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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    Implementation of PROMETHEUS 4‐step approach for evidence use in EFSA scientific assessments: benefits, issues, needs and solutions
    Aiassa, Elisa ; Martino, Laura ; Barizzone, Fulvio ; Ciccolallo, Laura ; Garcia, Ana ; Georgiadis, Marios ; Guajardo, Irene Muñoz ; Tomcikova, Daniela ; Alexander, Jan ; Calistri, Paolo ; Gundert‐remy, Ursula ; Hart, Andrew David ; Hoogenboom, Ron Laurentius ; Messean, Antoine ; Naska, Androniki ; Navarro, Maria Navajas ; Noerrung, Birgit ; Ockleford, Colin ; Wallace, Robert John ; Younes, Maged ; Abuntori, Blaize ; Alvarez, Fernando ; Aryeetey, Monica ; Baldinelli, Francesca ; Barrucci, Federica ; Bau, Andrea ; Binaglia, Marco ; Broglia, Alessandro ; Castoldi, Anna Federica ; Christoph, Eugen ; Sesmaisons‐Lecarré, Agnes De; Georgiadis, Nikolaos ; Gervelmeyer, Andrea ; Istace, Frederique ; López‐Gálvez, Gloria ; Manini, Paola ; Maurici, Daniela ; Merten, Caroline ; Messens, Winy ; Mosbach‐Schulz, Olaf ; Putzu, Claudio ; Bordajandi, Luisa Ramos ; Smeraldi, Camilla ; Tiramani, Manuela ; Martínez, Silvia Valtueña ; Sybren, Vos ; Hardy, Anthony Richard ; Hugas, Marta ; Kleiner, Juliane ; Seze, Guilhem De - \ 2018
    EFSA Supporting Publications 15 (2018)4. - ISSN 2397-8325
    In 2014, the European Food Safety Authority (EFSA) started the PROMETHEUS (PROmoting METHods for Evidence Use in Scientific assessments) project to improve further and increase the consistency of the methods it uses in its scientific assessments. The project defined a set of principles for the scientific assessment process and a 4‐step approach (plan/carry out/verify/report) for their fulfilment, which was tested in ten case studies, one from each EFSA panel. The present report describes the benefits, issues, needs and solutions related to the implementation of the 4‐step approach in EFSA, identified in a dedicated workshop in October 2017. The key benefits of the approach, which was deemed applicable to all types of EFSA scientific assessment including assessments of regulated products, are: 1) increased ‘scientific value’ of EFSA outputs, i.e. the extent of impartiality, methodological rigour, transparency and engagement; 2) guarantee of fitness‐for‐purpose, as it implies tailoring the methods to the specificities of each assessment; 3) efficiency gain, since preparing a protocol for the assessment upfront helps more streamlined processes throughout the implementation phase; 4) innovation, as the approach promotes the pioneering practice of ‘planning before doing’ (well established in primary research) for broad scientific assessments in regulatory science; and 5) increased harmonisation and consistency of EFSA assessments. The 4‐step approach was also considered an effective system for detecting additional methodological and/or expertise needs and a useful basis for further defining a quality management system for EFSA's scientific processes. The identified issues and solutions related to the implementation of the approach are: a) lack of engagement and need for effective communication on benefits and added value; b) need for further advances especially in the field of problem formulation/protocol development, evidence appraisal and evidence integration; c) need for specialised expertise in the previous aspects; and specific needs for d) assessments of regulated products and e) outsourced projects.
    Eighty Years of Mycopathologia: A Retrospective Analysis of Progress Made in Understanding Human and Animal Fungal Pathogens
    Chaturvedi, Vishnu ; Bouchara, Jean Philippe ; Hagen, Ferry ; Alastruey-Izquierdo, Ana ; Badali, Hamid ; Bocca, Anamelia Lorenzetti ; Cano-Lira, Jose F. ; Cao, Cunwei ; Chaturvedi, Sudha ; Chotirmall, Sanjay H. ; Diepeningen, Anne D. Van; Gangneux, Jean Pierre ; Guinea, Jesus ; Hoog, Sybren De; Ilkit, Macit ; Kano, Rui ; Liu, Weida ; Martinez-Rossi, Nilce M. ; Souza Carvalho Melhem, Marcia De; Ono, Mario Augusto ; Ran, Yuping ; Ranque, Stephane ; Almeida Soares, Celia Maria De; Sugita, Takashi ; Thomas, Philip A. ; Vecchiarelli, Anna ; Wengenack, Nancy L. ; Woo, Patrick C.Y. ; Xu, Jianping ; Zancope-Oliveira, Rosely M. - \ 2018
    Mycopathologia 183 (2018)6. - ISSN 0301-486X - p. 859 - 877.
    Mycopathologia was founded in 1938 to ‘diffuse the understanding of fungal diseases in man and animals among mycologists.’ This was an important mission considering that pathogenic fungi for humans and animals represent a tiny minority of the estimated 1.5–5 million fungal inhabitants on Earth. These pathogens have diverged from the usual saprotrophic lifestyles of most fungi to colonize and infect humans and animals. Medical and veterinary mycology is the subdiscipline of microbiology that dwells into the mysteries of parasitic, fungal lifestyles. Among the oldest continuing scientific publications on the subject, Mycopathologia had its share of ‘classic papers’ since the first issue was published in 1938. An analysis of the eight decades of notable contributions reveals many facets of host–pathogen interactions among 183 volumes comprising about 6885 articles. We have analyzed the impact and relevance of this body of work using a combination of citation tools (Google Scholar and Scopus) since no single citation metric gives an inclusive perspective. Among the highly cited Mycopathologia publications, those on experimental mycology accounted for the major part of the articles (36%), followed by diagnostic mycology (16%), ecology and epidemiology (15%), clinical mycology (14%), taxonomy and classification (10%), and veterinary mycology (9%). The first classic publication, collecting nearly 200 citations, appeared in 1957, while two articles published in 2010 received nearly 150 citations each, which is notable for a journal covering a highly specialized field of study. An empirical analysis of the publication trends suggests continuing interests in novel diagnostics, fungal pathogenesis, review of clinical diseases especially with relevance to the laboratory scientists, taxonomy and classification of fungal pathogens, fungal infections and carriage in pets and wildlife, and changing ecology and epidemiology of fungal diseases around the globe. We anticipate that emerging and re-emerging fungal pathogens will continue to cause significant health burden in the coming decades. It remains vital that scientists and physicians continue to collaborate by learning each other’s language for the study of fungal diseases, and Mycopathologia will strive to be their partner in this increasingly important endeavor to its 100th anniversary in 2038 and beyond.
    Impact of initial conditions versus external forcing in decadal climate predictions : A sensitivity experiment
    Corti, Susanna ; Palmer, Tim ; Balmaseda, Magdalena ; Weisheimer, Antje ; Drijfhout, Sybren ; Dunstone, Nick ; Hazeleger, Wilco ; Kröger, Jürgen ; Pohlmann, Holger ; Smith, Doug ; Storch, Jin Song Von; Wouters, Bert - \ 2015
    Journal of Climate 28 (2015)11. - ISSN 0894-8755 - p. 4454 - 4470.
    Climate models - Climate prediction - Decadal variability - Interdecadal variability - Model comparison - Oceanic variability

    The impact of initial conditions relative to external forcings in decadal integrations from an ensemble of state-of-the-art prediction models has been assessed using specifically designed sensitivity experiments (SWAP experiments). They consist of two sets of 10-yr-long ensemble hindcasts for two initial dates in 1965 and 1995 using either the external forcings from the "correct" decades or swapping the forcings between the two decades. By comparing the two sets of integrations, the impact of external forcing versus initial conditions on the predictability over multiannual time scales was estimated as the function of lead time of the hindcast. It was found that over time scales longer than about 1 yr, the predictability of sea surface temperatures (SSTs) on a global scale arises mainly from the external forcing. However, the correct initialization has a longer impact on SST predictability over specific regions such as the North Atlantic, the northwestern Pacific, and the Southern Ocean. The impact of initialization is even longer and extends to wider regions when below-surface ocean variables are considered. For the western and eastern tropical Atlantic, the impact of initialization for the 700-m heat content (HTC700) extends to as much as 9 years for some of the models considered. In all models the impact of initial conditions on the predictability of the Atlantic meridional overturning circulation (AMOC) is dominant for the first 5 years.

    Three‐dimensional correlated NMR study of Megasphaera elsdenii flavodoxin in the oxidized state
    Wijmenga, Sybren S. ; Mierlo, Carlo P.M. van - \ 1991
    European Journal of Biochemistry 195 (1991)3. - ISSN 0014-2956 - p. 807 - 822.

    The value of a three‐dimensional (3D) non‐selective total correlation/nuclear Overhauser enhancement spectroscopy (TOCSY‐NOESY) spectrum for making sequential resonance assignments in proteins is demonstrated using the relatively large Megasphaera elsdenii flavodoxin (molecular mass 15 kDa) in the oxidized state. An easy and concise method for the analysis of 3D‐NMR spectra and a strategy for the resonance assignment of 3D‐NMR protein spectra is introduced. In this context, non‐selective TOCSY‐NOESY is compared with selective TOCSY‐NOESY and non‐selective NOESY‐TOCSY. Sequential assignments in various secondary structure elements of flavodoxin are made using the method of analysis introduced. NOEs not previously identified in 2D‐NMR spectra due to resonance overlap are found in the 3D Clean‐TOCSY‐NOESY spectrum. Also additional side‐chain assignments could be made.

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