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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Patterns of covariance between airborne laser scanning metrics and Lorenz curve descriptors of tree size inequality
Valbuena, R. ; Maltamo, M. ; Martín-Fernández, S. ; Packalén, P. ; Pascual, C. ; Nabuurs, G.J. - \ 2013
Canadian Journal of Remote Sensing 39 (2013)Suppl. 1. - ISSN 1712-7971 - p. S18 - S31.
nearest-neighbor imputation - partial least-squares - forest structure - lidar data - stand - regression - inventory - northwest - selection - canopies
The Lorenz curve, as a descriptor of tree size inequality within a stand, has been suggested as a reliable means for characterizing forest structure and distinguishing even from uneven-sized areas. The aim of this study was to achieve a thorough understanding on the relations between airborne laser scanning (ALS) metrics and indicators based on Lorenz curve ordering: Gini coefficient (GC) and Lorenz asymmetry (S). Exploratory multivariate analysis was carried out using correlation tests, partial least squares (PLS), and an information-theoretic approach for multimodel inference (MMI). Best subset linear model was selected for GC and S prediction, as variable transformations yielded no improvement in the relation of ALS with the given response. Relative variable importance based on the MMI model showed that GC is best predicted by ALS metrics expressing canopy coverage, return dispersion, and low high percentile combinations. Although ALS metrics showed no correlation with S, they did so against its constituting components: the proportions of basal area (Mg) and stem density (xg) stocked above the mean quadratic diameter. The study of PLS loading vectors illustrated how ALS metrics explain variance in opposing directions for each of these components, so that their effects cancel each other out in the overall S. Cross-validation showed that only marginal differences are nevertheless found between predicting S directly or as the sum Mg and xg estimations. The differing relation of diverse ALS metrics was therefore observed for Mg and xg. The conclusions obtained by this research may assist in selecting relevant Lorenz curve descriptors for forest structure characterization, as well as in variable reduction strategies for their wall-to-wall prediction by means of ALS metrics.
Surface Temperature and Surface-Layer Turbulence in a Convective Boundary Layer
Garai, A. ; Pardyjak, E. ; Steeneveld, G.J. ; Kleissl, J. - \ 2013
Boundary-Layer Meteorology 148 (2013)1. - ISSN 0006-8314 - p. 51 - 72.
sensible heat-flux - energy balance algorithm - renewal analysis - model - grass - flow - environment - similarity - canopies - density
Previous laboratory and atmospheric experiments have shown that turbulence influences the surface temperature in a convective boundary layer. The main objective of this study is to examine land-atmosphere coupled heat transport mechanism for different stability conditions. High frequency infrared imagery and sonic anemometer measurements were obtained during the boundary layer late afternoon and sunset turbulence (BLLAST) experimental campaign. Temporal turbulence data in the surface-layer are then analyzed jointly with spatial surface-temperature imagery. The surface-temperature structures (identified using surface-temperature fluctuations) are strongly linked to atmospheric turbulence as manifested in several findings. The surface-temperature coherent structures move at an advection speed similar to the upper surface-layer or mixed-layer wind speed, with a decreasing trend with increase in stability. Also, with increasing instability the streamwise surface-temperature structure size decreases and the structures become more circular. The sequencing of surface- and air-temperature patterns is further examined through conditional averaging. Surface heating causes the initiation of warm ejection events followed by cold sweep events that result in surface cooling. The ejection events occur about 25 % of the time, but account for 60–70 % of the total sensible heat flux and cause fluctuations of up to 30 % in the ground heat flux. Cross-correlation analysis between air and surface temperature confirms the validity of a scalar footprint model.
A note on upscaling coniferous needle spectra to shoot spectral albedo
Rautiainen, M. ; Mottus, M. ; Yanez Rausell, L. ; Homolova, L. ; Malenovsky, Z. ; Schaepman, M.E. - \ 2012
Remote Sensing of Environment 117 (2012). - ISSN 0034-4257 - p. 469 - 474.
leaf-area index - scots pine - optical-properties - silhouette area - radiation - canopies - light - stands - model - simulations
Mutual shading of needles in coniferous shoots and small-scale variations in needle area density both within and between shoots violate conventional assumptions used in the definition of the elementary volume in radiative transfer models. In this paper, we test the hypothesis if it is possible to scale needle spectral albedo up to shoot spectral albedo using only one structural parameter: the spherically averaged shoot silhouette to total area ratio (STAR). To test the hypothesis, we measured both structural and spectral properties of ten Scots pine (Pinus sylvestris) shoots and their needles. Our results indicate that it is possible to upscale from needle to shoot spectral albedo using STAR. The upscaling model performed best in the VIS and SWIR regions, and for shoots with high STAR values. As STAR is linearly related to photon recollision probability, it is also possible to apply the upscaling model as integral part of radiative transfer models.
Towards a functional–structural plant model of cut-rose: simulation of light environment, light absorption, photosynthesis and interference with the plant structure
Buck-Sorlin, G.H. ; Visser, P.H.B. de; Henke, M. ; Sarlikioti, V. ; Heijden, G.W.A.M. van der; Marcelis, L.F.M. ; Vos, J. - \ 2011
Annals of Botany 108 (2011)6. - ISSN 0305-7364 - p. 1121 - 1134.
axillary buds - growth - interception - elongation - canopies - leaves - wheat - shoot - l.
Background and Aims The production system of cut-rose (Rosa × hybrida) involves a complex combination of plant material, management practice and environment. Plant structure is determined by bud break and shoot development while having an effect on local light climate. The aim of the present study is to cover selected aspects of the cut-rose system using functional–structural plant modelling (FSPM), in order to better understand processes contributing to produce quality and quantity. Methods The model describes the production system in three dimensions, including a virtual greenhouse environment with the crop, light sources (diffuse and direct sun light and lamps) and photosynthetically active radiation (PAR) sensors. The crop model is designed as a multiscaled FSPM with plant organs (axillary buds, leaves, internodes, flowers) as basic units, and local light interception and photosynthesis within each leaf. A Monte-Carlo light model was used to compute the local light climate for leaf photosynthesis, the latter described using a biochemical rate model. Key Results The model was able to reproduce PAR measurements taken at different canopy positions, different times of the day and different light regimes. Simulated incident and absorbed PAR as well as net assimilation rate in upright and bent shoots showed characteristic spatial and diurnal dynamics for different common cultivation scenarios. Conclusions The model of cut-rose presented allowed the creation of a range of initial structures thanks to interactive rules for pruning, cutting and bending. These static structures can be regarded as departure points for the dynamic simulation of production of flower canes. Furthermore, the model was able to predict local (per leaf) light absorption and photosynthesis. It can be used to investigate the physiology of ornamental plants, and provide support for the decisions of growers and consultants.
Consideration of smoothing techniques for hyperspectral remote sensing
Vaiphasa, C. - \ 2006
ISPRS Journal of Photogrammetry and Remote Sensing 60 (2006)2. - ISSN 0924-2716 - p. 91 - 99.
feature-selection - derivative analysis - vegetation - spectra - model - differentiation - discrimination - inversion - canopies - accuracy
Spectral smoothing filters are popularly used in a large number of modern hyperspectral remote sensing studies for removing noise from the data. However, most of these studies subjectively apply ad hoc measures to select filter types and their parameters. We argue that this subjectively minded approach is not appropriate for choosing smoothing methods for hyperspectral applications. In our case study, it is proved that smoothing filters can cause undesirable changes to statistical characteristics of the spectral data; thereby, affecting the results of the analyses that are based on statistical class models. If preserving statistical properties of the original hyperspectral data is desired, smoothing filters should then be used, if necessary, after careful consideration of which smoothing techniques will minimize disturbances to the statistical properties of the original data. A comparative t-test is proposed as a method for choosing a smoothing filter suitable for hyperspectral data at hand.
Leaf traits determine the growth-survival trade-off across rain forest tree species
Sterck, F.J. ; Poorter, L. ; Schieving, F. - \ 2006
American Naturalist 167 (2006)5. - ISSN 0003-0147 - p. 758 - 765.
shade tolerance - relative importance - tropical trees - carbon gain - plant - model - disturbance - canopies - spectrum - size
A dominant hypothesis explaining tree species coexistence in tropical forest is that trade-offs in characters allow species to adapt to different light environments, but tests for this hypothesis are scarce. This study is the first that uses a theoretical plant growth model to link leaf trade-offs to whole-plant performances and to differential performances across species in different light environments. Using data of 50 sympatric tree species from a Bolivian rain forest, we observed that specific leaf area and photosynthetic capacity codetermined interspecific height growth variation in a forest gap; that leaf survival rate determined the variation in plant survival rate under a closed canopy; that predicted height growth and plant survival rate matched field observations; and that fast-growing species had low survival rates for both field and predicted values. These results show how leaf trade-offs influence differential tree performance and tree species' coexistence in a heterogeneous light environment
Narrow band vegetation indices overcome the saturation problem in biomass estimation
Mutanga, O. ; Skidmore, A.K. - \ 2004
International Journal of Remote Sensing 25 (2004)19. - ISSN 0143-1161 - p. 3999 - 4014.
hyperspectral brdf data - red edge position - leaf-area index - spectral reflectance - chlorophyll content - classification - canopies - grass - ndvi
Remotely sensed vegetation indices such as NDVI, computed using the red and near infrared bands have been used to estimate pasture biomass. These indices are of limited value since they saturate in dense vegetation. In this study, we evaluated the potential of narrow band vegetation indices for characterizing the biomass of Cenchrus ciliaris grass measured at high canopy density. Three indices were tested: Modified Normalized Difference Vegetation Index (MNDVI), Simple Ratio (SR) and Transformed Vegetation Index (TVI) involving all possible two band combinations between 350 nm and 2500 nm. In addition, we evaluated the potential of the red edge position in estimating biomass at full canopy cover. Results indicated that the standard NDVI involving a strong chlorophyll absorption band in the red region and a near infrared band performed poorly in estimating biomass ( R(2) = 0.26). The MNDVIs involving a combination of narrow bands in the shorter wavelengths of the red edge ( 700 - 750 nm) and longer wavelengths of the red edge ( 750 - 780 nm), yielded higher correlations with biomass ( mean R(2) = 0.77 for the highest 20 narrow band NDVIs). When the three vegetation indices were compared, SR yielded the highest correlation coefficients with biomass as compared to narrow band NDVI and TVI ( average R(2) = 0.80, 0.77 and 0.77 for the first 20 ranked SR, NDVI and TVI respectively). The red edge position yielded comparable results to the narrow band vegetation indices involving the red edge bands. These results indicate that at high canopy density, pasture biomass may be more accurately estimated by vegetation indices based on wavelengths located in the red edge than the standard NDVI.
Extension of a biochemical model for the generalized stoichiometry of electron transport limited C3 photosynthesis
Yin, X. ; Oijen, M. van; Schapendonk, A.H.C.M. - \ 2004
Plant, Cell & Environment 27 (2004)10. - ISSN 0140-7791 - p. 1211 - 1222.
temperature response functions - gas-exchange - q-cycle - leaves - parameters - co2 - canopies - plants - assimilation - productivity
The widely used steady-state model of Farquhar et al. (Planta 149: 78-90, 1980) for C-3 photosynthesis was developed on the basis of linear whole-chain (non-cyclic) electron transport. In this model, calculation of the RuBP-regeneration limited CO2-assimilation rate depends on whether it is insufficient ATP or NADPH that causes electron transport limitation. A new, generalized equation that allows co-limitation of NADPH and ATP on electron transport is presented herein. The model is based on the assumption that other thylakoid pathways (the Q-cycle, cyclic photophosphorylation, and pseudocyclic electron transport) interplay with the linear chain to co-contribute to a balanced production of NADPH and ATP as required by stromal metabolism. The original model assuming linear electron transport limited either by NADPH or by ATP, predicts quantum yields for CO2 uptake that represent the highest and the lowest values, respectively, of the range given by the new equation. The applicability of the new equation is illustrated for a number of C-3 crop species, by curve fitting to gas exchange data in the literature. In comparison with the original model, the new model enables analysis of photosynthetic regulation via the electron transport pathways in response to environmental stresses.
A simple method to estimate radiation interception by nursery stock conifers: a case study of eastern white cedar
Pronk, A.A. ; Goudriaan, J. ; Stilma, E.S.C. ; Challa, H. - \ 2003
NJAS Wageningen Journal of Life Sciences 51 (2003)3. - ISSN 1573-5214 - p. 279 - 295.
thuja occidentalis - plantmateriaal - kroondak - interceptie - zonnestraling - schatting - planting stock - canopy - interception - solar radiation - estimation - leaf-area index - lai-2000 - photosynthesis - canopies - stands - model
A simple method was developed to estimate the fraction radiation intercepted by small eastern white cedar plants (Thuja occidentalis 'Brabant'). The method, which describes the crop canopy as rows of cuboids, was compared with methods used for estimating radiation interception by crops with homogeneous canopies and crops grown in rows. The extinction coefficient k was determined at different plant arrangements and an average k-value of 0.48 ± 0.03 (R2 = 0.89) was used in the calculations. Effects of changing plant characteristics and inter- and intra-row plant distances were explored. The fraction radiation intercepted that was estimated with the method for rows of cuboids was up to 20% and for row crops up to 8% lower than estimated with the method for homogeneous canopies at low plant densities and a LAI of 1. The fraction radiation intercepted by small plants of Thuja occidentals 'Brabant' was best estimated by the simple method described in this paper
Water vapour and carbon dioxide fluxes over bog vegetation
Jacobs, A.F.G. ; Ronda, R.J. ; Holtslag, A.A.M. - \ 2003
Agricultural and Forest Meteorology 116 (2003). - ISSN 0168-1923 - p. 103 - 112.
veenplanten - evapotranspiratie - micrometeorologie - fotosynthese - nitraten - modellen - ecohydrologie - bog plants - evapotranspiration - micrometeorology - photosynthesis - nitrates - models - ecohydrology - stomatal conductance - boundary-layer - model - transpiration - canopies - leaves
During a period of 18 months observations have been made above bog vegetation in The Netherlands. The observations have been used to evaluate an assimilation model in which nitrogen shortage has been taken into account
In this study we analyse observations of water vapour and carbon dioxide fluxes over bog vegetation in the Netherlands. The observations are used to evaluate an assimilation photosynthesis (so-called A-g(s)) model on the canopy scale. Next, a simple estimate for the soil respiration has been added to the A-g(s) model. Leaf sample analysis showed that nitrogen concentration was well below optimum conditions, so the A-g(s) model was adjusted appropriately. Transpiration calculations with the adjusted model result in an excellent agreement with the measurements over the bog area. The total simulated fluxes of plant assimilation and soil respiration have been compared with the measured total CO2 flux. The agreement between simulations and experiments appears to be reasonably good. For practical applications a simplified relationship has been derived between the transpiration and the net assimilation rates. This relation has been tested and appears to work well for practical purposes. (C) 2002 Elsevier Science B.V. All rights reserved.
Scale variability of atmospheric surface layer fluxes of energy and carbon over a tropical rain forest in southwest Amazonia; 1 diurnal conditions
Randow, C. von; Sá, L.D.A. ; Gannabathula, P.S.S.D. ; Manzi, A.O. ; Arlino, P.R.A. ; Kruijt, B. - \ 2002
Journal of Geophysical Research: Atmospheres 107 (2002)020. - ISSN 2169-897X - p. 8062 - 8062.
boundary-layer - wavelet analysis - turbulence - temperature - decomposition - similarity - modulation - canopies - aircraft - spectra
The aim of this study is to investigate the low-frequency characteristics of diurnal turbulent scalar spectra and cospectra near the Amazonian rain forest during the wet and dry seasons. This is because the available turbulent data are often nonstationary and there is no clear spectral gap to separate data into "mean" and "turbulent" parts. Daubechies-8 orthogonal wavelet is used to scale project turbulent signals in order to provide scale variance and covariance estimations. Based on the characteristics of the scale dependence of the scalar fluxes, some classification criteria of this scale dependence are investigated. The total scalar covariance of each 4-hour data run is partitioned in categories of scale covariance contributions. This permits the study of some statistical characteristics of the scalar turbulent fields in each one of these classes and, thus, to give an insight and a possible explanation of the origin of the variability of the scalar fields close to the Amazonian forest. The results have shown that a two-category classification is the most appropriate to describe the kind of observed fluctuations: "turbulent" and "mesoscale" contributions. The largest contribution of the sensible heat, latent heat, and CO2 covariance contributions occurs in the "turbulent" length scales. Mesoscale eddy motions, however, can contribute up to 30% of the total covariances under weak wind conditions. Analysis of scale correlation coefficient [r(Tvq)] between virtual temperature (Tv) and humidity (q) signals shows that the scale patterns of Tv and q variability are not similar and r(Tvq) <1 for all analyzed scales. Scale humidity skewness calculations are negative during the dry season and positive during the wet season. This suggests that different boundary layer moisture regimes occur during the dry and wet seasons.
Temperature sensitivity of photosynthesis in Lolium perenne swards: a comparison of two methods for deriving photosynthetic parameters from in vivo measurements
Dirks, B.O.M. ; Oijen, M. van; Schapendonk, A.H.C.M. ; Goudriaan, J. ; Wolf, J. - \ 2002
Photosynthetica 40 (2002)3. - ISSN 0300-3604 - p. 405 - 413.
carbon-dioxide - water-use - leaf - co2 - productivity - canopies - ryegrass - light - model
The seasonal variation in photosynthetic rate of grass swards is partly the result of changes in the environment and partly the result of changes in the photosynthetic capacity of the sward itself. We evaluated two types of photosynthesis equations regarding their capacity to analyse seasonal and short-term temperature effects on photosynthesis of ryegrass (Lolium perenne L.). Intact cores of a field-grown ryegrass sward were taken to the laboratory 10 d after cutting for measurement of photosynthesis under controlled conditions. This was done during two four-week periods, in summer and autumn. Net photosynthetic rate (PN) of the sward was lower in autumn than in summer. Both a simple negatively exponential photosynthesis irradiance-response curve and the Farquhar equations for photosynthesis were applied to the in vivo canopy measurements. Application of the irradiance-response curve showed that irradiance-saturated gross photosynthetic rate increased linearly with increasing temperature and was higher in summer than in autumn. The initial radiation use efficiency did not differ between the seasons but decreased with the temperature rise. This explains the observation that total canopy photosynthetic rate decreased after short-term temperature increases in both seasons. The parameters in Farquhar equations that represent the temperature sensitivity of the maximum electron transport rate and of the Michaelis-Menten constants for CO2 and O2 fixation could not be quantified satisfactorily. Parameterisation of the Farquhar equations was hampered by a lack of robust information on many biochemical parameters, and the use of simple empirical response-functions may be preferable in the case of in vivo canopy measurements on grass swards.
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