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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    Effects of eggshell temperature pattern during incubation on tibia characteristics of broiler chickens at slaughter age
    Güz, B.C. ; Molenaar, R. ; Jong, I.C. de; Kemp, B. ; Krimpen, M. van; Brand, H. van den - \ 2020
    Poultry Science 99 (2020)6. - ISSN 0032-5791 - p. 3020 - 3029.
    broiler chickens - eggshell temperature - incubation - leg health - tibia

    This study was designed to determine effects of eggshell temperature (EST) pattern in week 2 and week 3 of incubation on tibia development of broiler chickens at slaughter age. A total of 468 Ross 308 eggs were incubated at an EST of 37.8°C from incubation day (E) 0 to E7. Thereafter, a 2 × 2 factorial arrangement with 2 EST (37.8°C and 38.9°C) from E8 to E14 and 2 EST (36.7°C and 37.8°C) from E15 till hatch was applied. After hatching, chickens were reared until slaughter age with the 4 EST treatments and 8 replicates per treatment. At day 41 and 42, one male chicken per replicate per day was selected, and hock burn and food pad dermatitis were scored. Rotated tibia, tibia dyschondroplasia, epiphyseal plate abnormalities, bacterial chondronecrosis with osteomyelitis, and epiphysiolysis were assessed. Tibia weight, length, thickness, head thickness, and robusticity index were determined. X-ray analyses (osseous volume, pore volume, total volume, volume fraction, mineral content, and mineral density) and a 3-point bending test (ultimate strength, yield strength, stiffness, energy to fracture, and elastic modulus) were performed. A high EST (38.9°C) in week 2 of incubation, followed by a normal EST (37.8°C) in week 3 resulted in higher mineral content (P = 0.001), mineral density (P = 0.002), ultimate strength (P = 0.04), yield strength (P = 0.03), and stiffness (P = 0.05) compared with the other 3 EST groups (week 2 × week 3 interaction). A high EST (38.9°C) in week 2 of incubation, regardless of the EST in week 3, resulted in a higher tibia weight (P < 0.001), thickness (P = 0.05), osseous volume (P < 0.001), and total volume (P < 0.001) than a normal EST (37.8°C). It can be concluded that 1.1°C higher EST than normal in week 2 of incubation appears to stimulate tibia morphological, biophysical, and mechanical characteristics of broiler chickens at slaughter age. Additionally, a 1.1°C lower EST in week 3 of incubation appears to have negative effects on tibia characteristics, particularly in interaction with the EST in week 2 of incubation.

    A diagnostic tool for supporting policymaking on urban resilience
    Wardekker, Arjan ; Wilk, Bettina ; Brown, Valerie ; Uittenbroek, Caroline ; Mees, Heleen ; Driessen, Peter ; Wassen, Martin ; Molenaar, Arnoud ; Walda, Jim ; Runhaar, Hens - \ 2020
    Cities 101 (2020). - ISSN 0264-2751
    Choices - Diagnostic tool - Urban governance - Urban resilience

    Urban resilience has become a popular notion among urban policymakers and scientists, as a way to deal with the many complex issues that cities face. While it has positive connotations and resonates with local urban agendas, it is not always clear what it means and what factors contribute to resilience. Additionally, critical literature observes that people's views on what resilience means can differ strongly and the many choices that are made in planning and implementing resilience are often left implicit. In this paper, we describe a diagnostic tool that tackles these issues by (1) distilling resilience principles and narratives that provide a comprehensive picture of the different pathways that resilience-building could take, and (2) making explicit and facilitating reflection on the choices embedded in planning for urban resilience. We illustrate the tool with an application on urban flood risk management in Rotterdam. We conclude that the Resilience Diagnostic Tool is useful to reflect on the local goals of resilience-building, to diagnose choices made in urban plans, and to reflect on their consequences. It supports policymakers in making deliberate, transparent and goal-oriented choices on urban resilience.

    Condition and survival of discards in tickler chain beam trawl fisheries
    Schram, Edward ; Molenaar, Pieke ; Kleppe, Raoul ; Rijnsdorp, Adriaan - \ 2020
    IJmuiden : Wageningen Marine Research (Wageningen Marine Research report C034/20) - 31
    Dutch demersal fisheries in the North Sea is a mixed fishery that mainly targets Dover sole (Solea solea) with plaice (Pleuronectes platessa), turbot (Scophthalmus maximus), brill (Scophthalmus rhombus) and other species as valuable bycatches. The fleet currently uses two gear types: pulse beam trawls and conventional tickler chain beam trawls. Pulse beam trawlers operate with a temporary exemption from the EU prohibition to use electric stimulation in fishing gears, of which the last exemptions will expire in June 2021.To assess the consequences of transitions between pulse and tickler chain beam trawling for discards mortality, knowledge on the discards survival probabilities as well as the amount of discards is required for both gear types. The objective of the current study was to estimate discards survival probabilities for undersized plaice, sole, turbot, brill and thornback ray discarded by tickler chain beam trawl fisheries using fish condition as a proxy for survival probability. To this end the condition and reflex impairment of undersized fish in the catches of tickler chain beam trawlers were assessed and compared to similar data collected from pulse trawl fisheries. For spotted ray we assessed fish condition in tickler chain beam trawling but could not estimate its discards survival probability because a relation between survival probability and fish condition is lacking for this species. In this study direct mortality imposed by the tickler chain beam trawling ranged between 10 and 32% in flatfish species and was between 2-4 times higher than in pulse beam trawling. Direct mortality in ray species was lowest among the investigated species (2-8%) and did not differ between the two gear types. Differences in direct mortality were reflected in the condition scores. Direct mortality of sole was higher in tickler chain beam trawling (17%) than in pulse beam trawling (8%). Brill, turbot and plaice discarded by pulse beam trawling are in better condition than when discarded by tickler chain beam trawl fisheries. For sole no effect of gear type on fish condition could be detected. We consider the lower fish condition scores of brill, plaice and turbot from tickler chain beam trawling a direct reflection of the higher mechanical impact of this gear on the fish. For thornback ray and spotted ray no effect of gear type on fish condition could be detected. The predicted survival of plaice, brill and turbot discards indicate that discards survival could indeed be lower in tickler chain beam trawl fisheries compared to pulse beam trawl fisheries. For sole and thornback ray discards we found no evidence for such difference between gear types. The discards survival probabilities for tickler chain beam trawling as presented in this study should be considered as predictions based on the currently best available information instead of definite values. Actual measurements of discards survival at sea are needed to confirm and quantify survival probabilities in tickler chain beam trawling.
    The implications of a transition from tickler chain beam trawl to electric pulse trawl on the sustainability and ecosystem effects of the fishery for North Sea sole: an impact assessment
    Rijnsdorp, A.D. ; Boute, P. ; Tiano, J. ; Lankheet, M. ; Soetaert, K. ; Beier, U. ; Borger, E. de; Hintzen, N.T. ; Molenaar, P. ; Polet, H. ; Poos, J.J. ; Schram, E. ; Soetaert, M. ; Overzee, H. van; Wolfshaar, K. van de; Kooten, T. van - \ 2020
    IJmuiden : Wageningen Marine Research (Wageningen Marine Research report C037/20) - 108
    electro-fishing - pulse trawls - beam trawls - bottom-trawling - gear selectivity - discards - fish - benthos - geochemical functioning - footprint - impact indicators - fuel consumption
    ICES Working Group on Electrical Trawling (WGELECTRA)
    Boute, P.G. ; Bremner, J. ; Fox, C. ; Lankheet, M.J. ; Molenaar, P. ; Polet, H. ; Rijnsdorp, A.D. ; Schram, E. ; Servili, A. ; Stepputtis, D. ; Tiano, J.C. ; Opstal, M. van - \ 2020
    ICES (ICES Scientific Reports 37) - 108 p.
    An efficient procedure to assist in the re-parametrization of structurally unidentifiable models
    Joubert, D. ; Stigter, J.D. ; Molenaar, J. - \ 2020
    Mathematical Biosciences 323 (2020). - ISSN 0025-5564
    Correlated parameter sets - Re-parametrization - State transformation - Structural identifiability - Systems biology

    An efficient method that assists in the re-parametrization of structurally unidentifiable models is introduced. It significantly reduces computational demand by combining numerical and symbolic identifiability calculations. This hybrid approach facilitates the re-parametrization of large unidentifiable ordinary differential equation models, including models where state transformations are required. A model is first assessed numerically, to discover potential structurally unidentifiable parameters. We then use symbolic calculations to confirm the numerical results, after which we describe the algebraic relationships between the unidentifiable parameters. Finally, the unidentifiable parameters are substituted with new parameters and simplification ensures that all the unidentifiable parameters are eliminated from the original model structure. The novelty of this method is its utilisation of numerical results, which notably reduces the number of symbolic calculations required. We illustrate our procedure and the detailed re-parametrization process in 5 examples: (1) an immunological model, (2) a microbial growth model, (3) a lung cancer model, (4) a JAK/STAT model, and (5) a small linear model with a non-scalable re-parametrization.

    Temperature effects on egg and larval development rate in European smelt, Osmerus eperlanus, experiments and a 50 year hindcast
    Keller, A.M. ; Molenaar, P. ; Leeuw, J.J. ; Mooij, W.M. ; Rijnsdorp, A.D. ; Wolfshaar, K.E. - \ 2020
    Journal of Fish Biology (2020). - ISSN 0022-1112 - 12 p.
    This study investigates the effect of water temperature on the development rate of eggs and larvae, the duration of the endogenous feeding period and its consequences for recruitment of smelt (Osmerus eperlanus) in Dutch lakes IJsselmeer and Markermeer. This study measured temperature-dependent egg and larval development rates as well as mortality rates from fertilization till the moment of absorption of the yolk-sac and from yolk-sac depletion onwards in temperature-controlled indoor experiments. Using multinomial modelling the authors found significant differences in development time of egg development stages under different temperature regimes. Based on historic water temperatures, the model predicted that the larval endogenous feeding period has advanced at a rate of about 2.9 days per decade in a more than 50 year period since 1961, yet there was no change in the duration of the endogenous feeding period. As zooplankton is more responsive to daylight than water temperature cues, a mismatch between the peak of the onset of exogenous
    feeding of smelt and the peak of zooplankton blooms could lead to high mortality and therefore low recruitment of smelt. Such a mismatch might contribute to a decline in the smelt population in Lake IJsselmeer and Lake Markermeer.
    A review on yolk sac utilization in poultry
    Wagt, Ilonka van der; Jong, I.C. de; Mitchell, M.A. ; Molenaar, R. ; Brand, H. van den - \ 2020
    Poultry Science 99 (2020)4. - ISSN 0032-5791 - p. 2162 - 2175.
    During incubation, embryonic growth and development are dependent on nutrients deposited in the egg. The content of the yolk can be transferred to the embryo in 2 ways: directly into the intestine via the yolk stalk or through the highly vascularized yolk sac membrane. It has been suggested that, as a result of genetic selection and improved management, the increase in posthatch growth rate and concurrently the increase in metabolic rate of broiler chickens during the last 50 yr has also increased embryonic metabolism. A higher metabolic rate during incubation would imply a lower residual yolk weight and possibly lower energy reserve for the hatchling. This might affect posthatch development and performance. This review examined scientific publications published between 1930 and 2018 to compare residual yolk weight at hatch, metabolic heat production, and yolk utilization throughout incubation. This review aimed to investigate 1) whether or not residual yolk weight and composition has been changed during the 88-yr period considered and 2) which abiotic and biotic factors affect yolk utilization in poultry during incubation and the early posthatch period. It can be concluded that 1) residual yolk weight and the total solid amount of the residual yolk at hatch seem to be decreased in the recent decades. It cannot be concluded whether the (lack of) differences between old and modern strains are due to genetic selection, changed management and incubation conditions, or moment of sampling (immediately after hatch or at pulling). It is remarkable that with the genetic progress and improved management and incubation conditions over the last 88 yr, effects on yolk utilization efficiency and embryonic metabolic heat production are limited; 2) factors specially affecting residual yolk weight at hatch include egg size and incubation temperature, whereas breeder age has more influence on nutrient composition of the residual yolk.
    Structural identifiability of large systems biology models
    Joubert, Dominique - \ 2020
    Wageningen University. Promotor(en): J. Molenaar, co-promotor(en): J.D. Stigter. - Wageningen : Wageningen University - ISBN 9789463952262 - 173

    A fundamental principle of systems biology is its perpetual need for new technologies that can solve challenging biological questions. This precept will continue to drive the development of novel analytical tools. The virtuous cycle of biological progress can therefore only exist when experts from different disciplines including biology, chemistry, computer science, engineering, mathematics, and medicine collaborate.

    General opinion is however that one of the challenges facing the systems biology community is the lag in the development of such technologies. The topic of structural identifiability in particular has been of interest to the systems biology community. This is because researchers in this field often face experimental limitations. These limitations, combined with the fact that systems biology models can contain vast numbers of unknown parameters, necessitate an identifiability analysis. In reality, analysing the structural identifiability of systems biology models, even when they contain only a few states and system parameters, may be challenging. As these models increase in size and complexity, this difficulty is exasperated, and one becomes limited to only a few methods capable of analysing large ordinary differential equation models.

    In this thesis I study the use of a computationally efficient algorithm, well suited to the analysis of large models, in the model development process. The three related objectives of this thesis are: 1) develop an accurate method to asses the structural identifiability of large possibly nonlinear ordinary differential models, 2) implement thismethod in the preliminary design of experiments, and 3) use the method to address the topic of structural unidentifiability.

    To improve the method’s accuracy, I systematically study the role of individual factors, such as the number of experimentally measured sensors, on the sharpness of results. Based on the findings, I propose measures that can improve numerical accuracy.

    To address the second objective, I introduce an iterative identifiability algorithm that can determine minimal sets of outputs that need to be measured to ensure a model’s local structural identifiability. I also illustrate how one could potentially reduce the computational demand of the algorithm, enabling a user to detect minimal output sets of large ordinary differential equation models within minutes.

    For the last objective, I investigate the role of initial conditions in a model’s structural unidentifiability. I show that the method can detect problematic values for large ordinary differential equation models. I illustrate its role in reinstating the local structural identifiability of a model by identifying problematic initial conditions.

    I also show that the method can provide theoretical suggestions for the reparameterization of structurally unidentifiable models. The novelty of this work is that the algorithm allows for unknown initial conditions to be parameterised and accordingly, repameterisations requiring the transformation of states, associated with unidentifiable initial conditions, can easily be obtained. The computational efficiency of the method allows for the reparameterisation of large ordinary differential equation models in particular.

    To conclude, in this thesis I introduce an method that can be used during the model development process in an array of useful applications. These include: 1) determining minimal output sets, 2) reparameterising structurally unidentifiable models and 3) detecting problematic initial conditions. Each of these application can be implemented before any experiments are conducted and can play a potential role in the optimisation of the modelling process.

    Warmtebehandeling raapzaad onderzoek: promotie onderzoek Sergio Salazar Villanea
    Salazar Villanea, Sergio - \ 2020

    Promotieonderzoek Sergio Salazar Villanea

    Visualizing large-scale flow using synthetic aperture PIV
    Houwelingen, Josje van; Holten, Ad P.C. ; Clercx, Herman J.H. ; Kunnen, Rudie P.J. ; Molenaar, Jaap ; Water, Willem van de - \ 2020
    Experiments in fluids 61 (2020)1. - ISSN 0723-4864

    Abstract: We discuss the application of synthetic aperture particle image velocimetry for measuring the flow around human swimmers using small bubbles as tracer. We quantify the two-dimensional projection of the velocity field in planes perpendicular to the viewing direction of an array of six cameras. With help of simulations, modelled after the experiment, we address questions about depth selectivity and occlusion in dense bubble fields. Using vortex rings in the swimming pool, we provide a proof of principle of the method. It is further illustrated by the vorticity field produced by a human swimmer. Graphic abstract: [Figure not available: see fulltext.].

    Inclusive agriculture trade scan
    Guijt, Joost ; Molenaar, Jan Willem ; Sopov, Monika - \ 2019
    Wageningen : Wageningen Centre for Development Innovation - ISBN 9789463953375 - 18
    Mathematics, the science of my Life
    Molenaar, J. - \ 2019
    Wageningen : Wageningen University & Research - ISBN 9789463953078 - 25
    Experimentele Luchtdruk wing als vangsttechniek voor platvis
    Molenaar, Pieke - \ 2019
    Yerseke : Wageningen Marine Research (Wageningen Marine Research rapport C132/19) - 12
    Met het volledig verbieden van de pulstechniek wordt er binnen de Nederlandse visserijsector gekeken naar een alternatief voor elektrische (puls) of mechanische (wekker kettingen) stimulering om platvis te vangen. Een mogelijkheid werd gezien in het stimuleren van platvis door middel van perslucht. Om de werking en effectiviteit van dit idee te testen is door texelaar Piet Standaard een aqua dynamische luchtdruk wing ontwikkeld die de lucht richting de grond blaast. Om de werking van het innovatieve ontwerp te testen is er gekozen om een eerste experiment te doen met een schaalmodel in het Visserij Innovatie Centrum zuidwest Nederland (VIC). De uitgevoerde proeven met tong en schol laten zien dat in deze opstelling een zeer beperkt aantal vissen reageert op de luchtbellen. Ook dient de opstelling zeer dicht boven de bodem langs te gaan (8 cm) om effectief de luchtbellen onder snelheid de bodem te laten raken. De huidige opstelling lijkt nog geen alternatief voor wekkerkettingen of puls te bieden gezien de beperkte effectiviteit waarmee tong en schol gestimuleerd worden om de bodem te verlaten. Verder ontwikkeling en verbetering is noodzakelijk om tot een rendabele visserijmethode te komen.
    Working Group on Electrical Trawling (WGELECTRA)
    Bremner, Julie ; Boute, Pim G. ; Desender, Marieke ; Chiers, Koen ; Garcia, Clement ; Soetaert, Maarten ; Molenaar, Pieke ; Polet, Hans ; Rijnsdorp, Adriaan D. ; Tiano, Justin C. ; Opstal, Mattias van; Vansteenbrugge, Lies - \ 2019
    ICES (ICES Scientific Reports ) - 81 p.
    Pulsvissen veroorzaakt geen massale sterfte bodemleven
    Molenaar, Pieke ; Schram, Edward - \ 2019
    Aandacht voor kalver-opfok betaalt zich terug
    Gerrits, Walter - \ 2019
    EEHNC voor derde keer in Nederland: 'Small things' in de spotlights
    Edwards, Joan ; Pellikaan, Wilbert - \ 2019
    Eerste congres over voertechnologie: Primeur tijdens Victam International
    Hartog, Leonard den; Poel, Thomas van der - \ 2019
    Nutritionele waarde van maisstro
    He, Yuan - \ 2019

    promotie onderzoek Yuan He

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