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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    Multi-bucket optimization for integrated planning and scheduling in the perishable dairy supply chain
    Sel, C. ; Bilgen, B. ; Bloemhof, J.M. ; Vorst, J.G.A.J. van der - \ 2015
    Computers and Chemical Engineering 77 (2015). - ISSN 0098-1354 - p. 59 - 73.
    sequence-dependent changeovers - semicontinuous food-industries - yogurt production line - timed automata models - mixed-integer - batch plants - parallel machines - hybrid - algorithm - challenges
    This paper considers a dairy industry problem on integrated planning and scheduling of set yoghurt production. A mixed integer linear programming formulation is introduced to integrate tactical and operational decisions and a heuristic approach is proposed to decompose time buckets of the decisions. The decomposition heuristic improves computational efficiency by solving big bucket planning and small bucket scheduling problems. Further, mixed integer linear programming and constraint programming methodologies are combined with the algorithm to show their complementary strengths. Numerical studies using illustrative data with high demand granularity (i.e., a large number of small-sized customer orders) demonstrate that the proposed decomposition heuristic has consistent results minimizing the total cost (i.e., on average 8.75% gap with the best lower bound value found by MILP) and, the developed hybrid approach is capable of solving real sized instances within a reasonable amount of time (i.e., on average 92% faster than MILP in CPU time).
    Covariances Simultaneous Component Analysis: a new method within a framework for modeling covariances
    Smilde, A.K. ; Timmerman, M.E. ; Saccenti, E. ; Jansen, J.J. ; Hoefsloot, H.C.J. - \ 2015
    Journal of Chemometrics 29 (2015)5. - ISSN 0886-9383 - p. 277 - 288.
    metabolomics data - phenotypes - algorithm
    In modern omics research, it is more rule than exception that multiple data sets are collected in a study pertaining to the same biological organism. In such cases, it is worthwhile to analyze all data tables simultaneously to arrive at global information of the biological system. This is the area of data fusion or multi-set analysis, which is a lively research topic in chemometrics, bioinformatics, and biostatistics. Most methods of analyzing such complex data focus on group means, treatment effects, or time courses. There is also information present in the covariances among variables within a group, because this relates directly to individual differences, heterogeneity of responses, and changes of regulation in the biological system. We present a framework for analyzing covariance matrices and a new method that fits nicely in this framework. This new method is based on combining covariance prototypes using simultaneous components and is, therefore, coined Covariances Simultaneous Component Analysis (COVSCA). We present the framework and our new method in mathematical terms, thereby explaining the (dis)similarities of the methods. Systems biology models based on differential equations illustrate the type of variation generated in real-life biological systems and how this type of variation can be modeled within the framework and with COVSCA. The method is subsequently applied to two real-life data sets from human and plant metabolomics studies showing biologically meaningful results
    Modelling long-term (300¿ka) upland catchment response to multiple lava damming events
    Gorp, W. van; Temme, A.J.A.M. ; Veldkamp, A. ; Schoorl, J.M. - \ 2015
    Earth Surface Processes and Landforms 40 (2015)7. - ISSN 0197-9337 - p. 888 - 900.
    western turkey - landscape evolution - fluvial system - gediz river - environmental-change - volcanic disruption - thresholds - depressions - algorithm - pliocene
    Landscapes respond in complex ways to external drivers such as base level change due to damming events. In this study, landscape evolution modelling was used to understand and analyse long-term catchment response to lava damming events. PalaeoDEM reconstruction of a small Turkish catchment (45¿km2) that endured multiple lava damming events in the past 300¿ka, was used to derive long-term net erosion rates. These erosion rates were used for parameter calibration and led to a best fit parameter set. This optimal parameter set was used to compare net erosion landscape time series of four scenarios: (i) no uplift and no damming events; (ii) no uplift and three damming events; (iii) uplift and no damming events; and (iv) uplift and three damming events. Spatial evolution of net erosion and sediment storage of scenario (iii) and (iv) were compared. Simulation results demonstrate net erosion differences after 250 000¿years between scenarios with and without dams. Initially, trunk gullies show less net erosion in the scenario with damming events compared with the scenario without damming events. This effect of dampened erosion migrates upstream to smaller gullies and local slopes. Finally, an intrinsic incision pulse in the dam scenario results in a higher net erosion of trunk gullies while decoupled local slopes are still responding to the pre-incision landscape conditions. Sediment storage differences also occur on a 100¿ka scale. These differences behaved in a complex manner owing to different timings of the migration of erosion and sediment waves along the gullies for each scenario. Although the specific spatial and temporal sequence of erosion and deposition events is sensitive to local parameters, this model study shows the manner in which past short-lived events like lava dams have long-lasting effects on catchment evolution.
    The time-dependent two-echelon capacitated vehicle routing problem with environmental considerations
    Soysal, M. ; Bloemhof, J.M. ; Bektas, T. - \ 2015
    International Journal of Production Economics 164 (2015). - ISSN 0925-5273 - p. 366 - 378.
    road freight transportation - city logistics - emission - optimization - models - algorithm - windows - impact - costs
    Multi-echelon distribution strategies in which freight is delivered to customers via intermediate depots rather than direct shipments is an increasingly popular strategy in urban logistics. This is primarily to alleviate the environmental (e.g., energy usage and congestion) and social (e.g., traffic-related air pollution, accidents and noise) consequences of logistics operations. This paper presents a comprehensive MILP formulation for a time-dependent two-echelon capacitated vehicle routing problem (2E-CVRP) that accounts for vehicle type, traveled distance, vehicle speed, load, multiple time zones and emissions. A case study in a supermarket chain operating in the Netherlands shows the applicability of the model to a real-life problem. Several versions of the model, each differing with respect to the objective function, are tested to produce a number of selected key performance indicators (KPIs) relevant to distance, time, fuel consumption and cost. The paper offers insight on economies of environmentally-friendly vehicle routing in two-echelon distribution systems. The results suggest that an environmentally-friendly solution is obtained from the use of a two-echelon distribution system, whereas a single-echelon distribution system provides the least-cost solution.
    Derivation of Land Surface Albedo at High Resolution by Combining HJ-1A/B Reflectance Observations with MODIS BRDF Products
    Gao, B. ; Jia, L. ; Wang, T.X. - \ 2014
    Remote Sensing 6 (2014)9. - ISSN 2072-4292 - p. 8966 - 8985.
    remote-sensing data - bidirectional reflectance - retrieval - algorithm - meteosat - polder/adeos - simulation - models
    Land surface albedo is an essential parameter for monitoring global/regional climate and land surface energy balance. Although many studies have been conducted on global or regional land surface albedo using various remote sensing data over the past few decades, land surface albedo product with a high spatio-temporal resolution is currently very scarce. This paper proposes a method for deriving land surface albedo with a high spatio-temporal resolution (space: 30 m and time: 2-4 days). The proposed method works by combining the land surface reflectance data at 30 m spatial resolution obtained from the charge-coupled devices in the Huanjing-1A and -1B (HJ-1A/B) satellites with the Moderate Resolution Imaging Spectroradiometer (MODIS) land surface bidirectional reflectance distribution function (BRDF) parameters product (MCD43A1), which is at a spatial resolution of 500 m. First, the land surface BRDF parameters for HJ-1A/B land surface reflectance with a spatial-temporal resolutions of 30 m and 2-4 day are calculated on the basis of the prior knowledge from the MODIS BRDF product; then, the calculated high resolution BRDF parameters are integrated over the illuminating/viewing hemisphere to produce the white-and black-sky albedos at 30 m resolution. These results form the basis for the final land surface albedo derivation by accounting for the proportion of direct and diffuse solar radiation arriving at the ground. The albedo retrieved by this novel method is compared with MODIS land surface albedo products, as well as with ground measurements. The results show that the derived land surface albedo during the growing season of 2012 generally achieved a mean absolute accuracy of +/- 0.044, and a root mean square error of 0.039, confirming the effectiveness of the newly proposed method.
    Data-based perfect-deficit approach to understanding climate extremes and forest carbon assimilation capacity
    Wei, S. ; Yi, C. ; Hendrey, G. ; Eaton, T. ; Rustic, G. ; Wang, S. ; Liu, H. ; Krakauer, N.Y. ; Wang, W. ; Desai, A.R. ; Moors, E.J. - \ 2014
    Environmental Research Letters 9 (2014). - ISSN 1748-9326
    net ecosystem exchange - drought - respiration - algorithm - heat - reduction - feedbacks - model
    Several lines of evidence suggest that the warming climate plays a vital role in driving certain types of extreme weather. The impact of warming and of extreme weather on forest carbon assimilation capacity is poorly known. Filling this knowledge gap is critical towards understanding the amount of carbon that forests can hold. Here, we used a perfect-deficit approach to identify forest canopy photosynthetic capacity (CPC) deficits and analyze how they correlate to climate extremes, based on observational data measured by the eddy covariance method at 27 forest sites over 146 site-years. We found that droughts severely affect the carbon assimilation capacities of evergreen broadleaf forest (EBF) and deciduous broadleaf forest. The carbon assimilation capacities of Mediterranean forests were highly sensitive to climate extremes, while marine forest climates tended to be insensitive to climate extremes. Our estimates suggest an average global reduction of forest CPC due to unfavorable climate extremes of 6.3 Pg C (~5.2% of global gross primary production) per growing season over 2001–2010, with EBFs contributing 52% of the total reduction.
    Right-hand-side updating for fast computing of genomic breeding values
    Calus, M.P.L. - \ 2014
    Genetics, Selection, Evolution 46 (2014). - ISSN 0999-193X - 24 p.
    genetic value - prediction - selection - accuracy - reliability - algorithm - cattle
    Since both the number of SNPs (single nucleotide polymorphisms) used in genomic prediction and the number of individuals used in training datasets are rapidly increasing, there is an increasing need to improve the efficiency of genomic prediction models in terms of computing time and memory (RAM) required.
    Imputation of non-genotyped individuals based on genotyped relatives: assessing the imputation accuracy of a real case scenario in dairy cattle
    Bouwman, A.C. ; Hickey, J.M. ; Calus, M.P.L. ; Veerkamp, R.F. - \ 2014
    Genetics, Selection, Evolution 46 (2014). - ISSN 0999-193X - 11 p.
    genome-wide association - density genotypes - populations - selection - animals - pedigree - information - simulation - prediction - algorithm
    Background Imputation of genotypes for ungenotyped individuals could enable the use of valuable phenotypes created before the genomic era in analyses that require genotypes. The objective of this study was to investigate the accuracy of imputation of non-genotyped individuals using genotype information from relatives. Methods Genotypes were simulated for all individuals in the pedigree of a real (historical) dataset of phenotyped dairy cows and with part of the pedigree genotyped. The software AlphaImpute was used for imputation in its standard settings but also without phasing, i.e. using basic inheritance rules and segregation analysis only. Different scenarios were evaluated i.e.: (1) the real data scenario, (2) addition of genotypes of sires and maternal grandsires of the ungenotyped individuals, and (3) addition of one, two, or four genotyped offspring of the ungenotyped individuals to the reference population. Results The imputation accuracy using AlphaImpute in its standard settings was lower than without phasing. Including genotypes of sires and maternal grandsires in the reference population improved imputation accuracy, i.e. the correlation of the true genotypes with the imputed genotype dosages, corrected for mean gene content, across all animals increased from 0.47 (real situation) to 0.60. Including one, two and four genotyped offspring increased the accuracy of imputation across all animals from 0.57 (no offspring) to 0.73, 0.82, and 0.92, respectively. Conclusions At present, the use of basic inheritance rules and segregation analysis appears to be the best imputation method for ungenotyped individuals. Comparison of our empirical animal-specific imputation accuracies to predictions based on selection index theory suggested that not correcting for mean gene content considerably overestimates the true accuracy. Imputation of ungenotyped individuals can help to include valuable phenotypes for genome-wide association studies or for genomic prediction, especially when the ungenotyped individuals have genotyped offspring.
    Global Multimodel Analsysis of Drought in Runoff for the Second Half of the Twentieth Century
    Huijgevoort, M.H.J. van; Hazenberg, P. ; Lanen, H.A.J. van; Teuling, A.J. ; Clark, D.B. ; Folwell, S. ; Gosling, S. ; Uijlenhoet, R. - \ 2013
    Journal of Hydrometeorology 14 (2013)5. - ISSN 1525-755X - p. 1535 - 1552.
    environment simulator jules - conterminous united-states - hydrological drought - model description - scale - ensemble - streamflow - europe - variability - algorithm
    During the past decades large-scale models have been developed to simulate global and continental terrestrial water cycles. It is an open question whether these models are suitable to capture hydrological drought, in terms of runoff, on a global scale. A multimodel ensemble analysis was carried out to evaluate if 10 such large-scale models agree on major drought events during the second half of the twentieth century. Time series of monthly precipitation, monthly total runoff from 10 global hydrological models, and their ensemble median have been used to identify drought. Temporal development of area in drought for various regions across the globe was investigated. Model spread was largest in regions with low runoff and smallest in regions with high runoff. In vast regions, correlation between runoff drought derived from the models and meteorological drought was found to be low. This indicated that models add information to the signal derived from precipitation and that runoff drought cannot directly be determined from precipitation data alone in global drought analyses with a constant aggregation period. However, duration and spatial extent of major drought events differed between models. Some models showed a fast runoff response to rainfall, which led to deviations from reported drought events in slowly responding hydrological systems. By using an ensemble of models, this fast runoff response was partly overcome and delay in drought propagating from meteorological drought to drought in runoff was included. Finally, an ensemble of models also allows for consideration of uncertainty associated with individual model structures.
    Interpreting experimental data on egg production - applications of dynamic differential equations
    France, J. ; Lopez, S. ; Kebreab, E. ; Dijkstra, J. - \ 2013
    Poultry Science 92 (2013)9. - ISSN 0032-5791 - p. 2498 - 2508.
    drosophila-melanogaster - gastrointestinal-tract - quantitative genetics - mathematical-models - phosphorus - calcium - absorption - fertility - algorithm
    This contribution focuses on applying mathematical models based on systems of ordinary first-order differential equations to synthesize and interpret data from egg production experiments. Models based on linear systems of differential equations are contrasted with those based on nonlinear systems. Regression equations arising from analytical solutions to linear compartmental schemes are considered as candidate functions for describing egg production curves, together with aspects of parameter estimation. Extant candidate functions are reviewed, a role for growth functions such as the Gompertz equation suggested, and a function based on a simple new model outlined. Structurally, the new model comprises a single pool with an inflow and an outflow. Compartmental simulation models based on nonlinear systems of differential equations, and thus requiring numerical solution, are next discussed, and aspects of parameter estimation considered. This type of model is illustrated in relation to development and evaluation of a dynamic model of calcium and phosphorus flows in layers. The model consists of 8 state variables representing calcium and phosphorus pools in the crop, stomachs, plasma, and bone. The flow equations are described by Michaelis-Menten or mass action forms. Experiments that measure Ca and P uptake in layers fed different calcium concentrations during shell-forming days are used to evaluate the model. In addition to providing a useful management tool, such a simulation model also provides a means to evaluate feeding strategies aimed at reducing excretion of potential pollutants in poultry manure to the environment.
    Synergistic process design: Reducing drying energy consumption by optimal adsorbent selection
    Atuonwu, J.C. ; Straten, G. van; Deventer, H.C. van; Boxtel, A.J.B. van - \ 2013
    Industrial & Engineering Chemistry Research 52 (2013)18. - ISSN 0888-5885 - p. 6201 - 6210.
    water-vapor - adsorption dryer - optimization - efficiency - algorithm - behavior
    This work analyzes the synergy between two complementary unit operations - adsorbent dehumidification and drying - and presents a mixed integer nonlinear programming approach to optimize energy performance in a two-stage system. Combined with active constraint analysis, the adsorbent properties that promote energy performance are derived. Microporous adsorbents with higher sorption capacities at low vapor pressures and requiring higher regeneration temperatures are preferred for ambient air dehumidification in the first stage. For exhaust air dehumidification, mesoporous adsorbents with lower regeneration temperatures are preferred such that the exhaust air from the first regeneration stage can sufficiently regenerate them. For drying below 50 C, energy consumption reductions of about 70% are achieved compared to conventional dryers without adsorbent dehumidification depending on adsorbent properties. The results demonstrate the usefulness of superstructure optimization in matching the drying process with the capabilities of the adsorbents to enhance process synergy for improved energy efficiency. © 2013 American Chemical Society
    How much CO was emitted by the 2010 fires around Moscow?
    Krol, M.C. ; Peters, W. ; Hooghiemstra, P. ; George, M. ; Clerbaux, C. ; Hurtmans, D. ; McInerney, D. ; Sedano, F. ; Bergamaschi, P. ; Hajj, M. El; Kaiser, J.W. ; Fisher, D. ; Yeshov, V. ; Muller, J.P. - \ 2013
    Atmospheric Chemistry and Physics 13 (2013). - ISSN 1680-7316 - p. 4737 - 4747.
    russian wildfires - emissions - pollution - summer - iasi - assimilation - retrieval - satellite - algorithm - transport
    The fires around Moscow in July and August 2010 emitted a large amount of pollutants to the atmosphere. Here we estimate the carbon monoxide (CO) source strength of the Moscow fires in July and August by using the TM5-4DVAR system in combination with CO column observations of the Infrared Atmospheric Sounding Interferometer (IASI). It is shown that the IASI observations provide a strong constraint on the total emissions needed in the model. Irrespective of the prior emissions used, the optimised CO fire emission estimates from mid-July to mid-August 2010 amount to approximately 24 TgCO. This estimate depends only weakly (<15 %) on the assumed diurnal variations and injection height of the emissions. However, the estimated emissions might depend on unaccounted model uncertainties such as vertical transport. Our emission estimate of 22-27 TgCO during roughly one month of intense burning is less than suggested by another recent study, but substantially larger than predicted by the bottom-up inventories. This latter discrepancy suggests that bottom-up emission estimates for extreme peat burning events require improvements.
    Adaptive response of beam trawl fishers to rising fuel cost
    Poos, J.J. ; Turenhout, M.N.J. ; Oostenbrugge, J.A.E. van; Rijnsdorp, A.D. - \ 2013
    ICES Journal of Marine Science 70 (2013)3. - ISSN 1054-3139 - p. 675 - 684.
    fishing effort - effort allocation - energy use - north-sea - r package - model - algorithm - evolution - abundance - fleets
    Early recruitment indices based on larval fish data from the Continuous Plankton Recorder (CPR) have the potential to inform stock assessments of Ammodytes marinus in the North Sea. We evaluate whether the CPR data are reliable for sandeel larvae. Spatially, CPR larval data were comparable with catches by dedicated larval samplers (Gulf and bongo nets) during ICES coordinated surveys in 2004 and 2009. ICES data are also used to explore environmental influences on sandeel distributions. Temporally, CPR data correlate with larval data from plankton surveys off Stonehaven (1999–2005), with sandeel 0-group trawl data at the east Fair Isle ground (since 1984), and with recruitment data (since 1983) for the Dogger Banks stock assessment area. Therefore, CPR data may provide an early recruit index of relative abundance for the Dogger Banks assessment area, where the majority of the commercial catch of A. marinus is taken, and the Wee Bankie area that is particularly important for seabird foraging. While warm conditions may stimulate the production of sandeel larvae, their natural mortality is typically greater, in the Dogger Banks and Wadden Sea areas, when the larvae are hatched in warm years and/or with abundant 1-year-old sandeel that are likely to be cannibalistic
    Quality of core collections for effective utilisation of genetic resources review, discussion and interpretation
    Odong, T.L. ; Jansen, J. ; Eeuwijk, F.A. van; Hintum, T.J.L. van - \ 2013
    Theoretical and Applied Genetics 126 (2013)2. - ISSN 0040-5752 - p. 289 - 305.
    morphological descriptors - germplasm collection - sampling strategies - diversity - algorithm - establishment - accessions - selection - markers - sorghum
    Definition of clear criteria for evaluation of the quality of core collections is a prerequisite for selecting high-quality cores. However, a critical examination of the different methods used in literature, for evaluating the quality of core collections, shows that there are no clear guidelines on the choices of quality evaluation criteria and as a result, inappropriate analyses are sometimes made leading to false conclusions being drawn regarding the quality of core collections and the methods to select such core collections. The choice of criteria for evaluating core collections appears to be based mainly on the fact that those criteria have been used in earlier publications rather than on the actual objectives of the core collection. In this study, we provide insight into different criteria used for evaluating core collections. We also discussed different types of core collections and related each type of core collection to their respective evaluation criteria. Two new criteria based on genetic distance are introduced. The consequences of the different evaluation criteria are illustrated using simulated and experimental data. We strongly recommend the use of the distance-based criteria since they not only allow the simultaneous evaluation of all variables describing the accessions, but they also provide intuitive and interpretable criteria, as compared with the univariate criteria generally used for the evaluation of core collections. Our findings will provide genebank curators and researchers with possibilities to make informed choices when creating, comparing and using core collections
    Comparing optimized CO emission estimates using MOPITT or NOAA surface network observations
    Hooghiemstra, P.B. ; Krol, M.C. ; Bergamaschi, P. ; Laat, A.T.J. de; Werf, G.R. van der; Novelli, P.C. ; Deeter, M.N. ; Aben, I. ; Rockmann, T. - \ 2012
    Journal of Geophysical Research: Atmospheres 117 (2012). - ISSN 2169-897X - 23 p.
    variational data assimilation - zoom model tm5 - carbon-monoxide - tropospheric chemistry - inversion - validation - sciamachy - algorithm - pollution - aircraft
    This paper compares two global inversions to estimate carbon monoxide (CO) emissions for 2004. Either surface flask observations from the National Oceanic and Atmospheric Administration Earth System Research Laboratory (NOAA/ESRL) Global Monitoring Division (GMD) or CO total columns from the Measurement of Pollution in the Troposphere (MOPITT) instrument are assimilated in a 4D-Var framework. Inferred emission estimates from the two inversions are consistent over the Northern Hemisphere (NH). For example, both inversions increase anthropogenic CO emissions over Europe (from 46 to 94 Tg CO/yr) and Asia (from 222 to 420 Tg CO/yr). In the Southern Hemisphere (SH), three important findings are reported. First, due to their different vertical sensitivity, the stations-only inversion increases SH biomass burning emissions by 108 Tg CO/yr more than the MOPITT-only inversion. Conversely, the MOPITT-only inversion results in SH natural emissions (mainly CO from oxidation of NMVOCs) that are 185 Tg CO/yr higher compared to the stations-only inversion. Second, MOPITT-only derived biomass burning emissions are reduced with respect to the prior which is in contrast to previous (inverse) modeling studies. Finally, MOPITT derived total emissions are significantly higher for South America and Africa compared to the stations-only inversion. This is likely due to a positive bias in the MOPITT V4 product. This bias is also apparent from validation with surface stations and ground-truth FTIR columns. Our results show that a combined inversion is promising in the NH. However, implementation of a satellite bias correction scheme is essential to combine both observational data sets in the SH.
    Effect of the sampling design of ground control points on the geometric correction of remotely sensed imagery
    Wang, J. ; Ge, Y. ; Heuvelink, G.B.M. ; Zhou, C. ; Brus, D.J. - \ 2012
    International Journal of applied Earth Observation and Geoinformation 18 (2012). - ISSN 0303-2434 - p. 91 - 100.
    resolution satellite imagery - accuracy - registration - algorithm - model
    The acquirement of ground control points (GCPs) is a basic and important step in the geometric correction of remotely sensed imagery. In particular, the spatial distribution of GCPs may affect the accuracy and quality of image correction. In this paper, both a simulation experiment and actual-image analyses are carried out to investigate the effect of the sampling design for selecting GCPs on the geometric correction of remotely sensed imagery. Sampling designs compared are simple random sampling, spatial coverage sampling, and universal kriging model-based sampling. The experiments indicate that the sampling design of GCPs strongly affects the accuracy of the geometric correction. The universal kriging model-based sampling design considers the spatial autocovariance of regression residuals and yields the most accurate correction. This method is highly recommended as a new GCPs sampling design method for geometric correction of remotely sensed imagery.
    Estimating total suspended matter concentration in tropical waters of the Berau estuary, Indonesia
    Ambarwulan, W. ; Verhoef, W. ; Mannaerts, C.M. ; Salama, M.S. - \ 2012
    International Journal of Remote Sensing 33 (2012)16. - ISSN 0143-1161 - p. 4919 - 4936.
    ocean color - atmospheric correction - meris measurements - baltic sea - products - validation - algorithm - simulation - retrieval - skagerrak
    This study presents the application of a semi-empirical approach, based on the Kubelka–Munk (K-M) model, to retrieve the total suspended matter (TSM) concentration of water bodies from ocean colour remote sensing. This approach is validated with in situ data sets compiled from the tropical waters of Berau estuary, Indonesia. Compared to a purely empirical approach, the K-M model provides better results in the retrieval of TSM concentration on both data sets (in situ and Medium Resolution Imaging Spectrometer (MERIS)). In this study, the K-M model was calibrated with in situ measurements of remote-sensing reflectance (R rs) and TSM concentration. Next, the inverse K-M model was successfully applied to images taken by the MERIS instrument by generating regional maps of TSM concentration. MERIS top-of-atmosphere radiances were atmospherically corrected using the Moderate Spectral Resolution Atmospheric Transmittance (MODTRAN) radiative transfer model. The best correlation between R rs measured in situ and R rs MERIS was found to be at a wavelength of 620 nm. The TSM concentrations retrieved using the K-M model showed a lower root mean square error (RMSE), a higher coefficient of determination and a smaller relative error than those retrieved by the purely empirical approach.
    A laboratory goniometer system for measuring reflectance and emittance anisotropy
    Roosjen, P.P.J. ; Clevers, J.G.P.W. ; Bartholomeus, H. ; Schaepman, M.E. ; Schaepman-Strub, G. ; Jalink, H. ; Schoor, R. van der; Jong, A. de - \ 2012
    Sensors 12 (2012)12. - ISSN 1424-8220 - p. 17358 - 17371.
    bidirectional reflectance - radiance data - albedo - field - brdf - algorithm - surface - model - acquisition - vegetation
    In this paper, a laboratory goniometer system for performing multi-angular measurements under controlled illumination conditions is described. A commercially available robotic arm enables the acquisition of a large number of measurements over the full hemisphere within a short time span making it much faster than other goniometers. In addition, the presented set-up enables assessment of anisotropic reflectance and emittance behaviour of soils, leaves and small canopies. Mounting a spectrometer enables acquisition of either hemispherical measurements or measurements in the horizontal plane. Mounting a thermal camera allows directional observations of the thermal emittance. This paper also presents three showcases of these different measurement set-ups in order to illustrate its possibilities. Finally, suggestions for applying this instrument and for future research directions are given, including linking the measured reflectance anisotropy with physically-based anisotropy models on the one hand and combining them with field goniometry measurements for joint analysis with remote sensing data on the other hand. The speed and flexibility of the system offer a large added value to the existing pool of laboratory goniometers.
    Observation uncertainty of satellite soil moisture products determined with physically-based modeling
    Wanders, N. ; Karssenberg, D. ; Bierkens, M.F.P. ; Parinussa, R. ; Jeu, R. de; Dam, J.C. van; Jong, S. de - \ 2012
    Remote Sensing of Environment 127 (2012). - ISSN 0034-4257 - p. 341 - 356.
    passive microwave measurements - improving runoff prediction - vegetation optical depth - ers scatterometer - amsr-e - retrieval - assimilation - validation - algorithm - index
    Accurate estimates of soil moisture as initial conditions to hydrological models are expected to greatly increase the accuracy of flood and drought predictions. As in-situ soil moisture observations are scarce, satellite-based estimates are a suitable alternative. The validation of remotely sensed soil moisture products is generally hampered by the difference in spatial support of in-situ observations and satellite footprints. Unsaturated zone modeling may serve as a valuable validation tool because it could bridge the gap of different spatial supports. A stochastic, distributed unsaturated zone model (SWAP) was used in which the spatial support was matched to these of the satellite soil moisture retrievals. A comparison between point observations and the SWAP model was performed to enhance understanding of the model and to assure that the SWAP model could be used with confidence for other locations in Spain. A timeseries analysis was performed to compare surface soil moisture from the SWAP model to surface soil moisture retrievals from three different microwave sensors, including AMSR-E, SMOS and ASCAT. Results suggest that temporal dynamics are best captured by AMSR-E and ASCAT resulting in an averaged correlation coefficient of 0.68 and 0.71, respectively. SMOS shows the capability of capturing the long-term trends, however on short timescales the soil moisture signal was not captured as well as by the other sensors, resulting in an averaged correlation coefficient of 0.42. Root mean square errors for the three sensors were found to be very similar (± 0.05 m3m- 3). The satellite uncertainty is spatially correlated and distinct spatial patterns are found over Spain.
    ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins
    Luo, H. ; Lin, K. ; David, A. ; Nijveen, H. ; Leunissen, J.A.M. - \ 2012
    Nucleic acids research 40 (2012)D1. - ISSN 0305-1048 - p. D394 - D399.
    annotation resource - codon usage - sequences - database - evolution - genomes - selection - alanine - algorithm - proteomes
    ProRepeat ( is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together with 85 completely sequenced eukaryotic proteomes contained within the RefSeq collection. It contains non-redundant perfect tandem repeats, approximate tandem repeats and simple, low-complexity sequences, covering the majority of the amino acid tandem repeat patterns found in proteins. The ProRepeat web interface allows querying the repeat database using repeat characteristics like repeat unit and length, number of repetitions of the repeat unit and position of the repeat in the protein. Users can also search for repeats by the characteristics of repeat containing proteins, such as entry ID, protein description, sequence length, gene name and taxon. ProRepeat offers powerful analysis tools for finding biological interesting properties of repeats, such as the strong position bias of leucine repeats in the N-terminus of eukaryotic protein sequences, the differences of repeat abundance among proteomes, the functional classification of repeat containing proteins and GC content constrains of repeats’ corresponding codons.
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