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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    Distance Measurements on Orthogonally Spin-Labeled Membrane Spanning WALP23 Polypeptides
    Lueders, P. ; Jäger, H. ; Hemminga, M.A. ; Jeschke, G. ; Yulikov, M. - \ 2013
    The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 117 (2013)7. - ISSN 1520-6106 - p. 2061 - 2068.
    electron double-resonance - trichogin ga-iv - alpha-helical peptides - dipole-dipole interactions - islet amyloid polypeptide - field pulsed epr - hydrophobic mismatch - phospholipid membrane - gd3+ complexes - spectroscopy
    EPR-based Gd(III)-nitroxide distance measurements were performed on a series of membrane-incorporated orthogonally labeled WALP23 polypeptides. The obtained distance distributions were stable upon the change of detection frequency from 10 GHz (X-band) to 35 GHz (Q-band). The alpha-helical pitch of WALP23 polypeptide could be experimentally observed, despite the flexibility of the two spin labels. The spectroscopic properties of Gd(III) ions and nitroxide radicals allow detecting both types of paramagnetic species selectively in different EPR experiments. In particular, this spectroscopic selectivity allows for supplementing Gd(III)-nitroxide distance measurements with independent checks of polypeptide aggregation and with measurements of the local environment of the nitroxide spin labels. All mentioned additional checks do not require preparation of further samples, as it is the case in the experiments with pairs of identical nitroxide spin labels.
    Emission enhancement and lifetime modification of phosphorescence on silver nanoparticle aggregates
    Gill, R. ; Tian, L. ; Amerongen, H. van; Subramaniam, V. - \ 2013
    Physical Chemistry Chemical Physics 15 (2013). - ISSN 1463-9076 - p. 15734 - 15739.
    single-molecule fluorescence - oxygen generation - luminescence - spectroscopy - photochemistry - complexes - yields
    Silver nanoparticle aggregates have been shown to support very large enhancements of fluorescence intensity from organic dye molecules coupled with an extreme reduction in observed fluorescence lifetimes. Here we show that for the same type of aggregates, similar enhancement factors (similar to 75 x in intensity and similar to 3400 x in lifetime compared to the native radiative lifetime) are observed for a ruthenium-based phosphorescent dye (when taking into account the effect of charge and the excitation/emission wavelengths). Additionally, the inherently long native phosphorescence lifetimes practically enable more detailed analyses of the distribution of lifetimes (compared with the case with fluorescence decays). It was thus possible to unambiguously observe the deviation from mono-exponential decay which we attribute to emission from a distribution of fluorophores with different lifetimes, as we could expect from a random aggregation process. We believe that combining phosphorescent dyes with plasmonic structures, even down to the single dye level, will offer a convenient approach to better characterize plasmonic systems in detail.
    (Quasi-) 2D aggregation of polystyrene-b-dextran at the air-water interface
    Bosker, W.T.E. ; Cohen Stuart, M.A. ; Norde, W. - \ 2013
    Langmuir 29 (2013)8. - ISSN 0743-7463 - p. 2667 - 2675.
    diblock copolymer monolayers - surface micelle formation - block polyelectrolytes - air/water interface - molecular-dynamics - solid-state - behavior - brushes - polymers - spectroscopy
    Polystyrene-b-dextran (PS-b-Dextran) copolymers can be used to prepare dextran brushes at solid surfaces, applying Langmuir–Blodgett deposition. When recording the interfacial pressure versus area isotherms of a PS-b-Dextran monolayer, time-dependent hysteresis was observed upon compression and expansion. We argue that this is due to (quasi-) 2D aggregation of the copolymer at the air–water surface, with three contributions. First, at large area per molecule, a zero surface pressure is measured; we ascribe this to self-assembly of block copolymers into surface micelles. At intermediate area we identify a second regime (“desorption regime”) where aggregation into large patches occurs due to van der Waals attraction between PS blocks. At high surface pressure (“brush regime”) we observe hysteretic behavior attributed to H-bonding between dextran chains. When compared to hysteresis of other amphiphilic diblock copolymers (also containing PS, e.g., polystyrene-b-poly(ethylene oxide)) a general criterion can be formulated concerning the extent of hysteresis: when the hydrophobic (PS) block is of equal size as (or bigger than) the hydrophilic block, the hysteresis is maximal. The (quasi-) 2D aggregation of PS-b-Dextran has significant implications for the preparation of dextran brushes at solid surfaces using Langmuir–Blodgett deposition. For each grafting density the monolayer needs to relax, up to several hours, prior to transfer.
    Spectroscopy-supported digital soil mapping
    Mulder, V.L. - \ 2013
    Wageningen University. Promotor(en): Michael Schaepman; Sytze de Bruin. - [S.l. : S.n. - ISBN 9789461736901 - 188
    bodemkarteringen - bodem - cartografie - spectroscopie - remote sensing - bodemsamenstelling - soil surveys - soil - mapping - spectroscopy - remote sensing - soil composition

    Global environmental changes have resulted in changes in key ecosystem services that soils provide. It is necessary to have up to date soil information on regional and global scales to ensure that these services continue to be provided. As a result, Digital Soil Mapping (DSM) research priorities are among others, advancing methods for data collection and analyses tailored towards large-scale mapping of soil properties. Scientifically, this thesis contributed to the development of methodologies, which aim to optimally use remote and proximal sensing (RS and PS) for DSM to facilitate regional soil mapping. The main contributions of this work with respect to the latter are (I) the critical evaluation of recent research achievements and identification of knowledge gaps for large-scale DSM using RS and PS data, (II) the development of a sparse RS-based sampling approach to represent major soil variability at regional scale, (III) the evaluation and development of different state-of-the-art methods to retrieve soil mineral information from PS, (IV) the improvement of spatially explicit soil prediction models and (V) the integration of RS and PS methods with geostatistical and DSM methods.

    A review on existing literature about the use of RS and PS for soil and terrain mapping was presented in Chapter 2. Recent work indicated the large potential of using RS and PS methods for DSM. However, for large-scale mapping, current methods will need to be extended beyond the plot. Improvements may be expected in the fields of developing more quantitative methods, enhanced geostatistical analysis and improved transferability to other areas. From these findings, three major research interests were selected: (I) soil sampling strategies, (II) retrieval of soil information from PS and (III) spatially continuous mapping of soil properties at larger scales using RS.

    Budgetary constraints, limited time and available soil legacy data restricted the soil data acquisition, presented in Chapter 3. A 15.000 km2 area located in Northern Morocco served as test case. Here, a sample was collected using constrained Latin Hypercube Sampling (cLHS) of RS and elevation data. The RS data served as proxy for soil variability, as alternative for the required soil legacy data supporting the sampling strategy. The sampling aim was to optimally sample the variability in the RS data while minimizing the acquisition efforts. This sample resulted in a dataset representing major soil variability. The cLHS sample failed to express spatial correlation; constraining the LHS by a distance criterion favoured large spatial variability over short distances. The absence of spatial correlation in the sampled soil variability precludes the use of additional geostatistical analyses to spatially predict soil properties. Predicting soil properties using the cLHS sample is thus restricted to a modelled statistical relation between the sample and exhaustive predictor variables. For this, the RS data provided the necessary spatial information because of the strong spatial correlation while the spectral information provided the variability of the environment (Chapter 3 and 6). Concluding, the RS-based cLHS approach is considered a time and cost efficient method for acquiring information on soil resources over extended areas.

    This sample was further used for developing methods to derive soil mineral information from PS, and to characterize regional soil mineralogy using RS. In Chapter 4, the influences of complex scattering within the mixture and overlapping absorption features were investigated. This was done by comparing the success of PRISM’s MICA in determining mineralogy of natural samples and modelled spectra. The modelled spectra were developed by a linearly forward model of reflectance spectra, using the fraction of known constituents within the sample. The modelled spectra accounted for the co-occurrence of absorption features but eluded the complex interaction between the components. It was found that more minerals could be determined with higher accuracy using modelled reflectance. The absorption features in the natural samples were less distinct or even absent, which hampered the classification routine. Nevertheless, grouping the individual minerals into mineral categories significantly improved the classification accuracy. These mineral categories are particularly useful for regional scale studies, as key soil property for parent material characterization and soil formation. Characterizing regional soil mineralogy by mineral categories was further described in Chapter 6. Retrieval of refined information from natural samples, such as mineral abundances, is more complex; estimating abundances requires a method that accounts for the interaction between minerals within the intimate mixture. This can be done by addressing the interaction with a non-linear model (Chapter 5).

    Chapter 5 showed that mineral abundances in complex mixtures could be estimated using absorption features in the 2.1–2.4 µm wavelength region. First, the absorption behaviour of mineral mixtures was parameterized by exponential Gaussian optimization (EGO). Next, mineral abundances were successfully predicted by regression tree analysis, using these parameters as inputs. Estimating mineral abundances using prepared mixes of calcite, kaolinite, montmorillonite and dioctahedral mica or field samples proved the validity of the proposed method. Estimating mineral abundances of field samples showed the necessity to deconvolve spectra by EGO. Due to the nature of the field samples, the simple representation of the complex scattering behaviour by a few Gaussian bands required the parameters asymmetry and saturation to accurately deconvolve the spectra. Also, asymmetry of the EGO profiles showed to be an important parameter for estimating the abundances of the field samples. The robustness of the method in handling the omission of minerals during the training phase was tested by replacing part of the quartz with chlorite. It was found that the accuracy of the predicted mineral content was hardly affected. Concluding, the proposed method allowed for estimating more than two minerals within a mixture. This approach advances existing PS methods and has the potential to quantify a wider set of soil properties. With this method the soil science community was provided an improved inference method to derive and quantify soil properties

    The final challenge of this thesis was to spatially explicit model regional soil mineralogy using the sparse sample from Chapter 3. Prediction models have especially difficulties relating predictor variables to sampled properties having high spatial correlation. Chapter 6 presented a methodology that improved prediction models by using scale-dependent spatial variability observed in RS data. Mineral predictions were made using the abundances from X-ray diffraction analysis and mineral categories determined by PRISM. The models indicated that using the original RS data resulted in lower model performance than those models using scaled RS data. Key to the improved predictions was representing the variability of the RS data at the same scale as the sampled soil variability. This was realized by considering the medium and long-range spatial variability in the RS data. Using Fixed Rank Kriging allowed smoothing the massive RS datasets to these ranges. The resulting images resembled more closely the regional spatial variability of soil and environmental properties. Further improvements resulted from using multi-scale soil-landscape relationships to predict mineralogy. The maps of predicted mineralogy showed agreement between the mineral categories and abundances. Using a geostatistical approach in combination with a small sample, substantially improves the feasibility to quantitatively map regional mineralogy. Moreover, the spectroscopic method appeared sufficiently detailed to map major mineral variability. Finally, this approach has the potential for modelling various natural resources and thereby enhances the perspective of a global system for inventorying and monitoring the earth’s soil resources.

    With this thesis it is demonstrated that RS and PS methods are an important but also an essential source for regional-scale DSM. Following the main findings from this thesis, it can be concluded that: Improvements in regional-scale DSM result from the integrated use of RS and PS with geostatistical methods. In every step of the soil mapping process, spectroscopy can play a key role and can deliver data in a time and cost efficient manner. Nevertheless, there are issues that need to be resolved in the near future. Research priorities involve the development of operational tools to quantify soil properties, sensor integration, spatiotemporal modelling and the use of geostatistical methods that allow working with massive RS datasets. This will allow us in the near future to deliver more accurate and comprehensive information about soils, soil resources and ecosystem services provided by soils at regional and, ultimately, global scale.

    Jacobaea through the eyes of spectroscopy : identifying plant interactions with the (a)biotic environment by chemical variation effects on spectral reflectance patterns
    Almeida De Carvalho, S. - \ 2013
    Wageningen University. Promotor(en): Wim van der Putten; Andrew Skidmore, co-promotor(en): M. Macel; M. Schlerf. - S.l. : s.n. - ISBN 9789461737502 - 180
    senecio jacobaea - senecio erucifolius - pyrrolizidinealkaloïden - voedingsstoffen - spectraalanalyse - spectroscopie - bodemmicrobiologie - metabolieten - chemische analyse - plantensuccessie - senecio jacobaea - senecio erucifolius - pyrrolizidine alkaloids - nutrients - spectral analysis - spectroscopy - soil microbiology - metabolites - chemical analysis - plant succession

    Plants interact with a wide array of aboveground and belowground herbivores, pathogens, mutualists, and their natural enemies. These interactions are important drivers of spatio-temporal changes in vegetation, however, they may be difficult to be revealed without extensive sampling.In this thesis I investigated the potential of visible and near-infrared spectral measurements to detect plant chemical changes that may reflect interactions between plants and biotic or abiotic soil factors. First, I examined the relative contribution of pyrrolizidine alkaloids (PAs; these are defence compounds of Senecio-type plants against generalist herbivores) to the spectral reflectance features in the visible and short-wave infrared region. My hypothesis was that PAs can be predicted from specific spectral features of aboveground plant tissues. Since PA profiles and their relation to spectral features could be species specific I compared three different species, Jacobaea vulgaris, J. erucifolia and S. inaequidens subjected to nutrient and water treatments to stimulate plant chemical variation. Pyrrolizidine alkaloids were predicted best by spectral reflectance features in the case of Jacobaea vulgaris. I related the better results obtained with J. vulgaris to the existence of the correlation between PAs and nitrogen and the presence of the epoxide chemical structure in J. vulgaris.

    I also examined if different soil microbial communities influenced plant shoot spectral reflectance. I grew the same three plant species as before in sterilized soil and living soil collected from fields with J. vulgaris. I expected that soil biota would change shoot defence content and hyperspectral reflectance in plant species-specific ways. Indeed, the exposure to different soils caused plant chemical profiles to change and both chemical and spectral patterns discriminated plants according to the soil biotic conditions.

    I studied how primary and secondary plant metabolites varied during the growing season and vegetation successional stages. I used a well-studied chronosequence of abandoned arable fields and analysed the chemistry of both leaves and flowers of Jacobaea vulgaris throughout the seasons in fields of different successional status. My general hypothesis was that seasonal allocation of nutrients and defence metabolites to reproductive organs fitted the optimal defence theory, but that pattern was dependent on the successional stage of the vegetation. I found an interaction between season and succession stage, as plants from longer abandoned fields generally had flowers and leaves with higher N-oxides, especially in late Summer. Independent of the succession stage there was a seasonal allocation of nutrients and defence metabolites to flowers. Analyses of spectral reflectance of the field plants showed thatdefence compounds could be estimated more reliably in flowers, while in leaves primary compounds could be predicted best. Succession classes were successfully discriminated by the spectral patterns of flowers. Both chemical and spectral findings suggested that flowers are more sensitive to field ageing processes than leaves.

    Conclusions

    The estimation of pyrrolizidine alkaloids by spectral reflectance features was better in Jacobaea vulgaris than in Senecio inaequidens or Jacobaea erucifolia (chapter 2). Differences in soil communities affect plant leaves’ chemistry and spectral reflectance patterns (chapter 3). Jacobaea vulgarisplants from recent and longer-abandoned fields showed the largest differences in chemical concentration, composition of defence compounds, and spectral reflectance patterns. Flowers were more discriminatory than leaves (chapters 4 and 5). There is a potential to detect plant-biotic interactions by analyzing spectral reflectance patterns (this thesis).
    Multivariate data analysis as a PAT tool for early bioprocess development data
    Mercier, S.M. ; Diepenbroek, B. ; Dalm, M.C.F. ; Wijffels, R.H. ; Streefland, M. - \ 2013
    Journal of Biotechnology 167 (2013)13. - ISSN 0168-1656 - p. 262 - 270.
    monitoring batch processes - cell-culture - chemometrics - spectroscopy - prediction - quality - design
    Early development datasets are typically unstructured, incomplete and truncated, yet they are readily available and contain relevant process information which is not extracted using classical data analysis techniques. In this paper, we illustrate the power of multivariate data analysis (MVDA) as a Process Analytical Technology tool to analyze early development data of a PER.C6® cell cultivation process. MVDA increased our understanding of the process studied. Principal component analysis enabled a thorough exploration of the dataset, identifying causes for batch deviations and revealing sensitivity of the process to scale. These findings were previously undetected using traditional univariate analysis. The lack of structure and gaps in the early development datasets made it impossible to fit them to more advanced partial least square regression models. This paper clearly shows that MVDA should be routinely used to analyze early development data to reveal relevant information for later development and scale-up. The value of these early development runs can be greatly enhanced if the experiments are well-structured and accompanied with full process analytics. This up-front investment will result in shorter and more efficient process development paths, resulting in lower overall development costs for new biopharmaceutical products.
    Fast and Robust Method To Determine Phenoyl and Acetyl Esters of Polysaccharides by Quantitative 1H NMR
    Neumüller, K.G. ; Carvalho de Souza, A. ; Rijn, J. van; Appeldoorn, M.M. ; Streekstra, H. ; Schols, H.A. ; Gruppen, H. - \ 2013
    Journal of Agricultural and Food Chemistry 61 (2013)26. - ISSN 0021-8561 - p. 6282 - 6287.
    acids - nmr - spectroscopy - extracts
    The acetyl (AcE), feruloyl (FE), and p-coumaroyl (pCE) ester contents of different cereal and grass polysaccharides were determined by a quantitative 1H NMR-based method. The repeatability and the robustness of the method were demonstrated by analyzing different plant polysaccharide preparations. Good sensitivity and selectivity for AcE, FE, and pCE were observed. Moreover, an optimized and easy sample preparation allowed for simultaneous quantification of AcE, FE, and pCE. The method is suitable for high-throughput analysis, and it is a good alternative for currently used analytical procedures. A comparison of the method presented to a conventional HPLC-based method showed that the results obtained are in good agreement, whereas the combination of the optimized sample preparation and analysis by the 1H NMR-based methodology results in significantly reduced analysis time.
    Sacha Inchi (Plukenetia volubilis): a seed source of polyunsaturated fatty acids, tocopherols, phytoserols, phenolic compounds and antioxidant capacity
    Chirinos, R. ; Zuloeta, G. ; Pedreschi Plasencia, R.P. - \ 2013
    Food Chemistry 141 (2013)3. - ISSN 0308-8146 - p. 1732 - 1739.
    chemical-composition - oxidative stability - united-states - l. seeds - oil - foods - spectroscopy - cultivars - flaxseed - assay
    Fatty acids (FA), phytosterols, tocopherols, phenolic compounds, total carotenoids and hydrophilic and lipophilic ORAC antioxidant capacities were evaluated in 16 cultivars of Sacha inchi (SI) seeds with the aim to valorise them and offer more information on the functional properties of SI seeds. A high a linolenic (a-Ln) fatty acid content was found in all cultivars (¿3, 12.8–16.0 g/100 g seed), followed by linoleic (L) fatty acid (¿6, 12.4–14.1 g/100 g seed). The ratio ¿6/¿3 was within the 0.83–1.09 range. ¿- and d-tocopherols were the most important tocopherols, whereas the most representative phytosterols were ß-sitosterol and stigmasterol. Contents of total phenolics, total carotenoids and hydrophilic and lipophilic antioxidant capacities ranged from 64.6 to 80 mg of gallic acid equivalent/100 g seed; from 0.07 to 0.09 mg of ß-carotene equivalent/100 g of seed; from 4.3 to 7.3 and, from 1.0 to 2.8 µmol of Trolox equivalent/g of seed, respectively, among the evaluated SI cultivars. Results showed significant differences (p <0.05) among the evaluated SI cultivars in the contents of ¿3, ¿6, antioxidant capacities and other evaluated phytochemicals. SI seeds should be considered as an important dietary source of health promoting phytochemicals.
    Fouling mechanisms of dairy streams during membrane distillation
    Hausmann, A. ; Sanciolo, P. ; Vasiljevic, T. ; Weeks, M. ; Schroën, C.G.P.H. ; Gray, S. ; Duke, M. - \ 2013
    Journal of Membrane Science 441 (2013). - ISSN 0376-7388 - p. 102 - 111.
    calcium-phosphate - skimmed-milk - osmotic distillation - whey proteins - ultrafiltration - microfiltration - adsorption - stability - spectroscopy - precursors
    This study reports on fouling mechanisms of skim milk and whey during membrane distillation (MD) using polytetrafluoroethylene (PTFE) membranes. Structural and elemental changes along the fouling layer from the anchorpoint at the membrane to the topsurface of the fouling layer have been investigated using synchrotron IR micro-spectroscopy and electron microscopy with associated energy dispersive X-ray spectroscopy(EDS)Initial adhesion of single components on a membrane representing a PTFEsurface was observed in-situ utilizing reflectometry.Whey components were found to penetrate into the membrane matrix while skim milk fouling remained on top of the membrane. Whey proteins had weaker attractive interaction with the membrane and adhesion depended more on the presence of phosphorus near the membrane surface and throughout to establish the fouling layer. This work has given detailed insight into the fouling mechanisms of MD membranes in major dairy streams, essential for maintaining membrane distillation as operational for acceptable times, therewith allowing further development of this emerging technology.
    Magnetic Resonance in Food Science - Food for Thought
    Duynhoven, J.P.M. van; Belton, P.S. ; Webb, G.A. ; As, H. van - \ 2013
    London : RSC Books - ISBN 9781849736343 - 235
    voedselwetenschappen - voedingsmiddelen - kernspintomografie - diagnostische technieken - voedselverwerking - spectroscopie - afbeelden - voedselkwaliteit - voedselveiligheid - food sciences - foods - magnetic resonance imaging - diagnostic techniques - food processing - spectroscopy - imagery - food quality - food safety
    There are many challenges and problems in food science and magnetic resonance methods may be used to provide answers and deepen both fundamental and practical knowledge. This book presents innovations in magnetic resonance and in particular applications to understanding the functionality of foods, their processing and stability and their impact on health, perception and behaviour. Coverage includes structure and function, emphasizing respectively applications of spectroscopy/relaxometry and imaging/diffusometry; high resolution NMR spectroscopy as applied to quality and safety and foodomics; and dedicated information on perception and behaviour demonstrating the progress that has been made in applications of fMRI in this field.
    Validation of fatty acid predictions in milk using mid-infrared spectrometry across cattle breeds
    Maurice - Van Eijndhoven, M.H.T. ; Soyeurt, H. ; Dehareng, F. ; Calus, M.P.L. - \ 2013
    Animal 7 (2013)2. - ISSN 1751-7311 - p. 348 - 354.
    gas-liquid chromatography - bovine-milk - short-communication - genetic-parameters - spectroscopy - protein
    The aim of this study was to investigate the accuracy to predict detailed fatty acid (FA) composition of bovine milk by mid-infrared spectrometry, for a cattle population that partly differed in terms of country, breed and methodology used to measure actual FA composition compared with the calibration data set. Calibration equations for predicting FA composition using mid-infrared spectrometry were developed in the European project RobustMilk and based on 1236 milk samples from multiple cattle breeds from Ireland, Scotland and the Walloon Region of Belgium. The validation data set contained 190 milk samples from cows in the Netherlands across four breeds: Dutch Friesian, Meuse-Rhine-Yssel, Groningen White Headed (GWH) and Jersey (JER). The FA measurements were performed using gas–liquid partition chromatography (GC) as the gold standard. Some FAs and groups of FAs were not considered because of differences in definition, as the capillary column of the GC was not the same as used to develop the calibration equations. Differences in performance of the calibration equations between breeds were mainly found by evaluating the standard error of validation and the average prediction error. In general, for the GWH breed the smallest differences were found between predicted and reference GC values and least variation in prediction errors, whereas for JER the largest differences were found between predicted and reference GC values and most variation in prediction errors. For the individual FAs 4:0, 6:0, 8:0, 10:0, 12:0, 14:0 and 16:0 and the groups’ saturated FAs, short-chain FAs and medium-chain FAs, predictions assessed for all breeds together were highly accurate (validation R2 > 0.80) with limited bias. For the individual FAs cis-14:1, cis-16:1 and 18:0, the calibration equations were moderately accurate (R2 in the range of 0.60 to 0.80) and for the individual FA 17:0 predictions were less accurate (R2 <0.60) with considerable bias. FA concentrations in the validation data set of our study were generally higher than those in the calibration data. This difference in the range of FA concentrations, mainly due to breed differences in our study, can cause lower accuracy. In conclusion, the RobustMilk calibration equations can be used to predict most FAs in milk from the four breeds in the Netherlands with only a minor loss of accuracy.
    Remote sensing image processing
    Camps-Valls, Gustavo ; Tuia, Devis ; Gómez-Chova, Luis ; Jiménez, Sandra ; Malo, Jesús - \ 2012
    Morgan and Claypool Publishers (Synthesis Lectures on Image, Video, and Multimedia Processing ) - ISBN 9781608458196 - 194 p.
    biophysical parameter - classification - computer vision - Earth observation - feature selection and extraction - image statistics - machine learning - manifold learning - morphology - pattern recognition - regression - remote sensing - retrieval - segmentation - spectral signature - spectroscopy - statistical learning - unmixing - vision science

    Earth observation is the field of science concerned with the problem of monitoring and modeling the processes on the Earth surface and their interaction with the atmosphere.The Earth is continuously monitored with advanced optical and radar sensors.The images are analyzed and processed to deliver useful products to individual users, agencies and public administrations.To deal with these problems, remote sensing image processing is nowadays a mature research area, and the techniques developed in the field allow many real-life applications with great societal value.For instance, urban monitoring, fire detection or flood prediction can have a great impact on economical and environmental issues. To attain such objectives, the remote sensing community has turned into a multidisciplinary field of science that embraces physics, signal theory, computer science, electronics and communications. From a machine learning and signal/image processing point of view, all the applications are tackled under specific formalisms, such as classification and clustering, regression and function approximation, data coding, restoration and enhancement, source unmixing, data fusion or feature selection and extraction. This book covers some of the fields in a comprehensive way.

    Use of NMR metabolomic plasma profiling methodologies to identify illicit growth-promoting administrations
    Graham, S.F. ; Ruiz Aracama, A. ; Lommen, A. ; Cannizzo, F.T. ; Biolatti, B. ; Elliott, C.T. ; Mooney, M.H. - \ 2012
    Analytical and Bioanalytical Chemistry 403 (2012)2. - ISSN 1618-2642 - p. 573 - 582.
    veal calves - cattle - dexamethasone - spectroscopy - urine - h-1 - 17-beta-estradiol - metabolites - hormones - h-1-nmr
    Detection of growth-promoter use in animal production systems still proves to be an analytical challenge despite years of activity in the field. This study reports on the capability of NMR metabolomic profiling techniques to discriminate between plasma samples obtained from cattle treated with different groups of growth-promoting hormones (dexamethasone, prednisolone, oestradiol) based on recorded metabolite profiles. Two methods of NMR analysis were investigated-a Carr-Purcell-Meiboom-Gill (CPMG)-pulse sequence technique and a conventional H-1 NMR method using pre-extracted plasma. Using the CPMG method, 17 distinct metabolites could be identified from the spectra. H-1 NMR analysis of extracted plasma facilitated identification of 23 metabolites-six more than the alternative method and all within the aromatic region. Multivariate statistical analysis of acquired data from both forms of NMR analysis separated the plasma metabolite profiles into distinct sample cluster sets representative of the different animal study groups. Samples from both sets of corticosteroid-treated animals-dexamethasone and prednisolone-were found to be clustered relatively closely and had similar alterations to identified metabolite panels. Distinctive metabolite profiles, different from those observed within plasma from corticosteroid-treated animal plasma, were observed in oestradiol-treated animals and samples from these animals formed a cluster spatially isolated from control animal plasma samples. These findings suggest the potential use of NMR methodologies of plasma metabolite analysis as a high-throughput screening technique to aid detection of growth promoter use.
    Microscopic Origin of the Fast Blue-Green Luminescence from Chemically Synthesized Non-Oxidized Silicon Quantum Dots
    Dohnalová, K. ; Gregorkiewicz, T. ; Fucíková, A. ; Valenta, J. ; Umesh, C. ; Paulusse, J.M.J. ; Zuilhof, H. ; Humpolícková, J. ; Hof, M. van - \ 2012
    Small 8 (2012)20. - ISSN 1613-6810 - p. 3185 - 3191.
    light-emission - confinement regime - electronic states - si nanocrystals - porous silicon - photoluminescence - nanoparticles - alkyl - nanoclusters - spectroscopy
    The microscopic origin of the bright nanosecond blue-green photoluminescence (PL), frequently reported for synthesized organically terminated Si quantum dots (Si-QDs), has not been fully resolved, hampering potential applications of this interesting material. Here a comprehensive study of the PL from alkyl-terminated Si-QDs of 2-3 nm size, prepared by wet chemical synthesis is reported. Results obtained on the ensemble and those from the single nano-object level are compared, and they provide conclusive evidence that efficient and tunable emission arises due to radiative recombination of electron-hole pairs confined in the Si-QDs. This understanding paves the way towards applications of chemical synthesis for the development of Si-QDs with tunable sizes and bandgaps.
    Hexadecadienyl Monolayers on Hydrogen-Terminated Si(III): Faster Monolayer Formation and Improved Surface Coverage Using the Enyne Moiety
    Rijksen, B.M.G. ; Pujari, S.P. ; Scheres, L.M.W. ; Rijn, C.J.M. van; Baio, J.E. ; Weidner, T. ; Zuilhof, H. - \ 2012
    Langmuir 28 (2012)16. - ISSN 0743-7463 - p. 6577 - 6588.
    self-assembled monolayers - silicon surfaces - alkyl monolayers - organic monolayers - x-ray - molecular simulation - visible-light - si - spectroscopy - attachment
    To further improve the coverage of organic monolayers on hydrogen-terminated silicon (H–Si) surfaces with respect to the hitherto best agents (1-alkynes), it was hypothesized that enynes (H–C=C–HC-CH–R) would be even better reagents for dense monolayer formation. To investigate whether the increased delocalization of ß-carbon radicals by the enyne functionality indeed lowers the activation barrier, the kinetics of monolayer formation by hexadec-3-en-1-yne and 1-hexadecyne on H–Si(111) were followed by studying partially incomplete monolayers. Ellipsometry and static contact angle measurements indeed showed a faster increase of layer thickness and hydrophobicity for the hexadec-3-en-1-yne-derived monolayers. This more rapid monolayer formation was supported by IRRAS and XPS measurements that for the enyne show a faster increase of the CH2 stretching bands and the amount of carbon at the surface (C/Si ratio), respectively. Monolayer formation at room temperature yielded plateau values for hexadec-3-en-1-yne and 1-hexadecyne after 8 and 16 h, respectively. Additional experiments were performed for 16 h at 80° to ensure full completion of the layers, which allows comparison of the quality of both layers. Ellipsometry thicknesses (2.0 nm) and contact angles (111–112°) indicated a high quality of both layers. XPS, in combination with DFT calculations, revealed terminal attachment of hexadec-3-en-1-yne to the H–Si surface, leading to dienyl monolayers. Moreover, analysis of the Si2p region showed no surface oxidation. Quantitative XPS measurements, obtained via rotating Si samples, showed a higher surface coverage for C16 dienyl layers than for C16 alkenyl layers (63% vs 59%). The dense packing of the layers was confirmed by IRRAS and NEXAFS results. Molecular mechanics simulations were undertaken to understand the differences in reactivity and surface coverage. Alkenyl layers show more favorable packing energies for surface coverages up to 50–55%. At higher coverages, this packing energy rises quickly, and there the dienyl packing becomes more favorable. When the binding energies are included the difference becomes more pronounced, and dense packing of dienyl layers becomes more favorable by 2–3 kcal/mol. These combined data show that enynes provide the highest-quality organic monolayers reported on H–Si up to now.
    Charge transport across metal/molecular (alkyl) monolayer-Si junctions is dominated by the LUMO level
    Yaffe, O. ; Qi, Y. ; Scheres, L.M.W. ; Puniredd, S.R. ; Segev, L. ; Ely, T. ; Haick, H. ; Zuilhof, H. ; Vilan, A. ; Kronik, L. ; Kahn, A. ; Cahen, D. - \ 2012
    Physical Review. B : Condensed Matter and Materials Physics 85 (2012)4. - ISSN 1098-0121
    self-assembled monolayers - electronic transport - molecular electronics - organic-molecules - chain monolayers - spectroscopy - polyethylene - conductance - films - photoemission
    We compare the charge transport characteristics of heavy-doped p(++)- and n(++)-Si-alkyl chain/Hg junctions. Based on negative differential resistance in an analogous semiconductor-inorganic insulator/metal junction we suggest that for both p(++)- and n(++)-type junctions, the energy difference between the Fermi level and lowest unoccupied molecular orbital (LUMO), i.e., electron tunneling, controls charge transport. This conclusion is supported by results from photoelectron spectroscopy (ultraviolet photoemission spectroscopy, inverse photoelectron spectroscopy, and x-ray photoemission spectroscopy) for the molecule-Si band alignment at equilibrium, which clearly indicate that the energy difference between the Fermi level and the LUMO is much smaller than that between the Fermi level and the highest occupied molecular orbital (HOMO). Furthermore, the experimentally determined Fermi level - LUMO energy difference, agrees with the non-resonant tunneling barrier height, deduced from the exponential length attenuation of the current.
    An Investigation of Polyamides Based on Isoidide-2,5-dimethyleneamine as a Green Rigid Building Block with Enhanced Reactivity
    Wu, J. ; Jasinska-Walc, L. ; Dudenko, D. ; Rozanski, A. ; Hansen, M.R. ; Es, D.S. van; Koning, C.E. - \ 2012
    Macromolecules 45 (2012)23. - ISSN 0024-9297 - p. 9333 - 9346.
    solid-state-nmr - infrared temperature - renewable resources - brill transition - isosorbide - isohexide - polymers - mas - spectroscopy - crystals
    Novel, semicrystalline polyamides and copolyamides were synthesized from a new carbohydrate-based diamine, namely isoidide-2,5-dimethyleneamine (IIDMA). In combination with 1,6-hexamethylene diamine (1,6-HDA) as well as the biobased sebacic acid (SA) or brassylic acid (BrA), the desired copolyamides were obtained via melt polymerization of the nylon salts followed by a solid-state polycondensation (SSPC) process. Depending on the chemical compositions, the number average molecular weights (Mn) of the polyamides were in the range of 4000–49000 g/mol. With increasing IIDMA content in the synthesized copolyamides, their corresponding glass transition temperatures (Tg) increased from 50 °C to approximately 60–67 °C while the melting temperatures (Tm) decreased from 220 to 160 °C. The chemical structures of the polyamides were analyzed by NMR and FT-IR spectroscopy. Both differential scanning calorimetry (DSC) and wide-angle X-ray diffraction (WAXD) analyses revealed the semicrystalline character of these novel copolyamides. Variable-temperature (VT) 13C{1H} cross-polarization/magic-angle spinning (CP/MAS) NMR and FT-IR techniques were employed to study the crystal structures as well as the distribution of IIDMA moieties over the crystalline and amorphous phases of the copolyamides. The performed ab initio calculations reveal that the stability of the IIDMA moieties is due to a pronounced “boat” conformation of the bicyclic rings. The incorporation of methylene segments in between the isohexide group and the amide groups enables the hydrogen bonds formation and organization of the polymer chain fragments. Given the sufficiently high Tm values (200 °C) of the copolyamides containing less than 50% of IIDMA, these biobased semicrystalline copolyamides can be useful for engineering plastic applica
    Organic matter of subsoil horizons under broadleaved forest: Highly processed or labile and plant-derived?
    Vancampenhout, K. ; Vos, B. de; Wouters, K. ; Swennen, R. ; Buurman, P. - \ 2012
    Soil Biology and Biochemistry 50 (2012)july. - ISSN 0038-0717 - p. 40 - 46.
    pyrolysis-gc/ms - chemical-composition - carbon pool - soils - stabilization - spectroscopy - ecosystems - mechanisms - fractions - chemistry
    Between 30 and 63% of the soil organic matter (SOM) is stored below 30 cm, making subsoil-SOM an important source and sink in the global carbon cycle. Nevertheless, detailed information on the composition of subsoil-SOM remains scarce. This study aims to evaluate the chemical composition of SOM in topsoil and subsoil horizons in broadleaved forests on acid loamy soils. Six sites were chosen in Northern Belgium under beech, oak and hybrid poplar, on Gleysols, Umbrisols, Cambisols and Albeluvisols on loamy Quaternary deposits. Analytical pyrolysis–gas chromatography/mass spectrometry (pyrolysis–GC/MS) was performed on the dialyzed alkaline extract, which represents between 41 and 90% of the total organic carbon for the selected sites. All extracts show a significant shift in chemical composition between the topsoil and the subsoil. While topsoil-SOM mainly differs according to input and nutrient status, subsoil-SOM shows high relative amounts of alkanes and alkenes or polysaccharides for coarse and fine textured soils respectively. Lignins, lignin-derived phenols or aromatics were not major contributors to subsoil-SOM, regardless of soil type. Furthermore, results show that very labile plant-derived molecules are present in the subsoil, i.e. long-chain aliphatics and (cellulose-derived) anhydrosugars. The organic matter signature of the subsoil samples was evaluated for typical indications of fresh material, decay, podzolisation and anaerobic processes, and indicates root input and stabilization of certain labile plant-derived compounds against microbial decay to be important in the subsoil.
    Using a genetic algorithm as an optimal band selector in the mid and thermal infrared (2.5-14 µm) to discriminate vegetation species
    Ullah, S. ; Groen, T.A. ; Schlerf, M. ; Skidmore, A.K. ; Nieuwenhuis, W. ; Vaiphasa, C. - \ 2012
    Sensors 12 (2012)7. - ISSN 1424-8220 - p. 8755 - 8769.
    spectral discrimination - reflectance - spectroscopy - emissivity - imagery - leaves - identification - spectrometry - regression - plants
    Genetic variation between various plant species determines differences in their physio-chemical makeup and ultimately in their hyperspectral emissivity signatures. The hyperspectral emissivity signatures, on the one hand, account for the subtle physio-chemical changes in the vegetation, but on the other hand, highlight the problem of high dimensionality. The aim of this paper is to investigate the performance of genetic algorithms coupled with the spectral angle mapper (SAM) to identify a meaningful subset of wavebands sensitive enough to discriminate thirteen broadleaved vegetation species from the laboratory measured hyperspectral emissivities. The performance was evaluated using an overall classification accuracy and Jeffries Matusita distance. For the multiple plant species, the targeted bands based on genetic algorithms resulted in a high overall classification accuracy (90%). Concentrating on the pairwise comparison results, the selected wavebands based on genetic algorithms resulted in higher Jeffries Matusita (J-M) distances than randomly selected wavebands did. This study concludes that targeted wavebands from leaf emissivity spectra are able to discriminate vegetation species.
    Silver nanoparticle aggregates as highly efficient plasmonic antennas for fluorescence enhancement
    Gill, R. ; Tian, L. ; Somerville, W.R.C. ; Ru, E.C. Le; Amerongen, H. van; Subramaniam, V. - \ 2012
    The Journal of Physical Chemistry Part C: Nanomaterials and Interfaces 116 (2012)31. - ISSN 1932-7447 - p. 16687 - 16693.
    raman-scattering sers - field enhancement - optical antennas - hot-spots - surface - spectroscopy - molecule - nanoantennas - nanoshells - decay
    The enhanced local fields around plasmonic structures can lead to enhancement of the excitation and modification of the emission quantum yield of fluorophores. So far, high enhancement of fluorescence intensity from dye molecules was demonstrated using bow-tie gap antenna made by e-beam lithography. However, the high manufacturing cost and the fact that currently there are no effective ways to place fluorophores only at the gap prevent the use of these structures for enhancing fluorescence-based biochemical assays. We report on the simultaneous modification of fluorescence intensity and lifetime of dye-labeled DNA in the presence of aggregated silver nanoparticles. The nanoparticle aggregates act as efficient plasmonic antennas, leading to more than 2 orders of magnitude enhancement of the average fluorescence. This is comparable to the best-reported fluorescence enhancement for a single molecule but here applies to the average signal detected from all fluorophores in the system. This highlights the remarkable efficiency of this system for surface-enhanced fluorescence. Moreover, we show that the fluorescence intensity enhancement varies with the plasmon resonance position and measure a significant reduction (300×) of the fluorescence lifetime. Both observations are shown to be in agreement with the electromagnetic model of surface-enhanced fluorescence.
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