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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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

Repurposing isoxazoline veterinary drugs for control of vector-borne human diseases
Miglianico, Marie ; Eldering, Maarten ; Slater, Hannah ; Ferguson, Neil ; Ambrose, Pauline ; Lees, Rosemary S. ; Koolen, Karin M.J. ; Pruzinova, Katerina ; Jancarova, Magdalena ; Volf, Petr ; Koenraadt, Constantianus J.M. ; Duerr, Hans Peter ; Trevitt, Graham ; Yang, Baiyuan ; Chatterjee, Arnab K. ; Wisler, John ; Sturm, Angelika ; Bousema, Teun ; Sauerwein, Robert W. ; Schultz, Peter G. ; Tremblay, Matthew S. ; Dechering, Koen J. - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)29. - ISSN 0027-8424 - p. E6920 - E6926.
Insecticide - Isoxazoline - Malaria - Vector control - Zika fever

Isoxazolines are oral insecticidal drugs currently licensed fo ectoparasite control in companion animals. Here we propose thei use in humans for the reduction of vector-borne disease incidence Fluralaner and afoxolaner rapidly killed Anopheles, Aedes, an Culex mosquitoes and Phlebotomus sand flies after feeding on drug-supplemented blood meal, with IC50 values ranging from 33 to 575 nM, and were fully active against strains with preexist ing resistance to common insecticides. Based on allometric scalin of preclinical pharmacokinetics data, we predict that a single hu man median dose of 260 mg (IQR, 177–407 mg) for afoxolaner, o 410 mg (IQR, 278–648 mg) for fluralaner, could provide an insecti cidal effect lasting 50–90 days against mosquitoes and Phleboto mus sand flies. Computational modeling showed that seasona mass drug administration of such a single dose to a fraction of regional population would dramatically reduce clinical cases o Zika and malaria in endemic settings. Isoxazolines therefore rep resent a promising new component of drug-based vector control.

Reply to Anderson, Ellen, Hanazaki, Hunn, Rival, Si, Slater, Weiskopf
Ludwig, D.J. - \ 2018
Current Anthropology 59 (2018)4. - ISSN 0011-3204 - p. 430 - 438.
Fluctuations in populations of subsurface methane oxidizers in coordination with changes in electron acceptor availability
Magnabosco, C. ; Timmers, P.H.A. ; Lau, M.C.Y. ; Borgonie, G. ; Linage-Alvarez, B. ; Kuloyo, O. ; Alleva, R. ; Kieft, T.L. ; Slater, G.F. ; Heerden, E. van; Sherwood Lollar, B. ; Onstott, T.C. - \ 2018
FEMS microbiology ecology 94 (2018)7. - ISSN 0168-6496
Archaea - Metagenomics - Methane oxidation - Subsurface

The concentrations of electron donors and acceptors in the terrestrial subsurface biosphere fluctuate due to migration and mixing of subsurface fluids, but the mechanisms and rates at which microbial communities respond to these changes are largely unknown. Subsurface microbial communities exhibit long cellular turnover times and are often considered relatively static-generating just enough ATP for cellular maintenance. Here, we investigated how subsurface populations of CH4 oxidizers respond to changes in electron acceptor availability by monitoring the biological and geochemical composition in a 1339 m-below-land-surface (mbls) fluid-filled fracture over the course of both longer (2.5 year) and shorter (2-week) time scales. Using a combination of metagenomic, metatranscriptomic, and metaproteomic analyses, we observe that the CH4 oxidizers within the subsurface microbial community change in coordination with electron acceptor availability over time. We then validate these findings through a series of 13C-CH4 laboratory incubation experiments, highlighting a connection between composition of subsurface CH4 oxidizing communities and electron acceptor availability.

HESS Opinions: Science in today's media landscape - Challenges and lessons from hydrologists and journalists
Lutz, Stefanie R. ; Popp, Andrea ; Emmerik, Tim Van; Gleeson, Tom ; Kalaugher, Liz ; Möbius, Karsten ; Mudde, Tonie ; Walton, Brett ; Hut, Rolf ; Savenije, Hubert ; Slater, Louise J. ; Solcerova, Anna ; Stoof, Cathelijne R. ; Zink, Matthias - \ 2018
Hydrology and Earth System Sciences 22 (2018)7. - ISSN 1027-5606 - p. 3589 - 3599.

Media such as television, newspapers and social media play a key role in the communication between scientists and the general public. Communicating your science via the media can be positive and rewarding by providing the inherent joy of sharing your knowledge with a broader audience, promoting science as a fundamental part of culture and society, impacting decision- and policy-makers, and giving you a greater recognition by institutions, colleagues and funders. However, the interaction between scientists and journalists is not always straightforward. For instance, scientists may not always be able to translate their work into a compelling story, and journalists may sometimes misinterpret scientific output. In this paper, we present insights from hydrologists and journalists discussing the advantages and benefits as well as the potential pitfalls and aftermath of science-media interaction. As we perceive interacting with the media as a rewarding and essential part of our work, we aim to encourage scientists to participate in the diverse and evolving media landscape. With this paper, we call on the scientific community to support scientists who actively contribute to a fruitful science-media relationship..

Indigenous and Scientific Kinds
Ludwig, David - \ 2017
The British Journal for the Philosophy of Science 68 (2017)1. - ISSN 0007-0882 - p. 187 - 212.
The aim of this article is to discuss the relation between indigenous and scientific kinds on the basis of contemporary ethnobiological research. I argue that ethnobiological accounts of taxonomic convergence–divergence patters challenge common philosophical models of the relation between folk concepts and natural kinds. Furthermore, I outline a positive model of taxonomic convergence–divergence patterns that is based on Slater's ([2015]) notion of ‘stable property clusters’ and Franklin-Hall's ([2015]) discussion of natural kinds as ‘categorical bottlenecks’. Finally, I argue that this model is not only helpful for understanding the relation between indigenous and scientific kinds, but also makes substantial contributions to contemporary debates about natural kinds.
Impact of the shedding level on transmission of persistent infections in Mycobacterium avium subspecies paratuberculosis (MAP)
Slater, Noa ; Mitchell, Rebecca Mans ; Whitlock, Robert H. ; Fyock, Terry ; Pradhan, Abani Kumar ; Knupfer, Elena ; Schukken, Ynte Hein ; Louzoun, Yoram - \ 2016
Veterinary Research 47 (2016)1. - ISSN 0928-4249

Super-shedders are infectious individuals that contribute a disproportionate amount of infectious pathogen load to the environment. A super-shedder host may produce up to 10 000 times more pathogens than other infectious hosts. Super-shedders have been reported for multiple human and animal diseases. If their contribution to infection dynamics was linear to the pathogen load, they would dominate infection dynamics. We here focus on quantifying the effect of super-shedders on the spread of infection in natural environments to test if such an effect actually occurs in Mycobacterium avium subspecies paratuberculosis (MAP). We study a case where the infection dynamics and the bacterial load shed by each host at every point in time are known. Using a maximum likelihood approach, we estimate the parameters of a model with multiple transmission routes, including direct contact, indirect contact and a background infection risk. We use longitudinal data from persistent infections (MAP), where infectious individuals have a wide distribution of infectious loads, ranging upward of three orders of magnitude. We show based on these parameters that the effect of super-shedders for MAP is limited and that the effect of the individual bacterial load is limited and the relationship between bacterial load and the infectiousness is highly concave. A 1000-fold increase in the bacterial contribution is equivalent to up to a 2-3 fold increase in infectiousness.

The FAIR Guiding Principles for scientific data management and stewardship : Comment
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 - \ 2016
Scientific Data 3 (2016). - ISSN 2052-4463

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

Rapid Evolution of Virulence and Drug Resistance in the Emerging Zoonotic Pathogen Streptococcus suis
Holden, M.T.G. ; Hauser, H. ; Sanders, M. ; Hoa Ngo, Thi ; Cherevach, I. ; Cronin, A. ; Goodhead, I. ; Mungall, K. ; Quail, M.A. ; Price, C. ; Rabbinowitsch, E. ; Sharp, S. ; Croucher, N. ; Chieu, Tran Bich ; Nguyen, Thi Hoang Mai ; To, Song Diep ; Nguyen, Tran Chinh ; Kehoe, M. ; Leigh, J.A. ; Ward, P.N. ; Dowson, C.G. ; Whatmore, A.M. ; Chanter, N. ; Iversen, P. ; Gottschalk, M. ; Slater, J.D. ; Smith, H.E. ; Spratt, B.G. ; Jianguo, Xu ; Changyun, Ye ; Bentley, S. ; Barrell, B.G. ; Schultsz, C. ; Maskell, D.J. ; Parkhill, J. - \ 2009
PLoS ONE (2009). - ISSN 1932-6203 - 7 p.
Background - Streptococcus suis is a zoonotic pathogen that infects pigs and can occasionally cause serious infections in humans. S. suis infections occur sporadically in human Europe and North America, but a recent major outbreak has been described in China with high levels of mortality. The mechanisms of S. suis pathogenesis in humans and pigs are poorly understood. Methodology/Principal Findings - The sequencing of whole genomes of S. suis isolates provides opportunities to investigate the genetic basis of infection. Here we describe whole genome sequences of three S. suis strains from the same lineage: one from European pigs, and two from human cases from China and Vietnam. Comparative genomic analysis was used to investigate the variability of these strains. S. suis is phylogenetically distinct from other Streptococcus species for which genome sequences are currently available. Accordingly, ~40% of the ~2 Mb genome is unique in comparison to other Streptococcus species. Finer genomic comparisons within the species showed a high level of sequence conservation; virtually all of the genome is common to the S. suis strains. The only exceptions are three ~90 kb regions, present in the two isolates from humans, composed of integrative conjugative elements and transposons. Carried in these regions are coding sequences associated with drug resistance. In addition, small-scale sequence variation has generated pseudogenes in putative virulence and colonization factors. Conclusions/Significance - The genomic inventories of genetically related S. suis strains, isolated from distinct hosts and diseases, exhibit high levels of conservation. However, the genomes provide evidence that horizontal gene transfer has contributed to the evolution of drug resistance.
An integrated approach to recovery of intracellular products from yeasts by bead milling and precoat filtration.
Kloosterman, J. ; Wassenaar, P.D. van; Slater, N.H.K. ; Padt, A. van der - \ 1988
Chemical Engineering Journal 37 (1988). - ISSN 1385-8947 - p. B47 - B54.
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