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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    Data driven supply allocation to individual customers considering forecast bias
    Seitz, Alexander ; Grunow, Martin ; Akkerman, Renzo - \ 2020
    International Journal of Production Economics 227 (2020). - ISSN 0925-5273
    Allocation planning - Big data - Demand forecast bias - Demand fulfilment - Order promising - Supply chain planning

    We propose a data-driven allocation planning approach, which is designed for use in advanced planning systems as they are widely used in industrial environments. The approach exploits increasingly available data on individual customers and products by allocating supply on a highly granular level at high planning frequencies. It counteracts rationing gaming by customers, which we assume to be the reason for demand forecast biases. We create an incentive for truthful forecasting by not only allocating supply based on customer profitability but also based on forecast bias. In the long term, this approach gives access to a profit potential and an on-time service level increase. In the short term, however, setting such an incentive does not only have a positive impact on service levels but also leads to a decline in profits. Our methodology quantifies this trade off providing decision support for determining the extent to which the forecast bias should affect the allocation. In a numerical study based on the semiconductor industry, we demonstrate that the approach has a large long-term profit potential while having limited effect on short-term profits for significant service level incentives. The analysis further shows that the allocation efficiency increases with the granularity level and the predictive quality of the available data.

    Asgard archaea capable of anaerobic hydrocarbon cycling
    Seitz, Kiley W. ; Dombrowski, Nina ; Eme, Laura ; Spang, Anja ; Lombard, Jonathan ; Sieber, Jessica R. ; Teske, Andreas P. ; Ettema, Thijs J.G. ; Baker, Brett J. - \ 2019
    Nature Communications 10 (2019). - ISSN 2041-1723

    Large reservoirs of natural gas in the oceanic subsurface sustain complex communities of anaerobic microbes, including archaeal lineages with potential to mediate oxidation of hydrocarbons such as methane and butane. Here we describe a previously unknown archaeal phylum, Helarchaeota, belonging to the Asgard superphylum and with the potential for hydrocarbon oxidation. We reconstruct Helarchaeota genomes from metagenomic data derived from hydrothermal deep-sea sediments in the hydrocarbon-rich Guaymas Basin. The genomes encode methyl-CoM reductase-like enzymes that are similar to those found in butane-oxidizing archaea, as well as several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. We suggest that members of the Helarchaeota have the potential to activate and subsequently anaerobically oxidize hydrothermally generated short-chain hydrocarbons.

    Asgard archaea illuminate the origin of eukaryotic cellular complexity
    Zaremba-Niedzwiedzka, Katarzyna ; Caceres, Eva F. ; Saw, Jimmy H. ; Bäckström, Disa ; Juzokaite, Lina ; Vancaester, Emmelien ; Seitz, Kiley W. ; Anantharaman, Karthik ; Starnawski, Piotr ; Kjeldsen, Kasper U. ; Stott, Matthew B. ; Nunoura, Takuro ; Banfield, Jillian F. ; Schramm, Andreas ; Baker, Brett J. ; Spang, Anja ; Ettema, Thijs J.G. - \ 2017
    Nature 541 (2017)7637. - ISSN 0028-0836 - p. 353 - 358.

    The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the Asgard superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- A nd Heimdallarchaeota. Asgard archaea affiliate with eukaryotes in phylogenomic analyses, and their genomes are enriched for proteins formerly considered specific to eukaryotes. Notably, thorarchaeal genomes encode several homologues of eukaryotic membrane-trafficking machinery components, including Sec23/24 and TRAPP domains. Furthermore, we identify thorarchaeal proteins with similar features to eukaryotic coat proteins involved in vesicle biogenesis. Our results expand the known repertoire of eukaryote-specific proteins in Archaea, indicating that the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.

    A robust supply chain planning framework for revenue management in the semiconductor industry
    Seitz, Alexander ; Ehm, Hans ; Akkerman, Renzo ; Osman, Sarah - \ 2016
    Journal of Revenue and Pricing Management 15 (2016)6. - ISSN 1476-6930 - p. 523 - 533.
    dynamic pricing - forecast accuracy - order management - semiconductor industry - supply chain contracts - supply chain planning

    High demand uncertainties, long production lead times, and short product life cycles cause high risks for supply chain planning in the semiconductor industry. These affect all industries producing goods containing semiconductors. We present a robust supply chain planning framework for revenue management that consists of stable and flexible solutions for demand steering and dynamic pricing, extending current industry practice in several aspects. We introduce the concept of availabilities and capabilities, as well as various planning processes and process enablers. Based on our framework, we also highlight directions for future research.

    FlpS, the FNR-like protein of streptococcus suis is an essential, oxygen-sensing activator of the arginine deiminase system
    Willenborg, Jörg ; Koczula, Anna ; Fulde, Marcus ; Greeff, Astrid de; Beineke, Andreas ; Eisenreich, Wolfgang ; Huber, Claudia ; Seitz, Maren ; Valentin-Weigand, Peter ; Goethe, Ralph - \ 2016
    Pathogens 5 (2016)3. - ISSN 2076-0817
    Arginine deiminase system - FNR-like protein - Streptococcus suis

    Streptococcus (S.) suis is a zoonotic pathogen causing septicemia and meningitis in pigs and humans. During infection S. suis must metabolically adapt to extremely diverse environments of the host. CcpA and the FNR family of bacterial transcriptional regulators are important for metabolic gene regulation in various bacteria. The role of CcpA in S. suis is well defined, but the function of the FNR-like protein of S. suis, FlpS, is yet unknown. Transcriptome analyses of wild-type S. suis and a flpS mutant strain suggested that FlpS is involved in the regulation of the central carbon, arginine degradation and nucleotide metabolism. However, isotopologue profiling revealed no substantial changes in the core carbon and amino acid de novo biosynthesis. FlpS was essential for the induction of the arcABC operon of the arginine degrading pathway under aerobic and anaerobic conditions. The arcABC-inducing activity of FlpS could be associated with the level of free oxygen in the culture medium. FlpS was necessary for arcABC-dependent intracellular bacterial survival but redundant in a mice infection model. Based on these results, we propose that the core function of S. suis FlpS is the oxygen-dependent activation of the arginine deiminase system.

    Noise impact on European sea bass behavior : Temporal structure matters
    Neo, Yik Yaw ; Seitz, Johanna ; Kastelein, Ronald A. ; Winter, Hendrik V. ; Cate, Carel ten; Slabbekoorn, Hans - \ 2016
    In: The Effects of Noise on Aquatic Life II Springer New York LLC (Advances in Experimental Medicine and Biology ) - ISBN 9781493929801 - p. 763 - 766.
    Amplitude fluctuation - Anthropogenic sounds - Dicentrarchus labrax - Intermittency - Stress response

    Anthropogenic sounds come in different forms, varying not only in amplitude and frequency spectrum but also in temporal structure. Although fish are sensitive to the temporal characteristics of sound, little is known about how their behavior is affected by anthropogenic sounds of different temporal patterns. We investigated this question using groups of Dicentrarchus labrax (European sea bass) in an outdoor basin. Our data revealed that the temporal pattern of sound exposure is important in noise impact assessments.

    Momentum or kinetic energy - How do substrate properties influence the calculation of rainfall erosivity?
    Goebes, Philipp ; Seitz, Steffen ; Geißler, Christian ; Lassu, Tamás ; Peters, Piet ; Seeger, Manuel ; Nadrowski, Karin ; Scholten, Thomas - \ 2014
    Journal of Hydrology 517 (2014). - ISSN 0022-1694 - p. 310 - 316.
    Kinetic energy - Momentum - Rainfall erosivity - Rainfall simulation - Splash cup

    Rainfall erosivity is a key component in soil erosion by water. While kinetic energy and momentum are used to describe the erosivity of rainfall, and both are derived from mass and velocity of raindrops, it is not clear how different substrates transform this energy. In our study we conducted rainfall simulation experiments to determine splash detachment amounts of five substrates (coarse sand, medium sand, fine sand, PE balls, silt) for seven different rainfall intensities (52-116mmh -1 ). We used linear mixed-effect modeling (LME) to calculate erosivity predictors for each substrate. Additionally, we separated drop-size-velocity relationship into lower left and upper right quarter to investigate the effect of small and slow just as big and fast raindrops on splash detachment amounts.We suggest using momentum divided by drop diameter as a substrate-independent erosivity predictor. To consider different substrates specific erosivity parameters are needed. Heavier substrates like sand are best described by kinetic energy multiplied by diameter whereas lighter substrates like silt point to momentum divided by diameter to the power of 1.5. Furthermore, our results show that substrates are differently affected by the size and velocity of drops. While splash detachment of light substances can be reliably predicted by drop size and velocity for small and slow drops, drop size and velocity loses its predictive power in heavier substrates like sand.

    Temporal structure of sound affects behavioural recovery from noise impact in European seabass
    Neo, Y.Y. ; Seitz, J. ; Kastelein, R.A. ; Winter, H.V. ; Cate, C. ten; Slabbekoorn, H. - \ 2014
    Biological Conservation 178 (2014). - ISSN 0006-3207 - p. 65 - 73.
    zebrafish danio-rerio - seismic air-guns - dicentrarchus-labrax - fish distribution - startle response - atlantic salmon - high-intensity - rainbow-trout - teleost fish - marine fish
    Human activities in and around waters generate a substantial amount of underwater noise, which may negatively affect aquatic life including fish. In order to better predict and assess the consequences of the variety of anthropogenic sounds, it is essential to examine what sound features contribute to an impact. In this study, we tested if sounds with different temporal structure resulted in different behavioural changes in European seabass. Groups of four fish were exposed in an outdoor basin to a series of four sound treatments, which were either continuous or intermittent, with either consistent or fluctuating amplitude. The behavioural changes of the fish were analyzed by a video-tracking system. All sound treatments elicited similar behavioural changes, including startle responses, increased swimming speed, increased group cohesion and bottom diving. However, with all other sound conditions being the same, intermittent exposure resulted in significantly slower behavioural recovery to pre-exposure levels compared to continuous exposure. Our findings imply that the temporal structure of sound is highly relevant in noise impact assessments: intermittent sounds, such as from pile driving, may have a stronger behavioural impact on fish than continuous sounds, such as from drilling, even though the latter may have higher total accumulated energy. This study urges regulatory authorities and developers to pay more attention to the influence of temporal structure when assessing noise impacts. However, more studies are needed to examine other sound parameters and to determine the generality of our observations in other species and in other outdoor water bodies
    Ecological value of coastal habitats for commercially and ecologically important species
    Seitz, R.D. ; Wennhage, H. ; Bergstrom, U. ; Lipcius, R.M. ; Ysebaert, T. - \ 2014
    ICES Journal of Marine Science 71 (2014)3. - ISSN 1054-3139 - p. 648 - 665.
    lobster homarus-gammarus - crab cancer-pagurus - bivalve macoma-balthica - shrimp crangon-crangon - mussel mytilus-edulis - southern north-sea - scallop placopecten-magellanicus - anchovy engraulis-encrasicolus - fish assemblage structure - sprat sprattus-sprattus
    Many exploited fish and macroinvertebrates that utilize the coastal zone have declined, and the causes of these declines, apart from overfishing, remain largely unresolved. Degradation of essential habitats has resulted in habitats that are no longer adequate to fulfil nursery, feeding, or reproductive functions, yet the degree to which coastal habitats are important for exploited species has not been quantified. Thus, we reviewed and synthesized literature on the ecological value of coastal habitats (i.e. seagrass beds, shallow subtidal and intertidal habitats, kelp beds, shallow open water habitats, saltmarshes, mussel beds, macroalgal beds, rocky bottom, and mariculture beds) as feeding grounds, nursery areas, spawning areas, and migration routes of 59 taxa, for which the International Council for the Exploration of the Sea (ICES) gives management advice, and another 12 commercially or ecologically important species. In addition, we provide detailed information on coastal habitat use for plaice (Pleuronectes platessa), cod (Gadus morhua), brown shrimp (Crangon crangon), and European lobster (Homarus gammarus). Collectively, 44% of all ICES species utilized coastal habitats, and these stocks contributed 77% of the commercial landings of ICES-advice species, indicating that coastal habitats are critical to population persistence and fishery yield of ICES species. These findings will aid in defining key habitats for protection and restoration and provide baseline information needed to define knowledge gaps for quantifying the habitat value for exploited fish and invertebrates.
    Structure Matters: Correlating Temperature Dependent Electrical Transport through Alkyl Monolayers with Vibrational and Photoelectron Spectroscopies
    Shpaisman, H. ; Seitz, H. ; Yaffe, O. ; Roodenko, K. ; Scheres, L.M.W. ; Zuilhof, H. ; Chabal, Y.J. ; Sueyoshi, T. ; Kera, S. ; Ueno, N. ; Vilan, A. ; Cahen, D. - \ 2012
    Chemical Science 3 (2012). - ISSN 2041-6520 - p. 851 - 862.
    self-assembled monolayers - hydrogen-terminated silicon - h stretching modes - molecular junctions - charge-transport - through-bond - infrared-spectroscopy - electronic transport - organic monolayers - thiol monolayers
    Freezing out of molecular motion and increased molecular tilt enhance the efficiency of electron transport through alkyl chain monolayers that are directly chemically bound to oxide-free Si. As a result, the current across such monolayers increases as the temperature decreases from room temperature to [similar]80 K, i.e., opposite to thermally activated transport such as hopping or semiconductor transport. The 30-fold change for transport through an 18-carbon long alkyl monolayer is several times the resistance change for actual metals over this range. FTIR vibrational spectroscopic measurements indicate that cooling increases the packing density and reduces the motional freedom of the alkyl chains by first stretching the chains and then gradually tilting the adsorbed molecules away from the surface normal. Ultraviolet photoelectron spectroscopy shows drastic sharpening of the valence band structure as the temperature decreases, which we ascribe to decreased electron–phonon coupling. Although conformational changes are typical in soft molecular systems, in molecular electronics they are rarely observed experimentally or considered theoretically. Our findings, though, indicate that the molecular conformational changes are a prominent feature, which imply behavior that differs qualitatively from that described by models of electronic transport through inorganic mesoscopic solids
    Counterion localization in solutions of starlike polyelectrolytes and colloidal polyelectrolyte brushes: A self-consistent theory
    Leermakers, F.A.M. ; Ballauff, M. ; Borisov, O.V. - \ 2008
    Langmuir 24 (2008)18. - ISSN 0743-7463 - p. 10026 - 10034.
    branched polyelectrolytes - polymer brushes - simulations - micelles - model
    A quantitative analysis of the distribution of counterions in salt-free solutions of colloidal polyelectrolyte brushes and starlike polyelectrolytes is performed on the level of the Poisson¿Boltzmann approximation. Exact numerical solutions are obtained for starlike polyelectrolyte molecules composed of f = 20,¿.¿.¿., 50 arms with a fixed fractional charge ¿ per segment by applying the self-consistent field method of Scheutjens and Fleer (SF-SCF). The Wigner¿Seitz cell dimension defines the concentration of polyelectrolyte stars in the system. The numerical results are compared to predictions of an analytical mean field theory and related to experimental observations on the osmotic pressure in solutions of starlike polyelectrolytes and colloidal polyelectrolyte brushes.
    Galilean invariant lattice Boltzmann scheme for natural convection on square and rectangular lattices
    Sman, R.G.M. van der - \ 2006
    Physical Review. E, Statistical nonlinear, and soft matter physics 74 (2006)2. - ISSN 1539-3755 - 17 p.
    hydrodynamics - simulations - diffusion - relaxation - dispersion - models - cavity - number - flow
    In this paper we present lattice Boltzmann (LB) schemes for convection diffusion coupled to fluid flow on two-dimensional rectangular lattices. Via inverse Chapman-Enskog analysis of LB schemes including source terms, we show that for consistency with physics it is required that the moments of the equilibrium distributions equal those of the Maxwell-Boltzmann distribution. These constraints can be satisfied for the rectangular D2Q9 lattice for only fluid flow in the weakly compressible regime. The analysis of source terms shows that fluxes are really defined on the boundaries of the Wigner-Seitz cells, and not on the lattice sites where the densities are defined¿which is quite similar to the staggered grid finite-volume schemes. Our theoretical findings are confirmed by numerical solutions of benchmark problems for convection diffusion and natural convection. The lattice Boltzmann scheme shows remarkably good performance for convection diffusion, showing little to non-numerical diffusion or numerical dispersion, even at high grid Peclet numbers
    High-throughput identification of potential Arabidopsis MAP kinases substrates
    Feilner, T. ; Hultschig, C. ; Lee, J. ; Meyer, S. ; Immink, R.G.H. ; Koenig, A. ; Possling, A. ; Seitz, H. ; Beveridge, A. ; Scheel, D. ; Cahill, D.J. ; Lehrach, H. ; Kreutzberger, J. ; Kersten, B. - \ 2005
    Molecular and Cellular Proteomics 4 (2005)10. - ISSN 1535-9476 - p. 1558 - 1568.
    unnatural nucleotide specificity - antibody microarray technology - transcriptional regulation - fluorescence detection - innate immunity - phosphorylation - expression - stress - chips - scale
    Mitogen-activated protein kinase (MAPK) cascades are universal and highly conserved signal transduction modules in eucaryotes, including plants. These protein phosphorylation cascades link extracellular stimuli to a wide range of cellular responses. However, the underlying mechanisms are so far unknown, as information about phosphorylation substrates of plant MAPKs is lacking. In this study we addressed the challenging task to identify potential substrates for Arabidopsis thaliana mitogen-activated protein kinases 3 (MPK3) and 6 (MPK6), which are activated by many environmental stress factors. For this purpose, we developed a novel protein microarray-based proteomics method allowing high-throughput study of protein phosphorylation. We generated protein microarrays including 1,690 Arabidopsis proteins, which were obtained from the expression of an almost nonredundant uniclone set derived from an inflorescence meristem cDNA expression library. Microarrays were incubated with MPKs in the presence of radioactive ATP. Using a threshold-based quantification method to evaluate the microarray results, we were able to identify 48 potential substrates of MPK3 and 39 of MPK6. 26 of them are common for both kinases. One of the identified MPK6 substrates, 1-Aminocyclopropane-1-carboxylic acid synthase-6 (ACS-6) was just recently shown as the first plant MAPK substrate in vivo, demonstrating the potential of our method to identify substrates with physiological relevance. Furthermore, we revealed transcription factors, transcription regulators, splicing factors, receptors, histones and others as candidate substrates indicating that regulation in response to MAPK signaling is very complex and not restricted to the transcriptional level. Nearly all of the 48 potential MPK3 substrates were confirmed by other in vitro methods. As a whole, our approach allows to shortlist candidate substrates of MAP kinases as well as those of other protein kinases for further analysis. Follow-up in vivo experiments are essential to evaluate their physiological relevance
    An unambiguous nomenclature for xyloglucan-derived oligosaccharides.
    Fry, S.C. ; York, W.S. ; Albersheim, P. ; Darvill, A. ; Hayashi, T. ; Joseleau, J.P. ; Kato, Y. ; Pérez Lorences, E. ; Maclachlan, G.A. ; McNeil, M. ; Mort, A.J. ; Grant Reid, J.S. ; Seitz, H.U. ; Selvendran, R.R. ; Voragen, A.G.J. ; White, A.R. - \ 1993
    Physiologia Plantarum 89 (1993). - ISSN 0031-9317 - p. 1 - 3.
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