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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Molnetenhancer: Enhanced molecular networks by integrating metabolome mining and annotation tools
Ernst, Madeleine ; Kang, Kyo Bin ; Caraballo-Rodríguez, Andrés Mauricio ; Nothias, Louis Felix ; Wandy, Joe ; Chen, Christopher ; Wang, Mingxun ; Rogers, Simon ; Medema, Marnix H. ; Dorrestein, Pieter C. ; Hooft, Justin J.J. van der - \ 2019
Metabolites 9 (2019)7. - ISSN 2218-1989
Chemical classification - In silico workflows - Metabolite annotation - Metabolite identification - Metabolome mining - Molecular families - Networking - Substructures

Metabolomics has started to embrace computational approaches for chemical interpretation of large data sets. Yet, metabolite annotation remains a key challenge. Recently, molecular networking and MS2LDA emerged as molecular mining tools that find molecular families and substructures in mass spectrometry fragmentation data. Moreover, in silico annotation tools obtain and rank candidate molecules for fragmentation spectra. Ideally, all structural information obtained and inferred from these computational tools could be combined to increase the resulting chemical insight one can obtain from a data set. However, integration is currently hampered as each tool has its own output format and efficient matching of data across these tools is lacking. Here, we introduce MolNetEnhancer, a workflow that combines the outputs from molecular networking, MS2LDA, in silico annotation tools (such as Network Annotation Propagation or DEREPLICATOR), and the automated chemical classification through ClassyFire to provide a more comprehensive chemical overview of metabolomics data whilst at the same time illuminating structural details for each fragmentation spectrum. We present examples from four plant and bacterial case studies and show how MolNetEnhancer enables the chemical annotation, visualization, and discovery of the subtle substructural diversity within molecular families. We conclude that MolNetEnhancer is a useful tool that greatly assists the metabolomics researcher in deciphering the metabolome through combination of multiple independent in silico pipelines.

Toward the improvement of total nitrogen deposition budgets in the United States
Walker, J.T. ; Beachley, G. ; Amos, H.M. ; Baron, J.S. ; Bash, J. ; Baumgardner, R. ; Bell, M.D. ; Benedict, K.B. ; Chen, X. ; Clow, D.W. ; Cole, A. ; Coughlin, J.G. ; Cruz, K. ; Daly, R.W. ; Decina, S.M. ; Elliott, E.M. ; Fenn, M.E. ; Ganzeveld, L. ; Gebhart, K. ; Isil, S.S. ; Kerschner, B.M. ; Larson, R.S. ; Lavery, T. ; Lear, G.G. ; Macy, T. ; Mast, M.A. ; Mishoe, K. ; Morris, K.H. ; Padgett, P.E. ; Pouyat, R.V. ; Puchalski, M. ; Pye, H.O.T. ; Rea, A.W. ; Rhodes, M.F. ; Rogers, C.M. ; Saylor, R. ; Scheffe, R. ; Schichtel, B.A. ; Schwede, D.B. ; Sexstone, G.A. ; Sive, B.C. ; Sosa, R. ; Templer, P.H. ; Thompson, T. ; Tong, D. ; Wetherbee, G.A. ; Whitlow, T.H. ; Wu, Z. ; Yu, Z. ; Zhang, L. - \ 2019
Science of the Total Environment 691 (2019). - ISSN 0048-9697 - p. 1328 - 1352.
Ammonia - Dry deposition - Organic nitrogen - Oxidized nitrogen - Reactive nitrogen - Wet deposition

Frameworks for limiting ecosystem exposure to excess nutrients and acidity require accurate and complete deposition budgets of reactive nitrogen (Nr). While much progress has been made in developing total Nr deposition budgets for the U.S., current budgets remain limited by key data and knowledge gaps. Analysis of National Atmospheric Deposition Program Total Deposition (NADP/TDep) data illustrates several aspects of current Nr deposition that motivate additional research. Averaged across the continental U.S., dry deposition contributes slightly more (55%) to total deposition than wet deposition and is the dominant process (>90%) over broad areas of the Southwest and other arid regions of the West. Lack of dry deposition measurements imposes a reliance on models, resulting in a much higher degree of uncertainty relative to wet deposition which is routinely measured. As nitrogen oxide (NOx) emissions continue to decline, reduced forms of inorganic nitrogen (NHx = NH3 + NH4 +) now contribute >50% of total Nr deposition over large areas of the U.S. Expanded monitoring and additional process-level research are needed to better understand NHx deposition, its contribution to total Nr deposition budgets, and the processes by which reduced N deposits to ecosystems. Urban and suburban areas are hotspots where routine monitoring of oxidized and reduced Nr deposition is needed. Finally, deposition budgets have incomplete information about the speciation of atmospheric nitrogen; monitoring networks do not capture important forms of Nr such as organic nitrogen. Building on these themes, we detail the state of the science of Nr deposition budgets in the U.S. and highlight research priorities to improve deposition budgets in terms of monitoring and flux measurements, leaf- to regional-scale modeling, source apportionment, and characterization of deposition trends and patterns.

Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
Rogers, Simon ; Wei Ong, Cher ; Wandy, Joe ; Ernst, Madeleine ; Ridder, Lars ; Hooft, Justin J.J. Van Der - \ 2019
Faraday Discussions 218 (2019). - ISSN 1359-6640 - p. 284 - 302.
Complex metabolite mixtures are challenging to unravel. Mass spectrometry (MS) is a widely used and sensitive technique to obtain structural information on complex mixtures. However, just knowing the molecular masses of the mixture’s constituents is almost always insufficient for confident assignment of the associated chemical structures. Structural information can be augmented through MS fragmentation experiments whereby detected metabolites are fragmented giving rise to MS/MS spectra. However, how can we maximize the structural information we gain from fragmentation spectra? We recently proposed a substructure-based strategy to enhance metabolite annotation for complex mixtures by considering metabolites as the sum of (bio)chemically relevant moieties that we can detect through mass spectrometry fragmentation approaches. Our MS2LDA tool allows us to discover - unsupervised - groups of mass fragments and/or neutral losses termed Mass2Motifs that often correspond to substructures. After manual annotation, these Mass2Motifs can be used in subsequent MS2LDA analyses of new datasets, thereby providing structural annotations for many molecules that are not present in spectral databases. Here, we describe how additional strategies, taking advantage of i) combinatorial in-silico matching of experimental mass features to substructures of candidate molecules, and ii) automated machine learning classification of molecules, can facilitate semi-automated annotation of substructures. We show how our approach accelerates the Mass2Motif annotation process and therefore broadens the chemical space spanned by characterized motifs. Our machine learning model used to classify fragmentation spectra learns the relationships between fragment spectra and chemical features. Classification prediction on these features can be aggregated for all molecules that contribute to a particular Mass2Motif and guide Mass2Motif annotations. To make annotated Mass2Motifs available to the community, we also present motifDB: an open database of Mass2Motifs that can be browsed and accessed programmatically through an API. MotifDB is integrated within, allowing users to efficiently search for characterized motifs in their own experiments. We expect that with an increasing number of Mass2Motif annotations available through a growing database we can more quickly gain insight in the constituents of complex mixtures. That will allow prioritization towards novel or unexpected chemistries and faster recognition of known biochemical building blocks.
Food Aid for Nutrition: Narrative Review of Major Research Topics Presented at a Scientific Symposium Held October 21, 2017, at the 21st International Congress of Nutrition in Buenos Aires, Argentina
Caiafa, Kristine ; Dewey, Kathryn G. ; Michaelsen, Kim F. ; Pee, Saskia de; Collins, Steve ; Rogers, Beatrice Lorge ; El-Kour, Tatyana ; Walton, Shelley ; Webb, Patrick - \ 2019
Food and Nutrition Bulletin 40 (2019)1. - ISSN 0379-5721 - p. 111 - 123.
cost-effectiveness - evidence - food aid - global health - nutrition - public health

Background: Food aid is a valuable tool for meeting global nutrition goals, particularly for vulnerable populations of children and reproductive-aged women. On October 21, 2017, the Food Aid Quality Review Project hosted a scientific symposium at the 21st International Congress on Nutrition in Buenos Aires, Argentina, to take stock of what the global community has learned about selected topics in the research literature on food aid used to address malnutrition. Objective: This article presents the discussion that took place during the symposium, which was guided by presentations by 6 experts from the field of nutrition, food aid, and humanitarian response. Conclusion: The recent upsurge in research on food aid has advanced the collective knowledge of what food aid products and programs work for addressing nutrition, but there is much more to learn. Presentations in this symposium called for further inquiry on (1) different and novel food aid formulations, (2) the cost-effectiveness of products and programs, and (3) market-based approaches to food assistance. Continuing to expand the evidence base on these topics is critical to improving global nutrition programs.

Multicore Liquid Perfluorocarbon-Loaded Multimodal Nanoparticles for Stable Ultrasound and 19F MRI Applied to In Vivo Cell Tracking
Koshkina, Olga ; Lajoinie, Guillaume ; Baldelli Bombelli, Francesca ; Swider, Edyta ; Cruz, Luis J. ; White, Paul B. ; Schweins, Ralf ; Dolen, Yusuf ; Dinther, Eric A.W. van; Riessen, N.K. van; Rogers, Sarah E. ; Fokkink, Remco ; Voets, Ilja K. ; Eck, Ernst R.H. van; Heerschap, Arend ; Versluis, Michel ; Korte, Chris L. de; Figdor, Carl G. ; Vries, I.J.M. de; Srinivas, Mangala - \ 2019
Advanced Functional Materials 29 (2019)19. - ISSN 1616-301X
F MRI - cell therapy - cell tracking - multimodal imaging - perfluorocarbons - ultrasound

Ultrasound is the most commonly used clinical imaging modality. However, in applications requiring cell-labeling, the large size and short active lifetime of ultrasound contrast agents limit their longitudinal use. Here, 100 nm radius, clinically applicable, polymeric nanoparticles containing a liquid perfluorocarbon, which enhance ultrasound contrast during repeated ultrasound imaging over the course of at least 48 h, are described. The perfluorocarbon enables monitoring the nanoparticles with quantitative 19 F magnetic resonance imaging, making these particles effective multimodal imaging agents. Unlike typical core–shell perfluorocarbon-based ultrasound contrast agents, these nanoparticles have an atypical fractal internal structure. The nonvaporizing highly hydrophobic perfluorocarbon forms multiple cores within the polymeric matrix and is, surprisingly, hydrated with water, as determined from small-angle neutron scattering and nuclear magnetic resonance spectroscopy. Finally, the nanoparticles are used to image therapeutic dendritic cells with ultrasound in vivo, as well as with 19 F MRI and fluorescence imaging, demonstrating their potential for long-term in vivo multimodal imaging.

Homoeostatic maintenance of nonstructural carbohydrates during the 2015–2016 El Niño drought across a tropical forest precipitation gradient
Dickman, Lee Turin ; McDowell, Nate G. ; Grossiord, Charlotte ; Collins, Adam D. ; Wolfe, Brett T. ; Detto, Matteo ; Wright, S.J. ; Medina-Vega, José A. ; Goodsman, Devin ; Rogers, Alistair ; Serbin, Shawn P. ; Wu, Jin ; Ely, Kim S. ; Michaletz, Sean T. ; Xu, Chonggang ; Kueppers, Lara ; Chambers, Jeffrey Q. - \ 2019
Plant, Cell & Environment 42 (2019)5. - ISSN 0140-7791 - p. 1705 - 1714.
climate - ENSO - NSC - Panama - storage - sugars - tropics - vegetation

Nonstructural carbohydrates (NSCs) are essential for maintenance of plant metabolism and may be sensitive to short- and long-term climatic variation. NSC variation in moist tropical forests has rarely been studied, so regulation of NSCs in these systems is poorly understood. We measured foliar and branch NSC content in 23 tree species at three sites located across a large precipitation gradient in Panama during the 2015–2016 El Niño to examine how short- and long-term climatic variation impact carbohydrate dynamics. There was no significant difference in total NSCs as the drought progressed (leaf P = 0.32, branch P = 0.30) nor across the rainfall gradient (leaf P = 0.91, branch P = 0.96). Foliar soluble sugars decreased while starch increased over the duration of the dry period, suggesting greater partitioning of NSCs to storage than metabolism or transport as drought progressed. There was a large variation across species at all sites, but total foliar NSCs were positively correlated with leaf mass per area, whereas branch sugars were positively related to leaf temperature and negatively correlated with daily photosynthesis and wood density. The NSC homoeostasis across a wide range of conditions suggests that NSCs are an allocation priority in moist tropical forests.

Scenarios of Land Use and Land Cover Change and Their Multiple Impacts on Natural Capital in Tanzania
Capitani, Claudia ; Soesbergen, Arnout van; Mukama, Kusaga ; Malugu, Isaac ; Mbilinyi, Boniface ; Chamuya, Nurdin ; Kempen, Bas ; Malimbwi, Rogers ; Mant, Rebecca ; Munishi, Panteleo ; Njana, Marco Andrew ; Ortmann, Antonia ; Platts, Philip J. ; Runsten, Lisen ; Sassen, Marieke ; Sayo, Philippina ; Shirima, Deo ; Zahabu, Elikamu ; Burgess, Neil D. ; Marchant, Rob - \ 2019
Environmental Conservation 46 (2019)1. - ISSN 0376-8929 - p. 17 - 24.
Reducing emissions from deforestation and forest degradation plus the conservation of forest carbon stocks, sustainable management of forests and enhancement of forest carbon stocks in developing countries (REDD+) requires information on land-use and land-cover changes (LULCCs) and carbon emission trends from the past to the present and into the future. Here, we use the results of participatory scenario development in Tanzania to assess the potential interacting impacts on carbon stock, biodiversity and water yield of alternative scenarios where REDD+ is or is not effectively implemented by 2025, a green economy (GE) scenario and a business as usual (BAU) scenario, respectively. Under the BAU scenario, LULCCs will cause 296 million tonnes of carbon (MtC) national stock loss by 2025, reduce the extent of suitable habitats for endemic and rare species (mainly in encroached protected mountain forests) and change water yields. In the GE scenario, national stock loss decreases to 133 MtC. In this scenario, consistent LULCC impacts occur within small forest patches with high carbon density, water catchment capacity and biodiversity richness. Opportunities for maximizing carbon emission reductions nationally are largely related to sustainable woodland management, but also contain trade-offs with biodiversity conservation and changes in water availability.
A workshop on 'Dietary Sweetness-Is It an Issue?'
Wittekind, Anna ; Higgins, Kelly ; McGale, Lauren ; Schwartz, Camille ; Stamataki, Nikoleta S. ; Beauchamp, Gary K. ; Bonnema, Angela ; Dussort, Pierre ; Gibson, Sigrid ; Graaf, Cees de; Halford, Jason C.G. ; Marsaux, Cyril F.M. ; Mattes, Richard D. ; McLaughlin, John ; Mela, David J. ; Nicklaus, Sophie ; Rogers, Peter J. ; Macdonald, Ian A. - \ 2018
International Journal of Obesity 42 (2018)4. - ISSN 0307-0565 - p. 934 - 938.
This report summarises a workshop convened by ILSI Europe on 3 and 4 April 2017 to discuss the issue of dietary sweetness. The objectives were to understand the roles of sweetness in the diet, establish whether exposure to sweetness affects diet quality and energy intake, and consider whether sweetness per se affects health. Although there may be evidence for tracking of intake of some sweet components of the diet through childhood, evidence for tracking of whole diet sweetness, or through other stages of maturity are lacking. The evidence to date does not support adverse effects of sweetness on diet quality or energy intake, except where sweet food choices increase intake of free sugars. There is some evidence for improvements in diet quality and reduced energy intake where sweetness without calories replaces sweetness with calories. There is a need to understand the physiological and metabolic relevance of sweet taste receptors on the tongue, in the gut and elsewhere in the body, as well as possible differentiation in the effects of sustained consumption of individual sweeteners. Despite a plethora of studies, there is no consistent evidence for an association of sweetness sensitivity/preference with obesity or type 2 diabetes. A multifaceted integrated approach, characterising nutritive and sensory aspects of the whole diet or dietary patterns, may be more valuable in providing contextual insight. The outcomes of the workshop could be used as a scientific basis to inform the expert community and create more useful dialogue among health care professionals.
Avoiding pitfalls in interdisciplinary education
Holt, R.E. ; Woods, P.J. ; Ferreira, A.S.A. ; Bardarson, H. ; Bonanomi, S. ; Boonstra, W.J. ; Butler, W.E. ; Diekert, F.K. ; Fouzai, N. ; Holma, M. ; Kokkalis, A. ; Kvile, K. ; Macdonald, J.I. ; Malanski, E. ; Nieminen, E. ; Ottosen, K.M. ; Pedersen, M.W. ; Richter, A. ; Rogers, L. ; Romagnoni, G. ; Snickars, M. ; Törnroos, A. ; Weigel, B. ; Whittington, J.D. ; Yletyinen, J. - \ 2017
Climate Research 74 (2017)2. - ISSN 0936-577X - p. 121 - 129.
Climate change - Education - Interdisciplinarity - Learning mechanisms - Research network
As the world's social-environmental problems increasingly extend across boundaries, both disciplinary and political, there is a growing need for interdisciplinarity, not only in research per se, but also in doctoral education. We present the common pitfalls of interdisciplinary research in doctoral education, illustrating approaches towards solutions using the Nordic Centre for Research on Marine Ecosystems and Resources under Climate Change (NorMER) research network as a case study. We provide insights and detailed examples of how to overcome some of the challenges of conducting interdisciplinary research within doctoral studies that can be applied within any doctoral/postdoctoral education programme, and beyond. Results from a selfevaluation survey indicate that early-career workshops, annual meetings and research visits to other institutions were the most effective learning mechanisms, whereas single discipline-focused courses and coursework were among the least effective learning mechanisms. By identifying the strengths and weaknesses of components of NorMER, this case study can inform the design of future programmes to enhance interdisciplinarity in doctoral education, as well as be applied to science collaboration and academic research in general.
Towards ecosystem-based management : identifying operational food-web indicators for marine ecosystems
Tam, Jamie C. ; Link, Jason S. ; Rossberg, Axel G. ; Rogers, Stuart I. ; Levin, Philip S. ; Rochet, Marie-Joelle ; Bundy, Alida ; Belgrano, Andrea ; Libralato, Simone ; Tomczak, Maciej ; Wolfshaar, K.E. van de; Pranovi, Fabio ; Gorokhova, Elena ; Large, Scott I. ; Niquil, Nathalie ; Greenstreet, Simon P.R. ; Druon, Jean-Noel ; Lesutiene, Jurate ; Johansen, Marie ; Preciado, Izaskun ; Patricio, Joana ; Palialexis, Andreas ; Tett, Paul ; Johansen, Geir O. ; Houle, Jennifer ; Rindorf, Anna - \ 2017
ICES Journal of Marine Science 74 (2017)7. - ISSN 1054-3139 - p. 2040 - 2052.
ecoystem-based management - Good environmental status - Indicator selection - integrated ecosystem assessment - marine strategy framework directive
Modern approaches to Ecosystem-Based Management and sustainable use of marine resources must account for the myriad of pressures (interspecies, human and environmental) affecting marine ecosystems. The network of feeding interactions between co-existing species and populations (food webs) are an important aspect of all marine ecosystems and biodiversity. Here we describe and discuss a process to evaluate the selection of operational food-web indicators for use in evaluating marine ecosystem status. This process brought together experts in food-web ecology, marine ecology, and resource management, to identify available indicators that can be used to inform marine management. Standard evaluation criteria (availability and quality of data, conceptual basis, communicability, relevancy to management) were implemented
to identify practical food-web indicators ready for operational use and indicators that hold promise for future use in policy and management. The major attributes of the final suite of operational food-web indicators were structure and functioning. Indicators that represent resilience of the marine ecosystem were less developed. Over 60 potential food-web indicators were evaluated and the final selection of operational food-web indicators includes: the primary production required to sustain a fishery, the productivity of seabirds (or charismatic megafauna), zooplankton indicators, primary productivity, integrated trophic indicators, and the biomass of trophic guilds. More efforts
should be made to develop thresholds-based reference points for achieving Good Environmental Status. There is also a need for international
collaborations to develop indicators that will facilitate management in marine ecosystems used by multiple countries.
Recommendations and guidelines for a common European food waste policy framework
Vittuari, Matteo ; Azzurro, Paolo ; Gaiani, Sivia ; Gheoldus, Manuela ; Burgos, Stephanie ; Aramyan, Lusine ; Valeeva, Natalia ; Rogers, David ; Östergren, Karin ; Timmermans, Toine ; Bos-Brouwers, Hilke - \ 2016
Bologna : FUSIONS - ISBN 9789462579590 - 75
Improving sustainability in coffee and cocoa
Rijn, Fédes ; Ingram, Verina ; Rogers, Andrew ; Nuijt, Jan Hugo - \ 2016
Den Haag : Wageningen Economic Research (Wageningen Economic Research rapport 2016-089) - 32
Framework for Designing Robust Supply Chains
Vlajic, J.V. ; Vorst, J.G.A.J. van der; Haijema, R. - \ 2016
In: Developments in Logistics and Supply Chain Management / Pawar, Kulwant S., Rogers, Helen, Potter, Andrew, Naim, Mohamed, Palgrave Macmillan - ISBN 9781349558483 - p. 13 - 26.
Today’s business environment and harsh competitiveness force companies and entire supply chains to increase their efficiency as much as possible. As a consequence, supply chains have become highly sensitive to disruptions and less tolerant to deviations in operations, that is, supply chains have become more vulnerable (see Kleindorfer and Saad, 2005). Vulnerability of supply chains may result in less consistent supply chain performances, and consequently, their competitive power in the market may diminish. In order to maintain stability of supply chain performances, it is necessary to design robust supply chains. Robust supply chains should be able to continue to function well in the event of a disruption as well as in the normal business environment (see Dong, 2006; Tang, 2006; Waters, 2007). Generally, robustness of the supply chain depends on its capability to respond adequately to different kinds of risks of disturbances. Recently, supply chain vulnerability and robustness has become a hot research topic, and as such, it is still in its infancy. With this paper, we aim to contribute to the existing knowledge in these areas.
Does low-energy sweetener consumption affect energy intake and body weight? A systematic review, including meta-analyses, of the evidence from human and animal studies
Rogers, P.J. ; Hogenkamp, P.S. ; Graaf, Kees de; Higgs, S. ; Lluch, A. ; Ness, A.R. ; Penfold, C. ; Perry, R. ; Putz, P. ; Yeomans, M.R. ; Mela, D.J. - \ 2016
International Journal of Obesity 40 (2016)3. - ISSN 0307-0565 - p. 381 - 394.

By reducing energy density, low-energy sweeteners (LES) might be expected to reduce energy intake (EI) and body weight (BW). To assess the totality of the evidence testing the null hypothesis that LES exposure (versus sugars or unsweetened alternatives) has no effect on EI or BW, we conducted a systematic review of relevant studies in animals and humans consuming LES with ad libitum access to food energy. In 62 of 90 animal studies exposure to LES did not affect or decreased BW. Of 28 reporting increased BW, 19 compared LES with glucose exposure using a specific 'learning' paradigm. Twelve prospective cohort studies in humans reported inconsistent associations between LES use and body mass index (-0.002 kg m - 2 per year, 95% confidence interval (CI) -0.009 to 0.005). Meta-analysis of short-term randomized controlled trials (129 comparisons) showed reduced total EI for LES versus sugar-sweetened food or beverage consumption before an ad libitum meal (-94 kcal, 95% CI -122 to -66), with no difference versus water (-2 kcal, 95% CI -30 to 26). This was consistent with EI results from sustained intervention randomized controlled trials (10 comparisons). Meta-analysis of sustained intervention randomized controlled trials (4 weeks to 40 months) showed that consumption of LES versus sugar led to relatively reduced BW (nine comparisons; -1.35 kg, 95% CI -2.28 to -0.42), and a similar relative reduction in BW versus water (three comparisons; -1.24 kg, 95% CI -2.22 to -0.26). Most animal studies did not mimic LES consumption by humans, and reverse causation may influence the results of prospective cohort studies. The preponderance of evidence from all human randomized controlled trials indicates that LES do not increase EI or BW, whether compared with caloric or non-caloric (for example, water) control conditions. Overall, the balance of evidence indicates that use of LES in place of sugar, in children and adults, leads to reduced EI and BW, and possibly also when compared with water.

Trends in marine climate change research in the Nordic region since the first IPCC report
Pedersen, M.W. ; Kokkalis, A. ; Bardarson, H. ; Bonanomi, S. ; Boonstra, W.J. ; Butler, W.E. ; Diekert, F.K. ; Fouzai, N. ; Holma, M. ; Holt, R.E. ; Kvile, K. ; Nieminen, E. ; Ottosen, K.M. ; Richter, A.P. ; Rogers, L.A. ; Romagnoni, G. ; Snickars, M. ; Tornroos, A. ; Weigel, B. ; Whittington, J.D. ; Yletyinen, J. ; Ferreira, A.S.A. - \ 2016
Climatic Change 134 (2016)1. - ISSN 0165-0009 - p. 147 - 161.
Oceans are exposed to anthropogenic climate change shifting marine systems toward potential instabilities. The physical, biological and social implications of such shifts can be assessed within individual scientific disciplines, but can only be fully understood by combining knowledge and expertise across disciplines. For climate change related problems these research directions have been well-established since the publication of the first IPCC report in 1990, however it is not well-documented to what extent these directions are reflected in published research. Focusing on the Nordic region, we evaluated the development of climate change related marine science by quantifying trends in number of publications, disciplinarity, and scientific focus of 1362 research articles published between 1990 and 2011. Our analysis showed a faster increase in publications within climate change related marine science than in general marine science indicating a growing prioritisation of research with a climate change focus. The composition of scientific disciplines producing climate change related publications, which initially was dominated by physical sciences, shifted toward a distribution with almost even representation of physical and biological sciences with social sciences constituting a minor constant proportion. These trends suggest that the predominantly model-based directions of the IPCC have favoured the more quantitatively oriented natural sciences rather than the qualitative traditions of social sciences. In addition, despite being an often declared prerequisite to successful climate science, we found surprisingly limited progress in implementing interdisciplinary research indicating that further initiatives nurturing scientific interactions are required.
Verification of Egg Farming Systems from the Netherlands and New Zealand Using Stable Isotopes
Rogers, Karyne M. ; Ruth, Saskia Van; Alewijn, Martin ; Philips, Andy ; Rogers, Pam - \ 2015
Journal of Agricultural and Food Chemistry 63 (2015)38. - ISSN 0021-8561 - p. 8372 - 8380.
authenticity - barn - carbon - diet - egg albumen - free range - isotope - Netherlands - New Zealand - nitrogen - organic - supermarket

Stable isotopes were used to develop authentication criteria of eggs laid under cage, barn, free range, and organic farming regimens from The Netherlands and New Zealand. A training set of commercial poultry feeds and egg albumen from 49 poultry farms across The Netherlands was used to determine the isotopic variability of organic and conventional feeds and to assess trophic effects of these corresponding feeds and barn, free range, and organic farming regimens on corresponding egg albumen. A further 52 brands of New Zealand eggs were sampled from supermarket shelves in 2008 (18), 2010 (30), and 2014 (4) to characterize and monitor changes in caged, barn, free range, and organic egg farming regimens. Stable carbon (δ13C) and nitrogen (δ15N) isotopes of 49 commercial poultry feeds and their corresponding egg albumens reveals that Dutch poultry are fed exclusively on a plant-based feed and that it is possible to discriminate between conventional and organic egg farming regimens in The Netherlands. Similarly, it is possible to discriminate between New Zealand organic and conventional egg farming regimens, although in the initial screening in 2008, results showed that some organic eggs had isotope values similar to those of conventional eggs, suggesting hens were not exclusively receiving an organic diet. Dutch and New Zealand egg regimens were shown to have a low isotopic correlation between both countries, because of different poultry feed compositions. In New Zealand, both conventional and organic egg whites have higher δ15N values than corresponding Dutch egg whites, due to the use of fishmeal or meat and bone meal (MBM), which is banned in European countries. This study suggests that stable isotopes (specifically nitrogen) show particular promise as a screening and authentication tool for organically farmed eggs. Criteria to assess truthfulness in labeling of organic eggs were developed, and we propose that Dutch organic egg whites should have a minimum δ15N value of 4.8‰ to account for an organic plant derived diet. Monitoring of New Zealand egg isotopes over the past 7 years suggests that organic eggs should have a minimum δ15N value of 6.0‰, and eggs falling below this value should be investigated further by certification authorities.

What are the major global threats and impacts in marine environments? Investigating the contours of a shared perception among marine scientists from the bottom-up
Boonstra, W.J. ; Ottosen, K.M. ; Ferreira, A.S.A. ; Richter, A.P. ; Rogers, L.A. ; Pedersen, M.W. ; Kokkalis, A. ; Bardarson, H. ; Bonanomi, S. ; Butler, W. ; Diekert, F.K. ; Fouzai, N. ; Holma, M. ; Holt, R.E. ; Kvile, K. ; Malanski, E. ; Macdonald, J.I. ; Nieminen, E. ; Romagnoni, G. ; Snickars, M. ; Weigel, B. ; Woods, P. ; Yletyinen, J. ; Whittington, J.D. - \ 2015
Marine Policy 60 (2015). - ISSN 0308-597X - p. 197 - 201.
Marine scientists broadly agree on which major processes influence the sustainability of marine environments worldwide. Recent studies argue that such shared perceptions crucially shape scientific agendas and are subject to a confirmation bias. Based on these findings a more explicit engagement with scientists’ (shared) perceptions of global change in marine environments is called for. This paper takes stock of the shared understanding in marine science of the most pertinent, worldwide threats and impacts that currently affect marine environments. Using results from an email survey among leading academics in marine science this article explores if a shared research agenda in relation to global change in marine environments exists. The analysis demonstrates that marine scientists across disciplines are largely in agreement on some common features of global marine change. Nevertheless, the analysis also highlights where natural and social scientists diverge in their assessment. The article ends discussing what these findings imply for further improvement of interdisciplinary marine science.
A step-wise process of decision-making under uncertainty when implementing environmental policy
Knights, A.M. ; Culhane, F. ; Hussain, S.S. ; Papadopoulou, K.N. ; Piet, G.J. ; Raakaer, J. ; Rogers, S.I. ; Robinson, L.A. - \ 2014
Environmental Science & Policy 39 (2014). - ISSN 1462-9011 - p. 56 - 64.
climate-change - north-atlantic - change impacts - management - systems - biodiversity - ecosystems - pressure - diversity - support
An ecosystem approach forms the basis of many recent environmental policies. The underlying concept states that decision-makers must consider the environmental, social and economic costs and benefits in the course of deciding whether to implement a management action. Decision-making can be undermined by uncertainty. Here, we discuss potential sources of uncertainty and their effect on an ecosystem approach-driven environmental policy, the factors affecting the choice and potential for management actions to achieve their objectives, the challenges associated with setting realistic and achievable targets, and how we can prioritise management of detrimental activities. We also consider how human challenges such as the availability of infrastructure and political will and ways of measuring costs and benefits and Member State interactions could also undermine environmental management. Potential limitations along with areas where further effort may be required to support ecosystem-based management objectives are highlighted and the advantages of a structured step-wise interdisciplinary approach to ecosystem management is shown. (C) 2014 Elsevier Ltd. All rights reserved.
Quantifying plate-cleaning using 'The Restaurant of the Future'
Hinton, E.C. ; Brunstrom, J.M. ; Fay, S.H. ; Wilkinson, L.L. ; Ferriday, D. ; Rogers, P.J. ; Wijk, R.A. de - \ 2013
Appetite 63 (2013). - ISSN 0195-6663 - p. 31 - 35.
affects energy-intake - normal-weight women - food photographs - digital photography - size - consumption - overweight - accuracy - behavior - density
Laboratory-based studies of human dietary behaviour benefit from highly controlled conditions; however, this approach can lack ecological validity. Identifying a reliable method to capture and quantify natural dietary behaviours represents an important challenge for researchers. In this study, we scrutinised cafeteria-style meals in the ‘Restaurant of the Future.’ Self-selected meals were weighed and photographed, both before and after consumption. Using standard portions of the same foods, these images were independently coded to produce accurate and reliable estimates of (i) initial self-served portions, and (ii) food remaining at the end of the meal. Plate cleaning was extremely common; in 86% of meals at least 90% of self-selected calories were consumed. Males ate a greater proportion of their self-selected meals than did females. Finally, when participants visited the restaurant more than once, the correspondence between selected portions was better predicted by the weight of the meal than by its energy content. These findings illustrate the potential benefits of meal photography in this context. However, they also highlight significant limitations, in particular, the need to exclude large amounts of data when one food obscures another.
Implementing Pollution Source Control—Learning from the Innovation Process in English and Welsh Water Companies
Spiller, M. ; McIntosh, B.S. ; Seaton, R.A.F. ; Jeffrey, P. - \ 2013
Water Resources Management 27 (2013)1. - ISSN 0920-4741 - p. 75 - 94.
cooperative agreements - perspective - management - systems
Improving the stimulation and management of innovation by water utilities is a key mechanism through which the challenges of securing sustainable water and wastewater services will be achieved. This paper describes the process of adopting source control interventions (SCIs) by water and sewerage companies (WaSCs) in England and Wales. SCIs can be defined as efforts by water suppliers to control agricultural pollution where it arises. To investigate differences in the extent to which SCIs have and are being adopted across all ten WaSCs in England and Wales, Rogers’ five stage innovation model is used to structure and interpret results from a series of semi-structured interviews with raw water quality and catchment management personnel. Results suggest that to promote SCI innovation by WaSCs, regulation should be designed in two interdependent ways. First, regulation must generate awareness of a performance gap so as to set an agenda for change and initiate innovation. This can be achieved either through direct regulation or regulation which raises the awareness of an organisations performance gap, for example through additional monitoring. Simultaneously, regulation needs to create possibilities for implementation of innovation through enabling WaSCs to utilise SCIs where appropriate. Evidence from the research suggests that appropriate intermediary organisations can assist in this process by providing a resource of relevant and local knowledge and data. Future research should seek to characterise the factors affecting each stage in the WaSC innovation process both to confirm the conclusions of this study and to reveal more detail about various influences on innovation outcomes.
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