - ISSN 0300-5771 - p. 872 - 883i.
    Blood pressure - Global health - Hypertension - Non-communicable disease - Population health

    Background: Change in the prevalence of raised blood pressure could be due to both shifts in the entire distribution of blood pressure (representing the combined effects of public health interventions and secular trends) and changes in its high-blood-pressure tail (representing successful clinical interventions to control blood pressure in the hypertensive population). Our aim was to quantify the contributions of these two phenomena to the worldwide trends in the prevalence of raised blood pressure. Methods: We pooled 1018 population-based studies with blood pressure measurements on 88.6 million participants from 1985 to 2016. We first calculated mean systolic blood pressure (SBP), mean diastolic blood pressure (DBP) and prevalence of raised blood pressure by sex and 10-year age group from 20-29 years to 70-79 years in each study, taking into account complex survey design and survey sample weights, where relevant. We used a linear mixed effect model to quantify the association between (probittransformed) prevalence of raised blood pressure and age-group- and sex-specific mean blood pressure. We calculated the contributions of change in mean SBP and DBP, and of change in the prevalence-mean association, to the change in prevalence of raised blood pressure. Results: In 2005-16, at the same level of population mean SBP and DBP, men and women in South Asia and in Central Asia, the Middle East and North Africa would have the highest prevalence of raised blood pressure, and men and women in the highincome Asia Pacific and high-income Western regions would have the lowest. In most region-sex-age groups where the prevalence of raised blood pressure declined, one half or more of the decline was due to the decline in mean blood pressure. Where prevalence of raised blood pressure has increased, the change was entirely driven by increasing mean blood pressure, offset partly by the change in the prevalence-mean association. Conclusions: Change in mean blood pressure is the main driver of the worldwide change in the prevalence of raised blood pressure, but change in the high-blood-pressure tail of the distribution has also contributed to the change in prevalence, especially in older age groups.

    Survival of Phytophthora cinnamomi and Fusarium verticillioides in commercial potting substrates for ornamental plants
    Puértolas, Alexandra ; Boa, Eric ; Bonants, Peter J.M. ; Woodward, Steve - \ 2018
    Journal of Phytopathology 166 (2018)7-8. - ISSN 0931-1785 - p. 484 - 493.
    Fusarium - Ornamental plants - Peat - Peat-free - Phytophthora - Potting substrates - Survival
    Live plants, particularly when accompanied by soil or potting substrates, are considered the main pathway for international spread of plant pathogens. Modern, rapid shipping technologies for international plant trade increase the probability of plant pathogen survival during transport and the subsequent chances of disease outbreaks in new locations. The survival of two model pathogens, an Oomycete, Phytophthora cinnamomi, and a filamentous fungus, Fusarium verticillioides, was studied in two different commercial potting substrates (peat and peat-free) under glasshouse conditions in the absence of a plant host. Survival rates were analysed at 2, 7, 12 and 17 months after substrate inoculation. Fusarium verticillioides had the longest survival rate, and was still present at 17 months. In contrast, P. cinnamomi survived up to 7 months but was not recovered after 12 or 17 months. There was no significant difference in the number of colony-forming units (CFUs) of either pathogen in the two substrates, except at 2 months, when higher numbers were recovered from peat substrates.
    Ecological networks in managed ecosystems: Connecting structure to services
    Mulder, Christian ; Sechi, Valentina ; Woodward, Guy ; Bohan, David Andrew - \ 2017
    In: Adaptive Food Webs Cambridge University Press - ISBN 9781107182110 - p. 214 - 227.

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

    Alien Pathogens on the Horizon : Opportunities for Predicting their Threat to Wildlife
    Roy, Helen E. ; Hesketh, Helen ; Purse, Bethan V. ; Eilenberg, Jørgen ; Santini, Alberto ; Scalera, Riccardo ; Stentiford, Grant D. ; Adriaens, Tim ; Bacela-Spychalska, Karolina ; Bass, David ; Beckmann, Katie M. ; Bessell, Paul ; Bojko, Jamie ; Booy, Olaf ; Cardoso, Ana Cristina ; Essl, Franz ; Groom, Quentin ; Harrower, Colin ; Kleespies, Regina ; Martinou, Angeliki F. ; Oers, Monique M. van; Peeler, Edmund J. ; Pergl, Jan ; Rabitsch, Wolfgang ; Roques, Alain ; Schaffner, Francis ; Schindler, Stefan ; Schmidt, Benedikt R. ; Schönrogge, Karsten ; Smith, Jonathan ; Solarz, Wojciech ; Stewart, Alan ; Stroo, Arjan ; Tricarico, Elena ; Turvey, Katharine M.A. ; Vannini, Andrea ; Vilà, Montserrat ; Woodward, Stephen ; Wynns, Anja Amtoft ; Dunn, Alison M. - \ 2017
    Conservation Letters 10 (2017)4. - ISSN 1755-263X - p. 477 - 484.
    Environmental hazard - Horizon scanning - Invasive alien species - Legislation - Wildlife diseases
    According to the Convention on Biological Diversity, by 2020 invasive alien species (IAS) should be identified and their impacts assessed, so that species can be prioritized for implementation of appropriate control strategies and measures put in place to manage invasion pathways. For one quarter of the IAS listed as the "100 of the world's worst" environmental impacts are linked to diseases of wildlife (undomesticated plants and animals). Moreover, IAS are a significant source of "pathogen pollution" defined as the human-mediated introduction of a pathogen to a new host or region. Despite this, little is known about the biology of alien pathogens and their biodiversity impacts after introduction into new regions. We argue that the threats posed by alien pathogens to endangered species, ecosystems, and ecosystem services should receive greater attention through legislation, policy, and management. We identify 10 key areas for research and action, including those relevant to the processes of introduction and establishment of an alien pathogen and to prediction of the spread and associated impact of an alien pathogen on native biota and ecosystems. The development of interdisciplinary capacity, expertise, and coordination to identify and manage threats was seen as critical to address knowledge gaps.
    Removal of soya bean meal from wheat- and maize-based diets decreased litter moisture and foot pad dermatitis in turkeys
    Hocking, P.M. ; Veldkamp, T. ; Vinco, L.J. ; Woodward, P. ; Harkness, A. - \ 2016
    British Poultry Abstracts 12 (2016)1. - ISSN 1746-6202 - p. 15 - 16.
    Diversity of STs, plasmids and ESBL genes among Escherichia coli from humans, animals and food in Germany, the Netherlands and the UK
    Day, Michaela J. ; Rodríguez, Irene ; Essen-Zandbergen, Alieda van; Dierikx, Cindy ; Kadlec, Kristina ; Schink, Anne Kathrin ; Wu, Guanghui ; Chattaway, Marie A. ; DoNascimento, Vivienne ; Wain, John ; Helmuth, Reiner ; Guerra, Beatriz ; Schwarz, Stefan ; Threlfall, John ; Woodward, Martin J. ; Coldham, Nick ; Mevius, Dik ; Woodford, Neil - \ 2016
    Journal of Antimicrobial Chemotherapy 71 (2016)5. - ISSN 0305-7453 - p. 1178 - 1182.

    Objectives: This study aimed to compare ESBL-producing Escherichia coli causing infections in humans with infecting or commensal isolates from animals and isolates from food of animal origin in terms of the strain types, the ESBL gene present and the plasmids that carry the respective ESBL genes. Methods: A collection of 353 ESBL-positive E. coli isolates from the UK, the Netherlands and Germany were studied by MLST and ESBL genes were identified. Characterization of ESBL gene-carrying plasmids was performed using PCR-based replicon typing. Moreover, IncI1-Iγ and IncN plasmids were characterized by plasmid MLST. Results: The ESBL-producing E. coli represented 158 different STs with ST131, ST10 and ST88 being the most common. Overall, blaCTX-M-1 was the most frequently detected ESBL gene, followed by blaCTX-M-15, which was the most common ESBL gene in the human isolates. The most common plasmid replicon type overall was IncI1-Ig followed by multiple IncF replicons. Conclusions: ESBL genes were present in a wide variety of E. coli STs. IncI1-Iγ plasmids that carried the blaCTX-M-1 gene were widely disseminated amongst STs in isolates from animals and humans, whereas other plasmids and STs appeared to be more restricted to isolates from specific hosts.

    High water intake is associated with soya compared with non-soya protein sources and may be associated with foot pad dermatitis in growing turkeys
    Hocking, P.M. ; Veldkamp, T. ; Vinco, L.J. ; Woodward, P. - \ 2015
    British Poultry Abstracts 11 (2015)1. - ISSN 1746-6202 - p. 33 - 34.
    Replacing soya bean meal with alternative protein sources will reduce water consumption and may lead to dryer litter and decrease the incidence of foot pad dermatitis in growing turkeys
    Association of Cardiometabolic Multimorbidity With Mortality
    Angelantonio, Emanuele Di; Kaptoge, Stephen ; Wormser, David ; Willeit, Peter ; Butterworth, Adam S. ; Bansal, Narinder ; O’Keeffe, Linda M. ; Gao, Pei ; Wood, Angela M. ; Burgess, Stephen ; Freitag, Daniel F. ; Pennells, Lisa ; Peters, Sanne A. ; Hart, Carole L. ; Håheim, Lise Lund ; Gillum, Richard F. ; Nordestgaard, Børge G. ; Psaty, Bruce M. ; Yeap, Bu B. ; Knuiman, Matthew W. ; Nietert, Paul J. ; Kauhanen, Jussi ; Salonen, Jukka T. ; Kuller, Lewis H. ; Simons, Leon A. ; Schouw, Yvonne T. van der; Barrett-Connor, Elizabeth ; Selmer, Randi ; Crespo, Carlos J. ; Rodriguez, Beatriz ; Verschuren, Monique W.M. ; Salomaa, Veikko ; Svärdsudd, Kurt ; Harst, Pim Van Der; Björkelund, Cecilia ; Wilhelmsen, Lars ; Wallace, Robert B. ; Brenner, Hermann ; Amouyel, Philippe ; Barr, Elizabeth L.M. ; Iso, Hiroyasu ; Onat, Altan ; Trevisan, Maurizio ; agostino, Ralph B. D'; Cooper, Cyrus ; Kavousi, Maryam ; Welin, Lennart ; Roussel, Ronan ; Hu, Frank B. ; Sato, Shinichi ; Davidson, Karina W. ; Howard, Barbara V. ; Leening, Maarten J.G. ; Rosengren, Annika ; Dörr, Marcus ; Deeg, Dorly J.H. ; Kiechl, Stefan ; Stehouwer, Coen D.A. ; Nissinen, Aulikki ; Giampaoli, Simona ; Donfrancesco, Chiara ; Kromhout, Daan ; Price, Jackie F. ; Peters, Annette ; Meade, Tom W. ; Casiglia, Edoardo ; Lawlor, Debbie A. ; Gallacher, John ; Nagel, Dorothea ; Franco, Oscar H. ; Assmann, Gerd ; Dagenais, Gilles R. ; Jukema, Wouter J. ; Sundström, Johan ; Woodward, Mark ; Brunner, Eric J. ; Khaw, Kay-Tee ; Wareham, Nicholas J. ; Whitsel, Eric A. ; Njølstad, Inger ; Hedblad, Bo ; Wassertheil-Smoller, Sylvia ; Engström, Gunnar ; Rosamond, Wayne D. ; Selvin, Elizabeth ; Sattar, Naveed ; Thompson, Simon G. ; Danesh, John - \ 2015
    JAMA: The Journal of the American Medical Association 314 (2015)1. - ISSN 0098-7484 - p. 52 - 60.
    Importance The prevalence of cardiometabolic multimorbidity is increasing.

    Objective To estimate reductions in life expectancy associated with cardiometabolic multimorbidity.

    Design, Setting, and Participants Age- and sex-adjusted mortality rates and hazard ratios (HRs) were calculated using individual participant data from the Emerging Risk Factors Collaboration (689 300 participants; 91 cohorts; years of baseline surveys: 1960-2007; latest mortality follow-up: April 2013; 128 843 deaths). The HRs from the Emerging Risk Factors Collaboration were compared with those from the UK Biobank (499 808 participants; years of baseline surveys: 2006-2010; latest mortality follow-up: November 2013; 7995 deaths). Cumulative survival was estimated by applying calculated age-specific HRs for mortality to contemporary US age-specific death rates.

    Exposures A history of 2 or more of the following: diabetes mellitus, stroke, myocardial infarction (MI).

    Main Outcomes and Measures All-cause mortality and estimated reductions in life expectancy.
    Results In participants in the Emerging Risk Factors Collaboration without a history of diabetes, stroke, or MI at baseline (reference group), the all-cause mortality rate adjusted to the age of 60 years was 6.8 per 1000 person-years. Mortality rates per 1000 person-years were 15.6 in participants with a history of diabetes, 16.1 in those with stroke, 16.8 in those with MI, 32.0 in those with both diabetes and MI, 32.5 in those with both diabetes and stroke, 32.8 in those with both stroke and MI, and 59.5 in those with diabetes, stroke, and MI. Compared with the reference group, the HRs for all-cause mortality were 1.9 (95% CI, 1.8-2.0) in participants with a history of diabetes, 2.1 (95% CI, 2.0-2.2) in those with stroke, 2.0 (95% CI, 1.9-2.2) in those with MI, 3.7 (95% CI, 3.3-4.1) in those with both diabetes and MI, 3.8 (95% CI, 3.5-4.2) in those with both diabetes and stroke, 3.5 (95% CI, 3.1-4.0) in those with both stroke and MI, and 6.9 (95% CI, 5.7-8.3) in those with diabetes, stroke, and MI. The HRs from the Emerging Risk Factors Collaboration were similar to those from the more recently recruited UK Biobank. The HRs were little changed after further adjustment for markers of established intermediate pathways (eg, levels of lipids and blood pressure) and lifestyle factors (eg, smoking, diet). At the age of 60 years, a history of any 2 of these conditions was associated with 12 years of reduced life expectancy and a history of all 3 of these conditions was associated with 15 years of reduced life expectancy.

    Conclusions and Relevance Mortality associated with a history of diabetes, stroke, or MI was similar for each condition. Because any combination of these conditions was associated with multiplicative mortality risk, life expectancy was substantially lower in people with multimorbidity.
    Evidence of Evolving Extraintestinal Enteroaggregative Escherichia coli ST38 Clone
    Chattaway, M.A. ; Jenkins, C. ; Ciesielczuk, H. ; Day, M. ; DoNascimento, V. ; Day, M.M. ; Rodriguez, I. ; Essen-Zandbergen, A. van; Schink, A.K. ; Wu, G.H. ; Threlfall, J. ; Woodward, M.J. ; Coldham, N. ; Kadlec, K. ; Schwarz, S. ; Dierikx, C. ; Guerra, B. ; Helmuth, R. ; Mevius, D.J. ; Woodford, N. ; Wain, J. - \ 2014
    Emerging Infectious Diseases 20 (2014)11. - ISSN 1080-6040 - p. 1935 - 1937.
    strains
    Participatory Development and Analysis of a Fuzzy Cognitive Map of the Establishment of a Bio-Based Economy in the Humber Region.
    Penn, A.S. ; Knight, C.J.K. ; Lloyd, D.J.B. ; Avitabile, D. ; Kok, K. ; Schiller, F. ; Woodward, A. ; Druckman, A. ; Basson, L. - \ 2013
    PLoS ONE 8 (2013)11. - ISSN 1932-6203
    bayesian networks - river-basin - management - knowledge - models
    Fuzzy Cognitive Mapping (FCM) is a widely used participatory modelling methodology in which stakeholders collaboratively develop a ‘cognitive map’ (a weighted, directed graph), representing the perceived causal structure of their system. This can be directly transformed by a workshop facilitator into simple mathematical models to be interrogated by participants by the end of the session. Such simple models provide thinking tools which can be used for discussion and exploration of complex issues, as well as sense checking the implications of suggested causal links. They increase stakeholder motivation and understanding of whole systems approaches, but cannot be separated from an intersubjective participatory context. Standard FCM methodologies make simplifying assumptions, which may strongly influence results, presenting particular challenges and opportunities. We report on a participatory process, involving local companies and organisations, focussing on the development of a bio-based economy in the Humber region. The initial cognitive map generated consisted of factors considered key for the development of the regional bio-based economy and their directional, weighted, causal interconnections. A verification and scenario generation procedure, to check the structure of the map and suggest modifications, was carried out with a second session. Participants agreed on updates to the original map and described two alternate potential causal structures. In a novel analysis all map structures were tested using two standard methodologies usually used independently: linear and sigmoidal FCMs, demonstrating some significantly different results alongside some broad similarities. We suggest a development of FCM methodology involving a sensitivity analysis with different mappings and discuss the use of this technique in the context of our case study. Using the results and analysis of our process, we discuss the limitations and benefits of the FCM methodology in this case and in general. We conclude by proposing an extended FCM methodology, including multiple functional mappings within one participant-constructed graph.
    Distributional (In)Congruence of Biodiversity-Ecosystem Functioning
    Mulder, Christian ; Boit, Alice ; Mori, Shigeta ; Vonk, J.A. ; Dyer, Scott D. ; Faggiano, Leslie ; Geisen, Stefan ; González, Angélica L. ; Kaspari, Michael ; Lavorel, Sandra ; Marquet, Pablo A. ; Rossberg, Axel G. ; Sterner, Robert W. ; Voigt, Winfried ; Wall, Diana H. - \ 2012
    In: Global Change in Multispecies Systems Part 1 / Jacob, U., Woodward, G., Academic Press Inc. (Advances in Ecological Research ) - ISBN 9780123969927 - p. 1 - 88.

    The majority of research on biodiversity-ecosystem functioning in laboratories has concentrated on a few traits, but there is increasing evidence from the field that functional diversity controls ecosystem functioning more often than does species number. Given the importance of traits as predictors of niche complementarity and community structures, we (1) examine how the diversity sensu lato of forest trees, freshwater fishes and soil invertebrates might support ecosystem functioning and (2) discuss the relevance of productive biota for monophyletic assemblages (taxocenes).In terrestrial ecosystems, correlating traits to abiotic factors is complicated by the appropriate choice of body-size distributions. Angiosperm and gymnosperm trees, for example, show metabolic incongruences in their respiration rates despite their pronounced macroecological scaling. Scaling heterotrophic organisms within their monophyletic assemblages seems more difficult than scaling autotrophs: in contrast to the generally observed decline of mass-specific metabolic rates with body mass within metazoans, soil organisms such as protozoans show opposite mass-specific trends.At the community level, the resource demand of metazoans shapes multitrophic interactions. Hence, population densities and their food web relationships reflect functional diversity, but the influence of biodiversity on stability and ecosystem functioning remains less clear. We focused on fishes in 18 riverine food webs, where the ratio of primary versus secondary extinctions (hereafter, 'extinction partitioning') summarizes the responses of fish communities to primary species loss (deletions) and its consequences. Based on extinction partitioning, our high-diversity food webs were just as (or even more) vulnerable to extinctions as low-diversity food webs.Our analysis allows us to assess consequences of the relocation or removal of fish species and to help with decision-making in sustainable river management. The study highlights that the topology of food webs (and not simply taxonomic diversity) plays a greater role in stabilizing the food web and enhancing ecological services than is currently acknowledged.

    A Belowground Perspective on Dutch Agroecosystems: How Soil Organisms Interact to Support Ecosystem Services
    Mulder, C. ; Boit, A. ; Bonkowski, M. ; Ruiter, P.C. de; Mancinelli, G. ; Heijden, M.G.A. van der; Wijnen, H.J. van; Vonk, J.A. ; Rutgers, M. - \ 2011
    In: Advances in Ecological Research / Woodward, G., San Diego, USA : Elsevier Academic Press (Advances in Ecological Research 44) - ISBN 9780123747945 - p. 277 - 357.
    arable farming systems - stable-isotope ratios - ecological community description - direct counting method - belowground food webs - winter-wheat fields - body-size - fatty-acids - species richness - nitrogen mineralization
    1. New patterns and trends in land use are becoming increasingly evident in Europe's heavily modified landscape and else whereas sustainable agriculture and nature restoration are developed as viable long-term alternatives to intensively farmed arable land. The success of these changes depends on how soil biodiversity and processes respond to changes in management. To improve our understanding of the community structure and ecosystem functioning of the soil biota, we analyzed abiotic variables across 200 sites, and biological variables across 170 sites in The Netherlands, one of the most intensively farmed countries. The data were derived from the Dutch Soil Quality Network (DSQN), a long-term monitoring framework designed to obtain ecological insight into soil types (STs) and ecosystem types (ETs). 2. At the outset we describe STs and biota, and we estimate the contribution of various groups to the provision of ecosystem services. We focused on interactive effects of soil properties on community patterns and ecosystem functioning using food web models. Ecologists analyze soil food webs by means of mechanistic and statistical modelling, linking network structure to energy flow and elemental dynamics commonly based on allometric scaling. 3. We also explored how predatory and metabolic processes are constrained by body size, diet and metabolic type, and how these constraints govern the interactions within and between trophic groups. In particular, we focused on how elemental fluxes determine the strengths of ecological interactions, and the resulting ecosystem services, in terms of sustenance of soil fertility. 4. We discuss data mining, food web visualizations, and an appropriate categorical way to capture subtle interrelationships within the DSQN dataset. Sampled metazoans were used to provide an overview of below-ground processes and influences of land use. Unlike most studies to date we used data from the entire size spectrum, across 15 orders of magnitude, using body size as a continuous trait crucial for understanding ecological services. 5. Multimodality in the frequency distributions of body size represents a performance filter that acts as a buffer to environmental change. Large differences in the body-size distributions across ETs and STs were evident. Most observed trends support the hypothesis that the direct influence of ecological stoichiometry on the soil biota as an independent predictor (e.g. in the form of nutrient to carbon ratios), and consequently on the allometric scaling, is more dominant than either ET or ST. This provides opportunities to develop a mechanistic and physiologically oriented model for the distribution of species' body sizes, where responses of invertebrates can be predicted. 6. Our results highlight the different roles that organisms play in a number of key ecosystem services. Such a trait-based research has unique strengths in its rigorous formulation of fundamental scaling rules, as well as in its verifiability by empirical data. Nonetheless, it still has weaknesses that remain to be addressed, like the consequences of intraspecific size variation, the high degree of omnivory, and a possibly inaccurate assignment to trophic groups. 7. Studying the extent to which nutrient levels influence multitrophic interactions and how different land-use regimes affect soil biodiversity is clearly a fruitful area for future research to develop predictive models for soil ecosystem services under different management regimes. No similar efforts have been attempted previously for soil food webs, and our dataset has the potential to test and further verify its usefulness at an unprecedented space scale.
    COST action FP801- established and emerging Phytophthora: incresasing threats to woodland and forest ecosystems in Europe
    Woodward, S. ; Vannini, A. ; Werres, S. ; Osswald, W. ; Bonants, P.J.M. ; Jung, T. - \ 2011
    New Zealand Journal of Forestry Science 41S (2011). - ISSN 0048-0134 - p. 7 - 13.
    With the rapidly growing international trade in plants and ongoing impacts of climate change, impacts of plant pathogens in the genus Phytophthora are increasing, threatening the biodiversity and sustainability of European forest ecosystems. Through the European Cooperation in Science and Technology (COST) framework Action FP0801, scientists and disease-control experts are working on phytophthora in forest ecosystems with the overall aim of increasing understanding of the biology and ecology of Phytophthora species with potential to cause damage to European forestry. This knowledge will be used in the development of effective control and management protocols for the problems caused. Outcomes of the Action will be promoted in an effort to increase knowledge and awareness of the problem by disseminating information to end-users and authorities in the forestry sector, and to he general public. Four interrelated working groups have been established to (i) examine the ways n which Phytophthora species spread into and within Europe; (ii) determine how phytophthoras kill oody plants and elucidate mechanisms for host resistance; (iii) disseminate state-of-the-art rapid olecular diagnostic techniques, and (iv) seek sustainable protocols for management and control of he diseases. The project is expected to increase understanding of threats to forest ecosystems y phytophthora, improve the ability to rapidly detect phytophthora in environmental samples, and rovide sustainable management solutions to the diseases caused by these destructive organisms
    Virulotyping and antimicrobial resistance typing of Salmonella enterica serovars relevant to human health in Europe
    Huehn, S. ; Ragione, R.M. La; Anjum, F.M. ; Saunders, M. ; Woodward, M. ; Bunge, C. ; Helmuth, R. ; Hauser, E. ; Guerra, B. ; Beutlich, J. ; Brisabois, A. ; Peters, T. ; Svensson, L. ; Madajczak, G. ; Litrup, E. ; Imre, A. ; Herrera-Leon, S. ; Mevius, D.J. ; Newell, D.G. ; Malrony, B. - \ 2010
    Foodborne Pathogens and Disease 7 (2010). - ISSN 1535-3141 - p. 523 - 535.
    complete genome sequence - quinolone resistance - serotype enteritidis - peyers-patches - typhimurium - identification - expression - integrons - strains - gene
    The combination of virulence gene and antimicrobial resistance gene typing using DNA arrays is a recently developed genomics-based approach to bacterial molecular epidemiology. We have now applied this technology to 523 Salmonella enterica subsp. enterica strains collected from various host sources and public health and veterinary institutes across nine European countries. The strain set included the five predominant Salmonella serovars isolated in Europe (Enteritidis, Typhimurium, Infantis, Virchow, and Hadar). Initially, these strains were screened for 10 potential virulence factors (avrA, ssaQ, mgtC, siiD, sopB, gipA, sodC1, sopE1, spvC, and bcfC) by polymerase chain reaction. The results indicated that only 14 profiles comprising these genes (virulotypes) were observed throughout Europe. Moreover, most of these virulotypes were restricted to only one (n = 9) or two (n = 4) serovars. The data also indicated that the virulotype did not vary significantly with host source or geographical location. Subsequently, a representative subset of 77 strains was investigated using a microarray designed to detect 102 virulence and 49 resistance determinants. The results confirmed and extended the previous observations using the virulo-polymerase chain reaction screen. Strains belonging to the same serovar grouped together, indicating that the broader virulence-associated gene complement corresponded with the serovar. There were, however, some differences in the virulence gene profiles between strains belonging to an individual serovar. This variation occurred primarily within those virulence genes that were prophage encoded, in fimbrial clusters or in the virulence plasmid. It seems likely that such changes enable Salmonella to adapt to different environmental conditions, which might be reflected in serovar-specific ecology. In this strain subset a number of resistance genes were detected and were serovar restricted to a varying degree. Once again the profiles of those genes encoding resistance were similar or the same for each serovar in all hosts and countries investigated
    Development of a miniaturised microarray-based assay for the rapid identification of antimicrobial resistance genes in Gram-negative bacteria
    Batchelor, M. ; Hopkins, K.L. ; Liebana, E. ; Slickers, P. ; Ehricht, R. ; Mafura, M. ; Aerestrup, F. ; Mevius, D.J. ; Clifton-Hadley, F.A. ; Woodward, M. ; Davies, R. ; Threlfall, J. ; Anjum, F.M. - \ 2008
    International Journal of Antimicrobial Agents 31 (2008)5. - ISSN 0924-8579 - p. 440 - 451.
    escherichia-coli - beta-lactamases - staphylococcus-aureus - dna microarrays - humans - animals - england - wales
    We describe the development of a miniaturised microarray for the detection of antimicrobial resistance genes in Gram-negative bacteria. Included on the array are genes encoding resistance to aminoglycosides, trimethoprim, sulphonamides, tetracyclines and ß-lactams, including extended-spectrum ß-lactamases. Validation of the array with control strains demonstrated a 99% correlation between polymerase chain reaction and array results. There was also good correlation between phenotypic and genotypic results for a large panel of Escherichia coli and Salmonella isolates. Some differences were also seen in the number and type of resistance genes harboured by E. coli and Salmonella strains. The array provides an effective, fast and simple method for detection of resistance genes in clinical isolates suitable for use in diagnostic laboratories, which in future will help to understand the epidemiology of isolates and to detect gene linkage in bacterial populations.
    Advanced terrestrial ecosystem analysis and modelling (ATEAM)
    Schröter, D. ; Acosta-Michlik, L. ; Arnell, A.W. ; Araújo, M.B. ; Badeck, F. ; Bakker, Martha ; Bondeau, A. ; Brugmann, H. ; Carter, T. ; Vega de la-Leinert, A.C. ; Erhard, M. ; Espineira, G.Z. ; Ewert, F. ; Fritsch, U. ; Friedlingstein, P. ; Glendining, M. ; Gracia, C.A. ; Hickler, T. ; House, J. ; Hulme, M. ; Kankaanpää, S. ; Klein, R.J.T. ; Krukenberg, B. ; Lavorel, S. ; Leemans, R. ; Lindner, M. ; Liski, J. ; Metzger, M.J. ; Meyer, J. ; Mitchell, T. ; Mohren, G.M.J. ; Morales, P. ; Moreno, J.M. ; Reginster, I. ; Reidsma, P. ; Rounsevell, M. ; Pla, E. ; Pluimers, J.C. ; Prentice, I.C. ; Pussinen, A. ; Sánchez, A. ; Sabaté, S. ; Sitch, S. ; Smith, B. ; Smith, P. ; Sykes, M.T. ; Thonicke, K. ; Thuiller, W. ; Tuck, G. ; Werf, G. van der; Vayreda, J. ; Wattenbach, M. ; Wilson, D.W. ; Woodward, F.I. ; Zaehle, S. ; Zierl, B. ; Zudin, S. ; Cramer, W. - \ 2004
    Potsdam : Potsdam Institute for Climate Impact Research (PIK)
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