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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Report on EU socio-ecological systems
Ripoll Bosch, R. ; Giampietro, M. ; Cabello, V. ; Cadillo Benalcazar, J. ; Kovacic, Z. ; Boer, I.J.M. de; Felice, L. Di; Krol, M.S. ; Matthews, K. ; Miller, D. ; Muscat, A. ; Olde, E.M. de; Renner, A. ; Serrano-Tovar, T. ; Verburg, C.C.A. ; Wardell-Johnson, D. - \ 2019
EU - 324 p.
The sustainability agenda builds on key components (i.e. food, water, energy, land use, climate and environment) that are inherently interconnected in a Nexus. MAGIC uses an innovative approach to test the robustness of narratives about the Nexus in Europe and focuses on the EU’ sustainable strategy. The aim of this deliverable is to operationalize and test a tool-kit to structure the quantitative analysis of the metabolic pattern of social-ecological systems in relation to their sustainability and the Nexus, at different levels of aggregation and spatial scales (EU, country or regional level). We use “quantitative story telling” as an alternative approach to use scientific information generated and better inform policy-makers. This deliverable builds on the methodological approach and the basic features of the theoretical framework of accounting called Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism (MuSIASEM). The application of the tool-kit in this deliverable has the only goal of illustrating the potentiality of the approach. In a series of chapters we i) present the theoretical background and features of the tool-kit used to characterize the state-of-the-play (diagnostic analysis) with regard to the sustainability of SES; ii) provide an overview of the results obtained in the analysis of 8 EU countries (i.e. France, Germany, Italy, Netherlands, Romania, Spain, Sweden and United Kingdom); iii) demonstrate the capability of the toolkit to perform the anlysis at diffrent scales (in this case, at a lower aggregated level -NUTS2-); and iv) highlight the methodological breakthrough provided by relational analysis and its relevance for policy making with regard to the water-energy-food-environment Nexus.
Cognitive and Affective Predictors of Illinois Residents’ Perceived Risks from Gray Wolves
Landon, A. ; Jacobs, M.H. ; Miller, C.A. ; Vaske, J.J. ; Williams, B. - \ 2019
Society & Natural Resources (2019). - ISSN 0894-1920 - 20 p.
Increasing wolf populations are a concern for wildlife managers inthe Midwestern U.S. Understanding the psychological mechanismsthat contribute to public perceptions of risk will enable developmentof strategies that seek to mitigate these risks, and suggest where outreach efforts may facilitate acceptance of wolves. We examined the psychological factors that influence Illinois residents’ perceived risks from wolves. We hypothesized that individuals’ perceived risks from wolves were a function of their attitudes toward wolves, negative affect toward wolves, and basic beliefs about wildlife. Data were obtained from a survey of the Illinois public (n¼784). Negative affect and attitudes toward wolves were direct predictors of perceived risks. Basic beliefs predicted attitudes and negative affect toward wolves. Negative affect predicted attitudes. Basic beliefs had direct and indirect effects on perceived risks.
Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe
Frantz, Laurent A.F. ; Haile, James ; Lin, Audrey T. ; Scheu, Amelie ; Geörg, Christina ; Benecke, Norbert ; Alexander, Michelle ; Linderholm, Anna ; Mullin, Victoria E. ; Daly, Kevin G. ; Battista, Vincent M. ; Price, Max ; Gron, Kurt J. ; Alexandri, Panoraia ; Arbogast, Rose Marie ; Arbuckle, Benjamin ; Bǎlǎşescu, Adrian ; Barnett, Ross ; Bartosiewicz, László ; Baryshnikov, Gennady ; Bonsall, Clive ; Borić, Dušan ; Boroneanţ, Adina ; Bulatović, Jelena ; Çakirlar, Canan ; Carretero, José Miguel ; Chapman, John ; Church, Mike ; Crooijmans, Richard ; Cupere, Bea De; Detry, Cleia ; Dimitrijevic, Vesna ; Dumitraşcu, Valentin ; Plessis, Louis Du; Edwards, Ceiridwen J. ; Erek, Cevdet Merih ; Erim-Özdoǧan, Asli ; Ervynck, Anton ; Fulgione, Domenico ; Gligor, Mihai ; Götherström, Anders ; Gourichon, Lionel ; Groenen, Martien A.M. ; Helmer, Daniel ; Hongo, Hitomi ; Horwitz, Liora K. ; Irving-Pease, Evan K. ; Lebrasseur, Ophélie ; Lesur, Joséphine ; Malone, Caroline ; Manaseryan, Ninna ; Marciniak, Arkadiusz ; Martlew, Holley ; Mashkour, Marjan ; Matthews, Roger ; Matuzeviciute, Giedre Motuzaite ; Maziar, Sepideh ; Meijaard, Erik ; McGovern, Tom ; Megens, Hendrik Jan ; Miller, Rebecca ; Mohaseb, Azadeh Fatemeh ; Orschiedt, Jörg ; Orton, David ; Papathanasiou, Anastasia ; Pearson, Mike Parker ; Pinhasi, Ron ; Radmanović, Darko ; Ricaut, François Xavier ; Richards, Mike ; Sabin, Richard ; Sarti, Lucia ; Schier, Wolfram ; Sheikhi, Shiva ; Stephan, Elisabeth ; Stewart, John R. ; Stoddart, Simon ; Tagliacozzo, Antonio ; Tasić, Nenad ; Trantalidou, Katerina ; Tresset, Anne ; Valdiosera, Cristina ; Hurk, Youri Van Den; Poucke, Sophie Van; Vigne, Jean Denis ; Yanevich, Alexander ; Zeeb-Lanz, Andrea ; Triantafyllidis, Alexandros ; Gilbert, M.T.P. ; Schibler, Jörg ; Rowley-Conwy, Peter ; Zeder, Melinda ; Peters, Joris ; Cucchi, Thomas ; Bradley, Daniel G. ; Dobney, Keith ; Burger, Joachim ; Evin, Allowen ; Girdland-Flink, Linus ; Larson, Greger - \ 2019
Proceedings of the National Academy of Sciences of the United States of America 116 (2019)35. - ISSN 0027-8424 - p. 17231 - 17238.
Domestication - Evolution - Gene flow - Neolithic

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

Biotransformation and bioactivation reactions – 2018 literature highlights
Khojasteh, S.C. ; Bumpus, Namandjé N. ; Driscoll, James P. ; Miller, Grover P. ; Mitra, Kaushik ; Rietjens, Ivonne M.C.M. ; Zhang, Donglu - \ 2019
Drug Metabolism Reviews 51 (2019)2. - ISSN 0360-2532 - p. 121 - 161.

In the past three decades, ADME sciences have become an integral component of the drug discovery and development process. At the same time, the field has continued to evolve, thus, requiring ADME scientists to be knowledgeable of and engage with diverse aspects of drug assessment: from pharmacology to toxicology, and from in silico modeling to in vitro models and finally in vivo models. Progress in this field requires deliberate exposure to different aspects of ADME; however, this task can seem daunting in the current age of mass information. We hope this review provides a focused and brief summary of a wide array of critical advances over the past year and explains the relevance of this research (Table 1). We divided the articles into categories of (1) drug optimization, (2) metabolites and drug metabolizing enzymes, and (3) bioactivation. This annual review is the fourth of its kind (Baillie et al. 2016; Khojasteh et al. 2017, 2018). We have followed the same format we used in previous years in terms of the selection of articles and the authoring of each section. This effort in itself also continues to evolve. I am pleased that Rietjens, Miller, and Mitra have again contributed to this annual review. We would like to welcome Namandjé N. Bumpus, James P. Driscoll, and Donglu Zhang as authors for this year’s issue. We strive to maintain a balance of authors from academic and industry settings. We would be pleased to hear your opinions of our commentary, and we extend an invitation to anyone who would like to contribute to a future edition of this review. Cyrus Khojasteh, on behalf of the authors.

Sub-diurnal variability of the carbon dioxide and water vapor isotopologues at the field observational scale
Vilà-Guerau de Arellano, Jordi ; Koren, Gerbrand ; Ouwersloot, Huug G. ; Velde, Ivar van der; Röckmann, Thomas ; Miller, John B. - \ 2019
Agricultural and Forest Meteorology 275 (2019). - ISSN 0168-1923 - p. 114 - 135.
Boundary-layer dynamics - CO - Coupled soil-vegetation-atmosphere model - HO - Harvard Forest observations - Stable isotopologues - Sub-diurnal variability

We investigated the sub-diurnal variability of the carbon dioxide and water vapour isotopologues by modelling a representative case measured above the Harvard Forest. To this end, we developed a model that couples the local processes governed by soil and vegetation conditions to non-local atmospheric processes such as entrainment and long-range advection. The model formulation is based on solving the stable isotopologues 12CO2, 13CO2, C18OO, H2 16O and H2 18O as conserved variables. It also includes simultaneously solving the meteorological state variables coupled with their respective surface fluxes. Our model results indicate the need for a comprehensive observational data-set to ensure that the essential processes and interactions between the boundary-layer dynamics of a forest and the atmospheric boundary layer are satisfactorily reproduced. We present and discuss the temporal evolution of the budgets of 13CO2 and C18OO, in order to quantify the individual contributions made by soil, plant and entrainment dynamics. All these contributions turn out to be relevant, as they enable us to quantify how the energy, water and carbon fluxes on sub-daily scales are partitioned. Regarding the role played by entrainment, we carried out a set of three systematic experiments in which air, with different CO2 and H2O isotopic compositions originating in the residual layer, mix with the boundary-layer air. Our findings show that both the C18OO and H2 18O isotopic ratios and their respective isofluxes are influenced by the entrainment event. This result indicates that high frequency and accurate isotopologues surface measurements (seconds or minutes)can be used to quantify how non-local atmospheric processes modify isotopic composition at sub-daily scales.

Methane budget estimates in Finland from the CarbonTracker Europe-CH4 data assimilation system
Tsuruta, Aki ; Aalto, Tuula ; Backman, Leif ; Krol, Maarten C. ; Peters, Wouter ; Lienert, Sebastian ; Joos, Fortunat ; Miller, Paul A. ; Zhang, Wenxin ; Laurila, Tuomas ; Hatakka, Juha ; Leskinen, Ari ; Lehtinen, Kari E.J. ; Peltola, Olli ; Vesala, Timo ; Levula, Janne ; Dlugokencky, Ed ; Heimann, Martin ; Kozlova, Elena ; Aurela, Mika ; Lohila, Annalea ; Kauhaniemi, Mari ; Gomez-Pelaez, Angel J. - \ 2019
Tellus Series B: Chemical and Physical Meteorology (2019). - ISSN 0280-6509 - 21 p.
atmospheric CH - CH flux - data assimilation - Finland - flux estimation

We estimated the CH4 budget in Finland for 2004–2014 using the CTE-CH4 data assimilation system with an extended atmospheric CH4 observation network of seven sites from Finland to surrounding regions (Hyytiälä, Kjølnes, Kumpula, Pallas, Puijo, Sodankylä, and Utö). The estimated average annual total emission for Finland is 0.6 ± 0.5 Tg CH4 yr−1. Sensitivity experiments show that the posterior biospheric emission estimates for Finland are between 0.3 and 0.9 Tg CH4 yr−1, which lies between the LPX-Bern-DYPTOP (0.2 Tg CH4 yr−1) and LPJG-WHyMe (2.2 Tg CH4 yr−1) process-based model estimates. For anthropogenic emissions, we found that the EDGAR v4.2 FT2010 inventory (0.4 Tg CH4 yr−1) is likely to overestimate emissions in southernmost Finland, but the extent of overestimation and possible relocation of emissions are difficult to derive from the current observation network. The posterior emission estimates were especially reliant on prior information in central Finland. However, based on analysis of posterior atmospheric CH4, we found that the anthropogenic emission distribution based on a national inventory is more reliable than the one based on EDGAR v4.2 FT2010. The contribution of total emissions in Finland to global total emissions is only about 0.13%, and the derived total emissions in Finland showed no trend during 2004–2014. The model using optimized emissions was able to reproduce observed atmospheric CH4 at the sites in Finland and surrounding regions fairly well (correlation > 0.75, bias < ± ppb), supporting adequacy of the observations to be used in atmospheric inversion studies. In addition to global budget estimates, we found that CTE-CH4 is also applicable for regional budget estimates, where small scale (1x1 in this case) optimization is possible with a dense observation network.

The Glycaemic Index-Food-Frequency Questionnaire: Development and Validation of a Food Frequency Questionnaire Designed to Estimate the Dietary Intake of Glycaemic Index and Glycaemic Load : An Effort by the PREVIEW Consortium
Brouwer, E.M. ; Berendsen, A.M. ; Sluik, D. ; Wiel, A.M. van de; Raben, Anne ; Vries, J.H.M. de; Brand-Miller, Jennie ; Feskens, E.J.M. - \ 2019
Nutrients 11 (2019)1. - ISSN 2072-6643
Dietary glycaemic index (GI) and glycaemic load (GL) are indices used to quantify the effect of carbohydrate quality and quantity on postprandial glycaemia. GI/GL-health associations are widely studied but data on the validity of integrated GI/GL measurements are scarce. We evaluated the performance of a food-frequency questionnaire (FFQ) specifically developed to assess GI/GL. In total, 263 Dutch men and 212 women (aged 55 ± 11 years) completed a 58-item GI-FFQ, an 183-item general-FFQ and a 2-day 24 h-recall and donated blood for glycated haemoglobin (HbA1c) determination. The level of agreement between these methods was evaluated by (1) cross-classification, (2) correlations and (3) Bland and Altman plots. The three dietary assessment methods provided comparable mean intake estimates for total carbohydrates (range: 214–237 g/day), mono/disaccharides (100–107 g/day), polysaccharides (114–132 g/day), as well as bread, breakfast cereals, potatoes, pasta, rice, fruit, dairy, cakes/cookies and sweets. Mean (±SD) GI estimates were also comparable between the GI-FFQ (54 ± 3), general-FFQ (53 ± 4) and 24 h-recalls (53 ± 5). Mean (±SD) GI-FFQ GL (117 ± 37) was slightly lower than the general-FFQ GL (126 ± 38) and 24 h-recalls GL (127 ± 37). Classification of GI in quartiles was identical for the GI-FFQ and general-FFQ for 43% of the population (r = 0.58) and with 24 h-recalls for 35% of the population (de-attenuated r = 0.64). For GL, this was 48% (r = 0.65) and 44% (de-attenuated r = 0.74). Correlations between GI and HbA1c were low (r = −0.09 for GI-FFQ, r = −0.04 for general-FFQ and r = 0.07 for 24 h-recalls). In conclusion, compared to a general-FFQ and 24 h-recalls, the GI-FFQ showed a moderate to good relative validity for carbohydrates, carbohydrate-rich foods and GI/GL. No metric predicted HbA1c.
Embracing 3D Complexity in Leaf Carbon–Water Exchange
Earles, J.M. ; Buckley, Thomas N. ; Brodersen, Craig R. ; Busch, Florian A. ; Cano, F.J. ; Choat, Brendan ; Evans, John R. ; Farquhar, Graham D. ; Harwood, Richard ; Huynh, Minh ; John, Grace P. ; Miller, Megan L. ; Rockwell, Fulton E. ; Sack, Lawren ; Scoffoni, Christine ; Struik, Paul C. ; Wu, Alex ; Yin, Xinyou ; Barbour, Margaret M. - \ 2019
Trends in Plant Science 24 (2019)1. - ISSN 1360-1385 - p. 15 - 24.
3D - leaf anatomy - leaf hydraulic conductance - mesophyll conductance - photosynthesis

Leaves are a nexus for the exchange of water, carbon, and energy between terrestrial plants and the atmosphere. Research in recent decades has highlighted the critical importance of the underlying biophysical and anatomical determinants of CO2 and H2O transport, but a quantitative understanding of how detailed 3D leaf anatomy mediates within-leaf transport has been hindered by the lack of a consensus framework for analyzing or simulating transport and its spatial and temporal dynamics realistically, and by the difficulty of measuring within-leaf transport at the appropriate scales. We discuss how recent technological advancements now make a spatially explicit 3D leaf analysis possible, through new imaging and modeling tools that will allow us to address long-standing questions related to plant carbon–water exchange.

Biomarkers of Nutrition for Development (BOND): Vitamin B-12 Review
Allen, L.H. ; Miller, J. ; Groot, C.P.G.M. de; Rosenberg, I.H. ; Smith, A.D. ; Refsum, H. ; Raiten, D.J. - \ 2018
The Journal of Nutrition 148 (2018)suppl. 4. - ISSN 0022-3166 - p. 1995S - 2027S.
This report on vitamin B-12 (B12) is part of the Biomarkers of Nutrition for Development (BOND) Project, which provides state-of-the art information and advice on the selection, use, and interpretation of biomarkers of nutrient exposure, status, and function. As with the other 5 reports in this series, which focused on iodine, folate, zinc, iron, and vitamin A, this B12 report was developed with the assistance of an expert panel (BOND B12 EP) and other experts who provided information during a consultation. The experts reviewed the existing literature in depth in order to consolidate existing relevant information on the biology of B12, including known and possible effects of insufficiency, and available and potential biomarkers of status. Unlike the situation for the other 5 nutrients reviewed during the BOND project, there has been relatively little previous attention paid to B12 status and its biomarkers, so this report is a landmark in terms of the consolidation and interpretation of the available information on B12 nutrition. Historically, most focus has been on diagnosis and treatment of clinical symptoms of B12 deficiency, which result primarily from pernicious anemia or strict vegetarianism. More recently, we have become aware of the high prevalence of B12 insufficiency in populations consuming low amounts of animal-source foods, which can be detected with ≥1 serum biomarker but presents the new challenge of identifying functional consequences that may require public health interventions.
Cognitive and affective predictors of risks from wolves
Landon, A. ; Miller, C. ; Vaske, J.J. ; Jacobs, M.H. ; Williams, B. - \ 2018
Cognitive and affective predictors of risks from wolves
Landon, A. ; Miller, C. ; Vaske, J.J. ; Jacobs, M.H. - \ 2018
Biotransformation and bioactivation reactions – 2017 literature highlights
Khojasteh, S.C. ; Miller, Grover P. ; Mitra, Kaushik ; Rietjens, Ivonne M.C.M. - \ 2018
Drug Metabolism Reviews 50 (2018)3. - ISSN 0360-2532 - p. 221 - 255.

This annual review is the third one to highlight recent advances in the study and assessment of biotransformations and bioactivations (Table 1). We followed the same format as the previous years with selection and authoring each section (see Baillie et al. 2016; Khojasteh et al. 2017). We acknowledge that many universities no longer train students in mechanistic biotransformation studies reflecting a decline in the investment for those efforts by public funded granting institutions. We hope this work serves as a resource to appreciate the knowledge gained each year to understand and hopefully anticipate toxicological outcomes dependent on biotransformations and bioactivations. This effort itself also continues to evolve. I am pleased that Drs. Rietjens and Miller have again contributed to this annual review. We would like to welcome Kaushik Mitra as an author for this year’s issue, and we thank Deepak Dalvie for his contributions to last year’s edition. We have intentionally maintained a balance of authors such that two come from an academic setting and two come from industry. As always, please drop us a note if you find this review helpful. We would be pleased to hear your opinions of our commentary, and we extend an invitation to anyone who would like to contribute to a future edition of this review.

PREVIEW study—Influence of a behavior modification intervention (PREMIT) in over 2300 people with pre-diabetes : Intention, self-efficacy and outcome expectancies during the early phase of a lifestyle intervention
Huttunen-Lenz, Maija ; Hansen, Sylvia ; Christensen, Pia ; Larsen, Thomas Meinert ; Sandø-Pedersen, Finn ; Drummen, Mathijs ; Adam, Tanja C. ; Macdonald, Ian A. ; Taylor, Moira A. ; Martinez, J.A. ; Navas-Carretero, Santiago ; Handjiev, Svetoslav ; Poppitt, Sally D. ; Silvestre, Marta P. ; Fogelholm, Mikael ; Pietiläinen, Kirsi H. ; Brand-Miller, Jennie ; Berendsen, Agnes A.M. ; Raben, Anne ; Schlicht, Wolfgang - \ 2018
Psychology Research and Behavior Management 11 (2018). - ISSN 1179-1578 - p. 383 - 394.
Cognition - Diabetes mellitus - Goals - Habits - Weight loss

Purpose: Onset of type 2 diabetes (T2D) is often gradual and preceded by impaired glucose homeostasis. Lifestyle interventions including weight loss and physical activity may reduce the risk of developing T2D, but adherence to a lifestyle change is challenging. As part of an international T2D prevention trial (PREVIEW), a behavior change intervention supported participants in achieving a healthier diet and physically active lifestyle. Here, our aim was to explore the influence of this behavioral program (PREMIT) on social-cognitive variables during an 8-week weight loss phase. Methods: PREVIEW consisted of an initial weight loss, Phase I, followed by a weight-maintenance, Phase II, for those achieving the 8-week weight loss target of ≥ 8% from initial bodyweight. Overweight and obese (BMI ≥25 kg/m2) individuals aged 25 to 70 years with confirmed pre-diabetes were enrolled. Uni-and multivariate statistical methods were deployed to explore differences in intentions, self-efficacy, and outcome expectancies between those who achieved the target weight loss (“achievers”) and those who did not (“non-achievers”). Results: At the beginning of Phase I, no significant differences in intentions, self-efficacy and outcome expectancies between “achievers” (1,857) and “non-achievers” (163) were found. “Non-achievers” tended to be younger, live with child/ren, and attended the PREMIT sessions less frequently. At the end of Phase I, “achievers” reported higher intentions (healthy eating χ2 (1)=2.57; P <0.008, exercising χ2 (1)=0.66; P <0.008), self-efficacy (F(2; 1970)=10.27, P <0.005), and were more positive about the expected outcomes (F(4; 1968)=11.22, P <0.005). Conclusion: Although statistically significant, effect sizes observed between the two groups were small. Behavior change, however, is multi-determined. Over a period of time, even small differences may make a cumulative effect. Being successful in behavior change requires that the “new” behavior is implemented time after time until it becomes a habit. Therefore, having even slightly higher self-efficacy, positive outcome expectancies and intentions may over time result in considerably improved chances to achieve long-term lifestyle changes.

Tropical land carbon cycle responses to 2015/16 El Niño as recorded by atmospheric greenhouse gas and remote sensing data
Gloor, Emanuel ; Wilson, Chris ; Chipperfield, Martyn P. ; Chevallier, Frederic ; Buermann, Wolfgang ; Boesch, Hartmut ; Parker, Robert ; Somkuti, Peter ; Gatti, Luciana V. ; Correia, Caio ; Domingues, Lucas G. ; Peters, Wouter ; Miller, John ; Deeter, Merritt N. ; Sullivan, Martin J.P. - \ 2018
Philosophical Transactions of the Royal Society B. Biological sciences 373 (2018)1760. - ISSN 0962-8436 - 12 p.
carbon cycle - fire - global warming - tropical forests

The outstanding tropical land climate characteristic over the past decades is rapid warming, with no significant large-scale precipitation trends. This warming is expected to continue but the effects on tropical vegetation are unknown. El Niño-related heat peaks may provide a test bed for a future hotter world. Here we analyse tropical land carbon cycle responses to the 2015/16 El Niño heat and drought anomalies using an atmospheric transport inversion. Based on the global atmospheric CO2 and fossil fuel emission records, we find no obvious signs of anomalously large carbon release compared with earlier El Niño events, suggesting resilience of tropical vegetation. We find roughly equal net carbon release anomalies from Amazonia and tropical Africa, approximately 0.5 PgC each, and smaller carbon release anomalies from tropical East Asia and southern Africa. Atmospheric CO anomalies reveal substantial fire carbon release from tropical East Asia peaking in October 2015 while fires contribute only a minor amount to the Amazonian carbon flux anomaly. Anomalously large Amazonian carbon flux release is consistent with downregulation of primary productivity during peak negative near-surface water anomaly (October 2015 to March 2016) as diagnosed by solar-induced fluorescence. Finally, we find an unexpected anomalous positive flux to the atmosphere from tropical Africa early in 2016, coincident with substantial CO release.This article is part of a discussion meeting issue 'The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications'.

Understanding social innovation for the well-being of forest-dependent communities : A preliminary theoretical framework
Kluvánková, Tatiana ; Brnkaľáková, Stanislava ; Špaček, Martin ; Slee, Bill ; Nijnik, Maria ; Valero, Diana ; Miller, David ; Bryce, Rosalind ; Kozová, Mária ; Polman, Nico ; Szabo, Tomáš ; Gežík, Veronika - \ 2018
Forest Policy and Economics 97 (2018). - ISSN 1389-9341 - p. 163 - 174.
Forest-dependent community - SIMRA transdisciplinary framework - Social innovation - Social innovation factors
Demographic and Social-Cognitive Factors Associated with Weight Loss in Overweight, Pre-diabetic Participants of the PREVIEW Study
Hansen, Sylvia ; Huttunen-Lenz, Maija ; Sluik, Diewertje ; Brand-Miller, Jennie ; Drummen, Mathijs ; Fogelholm, Mikael ; Handjieva-Darlenska, Teodora ; Macdonald, Ian ; Martinez, Alfredo J. ; Larsen, Thomas Meinert ; Poppitt, Sally ; Raben, Anne ; Schlicht, Wolfgang - \ 2018
International Journal of Behavioral Medicine 25 (2018)6. - ISSN 1070-5503 - p. 682 - 692.
Behavioral determination - Lifestyle intervention - Social-cognitive factors - Weight loss

Purpose: Weight loss has been demonstrated to be a successful strategy in diabetes prevention. Although weight loss is greatly influenced by dietary behaviors, social-cognitive factors play an important role in behavioral determination. This study aimed to identify demographic and social-cognitive factors (intention, self-efficacy, outcome expectancies, social support, and motivation with regard to dietary behavior and goal adjustment) associated with weight loss in overweight and obese participants from the PREVIEW study who had pre-diabetes. Method: Prospective correlational data from 1973 adult participants were analyzed. The participants completed psychological questionnaires that assessed social-cognitive variables with regard to dietary behavior. Stepwise multiple regression analyses were performed to identify baseline demographic and social-cognitive factors associated with weight loss. Results: Overall, being male, having a higher baseline BMI, having a higher income, perceiving fewer disadvantages of a healthy diet (outcome expectancies), experiencing less discouragement for healthy eating by family and friends (social support), and lower education were independently linked to greater weight loss. When evaluating females and males separately, education was no longer associated with weight loss. Conclusion: The results indicate that a supportive environment in which family members and friends avoid discouraging healthy eating, with the application of a strategy that uses specific behavior change techniques to emphasize the benefits of outcomes, i.e., the benefits of a healthy diet, may support weight loss efforts. Weight loss programs should therefore always address the social environment of persons who try to lose body weight because family members and friends can be important supporters in reaching a weight loss goal.

CTDAS-Lagrange v1.0 : A high-resolution data assimilation system for regional carbon dioxide observations
He, Wei ; Velde, Ivar R. van der; Andrews, Arlyn E. ; Sweeney, Colm ; Miller, John ; Tans, Pieter ; Laan-Luijkx, Ingrid T. van der; Nehrkorn, Thomas ; Mountain, Marikate ; Ju, Weimin ; Peters, Wouter ; Chen, Huilin - \ 2018
Geoscientific Model Development 11 (2018)8. - ISSN 1991-959X - p. 3515 - 3536.

We have implemented a regional carbon dioxide data assimilation system based on the CarbonTracker Data Assimilation Shell (CTDAS) and a high-resolution Lagrangian transport model, the Stochastic Time-Inverted Lagrangian Transport model driven by the Weather Forecast and Research meteorological fields (WRF-STILT). With this system, named CTDAS-Lagrange, we simultaneously optimize terrestrial biosphere fluxes and four parameters that adjust the lateral boundary conditions (BCs) against CO2 observations from the NOAA ESRL North America tall tower and aircraft programmable flask packages (PFPs) sampling program. Least-squares optimization is performed with a time-stepping ensemble Kalman smoother, over a time window of 10 days and assimilating sequentially a time series of observations. Because the WRF-STILT footprints are pre-computed, it is computationally efficient to run the CTDAS-Lagrange system. To estimate the uncertainties in the optimized fluxes from the system, we performed sensitivity tests with various a priori biosphere fluxes (SiBCASA, SiB3, CT2013B) and BCs (optimized mole fraction fields from CT2013B and CTE2014, and an empirical dataset derived from aircraft observations), as well as with a variety of choices on the ways that fluxes are adjusted (additive or multiplicative), covariance length scales, biosphere flux covariances, BC parameter uncertainties, and model-data mismatches. In pseudo-data experiments, we show that in our implementation the additive flux adjustment method is more flexible in optimizing net ecosystem exchange (NEE) than the multiplicative flux adjustment method, and our sensitivity tests with real observations show that the CTDAS-Lagrange system has the ability to correct for the potential biases in the lateral BCs and to resolve large biases in the prior biosphere fluxes. Using real observations, we have derived a range of estimates for the optimized carbon fluxes from a series of sensitivity tests, which places the North American carbon sink for the year 2010 in a range from -0.92 to -1.26PgCyr-1. This is comparable to the TM5-based estimates of CarbonTracker (version CT2016, -0.91±1.10PgCyr-1) and CarbonTracker Europe (version CTE2016, -0.91±0.31PgCyr-1). We conclude that CTDAS-Lagrange can offer a versatile and computationally attractive alternative to these global systems for regional estimates of carbon fluxes, which can take advantage of high-resolution Lagrangian footprints that are increasingly easy to obtain.

Increased water-use efficiency and reduced CO2 uptake by plants during droughts at a continental scale
Peters, W. ; Velde, I.R. van der; Schaik, Erik van; Miller, John B. ; Ciais, Philippe ; Duarte, Henrique F. ; Laan-Luijkx, I.T. van der; Molen, M.K. van der; Scholze, M. ; Schaefer, Kevin ; Vidale, Pier Luigi ; Verhoef, Anne ; Wårlind, D. ; Zhu, Dan ; Tans, Pieter P. ; Vaughn, Bruce ; White, James W.C. - \ 2018
Nature Geoscience 11 (2018). - ISSN 1752-0894 - p. 744 - 748.
Severe droughts in the Northern Hemisphere cause a widespread decline of agricultural yield, the reduction of forest carbon uptake, and increased CO2 growth rates in the atmosphere. Plants respond to droughts by partially closing their stomata to limit their evaporative water loss, at the expense of carbon uptake by photosynthesis. This trade-off maximizes their water-use efficiency (WUE), as measured for many individual plants under laboratory conditions and field experiments. Here we analyse the 13C/12C stable isotope ratio in atmospheric CO2 to provide new observational evidence of the impact of droughts on the WUE across areas of millions of square kilometres and spanning one decade of recent climate variability. We find strong and spatially coherent increases in WUE along with widespread reductions of net carbon uptake over the Northern Hemisphere during severe droughts that affected Europe, Russia and the United States in 2001–2011. The impact of those droughts on WUE and carbon uptake by vegetation is substantially larger than simulated by the land-surface schemes of six state-of-the-art climate models. This suggests that drought-induced carbon–climate feedbacks may be too small in these models and improvements to their vegetation dynamics using stable isotope observations can help to improve their drought response.
The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera
Linard, Benjamin ; Crampton-Platt, Alex ; Moriniere, Jerome ; Timmermans, Martijn J.T.N. ; Andújar, Carmelo ; Arribas, Paula ; Miller, Kirsten E. ; Lipecki, Julia ; Favreau, Emeline ; Hunter, Amie ; Gómez-Rodríguez, Carola ; Barton, Christopher ; Nie, Ruie ; Gillett, Conrad P.D.T. ; Breeschoten, Thijmen ; Bocak, Ladislav ; Vogler, Alfried P. - \ 2018
Molecular Phylogenetics and Evolution 128 (2018). - ISSN 1055-7903 - p. 1 - 11.
Biodiversity discovery - Coleoptera - Mass-trapped samples - Metagenome skimming - Mitochondrial metagenomics

A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16,000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.

The Ozone Monitoring Instrument : Overview of 14 years in space
Levelt, Pieternel F. ; Joiner, Joanna ; Tamminen, Johanna ; Veefkind, J.P. ; Bhartia, Pawan K. ; Zweers, Deborah C.S. ; Duncan, Bryan N. ; Streets, David G. ; Eskes, Henk ; Der, Ronald A. Van; McLinden, Chris ; Fioletov, Vitali ; Carn, Simon ; Laat, Jos De; Deland, Matthew ; Marchenko, Sergey ; McPeters, Richard ; Ziemke, Jerald ; Fu, Dejian ; Liu, Xiong ; Pickering, Kenneth ; Apituley, Arnoud ; Abad, Gonzalo González ; Arola, Antti ; Boersma, Folkert ; Miller, Christopher Chan ; Chance, Kelly ; Graaf, Martin De; Hakkarainen, Janne ; Hassinen, Seppo ; Ialongo, Iolanda ; Kleipool, Quintus ; Krotkov, Nickolay ; Li, Can ; Lamsal, Lok ; Newman, Paul ; Nowlan, Caroline ; Suleiman, Raid ; Tilstra, Lieuwe Gijsbert ; Torres, Omar ; Wang, Huiqun ; Wargan, Krzysztof - \ 2018
Atmospheric Chemistry and Physics 18 (2018)8. - ISSN 1680-7316 - p. 5699 - 5745.
This overview paper highlights the successes of the Ozone Monitoring Instrument (OMI) on board the Aura satellite spanning a period of nearly 14 years. Data from OMI has been used in a wide range of applications and research resulting in many new findings. Due to its unprecedented spatial resolution, in combination with daily global coverage, OMI plays a unique role in measuring trace gases important for the ozone layer, air quality, and climate change. With the operational very fast delivery (VFD; direct readout) and near real-time (NRT) availability of the data, OMI also plays an important role in the development of operational services in the atmospheric chemistry domain.
Objectively measured physical activity and sedentary time are associated with cardiometabolic risk factors in adults with prediabetes : The PREVIEW study
Swindell, Nils ; Mackintosh, Kelly ; Mcnarry, Melitta ; Stephens, Jeffrey W. ; Sluik, Diewertje ; Fogelholm, Mikael ; Drummen, Mathijs ; Macdonald, Ian ; Martinez, J.A. ; Handjieva-Darlenska, Teodora ; Poppitt, Sally D. ; Brand-Miller, Jennie ; Larsen, Thomas M. ; Raben, Anne ; Stratton, Gareth - \ 2018
Diabetes Care 41 (2018)3. - ISSN 0149-5992 - p. 562 - 569.
OBJECTIVE The aim of the present cross-sectional study was to examine the association among physical activity (PA), sedentary time (ST), and cardiometabolic risk in adults with prediabetes. RESEARCH DESIGN AND METHODS Participants (n = 2,326; 25-70 years old, 67% female) from eight countries, with a BMI >25 kg · m22 and impaired fasting glucose (5.6-6.9 mmol · L21) or impaired glucose tolerance (7.8-11.0 mmol · L21 at 2 h), participated. Seven-day accelerometry objectively assessed PA levels and ST. RESULTS Multiple linear regression revealed that moderate-To-vigorous PA (MVPA) was negatively associated withHOMAof insulin resistance (HOMA-IR) (standardizedb =20.078 [95% CI20.128,20.027]), waist circumference (WC) (b =20.177 [20.122,20.134]), fasting insulin (b = 20.115 [20.158, 20.072]), 2-h glucose (b = 20.069 [20.112, 20.025]), triglycerides (b = 20.091 [20.138, 20.044]), and CRP (b = 20.086 [20.127, 20.045]). ST was positively associated with HOMA-IR (b = 0.175 [0.114, 0.236]), WC (b = 0.215 [0.026, 0.131]), fasting insulin (b = 0.155 [0.092, 0.219]), triglycerides (b = 0.106 [0.052, 0.16]), CRP (b = 0.106 [0.39, 0.172]), systolic blood pressure (BP) (b = 0.078 [0.026, 0.131]), and diastolic BP (b = 0.106 [0.39, 20.172]). Associations reported between total PA (counts · min21), and all risk factors were comparable or stronger than for MVPA: HOMA-IR (b = 20.151 [20.194, 20.107]), WC (b = 20.179 [20.224, 20.134]), fasting insulin (b = 20.139 [20.183, 20.096]), 2-h glucose (b = 20.088 [20.131, 20.045]), triglycerides (b = 20.117 [20.162, 20.071]), and CRP (b = 20.104 [20.146, 20.062]). CONCLUSIONS In adults with prediabetes, objectively measured PA and ST were associated with cardiometabolic risk markers. Total PA was at least as strongly associated with cardiometabolic risk markers as MVPA, which may imply that the accumulation of total PA over the day is as important as achieving the intensity of MVPA.
The CarbonTracker Data Assimilation System for CO2 and δ13C (CTDAS-C13 v1.0) : Retrieving information on land-atmosphere exchange processes
Velde, Ivar R. Van Der; Miller, John B. ; Molen, Michiel K. Van Der; Tans, Pieter P. ; Vaughn, Bruce H. ; White, James W.C. ; Schaefer, Kevin ; Peters, Wouter - \ 2018
Geoscientific Model Development 11 (2018)1. - ISSN 1991-959X - p. 283 - 304.
To improve our understanding of the global carbon balance and its representation in terrestrial biosphere models, we present here a first dual-species application of the CarbonTracker Data Assimilation System (CTDAS). The system's modular design allows for assimilating multiple atmospheric trace gases simultaneously to infer exchange fluxes at the Earth surface. In the prototype discussed here, we interpret signals recorded in observed carbon dioxide (CO2) along with observed ratios of its stable isotopologues 13CO2/12CO2 (δ13C). The latter is in particular a valuable tracer to untangle CO2 exchange from land and oceans. Potentially, it can also be used as a proxy for continent-wide drought stress in plants, largely because the ratio of 13CO2 and 12CO2 molecules removed from the atmosphere by plants is dependent on moisture conditions. The dual-species CTDAS system varies the net exchange fluxes of both 13CO2 and CO2 in ocean and terrestrial biosphere models to create an ensemble of 13CO2 and CO2 fluxes that propagates through an atmospheric transport model. Based on differences between observed and simulated 13CO2 and CO2 mole fractions (and thus δ13C) our Bayesian minimization approach solves for weekly adjustments to both net fluxes and isotopic terrestrial discrimination that minimizes the difference between observed and estimated mole fractions. With this system, we are able to estimate changes in terrestrial δ13C exchange on seasonal and continental scales in the Northern Hemisphere where the observational network is most dense. Our results indicate a decrease in stomatal conductance on a continent-wide scale during a severe drought. These changes could only be detected after applying combined atmospheric CO2 and δ13C constraints as done in this work. The additional constraints on surface CO2 exchange from δ13C observations neither affected the estimated carbon fluxes nor compromised our ability to match observed CO2 variations. The prototype presented here can be of great benefit not only to study the global carbon balance but also to potentially function as a data-driven diagnostic to assess multiple leaf-level exchange parameterizations in carbon-climate models that influence the CO2, water, isotope, and energy balance.
The sustainable seafood movement is a Governance concert, with the audience playing a key role
Barclay, Kate ; Miller, Alice - \ 2018
Sustainability 10 (2018)1. - ISSN 2071-1050
Corporate social responsibility - Ecolabels - Ethical consumption - Green marketing - Supply chain management - Sustainable seafood
Private standards, including ecolabels, have been posed as a governance solution for the global fisheries crisis. The conventional logic is that ecolabels meet consumer demand for certified "sustainable" seafood, with "good" players rewarded with price premiums or market share and "bad" players punished by reduced sales. Empirically, however, in the markets where ecolabeling has taken hold, retailers and brands-rather than consumers-are demanding sustainable sourcing, to build and protect their reputation. The aim of this paper is to devise a more accurate logic for understanding the sustainable seafood movement, using a qualitative literature review and reflection on our previous research. We find that replacing the consumer-driven logic with a retailer/brand-driven logic does not go far enough in making research into the sustainable seafood movement more useful. Governance is a "concert" and cannot be adequately explained through individual actor groups. We propose a new logic going beyond consumer- or retailer/brand-driven models, and call on researchers to build on the partial pictures given by studies on prices and willingness-to-pay, investigating more fully the motivations of actors in the sustainable seafood movement, and considering audience beyond the direct consumption of the product in question.
Global, regional, and national burden of neurological disorders during 1990–2015: a systematic analysis for the Global Burden of Disease Study 2015
Feigin, V.L. ; Krishnamurthi, R.V. ; Theadom, A.M. ; Abajobir, A.A. ; Mishra, S.R. ; Ahmed, M.B. ; Abate, K.H. ; Mengistie, M.A. ; Wakayo, T. ; Abd-Allah, F. ; Abdulle, A.M. ; Abera, S.F. ; Mohammed, K.E. ; Abyu, G.Y. ; Asgedom, S.W. ; Atey, T.M. ; Betsu, B.D. ; Mezgebe, H.B. ; Tuem, K.B. ; Woldu, M.A. ; Aichour, A.N. ; Aichour, I. ; Aichour, M.T. ; Akinyemi, R.O. ; Alabed, S. ; Al-Raddadi, R. ; Alvis-Guzman, N. ; Amare, A.T. ; Ansari, H. ; Anwari, P. ; Ärnlöv, J. ; Fereshtehnejad, S. ; Weiderpass, E. ; Havmoeller, R. ; Asayesh, H. ; Avila-Burgos, L. ; Avokpaho, E.F.G.A. ; Afrique, L.E.R.A.S. ; Azarpazhooh, M.R. ; Barac, A. ; Barboza, M. ; Barker-Collo, S.L. ; Bärnighausen, T. ; Farvid, M.S. ; Mohammed, S. ; Bedi, N. ; Beghi, E. ; Giussani, G. ; Bennett, D.A. ; Hay, S.I. ; Goulart, A.C. ; Santos, I.S. ; Bensenor, I.M. ; Lotufo, P.A. ; Berhane, A. ; Jeemon, P. ; Bhaumik, S. ; Dandona, L. ; Dandona, R. ; Kumar, G.A. ; Birlik, S.M. ; Biryukov, S. ; Casey, D. ; Foreman, K.J. ; Goldberg, E.M. ; Khalil, I.A. ; Kyu, H.H. ; Manhertz, T. ; Mokdad, A.H. ; Naghavi, M. ; Nguyen, G. ; Nichols, E. ; Smith, M. ; Carabin, H. ; Roth, G.A. ; Stanaway, J.D. ; Vos, T. ; Ellenbogen, R.G. ; Jakovljevic, M.B. ; Tirschwell, D.L. ; Zunt, J.R. ; Boneya, D.J. ; Hambisa, M. ; Bulto, L.N.B. ; Carabin, H. ; Castañeda-Orjuela, C.A. ; Catalá-López, F. ; Tabarés-Seisdedos, R. ; Chen, H. ; Chitheer, A.A. ; Chowdhury, R. ; Christensen, H. ; Deveber, G.A. ; Dharmaratne, S.D. ; Do, H.P. ; Nguyen, C.T. ; Nguyen, Q.L. ; Nguyen, T.H. ; Nong, V.M. ; Sheth, K.N. ; Dorsey, E.R. ; Eskandarieh, S. ; Fischer, F. ; Majeed, A. ; Steiner, T.J. ; Rawaf, S. ; Shakir, R. ; Shoman, H. ; Geleijnse, J.M. ; Gillum, R.F. ; Gona, P.N. ; Gugnani, H.C. ; Gupta, R. ; Hachinski, V. ; Hamadeh, R.R. ; Hankey, G.J. ; Hareri, H.A. ; Heydarpour, P. ; Sahraian, M.A. ; Kasaeian, A. ; Malekzadeh, R. ; Roshandel, G. ; Sepanlou, S.G. ; Hotez, P.J. ; Javanbakht, M. ; Jonas, J.B. ; Kalkonde, Y. ; Kandel, A. ; Karch, A. ; Kastor, A. ; Rahman, M.H.U. ; Keiyoro, P.N. ; Khader, Y.S. ; Khan, E.A. ; Khang, Y. ; Khoja, A.T.A. ; Tran, B.X. ; Khubchandani, J. ; Kim, D. ; Kim, Y.J. ; Kivimaki, M. ; Kokubo, Y. ; Kosen, S. ; Kravchenko, M. ; Piradov, M.A. ; Varakin, Y.Y. ; Defo, B.K. ; Kulkarni, C. ; Kumar, R. ; Larsson, A. ; Lavados, P.M. ; Li, Y. ; Liang, X. ; Liben, M.L. ; Lo, W.D. ; Logroscino, G. ; Loy, C.T. ; Mackay, M.T. ; Meretoja, A. ; Szoeke, C.E.I. ; Abd El Razek, H.M. ; Mantovani, L.G. ; Massano, J. ; Mazidi, M. ; McAlinden, C. ; Mehata, S. ; Mehndiratta, M.M. ; Memish, Z.A. ; Mendoza, W. ; Mensah, G.A. ; Wijeratne, T. ; Miller, T.R. ; Mohamed Ibrahim, N. ; Mohammadi, A. ; Moradi-Lakeh, M. ; Velasquez, I.M. ; Musa, K.I. ; Ngunjiri, J.W. ; Ningrum, D.N.A. ; Norrving, B. ; Stein, D.J. ; Noubiap, J.J.N. ; Ogbo, F.A. ; Renzaho, A.M.N. ; Owolabi, M.O. ; Pandian, J.D. ; Parmar, P.G. ; Pereira, D.M. ; Petzold, M. ; Phillips, M.R. ; Poulton, R.G. ; Pourmalek, F. ; Qorbani, M. ; Rafay, A. ; Rai, R.K. ; Rajsic, S. ; Ranta, A. ; Rezai, M.S. ; Rubagotti, E. ; Sachdev, P. ; Safiri, S. ; Sahathevan, R. ; Samy, A.M. ; Santalucia, P. ; Sartorius, B. ; Satpathy, M. ; Sawhney, M. ; Saylan, M.I. ; Shaikh, M.A. ; Shamsizadeh, M. ; Sheth, K.N. ; Shigematsu, M. ; Silva, D.A.S. ; Sobngwi, E. ; Sposato, L.A. ; Stovner, L.J. ; Suliankatchi Abdulkader, R. ; Tanne, D. ; Thrift, A.G. ; Topor-Madry, R. ; Truelsen, T. ; Ukwaja, K.N. ; Uthman, O.A. ; Yonemoto, N. ; Venketasubramanian, N. ; Vlassov, V.V. ; Wadilo, F. ; Wallin, M.T. ; Westerman, R. ; Wiysonge, C.S. ; Wolfe, C.D. ; Xavier, D. ; Xu, G. ; Yano, Y. ; Yimam, H.H. ; Yonemoto, N. ; Yu, C. ; Zaidi, Z. ; Zaki, M.E. - \ 2017
The Lancet Neurology 16 (2017)11. - ISSN 1474-4422 - p. 877 - 897.

Background Comparable data on the global and country-specific burden of neurological disorders and their trends are crucial for health-care planning and resource allocation. The Global Burden of Diseases, Injuries, and Risk Factors (GBD) Study provides such information but does not routinely aggregate results that are of interest to clinicians specialising in neurological conditions. In this systematic analysis, we quantified the global disease burden due to neurological disorders in 2015 and its relationship with country development level. Methods We estimated global and country-specific prevalence, mortality, disability-adjusted life-years (DALYs), years of life lost (YLLs), and years lived with disability (YLDs) for various neurological disorders that in the GBD classification have been previously spread across multiple disease groupings. The more inclusive grouping of neurological disorders included stroke, meningitis, encephalitis, tetanus, Alzheimer's disease and other dementias, Parkinson's disease, epilepsy, multiple sclerosis, motor neuron disease, migraine, tension-type headache, medication overuse headache, brain and nervous system cancers, and a residual category of other neurological disorders. We also analysed results based on the Socio-demographic Index (SDI), a compound measure of income per capita, education, and fertility, to identify patterns associated with development and how countries fare against expected outcomes relative to their level of development. Findings Neurological disorders ranked as the leading cause group of DALYs in 2015 (250·7 [95% uncertainty interval (UI) 229·1 to 274·7] million, comprising 10·2% of global DALYs) and the second-leading cause group of deaths (9·4 [9·1 to 9·7] million], comprising 16·8% of global deaths). The most prevalent neurological disorders were tension-type headache (1505·9 [UI 1337·3 to 1681·6 million cases]), migraine (958·8 [872·1 to 1055·6] million), medication overuse headache (58·5 [50·8 to 67·4 million]), and Alzheimer's disease and other dementias (46·0 [40·2 to 52·7 million]). Between 1990 and 2015, the number of deaths from neurological disorders increased by 36·7%, and the number of DALYs by 7·4%. These increases occurred despite decreases in age-standardised rates of death and DALYs of 26·1% and 29·7%, respectively; stroke and communicable neurological disorders were responsible for most of these decreases. Communicable neurological disorders were the largest cause of DALYs in countries with low SDI. Stroke rates were highest at middle levels of SDI and lowest at the highest SDI. Most of the changes in DALY rates of neurological disorders with development were driven by changes in YLLs. Interpretation Neurological disorders are an important cause of disability and death worldwide. Globally, the burden of neurological disorders has increased substantially over the past 25 years because of expanding population numbers and ageing, despite substantial decreases in mortality rates from stroke and communicable neurological disorders. The number of patients who will need care by clinicians with expertise in neurological conditions will continue to grow in coming decades. Policy makers and health-care providers should be aware of these trends to provide adequate services. Funding Bill & Melinda Gates Foundation.

Labor, social sustainability and the underlying vulnerabilities of work in Southeast Asia's seafood value chains
Bush, Simon R. ; Marschke, Melissa J. ; Belton, Ben - \ 2017
In: Routledge Handbook of Southeast Asian Development / McGregor, Andrew, Law, Lisa, Miller, Fiona, Taylor and Francis - ISBN 9781138848535 - p. 316 - 329.
Labor, social sustainability and the underlying vulnerabilities of work in Southeast Asia’s seafood value chains
Healthcare entitlements for citizens and transborder mobile peoples in Southeast Asia
Ormond, Meghann ; Khoon, Chan Chee ; Verghis, Sharuna - \ 2017
In: Routledge Handbook of Southeast Asian Development / McGregor, Andrew, Law, Lisa, Miller, Fiona, Abington : Routledge - ISBN 9781138848535 - p. 186 - 197.
The health of a population is shaped by a complex interplay of economic, political, social, cultural and biological factors that transcend national borders. In this chapter, we consider how these factors work together within the Association of Southeast Asian Nations (ASEAN), a supra-national regional political space encompassing a population of over 600 million across ten countries. Specifically, we query how economic liberalization and corollary increases in the movement of people, goods and services are challenging and transforming entrenched ideas about who is entitled to and responsible for health and social care within and across ASEAN member states’ national borders.
Association of sleep duration and quality with blood lipids : a systematic review and meta-analysis of prospective studies
Kruisbrink, Marlot ; Robertson, Wendy ; Ji, Chen ; Miller, Michelle A. ; Geleijnse, Johanna M. ; Cappuccio, Francesco P. - \ 2017
BMJ Open 7 (2017)12. - ISSN 2044-6055
blood lipids - cholesterol - meta-analysis - sleep duration - sleep quality - systematic review

OBJECTIVES: To assess the longitudinal evidence of the relationships between sleep disturbances (of quantity and quality) and dyslipidaemia in the general population and to quantify such relationships.

SETTING: Systematic review and meta-analysis following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.

METHODS: We performed a systematic search of PubMed and Embase (up to 9 September 2017), complemented with manual searches, of prospective population studies describing the association between sleep duration and quality and the incidence of dyslipidaemias. Relative risks (95% CIs) were extracted and pooled using a random effects model. Subgroup analyses by lipid type were performed. Heterogeneity and publication bias were also assessed. Quality was assessed with Downs and Black score.

PARTICIPANTS: Studies were included if they were prospective, had measured sleep quantity and/or quality at baseline and either incident cases of dyslipidaemia or changes in blood lipid fractions assessed prospectively.

PRIMARY OUTCOME MEASURES: Incidence of dyslipidaemia and changes in lipid fractions. Dyslipidaemia was defined as a high total cholesterol, triglycerides, low-density lipoprotein cholesterol or low high-density lipoprotein cholesterol compared with the reference group.

RESULTS: Thirteen studies were identified (eight using sleep duration, four sleep quality and one both). There was heterogeneity in the sleep quality aspects and types of lipids assessed. Classification of sleep duration (per hour/groups) also varied widely. In the pooled analysis of sleep duration (6 studies, 16 cohort samples; 30 033 participants; follow-up 2.6-10 years), short sleep was associated with a risk of 1.01 (95% CI 0.93 to 1.10) of developing dyslipidaemia, with moderate heterogeneity (I2=56%, P=0.003) and publication bias (P=0.035). Long sleep was associated with a risk of 0.98 (95% CI 0.87 to 1.10) for dyslipidaemia, with heterogeneity (I2=63%, P<0.001) and no significant publication bias (P=0.248).

CONCLUSION: The present analysis was unable to find supportive evidence of a significant relationship between sleep duration and the development of dyslipidaemia. However, heterogeneity and small number of studies limit the interpretation.

PROSPERO REGISTRATION NUMBER: CRD42016045242.

Transdisciplinary understanding of SI in MRAs
Kluvankova, Tatiana ; Gežik, Veronika ; Špaček, Martin ; Brnkalakova, Stanislava ; Slee, Bill ; Polman, N.B.P. ; Valero, Diana ; Bryce, Rosalind ; Alkhaled, Sophie ; Secco, Laura ; Burlando, Catie ; Kozova, Maria ; Miller, David ; Nijnik, Maria ; Perlik, Manfred ; Pisani, Elena ; Price, Martin ; Sarkki, Simo ; Weiss, Gerhard - \ 2017
SIMRA - 53 p.
Set of Methods to Assess SI Implications at Different Levels
Secco, Laura ; Pisani, Elena ; Burlando, Catie ; Re, Riccardo Da; Gatto, Paola ; Pettenella, Davide ; Vassilopoulos, Achilleas ; Akinsete, Ebun ; Koundouri, Phoebe ; Lopolito, Antonio ; Prosperi, Maurizio ; Tuomasiukka, Diana ; Herde, Micheal Den; Lovric, Marko ; Polman, N.B.P. ; Dijkshoorn-Dekker, M.W.C. ; Soma, K. ; Ludvig, Alice ; Weiss, Gerhard ; Zivojinovic, Ivana ; Sarkki, Simo ; Ravazzoli, Elisa ; Torre, Cristina Dalla; Streifeneder, Thomas ; Slee, Bill ; Nijnik, Maria ; Miller, David ; Barlagne, Carla ; Prokofieva, Irina - \ 2017
SIMRA - 203 p.
Diseases of Lily
Chastagner, G.A. ; Tuyl, J.M. van; Verbeek, M. ; Miller, William ; Westerdahl, Becky B. - \ 2017
In: Handbook of Florists' Crops Diseases, Handbook of Plant Disease Management / McGovern, R.J., Elmer, W.H., Springer International Publishing (Handbook of Plant Disease Management ) - ISBN 9783319323749 - 61 p.
Lilies (Lilium spp. and hybrids) are the second largest flower bulb crop in the Netherlands and the most important flower bulb crop in the world. They are grown for bulbs, as cut flowers, as container (potted) plants, or in gardens. Lilies are a vegetatively propagated crop and may be routinely increased by micropropagation (tissue culture) or through scaling (removal of bulb scales from which adventitious bulblets are produced). The propagules are subsequently grown in fields for 2 or 3 y to allow the bulbs to reach sufficient size (generally measured in circumference) for proper flowering and maximum horticultural quality. Although the majority of bulbs produced for worldwide distribution are grown mainly in the Netherlands, bulbs are also grown in other northern European countries, the USA, Asia, Israel, and southern hemisphere locations including Brazil, Australia, New Zealand, Tasmania, and Chile. There are a number of diseases caused by fungi, viruses, bacteria, and nematodes and physiological disorders that affect the production and quality of lily bulb and cut flower crops worldwide. Information on the distribution, epidemiology and management, of the common diseases and disorders is presented in this chapter.
Stakeholder and Citizen Participation in Bioeconomy Strategies : BioSTEP Guidelines for Practitioners
Davies, S. ; Miller, S. ; Bakker, H.C.M. de; Beekman, V. ; Overbeek, M.M.M. - \ 2017
BioSTEP - 12 p.
Primary Charge Separation in the Photosystem II Reaction Center Revealed by a Global Analysis of the Two-dimensional Electronic Spectra
Duan, Hong Guang ; Prokhorenko, Valentyn I. ; Wientjes, I.E. ; Croce, Roberta ; Thorwart, Michael ; Miller, R.J.D. - \ 2017
Scientific Reports 7 (2017). - ISSN 2045-2322 - 9 p.
The transfer of electronic charge in the reaction center of Photosystem II is one of the key building blocks of the conversion of sunlight energy into chemical energy within the cascade of the photosynthetic reactions. Since the charge transfer dynamics is mixed with the energy transfer dynamics, an effective tool for the direct resolution of charge separation in the reaction center is still missing. Here, we use experimental two-dimensional optical photon echo spectroscopy in combination with the theoretical calculation to resolve its signature. A global fitting analysis allows us to clearly and directly identify a decay pathway associated to the primary charge separation. In particular, it can be distinguished from regular energy transfer and occurs on a time scale of 1.5 ps under ambient conditions. This technique provides a general tool to identify charge separation signatures from the energy transport in two-dimensional optical spectroscopy.
Long-term population dynamics in a multi-species assemblage of large herbivores in East Africa
Kiffner, Christian ; Rheault, Helena ; Miller, Elizabeth ; Scheetz, Tanner ; Enriquez, Vivien ; Swafford, Rachelle ; Kioko, John ; Prins, Herbert H.T. - \ 2017
Ecosphere 8 (2017)12. - ISSN 2150-8925
Conservation Effectiveness - Declining Population Paradigm - Ecosystem Dynamics - Lake Manyara National Park - Shrub Encroachment - Ungulates
Wildlife population declines in Africa are widespread. However, species-specific population trends and dynamics in mammal community composition have rarely been described over long time periods. To describe population trends of 13 large herbivore species in Lake Manyara National Park (Tanzania) from 1959 to 2016 and to discover whether the herbivore community structure changed, we used general additive models and additional statistical methods to detect structural changes in the time series. Population dynamics were non-linear and population growth rates were not correlated with precipitation anomalies. Relatively steep population declines of three megaherbivores occurred during the 1980s and early 1990s, resulting in severe reductions in African elephant and buffalo populations and the local extinction of black rhinoceros. These declines coincided with reported peaks of illegal hunting of these species and expansion of agriculture at the periphery of the park. Population densities of elephant and buffalo seem to have stabilized in recent times, yet have not recovered to previous densities. In contrast, eight species (giraffe, zebra, waterbuck, wildebeest, warthog, impala, bushbuck, and baboon) have apparently fared well (similar or higher densities in most recent compared to first decade), despite having undergone substantial fluctuations over the past 58 yr. Population fluctuations in these species were likely caused by disease outbreaks, heavy bush encroachment, and reduced competition with buffalo. Possibly, declines in megaherbivore densities (mainly elephants) facilitated bush encroachment. Albeit grazers are still dominating in the herbivore community, the proportion of browsers is currently increasing, likely encouraged by dense vegetation in the shrub layer in large parts of the park. Overall, herbivore biomass density has declined by ~40% compared to the baseline estimate in the first decade of the time series. Our analyses and ancillary information provide evidence that this overall decline in the herbivore assemblage was triggered by human-induced reductions in megaherbivore population densities during the 1980s, either through excessive poaching, insularization of the park, or both. Likely, this had cascading and interacting effects on the vegetation structure and the herbivore assemblage. Thus, legacy effects of ineffective megaherbivore conservation efforts 30 yr ago are likely still affecting the ecology of this national park.
Evolution and patterns of global health financing 1995-2014 : Development assistance for health, and government, prepaid private, and out-of-pocket health spending in 184 countries
Dieleman, Joseph ; Campbell, Madeline ; Chapin, Abigail ; Eldrenkamp, Erika ; Fan, Victoria Y. ; Haakenstad, Annie ; Kates, Jennifer ; Liu, Yingying ; Matyasz, Taylor ; Micah, Angela ; Reynolds, Alex ; Sadat, Nafis ; Schneider, Matthew T. ; Sorensen, Reed ; Evans, Tim ; Evans, David ; Kurowski, Christoph ; Tandon, Ajay ; Abbas, Kaja M. ; Abera, Semaw Ferede ; Ahmad Kiadaliri, Aliasghar ; Ahmed, Kedir Yimam ; Ahmed, Muktar Beshir ; Alam, Khurshid ; Alizadeh-Navaei, Reza ; Alkerwi, A. ; Amini, Erfan ; Ammar, Walid ; Amrock, Stephen Marc ; Antonio, Carl Abelardo T. ; Atey, Tesfay Mehari ; Avila-Burgos, Leticia ; Awasthi, Ashish ; Barac, Aleksandra ; Bernal, Oscar Alberto ; Beyene, Addisu Shunu ; Beyene, Tariku Jibat ; Birungi, Charles ; Bizuayehu, Habtamu Mellie ; Breitborde, Nicholas J.K. ; Cahuana-Hurtado, Lucero ; Castro, Ruben Estanislao ; Catalá-López, Ferran ; Dalal, Koustuv ; Dandona, Lalit ; Dandona, Rakhi ; Jager, Pieter De; Dharmaratne, Samath D. ; Dubey, Manisha ; Sa Farinha, Carla Sofia E. ; Faro, Andre ; Feigl, Andrea B. ; Fischer, Florian ; Fitchett, Joseph Robert Anderson ; Foigt, Nataliya ; Giref, Ababi Zergaw ; Gupta, Rahul ; Hamidi, Samer ; Harb, Hilda L. ; Hay, Simon I. ; Hendrie, Delia ; Horino, Masako ; Jürisson, Mikk ; Jakovljevic, Mihajlo B. ; Javanbakht, Mehdi ; John, Denny ; Jonas, Jost B. ; Karimi, Seyed M. ; Khang, Young Ho ; Khubchandani, Jagdish ; Kim, Yun Jin ; Kinge, Jonas M. ; Krohn, Kristopher J. ; Kumar, G.A. ; Magdy Abd El Razek, Hassan ; Magdy Abd El Razek, Mohammed ; Majeed, Azeem ; Malekzadeh, Reza ; Masiye, Felix ; Meier, Toni ; Meretoja, Atte ; Miller, Ted R. ; Mirrakhimov, Erkin M. ; Mohammed, Shafiu ; Nangia, Vinay ; Olgiati, Stefano ; Osman, Abdalla Sidahmed ; Owolabi, Mayowa O. ; Patel, Tejas ; Paternina Caicedo, Angel J. ; Pereira, David M. ; Perelman, Julian ; Polinder, Suzanne ; Rafay, Anwar ; Rahimi-Movaghar, Vafa ; Rai, Rajesh Kumar ; Ram, Usha ; Ranabhat, Chhabi Lal ; Roba, Hirbo Shore ; Salama, Joseph ; Savic, Miloje ; Sepanlou, Sadaf G. ; Shrime, Mark G. ; Talongwa, Roberto Tchio ; Ao, Braden J. Te; Tediosi, Fabrizio ; Tesema, Azeb Gebresilassie ; Thomson, Alan J. ; Tobe-Gai, Ruoyan ; Topor-Madry, Roman ; Undurraga, Eduardo A. ; Vasankari, Tommi ; Violante, Francesco S. ; Werdecker, Andrea ; Wijeratne, Tissa ; Xu, Gelin ; Yonemoto, Naohiro ; Younis, Mustafa Z. ; Yu, Chuanhua ; Zaidi, Zoubida ; Sayed Zaki, Maysaa El; Murray, Christopher J.L. - \ 2017
The Lancet 389 (2017)10083. - ISSN 0140-6736 - p. 1981 - 2004.
Background: An adequate amount of prepaid resources for health is important to ensure access to health services and for the pursuit of universal health coverage. Previous studies on global health financing have described the relationship between economic development and health financing. In this study, we further explore global health financing trends and examine how the sources of funds used, types of services purchased, and development assistance for health disbursed change with economic development. We also identify countries that deviate from the trends. Methods: We estimated national health spending by type of care and by source, including development assistance for health, based on a diverse set of data including programme reports, budget data, national estimates, and 964 National Health Accounts. These data represent health spending for 184 countries from 1995 through 2014. We converted these data into a common inflation-adjusted and purchasing power-adjusted currency, and used non-linear regression methods to model the relationship between health financing, time, and economic development. Findings: Between 1995 and 2014, economic development was positively associated with total health spending and a shift away from a reliance on development assistance and out-of-pocket (OOP) towards government spending. The largest absolute increase in spending was in high-income countries, which increased to purchasing power-adjusted $5221 per capita based on an annual growth rate of 3.0%. The largest health spending growth rates were in upper-middle-income (5.9) and lower-middle-income groups (5.0), which both increased spending at more than 5% per year, and spent $914 and $267 per capita in 2014, respectively. Spending in low-income countries grew nearly as fast, at 4.6%, and health spending increased from $51 to $120 per capita. In 2014, 59.2% of all health spending was financed by the government, although in low-income and lower-middle-income countries, 29.1% and 58.0% of spending was OOP spending and 35.7% and 3.0% of spending was development assistance. Recent growth in development assistance for health has been tepid; between 2010 and 2016, it grew annually at 1.8%, and reached US$37.6 billion in 2016. Nonetheless, there is a great deal of variation revolving around these averages. 29 countries spend at least 50% more than expected per capita, based on their level of economic development alone, whereas 11 countries spend less than 50% their expected amount. Interpretation: Health spending remains disparate, with low-income and lower-middle-income countries increasing spending in absolute terms the least, and relying heavily on OOP spending and development assistance. Moreover, tremendous variation shows that neither time nor economic development guarantee adequate prepaid health resources, which are vital for the pursuit of universal health coverage.
Future and potential spending on health 2015-40 : Development assistance for health, and government, prepaid private, and out-of-pocket health spending in 184 countries
Dieleman, Joseph L. ; Campbell, Madeline ; Chapin, Abigail ; Eldrenkamp, Erika ; Fan, Victoria Y. ; Haakenstad, Annie ; Kates, Jennifer ; Li, Zhiyin ; Matyasz, Taylor ; Micah, Angela ; Reynolds, Alex ; Sadat, Nafis ; Schneider, Matthew T. ; Sorensen, Reed ; Abbas, Kaja M. ; Abera, Semaw Ferede ; Ahmad Kiadaliri, Aliasghar ; Ahmed, Muktar Beshir ; Alam, Khurshid ; Alizadeh-Navaei, Reza ; Alkerwi, A. ; Amini, Erfan ; Ammar, Walid ; Antonio, Carl Abelardo T. ; Atey, Tesfay Mehari ; Avila-Burgos, Leticia ; Awasthi, Ashish ; Barac, Aleksandra ; Berheto, Tezera Moshago ; Beyene, Addisu Shunu ; Beyene, Tariku Jibat ; Birungi, Charles ; Bizuayehu, Habtamu Mellie ; Breitborde, Nicholas J.K. ; Cahuana-Hurtado, Lucero ; Castro, Ruben Estanislao ; Catalá-López, Ferran ; Dalal, Koustuv ; Dandona, Lalit ; Dharmaratne, Rakhi Dandona Samath D. ; Dubey, Manisha ; Faro, Andé ; Feigl, Andrea B. ; Fischer, Florian ; Anderson Fitchett, Joseph R. ; Foigt, Nataliya ; Giref, Ababi Zergaw ; Gupta, Rahul ; Hamidi, Samer ; Harb, Hilda L. ; Hay, Simon I. ; Hendrie, Delia ; Horino, Masako ; Jürisson, Mikk ; Jakovljevic, Mihajlo B. ; Javanbakht, Mehdi ; John, Denny ; Jonas, Jost B. ; Karimi, Seyed M. ; Khang, Young Ho ; Khubchandani, Jagdish ; Kim, Yun Jin ; Kinge, Jonas M. ; Krohn, Kristopher J. ; Kumar, G.A. ; Leung, Ricky ; Magdy Abd El Razek, Hassan ; Magdy Abd El Razek, Mohammed ; Majeed, Azeem ; Malekzadeh, Reza ; Malta, Deborah Carvalho ; Meretoja, Atte ; Miller, Ted R. ; Mirrakhimov, Erkin M. ; Mohammed, Shafiu ; Molla, Gedefaw ; Nangia, Vinay ; Olgiati, Stefano ; Owolabi, Mayowa O. ; Patel, Tejas ; Paternina Caicedo, Angel J. ; Pereira, David M. ; Perelman, Julian ; Polinder, Suzanne ; Rafay, Anwar ; Rahimi-Movaghar, Vafa ; Rai, Rajesh Kumar ; Ram, Usha ; Ranabhat, Chhabi Lal ; Roba, Hirbo Shore ; Savic, Miloje ; Sepanlou, Sadaf G. ; Ao, Braden J. Te; Tesema, Azeb Gebresilassie ; Thomson, Alan J. ; Tobe-Gai, Ruoyan ; Topor-Madry, Roman ; Undurraga, Eduardo A. ; Vargas, Veronica ; Vasankari, Tommi ; Violante, Francesco S. ; Wijeratne, Tissa ; Xu, Gelin ; Yonemoto, Naohiro ; Younis, Mustafa Z. ; Yu, Chuanhua ; Zaidi, Zoubida ; Sayed Zaki, Maysaa El; Murray, Christopher J.L. - \ 2017
The Lancet 389 (2017)10083. - ISSN 0140-6736 - p. 2005 - 2030.
Background: The amount of resources, particularly prepaid resources, available for health can affect access to health care and health outcomes. Although health spending tends to increase with economic development, tremendous variation exists among health financing systems. Estimates of future spending can be beneficial for policy makers and planners, and can identify financing gaps. In this study, we estimate future gross domestic product (GDP), all-sector government spending, and health spending disaggregated by source, and we compare expected future spending to potential future spending. Methods: We extracted GDP, government spending in 184 countries from 1980-2015, and health spend data from 1995-2014. We used a series of ensemble models to estimate future GDP, all-sector government spending, development assistance for health, and government, out-of-pocket, and prepaid private health spending through 2040. We used frontier analyses to identify patterns exhibited by the countries that dedicate the most funding to health, and used these frontiers to estimate potential health spending for each low-income or middle-income country. All estimates are inflation and purchasing power adjusted. Findings: We estimated that global spending on health will increase from US$9.21 trillion in 2014 to $24.24 trillion (uncertainty interval [UI] 20.47-29.72) in 2040. We expect per capita health spending to increase fastest in upper-middle-income countries, at 5.3% (UI 4.1-6.8) per year. This growth is driven by continued growth in GDP, government spending, and government health spending. Lower-middle income countries are expected to grow at 4.2% (3.8-4.9). High-income countries are expected to grow at 2.1% (UI 1.8-2.4) and low-income countries are expected to grow at 1.8% (1.0-2.8). Despite this growth, health spending per capita in low-income countries is expected to remain low, at $154 (UI 133-181) per capita in 2030 and $195 (157-258) per capita in 2040. Increases in national health spending to reach the level of the countries who spend the most on health, relative to their level of economic development, would mean $321 (157-258) per capita was available for health in 2040 in low-income countries. Interpretation: Health spending is associated with economic development but past trends and relationships suggest that spending will remain variable, and low in some low-resource settings. Policy change could lead to increased health spending, although for the poorest countries external support might remain essential.
Mode of action based risk assessment of the botanical food-borne alkenylbenzenesapiol and myristicin
Alajlouni, Abdul - \ 2017
Wageningen University. Promotor(en): I.M.C.M. Rietjens, co-promotor(en): J.J.M. Vervoort; S. Wesseling. - Wageningen : Wageningen University - ISBN 9789463434584 - 212

Alkenylbenzenes including estragole, methyleugenol, safrole, elemicin, apiol, and myristicin are naturally occurring in many herbs such as parsley, dill, basil, tarragon, fennel and nutmeg (Kreydiyyeh and Usta, 2002, Smith et al., 2002, Semenov et al., 2007). Estragole, methyleugenol and safrole are genotoxic and carcinogenic in rodent bioassays inducing liver tumors (Boberg et al., 1986, Boberg et al., 1983, Drinkwater et al., 1976, Miller et al., 1983, Swanson et al., 1981, Wiseman et al., 1985, Wiseman et al., 1987, Wislocki et al., 1977). Because of that, the use of methyleugenol, safrole and estragole as pure substances in foodstuff has been prohibited in the EU from September 2008 onwards (European Commission (EC), 2008). For apiol and myristicin data for their risk assessment are limited and more research is needed to support the evaluation of the risk resulting from consumption of products containing these compounds (WHO, 2009). The aim of the current thesis was to perform a mode of action based risk assessment of exposure to low doses of apiol and myristicin by using physiologically based kinetic (PBK) modelling based read-across from other alkenylbenzenes and to use the results obtained for risk assessment of consumption of plant food supplements (PFS) and other botanical products containing parsley and dill.

Chapter 1 provides general background information to alkenylbenzenes especially apiol and myristicin, a description of the chemical, metabolic and toxicity characteristics of apiol and myristicin and other structurally related alkenylbenzenes, a brief outline of the method used for their risk assessment and a short introduction to PBK modelling. Besides that, Chapter 1 include the aim of the current thesis. In Chapter 2 and Chapter 3, PBK models for respectively apiol and myristicin in male rat and human were defined, enabling prediction of dose-dependent effects in bioactivation and detoxification of these alkenylbenzenes. The PBK model based predictions were subsequently compared to those for safrole enabling estimation of a BMDL10 for apiol and myristicin from read-across from the BMDL10 available for safrole, thereby enabling risk assessment of current dietary exposure to apiol. In Chapter 4 and 5, the risk assessment of exposure to apiol and related alkenylbenzenes through drinking of parsley and dill based herbal teas and consumption of parsley and dill containing PFS was performed using the BMDL10 values derived in Chapter 2 and 3. The results showed that consumption of parsley and dill based herbal teas and PFS would be a priority for risk management if consumed for longer periods of time. Chapter 6 includes a general discussion of the thesis results obtained and the future perspectives that describe the needs to further research, based on alternatives for animals testing, to improve the risk assessment approaches for different botanical preparations.

Altogether, the results obtained through different thesis chapters show that integration of different approaches provides the basis for a mode of action and PBK modelling based read-across from compounds for which tumor data are available to related compounds for which such data are lacking. This can contribute to the development of alternatives for animal testing and will facilitate the risk assessment of compounds for which in vivo toxicity studies on tumor formation data are unavailable.

Biotransformation and bioactivation reactions–2016 literature highlights
Khojasteh, S.C. ; Rietjens, Ivonne M.C.M. ; Dalvie, Deepak ; Miller, Grover - \ 2017
Drug Metabolism Reviews 49 (2017)3. - ISSN 0360-2532 - p. 285 - 317.
aldehyde oxidase - bioactivation - Biotransformation - cytochrome P450 - UGT
We are pleased to present a second annual issue highlighting a previous year’s literature on biotransformation and bioactivation. Each contributor to this issue worked independently to review the articles published in 2016 and proposed three to four articles, which he or she believed would be of interest to the broader research community. In each synopsis, the contributing author summarized the procedures, analyses and conclusions as described in the original manuscripts. In the commentary sections, our authors offer feedback and highlight aspects of the work that may not be apparent from an initial reading of the article. To be fair, one should still read the original article to gain a more complete understanding of the work conducted. Most of the articles included in this review were published in Drug Metabolism and Disposition or Chemical Research in Toxicology, but attempts were made to seek articles in 25 other journals. Importantly, these articles are not intended to represent a consensus of the best papers of the year, as we did not want to make any arbitrary standards for this purpose, but rather they were chosen by each author for their notable findings and descriptions of novel metabolic pathways or biotransformations. I am pleased that Drs. Rietjens and Dalvie have again contributed to this annual review. We would like to welcome Grover P Miller as an author for this year’s issue, and we thank Tom Baillie for his contributions to last year’s edition. We have intentionally maintained a balance of authors such that two come from an academic setting and two come from industry. Finally, please drop us a note if you find this review helpful. We would be pleased to hear your opinions of our commentary, and we extend an invitation to anyone who would like to contribute to a future edition of this review. This article is dedicated to Professor Thomas Baillie for his exceptional contributions to the field of drug metabolism.
Campylobacter pinnipediorum sp. Nov., isolated from pinnipeds, comprising Campylobacter pinnipediorum subsp. pinnipediorum subsp. nov. and Campylobacter pinnipediorum subsp. caledonicus subsp. nov
Gilbert, Maarten J. ; Miller, William G. ; St. Leger, Judy ; Chapman, Mary H. ; Timmerman, Arjen J. ; Duim, Birgitta ; Foster, Geoffrey ; Wagenaar, Jaap A. - \ 2017
International Journal of Systematic and Evolutionary Microbiology 67 (2017)6. - ISSN 1466-5026 - p. 1961 - 1968.
Average nucleotide identity - Campylobacter - Novel species - Pinnipeds - Urease - Whole genome sequencing

During independent diagnostic screenings of otariid seals in California (USA) and phocid seals in Scotland (UK), Campylobacter-like isolates, which differed from the established taxa of the genus Campylobacter, were cultured from abscesses and internal organs of different seal species. A polyphasic study was undertaken to determine the taxonomic position of these six isolates. The isolates were characterized by 16S rRNA gene and AtpA sequence analysis and by conventional phenotypic testing. The whole-genome sequences were determined for all isolates, and the average nucleotide identity (ANI) was determined. The isolates formed a separate phylogenetic clade, divergent from all other taxa of the genus Campylobacter and most closely related to Campylobactermucosalis. Although all isolates showed 100 % 16S rRNA gene sequence homology, AtpA and ANI analyses indicated divergence between the otariid isolates from California and the phocid isolates from Scotland, which warrants subspecies status for each clade. The two subspecies could also be distinguished phenotypically on the basis of catalase activity. This study shows clearly that the isolates obtained from pinnipeds represent a novel species within the genus Campylobacter, for which the name Campylobacter pinnipediorum sp. nov. is proposed. Within this novel species, the Californian isolates represent a separate subspecies, for which the name C. pinnipediorum subsp. pinnipediorum subsp. nov. is proposed. The type strain for both this novel species and subspecies is RM17260T (=LMG 29472T=CCUG 69570T). The Scottish isolates represent another subspecies, for which the name C. pinnipediorum subsp. caledonicus subsp. nov. is proposed. The type strain of this subspecies is M302/10/6T (=LMG 29473T=CCUG 68650T).

Indicators of the ‘wild seafood’ provisioning ecosystem service based on the surplus production of commercial fish stocks
Piet, G.J. ; Overzee, H.M.J. van; Miller, D.C.M. ; Gelabert, E.R. - \ 2017
Ecological Indicators 72 (2017). - ISSN 1470-160X - p. 194 - 202.
Ecosystem services - Fisheries management - Fishing mortality - Seafood provisioning - Spawning stock biomass - Sustainable exploitation

The ‘Wild Seafood’ Provisioning Service (WSPS), on which commercial fisheries rely, is probably one of the best studied marine ecosystem services due to its economic relevance and because extensive information sources exist for assessment purposes. Yet, the indicators often proposed are not suitable to describe the capacity of the ecosystem to deliver the WSPS. Therefore this study proposes surplus production (SP), a well-established concept in fisheries science, as the basis to calculate the capacity of marine ecosystems to provide the WSPS. SP is defined as the difference between stock production (through recruitment and body growth) and losses through natural mortality. This is, therefore, the production of the stock that could be harvested sustainably without decreasing the biomass. To assess the sustainability of the exploitation of the WSPS we also developed an indicator for this based on SP and compared it to existing fisheries management indicators. When both SP-based indicators showed a decreasing trend, contrasting with an increasing trend in the existing fisheries management indicators, the calculation of the SP-based indicators was scrutinized revealing that the weighting of the stocks into an aggregated indicator, strongly determines the indicator values, even up to the point that the trend is reversed. The aggregated indicators based on SP-weighted stocks can be considered complementary to existing fisheries management indicators as the former accurately reflect the capacity of the commercial fish to provide the WSPS and the sustainability of the exploitation of this service. In contrast the existing fisheries management indicators primarily reflect the performance of management towards achieving fisheries-specific policy goals.

Dataset of liver proteins of eu- and hypothyroid rats affected in abundance by any of three factors: in vivo exposure to hexabromocyclododecane (HBCD), thyroid status, gender differences
Miller, I. ; Renaut, J. ; Cambier, S. ; Murk, A.J. ; Gutleb, A.C. ; Serchi, T. - \ 2016
Data in Brief 8 (2016). - ISSN 2352-3409 - p. 1344 - 1347.
Gender-specific effects - HBCD - Hypothyroidism - Liver - Proteomics - Rat

Male Wistar rats with different thyroid status (eu-, hypothyroid) were exposed to 0, 3 or 30 mg/kg body weight of the flame retardant HBCD for 7 days and obtained data compared with a previous study in females, “Hexabromocyclododecane (HBCD) induced changes in the liver proteome of eu- and hypothyroid female rats” (Miller et al., 2016) [1]. Specifically, proteomic investigation of liver protein patterns obtained by 2D-DIGE was performed and differences between animals groups recorded, based on the factors exposure, thyroid status and gender. All proteins with significantly changed abundance in any of these comparisons were identified by mass spectrometry. General, hormone and proteomic data of both the present and the previous studies are discussed in Miller et al. (2016) [1] and in “Gender specific differences in the liver proteome of rats exposed to hexabromocyclododecane (HBCD)” Miller et al. (2016) [2].

D3.3: Good practice guidelines for stakeholder and citizen participation in bioeconomy strategies
Davies, Sara ; Ribeiro, Barbara ; Millar, Kate ; Miller, Stephen ; Vironen, Heidi ; Charles, David ; Griestop, Laura ; Hasenheit, Marius ; Kiresiewa, Zoritza ; Hoes, A.C. ; Overbeek, M.M.M. ; Bianchini, Chiara - \ 2016
EU - 35 p.
biobased economy - government policy - public participation - case studies - decision making - multi-stakeholder processes - overheidsbeleid - publieke participatie - gevalsanalyse - besluitvorming - multi-stakeholder processen
This document has been developed as part of Work Package 3 of the BioSTEP project, which has examined current participatory practices, involving both stakeholders and citizens, in bioeconomy strategies in six case studies, namely: Two case studies at national level (Finland and Germany); Four case studies at regional level (Bio-based Delta in the Netherlands, Saxony-Anhalt in Germany, Scotland in the United Kingdom, and the Veneto in Italy). Key documentary sources include international and national practice-based literature on stakeholder and public engagement, as well as other BioSTEP publications. Two earlier reports (Charles et al., 2016; Davies et al., 2016) provide a detailed overview of participation in these six case studies of national and regional bioeconomy strategies. Building on this work, as well as on a review of existing research on stakeholder and citizen engagement in the bioeconomy, this document sets out guidance and suggestions for designing and undertaking engagement with stakeholders and citizens in relation to national and regional bioeconomy strategies.
International Advances in Pesticide Application : at the School of Agriculture, Universitat Politècnica de Catalunya, Barcelona, Spain, on 13-15 January 2016
Balsari, P. ; Cooper, S.E. ; Gill, E. ; Glass, C.R. ; Jones, W. ; Magri, B. ; Miller, P.C.H. ; Mountford-Smith, D. ; Nuyttens, D. ; Robinson, T.H. ; Stock, D. ; Taylor, J.C. ; Zande, J.C. van de - \ 2016
The Association of Applied Biologists (Aspects of Applied Biology 132) - 430 p.
This international event marked the 14th occasion of this biennial conference and provided an opportunity to discuss pesticide (and bio-pesticide) application issues in an informal setting with platform and poster presentations. Key workers from research institutes, industry and regulatory authorities provided a unique mix of biological and engineering sciences.

Many governments of late have realised the importance of agricultural technologies with renewed emphasis on funding strategies aimed at developing new ideas and bringing developments to market. All this, in an effort to provide sustained development of their agricultural industry and food security while globally offering sustenance for an ever growing population. While much of these efforts gravitate towards the informatics and precision control technologies we should not forget the expanse that is crop protection and application technology’s part. The adoption of the holistic approaches of Integrated Pest Management offer growers’ avenues for control as the registration pressure on traditional chemistry continues to erode the farmers’ armoury. The diversion of attention towards the development of bio-pesticides by many major companies reinforces this shift in attitude and expectations, but may also encourage accepted application methods to be re-examined. While the use of larger more sophisticated machines in the application of pesticides and bio pesticides offer opportunities in maximising production on an industrial scale it must be remembered that assistance on a small scale can also offer considerable benefits. The papers presented here contribute to the wealth of knowledge needed to support a safe, sustainable and efficient industry.
Feed intake, growth, and body and carcass attributes of feedlot steers supplemented with two levels of calcium nitrate or urea
Hegarty, R.S. ; Miller, J. ; Oelbrandt, N. ; Li, L. ; Luijben, J.P.M. ; Robinson, D.L. ; Nolan, J.V. ; Perdok, H.B. - \ 2016
Journal of Animal Science 94 (2016)12. - ISSN 0021-8812 - p. 5372 - 5381.
Beef cattle - Body composition - Carcass - Feedlot - Nitrate - Urea

Nitrate supplementation has been shown to be effective in reducing enteric methane emission from ruminants, but there have been few large-scale studies assessing the effects of level of nitrate supplementation on feed intake, animal growth, or carcass and meat quality attributes of beef cattle. A feedlot study was conducted to assess the effects of supplementing 0.25 or 0.45% NPN in dietary DM as either urea (Ur) or calcium nitrate (CaN) on DMI, ADG, G:F, and carcass attributes of feedlot steers (n = 383). The levels of NPN inclusion were selected as those at which nitrate has previously achieved measurable mitigation of enteric methane. The higher level of NPN inclusion reduced ADG as did replacement of Ur with CaN (P <0.01). A combined analysis of DMI for 139 steers with individual animal intake data and pen-average intakes for 244 bunk-fed steers showed a significant interaction between NPN source and level (P = 0.02) with steers on the high-CaN diet eating less than those on the other 3 diets (P <0.001). Neither level nor NPN source significantly affected cattle G:F. There was a tendency (P = 0.05) for nitratesupplemented cattle to have a slower rate of eating (g DMI/min) than Ur-supplemented cattle. When adjusted for BW, neither NPN source nor inclusion level affected cross-sectional area of the LM or fatness measured on the live animal. Similarly, there were no significant main effects of treatments on dressing percentage or fat depth or muscling attributes of the carcass after adjustment for HCW (P > 0.05). Analysis of composited meat samples showed no detectable nitrates or nitrosamines in raw or cooked meat, and the level of nitrate detected in meat from nitrate-supplemented cattle was no higher than for Ur-fed cattle (P > 0.05). We conclude that increasing NPN inclusion from 0.25 to 0.45% NPN in dietary DM and replacing Ur with CaN decreased ADG in feedlot cattle without improving G:F.

Comparative Genomics of Campylobacter fetus from Reptilesand Mammals Reveals Divergent Evolution in Host-Associated Lineages
Gilbert, Maarten J. ; Miller, William G. ; Yee, Emma ; Zomer, Aldert ; Graaf-Van Bloois, Linda Van Der; Fitzgerald, C. ; Forbes, Ken J. ; Méric, Guillaume ; Sheppard, S. ; Wagenaar, J.A. ; Duim, Birgitta - \ 2016
Genome Biology and Evolution 8 (2016)6. - ISSN 1759-6653 - p. 2006 - 2019.
Campylobacter fetus currently comprises three recognized subspecies, which display distinct host association. Campylobacter fetus subsp. fetus and C. fetus subsp. venerealis are both associated with endothermic mammals, primarily ruminants, whereas C. fetus subsp. testudinum is primarily associated with ectothermic reptiles. Both C. fetus subsp. testudinum and C. fetus subsp. fetus have been associated with severe infections, often with a systemic component, in immunocompromised humans. To study the genetic factors associated with the distinct host dichotomy in C. fetus, whole-genome sequencing and comparison of mammal- and reptile-associated C. fetus was performed. The genomes of C. fetus subsp. testudinum isolated from either reptiles or humans were compared with elucidate the genetic factors associated with pathogenicity in humans. Genomic comparisons showed conservation of gene content and organization among C. fetus subspecies, but a clear distinction between mammal- and reptile-associated C. fetus was observed. Several genomic regions appeared to be subspecies specific, including a putative tricarballylate catabolism pathway, exclusively present in C. fetus subsp. testudinum strains. Within C. fetus subsp. testudinum, sapA, sapB, and sapAB type strains were observed. The recombinant locus iamABC (mlaFED) was exclusively associated with invasive C. fetus subsp. testudinum strains isolated from humans. A phylogenetic reconstruction was consistent with divergent evolution in host-associated strains and the existence of a barrier to lateral gene transfer between mammal- and reptile-associated C. fetus. Overall, this study shows that reptile-associated C. fetus subsp. testudinum is genetically divergent from mammal-associated C. fetus subspecies.
Studying the Mammalian Intestinal Microbiome Using Animal Models
Hugenholtz, F. ; Zhang, J. ; O'Toole, P.W. ; Smidt, H. - \ 2016
In: Manual of Environmental Microbiology / Yates, Marylyn V., Nakatsu, Cindy H., Miller, Robert V., Pillai, Suresh D., Washington DC : ASM Press - ISBN 9781555816025 - p. 4.4.2 - 1-4.4.2-10.
The gastrointestinal (GI) tract of humans and animals is colonized by microorganisms immediately after birth. The composition of the GI tract microbiota undergoes remarkable alterations during early age, reaches a relative stable status in adulthood, and is driven by external factors such as habitual diet, location along the intestine, antibiotic therapy and maternal microbiota, and intrinsic factors such as host species and genotype. Whereas usually faecal samples are used for assessing the impact on the microbiota in human intervention studies, in vitro and animal models provide an easier way to collect many (invasive) samples, have multiple comparisons and regulating the genotype background. Animal models, and in particular mammalian models, provide an alternative way to study the in vivo responses to beneficial, commensal and pathogenic microorganisms in the GI tract, including studies that aim to see the impact of the host system as well. The main animals used to study the mammalian GI tract are rodents (mainly mice and rats) and pigs. Rodent and pig models, including gnotobiotic and humanized rodents and pigs and minipigs, have been extensively employed in gut microbiota studies, and especially the piglet model has been suggested as an appropriate model for human infant studies. With pig models, several intestinal sampling techniques can be applied in kinetic microbiota studies, including small intestinal segment perfusion and cannulation. In many cases, to test a certain treatment, a tiered approach consisting of complementary methods is employed, comprising in vitro, in vivo animal models, eventually leading towards human intervention studies.
Genome-wide analysis identifies 12 loci influencing human reproductive behavior
Barban, Nicola ; Jansen, Rick ; Vlaming, Ronald de; Vaez, Ahmad ; Mandemakers, Jornt J. ; Tropf, Felix C. ; Shen, Xia ; Wilson, James F. ; Chasman, Daniel I. ; Nolte, Ilja M. ; Tragante, Vinicius ; Laan, Sander W. van der; Perry, John R.B. ; Kong, Augustine ; Ahluwalia, Tarunveer S. ; Albrecht, Eva ; Yerges-Armstrong, Laura ; Atzmon, Gil ; Auro, Kirsi ; Ayers, Kristin ; Bakshi, Andrew ; Ben-Avraham, Danny ; Berger, Klaus ; Bergman, Aviv ; Bertram, Lars ; Bielak, Lawrence F. ; Bjornsdottir, Gyda ; Bonder, Marc Jan ; Broer, Linda ; Bui, Minh ; Barbieri, Caterina ; Cavadino, Alana ; Chavarro, Jorge E. ; Turman, Constance ; Concas, Maria Pina ; Cordell, Heather J. ; Davies, Gail ; Eibich, Peter ; Eriksson, Nicholas ; Esko, Tõnu ; Eriksson, Joel ; Falahi, Fahimeh ; Felix, Janine F. ; Fontana, Mark Alan ; Franke, Lude ; Gandin, Ilaria ; Gaskins, Audrey J. ; Gieger, Christian ; Gunderson, Erica P. ; Guo, Xiuqing ; Hayward, Caroline ; He, Chunyan ; Hofer, Edith ; Huang, Hongyan ; Joshi, Peter K. ; Kanoni, Stavroula ; Karlsson, Robert ; Kiechl, Stefan ; Kifley, Annette ; Kluttig, Alexander ; Kraft, Peter ; Lagou, Vasiliki ; Lecoeur, Cecile ; Lahti, Jari ; Li-Gao, Ruifang ; Lind, Penelope A. ; Liu, Tian ; Makalic, Enes ; Mamasoula, Crysovalanto ; Matteson, Lindsay ; Mbarek, Hamdi ; McArdle, Patrick F. ; McMahon, George ; Meddens, S.F.W. ; Mihailov, Evelin ; Miller, Mike ; Missmer, Stacey A. ; Monnereau, Claire ; Most, Peter J. van der; Myhre, Ronny ; Nalls, Mike A. ; Nutile, Teresa ; Kalafati, Ioanna Panagiota ; Porcu, Eleonora ; Prokopenko, Inga ; Rajan, Kumar B. ; Rich-Edwards, Janet ; Rietveld, Cornelius A. ; Robino, Antonietta ; Rose, Lynda M. ; Rueedi, Rico ; Ryan, Kathleen A. ; Saba, Yasaman ; Schmidt, Daniel ; Smith, Jennifer A. ; Stolk, Lisette ; Streeten, Elizabeth ; Tönjes, Anke ; Thorleifsson, Gudmar ; Ulivi, Sheila ; Wedenoja, Juho ; Wellmann, Juergen ; Willeit, Peter ; Yao, Jie ; Yengo, Loic ; Zhao, Jing Hua ; Zhao, Wei ; Zhernakova, Daria V. ; Amin, Najaf ; Andrews, Howard ; Balkau, Beverley ; Barzilai, Nir ; Bergmann, Sven ; Biino, Ginevra ; Bisgaard, Hans ; Bønnelykke, Klaus ; Boomsma, Dorret I. ; Buring, Julie E. ; Campbell, Harry ; Cappellani, Stefania ; Ciullo, Marina ; Cox, Simon R. ; Cucca, Francesco ; Toniolo, Daniela ; Davey-Smith, George ; Deary, Ian J. ; Dedoussis, George ; Deloukas, Panos ; Duijn, Cornelia M. van; Geus, Eco J.C. de; Eriksson, Johan G. ; Evans, Denis A. ; Faul, Jessica D. ; Sala, Cinzia Felicita ; Froguel, Philippe ; Gasparini, Paolo ; Girotto, Giorgia ; Grabe, Hans-Jörgen ; Greiser, Karin Halina ; Groenen, Patrick J.F. ; Haan, Hugoline G. de; Haerting, Johannes ; Harris, Tamara B. ; Heath, Andrew C. ; Heikkilä, Kauko ; Hofman, Albert ; Homuth, Georg ; Holliday, Elizabeth G. ; Hopper, John ; Hyppönen, Elina ; Jacobsson, Bo ; Jaddoe, Vincent W.V. ; Johannesson, Magnus ; Jugessur, Astanand ; Kähönen, Mika ; Kajantie, Eero ; Kardia, Sharon L.R. ; Keavney, Bernard ; Kolcic, Ivana ; Koponen, Päivikki ; Kovacs, Peter ; Kronenberg, Florian ; Kutalik, Zoltan ; Bianca, Martina la; Lachance, Genevieve ; Iacono, William G. ; Lai, Sandra ; Lehtimäki, Terho ; Liewald, David C. ; Lindgren, Cecilia M. ; Liu, Yongmei ; Luben, Robert ; Lucht, Michael ; Luoto, Riitta ; Magnus, Per ; Magnusson, Patrik K.E. ; Martin, Nicholas G. ; McGue, Matt ; McQuillan, Ruth ; Medland, Sarah E. ; Meisinger, Christa ; Mellström, Dan ; Metspalu, Andres ; Traglia, Michela ; Milani, Lili ; Mitchell, Paul ; Montgomery, Grant W. ; Mook-Kanamori, Dennis ; Mutsert, Renée de; Nohr, Ellen A. ; Ohlsson, Claes ; Olsen, Jørn ; Ong, Ken K. ; Paternoster, Lavinia ; Pattie, Alison ; Penninx, Brenda W.J.H. ; Perola, Markus ; Peyser, Patricia A. ; Pirastu, Mario ; Polasek, Ozren ; Power, Chris ; Kaprio, Jaakko ; Raffel, Leslie J. ; Räikkönen, Katri ; Raitakari, Olli ; Ridker, Paul M. ; Ring, Susan M. ; Roll, Kathryn ; Rudan, Igor ; Ruggiero, Daniela ; Rujescu, Dan ; Salomaa, Veikko ; Schlessinger, David ; Schmidt, Helena ; Schmidt, Reinhold ; Schupf, Nicole ; Smit, Johannes ; Sorice, Rossella ; Spector, Tim D. ; Starr, John M. ; Stöckl, Doris ; Strauch, Konstantin ; Stumvoll, Michael ; Swertz, Morris A. ; Thorsteinsdottir, Unnur ; Thurik, A.R. ; Timpson, Nicholas J. ; Tung, Joyce Y. ; Uitterlinden, André G. ; Vaccargiu, Simona ; Viikari, Jorma ; Vitart, Veronique ; Völzke, Henry ; Vollenweider, Peter ; Vuckovic, Dragana ; Waage, Johannes ; Wagner, Gert G. ; Wang, Jie Jin ; Wareham, Nicholas J. ; Weir, David R. ; Willemsen, Gonneke ; Willeit, Johann ; Wright, Alan F. ; Zondervan, Krina T. ; Stefansson, Kari ; Krueger, Robert F. ; Lee, James J. ; Benjamin, Daniel J. ; Cesarini, David ; Koellinger, Philipp D. ; Hoed, Marcel den; Snieder, Harold ; Mills, Melinda C. - \ 2016
Nature Genetics 48 (2016)12. - ISSN 1061-4036 - p. 1462 - 1472.
The genetic architecture of human reproductive behavior—age at first birth (AFB) and number of children ever born (NEB)—has a strong relationship with fitness, human development, infertility and risk of neuropsychiatric disorders. However, very few genetic loci have been identified, and the underlying mechanisms of AFB and NEB are poorly understood. We report a large genome-wide association study of both sexes including 251,151 individuals for AFB and 343,072 individuals for NEB. We identified 12 independent loci that are significantly associated with AFB and/or NEB in a SNP-based genome-wide association study and 4 additional loci associated in a gene-based effort. These loci harbor genes that are likely to have a role, either directly or by affecting non-local gene expression, in human reproduction and infertility, thereby increasing understanding of these complex traits.
Teaching and learning reflexivity in problem-oriented inter- and transdisciplinary research
Fortuin, K.P.J. ; Koppen, C.S.A. van - \ 2016
In: Conference Proceedings. - Wageningen : Wageningen University & Research - p. 209 - 213.
A crucial skill for researchers involved in inter- and transdisciplinary projects is the ability to reflect not only on the problem and its solutions but also on the process of knowledge production itself. In other words, these researchers require reflexive skills. Reflexive skills refer to the ability of researchers to question the different sorts of knowledge used, to recognize the epistemological and normative aspects involved, and to reflect on their own and others' roles in these knowledge processes (Fortuin and van Koppen 2015). Literature shows that reflexivity in interdisciplinary and transdisciplinary research is important, yet difficult to learn (Miller et al. 2008, Godemann 2008, Kueffer et al. 2012). Reflexive skills need to be trained. Existing literature provides, however, little specific guidance on how to do so. The research presented in this paper aimed at developing and evaluating a teaching and learning strategy for reflexive skills in interdisciplinarity and transdisciplinarity specifically.
Comparative genomics of campylobacter iguaniorum to unravel genetic regions associated with reptilian hosts
Gilbert, Maarten J. ; Miller, William G. ; Yee, Emma ; Kik, Marja ; Zomer, Aldert L. ; Wagenaar, Jaap A. ; Duim, Birgitta - \ 2016
Genome Biology and Evolution 8 (2016)9. - ISSN 1759-6653 - p. 3022 - 3029.
Campylobacter Iguaniorum - Comparative Genomics - Evolution - Phylogeny - Recombination - Reptile

Campylobacter iguaniorum is most closely related to the species C. fetus, C. hyointestinalis, andC. lanienae. Reptiles, chelonians and lizards in particular, appear to be a primary reservoir of this Campylobacter species. Here we report the genome comparison of C. iguaniorumstrain 1485E, isolated from a bearded dragon (Pogona vitticeps), and strain 2463D, isolated froma green iguana (Iguana iguana), with the genomes of closely related taxa, in particular with reptile-Associated C. fetus subsp.Testudinum. In contrast to C. fetus, C. iguaniorum is lacking an S-layer encoding region. Furthermore, a defined lipooligosaccharide biosynthesis locus, encoding multiple glycosyltransferases and bounded by waa genes, is absent from C. iguaniorum. Instead, multiple predicted glycosylation regionswere identified inC. iguaniorum.One of these regions is>50 kb withdeviantG+Ccontent, suggesting acquisition via lateral transfer. These similar, but non-homologous glycosylation regions were located at the same position on the genome in both strains. Multiple genes encoding respiratory enzymes not identified to date within the C. fetus clade were present. C. iguaniorum shared highest homology with C. hyointestinalis and C. fetus. As in reptile-Associated C. fetus subsp.Testudinum, a putative tricarballylate catabolism locus was identified. However, despite colonizing a shared host, no recent recombination between both taxa was detected. This genomic study provides a better understanding of host adaptation, virulence, phylogeny, and evolution of C. iguaniorum and related Campylobacter taxa.

Host body size and the diversity of tick assemblages on Neotropical vertebrates
Esser, Helen J. ; Foley, Janet E. ; Bongers, Frans ; Herre, Edward Allen ; Miller, Matthew J. ; Prins, Herbert H.T. ; Jansen, Patrick A. - \ 2016
International Journal for Parasitology: Parasites and Wildlife 5 (2016)3. - ISSN 2213-2244 - p. 295 - 304.
20/80 Rule - Panama - Parasite fauna - Pareto principle - Proportional similarity - Species richness

Identifying the factors that influence the species diversity and distribution of ticks (Acari: Ixodida) across vertebrate host taxa is of fundamental ecological and medical importance. Host body size is considered one of the most important determinants of tick abundance, with larger hosts having higher tick burdens. The species diversity of tick assemblages should also be greater on larger-bodied host species, but empirical studies testing this hypothesis are lacking. Here, we evaluate this relationship using a comparative dataset of feeding associations from Panama between 45 tick species and 171 host species that range in body size by three orders of magnitude. We found that tick species diversity increased with host body size for adult ticks but not for immature ticks. We also found that closely related host species tended to have similar tick species diversity, but correcting for host phylogeny did not alter the relationships between host body size and tick species diversity. The distribution of tick species was highly aggregated, with approximately 20% of the host species harboring 80% of all tick species, following the Pareto principle or 20/80 Rule. Thus, the aggregated pattern commonly observed for tick burdens and disease transmission also holds for patterns of tick species richness. Our finding that the adult ticks in this system preferentially parasitize large-bodied host species suggests that the ongoing anthropogenic loss of large-bodied vertebrates is likely to result in host-tick coextinction events, even when immature stages feed opportunistically. As parasites play critical roles in ecological and evolutionary processes, such losses may profoundly affect ecosystem functioning and services.

Molecular ecological insights into neotropical bird-tick interactions
Miller, Matthew J. ; Esser, Helen J. ; Loaiza, Jose R. ; Herre, Edward Allen ; Aguilar, Celestino ; Quintero, Diomedes ; Alvarez, Eric ; Bermingham, Eldredge - \ 2016
PLoS ONE 11 (2016)5. - ISSN 1932-6203 - 17 p.

In the tropics, ticks parasitize many classes of vertebrate hosts. However, because many tropical tick species are only identifiable in the adult stage, and these adults usually parasitize mammals, most attention on the ecology of tick-host interactions has focused on mammalian hosts. In contrast, immature Neotropical ticks are often found on wild birds, yet difficulties in identifying immatures hinder studies of birds' role in tropical tick ecology and tick-borne disease transmission. In Panama, we found immature ticks on 227 out of 3,498 individually-sampled birds representing 93 host species (24% of the bird species sampled, and 13% of the Panamanian land bird fauna). Tick parasitism rates did not vary with rainfall or temperature, but did vary significantly with several host ecological traits. Likewise, Neotropical-Nearctic migratory birds were significantly less likely to be infested than resident species. Using a molecular library developed from morphologically-identified adult ticks specifically for this study, we identified eleven tick species parasitizing birds, indicating that a substantial portion of the Panamanian avian species pool is parasitized by a diversity of tick species. Tick species that most commonly parasitized birds had the widest diversity of avian hosts, suggesting that immature tick species are opportunistic bird parasites. Although certain avian ecological traits are positively associated with parasitism, we found no evidence that individual tick species show specificity to particular avian host ecological traits. Finally, our data suggest that the four principal vectors of Rocky Mountain Spotted Fever in the Neotropics rarely, if ever, parasitize Panamanian birds. However, other tick species that harbor newly-discovered rickettsial parasites of unknown pathogenicity are frequently found on these birds. Given our discovery of broad interaction between Panamanian tick and avian biodiversity, future work on tick ecology and the dynamics of emerging tropical tick-borne pathogens should explicitly consider wild bird as hosts.

Improving the knowledge basis for advice on North Sea horse mackerel : developing new methods to get insight on stock boundaries and abundance
Brunel, Thomas ; Farrell, Edward D. ; Kotterman, Michiel ; Kwadijk, Christiaan ; Verkempynck, Ruben ; Chen, Chun ; Miller, David - \ 2016
IJmuiden : Wageningen Marine Research (Wageningen Marine Research report C092/16) - 57
trachurus trachurus - fish stocks - fisheries - models - visstand - visserij - modellen
The North Sea horse mackerel stock is currently classified by ICES as a data poor stock, for which the catch advice is based on the trend in an abundance index. The development of an analytical stock assessment, necessary to give more accurate advice, is hampered by a number of limitations on the input data, among which the most important are the poor quality of catch-at-age data and the absence of a targeted survey for North Sea horse mackerel. The aim of this project was to study possibilities to improve the data quality used for an analytical stock assessment model.
A miniaturized optoelectronic system for rapid quantitative label-free detection of harmful species in food
Raptis, Ioannis ; Misiakos, Konstantinos ; Makarona, Eleni ; Salapatas, Alexandros ; Petrou, Panagiota ; Kakabakos, Sotirios ; Botsialas, Athanasios ; Jobst, Gerhard ; Haasnoot, Willem ; Fernandez-Alba, Amadeo ; Lees, Michelle ; Valamontes, Evangelos - \ 2016
In: Frontiers in Biological Detection: From Nanosensors to Systems VIII. - SPIE (Progress in Biomedical Optics and Imaging 37) - ISBN 9781628419597
food safety - lab-on-a-chip - Mach-Zehnder interferometry - optoelectronic chip

Optical biosensors have emerged in the past decade as the most promising candidates for portable, highly-sensitive bioanalytical systems that can be employed for in-situ measurements. In this work, a miniaturized optoelectronic system for rapid, quantitative, label-free detection of harmful species in food is presented. The proposed system has four distinctive features that can render to a powerful tool for the next generation of Point-of-Need applications, namely it accommodates the light sources and ten interferometric biosensors on a single silicon chip of a less-than-40mm2 footprint, each sensor can be individually functionalized for a specific target analyte, the encapsulation can be performed at the wafer-scale, and finally it exploits a new operation principle, Broad-band Mach-Zehnder Interferometry to ameliorate its analytical capabilities. Multi-analyte evaluation schemes for the simultaneous detection of harmful contaminants, such as mycotoxins, allergens and pesticides, proved that the proposed system is capable of detecting within short time these substances at concentrations below the limits imposed by regulatory authorities, rendering it to a novel tool for the near-future food safety applications.

Longer lifespan in male mice treated with a weakly estrogenic agonist, an antioxidant, an α-glucosidase inhibitor or a Nrf2-inducer
Strong, Randy ; Miller, Richard A. ; Antebi, Adam ; Astle, Clinton M. ; Bogue, Molly ; Denzel, Martin S. ; Fernandez, Elizabeth ; Flurkey, Kevin ; Hamilton, Karyn L. ; Lamming, Dudley W. ; Javors, Martin A. ; Magalhães, João Pedro de; Martinez, Paul Anthony ; McCord, Joe M. ; Miller, Benjamin F. ; Müller, Michael ; Nelson, James F. ; Ndukum, Juliet ; Rainger, G.E. ; Richardson, Arlan ; Sabatini, David M. ; Salmon, Adam B. ; Simpkins, James W. ; Steegenga, Wilma T. ; Nadon, Nancy L. ; Harrison, David E. - \ 2016
Aging Cell 15 (2016)5. - ISSN 1474-9718 - p. 872 - 884.
17-α-estradiol - acarbose - fish oil - metformin - NDGA - Protandim - rapamycin - UDCA

The National Institute on Aging Interventions Testing Program (ITP) evaluates agents hypothesized to increase healthy lifespan in genetically heterogeneous mice. Each compound is tested in parallel at three sites, and all results are published. We report the effects of lifelong treatment of mice with four agents not previously tested: Protandim, fish oil, ursodeoxycholic acid (UDCA) and metformin – the latter with and without rapamycin, and two drugs previously examined: 17-α-estradiol and nordihydroguaiaretic acid (NDGA), at doses greater and less than used previously. 17-α-estradiol at a threefold higher dose robustly extended both median and maximal lifespan, but still only in males. The male-specific extension of median lifespan by NDGA was replicated at the original dose, and using doses threefold lower and higher. The effects of NDGA were dose dependent and male specific but without an effect on maximal lifespan. Protandim, a mixture of botanical extracts that activate Nrf2, extended median lifespan in males only. Metformin alone, at a dose of 0.1% in the diet, did not significantly extend lifespan. Metformin (0.1%) combined with rapamycin (14 ppm) robustly extended lifespan, suggestive of an added benefit, based on historical comparison with earlier studies of rapamycin given alone. The α-glucosidase inhibitor, acarbose, at a concentration previously tested (1000 ppm), significantly increased median longevity in males and 90th percentile lifespan in both sexes, even when treatment was started at 16 months. Neither fish oil nor UDCA extended lifespan. These results underscore the reproducibility of ITP longevity studies and illustrate the importance of identifying optimal doses in lifespan studies.

Whole genome sequence analysis indicates recent diversification of mammal-associated Campylobacter fetus and implicates a genetic factor associated with H2S production
Graaf-van Bloois, Linda van der; Duim, Birgitta ; Miller, William G. ; Forbes, Ken J. ; Wagenaar, Jaap A. ; Zomer, Aldert - \ 2016
BMC Genomics 17 (2016)1. - ISSN 1471-2164
Bovine Genital Campylobacteriosis - Campylobacter fetus - Core genome SNP analysis - Cysteine transporter - HS production - Subspecies differentiation

Background: Campylobacter fetus (C. fetus) can cause disease in both humans and animals. C. fetus has been divided into three subspecies: C. fetus subsp. fetus (Cff), C. fetus subsp. venerealis (Cfv) and C. fetus subsp. testudinum (Cft). Subspecies identification of mammal-associated C. fetus strains is crucial in the control of Bovine Genital Campylobacteriosis (BGC), a syndrome associated with Cfv. The prescribed methods for subspecies identification of the Cff and Cfv isolates are: tolerance to 1 % glycine and H2S production. Results: In this study, we observed the deletion of a putative cysteine transporter in the Cfv strains, which are not able to produce H2S from L-cysteine. Phylogenetic reconstruction of the core genome single nucleotide polymorphisms (SNPs) within Cff and Cfv strains divided these strains into five different clades and showed that the Cfv clade and a Cff clade evolved from a single Cff ancestor. Conclusions: Multiple C. fetus clades were observed, which were not consistent with the biochemical differentiation of the strains. This suggests the need for a closer evaluation of the current C. fetus subspecies differentiation, considering that the phenotypic differentiation is still applied in BGC control programs.

Quantification of Stereochemical Communication in Metal–Organic Assemblies
Castilla, Ana M. ; Miller, Mark A. ; Nitschke, Jonathan R. ; Smulders, Maarten M.J. - \ 2016
Angewandte Chemie-International Edition 55 (2016)36. - ISSN 1433-7851 - p. 10616 - 10620.
cage compounds - diastereoselectivity - statistical mechanics - stereochemical communication - supramolecular chemistry

The derivation and application of a statistical mechanical model to quantify stereochemical communication in metal–organic assemblies is reported. The factors affecting the stereochemical communication within and between the metal stereocenters of the assemblies were experimentally studied by optical spectroscopy and analyzed in terms of a free energy penalty per “incorrect” amine enantiomer incorporated, and a free energy of coupling between stereocenters. These intra- and inter-vertex coupling constants are used to track the degree of stereochemical communication across a range of metal–organic assemblies (employing different ligands, peripheral amines, and metals); temperature-dependent equilibria between diastereomeric cages are also quantified. The model thus provides a unified understanding of the factors that shape the chirotopic void spaces enclosed by metal–organic container molecules.

D3.2: Case studies of regional bioeconomy strategies across Europe
Charles, David ; Davies, S. ; Miller, S. ; Clement, K. ; Overbeek, M.M.M. ; Hoes, A.C. ; Hasenheit, Marius ; Kiresiewa, Zoritza ; Kah, Stefan ; Bianchini, Chiara - \ 2016
EU - 80 p.
regional economics - regional development - economic development - biobased economy - european union - government policy - regionale economie - regionale ontwikkeling - economische ontwikkeling - europese unie - overheidsbeleid
This report provides a summary of issues raised in the four regional case studies: Scotland, South-West Netherlands, Saxony-Anhalt and Veneto. It examines the ways in which the bioeconomy has been defined in regional strategies and the ways in which those regional strategies have been initi-ated and implemented in the four regions. Each of the regions has a distinctive approach, specialis-ing around the particular assets and strengths of the region and its core stakeholders. Typically, re-gional strategies have been developed by regional government or by stakeholder groups sponsored by those governments, and hence the main objectives have been to promote economic development through the application of developments in the bioeconomy. A primary driver of strategy development has been the need to respond to the requirements of the EU smart specialisation strategies.
Gender specific differences in the liver proteome of rats exposed to short term and low-concentration hexabromocyclododecane (HBCD)
Miller, I. ; Diepenbroek, C. ; Rijntjes, E. ; Renaut, J. ; Teerds, K.J. ; Kwadijk, C. ; Cambier, S. ; Murk, A.J. ; Gutleb, A.C. ; Serchi, T. - \ 2016
Toxicology Research 5 (2016)5. - ISSN 2045-452X - p. 1273 - 1283.

The influence of short term (7-day) exposure of male rats to the brominated flame retardant hexabromocyclododecane (HBCD) was studied by investigation of the liver proteome, both in euthyroid and hypothyroid rats and by comparing results with general data on animal physiology and thyroid hormone, leptin, insulin and gonadotropin concentrations determined in parallel. Proteome analysis of liver tissue by two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) revealed that only small protein pattern changes were induced by exposure in males, on just a few proteins with different functions and not involved in pathways in common. This is in contrast to previous findings in similarly exposed eu- and hypothyroid female rats, where general metabolic pathways had been shown to be affected. The largest gender-dependent effects concerned basal concentrations of liver proteins already in control and hypothyroid animals, involving mainly the pathways which were also differently affected by HBCD exposure. Among them were differences in lipid metabolism, which-upon exposure to HBCD-may also be the reason for the considerably higher ratio of γ-HBCD accumulated in white adipose tissue of exposed female rats compared to males. The results further elucidate the already suggested different sensitivity of genders towards HBCD exposure on the protein level, and confirm the need for undertaking toxicological animal experiments in both genders.

Grazing lands in Sub-Saharan Africa and their potential role in climate change mitigation: What we do and don't know
Milne, E. ; Aynekulu, E. ; Bationo, A. ; Batjes, N.H. ; Boone, R. ; Conant, R. ; Davies, J. ; Hanan, N. ; Hoag, D. ; Herrick, J.E. ; Knausenberger, W. ; Neely, C. ; Njoka, J. ; Ngugi, M. ; Parton, B. ; Paustian, K. ; Reid, K. ; Said, M. ; Shepherd, K. ; Swift, D. ; Thornton, P. ; Williams, S. ; Miller, S. ; Nkonya, Ephraim - \ 2016
Environmental Development 19 (2016). - ISSN 2211-4645 - p. 70 - 74.
In 2014, the USAID project ‘Grazing lands, livestock and climate resilient mitigation in Sub-Saharan Africa’ held two workshops, hosted by the Colorado State University, which brought together experts from around the world. Two reports resulted from these workshops, one an assessment of the state of the science, and the other an inventory of related activities in the region to date.. In this short communication we summarize the main points of the first report – The state of the science (Milne and Williams, 2015). A second report is in preparation.
Regional atmospheric CO2 inversion reveals seasonal and geographic differences in Amazon net biome exchange
Alden, C.B. ; Miller, J.B. ; Gatti, L.V. ; Gloor, M.M. ; Laan-Luijkx, I.T. van der; Krol, M.C. ; Guan, K. ; Michalak, A.M. ; Touma, T. ; Andrew, A. ; Basso, L.S. ; Correia, C.S.C. ; Domingues, L.G. ; Joiner, J. ; Lyapustin, A. ; Peters, W. ; Shiga, Y.P. ; Thoning, K. ; Velde, I.R. van der; Leeuwen van, T.T. ; Yadav, V. ; Diffenbaugh, N.S. - \ 2016
Global Change Biology 22 (2016)10. - ISSN 1354-1013
Understanding tropical rainforest carbon exchange and its response to heat and drought is critical for quantifying the effects of climate change on tropical ecosystems, including global climate–carbon feedbacks. Of particular importance
for the global carbon budget is net biome exchange of CO2 with the atmosphere (NBE), which represents nonfire carbon fluxes into and out of biomass and soils. Subannual and sub-Basin Amazon NBE estimates have relied heavily on
process-based biosphere models, despite lack of model agreement with plot-scale observations. We present a new analysis of airborne measurements that reveals monthly, regional-scale (~1–8 9 106 km2) NBE variations. We
develop a regional atmospheric CO2 inversion that provides the first analysis of geographic and temporal variability in Amazon biosphere–atmosphere carbon exchange and that is minimally influenced by biosphere model-based first
guesses of seasonal and annual mean fluxes. We find little evidence for a clear seasonal cycle in Amazon NBE but do find NBE sensitivity to aberrations from long-term mean climate. In particular, we observe increased NBE (more carbon
emitted to the atmosphere) associated with heat and drought in 2010, and correlations between wet season NBE and precipitation (negative correlation) and temperature (positive correlation). In the eastern Amazon, pulses of
increased NBE persisted through 2011, suggesting legacy effects of 2010 heat and drought. We also identify regional differences in postdrought NBE that appear related to long-term water availability. We examine satellite proxies and
find evidence for higher gross primary productivity (GPP) during a pulse of increased carbon uptake in 2011, and lower GPP during a period of increased NBE in the 2010 dry season drought, but links between GPP and NBE
changes are not conclusive. These results provide novel evidence of NBE sensitivity to short-term temperature and moisture extremes in the Amazon, where monthly and sub-Basin estimates have not been previously available.
Understanding isoprene photooxidation using observations and modeling over a subtropical forest in the southeastern US
Su, Luping ; Patton, Edward G. ; Vilà-guerau De Arellano, Jordi ; Guenther, Alex B. ; Kaser, Lisa ; Yuan, Bin ; Xiong, Fulizi ; Shepson, Paul B. ; Zhang, Li ; Miller, David O. ; Brune, William H. ; Baumann, Karsten ; Edgerton, Eric ; Weinheimer, Andrew ; Misztal, Pawel K. ; Park, Jeong-Hoo ; Goldstein, Allen H. ; Skog, Kate M. ; Keutsch, Frank N. ; Mak, John E. - \ 2016
Atmospheric Chemistry and Physics 16 (2016)12. - ISSN 1680-7316 - p. 7725 - 7741.
The emission, dispersion, and photochemistry of isoprene (C5H8) and related chemical species in the convective boundary layer (CBL) during sunlit daytime were studied over a mixed forest in the southeastern United States by combining ground-based and aircraft observations. Fluxes of isoprene and monoterpenes were quantified at the top of the forest canopy using a high-resolution proton transfer reaction time-of-flight mass spectrometer (PTR-TOF-MS). Snapshot (∼  2 min sampling duration) vertical profiles of isoprene, methyl vinyl ketone (MVK) + methacrolein (MACR), and monoterpenes were collected from aircraft every hour in the CBL (100–1000 m). Both ground-based and airborne collected volatile organic compound (VOC) data are used to constrain the initial conditions of a mixed-layer chemistry model (MXLCH), which is applied to examine the chemical evolution of the O3–NOx–HOx–VOC system and how it is affected by boundary layer dynamics in the CBL. The chemical loss rate of isoprene (∼  1 h) is similar to the turbulent mixing timescale (0.1–0.5 h), which indicates that isoprene concentrations are equally dependent on both photooxidation and boundary layer dynamics. Analysis of a model-derived concentration budget suggests that diurnal evolution of isoprene inside the CBL is mainly controlled by surface emissions and chemical loss; the diurnal evolution of O3 is dominated by entrainment. The NO to HO2 ratio (NO : HO2) is used as an indicator of anthropogenic impact on the CBL chemical composition and spans a wide range (1–163). The fate of hydroxyl-substituted isoprene peroxyl radical (HOC5H8OO·; ISOPOO) is strongly affected by NO : HO2, shifting from NO-dominant to NO–HO2-balanced conditions from early morning to noontime. This chemical regime change is reflected in the diurnal evolution of isoprene hydroxynitrates (ISOPN) and isoprene hydroxy hydroperoxides (ISOPOOH).
Proteomics as a tool to gain more insight into sub-lethal toxicological effects
Miller, Ingrid - \ 2016
Wageningen University. Promotor(en): Tinka Murk, co-promotor(en): A.C. Gutleb; T. Serchi. - Wageningen : Wageningen University - ISBN 9789462578210 - 182
proteomics - laboratory methods - sublethal effects - toxic substances - endocrine disruptors - food consumption - toxicology - animal experiments - eiwitexpressieanalyse - laboratoriummethoden - subletale effecten - toxische stoffen - hormoonverstoorders - voedselconsumptie - toxicologie - dierproeven

This thesis focuses on a modern analytical method, proteomics, to investigate its use in the field of toxicological research. Proteomics is a high resolution method which separates all proteins present in a sample at a clearly defined state and compares this pattern to another one, under slightly different conditions (e.g. after exposure to a chemical). Protein changes may give rise to or reflect disease/harm of the individual and can be attributed to alterations in body functions/regulation systems. Analysis conditions and different varieties of proteomic methods are explained, and a brief introduction given where proteomics is already applied in toxicology. A specific investigation has been performed with the flame retardant HBCD (i.e. hexabromocyclododecane). It is a compound that accumulates in lipid tissue from where it is only slowly removed. Its mechanism of action is not yet completely understood and sometimes seems to be contradictory. Rats were exposed to HBCD in very low doses for just one week and liver proteins were compared to those of unexposed animals. As HBCD is suggested to disturb the thyroid system, both healthy and hypothyroid rats were investigated, of both genders. In female rats, not in males, some specific liver protein changes were seen in glucose/carbohydrate and lipid metabolism, and also in some stress related proteins. Changes were not dependent on the thyroid function of the females. These results are in line with previous findings that female rats were more susceptible to HBCD than males. In a further step, protein patterns of unexposed animals of both genders were compared, revealing gender-dependent differences that exceeded the effects seen in any of the other comparisons, mainly in the pathways that were also affected by HBCD in females. A previous proteomic study on serum proteins has also shown clear gender-dependent concentration differences in rats. This underlines the importance of performing studies both in female and male individuals. The detection of considerable gender-dependent protein alterations confirms that proteomics is a biochemical tool with high sensitivity and large potential also in toxicological research.

Inverse modeling of GOSAT-retrieved ratios of total column CH4 and CO2 for 2009 and 2010
Pandey, Sudhanshu ; Houweling, Sander ; Krol, Maarten ; Aben, Ilse ; Chevallier, Frédéric ; Dlugokencky, Edward J. ; Gatti, Luciana V. ; Gloor, Emanuel ; Miller, John B. ; Detmers, Rob ; Machida, Toshinobu ; Röckmann, Thomas - \ 2016
Atmospheric Chemistry and Physics 16 (2016)8. - ISSN 1680-7316 - p. 5043 - 5062.

This study investigates the constraint provided by greenhouse gas measurements from space on surface fluxes. Imperfect knowledge of the light path through the atmosphere, arising from scattering by clouds and aerosols, can create biases in column measurements retrieved from space. To minimize the impact of such biases, ratios of total column retrieved CH4 and CO2 (Xratio) have been used. We apply the ratio inversion method described in Pandey et al. (2015) to retrievals from the Greenhouse Gases Observing SATellite (GOSAT). The ratio inversion method uses the measured Xratio as a weak constraint on CO2 fluxes. In contrast, the more common approach of inverting proxy CH4 retrievals (Frankenberg et al., 2005) prescribes atmospheric CO2 fields and optimizes only CH4 fluxes. The TM5-4DVAR (Tracer Transport Model version 5-variational data assimilation system) inverse modeling system is used to simultaneously optimize the fluxes of CH4 and CO2 for 2009 and 2010. The results are compared to proxy inversions using model-derived CO2 mixing ratios (XCO2model) from CarbonTracker and the Monitoring Atmospheric Composition and Climate (MACC) Reanalysis CO2 product. The performance of the inverse models is evaluated using measurements from three aircraft measurement projects. Xratio and XCO2model are compared with TCCON retrievals to quantify the relative importance of errors in these components of the proxy XCH4 retrieval (XCH4proxy). We find that the retrieval errors in Xratio (mean Combining double low line 0.61%) are generally larger than the errors in XCO2model (mean Combining double low line 0.24 and 0.01% for CarbonTracker and MACC, respectively). On the annual timescale, the CH4 fluxes from the different satellite inversions are generally in agreement with each other, suggesting that errors in XCO2model do not limit the overall accuracy of the CH4 flux estimates. On the seasonal timescale, however, larger differences are found due to uncertainties in XCO2model, particularly over Australia and in the tropics. The ratio method stays closer to the a priori CH4 flux in these regions, because it is capable of simultaneously adjusting the CO2 fluxes. Over tropical South America, comparison to independent measurements shows that CO2 fields derived from the ratio method are less realistic than those used in the proxy method. However, the CH4 fluxes are more realistic, because the impact of unaccounted systematic uncertainties is more evenly distributed between CO2 and CH4. The ratio inversion estimates an enhanced CO2 release from tropical South America during the dry season of 2010, which is in accordance with the findings of Gatti et al. (2014) and Van der Laan et al. (2015). The performance of the ratio method is encouraging, because despite the added nonlinearity due to the assimilation of Xratio and the significant increase in the degree of freedom by optimizing CO2 fluxes, still consistent results are obtained with respect to other CH4 inversions.

Post-breeding migration routes of marine turtles from Bonaire and Klein Bonaire, Caribbean Netherlands
Becking, L.E. ; Christianen, M.J.A. ; Nava, M.I. ; Miller, N. ; Willis, S. ; Dam, R.P. Van - \ 2016
Endangered Species Research 30 (2016). - ISSN 1863-5407 - p. 117 - 124.
The management of small rookeries is key to conserving the regional genetic diversity of marine turtle populations and requires knowledge on population connectivity between breeding and foraging areas. To elucidate the geographic scope of the populations of marine turtles breeding at Bonaire and Klein Bonaire (Caribbean Netherlands) we examined the post-breeding migratory behavior of 5 female loggerheads Caretta caretta, 4 female green turtles Chelonia mydas, and 2 male and 13 female hawksbill turtles Eretmochelys imbricata during the years 2004-2013. After leaving Bonaire, the 24 tracked turtles frequented foraging grounds in 10 countries. The distances swum from Bonaire to the foraging areas ranged from 608 to 1766 km for loggerhead turtles, 198 to 3135 km for green turtles, and 197 to 3135 km for hawksbill turtles, together crossing the waters of 19 countries. Males represented the minority in this study, but we made 2 key observations that require further research: males remained in the vicinity of the breeding area for 3-5 mo, which is 2-5 times longer than females, and males migrated greater distances than previously recorded. Although the turtles dispersed widely across the Caribbean, there appeared to be 2 benthic foraging areas of particular importance to all 3 species of marine turtles breeding at Bonaire, namely the shallow banks east of Nicaragua and Honduras (n = 8 tracked turtles) and Los Roques, Venezuela (n = 3). Marine turtles breeding at Bonaire face threats from legal turtle harvesting, illegal take, and bycatch in the waters that they traverse across the Caribbean
Campylobacter fetus subspecies contain conserved type IV secretion systems on multiple genomic islands and plasmids
Graaf-Van Bloois, Linda Van Der; Miller, William G. ; Yee, Emma ; Wagenaar, Jaap A. ; Gorkiewisz, G. ; Forbes, Ken J. ; Zomer, Aldert ; Duim, Birgitta - \ 2016
PLoS ONE 11 (2016)4. - ISSN 1932-6203

The features contributing to differences in pathogenicity of the Campylobacter fetus subspecies are unknown. Putative factors involved in pathogenesis are located in genomic islands that encode a type IV secretion system (T4SS) and fic domain (filamentation induced by cyclic AMP) proteins, which may disrupt host cell processes. In the genomes of 27 C. fetus strains, three phylogenetically-different T4SS-encoding regions (T4SSs) were identified: one was located in both the chromosome and in extra-chromosomal plasmids; one was located exclusively in the chromosome; and one exclusively in extra-chromosomal plasmids.We observed that C. fetus strains can contain multiple T4SSs and that homologous T4SSs can be present both in chromosomal genomic islands (GI) and on plasmids in the C. fetus strains. The GIs of the chromosomally located T4SS differed mainly by the presence of fic genes, insertion sequence elements and phage-related or hypothetical proteins. Comparative analysis showed that T4SS sequences, inserted in the same locations, were conserved in the studied C. fetus genomes. Using phylogenetic analysis of the T4SSs, it was shown that C. fetus may have acquired the T4SS regions from other Campylobacter species by horizontal gene transfer. The identified T4SSs and fic genes were found in Cff and Cfv strains, although the presence of T4SSs and fic genes were significantly associated with Cfv strains. The T4SSs and fic genes could not be associated with S-layer serotypes or geographical origin of the strains.

Fisheries management controls for dab in The North Sea
Miller, D.C.M. ; Verkempynck, R. - \ 2016
IMARES (Report / IMARES C040/16) - 31 p.
Maximale Duurzame Oogst: wat betekent dat eigenlijk?
Miller, David - \ 2016
Dataset of liver proteins changed in eu- and hypothyroid female rats upon in vivo exposure to hexabromocyclododecane (HBCD)
Miller, I. ; Serchi, T. ; Cambier, S. ; Diepenbroek, C. ; Renaut, J. ; Berg, J.H.J. van den; Kwadijk, C. ; Gutleb, A.C. ; Rijntjes, E. ; Murk, A.J. - \ 2016
Data in Brief (2016). - ISSN 2352-3409 - p. 386 - 392.
HBCD - Hypothyroidism - Lipid metabolism - Liver - Proteomics - Rat

Female Wistar rats with different thyroid status (eu-, hypothyroid) were exposed to 0, 3 or 30 mg/kg body weight of the flame retardant HBCD for 7 days. Changes in protein patterns obtained by 2D-DIGE were evaluated, and different animal groups compared taking into account their exposure and thyroid status. Proteins significantly altered in abundance in any of these comparisons were identified by mass spectrometry. These data, together with hormone data of the animals, are discussed in "Hexa-bromocyclododecane (HBCD) induced changes in the liver proteome of eu- and hypothyroid female rats" (Miller et al., 2016) [1].

Hexabromocyclododecane (HBCD) induced changes in the liver proteome of eu- and hypothyroid female rats
Miller, I. ; Serchi, T. ; Cambier, S. ; Diepenbroek, C. ; Renaut, J. ; Berg, J.H.J. Van der; Kwadijk, C. ; Gutleb, A.C. ; Rijntjes, E. ; Murk, A.J. - \ 2016
Toxicology Letters 245 (2016). - ISSN 0378-4274 - p. 40 - 51.
HBCD - Hypothyroidism - Lipid metabolism - Liver - Proteomics - Rat

Hexabromocyclododecane (HBCD) is a brominated flame retardant known for its low acute toxicity as observed in animal experiments. However, HBCD exposure can affect liver functioning and thyroid hormone (TH) status. As exact mechanisms are unknown and only limited toxicological data exists, a gel-based proteomic approach was undertaken. In a eu- and hypothyroid female rat model, rats were exposed to 3 and 30 mg/kg. bw/day HBCD for 7 days via their diet, and exposure was related to a range of canonical endpoints (hormone status, body weight) available for these animals. Alterations in the liver proteome under HBCD exposure were determined in comparison with patterns of control animals, for both thyroid states. This revealed significantly changed abundance of proteins involved in metabolic processes (gluconeogenesis/glycolysis, amino acid metabolism, lipid metabolism), but also in oxidative stress responses, in both euthyroid and hypothyroid rats. The results provide a more detailed picture on the mechanisms involved in these alterations, e.g. at the protein level changes of the proposed influence of HBCD on the lipid metabolism. Present results show that proteomic approaches can provide further mechanistic insights in toxicological studies.

Nonequilibrium Thermodynamics of Interfaces
Sagis, L.M.C. - \ 2016
In: Computational Methods for Complex Liquid-Fluid Interfaces / Rahni, Mohammad Taeibi, Karbaschi, Mohsen, Reinhard, Miller, Boca Raton : CRC Press (Progress in Colloid and Interface Science ) - ISBN 9781498722087 - p. 41 - 58.
Contributors to dietary glycaemic index and glycaemic load in the Netherlands: the role of beer
Sluik, D. ; Atkinson, Fiona S. ; Brand-Miller, J. ; Fogelholm, M. ; Raben, A. ; Feskens, E.J.M. - \ 2016
The British journal of nutrition 115 (2016)7. - ISSN 0007-1145 - p. 1218 - 1225.
Diets high in glycaemic index (GI) and glycaemic load (GL) have been associated with a higher diabetes risk. Beer explained a large proportion of variation in GI in a Finnish and an American study. However, few beers have been tested according to International Organization for Standardization (ISO) methodology. We tested the GI of beer and estimated its contribution to dietary GI and GL in the Netherlands. GI testing of pilsner beer (Pilsner Urquell) was conducted at The University of Sydney according to ISO international standards with glucose as the reference food. Subsequently, GI and GL values were assigned to 2556 food items in the 2011 Dutch food composition table using a six-step methodology and consulting four databases. This table was linked to dietary data from 2106 adults in the Dutch National Food Consumption Survey 2007–2010. Stepwise linear regression identified contribution to inter-individual variation in dietary GI and GL. The GI of pilsner beer was 89 (sd 5). Beer consumption contributed to 9·6 and 5·3 % inter-individual variation in GI and GL, respectively. Other foods that contributed to the inter-individual variation in GI and GL included potatoes, bread, soft drinks, sugar, candy, wine, coffee and tea. The results were more pronounced in men than in women. In conclusion, beer is a high-GI food. Despite its relatively low carbohydrate content (approximately 4–5 g/100 ml), it still made a contribution to dietary GL, especially in men. Next to potatoes, bread, sugar and sugar-sweetened beverages, beer captured a considerable proportion of between-person variability in GI and GL in the Dutch diet.
Minimum aanlandingsmaat Brasem (Abramis brama)
Hal, R. van; Miller, D.C.M. - \ 2016
IJmuiden : IMARES (Rapport / IMARES C148/15a) - 17
abramis brama - grootte - visserij - lengte - ijsselmeer - size - fisheries - length - lake ijssel
Ter ondersteuning van een besluit aangaande een minimum aanlandingsmaat voor brasem, primair voor het IJsselmeer en Markermeer, heeft het ministerie van Economische Zaken IMARES verzocht een overzicht te geven van aanlandingsmaten voor brasem in andere landen en waar mogelijk de motivatie achter deze maten te geven. Er blijken in verschillende, voornamelijk oost, Europese landen minimum aanlandingsmaten te zijn ingesteld. Het is echter niet altijd duidelijk of deze voor de commerciële en/of recreatieve visserij gelden. De gegeven maten zijn niet eenduidig, in een deel van de geval gelden de maten voor de gehele vis (puntje neus tot eind staart) voor een ander deel gelden ze voor een kleiner deel van de vis (puntje neus tot begin staart). Het was voor ons niet altijd duidelijk welke meetmethode gebruikt wordt. De gevonden minimum aanlandingsmaten variëren tussen 20 en 45 cm. Er zijn helaas geen gegevens gevonden voor de onderbouwing van deze maten. Een mogelijke methode om een minimum aanlandingsmaat vast te stellen is gebruik te maken van gegevens die per lengte aangegeven welk deel van de populatie volwassen is. Op basis van deze gegevens kan een volwassenheid ogive worden bepaald. Deze was beschikbaar gebaseerd op IMARES survey en afslag gegevens van het IJsselmeer. Met behulp van deze ogive is de lengte waarop 50, 70 en 100% van de populatie brasem volwassen is bepaald. Bij de doelstelling “het zorgdragen van voortplanting” zijn dit maten die indicatief zou kunnen zijn voor een eventuele minimum aanlandingsmaat voor het IJsselmeer en Markermeer.
The role of traceability in transforming seafood governance in the global South
Bailey, M.L. ; Bush, S.R. ; Miller, A. ; Kochen, M. - \ 2016
Current Opinion in Environmental Sustainability 18 (2016). - ISSN 1877-3435 - p. 25 - 32.
Business-to-business traceability has historically played an important role in coordinating value chain activities and helping businesses to manage reputational risk. Its use and value, however, have recently extended beyond industry value chain actors alone, and traceability information may now contribute to improving government regulation, and via consumer-facing traceability (CFT) systems to sustainable seafood governance. Implementing traceability can be costly and requires coordination, consequently most systems utilized till date have been in the global North. Yet seafood value chains remain incredibly complex, and the majority of seafood is sourced from the South. This paper synthesizes the traceability literature through an informational governance perspective, analyzing if and how information can transform production practices while at the same time empowering producing nations. Traceability has gone beyond simply facilitating improved recall coordination, but the future value of traceability lies in how to design and organize systems in such a way that information flows can be harnessed to improve global seafood governance.
Closing the Incentive Gap: The Role of Public and Private Actors in Governing Indonesia's Tuna Fisheries
Bailey, M.L. ; Miller, A.M.M. ; Bush, S.R. ; Zwieten, P.A.M. van; Wiryawan, B. - \ 2016
Journal of Environmental Policy and Planning 18 (2016)2. - ISSN 1523-908X - p. 141 - 160.
Indonesia is one of the world's largest tuna producing countries, yet regulatory oversight remains weak and management is poor. Incentive-based approaches are a way to improve state-based resource management, but they often require strong government regulation. In this paper, we use principal–agent theory and the notion of the ‘incentive gap’ to explore how incentives could be brought to bear in Indonesia through a combination of private and public actors. With a shared fish stock like tuna, we argue that a double principal–agent problem emerges, where information, asymmetries between various players complicate management. We focus on the problems of adverse selection and moral hazard in three different tuna fisheries in Indonesia to identify the nature of the incentive gap, and comment on the mix of public and private actors currently engaged in tuna fishery governance towards reducing the gap. The double principal–agent problem is a useful yet underutilized framework to understand the dynamics of shared stocks management. In this first application to a developing country fishery, we conclude that information asymmetries cannot be overcome without the involvement of private actors, who are increasingly becoming important in aligning regional and global objectives with those of fishers themselves.
Mesoscale Lattice Boltzmann Model of Dispersions Stabilized by Surfactants
Meinders, M.B.J. ; Sman, R.G.M. van der - \ 2015
In: Computational Methods for Complex Liquid-Fluid Interfaces / Taeibi Rahni, Mohammad, Karbaschi, Mohsen, Miller, Reinhard, Boca Raton : CRC Press / Taylor & Francis - ISBN 9781498722087 - p. 295 - 308.
Modeling Foam Stability
Meinders, M.B.J. ; Sman, R.G.M. van der - \ 2015
In: Computational Methods for Complex Liquid-Fluid Interfaces / Taeibi Rahni, Mohammad, Karbaschi, Mohsen, Miller, Reinhard, CRC Press / Taylor & Francis (Progress in Colloid and Interface Science ) - ISBN 9781498722087 - p. 503 - 526.
Status and trends of St. Eustatius Coral reef ecosystem and fisheries: 2015 report card
Graaf, M. de; Piontek, S. ; Miller, D.C.M. ; Brunel, T.P.A. ; Nagelkerke, L.A.J. - \ 2015
IJmuiden : IMARES (Report / IMARES C167/15) - 41 p.
coral reefs - ecosystems - fisheries - algae - fishery management - pollution - habitat degradation - nature conservation - sint eustatius - koraalriffen - ecosystemen - visserij - algen - visserijbeheer - verontreiniging - habitatdegradatie - natuurbescherming
A message from magic to science: seeing how the brain can be tricked may strengthen our thinking
Osterblom, H. ; Scheffer, M. ; Westley, F.R. ; Esso, M.L. van; Miller, J. ; Bascompte, J. - \ 2015
Ecology and Society 20 (2015)4. - ISSN 1708-3087 - 4 p.
Art - Cognitive capacity - Cognitive limitations - Conclusion errors - Confirmation bias - Creative thinking - Illusion - Illusionist - Inattentive blindness - Magic - Magician - Priming - Science - Scientific discovery - Selective attention
Scientific discoveries rely on creative thinking, and several authors have explored similarities in and differences between creativity in the sciences and that in the arts. Here we explore possible ways in which science can learn from the arts, focusing specifically on experiences derived from the art of magic and on the limitations of human cognition. Generations of stage magicians or “illusionists” have made sophisticated use of the weaknesses in human systems of perception and interpretation. We highlight three important principles of magic tricks, including: (1) the audience see what it expects, (2) it is blind to all but the focus of attention, and (3) ideas spring predictably from a primed mind. These principles highlight a number of important tendencies, which we argue are shortcomings in the ability of scientists to perceive the world, and which scientists need to be aware of. Consciously addressing these shortcomings may help scientists improve their creativity, and will strengthen their capacity to address complex and global challenges. © 2015 by the author(s). Published here under license by the Resilience Alliance.
Campylobacter iguaniorum sp. nov., isolated from reptiles
Gilbert, Maarten J. ; Kik, Marja ; Miller, William G. ; Duim, Birgitta ; Wagenaar, Jaap A. - \ 2015
International Journal of Systematic and Evolutionary Microbiology 65 (2015)3. - ISSN 1466-5026 - p. 975 - 982.

During sampling of reptiles for members of the class Epsilonproteobacteria, strains representing a member of the genus Campylobacter not belonging to any of the established taxa were isolated from lizards and chelonians. Initial amplified fragment length polymorphism, PCR and 16S rRNA sequence analysis showed that these strains were most closely related to Campylobacter fetus and Campylobacter hyointestinalis. A polyphasic study was undertaken to determine the taxonomic position of five strains. The strains were characterized by 16S rRNA and atpA sequence analysis, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and conventional phenotypic testing. Whole-genome sequences were determined for strains 1485ET and 2463D, and the average nucleotide and amino acid identities were determined for these strains. The strains formed a robust phylogenetic clade, divergent from all other species of the genus Campylobacter. In contrast to most currently known members of the genus Campylobacter, the strains showed growth at ambient temperatures, which might be an adaptation to their reptilian hosts. The results of this study clearly show that these strains isolated from reptiles represent a novel species within the genus Campylobacter, for which the name Campylobacter iguaniorum sp. nov. is proposed. The type strain is 1485ET (=LMG 28143T=CCUG 66346T).

Response of the Amazon carbon balance to the 2010 drought derived with CarbonTracker South America
Laan-Luijkx, I.T. van der; Velde, I.R. van der; Krol, M.C. ; Gatti, L.V. ; Domingues, L.G. ; Correia, C.S.C. ; Miller, J.B. ; Gloor, M. ; Leeuwen, T.T. van; Kaiser, J.W. ; Wiedinmyer, C. ; Basu, S. ; Clerbaux, C. ; Peters, W. - \ 2015
Global Biogeochemical Cycles 29 (2015)7. - ISSN 0886-6236 - p. 1092 - 1108.
Two major droughts in the past decade had large impacts on carbon exchange in the Amazon. Recent analysis of vertical profile measurements of atmospheric CO2 and CO by Gatti et al. (2014) suggests that the 2010 drought turned the normally close-to-neutral annual Amazon carbon balance into a substantial source of nearly 0.5 PgC/yr, revealing a strong drought response. In this study, we revisit this hypothesis and interpret not only the same CO2/CO vertical profile measurements but also additional constraints on carbon exchange such as satellite observations of CO, burned area, and fire hot spots. The results from our CarbonTracker South America data assimilation system suggest that carbon uptake by vegetation was indeed reduced in 2010 but that the magnitude of the decrease strongly depends on the estimated 2010 and 2011 biomass burning emissions. We have used fire products based on burned area (Global Fire Emissions Database version 4), satellite-observed CO columns (Infrared Atmospheric Sounding Interferometer), fire radiative power (Global Fire Assimilation System version 1), and fire hot spots (Fire Inventory from NCAR version 1), and found an increase in biomass burning emissions in 2010 compared to 2011 of 0.16 to 0.24 PgC/yr. We derived a decrease of biospheric uptake ranging from 0.08 to 0.26 PgC/yr, with the range determined from a set of alternative inversions using different biomass burning estimates. Our numerical analysis of the 2010 Amazon drought results in a total reduction of carbon uptake of 0.24 to 0.50 PgC/yr and turns the balance from carbon sink to source. Our findings support the suggestion that the hydrological cycle will be an important driver of future changes in Amazonian carbon exchange.
Update of "Delineating catch quotas for Dutch demersal fisheries: a theoretical pilot study"
Poos, J.J. - \ 2015
IJmuiden : IMARES (Report / IMARES C139/15) - 19
demersal fisheries - fish catches - quotas - netherlands - demersale visserij - visvangsten - quota - nederland
A reduction of unwanted catches is a key element of the Common Fisheries Policy reform proposal (EC, 2010). To achieve this, a landing obligation (or discard ban) will be introduced, prohibiting the at-sea disposal of quota-regulated species. Instead these catches shall be brought back to shore and counted against a quota, where applicable. In 2014, upon request by the ministry, more clarity was sought on how catch quotas could be calculated and what they would look like for the most relevant fish species of the Dutch demersal fishery . The report of that study (Miller et al. 2014) provided an overview of total allowable catch allocations (TAC), national quota, landings and discards statistics for some of the most-relevant quota-regulated species caught by the Dutch demersal fleet. A number of scenarios of how the new catch quotas could be calculated were presented. The theoretical implications of these alternative scenarios for the Dutch fleet were described under the assumption of no change in relative stability. In 2015, the Ministry of Economic Affairs requested an update of Miller et al. (2014), and this report is the result of that update.
Animal board Invited Review: Genetic possibilities to reduce enteric methane emissions from ruminants
Pickering, N.K. ; Oddy, V.H. ; Basarab, J. ; Cammack, K. ; Hayes, B. ; Hegarty, R. ; Lassen, J. ; McEwan, J. ; Miller, S. ; Pinares-Patino, C. ; Haas, Y. de - \ 2015
Animal 9 (2015)9. - ISSN 1751-7311 - p. 1431 - 1440.
special topics-mitigation - nitrous-oxide emissions - dairy-cows - genomic selection - sheep - rumen - fermentation - accuracy - cattle - livestock
Measuring and mitigating methane (CH4) emissions from livestock is of increasing importance for the environment and for policy making. Potentially, the most sustainable way of reducing enteric CH4 emission from ruminants is through the estimation of genomic breeding values to facilitate genetic selection. There is potential for adopting genetic selection and in the future genomic selection, for reduced CH4 emissions from ruminants. From this review it has been observed that both CH4 emissions and production (g/day) are a heritable and repeatable trait. CH4 emissions are strongly related to feed intake both in the short term (minutes to several hours) and over the medium term (days). When measured over the medium term, CH4 yield (MY, g CH4/kg dry matter intake) is a heritable and repeatable trait albeit with less genetic variation than for CH4 emissions. CH4 emissions of individual animals are moderately repeatable across diets, and across feeding levels, when measured in respiration chambers. Repeatability is lower when short term measurements are used, possibly due to variation in time and amount of feed ingested prior to the measurement. However, while repeated measurements add value; it is preferable the measures be separated by at least 3 to 14 days. This temporal separation of measurements needs to be investigated further. Given the above issue can be resolved, short term (over minutes to hours) measurements of CH4 emissions show promise, especially on systems where animals are fed ad libitum and frequency of meals is high. However, we believe that for short-term measurements to be useful for genetic evaluation, a number (between 3 and 20) of measurements will be required over an extended period of time (weeks to months). There are opportunities for using short-term measurements in standardised feeding situations such as breath 'sniffers' attached to milking parlours or total mixed ration feeding bins, to measure CH4. Genomic selection has the potential to reduce both CH4 emissions and MY, but measurements on thousands of individuals will be required. This includes the need for combined resources across countries in an international effort, emphasising the need to acknowledge the impact of animal and production systems on measurement of the CH4 trait during design of experiments.
Vangstadviezen van ICES voor 2016 in de Noordzee
Miller, David - \ 2015
fish catches - north sea - fishery resources - guidelines - fishery management
Vangstadviezen van ICES voor 2015
Miller, David - \ 2015
Studying biosphere-atmosphere exchange of CO2 through Carbon-13 stable isotopes
Velde, I.R. van der - \ 2015
Wageningen University. Promotor(en): Maarten Krol; Wouter Peters, co-promotor(en): J.B. Miller. - Wageningen : Wageningen University - ISBN 9789462572935 - 143
kooldioxide - biosfeer - atmosfeer - isotopen - koolstofcyclus - klimaat - voorspellingen - carbon dioxide - biosphere - atmosphere - isotopes - carbon cycle - climate - forecasts

Summary Thesis ‘Studying biosphere-atmosphere exchange of CO2 through

carbon-13 stable isotopes’

Ivar van der Velde

Making predictions of future climate is difficult, mainly due to large uncertainties in the carbon cycle. The rate at which carbon is stored in the oceans and terrestrial biosphere is not keeping pace with the rapid increase in fossil fuel combustion and deforestation, resulting in an increase of atmospheric carbon dioxide (CO2). To gain a better understanding of the global carbon cycle we need to combine multiple sources of data into one consistent analysis, such as, forest and agricultural statistics, satellite data, atmospheric and ecological observations, and mechanistic models. This thesis describes fundamental research on some of the key components of the terrestrial carbon cycle, i.e., gross primary production (GPP) and terrestrial ecosystem respiration (TER) of CO2, which forms the key to improved prediction of net exchange. Droughts have been shown to strongly influence this exchange, and to interpret these responses adequately we have turned to a large collection of new atmospheric observations of CO2, and its 13C isotope (13CO2), to constrain key model components.

In Chapter 2 we studied the global budget of atmospheric CO2 and the ratio of 13CO2/12CO2 (δ13C) and investigated the main terrestrial drivers of interannual variability (IAV) responsible for the observed atmospheric δ13C variations. In this chapter we introduced the SiBCASA biogeochemical model that we provided with a detailed isotopic discrimination scheme (to calculate the natural preference of 12CO2 over 13CO2 in uptake processes), separate 12C and 13C biogeochemical pools, and satellite-observed fire disturbances. This model was able to calculate uptake of 13CO2 and 12CO2 and produced return fluxes from its differently aged carbon pools, contributing to the so-called disequilibrium flux. Our simulated terrestrial isotope processes, plant discrimination and disequilibrium, closely resembled previously published values and similarly suggested that discrimination variations in C3 type plants and year-to-year variations in C3 and C4 productivity are the main drivers of IAV. The year-to-year variability in the terrestrial disequilibrium flux was much lower than required to match variations in atmospheric observations, under the common assumption of low variability in net ocean CO2 exchange, constant discrimination, and a closed CO2 budget. It was unclear how to increase IAV in the terrestrial biosphere, which suggested that SiBCASA missed adequate drought responses resulting in a latent isotope discrimination and variability in C3/C4 plant productivity.

Implementation of carbon isotope cycling, biomass burning, and SiBCASA’s drought response were closely studied in Chapter 3. Our biomass burning emissions were similar as in CASA-GFED; both in magnitude and spatial patterns, and the implementation of isotope exchange gave a global mean discrimination value of approximately 15 ‰, and varied spatially depending on the photosynthetic pathway in the plant. These values compared well (annually and seasonally) with other published results. Similarly, the size of the terrestrial isotopic disequilibrium was close to that of other studies. As plants experience drought stress, they respond by closing their stomata to prevent the loss of water. This process also inhibits the uptake of CO2 and reduces the isotope discrimination against 13CO2 molecules. We found that the amplitude of drought response in SiBCASA was smaller than suggested by the measured isotope signatures. We also found that a slight increase in stomatal closure for large vapor pressure deficits amplified the variations in the respired isotope signature. Finally, we saw the need for modified starch/sugar storage pools to improve the propagation of isotopic discrimination anomalies to respiration on short-term time scales.

In Chapter 4 we developed a multi-tracer inversion system to interpret signals in atmospheric CO2 and δ13C observations simultaneously. We wanted to know whether drought stress in plants can induce changes in atmospheric δ13C and whether they are interpretable. Using inverse modeling we were able to refine the discrimination parameter for plants as it reflected detectable variations in atmospheric δ13C. The results showed that the isotope discrimination values were consistently smaller during large severe droughts in the Northern Hemisphere, exceeding the estimates from SiBCASA (i.e., a larger reduction). Decreased discrimination suggested an increase in the regional intrinsic water use efficiency, which was also recorded at a large number of measurement sites. The IAV in net ecosystem exchange was relatively insensitive as we allowed the variability of the discrimination parameter to increase more than 8-fold, but it also allowed significant correlation between annual net exchange and discrimination. This study suggested a larger effect of droughts on discrimination than previously thought and that the treatment of drought response in biosphere models needs to be improved.

Carbon cycle research is far from complete as many components are still largely uncertain, which prevents us from making better predictions of future climate. This thesis, however, highlights the importance of isotope observations to assess and improve biogeochemical models, especially with regard to the allocation and turnover of carbon, and responses to droughts.

Distributions, ex situ conservation priorities, and genetic resource potential of crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas]
Khoury, C.K. ; Heider, B. ; Castaneda-Alvarez, N.P. ; Achicanoy, H.A. ; Sosa, C.C. ; Miller, R.E. ; Scotland, R.W. ; Wood, J.R.I. ; Rossel, G. ; Eserman, L.A. ; Jarret, R.L. ; Yencho, G.C. ; Bernau, V. ; Juarez, H. ; Sotelo, S. ; Haan, S. de; Struik, P.C. - \ 2015
Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 14 p.
species distribution models - phylogenetic-relationships - beta-carotene - convolvulaceae - sequences - diversity - evolution - bias - challenges - tolerance
Crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas] have the potential to contribute to breeding objectives for this important root crop. Uncertainty in regard to species boundaries and their phylogenetic relationships, the limited availability of germplasm with which to perform crosses, and the difficulty of introgression of genes from wild species has constrained their utilization. Here, we compile geographic occurrence data on relevant sweetpotato wild relatives and produce potential distribution models for the species. We then assess the comprehensiveness of ex situ germplasm collections, contextualize these results with research and breeding priorities, and use ecogeographic information to identify species with the potential to contribute desirable agronomic traits. The fourteen species that are considered the closest wild relatives of sweetpotato generally occur from the central United States to Argentina, with richness concentrated in Mesoamerica and in the extreme Southeastern United States. Currently designated species differ among themselves and in comparison to the crop in their adaptations to temperature, precipitation, and edaphic characteristics and most species also show considerable intraspecific variation. With 79% of species identified as high priority for further collecting, we find that these crop genetic resources are highly under-represented in ex situ conservation systems and thus their availability to breeders and researchers is inadequate. We prioritize taxa and specific geographic locations for further collecting in order to improve the completeness of germplasm collections. In concert with enhanced conservation of sweetpotato wild relatives, further taxonomic research, characterization and evaluation of germplasm, and improving the techniques to overcome barriers to introgression with wild species are needed in order to mobilize these genetic resources for crop breeding.
Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature
Seaton, D.D. ; Smith, R.W. ; Young Hun Song, ; MacGregor, D.R. ; Stewart, K. ; Steel, G. ; Foreman, J. ; Penfield, S. ; Imaizumi, T. ; Miller, A.J. ; Halliday, K.J. - \ 2015
Molecular Systems Biology 11 (2015)1. - ISSN 1744-4292
Clock-regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best-understood clock output pathways in Arabidopsis, which control key regulators of flowering and elongation growth. In flowering, the model predicted regulatory links from the clock to CYCLING DOF FACTOR 1 (CDF1) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) transcription. Physical interaction data support these links, which create threefold feed-forward motifs from two clock components to the floral regulator FT. In hypocotyl growth, the model described clock-regulated transcription of PHYTOCHROME-INTERACTING FACTOR 4 and 5 (PIF4, PIF5), interacting with post-translational regulation of PIF proteins by phytochrome B (phyB) and other light-activated pathways. The model predicted bimodal and end-of-day PIF activity profiles that are observed across hundreds of PIF-regulated target genes. In the response to temperature, warmth-enhanced PIF4 activity explained the observed hypocotyl growth dynamics but additional, temperature-dependent regulators were implicated in the flowering response. Integrating these two pathways with the clock model highlights the molecular mechanisms that coordinate plant development across changing conditions.
Authority without credibility? Competition and conflict between ecolabels in tuna fisheries
Miller, A.M.M. ; Bush, S.R. - \ 2015
Journal of Cleaner Production 107 (2015). - ISSN 0959-6526 - p. 137 - 145.
Certification is widely seen as an innovative strategy for dealing with environmental problems in supply chains. As the number of labels available in the fisheries sector has increased, each with its own framing of sustainability, questions are being asked about their credibility. In tuna fisheries, contrasting approaches have led to conflict over, among other things, the credibility of competing labels. This paper investigates one such conflict between the Dolphin Safe and the Marine Stewardship Council certification schemes in the West and Central Pacific. It looks at how key practices like scientific rigour, inclusiveness, transparency/openness, impartiality/independence and impact contribute to label credibility and explains the importance of authority in understanding how certification schemes maintain influence within global production networks. The results demonstrate that despite substantially different levels of credibility within these networks, the application of an environmental standard is more connected to the authority of the standard setter than the credibility of the label. The paper concludes that understanding the more nuanced role of authority, both with and without credibility, offers new insights into the wider dynamics that shape environmental regulation in global production networks.
Location choice of academic entrepreneurs: Evidence from the US biotechnology industry
Kolympiris, C. ; Kalaitzandonakes, N. ; Miller, D. - \ 2015
Journal of Business Venturing 30 (2015)2. - ISSN 0883-9026 - p. 227 - 254.
foreign direct-investment - resource-based view - spin-out companies - united-states - spatial-distribution - university-research - product development - labor mobility - life sciences - agency costs
Where knowledge-based firms are located is important because entrepreneurship, firm creation and innovation are typically associated with regional economic development, wealth creation and increased employment. In this paper we examine where academic entrepreneurs locate their firms. We begin by developing a theoretical model that examines the location choice of the academic entrepreneur within the standard utility maximization theory. Academic entrepreneurs are assumed to maximize their utility by allocating their efforts between academic and entrepreneurial pursuits which, in turn, determine their future streams of income and end-period wealth. Optimal allocation turns out to be a function of both personal and external factors that condition the relevant payoffs and such factors can be empirically observed. We then use several candidate explanatory variables to examine those factors that may influence the firm location choice for 187 biopharmaceutical firms started by 275 academic entrepreneurs in the US. From our empirical analysis we find that location-specific factors such as proximity to certain knowledge assets and to the funding venture capital firms, affect the firm location choice of academic entrepreneurs. Nevertheless, entrepreneur-specific characteristics, such as their age, seem to dominate the choice of firm location.
Simulation testing the robustness of stock assessement models to error: some results from the ICES strategic initiative on stock assessment methods
Deroba, J.J. ; Butterworth, D.S. ; Methot, R.D. ; Dickey-Collas, M. ; Miller, D.C.M. ; Hintzen, N.T. - \ 2015
ICES Journal of Marine Science 72 (2015)1. - ISSN 1054-3139 - p. 19 - 30.
at-age analysis - management procedures - natural mortality - performance - uncertainty - fishery
The World Conference on Stock Assessment Methods (July 2013) included a workshop on testing assessment methods through simulations. The exercise was made up of two steps applied to datasets from 14 representative fish stocks from around the world. Step 1 involved applying stock assessments to datasets with varying degrees of effort dedicated to optimizing fit. Step 2 was applied to a subset of the stocks and involved characteristics of given model fits being used to generate pseudo-data with error. These pseudo-data were then provided to assessment modellers and fits to the pseudo-data provided consistency checks within (self-tests) and among (cross-tests) assessment models. Although trends in biomass were often similar across models, the scaling of absolute biomass was not consistent across models. Similar types of models tended to perform similarly (e.g. age based or production models). Self-testing and cross-testing of models are a useful diagnostic approach, and suggested that estimates in the most recent years of time-series were the least robust. Results from the simulation exercise provide a basis for guidance on future large-scale simulation experiments and demonstrate the need for strategic investments in the evaluation and development of stock assessment methods.
Endangered Species Act listing: three case studies of data deficiencies and consequences of ESA 'threatened' listing on research output
Weijerman, M.W. ; Birkeland, C. ; Piniak, G.A. ; Miller, M.W. ; Eakin, C.M. ; McElhany, P. ; Dunlap, M.J. ; Patterson, M. ; Brainard, R.E. - \ 2014
Current Opinion in Environmental Sustainability 7 (2014). - ISSN 1877-3435 - p. 15 - 21.
region-wide declines - deep-sea corals - climate-change - reefs
Determining whether a species warrants listing as threatened or endangered under the U.S. Endangered Species Act depends on the government's assessment of the species' extinction risk, usually in response to a petition. Deciding whether data are sufficient to make a listing determination is a challenging part of the process. We examined three case studies involving corals. A petition for deep-sea corals was rejected for full status review of the species, based on insufficient information on population trends and threats. Information on threats for 82 tropical corals was sufficient to propose listing of 66 species. Significant population declines and identified threats resulted in listing two Atlantic Acropora corals as 'Threatened'. There was no decrease in journal publication rate on the Acropora species after that listing, and no decrease in research permit applications in marine protected areas. However, the effects of listings on research that might help to sustain or recover species remains largely unknown.
Inconsistency of Phenotypic and Genomic Characteristics of Campylobacter fetus Subspecies Requires Reevaluation of Current Diagnostics
Bloois, L. van; Miller, W.G. ; Yee, E. ; Rijnsburger, M. ; Wagenaar, J.A. ; Duim, B. - \ 2014
Journal of Clinical Microbiology 52 (2014)12. - ISSN 0095-1137 - p. 4183 - 4188.
pcr assay - identification - time
Classifications of the Campylobacter fetus subspecies fetus and venerealis were first described in 1959 and were based on the source of isolation (intestinal versus genital) and the ability of the strains to proliferate in the genital tract of cows. Two phenotypic assays (1% glycine tolerance and H2S production) were described to differentiate the subspecies. Multiple molecular assays have been applied to differentiate the C. fetus subspecies, but none of these tests is consistent with the phenotypic identification methods. In this study, we defined the core genome and accessory genes of C. fetus, which are based on the closed genomes of five C. fetus strains. Phylogenetic analysis of the core genomes of 23 C. fetus strains of the two subspecies showed a division into two clusters. The phylogenetic core genome clusters were not consistent with the phenotypic classifications of the C. fetus subspecies. However, they were consistent with the molecular characteristics of the strains, which were determined by multilocus sequence typing, sap typing, and the presence/absence of insertion sequences and a type I restriction modification system. The similarity of the genome characteristics of three of the phenotypically defined C. fetus subsp. fetus strains to C. fetus subsp. venerealis strains, when considering the core genome and accessory genes, requires a critical evaluation of the clinical relevance of C. fetus subspecies identification by phenotypic assays.
Contribution of Dynamic Vegetation Phenology to Decadal Climate Predictability
Weiss, M. ; Miller, P.A. ; Hurk, B.J.J.M. van den; Noije, T. van; Stefanescu, S. ; Haarsma, R. ; Ulft, L.H. van; Hazeleger, W. ; Sager, P. Le; Smith, B. ; Schurgers, G. - \ 2014
Journal of Climate 27 (2014)22. - ISSN 0894-8755 - p. 8563 - 8577.
leaf-area index - ensemble forecasts - data assimilation - soil-moisture - model - prediction - system - impact - skill - oscillation
In this study, the impact of coupling and initializing the leaf area index from the dynamic vegetation model Lund-Potsdam-Jena General Ecosystem Simulator (LPJ-GUESS) is analyzed on skill of decadal predictions in the fully coupled atmosphere-land-ocean-sea ice model, the European Consortium Earth System Model (EC-Earth). Similar to the impact of initializing the model with the observed oceanic state, initializing the leaf area index (LAI) fields obtained from an offline LPJ-GUESS simulation forced by the observed atmospheric state leads to a systematic drift. A different treatment of the water and soil moisture budget in LPJ-GUESS is a likely cause of this drift. The coupled system reduces the cold bias of the reference model over land by reducing LAI (and the associated evaporative cooling), particularly outside the growing season. The coupling with the interactive vegetation module implies more degrees of freedom in the coupled model, which generates more noise that can mask a portion of the extra signal that is generated. The forecast reliability improves marginally, particularly early in the forecast. Ranked probability skill scores are also improved slightly in most areas analyzed, but the signal is not fully coherent over the forecast interval because of the relatively low number of ensemble members. Methods to remove the LAI drift and allow coupling of other variables probably need to be implemented before significant forecast skill can be expected.
Comparative population structure analysis of Campylobacter jejuni from human and poultry origin in Bangladesh
Islam, Z. ; Belkum, A. van; Wagenaar, J.A. ; Cody, A.J. ; Boer, A.G. de; Sarker, S.K. ; Jacobs, B.C. ; Talukder, K.A. ; Endtz, H.P. - \ 2014
European Journal of Clinical Microbiology and Infectious Diseases 33 (2014)12. - ISSN 0934-9723 - p. 2173 - 2181.
fragment-length polymorphism - guillain-barre-syndrome - field gel-electrophoresis - miller-fisher-syndromes - sequence typing system - short variable region - genetic diversity - molecular characterization - strains - epidemiology
Campylobacter jejuni is the most important cause of antecedent infections leading to Guillain-Barr, syndrome (GBS) and Miller Fisher syndrome (MFS). The objective of the present study was to define the genetic diversity, population structure, and potential role of poultry in the transmission of Campylobacter to humans in Bangladesh. We determined the population structure of C. jejuni isolated from poultry (n = 66) and patients with enteritis (n = 39) or GBS (n = 10). Lipooligosaccharide (LOS) typing showed that 50/66 (76 %) C. jejuni strains isolated from poultry could be assigned to one of five LOS locus classes (A-E). The distribution of neuropathy-associated LOS locus classes A, B, and C were 30/50 (60 %) among the typable strains isolated from poultry. The LOS locus classes A, B, and C were significantly associated with GBS and enteritis-related C. jejuni strains more than for the poultry strains [(31/38 (82 %) vs. 30/50 (60 %), p <0.05]. Multilocus sequence typing (MLST) defined 15 sequence types (STs) and six clonal complexes (CCs) among poultry isolates, including one ST-3740 not previously documented. The most commonly identified type, ST-5 (13/66), in chicken was seen only once among human isolates (1/49) (p <0.001). Amplified fragment length polymorphism (AFLP) revealed three major clusters (A, B, and C) among C. jejuni isolated from humans and poultry. There seems to be a lack of overlap between the major human and chicken clones, which suggests that there may be additional sources for campylobacteriosis other than poultry in Bangladesh.
Campylobacter fetus subsp. testudinum subsp. nov., isolated from humans and reptiles
Fitzgerald, C. ; Tu, Z.C. ; Patrick, M. ; Stiles, T. ; Lawson, A.J. ; Santovenia, M. ; Gilbert, M.J. ; Bergen, M. von; Joyce, K. ; Pruckler, J. ; Stroika, S. ; Duim, B. ; Miller, W.G. ; Loparev, V. ; Sinnige, J.C. ; Fields, P.I. ; Tauxe, R.V. ; Blaser, M.J. ; Wagenaar, J.A. - \ 2014
International Journal of Systematic and Evolutionary Microbiology 64 (2014). - ISSN 1466-5026 - p. 2944 - 2948.
genus campylobacter - pcr assay - differentiation - identification - strains - origins
A polyphasic study was undertaken to determine the taxonomic position of 13 Campylobacter fetus-like strains from humans (n=8) and reptiles (n=5). The results of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS and genomic data from sap analysis, 16S rRNA gene and hsp60 sequence comparison, pulsed-field gel electrophoresis, amplified fragment length polymorphism analysis, DNA-DNA hybridization and whole genome sequencing demonstrated that these strains are closely related to C. fetus but clearly differentiated from recognized subspecies of C. fetus. Therefore, this unique cluster of 13 strains represents a novel subspecies within the species C. fetus, for which the name Campylobacter fetus subsp. testudinum subsp. nov. is proposed, with strain 03-427(T) (=ATCC BAA-2539(T)=LMG 27499(T)) as the type strain. Although this novel taxon could not be differentiated from C. fetus subsp. fetus and C. fetus subsp. venerealis using conventional phenotypic tests, MALDI-TOF MS revealed the presence of multiple phenotypic biomarkers which distinguish Campylobacter fetus subsp. testudinum subsp. nov. from recognized subspecies of C. fetus.
Amendments for the second stage of the North Sea sole and plaice multi-annual plan (EC regulation 2007/676)
Miller, D.C.M. ; Coers, A. - \ 2014
IJmuiden : IMARES (Report / IMARES Wageningen UR C088.14) - 26
schol - tong (vis) - noordzee - visserijbeheer - visbestand - beleidsevaluatie - programma-evaluatie - milieu-analyse - plaice - dover soles - north sea - fishery management - fishery resources - policy evaluation - program evaluation - environmental analysis
A multiannual plan for sole and plaice in the North Sea was adopted by the EU Council in 2007. It describes two stages: a recovery plan during its first stage and a management plan during its second stage. This report compiles information from a number of studies subsequent to the implementation of the plan, which have been conducted by ICES and STECF in relation to the management of the North Sea sole and plaice stocks. These studies included management strategy evaluations aimed at investigating the effects of specific amendments to the current management plan and analyses to establish appropriate reference points for exploitation of the stocks in accordance with MSY.
Climate change and the assessment of expert knowledge: Does the ipcc model need updating?
Beck, S. ; Borie, M. ; Esguerra, A. ; Chilvers, A. ; Heubach, K. ; Hulme, M. ; Lidskog, R. ; Lövbrand, E. ; Marquard, E. ; Miller, C. ; Nadim, T. ; Nesshöver, C. ; Settele, J. ; Turnhout, E. ; Vasileiadou, E. ; Görg, C. - \ 2014
Bridges 40 (2014).
Bridges is the free, online magazine of the OSTA published by Office of Science & Technology Austria, located in Washington D.C.
Terrestrial cycling of (CO2)-C-13 by photosynthesis, respiration, and biomass burning in SiBCASA
Velde, I.R. van der; Miller, J.B. ; Schaefer, K. ; Werf, G.R. van der; Krol, M.C. ; Peters, W. - \ 2014
Biogeosciences 11 (2014). - ISSN 1726-4170 - p. 6553 - 6571.
carbon-isotope discrimination - surface parameterization sib2 - ecosystem respiration - interannual variability - biophysical parameters - stomatal conductance - co2 assimilation - atmospheric gcms - global fields - dioxide
We present an enhanced version of the SiBCASA terrestrial biosphere model that is extended with (a) biomass burning emissions from the SiBCASA carbon pools using remotely sensed burned area from the Global Fire Emissions Database (GFED), (b) an isotopic discrimination scheme that calculates 13C signatures of photosynthesis and autotrophic respiration, and (c) a separate set of 13C pools to carry isotope ratios into heterotrophic respiration. We quantify in this study the terrestrial exchange of CO2 and 13CO2 as a function of environmental changes in humidity and biomass burning. The implementation of biomass burning yields similar fluxes as CASA-GFED both in magnitude and spatial patterns. The implementation of isotope exchange gives a global mean discrimination value of 15.2‰, ranges between 4 and 20‰ depending on the photosynthetic pathway in the plant, and compares favorably (annually and seasonally) with other published values. Similarly, the isotopic disequilibrium is similar to other studies that include a small effect of biomass burning as it shortens the turnover of carbon. In comparison to measurements, a newly modified starch/sugar storage pool propagates the isotopic discrimination anomalies to respiration much better. In addition, the amplitude of the drought response by SiBCASA is lower than suggested by the measured isotope ratios. We show that a slight increase in the stomatal closure for large vapor pressure deficit would amplify the respired isotope ratio variability. Our study highlights the importance of isotope ratio observations of 13C to assess and improve biochemical models like SiBCASA, especially with regard to the allocation and turnover of carbon and the responses to drought.
The suitability of the North Sea as a habitat for Atlantic Bluefin Tuna
Miller, D.C.M. ; Reijden, K.J. van der; Jak, R.G. - \ 2014
IJmuiden : IMARES (Report / IMARES Wageningen UR C174/14) - 32
tuna - scombridae - habitats - habitat suitability - north sea - tonijn - habitatgeschiktheid - noordzee
Predicting major outcomes in type 1 diabetes: a model development and validation study
Soedamah-Muthu, S.S. ; Vergouwe, Y. ; Costacou, T. ; Miller, R.G. ; Zgibor, J. ; Chaturvedi, N. ; Snell-Bergeon, J.K. ; Maahs, D.M. ; Rewers, M. ; Forsblom, C. ; Harjutsalo, V. ; Groop, P.H. ; Fuller, J.H. ; Moons, K.G.M. ; Orchard, T.J. - \ 2014
Diabetologia 57 (2014)11. - ISSN 0012-186X - p. 2304 - 2314.
coronary-heart-disease - eurodiab prospective complications - all-cause mortality - cardiovascular-disease - pittsburgh epidemiology - risk-factors - intensive treatment - iddm complications - metabolic syndrome - association
Aims/hypothesis Type 1 diabetes is associated with a higher risk of major vascular complications and death. A reliable method that predicted these outcomes early in the disease process would help in risk classification. We therefore developed such a prognostic model and quantified its performance in independent cohorts. Methods Data were analysed from 1,973 participants with type 1 diabetes followed for 7 years in the EURODIAB Prospective Complications Study. Strong prognostic factors for major outcomes were combined in a Weibull regression model. The performance of the model was tested in three different prospective cohorts: the Pittsburgh Epidemiology of Diabetes Complications study (EDC, n¿=¿554), the Finnish Diabetic Nephropathy study (FinnDiane, n¿=¿2,999) and the Coronary Artery Calcification in Type 1 Diabetes study (CACTI, n¿=¿580). Major outcomes included major CHD, stroke, end-stage renal failure, amputations, blindness and all-cause death. Results A total of 95 EURODIAB patients with type 1 diabetes developed major outcomes during follow-up. Prognostic factors were age, HbA1c, WHR, albumin/creatinine ratio and HDL-cholesterol level. The discriminative ability of the model was adequate, with a concordance statistic (C-statistic) of 0.74. Discrimination was similar or even better in the independent cohorts, the C-statistics being: EDC, 0.79; FinnDiane, 0.82; and CACTI, 0.73. Conclusions/interpretation Our prognostic model, which uses easily accessible clinical features can discriminate between type 1 diabetes patients who have a good or a poor prognosis. Such a prognostic model may be helpful in clinical practice and for risk stratification in clinical trials.
Sub-regionalisation of fisheries governance: the case of the Western and Central Pacific Ocean tuna fisheries
Miller, A.M.M. ; Bush, S.R. ; Zwieten, P.A.M. van - \ 2014
Maritime Studies 13 (2014). - ISSN 1872-7859 - 20 p.
Shifting political alliances and new environmental challenges are prompting debate over processes of sub-regionalisation and whether the interplay between multiple scales of governance leads to positive synergistic outcomes or negative institutional disruption. Regional management of tuna fisheries in the Western and Central Pacific Ocean is an example where a web of treaties, conventions and institutional frameworks underlie international cooperation. Through examining the interplay between the regional Western and Central Pacific Fisheries Commission and sub-regional Parties to the Nauru Agreement, this paper explores the extent to which the PNA and WCPFC interact in the management of regional tuna fisheries. The results demonstrate that for contested marine resources such as fisheries, international sub-regions can go beyond functional units to also present wider opportunities to shift power relations in favour of small island states. Additionally, the presence of sub-regional groups like the PNA has served to challenge the performance of the WCPFC, stimulating greater debate and progress within the regional body. The paper concludes that the combined work of the PNA and the WCPFC puts them ahead on many issues and may represent a testing ground for a functional multilateralism utilising both regional and sub-regional governance platforms for the management of shared resources.
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