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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    CAPICE: A computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations
    Li, Shuang ; Velde, K.J. Van Der; Ridder, Dick De; Dijk, Aalt D.J. Van; Soudis, Dimitrios ; Zwerwer, Leslie R. ; Deelen, Patrick ; Hendriksen, Dennis ; Charbon, Bart ; Gijn, Marielle E. Van; Abbott, Kristin ; Sikkema-Raddatz, Birgit ; Diemen, Cleo C. Van; Kerstjens-Frederikse, Wilhelmina S. ; Sinke, Richard J. ; Swertz, Morris A. - \ 2020
    Genome Medicine 12 (2020)1. - ISSN 1756-994X
    Allele frequency - Clinical genetics - Exome sequencing - Genome diagnostics - Machine learning - Molecular consequence - Variant pathogenicity prediction

    Exome sequencing is now mainstream in clinical practice. However, identification of pathogenic Mendelian variants remains time-consuming, in part, because the limited accuracy of current computational prediction methods requires manual classification by experts. Here we introduce CAPICE, a new machine-learning-based method for prioritizing pathogenic variants, including SNVs and short InDels. CAPICE outperforms the best general (CADD, GAVIN) and consequence-type-specific (REVEL, ClinPred) computational prediction methods, for both rare and ultra-rare variants. CAPICE is easily added to diagnostic pipelines as pre-computed score file or command-line software, or using online MOLGENIS web service with API. Download CAPICE for free and open-source (LGPLv3) at https://github.com/molgenis/capice.

    Eindrapportage SARS-CoV-2 bij besmette nertsenbedrijven
    Stegeman, Arjan ; Poel, W.H.M. van der; Vreman, S. ; Honing-Hakze, R.W. van der; Harders, F.L. ; Tacken, M.G.J. ; Engelsma, M.Y. ; Hulst, M.M. ; Koopmans, Marion ; Oude Munnink, B.B. ; Sikkema, Reina S. ; Molenaar, Robert Jan ; Bouwstra, Ruth ; Smit, Lidwien ; Rooij, M. de; Stegeman, Arjan - \ 2020
    Wageningen University & Research - 14 p.
    animal welfare - animal production - mink - animal health - animal diseases - Coronavirus
    SARS-CoV-2 infection in farmed minks, the Netherlands, April and May 2020
    Oreshkova, Nadia ; Molenaar, Robert Jan ; Vreman, Sandra ; Harders, Frank ; Oude Munnink, Bas B. ; Hakze-van der Honing, Renate W. ; Gerhards, Nora ; Tolsma, Paulien ; Bouwstra, Ruth ; Sikkema, Reina S. ; Tacken, Mirriam G.J. ; Rooij, Myrna M.T. de; Weesendorp, Eefke ; Engelsma, Marc Y. ; Bruschke, Christianne J.M. ; Smit, Lidwien A.M. ; Koopmans, Marion ; Poel, Wim H.M. van der; Stegeman, Arjan - \ 2020
    Eurosurveillance 25 (2020)23. - ISSN 1025-496X
    interstitial pneumonia - mink - SARS-CoV-2 - transmission

    Respiratory disease and increased mortality occurred in minks on two farms in the Netherlands, with interstitial pneumonia and SARS-CoV-2 RNA in organ and swab samples. On both farms, at least one worker had coronavirus disease-associated symptoms before the outbreak. Variations in mink-derived viral genomes showed between-mink transmission and no infection link between the farms. Inhalable dust contained viral RNA, indicating possible exposure of workers. One worker is assumed to have attracted the virus from mink.

    Tackling the nitrogen problem in five stages
    Hermans, Tia ; Dijkstra, Jan ; Smits, Nina ; Groenestein, Karin ; Ogink, Nico ; Huijsmans, Jan ; Velthof, Gerard ; Jongschaap, Raymond ; Geerdink, Peter ; Munniks, Sandra ; Jongeneel, Roel ; Ravesloot, Marc - \ 2020

    interview met Tia Hermans en Jan Dijstra en Nina Smits

    Is nutrition science ready for the twenty-first century? Moving towards transdisciplinary impacts in a changing world
    Tufford, Adèle R. ; Calder, Philip C. ; Van’t Veer, Pieter ; Feskens, Edith F. ; Ockhuizen, Theo ; Kraneveld, Aletta D. ; Sikkema, Jan ; Vries, Jan de - \ 2020
    European Journal of Nutrition 59 (2020). - ISSN 1436-6207 - p. 1 - 10.

    Malnutrition in an obese world was the fitting title of the 13th Federation of European Nutrition Societies (FENS) conference held in October 2019. Many individuals do not eat a healthy, well-balanced diet, and this is now understood to be a major driver of increased disease risk and illness. Moreover, both our current eating patterns and the food system as a whole are environmentally unsustainable, threatening the planetary systems we depend on for survival. As we attempt to feed a growing global population, food systems will increasingly be confronted with their environmental impacts, with the added challenge of climate change-induced threats to food production. As we move into the third decade of the twenty-first century, these challenges demand that the nutrition research community reconsider its scope, concepts, methods, and societal role. At a pre-meeting workshop held at the FENS conference, over 70 researchers active in the field explored ways to advance the discipline’s capacity to address cross-cutting issues of personal, public and planetary health. Using the world cafe method, four themed discussion tables explored (a) the breadth of scientific domains needed to meet the current challenges, (b) the nature and definition of the shifting concepts in nutrition sciences, (c) the next-generation methods required and (d) communication and organisational challenges and opportunities. As a follow-up to earlier work [1], here we report the highlights of the discussions, and propose the next steps to advance responsible research and innovation in the domain of nutritional science.

    Organic will be mainstream (one day)
    Sukkel, Wijnand - \ 2020
    Innovatiesubsidie voor medicijnmakers
    Wijffels, Rene ; Adamo, Sarah D'; Barbosa, Maria ; Martens, Dirk ; Südfeld, Christian - \ 2020
    Role of national fossil fuel comparators in the nominal emission savings through bioenergy under the red-case study in six eu countries
    Banja, M. ; Sikkema, R. ; Spijker, E. ; Szendrei, K. - \ 2019
    In: European Biomass Conference and Exhibition Proceedings 2019. - ETA-Florence Renewable Energies (European Biomass Conference and Exhibition Proceedings ) - p. 1701 - 1709.
    Bioenergy - Climate-effectiveness - Energy transition - Fossil fuel comparator - Greenhouse gases - Life cycle analysis - Sustainability

    As part of the energy transition efforts, most bioenergy policies are strongly driven by the ambition to reduce greenhouse gas (GHG) emissions and substitute fossil fuels. The challenge is to properly select the fossil fuel “baseline” comparators for each form of bioenergy for any given national context. Based on existing literature as well as data and experiences gathered within EU co-funded research projects the paper presents the methodological approach for discussing the effect on nominal GHG emissions savings due to bioenergy under RED rules taking into consideration the national fossil fuels comparators. The paper assesses this effect in the 3-bioenergy markets (electricity, heating/cooling and transport) in Finland, Germany, Italy, Lithuania, the Netherlands and Poland. The paper assesses this effect for each sector separately without trying to compare them showing that project-specific and/or national fossil fuels comparators in the calculation of nominal GHG emission savings from bioenergy can have a more stimulating effect than generic EU comparators and the GHG reduction can be more accurately estimated depending on specific conditions in a country. The paper suggests that for including any other effects than CO2 emissions, it is relevant to select appropriate indicators and use adequate comparators, with enough reference data, for those effects.

    Intensive export agriculture comes up against environmental limits: making choices in the Mekong Delta
    Bosma, Roel - \ 2019
    Tot op de bodem
    Postma, J. - \ 2019
    In: KennisBASIS voor een duurzame toekomst / Roskamp, Harry, de Boo, Marion, Sikkema, Albert, Wageningen University & Research - p. 12 - 13.
    Less nitrogen is very doable: the nitrogen problem is not as black and white as it seems
    Migchels, Gerard ; Vries, Wim de; Aarnink, Andre ; Gies, Edo - \ 2019
    Closing cycles together
    Ploeg, Jandouwe van der - \ 2019
    ‘I’m looking for farms that are ready for 2050’: Professor Rogier Schulte on his lighthouse farms
    Schulte, Rogier - \ 2019
    Alarm in the Amazon
    Kruijt, Bart - \ 2019
    3D camera spots the sick cows
    Song, Xiangyu ; Tol, Rik van der; Bokkers, E.A.M. - \ 2019

    Met een 3D-camera is de conditie van koeten te bepalen, zodat ziekten beter zijn te voorkomen. Promovendus Xiangyu Song ontwierp een methodiek om uiterlijke gezondheidskenmerken van koeien automatisch vast te leggen.

    Closing the cycles together: calling at three regional innovation workplaces
    Scholten, Martin ; Durksz, Durk ; Huizen, Ingrid van; Boer, Imke de - \ 2019
    Insulating houses with fibre from pig manure
    Nikiforidis, Costas ; Oever, Martien van den - \ 2019
    Methane inhibitors in feed are a step in the right direction
    Dijkstra, Jan - \ 2019
    'Farmers can solve the ammonia problem'
    Migchels, Gerard - \ 2019
    'Extra nitrogen measurements won't replace RIVM model'
    Groenestein, Karin - \ 2019
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