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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Corrigendum to: A genome-wide association study identifies nucleotide variants at SIGLEC5 and DEFA1A3 as risk loci for periodontitis
Munz, Matthias ; Willenborg, Christina ; Richter, Gesa M. ; Jockel-Schneider, Yvonne ; Graetz, Christian ; Staufenbiel, Ingmar ; Wellmann, Jürgen ; Berger, Klaus ; Krone, Bastian ; Hoffmann, Per ; Velde, Nathalie Van Der; Uitterlinden, André G. ; Groot, C.P.G.M. De; Sawalha, Amr H. ; Direskeneli, Haner ; Saruhan-Direskeneli, Güher ; Guzeldemir-Akcakanat, Esra ; Keceli, Huseyin Gencay ; Laudes, Matthias ; Noack, Barbara ; Teumer, Alexander ; Holtfreter, Birte ; Kocher, Thomas ; Eickholz, Peter ; Meyle, Jörg ; Doerfer, Christof ; Bruckmann, Corinna ; Lieb, Wolfgang ; Franke, Andre ; Schreiber, Stefan ; Nohutcu, Rahime M. ; Erdmann, Jeanette ; Loos, Bruno G. ; Jepsen, Soeren ; Dommisch, Henrik ; Schaefer, Arne S. - \ 2018
Human Molecular Genetics 27 (2018)5. - ISSN 0964-6906 - p. 941 - 942.
How plausible is automatic annotation of scientific spreadsheets?
Vos, Martine De; Wielemaker, Jan ; Wielinga, Bob ; Schreiber, Guus ; Top, Jan - \ 2017
CEUR Workshop Proceedings 2065 (2017). - ISSN 1613-0073 - p. 26 - 31.
Domain knowledge - Heuristics - Knowledge engineering - Spreadsheets - Vocabularies
It is possible to automatically annotate a natural science spreadsheet using lexical matching, given that the tables in these spreadsheets meet a number of requirements regarding the content. Results of a survey show that most of the existing natural science spreadsheets deviate from the ideal situation. We propose to complement lexical matching with both heuristics and knowledge from external vocabularies to overcome these deviations.
Draft genome sequence of Sphingomonas sp. strain Sph1(2015), isolated from a fouled membrane filter used to produce drinking water
Vries, Hendrik J. de; Marshall, Ian P.G. ; Schreiber, Lars ; Plugge, Caroline M. - \ 2017
Genome Announcements 5 (2017)24. - ISSN 2169-8287

We report here the high-quality draft genome sequence of Sphingomonas sp. strain Sph1(2015), isolated from a fouled reverse osmosis membrane used for the production of high-quality drinking water. The draft sequence provides insights into the modus operandi of this strain to form biofilms on membrane surfaces. This knowledge offers tools to develop novel antifouling strategies

Streptococcus sp. genome sequencing
Palakawong Na Ayudthaya, S. ; Marshall, Ian P.G. ; Schreiber, Lars ; Plugge, C.M. - \ 2017
Streptococcus - PRJNA352333
Novel Streptococcus species, Streptococcus sp. 'caviae' strain:Cavy grass 6
Draft genome sequence of Streptococcus caviae strain Cavy grass 6T, isolated from domesticated guinea pig fecal samples
Ayudthaya, Susakul Palakawong Na ; Marshall, Ian P.G. ; Schreiber, Lars ; Plugge, Caroline M. - \ 2017
Genome Announcements 5 (2017)13. - ISSN 2169-8287 - 2 p.

Streptococcus caviae strain Cavy grass 6T, isolated from fecal samples of pet guinea pigs, can metabolize a range of plant mono- and disaccharides, as well as polymeric carbohydrates. Here, we report the draft genome sequence of this strain, which comprises 2.11 Mb.

A genome-wide association study identifies nucleotide variants at SIGLEC5 and DEFA1A3 as risk loci for periodontitis
Munz, Matthias ; Willenborg, Christina ; Richter, Gesa M. ; Jockel-Schneider, Yvonne ; Graetz, Christian ; Staufenbiel, Ingmar ; Wellmann, Jürgen ; Berger, Klaus ; Krone, Bastian ; Hoffmann, Per ; Velde, Nathalie Van Der; Uitterlinden, André G. ; Groot, Lisette de; Sawalha, Amr H. ; Direskeneli, Haner ; Saruhan-Direskeneli, Güher ; Guzeldemir-Akcakanat, Esra ; Keceli, Gencay ; Laudes, Matthias ; Noack, Barbara ; Teumer, Alexander ; Holtfreter, Birte ; Kocher, Thomas ; Eickholz, Peter ; Meyle, Jörg ; Doerfer, Christof ; Bruckmann, Corinna ; Lieb, Wolfgang ; Franke, Andre ; Schreiber, Stefan ; Nohutcu, Rahime M. ; Erdmann, Jeanette ; Loos, Bruno G. ; Jepsen, Soeren ; Dommisch, Henrik ; Schaefer, Arne S. - \ 2017
Human Molecular Genetics 26 (2017)13. - ISSN 0964-6906 - p. 2577 - 2588.
Periodontitis is one of themost common inflammatory diseases, with a prevalence of 11% worldwide for the severe forms and an
estimated heritability of 50%. The disease is characterized by destruction of the alveolar bone due to an aberrant host
inflammatory response to a dysbiotic oral microbiome. Previous genome-wide association studies (GWAS) have reported several
suggestive susceptibility loci. Here, we conducted a GWAS using a German and Dutch case-control sample of aggressive periodontitis
(AgP, 896 cases, 7,104 controls), a rare but highly severe and early-onset form of periodontitis, validated the associations in a
German sample of severe forms of the more moderate phenotype chronic periodontitis (CP) (993 cases, 1,419 controls). Positive
findings were replicated in a Turkish sample of AgP (223 cases, 564 controls). A locus at SIGLEC5 (sialic acid binding Ig-like lectin 5)
and a chromosomal region downstream of the DEFA1A3 locus (defensin alpha 1-3) showed association with both disease phenotypes
and were associated with periodontitis at a genome-wide significance level in the pooled samples, with P¼1.09E-08
(rs4284742,-G; OR¼1.34, 95% CI¼1.21–1.48) and P¼5.48E-10 (rs2738058,-T; OR¼1.28, 95% CI¼1.18–1.38), respectively. SIGLEC5 is
expressed in various myeloid immune cells and classified as an inhibitory receptor with the potential tomediate tyrosine phosphatases
SHP-1/-2 dependent signaling. Alpha defensins are antimicrobial peptides with expression in neutrophils andmucosal
surfaces and a role in phagocyte-mediated host defense. This study identifies the first shared genetic risk loci of AgP and CP
with genome-wide significance and highlights the role of innate and adaptive immunity in the etiology of periodontitis.
Combining information on structure and content to automatically annotate natural science spreadsheets
Vos, Martine de; Wielemaker, Jan ; Rijgersberg, Hajo ; Schreiber, Guus ; Wielinga, Bob ; Top, Jan - \ 2017
International Journal of Human-Computer Studies 103 (2017). - ISSN 1071-5819 - p. 63 - 76.
Domain Model - Implicit knowledge - Methodology - Spreadsheets - Units of measure - Vocabularies

In this paper we propose several approaches for automatic annotation of natural science spreadsheets using a combination of structural properties of the tables and external vocabularies. During the design process of their spreadsheets, domain scientists implicitly include their domain model in the content and structure of the spreadsheet tables. However, this domain model is essential to unambiguously interpret the spreadsheet data. The overall objective of this research is to make the underlying domain model explicit, to facilitate evaluation and reuse of these data. We present our annotation approaches by describing five structural properties of natural science spreadsheets, that may pose challenges to annotation, and at the same time, provide additional information on the content. For example, the main property we describe is that, within a spreadsheet table, semantically related terms are grouped in rectangular blocks. For each of the five structural properties we suggest an annotation approach, that combines heuristics on the property with knowledge from external vocabularies. We evaluate our approaches in a case study, with a set of existing natural science spreadsheets, by comparing the annotation results with a baseline based on purely lexical matching. Our case study results show that combining information on structural properties of spreadsheet tables with lexical matching to external vocabularies results in higher precision and recall of annotation of individual terms. We show that the semantic characterization of blocks of spreadsheet terms is an essential first step in the identification of relations between cells in a table. As such, the annotation approaches presented in this study provide the basic information that is needed to construct the domain model of scientific spreadsheets.

Texture synthesis using convolutional neural networks with long-range consistency and spectral constraints
Schreiber, Shaun ; Geldenhuys, Jaco ; Villiers, Hendrik De - \ 2017
In: 2016 Pattern Recognition Association of South Africa and Robotics and Mechatronics International Conference, PRASA-RobMech 2016. - Institute of Electrical and Electronics Engineers Inc. - ISBN 9781509033355 - 6 p.

Procedural texture generation enables the creation of more rich and detailed virtual environments without the help of an artist. However, finding a flexible generative model of real world textures remains an open problem. We present a novel Convolutional Neural Network based texture model consisting of two summary statistics (the Gramian and Translation Gramian matrices), as well as spectral constraints. We investigate the Fourier Transform or Window Fourier Transform in applying spectral constraints, and find that the Window Fourier Transform improved the quality of the generated textures. We demonstrate the efficacy of our system by comparing generated output with that of related state of the art systems.

Requirements for the domain model of environmental computational spreadsheets
Top, J.L. ; Vos, M. de; Wielemaker, J. ; Schreiber, M. - \ 2015
A methodology for constructing the calculation model of scientific spreadsheets
Vos, M. de; Wielemaker, J. ; Schreiber, G. ; Wielinga, B. ; Top, J.L. - \ 2015
Spreadsheets models are frequently used by scientists to analyze research data. These models are typically described in a paper or a report, which serves as single source of information on the underlying research project. As the calculation workflow in these models is not made explicit, readers are not able to fully understand how the research results are calculated, and trace them back to the underlying spreadsheets. This paper proposes a methodology for semi-automatically deriving the calculation workflow underlying a set of spreadsheets. The starting point of our methodology is the cell dependency graph, representing all spreadsheet cells and connections. We automatically aggregate all cells in the graph that represent instances and duplicates of the same quantities, based on analysis of the formula syntax. Subsequently, we use a set of heuristics, incorporating knowledge on spreadsheet design, computational procedures and domain knowledge, to select those quantities, that are relevant for understanding the calculation workflow. We explain and illustrate our methodology by actually applying it on three sets of spreadsheets from existing research projects in the domains of environmental and life science. Results from these case studies show that our constructed calculation models approximate the ground truth calculation workflows, both in terms of content and size, but are not a perfect match.
Effects of ß-Lactam Antibiotics and Fluoroquinolones on Human Gut Microbiota in Relation to Clostridium difficile Associated Diarrhea
Knecht, H. ; Neulinger, S.C. ; Heinsen, F.A. ; Knecht, C. ; Schilhabel, A. ; Schmitz, R.A. ; Zimmermann, A. ; Martins dos Santos, V.A.P. ; Ferrer, R. ; Rosenstiel, P.C. ; Schreiber, S. ; Friedrichs, A.K. ; Ott, S.J. - \ 2014
PLoS ONE 9 (2014)2. - ISSN 1932-6203
irritable-bowel-syndrome - ribosomal-rna - colonization resistance - intestinal microbiota - fecal microbiota - fatty-acids - disease - diversity - differs - risk
Clostridium difficile infections are an emerging health problem in the modern hospital environment. Severe alterations of the gut microbiome with loss of resistance to colonization against C. difficile are thought to be the major trigger, but there is no clear concept of how C. difficile infection evolves and which microbiological factors are involved. We sequenced 16S rRNA amplicons generated from DNA and RNA/cDNA of fecal samples from three groups of individuals by FLX technology: (i) healthy controls (no antibiotic therapy); (ii) individuals receiving antibiotic therapy (Ampicillin/Sulbactam, cephalosporins, and fluoroquinolones with subsequent development of C. difficile infection or (iii) individuals receiving antibiotic therapy without C. difficile infection. We compared the effects of the three different antibiotic classes on the intestinal microbiome and the effects of alterations of the gut microbiome on C. difficile infection at the DNA (total microbiota) and rRNA (potentially active) levels. A comparison of antibiotic classes showed significant differences at DNA level, but not at RNA level. Among individuals that developed or did not develop a C. difficile infection under antibiotics we found no significant differences. We identified single species that were up- or down regulated in individuals receiving antibiotics who developed the infection compared to non-infected individuals. We found no significant differences in the global composition of the transcriptionally active gut microbiome associated with C. difficile infections. We suggest that up- and down regulation of specific bacterial species may be involved in colonization resistance against C. difficile providing a potential therapeutic approach through specific manipulation of the intestinal microbiome.
Population models quantifying the value of coastal habitats for exploited species
Lipcius, R. ; Eggleston, D.B. ; Fodrie, J. ; Moore, J. ; Schreiber, J. ; Meer, J. van der; Wolfshaar, K.E. van de; Vasconcelos, R.P. - \ 2013
Reykjavik : ICES
Comparison of static chambers to measure CH4 emissions from soils
Pihlatie, M.K. ; Christiansen, J.R. ; Aaltonen, H. ; Korhonen, J.F.J. ; Nordbo, A. ; Rasilo, T. ; Benanti, G. ; Giebels, M. ; Helmy, M. ; Sheehy, J. ; Jones, S. ; Juszczak, R. ; Klefoth, R.R. ; Lobo-do-Vale, R. ; Rosa, A.P. ; Schreiber, P. ; Serca, D. ; Vicca, S. ; Wolf, B. ; Pumpanen, J. - \ 2013
Agricultural and Forest Meteorology 171-172 (2013). - ISSN 0168-1923 - p. 124 - 136.
gas-exchange - flux measurements - co2 efflux - atmosphere - respiration - apparatus - biases
The static chamber method (non-flow-through-non-steady-state chambers) is the most common method to measure fluxes of methane (CH4) from soils. Laboratory comparisons to quantify errors resulting from chamber design, operation and flux calculation methods are rare. We tested fifteen chambers against four flux levels (FL) ranging from 200 to 2300 mu g CH4 M-2 II-1. The measurements were conducted on a calibration tank using three quartz sand types with soil porosities of 53% (dry fine sand, S1), 47% (dry coarse sand, S2), and 33% (wetted fine sand, S3). The chambers tested ranged from 0.06 to 1.8 m in height, and 0.02 to 0.195 m(3) in volume, 7 of them were equipped with a fan, and 1 with a vent-tube. We applied linear and exponential flux calculation methods to the chamber data and compared these chamber fluxes to the reference fluxes from the calibration tank. The chambers underestimated the reference fluxes by on average 33% by the linear flux calculation method (R-Iin), whereas the chamber fluxes calculated by the exponential flux calculation method (R-exp) did not significantly differ from the reference fluxes (p
"Hot standards" for the thermoacidophilic archaeon Sulfolobus solfataricus
Zaparty, M. ; Esser, D. ; Gertig, S. ; Haferkamp, P. ; Kouril, T. ; Sierocinski, P. ; Pham, T.K. ; Manica, A. ; Reimann, J. ; Schreiber, K. ; Teichmann, D. ; Wolferen, M.E. van; Jan, M. von; Wieloch, P. ; Albers, S.V. ; Driessen, A.J.M. ; Klenk, H.P. ; Schleper, C. ; Schomburg, D. ; Oost, J. van der; Wright, P.C. ; Siebers, B. - \ 2010
Extremophiles 14 (2010)1. - ISSN 1431-0651 - p. 119 - 142.
entner-doudoroff pathway - central carbohydrate-metabolism - dna microarray analysis - hyperthermophilic archaeon - membrane proteome - genus sulfolobus - high-temperature - systems biology - silicon cell - key-enzyme
Within the archaea, the thermoacidophilic crenarchaeote Sulfolobus solfataricus has become an important model organism for physiology and biochemistry, comparative and functional genomics, as well as, more recently also for systems biology approaches. Within the Sulfolobus Systems Biology ("SulfoSYS")-project the effect of changing growth temperatures on a metabolic network is investigated at the systems level by integrating genomic, transcriptomic, proteomic, metabolomic and enzymatic information for production of a silicon cell-model. The network under investigation is the central carbohydrate metabolism. The generation of high-quality quantitative data, which is critical for the investigation of biological systems and the successful integration of the different datasets, derived for example from high-throughput approaches (e.g., transcriptome or proteome analyses), requires the application and compliance of uniform standard protocols, e.g., for growth and handling of the organism as well as the "-omics" approaches. Here, we report on the establishment and implementation of standard operating procedures for the different wet-lab and in silico techniques that are applied within the SulfoSYS-project and that we believe can be useful for future projects on Sulfolobus or (hyper)thermophiles in general. Beside established techniques, it includes new methodologies like strain surveillance, the improved identification of membrane proteins and the application of crenarchaeal metabolomics
Bibliography
Jong, E. de; Schreiber, H. - \ 2009
In: Reading the American Landscape. An index of Books and Images / de Jong, E.A., A. Braak, ter, Hamers, D., Hoogewoning, A., Schreiber, H., van der Salm, F., Sijmons, D.F., Rotterdam : NAi-publishers - ISBN 9789056627034 - p. 635 - 670.
Bibliografie
Jong, E. de; Schreiber, H. - \ 2009
In: Bladeren door het Amerikaanse landschap. Een index van boeken en beelden / de Jong, E.A., A. Braak, ter, Hamers, D., Hoogewoning, A., Schreiber, H., van der Salm, F., Sijmons, D.F., Rotterdam : NAi Uitgevers - ISBN 9789056627027 - p. 635 - 670.
Een Renaissance van het ontworpen landschap
Jong, E. de - \ 2009
In: Bladeren door het Amerikaanse landschap. Een index van boeken en beelden / de Jong, E.A., A. Braak, ter, Hamers, D., Hoogewoning, A., Schreiber, H., van der Salm, F., Sijmons, D.F., Rotterdam : NAi-publishers - ISBN 9789056627027 - p. 188 - 195.
A Renaissance of Designed Landscape
Jong, E. de - \ 2009
In: Reading the American Landscape. An index of Books and Images / de Jong, E.A., A. Braak, ter, Hamers, D., Hoogewoning, A., Schreiber, H., van der Salm, F., Sijmons, D.F., Rotterdam : NAi-publishers - ISBN 9789056627034 - p. 188 - 195.
Fruit-Surface Flavonoid Accumulation in Tomato Is Controlled by a SlMYB12-Regulated Transcriptional Network
Adato, A. ; Mandel, T. ; Mintz-Orion, S. ; Venger, I. ; Levy, D. ; Yativ, M. ; Dominguez, E. ; Wang, Z. ; Vos, C.H. de; Jetter, R. ; Schreiber, L. ; Heredia, A. ; Rogachev, I. ; Aharoni, A. - \ 2009
Plos Genetics 5 (2009)12. - ISSN 1553-7404 - 23 p.
affects vegetative development - phenylpropanoid biosynthesis - liquid-chromatography - arabidopsis-thaliana - gene - expression - evolution - identification - metabolism - regulator
The cuticle covering plants' aerial surfaces is a unique structure that plays a key role in organ development and protection against diverse stress conditions. A detailed analysis of the tomato colorless-peel y mutant was carried out in the framework of studying the outer surface of reproductive organs. The y mutant peel lacks the yellow flavonoid pigment naringenin chalcone, which has been suggested to influence the characteristics and function of the cuticular layer. Large-scale metabolic and transcript profiling revealed broad effects on both primary and secondary metabolism, related mostly to the biosynthesis of phenylpropanoids, particularly flavonoids. These were not restricted to the fruit or to a specific stage of its development and indicated that the y mutant phenotype is due to a mutation in a regulatory gene. Indeed, expression analyses specified three R2R3-MYB–type transcription factors that were significantly down-regulated in the y mutant fruit peel. One of these, SlMYB12, was mapped to the genomic region on tomato chromosome 1 previously shown to harbor the y mutation. Identification of an additional mutant allele that co-segregates with the colorless-peel trait, specific down-regulation of SlMYB12 and rescue of the y phenotype by overexpression of SlMYB12 on the mutant background, confirmed that a lesion in this regulator underlies the y phenotype. Hence, this work provides novel insight to the study of fleshy fruit cuticular structure and paves the way for the elucidation of the regulatory network that controls flavonoid accumulation in tomato fruit cuticle
Reading the American Landscape. An Index of Books and Images
Jong, E. de; Schreiber, H. ; Sijmons, D.F. ; Hoogewoning, A. - \ 2009
Rotterdam : NAi-publishers - ISBN 9789056627034 - 992
landschap - landschapsarchitectuur - vs - illustraties - foto's - landschapselementen - nationale landschappen - natuurlandschap - landscape - landscape architecture - usa - illustrations - photographs - landscape elements - national landscapes - natural landscape
From city high-rise to southern desert, from urban sprawl to virgin canyons, the American landscape is endless in its variety. On the initiative of the Netherlands Foundation for Visual Arts, Design and Architecture, a group of landscape architects, architects, urban designers, artists and critics travelled through this imposing landscape, drawing inspiration for their own work from its history and transformations. Their journey is recorded in Reading the American Landscape, which includes essays by the members of the group and a number of American landscape researchers. The backbone of the book is a bibliography compiled specially for the study trip, from which the authors each took one title as the starting point for their essays. The result is a remarkable series of reflections on American landscape architecture and public space, with visual essays by the artists and photographers who were part of the group. The bibliography is brought to life in over 6500 photographs, pointing beyond words to a landscape that can only be truly grasped in its infinite expanse.
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