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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Distribution maps of cetacean and seabird populations in the North‐East Atlantic
Waggitt, J.J. ; Evans, P.G.H. ; Andrade, J. ; Banks, A.N. ; Boisseau, O. ; Bolton, M. ; Bradbury, G. ; Brereton, T. ; Camphuysen, C.J. ; Durinck, J. ; Felce, T. ; Fijn, R.C. ; Garcia‐baron, I. ; Garthe, S. ; Geelhoed, S.C.V. ; Gilles, A. ; Goodall, M. ; Haelters, J. ; Hamilton, S. ; Hartny‐mills, L. ; Hodgins, N. ; James, K. ; Jessopp, M. ; Kavanagh, A.S. ; Leopold, M. ; Lohrengel, K. ; Louzao, M. ; Markones, N. ; Martinez‐cediera, J. ; O’cadhla, O. ; Perry, S.I. ; Pierce, G.J. ; Ridoux, V. ; Robinson, K.P. ; Santos, M.B. ; Saavedra, C. ; Skov, H. ; Stienen, E.W.M. ; Sveegaard, S. ; Thompson, P. ; Vanermen, N. ; Wall, D. ; Webb, A. ; Wilson, J. ; Wanless, S. ; Hiddink, J.G. - \ 2019
Journal of Applied Ecology (2019). - ISSN 0021-8901 - 45 p.
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.

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

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

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.
Studying the impact of the Eurozone's Great Recession on health: Methodological choices and challenges
Thompson, Kristina ; Ophem, Johan van; Wagemakers, Annemarie - \ 2019
Economics and Human Biology 35 (2019). - ISSN 1570-677X - p. 162 - 184.
Eurozone - Great Recession - Health - Literature review - Wealth

Europe's Great Recession provides an opportunity to study the impact of increased financial insecurity on health. A number of studies explored the impact of the Recession on health, but they often reached different conclusions. To understand the root of this debate, we undertook a systematic literature review. Articles were analysed thematically based on: geography, data type, operationalisations of wealth and health, and study design. A critical appraisal was also undertaken. Forty-two studies, published from January 2010 to October 2018, were included in our review. Twenty-six of the forty-two studies found that the Great Recession worsened physical health indicators in the Eurozone. In terms of geography, a large concentration of studies focussed on Spain and Greece, indicating that there may be a gap in understanding the health consequences for EU countries with less severe experiences of the Recession. Regarding data type, nearly all studies used secondary datasets, possibly meaning that studies were constrained by the data available. In terms of operationalisations of wealth and health, a majority of studies used single/simple measures of both, so that these multi-faceted concepts were not fully reflected. Further, fewer than half included studies used panel data, with the remaining studies unable to undertake more causal analyses. The results of the critical appraisal showed that lower-quality studies tended to not find a negative impact of the Recession on health, whereas higher quality studies generally did. In future, we recommend conducting cross-country comparisons, using (inter)nationally-representative panel data conducted over a minimum of a ten-year time horizon, and employing multi-faceted operationalisations of wealth and health. This could provide more common ground across studies, and a clearer indication of whether the Recession impacted health.

Students’, colleagues’ and research partners’ experience about work and accomplishments from collaborating with Robin Thompson
Hickey, John ; Hill, William G. ; Blasco, Agustin ; Cameron, Neil ; Cullis, Brian ; McGuirk, Brian ; Mäntysaari, Esa ; Ruane, John ; Simm, Geoff ; Veerkamp, Roel ; Visscher, Peter M. ; Wray, Naomi R. - \ 2019
Journal of Animal Breeding and Genetics 136 (2019)4. - ISSN 0931-2668 - p. 301 - 309.
Digital mapping of peatlands – A critical review
Minasny, Budiman ; Berglund, Örjan ; Connolly, John ; Hedley, Carolyn ; Vries, Folkert de; Gimona, Alessandro ; Kempen, Bas ; Kidd, Darren ; Lilja, Harry ; Malone, Brendan ; McBratney, Alex ; Roudier, Pierre ; O'Rourke, Sharon ; Rudiyanto, ; Padarian, José ; Poggio, Laura ; Caten, Alexandre ten; Thompson, Daniel ; Tuve, Clint ; Widyatmanti, Wirastuti - \ 2019
Earth-Science Reviews 196 (2019). - ISSN 0012-8252

Peatlands offer a series of ecosystem services including carbon storage, biomass production, and climate regulation. Climate change and rapid land use change are degrading peatlands, liberating their stored carbon (C) into the atmosphere. To conserve peatlands and help in realising the Paris Agreement, we need to understand their extent, status, and C stocks. However, current peatland knowledge is vague—estimates of global peatland extent ranges from 1 to 4.6 million km2, and C stock estimates vary between 113 and 612 Pg (or billion tonne C). This uncertainty mostly stems from the coarse spatial scale of global soil maps. In addition, most global peatland estimates are based on rough country inventories and reports that use outdated data. This review shows that digital mapping using field observations combined with remotely-sensed images and statistical models is an avenue to more accurately map peatlands and decrease this knowledge gap. We describe peat mapping experiences from 12 countries or regions and review 90 recent studies on peatland mapping. We found that interest in mapping peat information derived from satellite imageries and other digital mapping technologies is growing. Many studies have delineated peat extent using land cover from remote sensing, ecology, and environmental field studies, but rarely perform validation, and calculating the uncertainty of prediction is rare. This paper then reviews various proximal and remote sensing techniques that can be used to map peatlands. These include geophysical measurements (electromagnetic induction, resistivity measurement, and gamma radiometrics), radar sensing (SRTM, SAR), and optical images (Visible and Infrared). Peatland is better mapped when using more than one covariate, such as optical and radar products using nonlinear machine learning algorithms. The proliferation of satellite data available in an open-access format, availability of machine learning algorithms in an open-source computing environment, and high-performance computing facilities could enhance the way peatlands are mapped. Digital soil mapping allows us to map peat in a cost-effective, objective, and accurate manner. Securing peatlands for the future, and abating their contribution to atmospheric C levels, means digitally mapping them now.

Which game narratives do adolescents of different gameplay and sociodemographic backgrounds prefer? A mixed-methods analysis
Schwarz, Ayla ; Mertens, Lieze ; Simons, Monique ; Spook, Jorinde E. ; Thompson, Debbe ; Cardon, Greet ; Bourdeaudhuij, Ilse De; Chastin, Sebastien F.M. ; Desmet, Ann - \ 2019
Games for Health Journal 8 (2019)3. - ISSN 2161-783X - p. 195 - 204.
Adolescents - Digital games - Health promotion - Mixed method - Narratives - Serious games

Objective: The aim of this study was to investigate which narrative elements of digital game narratives are preferred by the general adolescent population, and to examine associations with gender, socioeconomic status (SES), and gameplay frequency. Further, the study aims to discuss how results can be translated to serious digital games. Materials and Methods: Adolescents were recruited through school to complete a survey on narrative preferences in digital games. The survey included questions on sociodemographic information, frequency of gameplay, and an open-ended question on what could be an appealing narrative for them. Data were analyzed in a mixed-methods approach, using thematic analysis and chi-square analyses to determine narrative preferences and the associations between game narrative elements and player characteristics (gender, SES, and frequency of gameplay). Results: The sample consisted of 446 adolescents (12-15 years old) who described 30 narrative subthemes. Preferences included human characters as protagonists; nonhuman characters only as antagonists; realistic settings, such as public places or cities; and a strong conflict surrounding crime, catastrophe, or war. Girls more often than boys defined characters by their age, included avatars, located the narrative in private places, developed profession-related skills, and included a positive atmosphere. Adolescents of nonacademic education more often than adolescents of academic education defined characters by criminal actions. Infrequent players more often included human characters defined by their age than frequent players. After performing a Bonferroni correction, narrative preferences for several gender differences remained. Conclusion: Different narrative elements related to subgroups of adolescents by gender, SES, and frequency of gameplay. Customization of narratives in serious digital health games should be warranted for boys and girls; yet, further research is needed to specify how to address girls in particular.

Hierarchically structured composites and porous materials from soft templates : Fabrication and applications
Thompson, Benjamin R. ; Horozov, Tommy S. ; Stoyanov, Simeon D. ; Paunov, Vesselin N. - \ 2019
Journal of Materials Chemistry. A, Materials for energy and sustainability 7 (2019)14. - ISSN 2050-7488 - p. 8030 - 8049.

Recent experimental methods for fabrication of hierarchically porous and structured composites are reviewed. The main focus is on recent examples of how different soft templating materials, like emulsions, surfactant phases, breath figures, biological templates, liquid marbles and hydrogel bead slurries can be used to fabricate hierarchically porous materials with tuneable porosity, pore sizes and ratios of different sized pores. Approaches for tuning the physical properties (mechanical, thermal, acoustic) of these innovative materials as well as controlling the porosity, pore size and microstructure are discussed. We also show a variety of applications of hierarchically structured composites in catalysis, energy storage, usage and conversion, removal of pollutants, sensors, biomaterials, smart soaps, and structuring of consumer products.

Addendum: The FAIR Guiding Principles for scientific data management and stewardship
Wilkinson, Mark D. ; Dumontier, Michel ; Aalbersberg, Ijsbrand Jan ; Appleton, Gabrielle ; Axton, Myles ; Baak, Arie ; Blomberg, Niklas ; Boiten, Jan Willem ; Silva Santos, Luiz Bonino Da; Bourne, Philip E. ; Bouwman, Jildau ; Brookes, Anthony J. ; Clark, Tim ; Crosas, Mercè ; Dillo, Ingrid ; Dumon, Olivier ; Edmunds, Scott ; Evelo, Chris T. ; Finkers, Richard ; Gonzalez-Beltran, Alejandra ; Gray, Alasdair J.G. ; Groth, Paul ; Goble, Carole ; Grethe, Jeffrey S. ; Heringa, Jaap ; Hoen, Peter A.C. 't; Hooft, Rob ; Kuhn, Tobias ; Kok, Ruben ; Kok, Joost ; Lusher, Scott J. ; Martone, Maryann E. ; Mons, Albert ; Packer, Abel L. ; Persson, Bengt ; Rocca-Serra, Philippe ; Roos, Marco ; Schaik, Rene van; Sansone, Susanna Assunta ; Schultes, Erik ; Sengstag, Thierry ; Slater, Ted ; Strawn, George ; Swertz, Morris A. ; Thompson, Mark ; Lei, Johan van der; Mulligen, Erik van; Velterop, Jan ; Waagmeester, Andra ; Wittenburg, Peter ; Wolstencroft, Katherine ; Zhao, Jun ; Mons, Barend - \ 2019
Scientific Data 6 (2019). - ISSN 2052-4463

Integrated multi-omics approach reveals a role of ALDH1A1 in lipid metabolism in human colon cancer cells
Charkoftaki, Georgia ; Thompson, David C. ; Golla, Jaya Prakash ; Garcia-Milian, Rolando ; Lam, T.T. ; Engel, Jasper ; Vasiliou, Vasilis - \ 2019
Chemico-Biological Interactions 304 (2019). - ISSN 0009-2797 - p. 88 - 96.
Disentangling the genetics of lean mass
Karasik, David ; Zillikens, M.C. ; Hsu, Yi Hsiang ; Aghdassi, Ali ; Akesson, Kristina ; Amin, Najaf ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Bochud, Murielle ; Borecki, Ingrid B. ; Broer, Linda ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos-Obando, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Chambers, John C. ; Chen, Zhao ; Cho, Nam H. ; Choi, Hyung Jin ; Chou, Wen Chi ; Cummings, Steven R. ; Groot, Lisette C.P.G.M. De; Jager, Phillip L. De; Demuth, Ilja ; Diatchenko, Luda ; Econs, Michael J. ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Eriksson, Joel ; Eriksson, Johan G. ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Gieger, Christian ; Grallert, Harald ; Gudnason, Vilmundur ; Lenore, Launer J. ; Hayward, Caroline ; Hofman, Albert ; Homuth, Georg ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Johnson, Toby ; Biffar, Reiner ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpeläinen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koller, Daniel L. ; Kooner, Jaspal S. ; Kraus, William E. ; Kritchevsky, Stephen ; Kutalik, Zoltán ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Lerch, Markus M. ; Lewis, Joshua R. ; Lill, Christina ; Lind, Lars ; Lindgren, Cecilia ; Liu, Yongmei ; Livshits, Gregory ; Ljunggren, Östen ; Loos, Ruth J.F. ; Lorentzon, Mattias ; Luan, Jian An ; Luben, Robert N. ; Malkin, Ida ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Nethander, Maria ; Newman, Anne B. ; Oconnell, Jeffery R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Prince, Richard L. ; Psaty, Bruce M. ; Räikkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Rivadeneira, Fernando ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schipf, Sabine ; Shin, Chan Soo ; Smith, Albert V. ; Smith, Shad B. ; Soranzo, Nicole ; Spector, Timothy D. ; StanÄ Áková, Alena ; Stefansson, Kari ; Steinhagen-Thiessen, Elisabeth ; Stolk, Lisette ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorleifsson, Gudmar ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Uitterlinden, André G. ; Duijn, Cornelia M. Van; Schoor, Natasja M. Van; Vandenput, Liesbeth ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; J Wareham, Nicholas ; Waterworth, Dawn ; Weedon, Michael N. ; Wichmann, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Yerges-Armstrong, Laura M. ; Yu, Lei ; Zhang, Weihua ; Zhao, Jing Hua ; Zhou, Yanhua ; Nielson, Carrie M. ; Harris, Tamara B. ; Demissie, Serkalem ; Kiel, Douglas P. ; Ohlsson, Claes - \ 2019
American Journal of Clinical Nutrition 109 (2019)2. - ISSN 0002-9165 - p. 276 - 278.
body composition - body fat - meta-Analysis of genome-wide association studies - metabolic profile - skeletal muscle

Background Lean body mass (LM) plays an important role in mobility and metabolic function. We previously identified five loci associated with LM adjusted for fat mass in kilograms. Such an adjustment may reduce the power to identify genetic signals having an association with both lean mass and fat mass. Objectives To determine the impact of different fat mass adjustments on genetic architecture of LM and identify additional LM loci. Methods We performed genome-wide association analyses for whole-body LM (20 cohorts of European ancestry with n = 38,292) measured using dual-energy X-ray absorptiometry) or bioelectrical impedance analysis, adjusted for sex, age, age 2, and height with or without fat mass adjustments (Model 1 no fat adjustment; Model 2 adjustment for fat mass as a percentage of body mass; Model 3 adjustment for fat mass in kilograms). Results Seven single-nucleotide polymorphisms (SNPs) in separate loci, including one novel LM locus (TNRC6B), were successfully replicated in an additional 47,227 individuals from 29 cohorts. Based on the strengths of the associations in Model 1 vs Model 3, we divided the LM loci into those with an effect on both lean mass and fat mass in the same direction and refer to those as "sumo wrestler" loci (FTO and MC4R). In contrast, loci with an impact specifically on LM were termed "body builder" loci (VCAN and ADAMTSL3). Using existing available genome-wide association study databases, LM increasing alleles of SNPs in sumo wrestler loci were associated with an adverse metabolic profile, whereas LM increasing alleles of SNPs in "body builder" loci were associated with metabolic protection. Conclusions In conclusion, we identified one novel LM locus (TNRC6B). Our results suggest that a genetically determined increase in lean mass might exert either harmful or protective effects on metabolic traits, depending on its relation to fat mass.

Comparison of Pesticide Exposure in Honey Bees (Hymenoptera : Apidae) and Bumble Bees (Hymenoptera: Apidae): Implications for Risk Assessments
Gradish, Angela E. ; Steen, Jozef Van Der; Scott-Dupree, Cynthia D. ; Cabrera, Ana R. ; Cutler, G.C. ; Goulson, Dave ; Klein, Olaf ; Lehmann, David M. ; Lückmann, Johannes ; O'Neill, Bridget ; Raine, Nigel E. ; Sharma, Bibek ; Thompson, Helen - \ 2019
Environmental Entomology 48 (2019)1. - ISSN 0046-225X - p. 12 - 21.
bumble bee - honey bee - pesticide exposure - risk assessment

To date, regulatory pesticide risk assessments have relied on the honey bee (Apis mellifera L.) (Hymenoptera: Apidae) as a surrogate test species for estimating the risk of pesticide exposure to all bee species. However, honey bees and non-Apis bees may differ in their susceptibility and exposure to pesticides. In 2017, a workshop ('Pesticide Exposure Assessment Paradigm for Non-Apis Bees') was held to assess if honey bee risk assessment frameworks are reflective of non-Apis bee pesticide exposure. In this article, we summarize the workshop discussions on bumble bees (Bombus spp.). We review the life history and foraging behavior of bumble bees and honey bees and discuss how these traits may influence routes and levels of exposure for both taxa. Overall, the major pesticide exposure routes for bumble bees and honey bees are similar; however, bumble bees face additional exposure routes (direct exposure of foraging queens and exposure of larvae and adults to soil residues). Furthermore, bumble bees may receive comparatively higher pesticide doses via contact or oral exposure. We conclude that honey bee pesticide risk assessments may not always be protective of bumble bees, especially queens, in terms of exposure. Data needed to reliably quantify pesticide exposure for bumble bees (e.g., food consumption rates, soil residue levels) are lacking. Addressing these knowledge gaps will be crucial before bumble bee exposure can be incorporated into the pesticide risk assessment process. Because bumble bees exhibit appreciable interspecific variation in colony and behavioral characteristics, data relevant to pesticide exposure should be generated for multiple species.

Economic evaluation of 4 bovine leukemia virus control strategies for Alberta dairy farms
Kuczewski, Alessa ; Hogeveen, Henk ; Orsel, Karin ; Wolf, Robert ; Thompson, Jada ; Spackman, Eldon ; Meer, Frank van der - \ 2019
Journal of Dairy Science 102 (2019)3. - ISSN 0022-0302 - p. 2578 - 2592.
bovine leukemia virus - dairy economics - economic evaluation - leukosis

Bovine leukemia virus (BLV) is a production-limiting disease common in North American dairy herds. To make evidence-based recommendations to Canadian dairy producers and their consultants regarding cost and financial benefits of BLV on-farm control, an economic model that takes the supply-managed milk quota system into account is necessary. Alberta-specific input variables were used for the presented analysis. A decision tree model program was used to evaluate economic aspects of decreasing a 40% BLV within-herd prevalence on dairy farms by implementing various control strategies over 10 yr. Investigated strategies were (1) all management strategies, including 3 options for colostrum management; (2) some management strategies; (3) test and cull; and (4) test and segregate. Each of these strategies was compared with a no control on-farm approach. The prevalence for this no-control approach was assumed to stay constant over time. Each control strategy incurred specific yearly cost and yielded yearly decreases in prevalence, thereby affecting yearly partial net revenue. Infection with BLV was assumed to decrease milk production, decrease cow longevity, and increase condemnation of carcasses at slaughter from cattle with enzootic bovine leukosis, thereby decreasing net revenue. Cows infected with BLV generated a yearly mean partial net revenue of Can$7,641, whereas noninfected cows generated Can$8,276. Mean cost for the control strategies ranged from Can$193 to 847 per animal over 10 yr in a 146-animal herd. Net benefits of controlling BLV on farm, as compared with not controlling BLV, per cow in a 146-animal herd over a 10-yr period for each strategy was: Can$1,315 for all management strategies (freezer); Can$1,243 for all management strategies (pasteurizer); Can$785 for all management strategies (powdered colostrum); Can$1,028 for some management strategies; Can$1,592 for test and cull; and Can$1,594 for test and segregate. Consequently, on-farm BLV control was financially beneficial. Even though negative net benefits were possible and expected for some iterations, our sensitivity analysis highlighted the overall robustness of our model. In summary, this model provided evidence that Canadian dairy farmers should be encouraged to control BLV on their farm.

Balance of Emission and Dynamical Controls on Ozone During the Korea-United States Air Quality Campaign From Multiconstituent Satellite Data Assimilation
Miyazaki, K. ; Sekiya, T. ; Fu, D. ; Bowman, K.W. ; Kulawik, S.S. ; Sudo, K. ; Walker, T. ; Kanaya, Y. ; Takigawa, M. ; Ogochi, K. ; Eskes, H. ; Boersma, K.F. ; Thompson, A.M. ; Gaubert, B. ; Barre, J. ; Emmons, L.K. - \ 2019
Journal of Geophysical Research: Atmospheres 124 (2019)1. - ISSN 2169-897X - p. 387 - 413.
air quality - Asia - data assimilation - emission - ozone - satellite

Global multiconstituent concentration and emission fields obtained from the assimilation of the satellite retrievals of ozone, CO, NO2, HNO3, and SO2 from the Ozone Monitoring Instrument (OMI), Global Ozone Monitoring Experiment 2, Measurements of Pollution in the Troposphere, Microwave Limb Sounder, and Atmospheric Infrared Sounder (AIRS)/OMI are used to understand the processes controlling air pollution during the Korea-United States Air Quality (KORUS-AQ) campaign. Estimated emissions in South Korea were 0.42 Tg N for NOx and 1.1 Tg CO for CO, which were 40% and 83% higher, respectively, than the a priori bottom-up inventories, and increased mean ozone concentration by up to 7.5 ± 1.6 ppbv. The observed boundary layer ozone exceeded 90 ppbv over Seoul under stagnant phases, whereas it was approximately 60 ppbv during dynamical conditions given equivalent emissions. Chemical reanalysis showed that mean ozone concentration was persistently higher over Seoul (75.10 ± 7.6 ppbv) than the broader KORUS-AQ domain (70.5 ± 9.2 ppbv) at 700 hPa. Large bias reductions (>75%) in the free tropospheric OH show that multiple-species assimilation is critical for balanced tropospheric chemistry analysis and emissions. The assimilation performance was dependent on the particular phase. While the evaluation of data assimilation fields shows an improved agreement with aircraft measurements in ozone (to less than 5 ppbv biases), CO, NO2, SO2, PAN, and OH profiles, lower tropospheric ozone analysis error was largest at stagnant conditions, whereas the model errors were mostly removed by data assimilation under dynamic weather conditions. Assimilation of new AIRS/OMI ozone profiles allowed for additional error reductions, especially under dynamic weather conditions. Our results show the important balance of dynamics and emissions both on pollution and the chemical assimilation system performance.

Modelling strategies for assessing and increasing the effectiveness of new phenotyping techniques in plant breeding
Eeuwijk, Fred A. van; Bustos-Korts, Daniela ; Millet, Emilie J. ; Boer, Martin P. ; Kruijer, Willem ; Thompson, Addie ; Malosetti, Marcos ; Iwata, Hiroyoshi ; Quiroz, Roberto ; Kuppe, Christian ; Muller, Onno ; Blazakis, Konstantinos N. ; Yu, Kang ; Tardieu, Francois ; Chapman, Scott C. - \ 2019
Plant Science 282 (2019). - ISSN 0168-9452 - p. 23 - 39.
Crop growth model - Genomic prediction - Genotype-by-environment-interaction - Genotype-to-phenotype model - Mixed model - Multi-environment model - Multi-trait model - Phenotyping - Phenotyping platform - Physiology - Plant breeding - Prediction - Reaction norm - Response surface - Statistical genetics

New types of phenotyping tools generate large amounts of data on many aspects of plant physiology and morphology with high spatial and temporal resolution. These new phenotyping data are potentially useful to improve understanding and prediction of complex traits, like yield, that are characterized by strong environmental context dependencies, i.e., genotype by environment interactions. For an evaluation of the utility of new phenotyping information, we will look at how this information can be incorporated in different classes of genotype-to-phenotype (G2P) models. G2P models predict phenotypic traits as functions of genotypic and environmental inputs. In the last decade, access to high-density single nucleotide polymorphism markers (SNPs) and sequence information has boosted the development of a class of G2P models called genomic prediction models that predict phenotypes from genome wide marker profiles. The challenge now is to build G2P models that incorporate simultaneously extensive genomic information alongside with new phenotypic information. Beyond the modification of existing G2P models, new G2P paradigms are required. We present candidate G2P models for the integration of genomic and new phenotyping information and illustrate their use in examples. Special attention will be given to the modelling of genotype by environment interactions. The G2P models provide a framework for model based phenotyping and the evaluation of the utility of phenotyping information in the context of breeding programs.

Soil property and class maps of the conterminous United States at 100-meter spatial resolution
Ramcharan, Amanda ; Hengl, Tomislav ; Nauman, Travis ; Brungard, Colby ; Waltman, Sharon ; Wills, Skye ; Thompson, James - \ 2018
Soil Science Society of America Journal 82 (2018)1. - ISSN 0361-5995 - p. 186 - 201.

With growing concern for the depletion of soil resources, conventional soil maps need to be updated and provided at finer and finer resolutions to be able to support spatially explicit human-landscape models. Three US soil point datasets-the National Cooperative Soil Survey Characterization Database, the National Soil Information System, and the Rapid Carbon Assessment dataset-were combined with a stack of over 200 environmental datasets and gSSURGO polygon maps to generate complete coverage gridded predictions at 100-m spatial resolution of six soil properties (percentage of organic C, total N, bulk density, pH, and percentage of sand and clay) and two US soil taxonomic classes (291 great groups [GGs] and 78 modified particle size classes [mPSCs]) for the conterminous United States. Models were built using parallelized random forest and gradient boosting algorithms as implemented in the ranger and xgboost packages for R. Soil property predictions were generated at seven standard soil depths (0, 5, 15, 30, 60, 100, and 200 cm). Prediction probability maps for US soil taxonomic classifications were also generated. Cross validation results indicated an out-of-bag classification accuracy of 60% for GGs and 66% for mPSCs; for soil properties, RMSE for leave-location-out cross-validation was 0.74 (R2 = 0.68), 17.8 wt% (R2 = 0.57), 12 wt% (R2 = 0.46), 3.63 wt% (R2 = 0.41), 0.2 g cm-3 (R2 = 0.42), and 0.27 wt% (R2 = 0.39) for pH, percent sand and clay, weight percentage of organic C, bulk density, and weight percentage of total N, respectively. Nine independent validation datasets were used to assess prediction accuracies for soil class models, and results ranged between 24 and 58% and between 24 and 93% for GG and mPSC prediction accuracies, respectively. Although mapping accuracies were variable and likely lower than gSSURGO in some areas, this modeling approach can enable easier integration of soil information with spatially explicit models compared with multicomponent map units.

Covariance functions and random regression
Veerkamp, Roel - \ 2018
Smart soaps : Stimulus responsive soap-hydrogel bead composites for controlled dissolution and release of actives
Thompson, Benjamin R. ; Rutkevičius, Marius ; Horozov, Tommy S. ; Stoyanov, Simeon D. ; Paunov, Vesselin N. - \ 2018
Materials Chemistry Frontiers 2 (2018)2. - ISSN 2052-1537 - p. 402 - 409.

We designed pressure responsive soap-hydrogel bead composites by incorporating agar hydrogel beads of different size distributions within a molten soap matrix at various volume fractions. Upon cooling, the combined suspension of hydrogel beads into the molten soap was set into a composite of soap matrix. We demonstrate pressure driven syneresis of water from the soap-hydrogel bead composites upon compression. This allowed a release of active components embedded in the hydrogel beads upon application of pressure on these ''smart'' soap composites. We found that the dissolution rate of these composites generally increases with the volume percentage of hydrogel beads. We achieved a composite dissolution rate approximately 2.8 times higher than the soap control sample without hydrogel beads. However, the composite dissolution rate was independent of the size of the embedded hydrogel beads. We studied the release rates of active components encapsulated within the hydrogel beads used to prepare the composites. It was found that the release rate can be controlled in three different ways: varying the hydrogel beads size, using different concentrations of the gelling polymer used to make the hydrogel and also by co-encapsulating an oppositely charged polyelectrolyte along with the active encapsulated species. We found that the composites compressional strength decreased with an increasing volume percentage of hydrogel beads incorporated within the soap composite. Young's modulus showed a maximum when 7.5% by volume of hydrogel beads were used for composite preparation. These fast-dissolving soap-hydrogel composites contain significantly less raw materials and would reduce the pollution of waste water with surface active components. We envisage that soap-hydrogel bead composites could improve the sustainability of the soap-producing industry and could find their application within the hotel business, where they could reduce costs and the waste of millions of partially used soap bars discarded on a daily basis.

A genome-wide association study for natural antibodies measured in blood of Canadian Holstein cows
Klerk, Britt de; Emam, Mehdi ; Thompson-Crispi, Kathleen A. ; Sargolzaei, Mehdi ; Poel, Johan J. van der; Mallard, Bonnie A. - \ 2018
BMC Genomics 19 (2018)1. - ISSN 1471-2164
Dairy cattle - Genome-wide-association study - Immune system - Immunoglobulin class switching - Natural antibody - Vesicle trafficking

Background: Natural antibodies (NAb) are an important component of the innate immune system, and fight infections as a part of the first line defence. NAb are poly-reactive and can respond non-specifically to antigens. Therefore, NAb may be a key trait when evaluating an animal’s potential natural disease resistance. Variation in NAb is caused by both genetic and environmental factors. In this study genetic parameters of NAb were estimated and a genome-wide association study (GWAS) was performed to gain further understanding on the genes that are responsible for the observed genetic variation of NAb in Canadian Holsteins. Results: In total, blood samples of 1327 cows from 64 farms were studied. NAb binding to keyhole limpet hemocyanin (KLH) were determined via indirect ELISA. Immunoglobulin (Ig) isotypes, IgG and IgM, were evaluated. From the sample population, 925 cows were genotyped for 45,187 markers and each individual marker was tested to detect genetic variation in NAb levels. The relationships among animals was accounted for with genomic relationship. Results show heritabilities of 0.27 ± 0.064 (IgG) and 0.31 ± 0.065 (IgM). In total, 23 SNPs were found to be associated with IgG, but no SNPs were associated with IgM (FDR p-value < 0.05). The significant SNPs were located on autosomal chromosomes 1, 20 and 21 of the cow genome. Functional annotation analysis of the positional candidate genes revealed two sets of genes with biologically relevant functions related to NAb. In one set, seven genes with crucial roles in the production of antibody in B cells were associated with the trafficking of vesicles inside the cells between organelles. In the second set, two genes among positional candidate genes were associated with isotype class-switching and somatic hypermutation of B cells. Conclusions: This study demonstrated the possibility of increasing NAb through selective breeding. In addition, the effects of two candidate pathways are proposed for further investigation of NAb production in Holsteins.

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