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.

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

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

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, Titus C. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
Nature Biotechnology 37 (2019)8. - ISSN 1087-0156 - p. 852 - 857.
Special Section: Moving from Citizen to Civic Science to Address Wicked Conservation Problems
Dillon, Justin ; Stevenson, Robert B. ; Wals, Arjen E.J. - \ 2016
Conservation Biology 30 (2016)3. - ISSN 0888-8892 - 6 p.
Genetic variants of FADS gene cluster, plasma LC-PUFA levels and the association with cognitive function of under-two-year-old Sasaknese Indonesian children
Fahmida, Umi ; Htet, Min Kyaw ; Adhiyanto, Chris ; Kolopaking, Risatianti ; Yudisti, Miza Agria ; Maududi, Allay ; Suryandari, Dwi Anita ; Dillon, Drupadi ; Afman, Lydia ; Müller, Michael - \ 2015
Asia Pacific Journal of Clinical Nutrition 24 (2015)2. - ISSN 0964-7058 - p. 323 - 328.
Cognitive function - FADS - Indonesia - LC-PUFA - Under-two-year-old children

Background/Aims: Long-chain polyunsaturated fatty acids (LC-PUFA) are regarded as essential for child cognition. Genetic variation in fatty acid (FA) desaturase enzyme (FADS) has been recognized as an important effect modifier in the relation between LC-PUFA and child cognitive function. This study aimed to identify the distribution of genetic variant (genotype) SNP rs174468 and to assess plasma FA and developmental outcome by the genotype among under-2 year old Sasaknese Indonesian children. Methods: Data was collected at baseline of a randomized trial (NUPICO, clinicaltrials.gov NCT01504633) in East Lombok district, Indonesia. Breastfed, 12- 17 month old children were recruited and 240 subjects were included in the study. Child cognition was assessed as Bayley Mental Developmental Index (MDI). Results: From 206 subjects whose blood samples can be collected, only two genotypes were found (90.3% GG homozygotes, 9.7% AG heterozygotes), and minor allele AG was significantly associated with higher level of arachidonic acid (20:4 n-6), n-6 LC-PUFA and FADS1 index. MDI score was associated with a FADS2 index (DHA:EPA ratio) but not genotype (Adjusted R-square= 0.043). Conclusions: FADS2 index was associated with cognitive function. No difference was found between children with GG and AG genotypes who were all breastfed and not low birth weight.

Propojení přírodovědného a environmentálního vzdělávání
Wals, A.E.J. ; Brody, M. ; Dillon, J. ; Stevenson, R.B. - \ 2015
Envigogika 10 (2015)2. - ISSN 1802-3061 - 5 p.
Environmental education - science education - civic science
What is written about in Science journal? A paraphrase of the article: Wals, Arjen E. J., Michael Brody, Justin Dillon, Robert B. Stevenson (2014). Convergence Between Science and Environmental Education. Science, 344(6184), 583–584. DOI:10.1126/science.1250515
Foreword
Wals, A.E.J. ; Dillon, J. - \ 2015
In: Educating Science Teachers for Sustainability / Stratton, Susan K., Hagevik, Rita, Feldman, Allan, Bloom, Mark, Cham : Springer International Publishing Switzerland (ASTE Series in Science Education ) - ISBN 9783319164106 - p. 1 - 3.
Multi-species swards and multi scale strategies for multifunctional grassland-base ruminant production systems: An overview of the FP7-MultiSward project
Peyraud, J.L. ; Pol - Van Dasselaar, A. Van Den; Collins, R.P. ; Huguenin-Elie, O. ; Dillon, P. ; Peeters, B.P.H. - \ 2014
In: 25th EGF General Meeting on “EGF at 50: The Future of European Grasslands. - Zurich, Switzerland : European Grassland Federation EGF - p. 695 - 715.
Life cycle assessment of energy use on Irish dairy farms
Upton, J. ; Humphreys, J. ; Groot Koerkamp, P.W.G. ; French, P. ; Dillon, P. ; Boer, I.J.M. de - \ 2014
In: Proceedings of the Agricultural Research Forum 2014. - - p. 48 - 48.
Convergence between science and environmental education
Wals, A.E.J. ; Brody, M. ; Dillon, J. ; Stevenson, R.B. - \ 2014
Science 344 (2014)6184. - ISSN 0036-8075 - p. 583 - 584.
citizen science - public engagement - green
Urgent issues such as climate change, food scarcity, malnutrition, and loss of biodiversity are highly complex and contested in both science and society (1). To address them, environmental educators and science educators seek to engage people in what are commonly referred to as sustainability challenges. Regrettably, science education (SE), which focuses primarily on teaching knowledge and skills, and environmental education (EE), which also stresses the incorporation of values and changing behaviors, have become increasingly distant. The relationship between SE and EE has been characterized as “distant, competitive, predatorprey and host-parasite” (2). We examine the potential for a convergence of EE and SE that might engage people in addressing fundamental socioecological challenges.
Learning and Knowing in Pursuit of Sustainability: Concepts and Tools for Trans-Disciplinary Environmental Research
Peters, S. ; Wals, A.E.J. - \ 2013
In: Trading Zones in Environmental Education: Creating Trans-disciplinary Dialogue / Krasny, M., Dillon, J., New York : Peter Lang - ISBN 9781433111792 - p. 79 - 104.
Energy demand on dairy farms in Ireland
Upton, J.R. ; Humphreys, J. ; Groot Koerkamp, P.W.G. ; French, P. ; Dillon, P. ; Boer, I.J.M. de - \ 2013
Journal of Dairy Science 96 (2013)10. - ISSN 0022-0302 - p. 6489 - 6498.
life-cycle assessment - milk-production - impact
Reducing electricity consumption in Irish milk production is a topical issue for 2 reasons. First, the introduction of a dynamic electricity pricing system, with peak and off-peak prices, will be a reality for 80% of electricity consumers by 2020. The proposed pricing schedule intends to discourage energy consumption during peak periods (i.e., when electricity demand on the national grid is high) and to incentivize energy consumption during off-peak periods. If farmers, for example, carry out their evening milking during the peak period, energy costs may increase, which would affect farm profitability. Second, electricity consumption is identified in contributing to about 25% of energy use along the life cycle of pasture-based milk. The objectives of this study, therefore, were to document electricity use per kilogram of milk sold and to identify strategies that reduce its overall use while maximizing its use in off-peak periods (currently from 0000 to 0900 h). We assessed, therefore, average daily and seasonal trends in electricity consumption on 22 Irish dairy farms, through detailed auditing of electricity-consuming processes. To determine the potential of identified strategies to save energy, we also assessed total energy use of Irish milk, which is the sum of the direct (i.e., energy use on farm) and indirect energy use (i.e., energy needed to produce farm inputs). On average, a total of 31.73 MJ was required to produce 1 kg of milk solids, of which 20% was direct and 80% was indirect energy use. Electricity accounted for 60% of the direct energy use, and mainly resulted from milk cooling (31%), water heating (23%), and milking (20%). Analysis of trends in electricity consumption revealed that 62% of daily electricity was used at peak periods. Electricity use on Irish dairy farms, therefore, is substantial and centered around milk harvesting. To improve the competitiveness of milk production in a dynamic electricity pricing environment, therefore, management changes and technologies are required that decouple energy use during milking processes from peak periods
Economic values for yield, survival, calving interval and beef daily gain for three breeds in Slovenia
Haas, Y. de; Veerkamp, R.F. ; Shalloo, L. ; Dillon, P. ; Kuipers, A. ; Klopcic, M. - \ 2013
Livestock Science 157 (2013)2-3. - ISSN 1871-1413 - p. 397 - 407.
production circumstances - output limitations - production traits - selection - milk - fertility - objectives - efficiency - situations - weights
Breeding indices need to be looked at periodically to evaluate the objective of the breeding program. In recent times the economic perspective of the breeding program has received a higher priority in deciding breeding objectives than in the past. However, prices of input and output products are becoming more difficult to predict with increased fluctuations in most prices, which adds a level of complexity to their inclusion in the selection index. With these challenges in mind, the breeding program in a new EU country (Slovenia) was evaluated. All three national Breeding Associations joined the deliberations. The aim of this study was to develop an economic selection index for three breeds (Simmental, Brown Swiss and Holstein-Friesian) in Slovenia. Because farming circumstances differ within Slovenia, differences in the production systems were also taken into account; e.g., flat land vs. hilly/mountainous areas, and for conventional vs. organic farming. Economic values (€) were calculated for milk, fat and protein yields (€/cow/year/kg), survival (€/cow/year/%survival), calving interval (€/cow/year/day), and beef daily gain (€/cow/year/kg). Economic values were calculated by changing one of these traits whilst keeping the other traits at the default level. Economic indices were calculated using a farm economic model (Moorepark Dairy Systems Model). Herd parameters (e.g., number of milking cows, replacements, young stock and calving pattern), milk production, feed requirements and ration, land use and labour requirements were re-parameterised in order to be relevant to the Slovenian circumstances. Absolute economic values were slightly negative for milk yield for all breeds (-0.02 to -0.04€ per kg milk), but positive for milk components (0.55 to 1.45€ per kg fat, and 2.89 to 3.38€ per kg protein). High absolute economic values were calculated for survival (7.37 to 9.55€ per %). Absolute economic values for calving interval were approximately -1€ per day for all breeds, while the economic value for beef daily gain was 0.14€ per kg for Brown Swiss and 0.32€ per kg for Simmental. The constructed economic indices ranked bulls in a significantly different manner than how the Slovenian Total Merit Indices ranked the bulls. The economic indices were robust towards changes in prices and farming system. Ranking was most sensitive towards variation in milk price. Assumptions concerning feed intake in relation to growth influenced the economic value for beef daily gain. Assumptions regarding the farming system (i.e., organic farming systems) only slightly affected the ranking of the bulls.
The Evolving Characteristics of Environmental Education Research
Stevenson, B. ; Dillon, J. ; Wals, A.E.J. ; Brody, M. - \ 2013
In: International Handbook of Research on Environmental Education / Stevenson, R.B., Brody, M., Dillon, J., Wals, A.E.J., London : Routledge - ISBN 9780415892384 - p. 512 - 517.
Situating the Handbook in the Evolving Characteristics of Environmental Education Research
Stevenson, R.B. ; Dillon, J. ; Wals, A.E.J. ; Brody, M. - \ 2013
In: International Handbook of Environmental Education Research / Stevenson, B., Brody, M., Dillon, J., Wals, A.E.J., London, UK : Routledge - ISBN 9780415892391 - p. 508 - 513.
Probing Normative Research in Environmental Education: Ideas about Education and Ethics
Jickling, B. ; Wals, A.E.J. - \ 2013
In: International Handbook of Environmental Education Research / Stevenson, R.B., Brody, M., Dillon, J., Wals, A.E.J., London : Routledge - ISBN 9780415892384 - p. 74 - 86.
Introduction: An Orientation to Environmental Education and the Handbook
Stevenson, R.B. ; Brody, M. ; Dillon, J. ; Wals, A.E.J. - \ 2013
In: International Handbook of Environmental Education Research / Stevenson, R.B., Brody, M., Dillon, J., Wals, A.E.J., London : Routledge - ISBN 9780415892384 - p. 1 - 6.
Tentative Directions for Environmental Education Research in Uncertain Times
Wals, A.E.J. ; Stevenson, R.B. ; Brody, M. ; Dillon, J. - \ 2013
In: International Handbook of Research on Environmental Education / Stevenson, R.B., Brody, M., Dillon, J., Wals, A.E.J., New York : Routledge - ISBN 9780415892384 - p. 542 - 548.
Conventional and Emerging Learning Theories: Implications and Choices for Educational Researchers with a Planetary Consciousness
Wals, A.E.J. ; Dillon, J. - \ 2013
In: International Handbook of Environmental Education Research / Stevenson, R.B., Brody, M., Dillon, J., Wals, A.E.J., New York : Routledge - ISBN 9780415892384 - p. 253 - 261.
International Handbook of Research on Environmental Education
Stevenson, R.B. ; Brody, M. ; Dillon, J. ; Wals, A.E.J. - \ 2012
London : Routledge - ISBN 9780415892384 - 592
milieueducatie - milieuwetenschappen - onderzoek - onderwijzen - leren - milieu - duurzaamheid (sustainability) - wereld - handboeken - environmental education - environmental sciences - research - teaching - learning - environment - sustainability - world - handbooks
The environment and contested notions of sustainability are increasingly topics of public interest, political debate, and legislation across the world. Environmental education journals now publish research from a wide variety of methodological traditions that show linkages between the environment, health, development, and education. The growth in scholarship makes this an opportune time to review and synthesize the knowledge base of the environmental education (EE) field. The purpose of this 51-chapter handbook is not only to illuminate the most important concepts, findings and theories that have been developed by EE research, but also to critically examine the historical progression of the field, its current debates and controversies, what is still missing from the EE research agenda, and where that agenda might be headed. Published for the American Educational Research Association (AERA).
Economic selection indexes for various breeds under different farming and production systems in Slovenia
Klopcic, M. ; Veerkamp, R.F. ; Zgur, S. ; Kuipers, A. ; Dillon, P. ; Haas, Y. de - \ 2011
In: Book of Abstracts of the 62nd Annual Meeting of the European Federation of Animal Science, Stavanger, Norway, 29 August - 2 September, 2011. - Wageningen Academic Publishers - ISBN 9789086861774 - p. 127 - 127.
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