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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    Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
    Kang, Kyo Bin ; Ernst, Madeleine ; Hooft, Justin J.J. van der; Silva, Ricardo R. da; Park, Junha ; Medema, Marnix H. ; Sung, Sang Hyun ; Dorrestein, Pieter C. - \ 2019
    The Plant Journal (2019). - ISSN 0960-7412
    annotation - classification - mass spectrometry - Rhamnaceae - specialized metabolites - technical advance

    Plants produce a myriad of specialized metabolites to overcome their sessile habit and combat biotic as well as abiotic stresses. Evolution has shaped the diversity of specialized metabolites, which then drives many other aspects of plant biodiversity. However, until recently, large-scale studies investigating the diversity of specialized metabolites in an evolutionary context have been limited by the impossibility of identifying chemical structures of hundreds to thousands of compounds in a time-feasible manner. Here we introduce a workflow for large-scale, semi-automated annotation of specialized metabolites and apply it to over 1000 metabolites of the cosmopolitan plant family Rhamnaceae. We enhance the putative annotation coverage dramatically, from 2.5% based on spectral library matches alone to 42.6% of total MS/MS molecular features, extending annotations from well-known plant compound classes into dark plant metabolomics. To gain insights into substructural diversity within this plant family, we also extract patterns of co-occurring fragments and neutral losses, so-called Mass2Motifs, from the dataset; for example, only the Ziziphoid clade developed the triterpenoid biosynthetic pathway, whereas the Rhamnoid clade predominantly developed diversity in flavonoid glycosides, including 7-O-methyltransferase activity. Our workflow provides the foundations for the automated, high-throughput chemical identification of massive metabolite spaces, and we expect it to revolutionize our understanding of plant chemoevolutionary mechanisms.

    Potato Virus Y Detection in Seed Potatoes Using Deep Learning on Hyperspectral Images
    Polder, G. ; Blok, P.M. ; Villiers, H.A.C. de; Wolf, J.M. van der; Kamp, J.A.L.M. - \ 2019
    Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
    crop resistance - Phenotyping - hyperspectral imaging - classification - Convolutional neural network - Solanum tuberosum
    Virus diseases are of high concern in the cultivation of seed potatoes. Once found inthe field, virus diseased plants lead to declassification or even rejection of the seed lotsresulting in a financial loss. Farmers put in a lot of effort to detect diseased plants andremove virus-diseased plants from the field. Nevertheless, dependent on the cultivar,virus diseased plants can be missed during visual observations in particular in an earlystage of cultivation. Therefore, there is a need for fast and objective disease detection.Early detection of diseased plants with modern vision techniques can significantlyreduce costs. Laboratory experiments in previous years showed that hyperspectral imaging clearly could distinguish healthy from virus infected potato plants. This paper reports on our first real field experiment. A new imaging setup was designed, consisting of a hyperspectral line-scan camera. Hyperspectral images were taken in the field with a line interval of 5 mm. A fully convolutional neural network was adapted for hyperspectral images and trained on two experimental rows in the field. The trained network was validated on two other rows, with different potato cultivars. For three of the four row/date combinations the precision and recall compared to conventional disease assessment exceeded 0.78 and 0.88, respectively. This proves the suitability of this method for real world disease detection.
    Dense semantic labeling of subdecimeter resolution images with convolutional neural networks
    Volpi, Michele ; Tuia, Devis - \ 2017
    IEEE Transactions on Geoscience and Remote Sensing 55 (2017)2. - ISSN 0196-2892 - p. 881 - 893.
    Aerial images - classification - convolutional neural networks (CNNs) - deconvolution networks - deep learning - semantic labeling - subdecimeter resolution

    Semantic labeling (or pixel-level land-cover classification) in ultrahigh-resolution imagery (<10 cm) requires statistical models able to learn high-level concepts from spatial data, with large appearance variations. Convolutional neural networks (CNNs) achieve this goal by learning discriminatively a hierarchy of representations of increasing abstraction. In this paper, we present a CNN-based system relying on a downsample-then-upsample architecture. Specifically, it first learns a rough spatial map of high-level representations by means of convolutions and then learns to upsample them back to the original resolution by deconvolutions. By doing so, the CNN learns to densely label every pixel at the original resolution of the image. This results in many advantages, including: 1) the state-of-the-art numerical accuracy; 2) the improved geometric accuracy of predictions; and 3) high efficiency at inference time. We test the proposed system on the Vaihingen and Potsdam subdecimeter resolution data sets, involving the semantic labeling of aerial images of 9- and 5-cm resolution, respectively. These data sets are composed by many large and fully annotated tiles, allowing an unbiased evaluation of models making use of spatial information. We do so by comparing two standard CNN architectures with the proposed one: standard patch classification, prediction of local label patches by employing only convolutions, and full patch labeling by employing deconvolutions. All the systems compare favorably or outperform a state-of-the-art baseline relying on superpixels and powerful appearance descriptors. The proposed full patch labeling CNN outperforms these models by a large margin, also showing a very appealing inference time.

    Optimal Transport for Domain Adaptation
    Courty, Nicolas ; Flamary, Remi ; Tuia, Devis ; Rakotomamonjy, Alain - \ 2017
    IEEE Transactions on Pattern Analysis and Machine Intelligence 39 (2017)9. - ISSN 0162-8828 - p. 1853 - 1865.
    classification - optimal transport - transfer learning - Unsupervised domain adaptation - visual adaptation

    Domain adaptation is one of the most challenging tasks of modern data analytics. If the adaptation is done correctly, models built on a specific data representation become more robust when confronted to data depicting the same classes, but described by another observation system. Among the many strategies proposed, finding domain-invariant representations has shown excellent properties, in particular since it allows to train a unique classifier effective in all domains. In this paper, we propose a regularized unsupervised optimal transportation model to perform the alignment of the representations in the source and target domains. We learn a transportation plan matching both PDFs, which constrains labeled samples of the same class in the source domain to remain close during transport. This way, we exploit at the same time the labeled samples in the source and the distributions observed in both domains. Experiments on toy and challenging real visual adaptation examples show the interest of the method, that consistently outperforms state of the art approaches. In addition, numerical experiments show that our approach leads to better performances on domain invariant deep learning features and can be easily adapted to the semi-supervised case where few labeled samples are available in the target domain.

    Spatial classification with fuzzy lattice reasoning
    Mavridis, Constantinos ; Athanasiadis, I.N. - \ 2017
    In: Proceedings of the 1st International Conference on Internet of Things and Machine Learning. - ACM - ISBN 9781450352437
    Fuzzy Lattice Reasoning - classification - spatial data - spatial data mining - spatial classification - linear arrangement - data mining
    This work extends the Fuzzy Lattice Reasoning (FLR) Classifier to manage spatial attributes, and spatial relationships. Specifically, we concentrate on spatial entities, as countries, cities, or states. Lattice Theory requires the elements of a Lattice to be partially ordered. To match such requirement, spatial entities are represented as a graph, whose number of nodes is equal to the amount of unique values of the spatial attribute elements. Then, the graph nodes are linearly arranged to formulate a partially ordered set; and thus be included in the Fuzzy Lattice classifier. The overall problem of incorporating spatial attributes in FLR was deduced to a Minimum Linear Arrangement problem. A corresponding open-source implementation in R has been made available on CRAN repository. The proposed method was evaluated using an open spatial dataset from the National Ambient Air Quality Standards (NAAQS). We investigated whether the addition of the spatial attribute contributed to any improvements in classification accuracy; and how linear arrangement alternatives may affect it. Experimental results showed that classification accuracy is above 85% in all cases, and the use of spatial attributes resulted to an increased accuracy of 92%. Alternative linear arrangements did not contribute significantly in improving classification accuracy in this case study.
    Trajectories of agricultural change in southern Mali
    Falconnier, G.N. - \ 2016
    Wageningen University. Promotor(en): Ken Giller, co-promotor(en): Katrien Descheemaeker; T.A. van Mourik. - Wageningen : Wageningen University - ISBN 9789462577596 - 209
    agriculture - agricultural development - farms - classification - self sufficiency - food - income - intensification - farming systems - intensive production - mali - landbouw - landbouwontwikkeling - landbouwbedrijven - classificatie - zelfvoorziening - voedsel - inkomen - intensivering - bedrijfssystemen - intensieve productie - mali

    Key words: longitudinal study, farm typology, food self-sufficiency, income, legumes, ex-ante analysis, participatory research, scenario.

    Smallholder agriculture in sub-Saharan Africa provides basis of rural livelihoods and food security, yet farmers have to cope with land constraints, variable rainfall and unstable institutional support. This study integrates a diversity of approaches (household typology and understanding of farm trajectories, on-farm trials, participatory ex-ante trade-off analysis) to design innovative farming systems to confront these challenges. We explored farm trajectories during two decades (1994 to 2010) in the Koutiala district in southern Mali, an area experiencing the land constraints that exert pressure in many other parts of sub-Saharan Africa. We classified farms into four types differing in land and labour productivity and food self-sufficiency status. During the past two decades, 17% of the farms stepped up to a farm type with greater productivity, while 70% of the farms remained in the same type, and only 13% of the farms experienced deteriorating farming conditions. Crop yields did not change significantly over time for any farm type and labour productivity decreased. Together with 132 farmers in the Koutiala district, we tested a range of options for sustainable intensification, including intensification of cereal (maize and sorghum) and legume (groundnut, soyabean and cowpea) sole crops and cereal-legume intercropping over three years and cropping seasons (2012-2014) through on-farm trials. Experiments were located across three soil types that farmers identified – namely black, sandy and gravelly soils. Enhanced agronomic performance was achieved when targeting legumes to a given soil type and/or place in the rotation: the biomass production of the cowpea fodder variety was doubled on black soils compared with gravelly soils and the additive maize/cowpea intercropping option after cotton or maize resulted in no maize grain penalty, and 1.38 t ha−1 more cowpea fodder production compared with sole maize. Farm systems were re-designed together with the farmers involved in the trials. A cyclical learning model combining the on-farm testing and participatory ex-ante analysis was used during four years (2012-2015). In the first cycle of 2012-2014, farmers were disappointed by the results of the ex-ante trade-off analysis, i.e marginal improvement in gross margin when replacing sorghum with soybean and food self-sufficiency trade-offs when intercropping maize with cowpea. In a second cycle in 2014-2015 the farm systems were re-designed using the niche-specific (soil type/previous crop combinations) information on yield and gross margin, which solved the concerns voiced by farmers during the first cycle. Farmers highlighted the saliency of the niches and the re-designed farm systems that increased farm gross margin by 9 to 29% (depending on farm type and options considered) without compromising food self-sufficiency. The involvement of farmers in the co-learning cycles allowed establishment of legitimate, credible and salient farm reconfiguration guidelines that could be scaled-out to other communities within the “old cotton basin”. Five medium-term contrasting socio-economic scenarios were built towards the year 2027, including hypothetical trends in policy interventions and change towards agricultural intensification. A simulation framework was built to account for household demographic dynamics and crop/livestock production variability. In the current situation, 45% of the 99 households of the study village were food self-sufficient and above the 1.25 US$ day-1 poverty line. Without change in farmer practices and additional policy intervention, only 16% of the farms would be both food self-sufficient and above the poverty line in 2027. In the case of diversification with legumes combined with intensification of livestock production and support to the milk sector, 27% of farms would be food self-sufficient and above the poverty line. Additional broader policy interventions to favour out-migration would be needed to lift 69% of the farms out of poverty. Other additional subsidies to favour yield gap narrowing of the main crops would lift 92% of the farm population out of poverty. Whilst sustainable intensification of farming clearly has a key role to play in ensuring food self-sufficiency, and is of great interest to local farmers, in the face of increasing population pressure other approaches are required to address rural poverty. These require strategic and multi-sectoral approaches that address employment within and beyond agriculture, in both rural and urban areas.

    Een evaluatie van de maatlatten R6 en R7 voor de Kader Richtlijn Water
    Griffioen, A.B. ; Vries, I. de - \ 2016
    IMARES (Rapport / IMARES C087/15) - 28
    rivieren - kaderrichtlijn water - waterbeheer - classificatie - waterkwaliteit - aquatische ecologie - monitoring - rivers - water framework directive - water management - classification - water quality - aquatic ecology - monitoring
    De watertypes R6 en R7 in de Kader Richtlijn Water (KRW) classificering verschillen qua grootte van het waterlichaam en structuur. Het watertype R7 staat voor de grote rivieren met een hoofdstroom en nevengeulen. Rivieren als de Rijn, Waal en IJssel zijn hier voorbeelden van. Het watertype R6 staat voor langzaam stromende kleinere rivieren. In de praktijk kunnen beide riviertypen in elkaar overgaan en is het goed mogelijk dat het visbestand een grote overlap kent, maar volgens verschillende maatlatten worden beoordeeld. Dit onderzoek heeft tot doel het inzichtelijk maken van de indeling in beide watertypes. Ook wordt er gekeken naar de verschillen tussen de watertypen R6 en R7.
    Identifying and naming plant-pathogenic fungi: past, present, and future
    Crous, P.W. ; Hawksworth, D.L. ; Wingfield, M.J. - \ 2015
    Annual Review of Phytopathology 53 (2015). - ISSN 0066-4286 - p. 247 - 267.
    molecular systematics - polyphyletic nature - polyphasic approach - mycorrhizal fungi - species concepts - taxonomy - genus - classification - identification - chromatography
    Scientific names are crucial in communicating knowledge about fungi. In plant pathology, they link information regarding the biology, host range, distribution, and potential risk. Our understanding of fungal biodiversity and fungal systematics has undergone an exponential leap, incorporating genomics, web-based systems, and DNA data for rapid identification to link species to metadata. The impact of our ability to recognize hitherto unknown organisms on plant pathology and trade is enormous and continues to grow. Major challenges for phytomycology are intertwined with the Genera of Fungi project, which adds DNA barcodes to known biodiversity and corrects the application of old, established names via epi- or neotypification. Implementing the one fungus–one name system and linking names to validated type specimens, cultures, and reference sequences will provide the foundation on which the future of plant pathology and the communication of names of plant pathogens will rest.
    NSO-typering 2015; Typering van agrarische bedrijven in Nederland
    Everdingen, W.H. van - \ 2015
    Den Haag : LEI Wageningen UR (Nota / LEI 2015-084) - 36
    landbouw bedrijven - bedrijven - bedrijfsvergelijking in de landbouw - bedrijfsvoering - opbrengsten - inkomsten uit het landbouwbedrijf - bedrijfsgrootte in de landbouw - bedrijfsgegevens - standaardisering - classificatie - agrarische economie - farming - businesses - farm comparisons - management - yields - farm income - farm size - farm accountancy data - standardization - classification - agricultural economics
    In 2014 is voor de Nederlandse variant een nieuw kengetal geïntroduceerd: de Standaard Verdiencapaciteit (SVC) van bedrijven. Dat kengetal is ontwikkeld vanwege verschillen in marge tussen de sectoren. Met de SVC is de bedrijfsgrootte van bedrijven over bedrijfstypen heen meer gerelateerd aan arbeidsinzet en resultaat dan bij de Standaardopbrengst (SO) het geval is. De classificatie is gekoppeld aan de Landbouwtelling. De normen worden berekend voor de categorieën dieren en gewassen die in de Landbouwtelling worden uitgevraagd. Het doel van dit document is inzicht verschaffen in de achtergronden, rekenschema’s, indelingen en normen die bij de typering in gebruik zijn rond de Landbouwtelling van 2015. Achtereenvolgens komen in de volgende paragrafen de Standaardopbrengst (1), de NSO-typering (2), de Standaard Verdiencapaciteit (3) en het gebruik van de gegevens (4) aan bod.
    Mapping Soil Properties of Africa at 250 m resolution: random forest significantly improve current predictions
    Hengl, T. ; Heuvelink, G.B.M. ; Kempen, B. ; Leenaars, J.G.B. ; Walsh, M.G. ; Shepherd, K.D. ; Sila, A. ; Macmillan, R.A. ; Mendes de Jesus, J.S. ; Tamene, L. ; Tondoh, J.E. - \ 2015
    PLoS ONE 10 (2015)6. - ISSN 1932-6203
    continental-scale - maps - classification - surveillance - management - models - carbon - trees
    80% of arable land in Africa has low soil fertility and suffers from physical soil problems. Additionally, significant amounts of nutrients are lost every year due to unsustainable soil management practices. This is partially the result of insufficient use of soil management knowledge. To help bridge the soil information gap in Africa, the Africa Soil Information Service (AfSIS) project was established in 2008. Over the period 2008–2014, the AfSIS project compiled two point data sets: the Africa Soil Profiles (legacy) database and the AfSIS Sentinel Site database. These data sets contain over 28 thousand sampling locations and represent the most comprehensive soil sample data sets of the African continent to date. Utilizing these point data sets in combination with a large number of covariates, we have generated a series of spatial predictions of soil properties relevant to the agricultural management—organic carbon, pH, sand, silt and clay fractions, bulk density, cation-exchange capacity, total nitrogen, exchangeable acidity, Al content and exchangeable bases (Ca, K, Mg, Na). We specifically investigate differences between two predictive approaches: random forests and linear regression. Results of 5-fold cross-validation demonstrate that the random forests algorithm consistently outperforms the linear regression algorithm, with average decreases of 15–75% in Root Mean Squared Error (RMSE) across soil properties and depths. Fitting and running random forests models takes an order of magnitude more time and the modelling success is sensitive to artifacts in the input data, but as long as quality-controlled point data are provided, an increase in soil mapping accuracy can be expected. Results also indicate that globally predicted soil classes (USDA Soil Taxonomy, especially Alfisols and Mollisols) help improve continental scale soil property mapping, and are among the most important predictors. This indicates a promising potential for transferring pedological knowledge from data rich countries to countries with limited soil data.
    A Bayesian approach to combine Landsat and ALOS PALSAR time series for near real-time deforestation detection
    Reiche, J. ; Bruin, S. de; Hoekman, D.H. ; Verbesselt, J. ; Herold, M. - \ 2015
    Remote Sensing 7 (2015). - ISSN 2072-4292 - p. 4973 - 4996.
    conditional-probability networks - remotely-sensed images - forest cover loss - tropical deforestation - brazilian amazon - accuracy assessment - classification - sar - disturbance - fusion
    To address the need for timely information on newly deforested areas at medium resolution scale, we introduce a Bayesian approach to combine SAR and optical time series for near real-time deforestation detection. Once a new image of either of the input time series is available, the conditional probability of deforestation is computed using Bayesian updating, and deforestation events are indicated. Future observations are used to update the conditional probability of deforestation and, thus, to confirm or reject an indicated deforestation event. A proof of concept was demonstrated using Landsat NDVI and ALOS PALSAR time series acquired at an evergreen forest plantation in Fiji. We emulated a near real-time scenario and assessed the deforestation detection accuracies using three-monthly reference data covering the entire study site. Spatial and temporal accuracies for the fused Landsat-PALSAR case (overall accuracy = 87.4%; mean time lag of detected deforestation = 1.3 months) were consistently higher than those of the Landsat- and PALSAR-only cases. The improvement maintained even for increasing missing data in the Landsat time series.
    Hypothesis: the sound of the individual metabolic phenotype? Acoustic detection of NMR experiments
    Cacciatore, S. ; Saccenti, E. ; Piccioli, M. - \ 2015
    OMICS - A Journal of Integrative Biology 19 (2015)3. - ISSN 1536-2310 - p. 147 - 156.
    breast-cancer - personalized medicine - disease - profiles - models - health - time - classification - identification - metabonomics
    We present here an innovative hypothesis and report preliminary evidence that the sound of NMR signals could provide an alternative to the current representation of the individual metabolic fingerprint and supply equally significant information. The NMR spectra of the urine samples provided by four healthy donors were converted into audio signals that were analyzed in two audio experiments by listeners with both musical and non-musical training. The listeners were first asked to cluster the audio signals of two donors on the basis of perceived similarity and then to classify unknown samples after having listened to a set of reference signals. In the clustering experiment, the probability of obtaining the same results by pure chance was 7.04% and 0.05% for non-musicians and musicians, respectively. In the classification experiment, musicians scored 84% accuracy which compared favorably with the 100% accuracy attained by sophisticated pattern recognition methods. The results were further validated and confirmed by analyzing the NMR metabolic profiles belonging to two other different donors. These findings support our hypothesis that the uniqueness of the metabolic phenotype is preserved even when reproduced as audio signal and warrants further consideration and testing in larger study samples
    Remote sensing of epibenhtic shellfish using synthetic aperture radar satellite imagery
    Nieuwhof, S. ; Herman, P.M.J. ; Dankers, N.M.J.A. ; Troost, K. ; Wal, D. van der - \ 2015
    Remote Sensing 7 (2015)4. - ISSN 2072-4292 - p. 3710 - 3734.
    bare soil surfaces - mussel beds - wadden sea - ecosystem engineers - intertidal flats - tidal flats - sar data - roughness - classification - moisture
    On intertidal mudflats, reef-building shellfish, like the Pacific oyster and the blue mussel, provide a myriad of ecosystem services. Monitoring intertidal shellfish with high spatiotemporal resolution is important for fisheries, coastal management and ecosystem studies. Here, we explore the potential of X- (TerraSAR-X) and C-band (Radarsat-2) dual-polarized SAR data to map shellfish densities, species and coverage. We investigated two backscatter models (the integral equation model (IEM) and Oh’s model) for inversion possibilities. Surface roughness (vertical roughness RMSz and correlation length L) was measured of bare sediments and shellfish beds, which was then linked to shellfish density, presence and species. Oysters, mussels and bare sediments differed in RMSz, but because the backscatter saturates at relatively low RMSz values, it was not possible to retrieve shellfish density or species composition from X- and C-band SAR. Using a classification based on univariate and multivariate logistic regression of the field and SAR image data, we constructed maps of shellfish presence (Kappa statistics for calibration 0.56–0.74 for dual-polarized SAR), which were compared with independent field surveys of the contours of the beds (Kappa statistics of agreement 0.29–0.53 when using dual-polarized SAR). We conclude that spaceborne SAR allows one to monitor the contours of shellfish-beds (thus, distinguishing shellfish substrates from bare sediment and dispersed single shellfish), but not densities and species. Although spaceborne SAR cannot replace ground surveys entirely, it could very well offer a significant improvement in efficiency.
    Discrimination of Polish unifloral honeys using overall PTR-MS and HPLC fingerprints combined with chemometrics
    Kus, P.M. ; Ruth, S.M. van - \ 2015
    Food Science and Technology = Lebensmittel-Wissenschaft und Technologie 62 (2015)1. - ISSN 0023-6438 - p. 69 - 75.
    reaction-mass spectrometry - origin determination - botanical origin - electronic nose - floral markers - l. honey - volatile - classification - identification - flavonoids
    A total of 62 honey samples of six floral origins (rapeseed, lime, heather, cornflower, buckwheat and black locust) were analysed by means of proton transfer reaction mass spectrometry (PTR-MS) and HPLC-DAD. The data were evaluated by principal component analysis and k-nearest neighbours classification in order to examine consistent differences in analytical fingerprints between various honeys allowing their discrimination. The study revealed, that both techniques were able to distinguish the floral origins, however the HPLC shows advantage over PTR-MS providing substantially better differentiation of all analysed honey types. Especially HPLC fingerprints recorded at 210 nm were most suitable for discrimination of botanical origin with the use of chemometric analysis. The obtained classification rates were: 100%, 93%, 100%, 83%, 100%, 100% (HPLC) and 69%, 67%, 78%, 67%, 100%, 88% (PTR-MS) for rapeseed, lime, heather, cornflower, buckwheat and black locust, respectively. Even if performance of PTR-MS in general was lower than HPLC, it might be useful for fast on-line screening of buckwheat honey.
    Multi-model radiometric slope correction of SAR images of complex terrain using a two-stage semi-empirical approach
    Hoekman, D.H. ; Reiche, J. - \ 2015
    Remote Sensing of Environment 156 (2015). - ISSN 0034-4257 - p. 1 - 10.
    radar imagery - topography - forest - classification - backscatter - validation
    Practical approaches for the implementation of terrain type dependent radiometric slope correction for SAR data are introduced. Radiometric slope effects are modelled as the products of two models. The first is a simple physical model based on the assumption of a uniform opaque layer of isotropic scatterers, which is independent of terrain type, frequency and polarization. It accounts for the slope-induced variation in the number of scatterers per resolution cell. The second is a semi-empirical model, which accounts for the variation in scattering mechanisms, dependent on terrain type, frequency and polarization. PALSAR FBD (L-band, HH- and HV-polarization) data are used at two test sites in Brazil and Fiji. Results for the Brazilian area, which has slopes up to 25°, show that remaining slope effects for the multi-model case are much smaller than 0.1 dB, for all land cover types. This is much better than the best single-model approach where remaining slope effects can be very small for forests but be as large as 1.77 dB for woodland in HH-polarization. Results for the Fiji area, which has different vegetation types, are very similar. The potential large improvement, using this multi-model approach, in the accuracy of biomass estimation for transparent or open canopies is discussed. It is also shown that biomass change on slopes can be systematically under- or overestimated because of associated change in scattering mechanism.
    Fusing Landsat and SAR time series to detect deforestation in the tropics
    Reiche, J. ; Verbesselt, J. ; Hoekman, D.H. ; Herold, M. - \ 2015
    Remote Sensing of Environment 156 (2015). - ISSN 0034-4257 - p. 276 - 293.
    forest cover loss - alos palsar data - operational performance - accuracy assessment - multiscale texture - brazilian amazonia - missing data - jers-1 sar - satellite - classification
    Fusion of optical and SAR time series imagery has the potential to improve forest monitoring in tropical regions, where cloud cover limits optical satellite time series observations. We present a novel pixel-based Multi-sensor Time-series correlation and Fusion approach (MulTiFuse) that exploits the full observation density of optical and SAR time series. We model the relationship of two overlapping univariate time series using an optimized weighted correlation. The resulting optimized regression model is used to predict and fuse two time series. Using the MulTiFuse approach we fused Landsat NDVI and ALOS PALSAR L-band backscatter time series. We subsequently used the fused time series in a multi-sensor change detection framework to detect deforestation between 01/2008 - 09/2010 at a managed forest plantation in the tropics (Pinus caribea; 2859 ha). 3-monthly reference data covering the entire study area was used to validate and assess spatial and temporal accuracy. We tested the impact of persistent cloud cover by increasing the per-pixel missing data percentage of the NDVI time series stepwise from ~ 53% (~ 6 observations/year) up to 95% (~ 0.5 observation/year) while fusing with a consistent PALSAR time series of ~ 2 observations/year. A significant linear correlation was found between the Landsat NDVI and ALOS PALSAR L-band SAR time series observables for logged forest. The multi-temporal filtered PALSAR HVHH backscatter ratio time series (HVHHmt) was most strongly correlated with the NDVI time series. While for Landsat-only the spatial and temporal accuracy of detected deforestation decreased significantly with increasing missing data, the accuracies for the fused NDVI-PALSAR case remained high and were observed to be above the NDVI- and PALSAR-only cases for all missing data percentages. For the fused NDVI-HVHHmt time series the overall accuracy was 95.5% with a 1.59 month mean time lag of detected changes. The MulTiFuse approach is robust and automated, and it provides the opportunity to use the upcoming data streams of free-of charge, medium resolution optical and SAR satellite imagery in a beneficial way for improved tropical forest monitoring.
    Non-linear low-rank and sparse representation for hyperspectral image analysis
    Morsier, Frank De; Tuia, Devis ; Borgeaucft, Maurice ; Gass, Volker ; Thiran, Jean Philippe - \ 2014
    In: International Geoscience and Remote Sensing Symposium (IGARSS). - Institute of Electrical and Electronics Engineers Inc. (International Geoscience and Remote Sensing Symposium (IGARSS) ) - ISBN 9781479957750 - p. 4648 - 4651.
    classification - kernel - low-rank - manifold clustering - sparse - unsupervised

    In this paper, we tackle the problem of unsupervised classification of hyperspectral images. We propose a clustering method based on graphs representing the data structure, which is assumed to be an union of multiple manifolds. The method constraints the pixels to be expressed as a low-rank and sparse combination of the others in a reproducing kernel Hilbert spaces (RKHS). This captures the global (low-rank) and local (sparse) structures. Spectral clustering is applied on the graph to assign the pixels to the different manifolds. A large scale approach is proposed, in which the optimization is first performed on a subset of the data and then it is applied to the whole image using a non-linear collaborative representation respecting the manifolds structure. Experiments on two hyperspectral images show very good unsupervised classification results compared to competitive approaches.

    Importance of bistatic SAR features from TanDEM-X for forest mapping and monitoring
    Schlund, M. ; Poncet, F. von; Hoekman, D.H. ; Kuntz, S. ; Schmullius, C. - \ 2014
    Remote Sensing of Environment 151 (2014)sp. issue. - ISSN 0034-4257 - p. 16 - 26.
    land-cover - southeast-asia - feature-selection - polarimetric sar - tropical-forest - decision tree - alos palsar - rain-forest - sir-c - classification
    Deforestation and forest degradation are one of the important sources for human induced carbon dioxide emissions and their rates are highest in tropical forests. For man-kind, it is of great importance to track land-use conversions like deforestation, e.g. for sustainable forest management and land use planning, for carbon balancing and to support the implementation of international initiatives like REDD + (Reducing Emissions from Deforestation and Degradation). SAR (synthetic aperture radar) sensors are suitable to reliably and frequently monitor tropical forests due to their weather independence. The TanDEM-X mission (which is mainly aimed to create a unique global high resolution digital elevation model) currently operates two X-band SAR satellites, acquiring interferometric SAR data for the Earth's entire land surface multiple times. The operational mission provides interferometric data as well as mono- and bistatic scattering coefficients. These datasets are homogenous, globally consistent and are acquired in high spatial resolution. Hence, they may offer a unique basic dataset which could be useful in land cover monitoring. Based on first datasets available from the TanDEM-X mission, the main goal of this research is to investigate the information content of TanDEM-X data for mapping forests and other land cover classes in a tropical peatland area. More specifically, the study explores the utility of bistatic features for distinguishing between open and closed forest canopies, which is of relevance in the context of deforestation and forest degradation monitoring. To assess the predominant information content of TanDEM-X data, the importance of information derived from the bistatic system is compared against the monostatic case, usually available from SAR systems. The usefulness of the TanDEM-X mission data, i.e. scattering coefficients, derived textural information and interferometric coherence is investigated via a feature selection process. The resulting optimal feature sets representing a monostatic and a bistatic SAR dataset were used in a subsequent classification to assess the added value of the bistatic TanDEM-X features in the separability of land cover classes. The results obtained indicated that especially the interferometric coherence significantly improved the separability of thematic classes compared to a dataset of monostatic acquisition. The bistatic coherence was mainly governed by volume decorrelation of forest canopy constituents and carries information about the canopy structure which is related to canopy cover. In contrast, the bistatic scattering coefficient had no significant contribution to class separability. The classification with coherence and textural information outperformed the classification with the monostatic scattering coefficient and texture by more than 10% and achieved an overall accuracy of 85%. These results indicate that TanDEM-X can serve as a valuable and consistent source for mapping and monitoring tropical forests.
    Do Current European Policies Prevent Soil Threats and Support Soil Functions?
    Glaesner, N. ; Helming, K. ; Vries, W. de - \ 2014
    Sustainability 6 (2014)12. - ISSN 2071-1050 - p. 9538 - 9563.
    ecosystem services - sustainable intensification - management - agriculture - protection - framework - quality - carbon - classification - conservation
    There is currently no legislation at the European level that focuses exclusively on soil conservation. A cross-policy analysis was carried out to identify gaps and overlaps in existing EU legislation that is related to soil threats and functions. We found that three soil threats, namely compaction, salinization and soil sealing, were not addressed in any of the 19 legislative policies that were analyzed. Other soil threats, such as erosion, decline in organic matter, loss of biodiversity and contamination, were covered in existing legislation, but only a few directives provided targets for reducing the soil threats. Existing legislation addresses the reduction of the seven soil functions that were analyzed, but there are very few directives for improving soil functions. Because soil degradation is ongoing in Europe, it raises the question whether existing legislation is sufficient for maintaining soil resources. Addressing soil functions individually in various directives fails to account for the multifunctionality of soil. This paper suggests that a European Soil Framework Directive would increase the effectiveness of conserving soil functions in the EU.
    Agroforestry solutions to address climate change and food security challenges in Africa
    Mbow, C. ; Neufeldt, H. ; Noordwijk, M. van; Minang, P.A. ; Kowero, G. ; Luedeling, E. - \ 2014
    Current Opinion in Environmental Sustainability 6 (2014). - ISSN 1877-3435 - p. 61 - 67.
    sub-saharan africa - forest degradation - land degradation - climate-change - west-africa - agriculture - systems - intensification - classification - security
    Trees inside and outside forests contribute to food security in Africa in the face of climate variability and change. They also provide environmental and social benefits as part of farming livelihoods. Varied ecological and socio-economic conditions have given rise to specific forms of agroforestry in different parts of Africa. Policies that institutionally segregate forest from agriculture miss opportunities for synergy at landscape scale. More explicit inclusion of agroforestry and the integration of agriculture and forestry agendas in global initiatives on climate change adaptation and mitigation can increase their effectiveness. We identify research gaps and overarching research questions for the contributions in this special issue that may help shape current opinion in environmental sustainability.
    Harmonisatie diercategorieën
    Groenestein, C.M. ; Bruggen, C. van; Luesink, H.H. - \ 2014
    Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-technical report 16) - 36
    vee - classificatie - stikstof - fosfor - dierlijke meststoffen - wetgeving - nederland - rundvee - varkens - pluimvee - schapen - geiten - paarden - ezels - livestock - classification - nitrogen - phosphorus - animal manures - legislation - netherlands - cattle - pigs - poultry - sheep - goats - horses - donkeys
    Voor wettelijke regelingen, tellingen en monitoringstudies worden in Nederland verschillende indelingen gebruikt voor landbouwhuisdieren. Dat leidt soms tot verwarring en is inefficiënt, vooral omdat gegevens niet eenvoudig uitgewisseld kunnen worden en er aparte bestanden beheerd moeten worden. Op verzoek van het ministerie van Economische Zaken heeft de Commissie van Deskundigen Meststoffenwet (CDM) een voorstel gemaakt voor een geharmoniseerde en vereenvoudigde indeling van diercategorieën, vooral voor de Uitvoeringsregeling Meststoffenwet. In het voorstel is de huidige indeling van diercategorieën van de Landbouwtelling en de Farm Structure Survey (FSS) van de Europese Commissie als uitgangspunt genomen. In totaal zijn 117 diercategorieën verdeeld over zeven hoofdcategorieën onder de loep genomen. Per hoofdcategorie is een nieuwe, vereenvoudigde indeling voorgesteld. Het resultaat is een voorstel met 60 diercategorieën van in Nederland gehouden landbouwhuisdieren. Het aantal hoofdcategorieën (7) is gelijk gebleven, maar het aantal subcategorieën is fors verminderd. De grootste veranderingen worden voorgesteld bij varkens, van de oorspronkelijke tien categorieën blijven er zes over
    A fully traits-based approach to modeling global vegetation distribution
    Bodegom, P.M. van; Douma, J.C. ; Verheijen, L.M. - \ 2014
    Proceedings of the National Academy of Sciences of the United States of America 111 (2014)38. - ISSN 0027-8424 - p. 13733 - 13738.
    earth system model - climate-change - plant traits - economics spectrum - functional traits - amazonian forest - photosynthesis - classification - co2 - acclimation
    Dynamic Global Vegetation Models (DGVMs) are indispensable for our understanding of climate change impacts. The application of traits in DGVMs is increasingly refined. However, a comprehensive analysis of the direct impacts of trait variation on global vegetation distribution does not yet exist. Here, we present such analysis as proof of principle. We run regressions of trait observations for leaf mass per area, stem-specific density, and seed mass from a global database against multiple environmental drivers, making use of findings of global trait convergence. This analysis explained up to 52% of the global variation of traits. Global trait maps, generated by coupling the regression equations to gridded soil and climate maps, showed up to orders of magnitude variation in trait values. Subsequently, nine vegetation types were characterized by the trait combinations that they possess using Gaussian mixture density functions. The trait maps were input to these functions to determine global occurrence probabilities for each vegetation type. We prepared vegetation maps, assuming that the most probable (and thus, most suited) vegetation type at each location will be realized. This fully traits-based vegetation map predicted 42% of the observed vegetation distribution correctly. Our results indicate that a major proportion of the predictive ability of DGVMs with respect to vegetation distribution can be attained by three traits alone if traits like stem-specific density and seed mass are included. We envision that our traits-based approach, our observation-driven trait maps, and our vegetation maps may inspire a new generation of powerful traits-based DGVMs.
    Effects of selective digestive decontamination (SDD) on the gut resistome
    Buelow, E. ; Bello Gonzalez, T.D.G. ; Versluis, D. ; Oostdijk, E.A.N. ; Ogilvie, L.A. ; Mourik, M.S.M. van; Oosterink, L. ; Passel, M.W.J. van; Smidt, H. ; D’Andrea, M.M. ; Been, M. de; Jones, B.V. ; Willems, R.J.L. ; Bonten, M.J.M. ; Schaik, W. - \ 2014
    Journal of Antimicrobial Chemotherapy 69 (2014)8. - ISSN 0305-7453 - p. 2215 - 2223.
    intensive-care units - antimicrobial resistance - microbiota - tract - microarray - metagenome - sequences - bacterial - classification - generation
    Objectives Selective digestive decontamination (SDD) is an infection prevention measure for critically ill patients in intensive care units (ICUs) that aims to eradicate opportunistic pathogens from the oropharynx and intestines, while sparing the anaerobic flora, by the application of non-absorbable antibiotics. Selection for antibiotic-resistant bacteria is still a major concern for SDD. We therefore studied the impact of SDD on the reservoir of antibiotic resistance genes (i.e. the resistome) by culture-independent approaches. Methods We evaluated the impact of SDD on the gut microbiota and resistome in a single ICU patient during and after an ICU stay by several metagenomic approaches. We also determined by quantitative PCR the relative abundance of two common aminoglycoside resistance genes in longitudinally collected samples from 12 additional ICU patients who received SDD. Results The patient microbiota was highly dynamic during the hospital stay. The abundance of antibiotic resistance genes more than doubled during SDD use, mainly due to a 6.7-fold increase in aminoglycoside resistance genes, in particular aph(2¿)-Ib and an aadE-like gene. We show that aph(2¿)-Ib is harboured by anaerobic gut commensals and is associated with mobile genetic elements. In longitudinal samples of 12 ICU patients, the dynamics of these two genes ranged from a ~104 fold increase to a ~10-10 fold decrease in relative abundance during SDD. Conclusions ICU hospitalization and the simultaneous application of SDD has large, but highly individualized, effects on the gut resistome of ICU patients. Selection for transferable antibiotic resistance genes in anaerobic commensal bacteria could impact the risk of transfer of antibiotic resistance genes to opportunistic pathogens.
    Influence of setup and carbon source on the bacterial community of biocathodes in microbial electrolysis cells
    Croesea, E. ; Jeremiasse, A.W. ; Marshall, I.P.G. ; Spormann, A.M. ; Euverink, G.J.W. ; Geelhoed, J.S. ; Stams, A.J.M. ; Plugge, C.M. - \ 2014
    Enzyme and Microbial Technology 61-62 (2014). - ISSN 0141-0229 - p. 67 - 75.
    hydrogen-production - fuel-cells - desulfovibrio-vulgaris - sp-nov. - sequence data - gen. nov. - diversity - system - classification - acetate
    The microbial electrolysis cell (MEC) biocathode has shown great potential as alternative for expensive metals as catalyst for H2 synthesis. Here, the bacterial communities at the biocathode of five hydrogen producing MECs using molecular techniques were characterized. The setups differed in design (large versus small) including electrode material and flow path and in carbon source provided at the cathode (bicarbonate or acetate). A hydrogenase gene-based DNA microarray (Hydrogenase Chip) was used to analyze hydrogenase genes present in the three large setups. The small setups showed dominant groups of Firmicutes and two of the large setups showed dominant groups of Proteobacteria and Bacteroidetes. The third large setup received acetate but no sulfate (no sulfur source). In this setup an almost pure culture of a Promicromonospora sp. developed. Most of the hydrogenase genes detected were coding for bidirectional Hox-type hydrogenases, which have shown to be involved in cytoplasmatic H2 production.
    A Unimodal Species Response Model Relating Traits to Environment with Application to Phytoplankton Communities.
    Jamil, T. ; Kruk, C. ; Braak, C.J.F. ter - \ 2014
    PLoS ONE 9 (2014)5. - ISSN 1932-6203 - 14 p.
    bayesian variable selection - climate-change - ecology - lake - variability - strategies - diversity - habitat - classification - regression
    In this paper we attempt to explain observed niche differences among species (i.e. differences in their distribution along environmental gradients) by differences in trait values (e.g. volume) in phytoplankton communities. For this, we propose the trait-modulated Gaussian logistic model in which the niche parameters (optimum, tolerance and maximum) are made linearly dependent on species traits. The model is fitted to data in the Bayesian framework using OpenBUGS (Bayesian inference Using Gibbs Sampling) to identify according to which environmental variables there is niche differentiation among species and traits. We illustrate the method with phytoplankton community data of 203 lakes located within four climate zones and associated measurements on 11 environmental variables and six morphological species traits of 60 species. Temperature and chlorophyll-a (with opposite signs) described well the niche structure of all species. Results showed that about 25% of the variance in the niche centres with respect to chlorophyll-a were accounted for by traits, whereas niche width and maximum could not be predicted by traits. Volume, mucilage, flagella and siliceous exoskeleton are found to be the most important traits to explain the niche centres. Species were clustered in two groups with different niches structures, group 1 high temperature-low chlorophyll-a species and group 2 low temperature-high chlorophyll-a species. Compared to group 2, species in group 1 had larger volume but lower surface area, had more often flagella but neither mucilage nor siliceous exoskeleton. These results might help in understanding the effect of environmental changes on phytoplankton community. The proposed method, therefore, can also apply to other aquatic or terrestrial communities for which individual traits and environmental conditioning factors are available.
    Biogeographic patterns of base-rich fen vegetation across Europe
    Jiménez-Alfaro, B. ; Hájek, M. ; Ejrnaes, R. ; Rodwell, J. ; Pawlikowski, P. ; Weeda, E.J. - \ 2014
    Applied Vegetation Science 17 (2014)2. - ISSN 1402-2001 - p. 367 - 380.
    environmental gradients - ecological gradients - plant associations - vascular plants - temperate zone - plot size - north - classification - mires - water
    Questions What is the distribution of base-rich fen vegetation and the specialist species along European biogeographic regions? How do the gradients in species composition correlate to geography and climate at continental scale? What are the implications of such patterns for the classification of these habitats? Location Fifteen countries of Central, Western and Northern Europe. Methods We compiled a vegetation plot database of base-rich fens and related communities including vascular plants and bryophytes. The initial data set with 6943 plots was filtered according to the presence of specialists using discriminant analysis. We used DCA to analyse the correlation of species composition with geography and climate, and kriging interpolation for mapping gradients in the study area. Modified TWINSPAN was used to detect major vegetation groups. The results of the whole data set (plot size 1–100 m2) were compared with those obtained from two subsets with plots of 1–5 m2 and 6–30 m2. Results Most of the specialists were distributed among all the biogeographic regions, but many were more represented in the Alpine than in the Atlantic, Boreal and Continental regions. Variation in species composition was mainly correlated to temperature, precipitation and latitude in the three data sets, showing a major gradient from (1) alpine belt fens characterized by spring species to (2) small sedge fens mainly distributed in mountain regions and (3) boreo-temperate fens reflecting waterlogged conditions. Conclusions Base-rich fen communities are widely distributed across European biogeographic regions, but the Alpine region can be considered as the compositional centre of this vegetation type. Large-scale gradients of species composition are mainly explained by climate, while the influence of latitude is probably correlated to increasing water table in the boreo-temperate regions. These gradients can be better understood by differentiating three major vegetation types, which should be considered when establishing classification systems of base-rich fens in Europe.
    Fusion of pan-tropical biomass maps using weighted averaging and regional calibration data
    Ge, Y. ; Avitabile, V. ; Heuvelink, G.B.M. ; Wang, J. ; Herold, M. - \ 2014
    International Journal of applied Earth Observation and Geoinformation 31 (2014). - ISSN 0303-2434 - p. 13 - 24.
    remotely-sensed imagery - land-cover datasets - multisensor data - forest biomass - carbon-dioxide - sensing data - soil maps - classification - deforestation - validation
    Biomass is a key environmental variable that influences many biosphere–atmosphere interactions. Recently, a number of biomass maps at national, regional and global scales have been produced using different approaches with a variety of input data, such as from field observations, remotely sensed imagery and other spatial datasets. However, the accuracy of these maps varies regionally and is largely unknown. This research proposes a fusion method to increase the accuracy of regional biomass estimates by using higher-quality calibration data. In this fusion method, the biases in the source maps were first adjusted to correct for over- and underestimation by comparison with the calibration data. Next, the biomass maps were combined linearly using weights derived from the variance–covariance matrix associated with the accuracies of the source maps. Because each map may have different biases and accuracies for different land use types, the biases and fusion weights were computed for each of the main land cover types separately. The conceptual arguments are substantiated by a case study conducted in East Africa. Evaluation analysis shows that fusing multiple source biomass maps may produce a more accurate map than when only one biomass map or unweighted averaging is used.
    Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans
    Visser, M. ; Parshina, S.N. ; Alves, J.I. ; Sousa, D.Z. ; Pereira, I.A.C. ; Muyzer, G. ; Kuever, J. ; Lebedinsky, A.V. ; Koehorst, J.J. ; Worm, P. ; Plugge, C.M. ; Schaap, P.J. ; Goodwin, L.A. ; Lapidus, A. ; Kyrpides, N.C. ; Detter, J.C. ; Woyke, T. ; Chain, P. ; Davenport, K.W. ; Spring, S. ; Rohde, M. ; Klenk, H.P. ; Stams, A.J.M. - \ 2014
    Standards in Genomic Sciences 9 (2014)3. - ISSN 1944-3277 - p. 655 - 675.
    reducing bacterium - sp nov. - sequence - growth - classification - hydrogenase - evolution - standard - archaea - system
    Desulfotomaculum nigrificans and D. carboxydivorans are moderately thermophilic members of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. They are phylogenetically very closely related and belong to ‘subgroup a’ of the Desulfotomaculum cluster 1. D. nigrificans and D. carboxydivorans have a similar growth substrate spectrum; they can grow with glucose and fructose as electron donors in the presence of sulfate. Additionally, both species are able to ferment fructose, although fermentation of glucose is only reported for D. carboxydivorans. D. nigrificans is able to grow with 20% carbon monoxide (CO) coupled to sulfate reduction, while D. carboxydivorans can grow at 100% CO with and without sulfate. Hydrogen is produced during growth with CO by D. carboxydivorans. Here we present a summary of the features of D. nigrificans and D. carboxydivorans together with the description of the complete genome sequencing and annotation of both strains. Moreover, we compared the genomes of both strains to reveal their differences. This comparison led us to propose a reclassification of D. carboxydivorans as a later heterotypic synonym of D. nigrificans
    Ecosystem Services as a Contested Concept: A Synthesis of Critique and Counter-arguments
    Schröter, M. ; Zanden, E.H. van der; Oudenhoven, A.P.E. van; Remme, R.P. ; Serna-Chavez, H.M. ; Groot, R.S. de; Opdam, P. - \ 2014
    Conservation Letters 7 (2014)6. - ISSN 1755-263X - p. 514 - 523.
    sustainability research - saving nature - biodiversity - conservation - science - policy - benefits - classification - agriculture - valuation
    We describe and reflect on seven recurring critiques of the concept of ecosystem services and respective counter-arguments. First, the concept is criticized for being anthropocentric while others argue that it goes beyond instrumental values. Second, some argue that the concept promotes an exploitative human-nature relationship, while others state that it re-connects society to ecosystems, emphasizing humanity's dependence on nature. Third, concerns exist that the concept may conflict with biodiversity conservation objectives while others emphasize complementarity. Fourth, the concept is questioned because of its supposed focus on economic valuation, while others argue that ecosystem services science includes many values. Fifth, the concept is criticized for promoting commodification of nature, while others point out that most ecosystem services are not connected to market-based instruments. Sixth, vagueness of definitions and classifications are stated to be a weakness, while others argue that vagueness enhances transdisciplinary collaboration. Seventh, some criticize the normative nature of the concept implying that all outcomes of ecosystem processes are desirable. The normative nature is indeed typical for the concept, but should not be problematic when acknowledged. By disentangling and contrasting different arguments we hope to contribute to a more structured debate between opponents and proponents of the ecosystem services concept.
    Mapping a priori defined plant associations using remotely sensed vegetation characteristics
    Roelofsen, H.D. ; Kooistra, L. ; Bodegom, P.M. van; Verrelst, J. ; Krol, J. ; Witte, J.M.P. - \ 2014
    Remote Sensing of Environment 140 (2014). - ISSN 0034-4257 - p. 639 - 651.
    ellenberg indicator values - continuous floristic gradients - hyperspectral imagery - imaging spectroscopy - endmember selection - tropical forests - aviris data - classification - regression - moisture
    Incorporation of a priori defined plant associations into remote sensing products is a major challenge that has only recently been confronted by the remote sensing community. We present an approach to map the spatial distribution of such associations by using plant indicator values (IVs) for salinity, moisture and nutrients as an intermediate between spectral reflectance and association occurrences. For a 12 km2 study site in the Netherlands, the relations between observed IVs at local vegetation plots and visible and near-infrared (VNIR) and short-wave infrared (SWIR) airborne reflectance data were modelled using Gaussian Process Regression (GPR) (R2 0.73, 0.64 and 0.76 for salinity, moisture and nutrients, respectively). These relations were applied to map IVs for the complete study site. Association occurrence probabilities were modelled as function of IVs using a large database of vegetation plots with known association and IVs. Using the mapped IVs, we calculated occurrence probabilities of 19 associations for each pixel, resulting in both a crisp association map with the most likely occurring association per pixel, as well as occurrence probability maps per association. Association occurrence predictions were assessed by a local vegetation expert, which revealed that the occurrences of associations situated at frequently predicted indicator value combinations were over predicted. This seems primarily due to biases in the GPR predicted IVs, resulting in associations with envelopes located in extreme ends of IVs being scarcely predicted. Although the results of this particular study were not fully satisfactory, the method potentially offers several advantages compared to current vegetation classification techniques, like site-independent calibration of association probabilities, site-independent selection of associations and the provision of IV maps and occurrence probabilities per association. If the prediction of IVs can be improved, this method may thus provide a viable roadmap to bring a priori defined plant associations into the domain of remote sensing.
    Accounting for capacity and flow of ecosystem services: A conceptual model and a case study for Telemark, Norway
    Schroter, M. ; Barton, D.N. ; Remme, R.P. ; Hein, L.G. - \ 2014
    Ecological Indicators 36 (2014). - ISSN 1470-160X - p. 539 - 551.
    supply-and-demand - decision-making - framework - classification - indicators - scales - land - sustainability - management - valuation
    Understanding the flow of ecosystem services and the capacity of ecosystems to generate these services is an essential element for understanding the sustainability of ecosystem use as well as developing ecosystem accounts. We conduct spatially explicit analyses of nine ecosystem services in Telemark County, Southern Norway. The ecosystem services included are moose hunting, sheep grazing, timber harvest, forest carbon sequestration and storage, snow slide prevention, recreational residential amenity, recreational hiking and existence of areas without technical interference. We conceptually distinguish capacity to provide ecosystem services from the actual flow of services, and empirically assess both. This is done by means of different spatial models, developed with various available datasets and methods, including (multiple layer) look-up tables, causal relations between datasets (including satellite images), environmental regression and indicators derived from direct measurements. Capacity and flow differ both in spatial extent and in quantities. We discuss five conditions for a meaningful spatial capacity–flow-balance. These are (1) a conceptual difference between capacity and flow, (2) spatial explicitness of capacity and flow, (3) the same spatial extent of both, (4) rivalry or congestion, and (5) measurement with aligned indicators. We exemplify spatially explicit balances between capacity and flow for two services, which meet these five conditions. Research in the emerging field of mapping ES should focus on the development of compatible indicators for capacity and flow. The distinction of capacity and flow of ecosystem services provides a parsimonious estimation of over- or underuse of the respective service. Assessment of capacity and flow in a spatially explicit way can thus support monitoring sustainability of ecosystem use, which is an essential element of ecosystem accounting.
    Active learning: Any value for classification of remotely sensed data?
    Crawford, Melba M. ; Tuia, Devis ; Yang, Hsiuhan Lexie - \ 2013
    Proceedings of the IEEE 101 (2013)3. - ISSN 0018-9219 - p. 593 - 608.
    Active learning - adaptation - classification - high-resolution multispectral - hyperspectral - multiview - spatial learning - support vector machines (SVMs)

    Active learning, which has a strong impact on processing data prior to the classification phase, is an active research area within the machine learning community, and is now being extended for remote sensing applications. To be effective, classification must rely on the most informative pixels, while the training set should be as compact as possible. Active learning heuristics provide capability to select unlabeled data that are the 'most informative' and to obtain the respective labels, contributing to both goals. Characteristics of remotely sensed image data provide both challenges and opportunities to exploit the potential advantages of active learning. We present an overview of active learning methods, then review the latest techniques proposed to cope with the problem of interactive sampling of training pixels for classification of remotely sensed data with support vector machines (SVMs). We discuss remote sensing specific approaches dealing with multisource and spatially and time-varying data, and provide examples for high-dimensional hyperspectral imagery.

    Phylogeny and systematics of Demospongiae in light of new small-subunit ribosomal DNA (18S) sequences
    Redmond, N.E. ; Morrow, C. ; Thacker, R.W. ; Diaz, M.C. ; Boury-Esnaul, N. ; Cardenas, P.D. ; Hajdu, E. ; Lobo-Hajdu, G. ; Picton, B.E. ; Pomponi, S.A. ; Kayal, E. ; Collins, A.G. - \ 2013
    Integrative and Comparative Biology 53 (2013)3. - ISSN 1540-7063 - p. 388 - 415.
    glass sponges porifera - phylum porifera - molecular phylogeny - animal phylogeny - gene-sequences - fossil record - evolution - hexactinellida - classification - verongida
    The most diverse and species-rich class of the phylum Porifera is Demospongiae. In recent years, the systematics of this clade, which contains more than 7000 species, has developed rapidly in light of new studies combining molecular and morphological observations. We add more than 500 new, nearly complete 18S sequences (an increase of more than 200%) in an attempt to further enhance understanding of the phylogeny of Demospongiae. Our study specifically targets representation of type species and genera that have never been sampled for any molecular data in an effort to accelerate progress in classifying this diverse lineage. Our analyses recover four highly supported subclasses of Demospongiae: Keratosa, Myxospongiae, Haploscleromorpha, and Heteroscleromorpha. Within Keratosa, neither Dendroceratida, nor its two families, Darwinellidae and Dictyodendrillidae, are monophyletic and Dictyoceratida is divided into two lineages, one predominantly composed of Dysideidae and the second containing the remaining families (Irciniidae, Spongiidae, Thorectidae, and Verticillitidae). Within Myxospongiae, we find Chondrosida to be paraphyletic with respect to the Verongida. We amend the latter to include species of the genus Chondrosia and erect a new order Chondrillida to contain remaining taxa from Chondrosida, which we now discard. Even with increased taxon sampling of Haploscleromorpha, our analyses are consistent with previous studies; however, Haliclona species are interspersed in even more clades. Haploscleromorpha contains five highly supported clades, each more diverse than previously recognized, and current families are mostly polyphyletic. In addition, we reassign Janulum spinispiculum to Haploscleromorpha and resurrect Reniera filholi as Janulum filholi comb. nov. Within the large clade Heteroscleromorpha, we confirmed 12 recently identified clades based on alternative data, as well as a sister-group relationship between the freshwater Spongillida and the family Vetulinidae. We transfer Stylissa flabelliformis to the genus Scopalina within the family Scopalinidae, which is of uncertain position. Our analyses uncover a large, strongly supported clade containing all heteroscleromorphs other than Spongillida, Vetulinidae, and Scopalinidae. Within this clade, there is a major division separating Axinellidae, Biemnida, Tetractinellida, Bubaridae, Stelligeridae, Raspailiidae, and some species of Petromica, Topsentia, and Axinyssa from Agelasida, Polymastiidae, Placospongiidae, Clionaidae, Spirastrellidae, Tethyidae, Poecilosclerida, Halichondriidae, Suberitidae, and Trachycladus. Among numerous results: (1) Spirophorina and its family Tetillidae are paraphyletic with respect to a strongly supported Astrophorina within Tetractinellida; (2) Agelasida is the earliest diverging lineage within the second clade listed above; and (3) Merlia and Desmacella appear to be the earliest diverging lineages of Poecilosclerida.
    Segmentation of Rumex obtusifolius using Gaussian Markov random fields
    Atni Hiremath, S. ; Tolpekin, V.A. ; Heijden, G. van der; Stein, A. - \ 2013
    Machine Vision Applications 24 (2013)4. - ISSN 0932-8092 - p. 845 - 854.
    energy minimization - texture features - weed-control - graph cuts - classification - systems - imagery - vision
    Rumex obtusifolius is a common weed that is difficult to control. The most common way to control weeds-using herbicides-is being reconsidered because of its adverse environmental impact. Robotic systems are regarded as a viable non-chemical alternative for treating R. obtusifolius and also other weeds. Among the existing systems for weed control, only a few are applicable in real-time and operate in a controlled environment. In this study, we develop a new algorithm for segmentation of R. obtusifolius using texture features based on Markov random fields that works in real-time under natural lighting conditions. We show its performance by comparing it with an existing real-time algorithm that uses spectral power as texture feature. We show that the new algorithm is not only accurate with detection rate of 97.8 % and average error of 56 mm in estimating the location of the tap-root of the plant, but is also fast taking just 0.18 s to process an image of size pixels making it feasible for real-time applications.
    Long-Term Physical Functioning and Its Association With Somatic Comorbidity and Comorbid Depression in Patients With Established Rheumatoid Arthritis: A Longitudinal Study
    Hoek, J. ; Roorda, L.D. ; Boshuizen, H.C. ; Hees, J. van; Rupp, I. ; Tijhuis, G.J. ; Dekker, J. ; Bos, G.A.M. van den - \ 2013
    Arthritis Care & Research 65 (2013)7. - ISSN 2151-464X - p. 1157 - 1165.
    quality-of-life - chronic disease - health survey - co-morbidity - metaanalysis - prevalence - classification - outcomes - impact - sf-36
    ObjectiveTo describe long-term physical functioning and its association with somatic comorbidity and comorbid depression in patients with established rheumatoid arthritis (RA). MethodsLongitudinal data over a period of 11 years were collected from 882 patients with RA at study inclusion. Patient-reported outcomes were collected in 1997, 1998, 1999, 2002, and 2008. Physical functioning was measured with the Health Assessment Questionnaire and the physical component summary score of the Short Form 36 health survey. Somatic comorbidity was measured by a questionnaire including 12 chronic diseases. Comorbid depression was measured with the Center for Epidemiologic Studies Depression Scale. We distinguished 4 groups of patients based on comorbidity at baseline. ResultsSeventy-two percent of the patients at baseline were women. The mean +/- SD age was 59.3 +/- 14.8 years and the median disease duration was 5.0 years (interquartile range 2.0-14.0 years). For the total group of patients with RA, physical functioning improved over time. Patients with somatic comorbidity, comorbid depression, or both demonstrated worse physical functioning than patients without comorbidity at all data collection points. Both groups with comorbid depression had the lowest scores. Only patients with both somatic comorbidity and comorbid depression showed significantly less improvement in physical functioning over time. ConclusionBoth somatic comorbidity and comorbid depression were negatively associated with physical functioning during an 11-year followup period. Furthermore, their combination seems to be especially detrimental to physical functioning over time. These results emphasize the need to take somatic comorbidity and comorbid depression into account in the screening and treatment of patients with RA.
    Red list assessment of European habitat types. A feasibility study
    Rodwell, J.S. ; Janssen, J.A.M. ; Gubbay, S. ; Schaminee, J.H.J. - \ 2013
    European Commission DG Environment - 78
    habitats - biodiversiteit - flora - bedreigde soorten - classificatie - europese unie - biodiversity - endangered species - classification - european union
    This report presents an achievable methodology for the Red List assessment of European habitats in terrestrial, freshwater and marine realms, outlines a process that will deliver such evaluations and gives an indication of resources needed. It shows how the EUNIS habitat classification can be employed as an assessment typology, recommends criteria for quantity and quality, assessment of the past trend and current state, and advises including supplementary information on drivers, threats and restorability. The report recommends thresholds and assessment categories that are fully compatible with developing IUCN proposals. As a basis for its recommendations, the report reviews the kinds of typology that are used for habitat description – classifications based on fine-scale species assemblages, mid-scale habitat/biotope classifications and broad-scale ecosystem typologies. It reviews how far each typology has been used for Red List assessment and discusses the various scales on which such evaluations have been made. Relationships between these typologies and classifications used in the Habitats Directive and Marine Strategy Framework Directive are discussed. The report then outlines the core criteria and the thresholds that have been used so far for Red List assessment: quantity (Area of Occupancy, Extent of Occurrence, dispersal/fragmentation, endemism and stand size), quality (speciesrichness, presence of rare, threatened or endemic species, structure, function & landscape context) and trends (in both quantity and quality, both back in time and forwards). It also considers various supplementary criteria that have been used for some Red List assessments: scales of naturalness/hemeroby, drivers and threats, degrees of resilience and restoration capacity. Actual Red List evaluation processes are then described, in the developing IUCN programme for ecosystems and among other approaches, and the role of expert judgment and peer review in assessment is discussed. There is then a critical review of the assessment categories employed for Red Listing: extinct (completely destroyed, extirpated), critically endangered (immediately threatened, severely declined), endangered (threatened, significantly declined), vulnerable (potentially endangered), least concern (secure, not endangered), increasing and data-deficient. The report outlines some of the major data sources available to inform expert judgement: vegetation plot data for terrestrial and freshwater habitats, the Map of the Natural Vegetation of Europe, other terrestrial maps, marine data sources and the Article 17 reporting database. It then outlines relationships between Red List assessment and ecosystem services. The report provides an assessment Fact Sheet and provides two Case Studies which outline available data, deficiencies of information and feasibility of assessment. Finally, there is a comprehensive bibliography of all references.
    Sodiomyces alkalinus, a new holomorphic alkaliphilic ascomycete within the Plectoshaerellaceae
    Grum-Grzhimaylo, A. ; Debets, A.J.M. ; Diepeningen, A.D. van; Georgieva, M.L. ; Bilanenko, E.N. - \ 2013
    Persoonia 31 (2013). - ISSN 0031-5850 - p. 147 - 158.
    classification - inference - trees - fungi
    In this study we reassess the taxonomic reference of the previously described holomorphic alkaliphilic fungus Heleococcum alkalinum isolated from soda soils in Russia, Mongolia and Tanzania. We show that it is not an actual member of the genus Heleococcum (order Hypocreales) as stated before and should, therefore, be excluded from it and renamed. Multi-locus gene phylogeny analyses (based on nuclear ITS, 5.8S rDNA, 28S rDNA, 18S rDNA, RPB2 and TEF1-alpha) have displayed this fungus as a new taxon at the genus level within the family Plectosphaerellaceae, Hypocreomycetidae, Ascomycota. The reference species of actual Heleococcum members showed clear divergence from the strongly supported Heleococcum alkalinum position within the Plectosphaerellaceae, sister to the family Glomerellaceae. Eighteen strains isolated from soda lakes around the world show remarkable genetic similarity promoting speculations on their possible evolution in harsh alkaline environments. We established the pH growth optimum of this alkaliphilic fungus at c. pH 10 and tested growth on 30 carbon sources at pH 7 and 10. The new genus and species, Sodiomyces alkalinus gen. nov. comb. nov., is the second holomorphic fungus known within the family, the first one being Plectosphaerella – some members of this genus are known to be alkalitolerant. We propose the Plectosphaerellaceae family to be the source of alkaliphilic filamentous fungi as also the species known as Acremonium alcalophilum belongs to this group
    Typology and indicators of ecosystem services for marine spatial planning and management
    Bohnke-Henrichs, A. ; Baulcomb, C. ; Koss, R. ; Hussain, S. ; Groot, R.S. de - \ 2013
    Journal of Environmental Management 130 (2013)11. - ISSN 0301-4797 - p. 135 - 145.
    economic valuation - biodiversity - coastal - goods - area - classification - conservation - benefits
    The ecosystem services concept provides both an analytical and communicative tool to identify and quantify the link between human welfare and the environment, and thus to evaluate the ramifications of management interventions. Marine spatial planning (MSP) and Ecosystem-based Management (EBM) are a form of management intervention that has become increasingly popular and important globally. The ecosystem service concept is rarely applied in marine planning and management to date which we argue is due to the lack of a well-structured, systematic classification and assessment of marine ecosystem services. In this paper we not only develop such a typology but also provide guidance to select appropriate indicators for all relevant ecosystem services. We apply this marine-specific ecosystem service typology to MSP and EBM. We thus provide not only a novel theoretical construct but also show how the ecosystem services concept can be used in marine planning and management.
    Feature level fusion of multi-temporal ALOS PALSAR and Landsat data for mapping and monitoring of tropical deforestation and forest degradation
    Reiche, J. ; Souza, C. ; Hoekman, D.H. ; Verbesselt, J. ; Haimwant, P. ; Herold, M. - \ 2013
    IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing 6 (2013)5. - ISSN 1939-1404 - p. 2159 - 2173.
    brazilian amazonia - sar - imagery - classification - emissions - countries - accuracy - band
    Many tropical countries suffer from persistent cloud cover inhibiting spatially consistent reporting of deforestation and forest degradation for REDD+. Data gaps remain even when compositing Landsat-like optical satellite imagery over one or two years. Instead, medium resolution SAR is capable of providing reliable deforestation information but shows limited capacity to identify forest degradation. This paper describes an innovative approach for feature fusion of multi-temporal and medium-resolution SAR and optical sub-pixel fraction information. After independently processing SAR and optical input data streams the extracted SAR and optical sub-pixel fraction features are fused using a decision tree classifier. ALOS PALSAR Fine Bean Dual and Landsat imagery of 2007 and 2010 acquired over the main mining district in central Guyana have been used for a proof-of-concept demonstration observing overall accuracies of 88% and 89.3% formapping forest land cover and detecting deforestation and forest degradation, respectively. Deforestation and degradation rates of 0.1% and 0.08% are reported for the observation period. Data gaps due to mainly clouds and Landsat ETM+ SLC-off that remained after compositing a set of single-period Landsat scenes, but also due to SAR layover and shadow could be reduced from 7.9% to negligible 0.01% while maintaining the desired thematic detail of detecting deforestation and degradation. The paper demonstrates the increase of both spatial completeness and thematic detail when applying the methodology, compared with potential Landsat-only or PALSAR-only approaches for a heavy cloud contaminated tropical environment. It indicates the potential for providing the required accuracy of activity data for REDD+ MRV.
    Co-existence of Distinct Prion Types Enables Conformational Evolution of Human PrPSc by Competitive Selection
    Haldiman, T. ; Kim, C. ; Cohen, Y. ; Chen, W. ; Blevins, J. ; Qing, L. ; Cohen, M.L. ; Langeveld, J.P.M. ; Telling, G.C. ; Kong, Q. ; Safar, J.G. - \ 2013
    Journal of Biological Chemistry 288 (2013). - ISSN 0021-9258 - p. 29846 - 29861.
    creutzfeldt-jakob-disease - transmissible mink encephalopathy - chronic wasting disease - dependent immunoassay - strain variation - transgenic mice - molecular-basis - protein - scrapie - classification
    The unique phenotypic characteristics of mammalian prions are thought to be encoded in the conformation of pathogenic prion proteins (PrPSc). The molecular mechanism responsible for the adaptation, mutation, and evolution of prions observed in cloned cells and upon crossing the species barrier remains unsolved. Using biophysical techniques and conformation-dependent immunoassays in tandem, we isolated two distinct populations of PrPSc particles with different conformational stabilities and aggregate sizes, which frequently co-exist in the most common human prion disease, sporadic Creutzfeldt-Jakob disease (sCJD). The protein misfolding cyclic amplification (PMCA) replicates each of the PrPSc particle types independently, and leads to the competitive selection of those with lower initial conformational stability. In serial propagation with a nonglycosylated mutant PrPC substrate, the dominant PrPSc conformers are subject to further evolution by natural selection of the subpopulation with the highest replication rate due to its lowest stability. Cumulatively, the data show that sCJD PrPSc is not a single conformational entity, but a dynamic collection of two distinct populations of particles. This implies the co-existence of different prions, whose adaptation and evolution are governed by the selection of progressively less stable, faster replicating PrPSc conformers.
    Automated identification of animal species in camera trap images
    Yu, X. ; Wang, J. ; Kays, R. ; Jansen, P.A. ; Wang, T. ; Huang, T. - \ 2013
    EURASIP Journal on Image and Video Processing 2013 (2013). - ISSN 1687-5281 - 10 p.
    classification
    Image sensors are increasingly being used in biodiversity monitoring, with each study generating many thousands or millions of pictures. Efficiently identifying the species captured by each image is a critical challenge for the advancement of this field. Here, we present an automated species identification method for wildlife pictures captured by remote camera traps. Our process starts with images that are cropped out of the background. We then use improved sparse coding spatial pyramid matching (ScSPM), which extracts dense SIFT descriptor and cell-structured LBP (cLBP) as the local features, that generates global feature via weighted sparse coding and max pooling using multi-scale pyramid kernel, and classifies the images by a linear support vector machine algorithm. Weighted sparse coding is used to enforce both sparsity and locality of encoding in feature space. We tested the method on a dataset with over 7,000 camera trap images of 18 species from two different field cites, and achieved an average classification accuracy of 82%. Our analysis demonstrates that the combination of SIFT and cLBP can serve as a useful technique for animal species recognition in real, complex scenarios.
    An evaluation of WRF's ability to reproduce the surface wind over complex terrain based on typical circulation patterns.
    Jiménez, P.A. ; Dudhia, J. ; González-Rouco, J.F. ; Montávez, J.P. ; Garcia-Bustamante, E. ; Navarro, J. ; Vilà-Guerau de Arellano, J. ; Munoz-Roldán, A. - \ 2013
    Journal of Geophysical Research: Atmospheres 118 (2013)14. - ISSN 2169-897X - p. 7651 - 7669.
    regional climate model - cluster-analysis - quality-assurance - mesoscale model - united-states - variability - validation - reanalysis - classification - simulation
    [1] The performance of the Weather Research and Forecasting (WRF) model to reproduce the surface wind circulations over complex terrain is examined. The atmospheric evolution is simulated using two versions of the WRF model during an over 13¿year period (1992 to 2005) over a complex terrain region located in the northeast of the Iberian Peninsula. A high horizontal resolution of 2km is used to provide an accurate representation of the terrain features. The multiyear evaluation focuses on the analysis of the accuracy displayed by the WRF simulations to reproduce the wind field of the six typical wind patterns (WPs) identified over the area in a previous observational work. Each pattern contains a high number of days which allows one to reach solid conclusions regarding the model performance. The accuracy of the simulations to reproduce the wind field under representative synoptic situations, or pressure patterns (PPs), of the Iberian Peninsula is also inspected in order to diagnose errors as a function of the large-scale situation. The evaluation is accomplished using daily averages in order to inspect the ability of WRF to reproduce the surface flow as a result of the interaction between the synoptic scale and the regional topography. Results indicate that model errors can originate from problems in the initial and lateral boundary conditions, misrepresentations at the synoptic scale, or the realism of the topographic features.
    Phylogeny of Tetillidae (Porifera, Demospongiae, Spirophorida) based on three molecular markers
    Szitenberg, A. ; Becking, L.E. ; Vargas, S. ; Fernandez, J. ; Santodomingo, N. - \ 2013
    Molecular Phylogenetics and Evolution 67 (2013)2. - ISSN 1055-7903 - p. 509 - 519.
    multiple sequence alignment - antarctic sponges - mixed models - mitochondrial - tree - dna - classification - astrophorida - evolution - alloclada
    Tetillidae are spherical to elliptical cosmopolitan demosponges. The family comprises eight genera: namely, Acanthotetilla Burton, 1959, Amphitethya Lendenfeld, 1907, CinachyraSollas, 1886, CinachyrellaWilson, 1925, Craniella Schmidt, 1870, Fangophilina Schmidt, 1880, Paratetilla Dendy, 1905, and Tetilla Schmidt, 1868. These genera are characterized by few conflicting morphological characters, resulting in an ambiguity of phylogenetic relationships. The phylogeny of tetillid genera was investigated using the cox1, 18S rRNA and 28S rRNA (C1–D2 domains) genes in 88 specimens (8 genera, 28 species). Five clades were identified: (i) Cinachyrella, Paratetilla and Amphitethya species, (ii) Cinachyrella levantinensis, (iii) Tetilla, (iv) Craniella, Cinachyra and Fangophilina and (v) Acanthotetilla. Consequently, the phylogenetic analysis supports the monophyly of Tetilla, a genus lacking any known morphological synapomorphy. Acanthotetilla is also recovered. In contrast, within the first clade, species of the genera Paratetilla and Amphitethya were nested within Cinachyrella. Similarly, within the fourth clade, species of the genera Cinachyra and Fangophilina were nested within Craniella. As previously postulated by taxonomists, the loss of ectodermal specialization (i.e., a cortex) has occurred several times independently. Nevertheless, the presence or absence of a cortex and its features carry a phylogenetic signal. Surprisingly, the common view that assumes close relationships among sponges with porocalices (i.e., surface depressions) is refuted.
    Hydrological drought across the world: impact of climate and physical catchment structure
    Lanen, H.A.J. van; Wanders, N. ; Tallaksen, L.M. ; Loon, A.F. van - \ 2013
    Hydrology and Earth System Sciences 17 (2013)5. - ISSN 1027-5606 - p. 1715 - 1732.
    water availability - european runoff - united-states - groundwater - flow - model - simulations - trends - classification - propagation
    Large-scale hydrological drought studies have demonstrated spatial and temporal patterns in observed trends, and considerable difference exists among global hydrological models in their ability to reproduce these patterns. In this study a controlled modeling experiment has been set up to systematically explore the role of climate and physical catchment structure (soils and groundwater systems) to better understand underlying drought-generating mechanisms. Daily climate data (1958-2001) of 1495 grid cells across the world were selected that represent Koppen-Geiger major climate types. These data were fed into a conceptual hydrological model. Nine realizations of physical catchment structure were defined for each grid cell, i.e., three soils with different soil moisture supply capacity and three groundwater systems (quickly, intermediately and slowly responding). Hydrological drought characteristics (number, duration and standardized deficit volume) were identified from time series of daily discharge. Summary statistics showed that the equatorial and temperate climate types (A-and C-climates) had about twice as many drought events as the arid and polar types (B-and E-climates), and the durations of more extreme droughts were about half the length. Selected soils under permanent grassland were found to have a minor effect on hydrological drought characteristics, whereas groundwater systems had major impact. Groundwater systems strongly controlled the hydrological drought characteristics of all climate types, but particularly those of the wetter A-, C-and D-climates because of higher recharge. The median number of droughts for quickly responding groundwater systems was about three times higher than for slowly responding systems. Groundwater systems substantially affected the duration, particularly of the more extreme drought events. Bivariate probability distributions of drought duration and standardized deficit for combinations of Koppen-Geiger climate, soil and groundwater system showed that the responsiveness of the groundwater system is as important as climate for hydrological drought development. This urges for an improvement of subsurface modules in global hydrological models to be more useful for water resources assessments. A foreseen higher spatial resolution in large-scale models would enable a better hydrogeological parameterization and thus inclusion of lateral flow.
    Soil maps of The Netherlands
    Hartemink, A.E. ; Sonneveld, M.P.W. - \ 2013
    Geoderma 204-205 (2013). - ISSN 0016-7061 - p. 1 - 9.
    water-table - seasonal fluctuation - survey information - classification - evaluate
    The Netherlands has a long history of soil research. Over the past 150 years, seven national soil maps have been produced at scales ranging from 1:50,000 to 1:1,000,000. The maps were based on different conceptual models which reflected advances in soil science as well as societal demands. There are four phases in the development of soil mapping in The Netherlands. The first three are: (i) the geological phase (1837–1937), (ii) the physiographic phase (1937–1962) and (iii) the morphometric phase (1962–1995). The earliest soil maps, made in the mid-1800s, were largely based on surface geology. In 1950 the first national soil map was published based on physiographic soil mapping. From the 1960s onwards, mapping followed a pedogenetic–morphometric approach and these maps have been widely used in land use planning, hydrologic studies, re-allotments, and agricultural land evaluations. An increase in environmental awareness with the need to assess environmental impacts and developments in information technology induced the digital soil information phase (1995–present). New technologies have improved the collection, storage, analysis and presentation of soil geographic information. It is concluded that initial soil mapping in The Netherlands had a strong agricultural focus but that the current maps are used in a wide range of applications.
    Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes
    Kourmpetis, Y.A.I. ; Dijk, A.D.J. van; Braak, C.J.F. ter - \ 2013
    Algorithms for Molecular Biology 8 (2013)1. - ISSN 1748-7188
    arabidopsis-thaliana - integration - annotation - regression - network - classification - association - terms - tool
    Gene Ontology (GO) is a hierarchical vocabulary for the description of biological functions and locations, often employed by computational methods for protein function prediction. Due to the structure of GO, function predictions can be self- contradictory. For example, a protein may be predicted to belong to a detailed functional class, but not in a broader class that, due to the vocabulary structure, includes the predicted one.We present a novel discrete optimization algorithm called Functional Annotation with Labeling CONsistency (FALCON) that resolves such contradictions. The GO is modeled as a discrete Bayesian Network. For any given input of GO term membership probabilities, the algorithm returns the most probable GO term assignments that are in accordance with the Gene Ontology structure. The optimization is done using the Differential Evolution algorithm. Performance is evaluated on simulated and also real data from Arabidopsis thaliana showing improvement compared to related approaches. We finally applied the FALCON algorithm to obtain genome-wide function predictions for six eukaryotic species based on data provided by the CAFA (Critical Assessment of Function Annotation) project
    A high-resolution and harmonized model approach for reconstructing and analysing historic land changes in Europe
    Fuchs, R. ; Herold, M. ; Verburg, P.H. ; Clevers, J.G.P.W. - \ 2013
    Biogeosciences 10 (2013). - ISSN 1726-4170 - p. 1543 - 1559.
    mediterranean landscapes - atmospheric co2 - cover changes - future - carbon - maps - classification - emissions - centuries
    Human-induced land use changes are nowadays the second largest contributor to atmospheric carbon dioxide after fossil fuel combustion. Existing historic land change reconstructions on the European scale do not sufficiently meet the requirements of greenhouse gas (GHG) and climate assessments, due to insufficient spatial and thematic detail and the consideration of various land change types. This paper investigates if the combination of different data sources, more detailed modelling techniques, and the integration of land conversion types allow us to create accurate, high-resolution historic land change data for Europe suited for the needs of GHG and climate assessments. We validated our reconstruction with historic aerial photographs from 1950 and 1990 for 73 sample sites across Europe and compared it with other land reconstructions like Klein Goldewijk et al. (2010, 2011), Ramankutty and Foley (1999), Pongratz et al. (2008) and Hurtt et al. (2006). The results indicate that almost 700 000 km2 (15.5%) of land cover in Europe has changed over the period 1950–2010, an area similar to France. In Southern Europe the relative amount was almost 3.5% higher than average (19%). Based on the results the specific types of conversion, hot-spots of change and their relation to political decisions and socio-economic transitions were studied. The analysis indicates that the main drivers of land change over the studied period were urbanization, the reforestation program resulting from the timber shortage after the Second World War, the fall of the Iron Curtain, the Common Agricultural Policy and accompanying afforestation actions of the EU. Compared to existing land cover reconstructions, the new method considers the harmonization of different datasets by achieving a high spatial resolution and regional detail with a full coverage of different land categories. These characteristics allow the data to be used to support and improve ongoing GHG inventories and climate research
    Mapping land cover gradients through analysis of hyper-temporal NDVI imagery
    Ali, A. ; Bie, C.A.J.M. de; Skidmore, A.K. ; Scarrott, R.G. ; Hamad, A. ; Venus, V. ; Lymberakis, P. - \ 2013
    International Journal of applied Earth Observation and Geoinformation 23 (2013). - ISSN 0303-2434 - p. 301 - 312.
    multitemporal modis images - remotely-sensed imagery - time-series - fuzzy-sets - species composition - accuracy assessment - neural-networks - classification - vegetation - boundaries
    The green cover of the earth exhibits various spatial gradients that represent gradual changes in space of vegetation density and/or in species composition. To date, land cover mapping methods differentiate at best, mapping units with different cover densities and/or species compositions, but typically fail to express such differences as gradients. Present interpretation techniques still make insufficient use of freely available spatial-temporal Earth Observation (EO) data that allow detection of existing land cover gradients. This study explores the use of hyper-temporal NDVI imagery to detect and delineate land cover gradients analyzing the temporal behavior of NDVI values. MODIS-Terra MVC-images (250 m, 16-day) of Crete, Greece, from February 2000 to July 2009 are used. The analysis approach uses an ISODATA unsupervised classification in combination with a Hierarchical Clustering Analysis (HCA). Clustering of class-specific temporal NDVI profiles through HCA resulted in the identification of gradients in landcover vegetation growth patterns. The detected gradients were arranged in a relational diagram, and mapped. Three groups of NDVI-classes were evaluated by correlating their class-specific annual average NDVI values with the field data (tree, shrub, grass, bare soil, stone, litter fraction covers). Multiple regression analysis showed that within each NDVI group, the fraction cover data were linearly related with the NDVI data, while NDVI groups were significantly different with respect to tree cover (adj. R 2 = 0.96), shrub cover (adj. R 2 = 0.83), grass cover (adj. R 2 = 0.71), bare soil (adj. R 2 = 0.88), stone cover (adj. R 2 = 0.83) and litter cover (adj. R 2 = 0.69) fractions. Similarly, the mean Sorenson dissimilarity values were found high and significant at confidence interval of 95% in all pairs of three NDVI groups. The study demonstrates that hyper-temporal NDVI imagery can successfully detect and map land cover gradients. The results may improve land cover assessment and aid in agricultural and ecological studies.
    Use of agro-climatic zones to upscale simulated crop yield potential
    Wart, J. van; Bussel, L.G.J. van; Wolf, J. ; Licker, R. ; Grassini, P. ; Nelson, A. ; Boogaard, H.L. ; Gerber, J. ; Mueller, N.D. ; Claessens, L.F.G. ; Ittersum, M.K. van; Cassman, K.G. - \ 2013
    Field Crops Research 143 (2013). - ISSN 0378-4290 - p. 44 - 55.
    global land areas - climate-change - agroecological zones - management - impacts - classification - agriculture - patterns - system - world
    Yield gap analysis, which evaluates magnitude and variability of difference between crop yield potential (Yp) or water limited yield potential (Yw) and actual farm yields, provides a measure of untapped food production capacity. Reliable location-specific estimates of yield gaps, either derived from research plots or simulation models, are available only for a limited number of locations and crops due to cost and time required for field studies or for obtaining data on long-term weather, crop rotations and management practices, and soil properties. Given these constraints, we compare global agro-climatic zonation schemes for suitability to up-scale location-specific estimates of Yp and Yw, which are the basis for estimating yield gaps at regional, national, and global scales. Six global climate zonation schemes were evaluated for climatic homogeneity within delineated climate zones (CZs) and coverage of crop area. An efficient CZ scheme should strike an effective balance between zone size and number of zones required to cover a large portion of harvested area of major food crops. Climate heterogeneity was very large in CZ schemes with less than 100 zones. Of the other four schemes, the Global Yield Gap Atlas Extrapolation Domain (GYGA-ED) approach, based on a matrix of three categorical variables (growing degree days, aridity index, temperature seasonality) to delineate CZs for harvested area of all major food crops, achieved reasonable balance between number of CZs to cover 80% of global crop area and climate homogeneity within zones. While CZ schemes derived from two climate-related categorical variables require a similar number of zones to cover 80% of crop area, within-zone heterogeneity is substantially greater than for the GYGA-ED for most weather variables that are sensitive drivers of crop production. Some CZ schemes are crop-specific, which limits utility for up-scaling location-specific evaluation of yield gaps in regions with crop rotations rather than single crop species.
    A proposal for including humus forms in the World Reference Base for soil resources (WRB-FAO)
    Jabiol, B. ; Zanella, A. ; Ponge, J.F. ; Sarton, G. ; Englisch, M. ; Delft, S.P.J. van; Waal, R.W. de; Claire-Le Bayon, R. - \ 2013
    Geoderma 192 (2013). - ISSN 0016-7061 - p. 286 - 294.
    earthworm invasion - organic-matter - forest - classification - vegetation - france
    The morpho-functional classification of humus forms proposed in a previous issue by Zanella and collaborators for Europe has been extended and modified, without any change in diagnostic horizons, in order to embrace a wide array of humus forms at worldwide level and to complete and make more effective the World Reference Base for Soil Resources. For that purpose 31 Humus Form Reference Groups (HFRGs) and a set of prefix and suffix qualifiers are proposed, following the rules erected for the WRB. An exhaustive classification key, respecting the principles of WRB, is suggested and examples of classification are given for some already well known humus forms.
    Environmental stratifications as the basis for national, European and global ecological monitoring
    Metzger, M.J. ; Brus, D.J. ; Bunce, R.G.H. ; Carey, P.D. ; Goncalves, J. ; Honrado, J. ; Jongman, R.H.G. ; Trabucco, A. ; Zomer, R. - \ 2013
    Ecological Indicators 33 (2013). - ISSN 1470-160X - p. 26 - 35.
    conterminous united-states - countryside survey - observing system - temporal trend - biodiversity - classification - design - earth - land - landscapes
    There is growing urgency for integration and coordination of global environmental and ecological data and indicators required to respond to the ‘grand challenges’ the planet is facing, including climate change and biodiversity decline. A consistent stratification of land into relatively homogenous strata provides a valuable spatial framework for comparison and analysis of ecological and environmental data across large heterogeneous areas. We discuss how statistical stratification can be used to design national, European and global biodiversity observation networks. The value of strategic ecological survey based on stratified samples is first illustrated using the United Kingdom (UK) Countryside Survey, a national monitoring programme that has measured ecological change in the UK countryside for the last 35 years. We then present a design for a European-wide sampling design for monitoring common habitats, and discuss ways of extending these approaches globally, supported by the recently developed Global Environmental Stratification. The latter provides a robust spatial analytical framework for the identification of gaps in current monitoring efforts, and systematic design of new complementary monitoring and research. Examples from Portugal and the transboundary Kailash Sacred Landscape in the Himalayas illustrate the potential use of this stratification, which has been identified as a focal geospatial dataset within the Group on Earth Observation Biodiversity Observation Network (GEO BON).
    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.

    Freshwater resources management in coastal zones in different climates
    Blom-Zandstra, Greet - \ 2012
    water quality - fresh water - classification - quality standards - marine areas - freshwater ecology - drinking water
    Taxonomic revision of Myrosma (Marantaceae)
    Vieira, S. ; Maas, P.J.M. ; Borchsenius, F. - \ 2012
    Blumea 57 (2012)2. - ISSN 0006-5196 - p. 125 - 130.
    central-american marantaceae - classification - phylogeny
    Myrosma is a genus of rosulate herbs characterized by a compact and strongly monosymmetric inflorescence with conspicuous, white to pale green, mostly membranous bracts, in the axil of which is a single flower pair. The genus is widely distributed throughout Central Brazil, northern South America, and the Caribbean region. It occurs mostly in savannah environments but can also be found in humid and shaded habitats. We present a taxonomic revision of Myrosma recognizing a single species, Myrosma cannifolia L.f. A complete description of that species is provided with notes on its ecology, distribution, and variation. Three species and one variety are reduced into synonymy and four names are lectotypified. A complete nomenclatural account for all combinations including the name Myrosma is given.
    Phytoplankton species predictability increases towards warmer regions
    Kruk, C. ; Segura, A.M. ; Peeters, E.T.H.M. ; Huszar, V.L.M. ; Costa, L.S. ; Kosten, S. ; Lacerot, G. ; Scheffer, M. - \ 2012
    Limnology and Oceanography 57 (2012)4. - ISSN 0024-3590 - p. 1126 - 1135.
    latitudinal diversity gradient - fresh-water phytoplankton - multispecies competition - community - plankton - classification - biodiversity - disturbance - limitation - dispersal
    We explored systematic patterns in predictability of phytoplankton species from 83 lakes over a gradient ranging from subpolar to tropical regions in South America. We estimated the explained variance (proxy of predictability) of the presence and biomass (estimated as biovolume) of species using multiple regressions from commonly measured environmental variables such as nutrient levels, light, mixing depth, temperature, and zooplankton biomass. Both the presence and biomass of species occurring at least in 10 lakes were quite well predicted from the environmental variables, with average values of 35% and 58%, respectively. Predictability was not systematically related to phylogenetic affiliation or particular functional groups as defined by morphology. However, biomass predictability decreased with increasing occurrence, and improved with larger species size (maximum linear dimension). Species that were predictable in terms of biomass (R-2 >= 0.5, p
    Sequence-function-stability relationships in proteins from datasets of functionally annotated variants: The case of TEM beta-lactamases
    Abriata, L.A. ; Salverda, M.L.M. ; Tomatis, P.E. - \ 2012
    FEBS Letters 586 (2012)19. - ISSN 0014-5793 - p. 3330 - 3335.
    antibiotic-resistance - directed evolution - natural evolution - chemical-properties - global suppressor - in-vitro - enterobacteriaceae - classification - prediction - pathways
    A dataset of TEM lactamase variants with different substrate and inhibition profiles was compiled and analyzed. Trends show that loops are the main evolvable regions in these enzymes, gradually accumulating mutations to generate increasingly complex functions. Notably, many mutations present in evolved enzymes are also found in simpler variants, probably originating functional promiscuity. Following a function-stability tradeoff, the increase in functional complexity driven by accumulation of mutations fosters the incorporation of other stability-restoring substitutions, although our analysis suggests they might not be as "global" as generally accepted and seem instead specific to different networks of protein sites. Finally, we show how this dataset can be used to model functional changes in TEMs based on the physicochemical properties of the amino acids.
    Development and application of a SYBR green RT-PCR for first line screening and quantification of porcine sapovirus infection
    Mauroy, A. ; Poel, W.H.M. van der; Honing-Hakze, R.W. van der; Thys, C. ; Thiry, E. - \ 2012
    BMC Veterinary Research 8 (2012). - ISSN 1746-6148 - 11 p.
    virus-like particles - genetic diversity - enteric caliciviruses - epidemiology - noroviruses - recombination - pigs - classification - europe - assays
    Background: Sapoviruses are single stranded positive sense RNA viruses belonging to the family Caliciviridae. The virus is detected in different species including the human and the porcine species as an enteric pathogen causing asymptomatic to symptomatic enteritis. In this study, we report the development of a rapid real time qRT-PCR based on SYBR Green chemistry for the diagnosis of porcine sapovirus infection in swine. Results: The method allows the detection of porcine sapoviruses and the quantification of the genomic copies present in stool samples. During its development, the diagnostic tool showed good correlation compared with the gold standard conventional RT-PCR and was ten-fold more sensitive. When the method was applied to field samples, porcine noroviruses from genogroup 2 genotype 11b were also detected. The method was also applied to swine samples from the Netherlands that were positive for PoSaV infection. Phylogenetic results obtained from the samples showed that PoSaV sequences were genetically related to the currently described genogroup III, to the proposed genogroup VII and also to the MI-QW19 sequence (close to the human SaV sequences). Conclusions: A rapid, sensitive, and reliable diagnosis method was developed for porcine sapovirus diagnosis. It correlated with the gold standard conventional RT-PCR. Specificity was good apart for genogroup 2 genotype 11b porcine noroviruses. As a first line screening diagnosis method, it allows a quicker and easier decision on doubtful samples.
    The Rubetum taxandriae ass. nov. (Lonicero-Rubion silvatici, Lonicero-Rubetea plicati), a new bramble association from the Belgian and Dutch Campine
    Haveman, R. ; Ronde, I. de; Weeda, E.J. - \ 2012
    Tuexenia 32 (2012). - ISSN 0722-494X - p. 55 - 65.
    classification
    Bramble scrubs are among the least known and understood vegetation types in Europe. In the Dutch National Vegetation Overview, three associations belonging to the Lonicero-Rubion silvatici were distinguished, viz. the Rubetum grati, Rubetum silvatici, and Rubetum pedemontani. During several vegetation mapping projects and Rubus excursions, a distinct type of bramble scrub was recorded repeatedly in the Campine in the province Noord-Brabant in the southern part of the Netherlands. In this paper, this scrub is described as a new association, the Rubetum taxandriae Haveman, de Ronde & Weeda, with R. taxandriae, R. campaniensis, and R. baronicus as character species, and R. insectifolius as regional character species. Variation, ecology and distribution of this new association are given and discussed, and two subassociations are distinguished. The differences with the Rubetum silvatici, to which this community was believed to belong, are discussed. Based on an earlier analysis of the centres of diversity of the genus Rubus in the Netherlands, it is supposed that the Rubetum silvatici in its circumscription in the Dutch National Vegetation Overview can be divided in more regionally distributed communities, partly as subassociations of the Rubetum silvatici, partly as independent associations.
    Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DLT)
    Spring, S. ; Visser, M. ; Lu, M. ; Copeland, A. ; Lapidus, A. ; Lucas, S. ; Cheng, J.F. ; Han, C. ; Tapia, R. ; Goodwin, L.A. ; Pitluck, S. ; Ivanova, N. ; Land, M. ; Hauser, L. ; Larimer, F. ; Rohde, M. ; Göker, M. ; Detter, J.C. ; Kyrpides, N. ; Woyke, T. ; Schaap, P.J. ; Plugge, C.M. ; Muyzer, G. ; Kuever, J. ; Pereira, I.A.C. ; Parshina, S.N. ; Bernier-Latmani, R. ; Stams, A.J.M. ; Klenk, H.P. - \ 2012
    Standards in Genomic Sciences 7 (2012). - ISSN 1944-3277 - p. 304 - 319.
    bacterial names - classification - hydrogenases - database - archaea - system - site - tool
    Strain DLT (= DSM 2154 = ATCC 23193 = NCIMB 8452) is the type strain of the species Desulfotomaculum ruminis [1], one out of current-ly 30 species with validly published names in the paraphyletic genus Desulfotomaculum [2,3]. Strain DLT was initially isolated by G. S. Coleman in the 1950s from the rumen of hay-fed sheep [4]. Dissimilatory reduction of sulfate to sulfide in the rumen was first demonstrated by Lewis [5], who dosed fistulated sheep with sulfate and deter-mined the amount of sulfide produced. As high amounts of sulfide may be toxic to animals, bacte-rial sulfate-reduction in ruminants was a concern due to the presence of sulfate in grass and hay. D. ruminis represented the first pure culture of a sul-fate-reducing bacterium isolated from the rumen. The genus name was derived from the Latin words 'de', from, ‘sulfur’, sulfur, and 'tomaculum', a kind of sausage, meaning 'a sausage-shaped sul-fate reducer' [2,6]. The species epithet is derived from the Latin word 'rumen', throat, first stomach (rumen) of a ruminant, meaning of a rumen [1,2]. Here, we present a summary classification and a set of features for D. ruminis strain DLT, together with the description of the complete genomic se-quencing and annotation. The complete genome sequence of strain DLT will provide valuable in-formation for defining a more adequate descrip-tion of the currently paraphyletic genus Desulfotomaculum
    Structural and mechanistic insight into N-glycan processing by endo-a-mannosidase
    Thompson, A.J. ; Williams, R.J. ; Hakki, Z. ; Alonzi, D.S. ; Wennekes, T. ; Gloster, T.M. ; Songsrirote, K. ; Thomas-Oates, E. ; Wrodnigg, T.M. ; Spreitz, J. ; Stütz, A.E. ; Butters, T.D. ; Williams, S.J. ; Davies, G.J. - \ 2012
    Proceedings of the National Academy of Sciences of the United States of America 109 (2012)3. - ISSN 0027-8424 - p. 781 - 786.
    asparagine-linked oligosaccharides - glucosidase-ii-deficient - glycoprotein-biosynthesis - endomannosidase pathway - endoplasmic-reticulum - glycoside hydrolases - quality-control - inhibitors - cells - classification
    N-linked glycans play key roles in protein folding, stability, and function. Biosynthetic modification of N-linked glycans, within the endoplasmic reticulum, features sequential trimming and readornment steps. One unusual enzyme, endo-a-mannosidase, cleaves mannoside linkages internally within an N-linked glycan chain, short circuiting the classical N-glycan biosynthetic pathway. Here, using two bacterial orthologs, we present the first structural and mechanistic dissection of endo-a-mannosidase. Structures solved at resolutions 1.7–2.1 Å reveal a (ß/a)8 barrel fold in which the catalytic center is present in a long substrate-binding groove, consistent with cleavage within the N-glycan chain. Enzymatic cleavage of authentic Glc1/3Man9GlcNAc2 yields Glc1/3-Man. Using the bespoke substrate a-Glc-1,3-a-Man fluoride, the enzyme was shown to act with retention of anomeric configuration. Complexes with the established endo-a-mannosidase inhibitor a-Glc-1,3-deoxymannonojirimycin and a newly developed inhibitor, a-Glc-1,3-isofagomine, and with the reducing-end product a-1,2-mannobiose structurally define the -2 to +2 subsites of the enzyme. These structural and mechanistic data provide a foundation upon which to develop new enzyme inhibitors targeting the hijacking of N-glycan synthesis in viral disease and cancer.
    Pyrolysis-Gas Chromatography/Mass Spectrometry Characterization of Humic Acids in Coastal Spodosols from Southeastern Brazil
    Buurman, P. ; Vidal-Torrado, P. ; Martin-Neto, L. - \ 2012
    Soil Science Society of America Journal 76 (2012)3. - ISSN 0361-5995 - p. 961 - 971.
    soil organic-matter - cardoso island sp - restinga vegetation - incipient podzols - b-horizons - micromorphology - gc/ms - classification - accumulation - fractions
    This study on humic acids (HAs) of podzol horizons from the southeastern region of Brazil investigated the accumulation and degradation of soil organic matter (SOM) in warm-climate podzols. Humic acids from sandy coastal Spodosols (Histic Alaquod and Arenic Alorthod) from Cardoso Island in Sao Paulo State were characterized by pyrolysis in combination with gas chromatography and mass spectrometry (Py-GC/MS). The soils developed on quartziticsandynutrient-poor parent materials under restinga forest in a coastal area. The Py-GC/MS results show that the chemical composition of HAs in B horizons in one out of three profiles was influenced by both dissolved organic C (DOC) and C from in situ decaying roots. Carbon derived from DOC dominated in the deepest part of the B horizons. In the Arenic Alorthod (H9) profileSOM from the B horizon seemed to be largely derived from roots. The DOC-derived SOM was characterized by large contributions of phenolmethylphenolsand degraded polysaccharide productswhile root contributions were mainly characterized by lignin products. Aliphatics were most abundant in A horizons (E and EB horizons were not analyzed). Both DOC-derived and lignin-derived SOM showed distinct degradation patterns. The Py-GC/MS results corroborate those obtained by 13C variable amplitude cross polarization magic angle spinning nuclear magnetic resonance spectroscopy and Fourier-transform infrared spectroscopy. Molecular chemistry showed that podzol B horizons are variable in compositionand local influencessuch as drainage and vertical or lateral water transportand SOM decomposition play an important role in podzolization processes in warm climates.
    Soil type mapping using the generalised linear geostatistical model: A case study in a Dutch cultivated peatland
    Kempen, B. ; Brus, D.J. ; Heuvelink, G.B.M. - \ 2012
    Geoderma 189-190 (2012). - ISSN 0016-7061 - p. 540 - 553.
    markov random-fields - spatial prediction - categorical variables - information - classification - regression - uncertainty - knowledge - trend - maps
    We present the generalised linear geostatistical model (GLGM) for soil type mapping and investigate if spatial prediction with this model results in a soil map of greater accuracy than a map obtained using a non-spatial model, i.e. a model that ignores spatial dependence in the soil type variable. The GLGM is central to the framework of model-based geostatistics. We adopted a pragmatic approach in which the five soil types in a cultivated peatland were separately modelled with a binomial logit-linear GLGM. Prediction with soil type-specific GLGMs resulted in five binomial probabilities at each prediction location, which were standardised to multinomial probabilities by selecting the soil type with maximal probability. A soil map was created from the predicted probabilities. In addition, two non-spatial models were used to map soil type. These were the multinomial logit model and the generalised linear model for Bernoulli-distributed data. Validation with independent probability sample data showed that use of a spatial model for digital soil type mapping did not result in more accurate predictions than those with the non-spatial models.
    An accurate retrieval of leaf water content from mid to thermal infrared spectra using continuous wavelet analysis
    Ullah, S. ; Skidmore, A.K. ; Naeem, M. ; Schlerf, M. - \ 2012
    Science of the Total Environment 437 (2012). - ISSN 0048-9697 - p. 145 - 152.
    remote-sensing imagery - hyperspectral data - mu-m - spatial heterogeneity - reflectance data - transform - vegetation - leaves - classification - compression
    Leaf water content determines plant health, vitality, photosynthetic efficiency and is an important indicator of drought assessment. The retrieval of leaf water content from the visible to shortwave infrared spectra is well known. Here for the first time, we estimated leaf water content from the mid to thermal infrared (2.5-14.0µm) spectra, based on continuous wavelet analysis. The dataset comprised 394 spectra from nine plant species, with different water contents achieved through progressive drying. To identify the spectral feature most sensitive to the variations in leaf water content, first the Directional Hemispherical Reflectance (DHR) spectra were transformed into a wavelet power scalogram, and then linear relations were established between the wavelet power scalogram and leaf water content. The six individual wavelet features identified in the mid infrared yielded high correlations with leaf water content (R 2=0.86 maximum, 0.83 minimum), as well as low RMSE (minimum 8.56%, maximum 9.27%). The combination of four wavelet features produced the most accurate model (R 2=0.88, RMSE=8.00%). The models were consistent in terms of accuracy estimation for both calibration and validation datasets, indicating that leaf water content can be accurately retrieved from the mid to thermal infrared domain of the electromagnetic radiation.
    Evaluating competing hypotheses for the origin and dynamics of river anastomosis
    Kleinhans, M.G. ; Haas, T. de; Lavooi, E. ; Makaske, B. - \ 2012
    Earth Surface Processes and Landforms 37 (2012)12. - ISSN 0197-9337 - p. 1337 - 1351.
    rhine-meuse delta - upper columbia river - british-columbia - sediment transport - channel - netherlands - avulsion - canada - classification - bifurcation
    Anastomosing rivers have multiple interconnected channels that enclose flood basins. Various theories potentially explain this pattern, including an increased discharge conveyance and sediment transport capacity of multiple channels, deltaic branching, avulsion forced by base-level rise, or a tendency to avulse due to upstream sediment overloading. The former two imply a stable anabranching channel pattern, whereas the latter two imply disequilibrium and evolution towards a single-channel pattern in the absence of avulsion. Our objective is to test these hypotheses on morphodynamic scenario modelling and data of a well-documented case study: the upper Columbia River. Proportions of channel and floodplain sediments along the river valley were derived from surface mapping. Initial and boundary conditions for the modelling were derived from field data. A 1D network model was built based on gradually varied flow equations, sediment transport prediction, mass conservation, transverse slope and spiral meander flow effects at the bifurcations. The number of channels and crevasse splays decreases in a downstream direction. Also, measured sediment transport is higher at the upstream boundary than downstream. These observations concur with bed sediment overloading from upstream, which can have caused channel aggradation above the surrounding floodplain and subsequent avulsion. The modelling also indicates that avulsion was likely caused by upstream overloading. In the model, multi-channel systems inevitably evolve towards single-channel systems within centuries. The reasons are that symmetric channel bifurcations are inherently unstable, while confluenced channels have relatively less friction than two parallel channels, so that more discharge is conveyed through the path with more confluences and less friction. Furthermore, the present longitudinal profile curvature of the valley could only be reproduced in the model by temporary overfeeding.
    Revised taxonomy of Phoma and allied genera
    Gruyter, J. de - \ 2012
    Wageningen University. Promotor(en): Pedro Crous; Pierre de Wit. - S.l. : s.n. - ISBN 9789461733887 - 180
    phoma - taxonomie - classificatie - pleosporales - moleculaire detectie - moleculaire fylogenetica - moleculaire taxonomie - phoma - taxonomy - classification - pleosporales - molecular detection - molecular phylogenetics - molecular taxonomy

    The anamorphic genus Phoma includes many important plant pathogens. The identification of Phoma species based on studies in pure culture is difficult and time consuming and the in vitro characters are often variable. Moreover, the present classification of Phoma species
    into sections is ambiguous and morphological characters are shared with related genera. In the present study the molecular phylogeny of species of Phoma and allied genera was examined and the results obtained were used to revise the taxonomy. The DNA sequence data obtained provide tools for the development of detection and identification methods.
    Chapter 1 provides a general introduction of the anamorph genus Phoma and the research that has been performed in The Netherlands during the last decades is described. Phoma is characterised by producing hyaline conidia in fruiting bodies called pycnidia. The genus includes
    many important plant pathogens. The taxonomy of Phoma has been studied intensively at the Plant Protection Service in the Netherlands for more than 50 years, resulting in the development of a generic concept in 1997 as an outline for identification of Phoma species. In this concept species of the genus Phoma are classified based on their morphological characters into the nine sections Phoma, Heterospora, Macrospora, Paraphoma, Peyronellaea, Phyllostictoides, Pilosa, Plenodomus and Sclerophomella. The species placed in each of the sections were
    systematically described culminating in the publication of the “Phoma Identification Manual” in 2004, with the descriptions of 223 specific and infra-specific taxa of Phoma, and more than 1000 synonyms in other coelomycetous genera. In the Netherlands the late Gerhard Boerema, former head of the Mycology Department at the Plant Protection Service, has been the driving
    force behind this Phoma research for decades.
    The Phoma Identification Manual is a valuable tool for the morphological identification of isolates, but in vitro studies are very time consuming and need a high level of expertise.
    Moreover, the classification of Phoma species in sections based on morphological characters appeared artificial and several species can be classified in more than one section because of their multiple “section-specific” characters. In addition, distinctive characters of Phoma sections are shared among morphologically related coelomycetous genera including Ascochyta, Asteromella, Microsphaeropsis, Phomopsis, Phyllosticta, Pleurophoma, Pyrenochaeta and Stagonospora. Phoma sections are related to diverse teleomorph genera including Didymella,
    Leptosphaeria, Mycosphaerella and Pleospora. Synanamorphs of Phoma species have been
    recognised amongst the genera Phaeomoniella, Stagonosporopsis, Epicoccum, Phialophora
    and Sclerotium illustrating their heterogeneity.
    A large, well-studied Phoma culture collection established at the Plant Protection Service and the “Centraalbureau voor Schimmelcultures” includes more than 1100 strains of Phoma species. This collection formed the basis of an intensive molecular phylogenetic study of the genus Phoma and morphologically similar genera, which commenced in 2006. Furthermore, a literature study identified sequences of genes that are suitable for phylogenic studies and elucidation of the evolutionary history of the genus Phoma.
    Several potentially informative regions of the genome were sequenced in the first phase
    of the project as has been described in chapters 2–4. The phylogeny and DNA sequence data obtained have provided tools for the development of fast and reliable molecular detection and identification methods. The development of Real-time TaqMan PCR methods for the detection and identification of two important plant pathogenic (quarantine) species formerly described in Phoma, Stagonosporopsis andigena and S. crystalliniformis, is described in Chapter 5.
    In chapter 2 several genes were studied to elucidate the molecular phylogeny of Phoma and allied genera. Sequence data of the 18S nrDNA (SSU) and 28S nrDNA (LSU) regions of the type species of the Phoma sections and morphologically similar coelomycetes and related teleomorphs were compared. The results justified the introduction of the new family Didymellaceae to
    accommodate the generic type species Didymella exigua and Phoma herbarum. The type species of the Phoma sections Phyllostictoides, Sclerophomella, Macrospora and Peyronellaea also grouped in Didymellaceae.
    The generic type species Ascochyta pisi and Microsphaeropsis olivacea also grouped in
    Didymellaceae and it shows that these genera are closely allied to Phoma. The type species of Phoma sections Heterospora, Paraphoma, Pilosa and Plenodomus grouped in various families outside Didymellaceae and were subject of following studies.
    Chapter 3 provides a molecular phylogenetic re-evaluation on Phoma-like species that appeared only distantly related to the generic type species Phoma herbarum and its related Didymella teleomorph (Didymellaceae). Phoma section Paraphoma, characterised by setose pycnidia, resembles species of Pyrenochaeta and Pleurophoma. Sequence data from the SSU and LSU regions of the species classified in Phoma section Paraphoma were compared with those of representative isolates of Pyrenochaeta and Pleurophoma, and with those of the type
    species of the Phoma sections Phoma, Pilosa and Plenodomus. Unnamed, often sterile Phomalike
    strains in the collections were included. The molecular phylogeny of species that were classified in Phoma section Paraphoma appeared to be highly polyphyletic and a thorough reclassification of the species is provided. Paraphoma was reinstalled and grouped with the new
    genera Neosetophoma and Setophoma in Phaeosphaeriaceae. Pyrenochaeta and the new genus
    Pyrenochaetopsis, including mainly taxa formerly described in Phoma section Paraphoma, were closely allied in Cucurbitariaceae.
    In chapter 4 the molecular phylogeny of species of Phoma sections Plenodomus, Pleospora and Heterospora was determined using LSU, SSU and ITS. In a “one species = one name” approach, the species described in Phoma section Plenodomus and its teleomorph Leptosphaeria
    were reclassified in Leptosphaeria, Plenodomus and the new genera Paraleptosphaeria and Subplenodomus in Leptosphaeriaceae. Two species of Phoma section Heterospora, the type species Phoma heteromorphospora and its allied species Ph. dimorphospora, were transferred
    to the new genus Heterospora that also grouped in Leptosphaeriaceae. Leptosphaeria doliolum
    comprises a species complex that was revised based on multilocus sequence data of LSU, ITS,
    SSU, ß-tubulin, and chitin synthase 1. The molecular phylogeny of species classified in Ascochyta
    and Phoma, section Pilosa in Pleosporaceae that produce morphologically similar pilose pycnidia, was determined based on analysis of actin sequence data. Several Phoma-like species
    grouped outside the suborder Pleosporineae in a LSU sequence analysis and were transferred
    to the genera Aposphaeria (Melanommataceae), Paraconiothyrium (Montagnulaceae) and Westerdykella (Sporormiaceae). Coniothyrium palmarum and related species were described in Coniothyriaceae. The new genera Medicopsis (Trematosphaeriaceae) and Nigrograna, of which the family is still unknown, are introduced to accommodate two medically important
    species formerly classified in Pyrenochaeta.
    In chapter 5 specific real-time (TaqMan) PCR assays were developed for the detection of the pathogens Stagonosporopsis andigena and S. crystalliniformis in leaves of potato and tomato.
    The molecular phylogeny with related species of Stagonosporopsis, Boeremia and Phoma based on sequence polymorphisms in the actine gene, was determined. The reliability of the DNA extraction and TaqMan PCRs for the detection of S. andigena and S. crystalliniformis in leaf material was tested in performance studies and demonstrated the specificity, analytical
    sensitivity, reproducibility, repeatability and robustness of both assays.

    Which Factors Affect the Success or Failure of Eradication Campaigns against Alien Species?
    Pluess, T. ; Jarošík, V. ; Pysek, P. ; Cannon, R. ; Pergl, J. ; Breukers, A. ; Bacher, S. - \ 2012
    PLoS ONE 7 (2012)10. - ISSN 1932-6203
    biological invasions - plant - europe - classification - introductions - management - patterns - system - impact - birds
    Although issues related to the management of invasive alien species are receiving increasing attention, little is known about which factors affect the likelihood of success of management measures. We applied two data mining techniques, classification trees and boosted trees, to identify factors that relate to the success of management campaigns aimed at eradicating invasive alien invertebrates, plants and plant pathogens. We assembled a dataset of 173 different eradication campaigns against 94 species worldwide, about a half of which (50.9%) were successful. Eradications in man-made habitats, greenhouses in particular, were more likely to succeed than those in (semi-)natural habitats. In man-made habitats the probability of success was generally high in Australasia, while in Europe and the Americas it was higher for local infestations that are easier to deal with, and for international campaigns that are likely to profit from cross-border cooperation. In (semi-) natural habitats, eradication campaigns were more likely to succeed for plants introduced as an ornamental and escaped from cultivation prior to invasion. Averaging out all other factors in boosted trees, pathogens, bacteria and viruses were most, and fungi the least likely to be eradicated; for plants and invertebrates the probability was intermediate. Our analysis indicates that initiating the campaign before the extent of infestation reaches the critical threshold, starting to eradicate within the first four years since the problem has been noticed, paying special attention to species introduced by the cultivation pathway, and applying sanitary measures can substantially increase the probability of eradication success. Our investigations also revealed that information on socioeconomic factors, which are often considered to be crucial for eradication success, is rarely available, and thus their relative importance cannot be evaluated. Future campaigns should carefully document socioeconomic factors to enable tests of their importance.
    MM2-Thalamic Creutzfeldt-Jacob Disease: Neuropathological, Biochemical and Transmission Studies Identify a Distinctive Prion Strain
    Moda, F. ; Suardi, S. ; Fede, G. Di; Indaco, A. ; Limido, L. ; Vimercati, C. ; Ruggerone, M. ; Campagnani, I. ; Langeveld, J.P.M. ; Terruzzi, A. ; Brambilla, A. ; Zerbi, P. ; Fociani, P. ; Bishop, T. ; Will, G.W. ; Manson, J.C. ; Giaccone, G. ; Tagliavini, F. - \ 2012
    Brain Pathology 22 (2012)5. - ISSN 1015-6305 - p. 662 - 669.
    sporadic fatal insomnia - prpsc types - protein - variant - brain - classification - cooccurrence - degeneration - coexistence - scrapie
    In CreutzfeldtJakob disease (CJD), molecular typing based on the size of the protease resistant core of the disease-associated prion protein (PrPSc) and the M/V polymorphism at codon 129 of the PRNP gene correlates with the clinico-pathologic subtypes. Approximately 95% of the sporadic 129MM CJD patients are characterized by cerebral deposition of type 1 PrPSc and correspond to the classic clinical CJD phenotype. The rare 129MM CJD patients with type 2 PrPSc are further subdivided in a cortical and a thalamic form also indicated as sporadic fatal insomnia. We observed two young patients with MM2-thalamic CJD. Main neuropathological features were diffuse, synaptic PrP immunoreactivity in the cerebral cortex and severe neuronal loss and gliosis in the thalamus and olivary nucleus. Western blot analysis showed the presence of type 2A PrPSc. Challenge of transgenic mice expressing 129MM human PrP showed that MM2-thalamic sporadic CJD (sCJD) was able to transmit the disease, at variance with MM2-cortical sCJD. The affected mice showed deposition of type 2A PrPSc, a scenario that is unprecedented in this mouse line. These data indicate that MM2-thalamic sCJD is caused by a prion strain distinct from the other sCJD subtypes including the MM2-cortical form.
    Species, functional groups, and habitat preferences of birds in five agroforestry classes in Tabasco, Mexico
    Wal, J.C. van der; Peña-Álvarez, B. ; Arriaga-Weiss, S.L. ; Hernández-Daumás, S. - \ 2012
    The Wilson Journal of Ornithology 124 (2012)3. - ISSN 1559-4491 - p. 558 - 571.
    tropical forest - cacao plantations - coffee production - atlantic forest - biodiversity - diversity - landscapes - abundance - classification - conservation
    We studied species, functional groups, and habitat preferences of birds in five classes of agroforestry systems: agroforests, animal agroforestry, linear agroforestry, sequential agroforestry, and crops under tree cover in Tabasco, Mexico. Sampling sites were >2 km from natural forest fragments. Observations were made at 38 sites using 30-min point and transect counts in the morning and afternoon in the rainy season, season of northern winds, and dry season from June 2008 to May 2009. We observed 3,551 birds, which were assigned to 102 species: 72 were resident and 30 were migratory species. Overall efficiency of sampling was 82.4% and varied from 68.7% in linear agroforestry to 81.5% in animal agroforestry. Total species richness varied from 43 in sequential agroforestry to 64 in animal agroforestry. Species richness and Shannon diversity indices revealed no differences among agroforestry classes. Bird communities in animal agroforestry, linear agroforestry, and sequential agroforestry had similar species compositions, as did agroforests and crops under tree cover. Birds in all agroforestry classes were mainly forest generalists, although specialists of open areas were common, particularly in animal and sequential agroforestry. Only one individual of a forest specialist species was observed during sampling. Migrant species were mostly forest generalists, but some open area specialists occurred in animal agroforestry. Resident birds were distributed over all foraging guilds in all agroforestry classes, whereas migrants were mainly foliage-gleaning insectivores. Foraging guilds had different relative abundances among agroforestry classes. Structural diversity of agroforestry classes did not seem to influence bird species richness. Forest specialist species were virtually absent in agroforestry classes, but the avifauna in agroforestry is diverse and valuable in itself
    The role of textures to improve the detection accuracy of Rumex obtusifolius in robotic systems
    Hiremath, S. ; Heijden, G.W.A.M. van der; Evert, F.K. van; Stein, A. - \ 2012
    Weed Research 52 (2012)5. - ISSN 0043-1737 - p. 430 - 440.
    classification - weed - segmentation - grassland - features - cooccurrence - images - gabor - color
    Rumex obtusifolius is a common weed that is difficult to control in organic farming systems. Among the proposed non-chemical treatment methods, robotic systems to mechanically remove the weed have potential for its automatic detection and removal. This article considers a recently developed robot with a real-time vision system capable of detecting R. obtusifolius in a pasture with the objective of improving its detection accuracy. We show that the texture measure used by the current system is equivalent to local variance and has limited value for detecting R. obtusifolius in a complex background like pasture. To improve the system, two different sets of visual texture features corresponding to Gray level Co-occurence Matrix (GLCM) and Laws’ filter masks were investigated. Through feature selection, we determined that GLCM features of contrast, entropy and correlation were the best among the two sets of features and were 25% more accurate in estimating the taproot location than the current system. We incorporated these texture features in a new segmentation algorithm and demonstrated its robustness by testing it on a data set of 92 images with high complexity in terms of variation in illumination and weed size. The new segmentation algorithm had a detection accuracy of 90%, with an average error of 141 mm in the estimation of the location of the taproot of R. obtusifolius, compared with 308 mm with the former algorithm
    Phytogeographical analysis and checklist of the vascular plants of Loango National Park, Gabon
    Harris, D.J. ; Armstrong, K.E. ; Walters, M. ; Wilks, C. ; Mouandza Mbembo, J.C. ; Niangadouma, J. ; Wieringa, J.J. ; Breteler, F.J. - \ 2012
    Plant Ecology and Evolution 145 (2012)2. - ISSN 2032-3913 - p. 242 - 257.
    miocene expansion - c-4 grasslands - africa - classification - leguminosae
    Background and aims - Floristic inventories are the primary means by which the plant diversity of an area can be understood and are important in underpinning management plans for conservation. One of the priorities set out for Loango National Park (LNP) in an IUCN assessment of Gabon's protected areas was to produce a vascular plant checklist. Therefore, the primary goal of this research was to significantly increase the number of specimens for the park and make a concentrated effort to increase knowledge of plant diversity in the area. The secondary goal of this study was to analyse the flora of LNP in terms of phytogeography and endemism. Methods - A specimen-based botanical inventory was carried out in LNP (1005 herbarium specimens collected for this study were added to 752 existing records) and vegetation observations were made. Phytogeographical analyses were also performed using two different methods and datasets for comparison. Key results - A preliminary checklist of 686 species of vascular plants of LNP is presented, making a significant contribution to our knowledge of the flora of Gabon with more than twenty new country records. Conclusions -There is a surprisingly high proportion (15%) of the overall Gabonese flora recorded from within the park in this preliminary checklist. Further inventory within the park will undoubtedly produce a much higher percentage of the flora of the whole country. This high proportion is explained in part by the combination of restricted coastal endemics, diversity of habitats, and dynamic biological and physical processes. Phytogeographical analyses reveal different floristic relationships between the forest and savanna components of the flora suggesting different origins of these two biomes in coastal Gabon. The forest species are typically Guineo-Congolian in distribution and the savanna species are Sudano- Zambezian or widespread in distribution. Together, the faunal elements and the high diversity of the flora of Loango National Park make it a globally important site for conservation.
    A concise bibliographic overview of Annonaceae
    Erkens, R.H.J. ; Mennega, E.A. ; Westra, L.I.T. - \ 2012
    Botanical Journal of the Linnean Society 169 (2012)1. - ISSN 0024-4074 - p. 41 - 73.
    for-plant-conservation - taxonomists - science - classification - phylogenetics - collections - family - policy
    It is important that taxonomic knowledge is disseminated by those who possess it. This can be carried out via online databases, printed publications or training in taxonomic practice. For Annonaceae, the online database AnnonBase includes all published names of Annonaceae at any rank worldwide. Recently, an updated index to genera, species and infraspecific taxa of Neotropical Annonaceae was published in hard copy. This manuscript contains a concise update to the Bibliography of Annonaceae published by the late E. A. Mennega in 1993. Since his publication, much work has been carried out on systematics and evolution of Annonaceae, with the advent of molecular phylogenetics providing an additional stimulus. Here, however, we concentrate only on taxonomic papers focusing specifically on the description and circumscription of taxa (e.g. revisions, monographs, floras, checklists, descriptions of new species or phylogenetic studies that show monophyly/polyphyly/paraphyly of genera). The index should provide an easy entrance into the most important taxonomic literature on Annonaceae from 1900 onwards for the trained and untrained taxonomist with an interest in Annonaceae.
    Authentication of Organic Feed by Near-Infrared Spectroscopy Combined with Chemometrics A Feasibilily Study
    Tres, A. ; Veer, J.C. van der; Perez-Marin, M.D. ; Ruth, S.M. van; Garrido-Varo, A. - \ 2012
    Journal of Agricultural and Food Chemistry 60 (2012)33. - ISSN 0021-8561 - p. 8129 - 8133.
    orthogonal signal correction - reflectance spectroscopy - compound feedingstuffs - ingredient composition - products - spectra - classification - samples - meat - oil
    Organic products tend to retail at a higher price than their conventional counterparts, which makes them susceptible to fraud. In this study we evaluate the application of near-infrared spectroscopy (NIRS) as a rapid, cost-effective method to verify the organic identity of feed for laying hens. For this purpose a total of 36 organic and 60 conventional feed samples from The Netherlands were measured by NIRS. A binary classification model (organic vs conventional feed) was developed using partial least squares discriminant analysis. Models were developed using five different data preprocessing techniques, which were externally validated by a stratified random resampling strategy using 1000 realizations. Spectral regions related to the protein and fat content were among the most important ones for the classification model. The models based on data preprocessed using direct orthogonal signal correction (DOSC), standard normal variate (SNV), and first and second derivatives provided the most successful results in terms of median sensitivity (0.91 in external validation) and median specificity (1.00 for external validation of SNV models and 0.94 for DOSC and first and second derivative models). A previously developed model, which was based on fatty acid fingerprinting of the same set of feed samples, provided a higher sensitivity (1.00). This shows that the NIRS-based approach provides a rapid and low-cost screening tool, whereas the fatty acid fingerprinting model can be used for further confirmation of the organic identity of feed samples for laying hens. These methods provide additional assurance to the administrative controls currently conducted in the organic feed sector
    Proton transfer reaction-mass spectrometry volatile organic compound fingerprinting for monovarietal extra virgin olive oil identification
    Ruiz-Samblas, C. ; Tres, A. ; Koot, A.H. ; Ruth, S.M. van; Gonzalez-Casado, A. ; Cuadros-Rodriguez, L. - \ 2012
    Food Chemistry 134 (2012)1. - ISSN 0308-8146 - p. 589 - 596.
    geographical origin - ptr-ms - quality - authentication - classification - cultivars
    Proton transfer reaction-mass spectrometry (PTR-MS) is a relatively new technique that allows the fast and accurate qualification of the volatile organic compound (VOC) fingerprint. This paper describes the analysis of thirty samples of extra virgin olive oil, of five different varieties of olive fruit (Arbequina, Cornicabra, Frantoio, Hojiblanca, and Picual) by PTR-MS. A multivariate pattern recognition method (partial least square-discriminant analysis, PLS-DA) was applied on the full spectra fingerprint of the PTR-MS measurements. The multivariate model was doubly validated: firstly by means of internal validation (cross-validation) and secondly with an external validation data set. The results showed that the five varieties could be successfully distinguished within them. The proposed method provides a new valuable tool for extra virgin olive oil classification according to variety, and it could serve as a screening technique for the authentication of monovarietal extra-virgin olive oil and as a methodology to confirm that a variety is in agreement with claimed identity.
    Macrophotographic wood atlas of Annonaceae.
    Koek-Noorman, J. ; Westra, L.I.T. - \ 2012
    Botanical Journal of the Linnean Society 169 (2012)1. - ISSN 0024-4074 - p. 135 - 189.
    flowering plants - genera - classification - evolution - families - genus
    In this article, a general description of the microscopic wood anatomy of Annonaceae is given. We provide a description of the wood anatomical features of the family and of all subfamilies and tribes, all from material in the Utrecht Wood collection. Hand-lens images can be an important help in identification, not only at the family level, but also at the level of genera or below, notwithstanding the fact that the number of characters that can be easily observed in end-grain photographs is restricted. The differences are often slight and difficult to summarize in a few words, making illustrations an indispensable tool. Therefore, we provide end-grain photographs of cross-sections of wood of 66 genera and > 90 species of Annonaceae. The variation seen in lens key characters is discussed against the framework of the current phylogenetic tree of the family. Additional remarks on microscopic features are given when appropriate
    Serum protein profiles as potential biomarkers for infectious disease status in pigs
    Koene, M.G.J. ; Mulder, H.A. ; Stockhofe, N. ; Kruijt, L. ; Smits, M.A. - \ 2012
    BMC Veterinary Research 8 (2012). - ISSN 1746-6148 - 14 p.
    low-abundance proteins - acute-phase proteins - clinical proteomics - mass-spectrometry - ovine serum - discovery - classification - technology - enrichment - samples
    Background: In veterinary medicine and animal husbandry, there is a need for tools allowing the early warning of diseases. Preferably, tests should be available that warn farmers and veterinarians during the incubation periods of disease and before the onset of clinical signs. The objective of this study was to explore the potential of serum protein profiles as an early biomarker for infectious disease status. Serum samples were obtained from an experimental pig model for porcine circovirus-associated disease (PCVAD), consisting of Porcine Circovirus type 2 (PCV2) infection in combination with either Porcine Parvovirus (PPV) or Porcine Reproductive and Respiratory Syndrome virus (PRRSV). Sera were collected before and after onset of clinical signs at day 0, 5 and 19 post infection. Serum protein profiles were evaluated against sera from non-infected control animals. Results: Protein profiles were generated by SELDI-TOF mass spectrometry in combination with the Proteominer (TM) technology to enrich for low-abundance proteins. Based on these protein profiles, the experimentally infected pigs could be classified according to their infectious disease status. Before the onset of clinical signs 88% of the infected animals could be classified correctly, after the onset of clinical sigs 93%. The sensitivity of the classification appeared to be high. The protein profiles could distinguish between separate infection models, although specificity was moderate to low. Classification of PCV2/PRRSV infected animals was superior compared to PCV2/PPV infected animals. Limiting the number of proteins in the profiles (ranging from 568 to 10) had only minor effects on the classification performance. Conclusions: This study shows that serum protein profiles have potential for detection and identification of viral infections in pigs before clinical signs of the disease become visible.
    Phenology related measures and indicators at varying spatial scales : investigation of phenology information for forest classification using SPOT VGT and MODIS NDVI data
    Clerici, N. ; Weissteiner, C.J. ; Halabuk, A. ; Hazeu, G.W. ; Roerink, G.J. ; Mücher, S. - \ 2012
    Wageningen : Alterra (Alterra-rapport 2259)
    fenologie - bossen - habitats - modellen - bladeren - classificatie - phenology - forests - habitats - models - leaves - classification
    Descriptions of the European environmental zones and strata
    Metzger, M.J. ; Shkaruba, A.D. ; Jongman, R.H.G. ; Bunce, R.G.H. - \ 2012
    Wageningen : Alterra (Alterra report 2281) - 152
    klimaatzones - bodem - vegetatie - geologie - zonering - classificatie - europa - climatic zones - soil - vegetation - geology - zoning - classification - europe
    Too good to be true: pitfalls of usingmean Ellenberg indicator values in vegetation analyses
    Zeleny, D. ; Schaffers, A.P. - \ 2012
    Journal of Vegetation Science 23 (2012)3. - ISSN 1100-9233 - p. 419 - 431.
    species pools - classification - ordination - plants - ecology
    Question: Mean Ellenberg indicator values (EIVs) inherit information about compositional similarity, because during their calculation species abundances (or presence–absences) are used as weights. Can this similarity issue actually be demonstrated, does it bias results of vegetation analyses correlating mean EIVs with other aspects of species composition and how often are biased studies published? Methods: In order to separate information on compositional similarity possibly present in mean EIVs, a new variable was introduced, calculated as a weighted average of randomized species EIVs. The performance of these mean randomized EIVs was compared with that of the mean real EIVs on the one hand and random values (randomized mean EIVs) on the other. To demonstrate the similarity issue, differences between samples were correlated with dissimilarity matrices based on various indices. Next, the three mean EIV variables were tested in canonical correspondence analysis (CCA), detrended correspondence analysis (DCA), analysis of variance (ANOVA) between vegetation clusters, and in regression on species richness. Subsequently, a modified permutation test of significance was proposed, taking the similarity issue into account. In addition, an inventory was made of studies published in the Journal of Vegetation Science and Applied Vegetation Science between 2000 and 2010 likely reporting biased results due to the similarity issue. Results: Using mean randomized EIVs, it is shown that compositional similarity is inherited into mean EIVs and most resembles the inter-sample distances in correspondence analysis, which itself is based on iterative weighted averaging. The use of mean EIVs produced biased results in all four analysis types examined: unrealistic (too high) explained variances in CCA, too many significant correlations with ordination axes in DCA, too many significant differences between cluster analysis groups and too high coefficients of determination in regressions on species richness. Modified permutation tests provided ecologically better interpretable results. From 95 studies using Ellenberg indicator values, 36 reported potentially biased results. Conclusions: No statistical inferences should bemade in analyses relatingmean EIVs with other variables derived from the species composition as this can produce highly biased results, leading to misinterpretation. Alternatively, a modified permutation test using mean randomized EIVs can sometimes be used.
    Identifying plant species using mid-wave infrared (2.5-6µm) and thermal infrared (8-14µm) emissivity spectra
    Ullah, S. ; Schlerf, M. ; Skidmore, A.K. ; Hecker, C. - \ 2012
    Remote Sensing of Environment 118 (2012)4. - ISSN 0034-4257 - p. 95 - 102.
    salt-marsh vegetation - hyperspectral data - biomass estimation - reflectance - discrimination - indexes - imagery - leaves - classification - spectroscopy
    Plant species discrimination using remote sensing is generally limited by the similarity of their reflectance spectra in the visible, NIR and SWIR domains. Laboratory measured emissivity spectra in the mid infrared (MIR; 2.5µm-6µm) and the thermal infrared (TIR; 8µm-14µm) domain of different plant species, however, reveal significant differences. It is anticipated that with the advances in airborne and space borne hyperspectral thermal sensors, differentiation between plant species may improve. The laboratory emissivity spectra of thirteen common broad leaved species, comprising 3024 spectral bands in the MIR and TIR, were analyzed. For each wavelength the differences between the species were tested for significance using the one way analysis of variance (ANOVA) with the post-hoc Tukey HSD test. The emissivity spectra of the analyzed species were found to be statistically different at various wavebands. Subsequently, six spectral bands were selected (based on the histogram of separable pairs of species for each waveband) to quantify the separability between each species pair based on the Jefferies Matusita (JM) distance. Out of 78 combinations, 76 pairs had a significantly different JM distance. This means that careful selection of hyperspectral bands in the MIR and TIR (2.5µm-14µm) results in reliable species discrimination.
    A methodology to select particle morpho-chemical characteristics to use in source apportionment of particulate matter from livestock houses
    Cambra-Lopez, M. ; Hermosilla, T. ; Aarnink, A. ; Ogink, N.W.M. - \ 2012
    Computers and Electronics in Agriculture 81 (2012). - ISSN 0168-1699 - p. 14 - 23.
    dust particles - classification - buildings - accuracy - identification - generation - poultry - area
    Intensive poultry and pig houses are major point sources of particulate matter (PM) emissions. The knowledge on the contribution of individual sources to PM in different fractions is essential to improve PM reduction from livestock houses. We developed a methodology to investigate which input data (particle chemical, morphological or combined characteristics) were best to distinguish amongst specific sources of airborne PM in livestock houses. We used a validation procedure with classification rules based on decision trees and analyzed misclassification errors. The PM from two livestock species (poultry and pigs), and in two different fractions (fine and coarse) was studied. Results showed the selection of the best input data varied with the sources, which depend on livestock species. Using only particle chemical characteristics resulted in higher overall classification accuracies (62–68%) than using only morphological characteristics (40–64%) in poultry and pigs. Particle morphological characteristics can add value when sources show distinctive and well defined morphologies or differ in size. Using combined chemical and morphological resulted in the highest overall classification accuracies (average of 69% of particles correctly assigned to their source) and lowest misclassification errors. This study provides a methodological approach to assess input data and identifies the most effective characteristics to apportion PM in livestock houses. These data are promising to determine the contribution of different sources to PM in livestock houses and give insight in under- and overestimation errors in the source apportionment
    Mapping the irrigated rice cropping patterns of the Mekong delta, Vietnam through hyper-temporal SPOT NDVI image analysis
    Nguyen, Thi Thu Ha ; Bie, C.A.J.M. de; Ali, A. ; Smaling, E.M.A. ; Hoanh, C.T. - \ 2012
    International Journal of Remote Sensing 33 (2012)2. - ISSN 0143-1161 - p. 415 - 434.
    multitemporal modis images - time-series - agriculture - areas - china - south - classification - expansion - systems - fields
    Successful identification and mapping of different cropping patterns under cloudy conditions of a specific crop through remote sensing provides important baseline information for planning and monitoring. In Vietnam, this information is either missing or unavailable; several ongoing projects studying options with radar to avoid earth observation problems caused by the prevailing cloudy conditions have to date produced only partial successes. In this research, optical hyper-temporal Satellite Pour l'Observation de la Terre (SPOT) VEGETATION (SPOT VGT) data (1998–2008) were used to describe and map variability in irrigated rice cropping patterns of the Mekong delta. Divergence statistics were used to evaluate signature separabilities of normalized difference vegetation index (NDVI) classes generated from the iterative self-organizing data analysis technique algorithm (ISODATA) classification of 10-day SPOT NDVI image series. Based on this evaluation, a map with 77 classes was selected. Out of these 77 mapped classes, 26 classes with prior knowledge that they represent rice were selected to design the sampling scheme for fieldwork and for crop calendar characterization. Using the collected information of 112 farmers’ fields belonging to the 26 selected classes, the map produced provides highly accurate information on rice cropping patterns (94% overall accuracy, 0.93 Kappa coefficient). We found that the spatial distributions of the triple and the double rice cropping systems are highly related to the flooding regime from the Hau and Tien rivers. Areas that are highly vulnerable to flooding in the upper part and those that are saline in the north-western part of the delta mostly have a double rice cropping system, whilst areas in the central and the south-eastern parts mostly have a triple rice cropping system. In turn, the duration of flooding is highly correlated with the decision by farmers to cultivate shorter or longer duration rice varieties. The overall spatial variability mostly coincides with administrative units, indicating that crop pattern choices and water control measures are locally synchronized. Water supply risks, soil acidity and salinity constraints and the anticipated highly fluctuating rice market prices all strongly influence specific farmers’ choices of rice varieties. These choices vary considerably annually, and therefore grown rice varieties are difficult to map. Our study demonstrates the high potential of optical hyper-temporal images, taken on a daily basis, to differentiate and map a high variety of irrigated rice cropping patterns and crop calendars at a high level of accuracy in spite of cloudy conditions
    The ferulic acid esterases of Chrysosporium lucknowense C1: Purification, characterization and their potential application in biorefinery
    Kuhnel, S. ; Pouvreau, L.A.M. ; Appeldoorn, M.M. ; Hinz, S.W.A. ; Schols, H.A. ; Gruppen, H. - \ 2012
    Enzyme and Microbial Technology 50 (2012)1. - ISSN 0141-0229 - p. 77 - 85.
    sugar-beet pulp - plant-cell walls - aspergillus-niger - maize bran - feruloylated oligosaccharides - structural-characterization - wheat bran - degradation - classification - arabinoxylans
    Three ferulic acid esterases from the filamentous fungus Chrysosporium lucknowense C1 were purified and characterized. The enzymes were most active at neutral pH and temperatures up to 45 °C. All enzymes released ferulic acid and p-coumaric acid from a soluble corn fibre fraction. Ferulic acid esterases FaeA1 and FaeA2 could also release complex dehydrodiferulic acids and dehydrotriferulic acids from corn fibre oligomers, but released only 20% of all ferulic acid present in sugar beet pectin oligomers. Ferulic acid esterase FaeB2 released almost no complex ferulic acid oligomers from corn fibre oligomers, but 60% of all ferulic acid from sugar beet pectin oligomers. The ferulic acid esterases were classified based on both, sequence similarity and their activities toward synthetic substrates. The type A ferulic acid esterases FaeA1 and FaeA2 are the first members of the phylogenetic subfamily 5 to be biochemically characterized. Type B ferulic acid esterase FaeB2 is a member of subfamily 6.
    A method to assess ecosystem services developed from soil attributes with stakeholders and data of four arable farms
    Rutgers, M. ; Wijnen, H.J. van; Schouten, A.J. ; Mulder, C. ; Kuiten, A.M.P. ; Brussaard, L. ; Breure, A.M. - \ 2012
    Science of the Total Environment 415 (2012). - ISSN 0048-9697 - p. 39 - 48.
    classification - provision - land
    Ecosystem-service indicators and related accounting units are crucial for the development of decision frameworks for sustainable land management systems. With a management concept using ecosystem services, land-use expectations can be linked to quantifiable soil features in a defendable and transparent way. A method to define a set of site-specific ecosystem services and indication system for quantification was set-up and run. First, we interviewed a wide group of land users profiting from ecosystem services of the soil at four arable farms in the polder Hoeksche Waard (S-SE of Rotterdam, the Netherlands). Subsequently, site-specific ecosystem services were defined and weighted according to land use expectations at different spatial and temporal scales. Second, a practical set of indicators was taken from 'Best Professional Judgment' and used to quantify the performance of the ecosystem services for these four farms. The indicators were derived from biotic and abiotic soil parameters. The performance of ecosystem services was related to a reference situation (MEP: maximum ecological potential) with the same land use and soil type combination (i.e., arable fields on silt loam) taken from the database of our national soil survey. In many cases, the performance of ecosystem services was relatively poor if compared to MEP. However, the performances of natural attenuation and/or climate-related services were better. In addition, the different management of these farms (i.e. conventional, intensive and organic farming) was reflected in the performance of the ecosystem services of their soils. Third, land management measures to improve the targeted ecosystem services were incorporated in the outlined method, but not worked out with illustrative field data in this study. Together with concordant data, we show opportunities for a quantification of ecosystem services to improve land-users' awareness and to assess management sustainability. © 2011 Elsevier B.V. All rights reserved.
    Extracting topographic characteristics of landforms typical of Canadian agricultural landscapes for agri-environmental modeling. I. Methodology
    Li, S. ; Lobb, D.A. ; McConkey, B.G. ; MacMillan, R.A. ; Moulin, A. ; Fraser, W.R. - \ 2011
    Canadian Journal of Soil Science 91 (2011)2. - ISSN 0008-4271 - p. 251 - 266.
    fuzzy-logic - classification - saskatchewan - terrain - erosion
    Soil and topographic information are key inputs for many agri-environmental models and there are linkages between soil and topography at the Field scale. A major source of soil data is soil databases established based on field soil survey. Although both soil and topographic information are recorded in field soil surveys, the nominal nature of the topographic data has limited their use in agri-environmental models. in this study, we developed a methodology to extract various topographic derivatives and to classify the landscape into landform elements with distinctive topographic characteristics based on detailed analyses of fine resolution digital elevation models. Data obtained from these analyses were used to calculate a representative two-dimensional hillslope of five segments, each with a defined length and slope gradient. A set of modal hillslopes was developed to describe topographic variability. Additional topographic parameters, ratios and indices were calculated to reflect different aspects of topographic characteristics and also to build connections between different agri-environmental models. in particular, a topographic complexity index was developed as a quantitative measure of the degrees of divergence and convergence. This paper describes the methodology using one site as an example. Application of this methodology to other landforms in agricultural land of Canada is reported in a companion paper
    Assessing effects of temporal compositing and varying observation periods for large-area land-cover mapping in semi-arid ecosystems: Implications for global monitoring
    Huttich, C. ; Herold, M. ; Wegmann, M. ; Cord, A. ; Strobach, B. ; Schmullius, C. ; Dech, S. - \ 2011
    Remote Sensing of Environment 115 (2011)10. - ISSN 0034-4257 - p. 2445 - 2459.
    time-series - african savannas - avhrr data - data sets - vegetation dynamics - igbp discover - random forest - classification - kalahari - tree
    Land-cover is an important parameter in analyzing the state and dynamics of natural and anthropogenic terrestrial ecosystems. Land-cover classes related to semi-arid savannas currently exhibit among the greatest uncertainties in available global land cover datasets. This study focuses on the Kalahari in northeastern Namibia and compares the effects of different composite lengths and observation periods with class-wise mapping accuracies derived from multi-temporal MODIS time series classifications to better understand and overcome quality gaps in mapping semi-arid land-cover types. We further assess the effects of precipitation patterns on mapping accuracy using Tropical Rainfall Measuring Mission (TRMM) observation data. Botanical field samples, translated into the UN Land Cover Classification System (LCCS), were used for training and validation. Different sets of composites (16-day to three-monthly) were generated from MODIS (MOD13Q1) data covering the sample period from 2004 to 2007. Land-cover classifications were performed cumulatively based on annual and inter-annual feature sets with the use of random forests. Woody vegetation proved to be more stable in terms of omission and commission errors compared to herbaceous vegetation types. Generally, mapping accuracy increases with increasing length of the observation period. Analyses of variance (ANOVA) verified that inter-annual classifications significantly improved class-wise mapping accuracies, and confirmed that monthly composites achieved the best accuracy scores for both annual and inter-annual classifications. Correlation analyses using piecewise linear models affirmed positive correlations between cumulative mapping accuracy and rainfall and indicated an influence of seasonality and environmental cues on the mapping accuracies. The consideration of the inter-seasonal variability of vegetation activity and phenology cycling in the classification process further increases the overall classification performance of savanna classes in large-area land-cover datasets. Implications for global monitoring frameworks are discussed based on a conceptual model of the relationship between observation period and accuracy
    EU habitats of interest: an insight into Atlantic and Mediterranean beach and foredunes
    Feola, S. ; Carranza, M.L. ; Schaminee, J.H.J. ; Acosta, A.T.R. ; Janssen, J.A.M. - \ 2011
    Biodiversity and Conservation 20 (2011)7. - ISSN 0960-3115 - p. 1457 - 1468.
    ellenberg indicator values - coastal dunes - vegetation - europe - conservation - netherlands - management - classification - connectivity - ecosystems
    Abstract We compared the Atlantic and Mediterranean beach and foredune habitats of European interest, focusing on floristic, structural and ecological features. We selected two representative sites of Atlantic (The Netherlands) and Mediterranean (Italy) coastal dunes. From a georeferenced vegetation database, samples of: (a) annual vegetation on drift lines (European Union habitat type 1210), (b) embryonic shifting dunes (2110), and (c) shifting dunes along the shoreline with Ammophila arenaria (2120), were selected. Floristic representativity and comparability of plot sizes were considered. For each habitat, the frequency and the fidelity of the species, the life form frequency spectra and Ellenberg ecological indicator values were assessed. We found a consistent floristic differentiation between the Atlantic and the Mediterranean coastal dune habitats and only a small set of shared species. The Italian and the Dutch annual vegetation of drift lines (1210) register a high structural similarity that strongly declines landwards. Floristic composition, life forms and Ellenberg indicator values show higher similarities among different foredune habitats of the same site than between homologous habitats of the Mediterranean and Atlantic coasts. The results confirm the current description and distribution of the habitat of European interest annual vegetation of drift lines (1210). On the other hand, the floristic, structural and ecological differences between the Atlantic and the Mediterranean
    Vegetation survey: a new focus for Applied Vegetation Science
    Chytry, M. ; Schaminee, J.H.J. ; Schwabe, A. - \ 2011
    Applied Vegetation Science 14 (2011)4. - ISSN 1402-2001 - p. 435 - 439.
    classification - syntaxonomy - communities - databases - system
    Vegetation survey is an important research agenda in vegetation science. It defines vegetation types and helps understand differences among them, which is essential for both basic ecological research and applications in biodiversity conservation and environmental monitoring. In this editorial, we reflect on the historical development and current state of vegetation survey worldwide and introduce the Special Feature ‘Vegetation Survey’, as well as the new section of the same name in Applied Vegetation Science. The current Special Feature contains eight vegetation survey studies from North America, New Zealand, Europe and Asia. Most of these studies describe diversity of important vegetation types across large areas and some are also innovative from the methodological viewpoint. They illustrate current trends in vegetation survey in different parts of the world and also represent some examples of the type of studies that we wish to publish in the ‘Vegetation Survey’ section in future issues of Applied Vegetation Science.
    Application of fuzzy logic to Boolean models for digital soil assessment
    Gruijter, J.J. de; Walvoort, D.J.J. ; Bragato, G. - \ 2011
    Geoderma 166 (2011)1. - ISSN 0016-7061 - p. 15 - 33.
    land suitability - classification - interpolation - set
    Boolean models based on expert knowledge are often used to classify soils into a limited number of classes of a difficult-to-measure soil attribute. Although the primary data used for these classifications contain information on whether the soil is a typical class member or a boundary case between two classes, this is not retained in the final result. Such information is relevant in land use planning and soil management as it enables more flexible decision taking, but in the pre-digital era it was unfeasible to prevent the loss of it. We can now retain this information by fuzzifying the Boolean model using fuzzy logic. Choices must then be made on the type of membership function, logical operators, and formulation of the assessment rules. From a review of the main types of membership functions we conclude that piecewise linear functions are most appropriate in practical applications. Combinations of different fuzzy union (or) and intersection (and) connectives were tested on a 2-dimensional example. Nearly all combinations gave results that partly contradict the associated a priori knowledge, the exception being the Bounded sum connective for or, and the Product connective for and. We also found that in formulating the rules, overlap of predictor classes and negation should be avoided. Unrestricted choice of fuzzy connectives and rule formulation will generally lead to inconsistencies. The selected methods were tested in two case studies: one on suitability for seed-potatoes in an Italian region and one on suitability for grass farming in a Dutch region. The maps produced with the fuzzy and Boolean models are broadly similar. However, maps from the fuzzy models indicate that some areas represent a transition between two original Boolean classes, thereby providing relevant additional information. In the case study on seed-potatoes the quantitative prediction errors of the original Boolean suitability map were greatly reduced by the fuzzification.
    A molecular, morphological and ecological re-appraisal of Venturiales¿a new order of Dothideomycetes
    Zhang, Y. ; Crous, P.W. ; Schoch, C.L. ; Bahkali, A.H. ; Guo, L.D. ; Hyde, K.D. - \ 2011
    Fungal Diversity 51 (2011)1. - ISSN 1560-2745 - p. 249 - 277.
    phylogenetic trees - bayesian-inference - sequence-data - apple scab - sp-nov - venturiaceae - genera - fungi - herpotrichiellaceae - classification
    The Venturiaceae was traditionally assigned to Pleosporales although its diagnostic characters readily distinguish it from other pleosporalean families. These include a parasitic or saprobic lifestyle, occurring on leaves or stems of dicotyledons; small to medium-sized ascomata, often with setae; deliquescing pseudoparaphyses; 8-spored, broadly cylindrical to obclavate asci; 1-septate, yellowish, greenish or pale brown to brown ascospores; and hyphomycetous anamorphs. Phylogenetically, core genera of Venturiaceae form a monophyletic clade within Dothideomycetes, and represent a separate sister lineage from current orders, thus a new order—Venturiales is introduced. A new family, Sympoventuriaceae, is introduced to accommodate taxa of a well-supported subclade within Venturiales, which contains Sympoventuria, Veronaeopsis simplex and Fusicladium-like species. Based on morphology and DNA sequence analysis, eight genera are included in Venturiaceae, viz. Acantharia, Apiosporina (including Dibotryon), Caproventuria, Coleroa, Pseudoparodiella, Metacoleroa, Tyrannosorus and Venturia. Molecular phylogenetic information is lacking for seven genera previously included in Venturiales, namely Arkoola, Atopospora, Botryostroma, Lasiobotrys, Trichodothella, Trichodothis and Rhizogenee and these are discussed, but their inclusion in Venturiaceae is doubtful. Crotone, Gibbera, Lineostroma, Phaeocryptopus, Phragmogibbera, Platychora, Polyrhizon, Rosenscheldiella, Uleodothis and Xenomeris are excluded from Venturiales, and their ordinal placement needs further investigation. Zeuctomorpha is treated as a synonym of Acantharia.
    Trend analysis of copper and zinc in animal feed
    Adamse, P. ; Egmond, H.J. van; Polanen, A. van; Bikker, P. ; Jong, J. de - \ 2011
    Wageningen : Rikilt - Institute of Food Safety (Report / RIKILT 2011.012)
    veevoeder - voersamenstelling - sporenelementen - koper - zink - chemische analyse - classificatie - fodder - feed formulation - trace elements - copper - zinc - chemical analysis - classification
    The EC has introduced maximum inclusion levels of copper and zinc salts in animal diets from 1970 onwards and reduced these levels in recent years. In this report historical values are used to give insight into trends in levels of copper and zinc in compound feeds for animals in the Netherlands. The results of these analyses will enable the nVWA (Dutch Food and Consumer Product Safety Authority) to develop a more risk-directed sampling strategy in the National Feed Monitoring program. Over 2000 feed samples are analysed for this report. The data for this analysis are from the period between 2001 and 2009. The copper and zinc data-set contains mostly feeds for piglets, (older) pigs, sheep and to a lesser extent bovine and other species.
    Possibilities and limitations of artificial neural networks for sub-pixel mapping of land cover
    Nigussie, D. ; Zurita Milla, R. ; Clevers, J.G.P.W. - \ 2011
    International Journal of Remote Sensing 32 (2011)22. - ISSN 0143-1161 - p. 7203 - 7226.
    remotely-sensed imagery - classification - resolution - meris - fusion
    Although developments in remote sensing have greatly improved land cover mapping, the mixed pixel problem has not yet been fully addressed. Soft classification techniques have been introduced to address the problem, but they do not show the spatial location of the class proportions in a pixel. Subpixel mapping has been introduced to address the drawbacks of soft classifications. In this work, the feedforward backpropagating neural network (FFBPNN) was used for subpixel mapping. A set of class proportion images, which are to be treated as soft classification results, were created from a high spatial resolution (25 m) land cover dataset. For this purpose, the land cover dataset was aggregated both thematically (into two, four or eight land cover classes) and spatially (into proportion images with pixel sizes of 75, 150 and 300 m). This resulted in nine different combinations that were considered here as study cases. Several FFBPNNs were trained using these proportion images and the original land cover dataset (which was used as a target). Subsequently, the best networks were used to reconstruct high spatial resolution land cover maps of two heterogeneous areas in the south of The Netherlands. The overall accuracies obtained revealed that the networks were influenced by the spatial frequency, shape and size of the different land cover types. Moreover, it was revealed that most of the errors were on the class boundaries where highly mixed pixels are to be expected. The accuracies spanned a wide range of values depending on the complexity of the cases. Although it was not possible to exhaustively explore all network architectures, the results demonstrate the potential of the FFBPNN for subpixel mapping.
    Phytoplankton community composition can be predicted best in terms of morphological groups
    Kruk, C. ; Peeters, E.T.H.M. ; Nes, E.H. van; Huszar, V.M. ; Costa, L.S. ; Scheffer, M. - \ 2011
    Limnology and Oceanography 56 (2011)1. - ISSN 0024-3590 - p. 110 - 118.
    functional types - body-size - plankton - ecology - lake - diversity - classification - nutrient - evolution - patterns
    We explored how well the aggregated biovolume of groups of species can be predicted from environmental variables using three different classification approaches: morphology-based functional groups, phylogenetic groups, and functional groups proposed by Reynolds. We assessed the relationships between biovolume of each group and environmental conditions using canonical correlation analyses as well as multiple linear regressions, using data from 211 lakes worldwide ranging from subpolar to tropical regions. We compared the results of these analyses with those obtained for single species following the same protocol. While some species appear relatively predictable, a vast majority of the species showed no clear relationship to the environmental conditions we had measured. However, both the multivariate and the regression analyses indicated that morphology-based groups can be predicted better from environmental conditions than groups based on the other classification methods. This suggests that morphology captures ecological function of phytoplankton well, and that functional groups based on morphology may be the most suitable focus for predicting the composition of communities
    Data integration and network reconstruction with ~omics data using Random Forest regression in potato
    Acharjee, A. ; Kloosterman, B.A. ; Vos, R.C.H. de; Werij, J.S. ; Bachem, C.W.B. ; Visser, R.G.F. ; Maliepaard, C.A. - \ 2011
    Analytica Chimica Acta 705 (2011)1-2. - ISSN 0003-2670 - p. 56 - 63.
    mass-spectrometry - systems biology - microarray data - classification - metabolomics - proteomics - tomato - qtl - biomarkers - phenotypes
    In the post-genomic era, high-throughput technologies have led to data collection in fields like transcriptomics, metabolomics and proteomics and, as a result, large amounts of data have become available. However, the integration of these ~omics data sets in relation to phenotypic traits is still problematic in order to advance crop breeding. We have obtained population-wide gene expression and metabolite (LC–MS) data from tubers of a diploid potato population and present a novel approach to study the various ~omics datasets to allow the construction of networks integrating gene expression, metabolites and phenotypic traits. We used Random Forest regression to select subsets of the metabolites and transcripts which show association with potato tuber flesh color and enzymatic discoloration. Network reconstruction has led to the integration of known and uncharacterized metabolites with genes associated with the carotenoid biosynthesis pathway. We show that this approach enables the construction of meaningful networks with regard to known and unknown components and metabolite pathways.
    Functional classification of spatially heterogeneous environments: the Land Cover Mosaic approach in remote sensing
    Obbink, M.H. - \ 2011
    Wageningen University. Promotor(en): M. Molenaar, co-promotor(en): Jan Clevers. - [S.l.] : S.n. - ISBN 9789085859956 - 304
    remote sensing - heterogeniteit - tropische regenbossen - ruimtelijke variatie - classificatie - landschapsecologie - besluitvorming - remote sensing - heterogeneity - tropical rain forests - spatial variation - classification - landscape ecology - decision making

    Tropical rainforest areas are difficult to classify in the digital analysis of remote sensing data because of spatial heterogeneity. Often many technical solutions are adopted to reduce the ‘problem’ of spatial heterogeneity. This thesis describes theory and methods that now use this heterogeneity during the digital image classification. With spatial heterogeneity, spatial aggregation levels such as patches,patch-mosaics and landscapes can be distinguished. Consequently, vegetation patterns can be related to functional management units at different decision-levels. The developed theory and methods thus save two birds with one stone: (a) the classification is completely digitally, and (b) the classification provides information on deforestation that meets the needs of decision-makers. This thesis further recommends approaching all land cover classifications from a heterogeneous perspective for understanding and controlling environmental processes on a global level. This can enhance a sustainable development of tropical rainforest areas for the benefit of future generations.

    Spatial autocorrelation in predictors reduces the impact of positional uncertainty in occurrence data on species distribution modelling
    Naimi, B. ; Skidmore, A.K. ; Groen, T.A. ; Hamm, N.A.S. - \ 2011
    Journal of Biogeography 38 (2011)8. - ISSN 0305-0270 - p. 1497 - 1509.
    adaptive regression splines - ecological theory - classification - errors - performance - prevalence - criteria - account - maxent
    Aim To investigate the impact of positional uncertainty in species occurrences on the predictions of seven commonly used species distribution models (SDMs), and explore its interaction with spatial autocorrelation in predictors. Methods A series of artificial datasets covering 155 scenarios including different combinations of five positional uncertainty scenarios and 31 spatial autocorrelation scenarios were simulated. The level of positional uncertainty was defined by the standard deviation of a normally distributed zero-mean random variable. Each dataset included two environmental gradients (predictor variables) and one set of species occurrence sample points (response variable). Seven commonly used models were selected to develop SDMs: generalized linear models, generalized additive models, boosted regression trees, multivariate adaptive regression spline, random forests, genetic algorithm for rule-set production and maximum entropy. A probabilistic approach was employed to model and simulate five levels of error in the species locations. To analyse the propagation of positional uncertainty, Monte Carlo simulation was applied to each scenario for each SDM. The models were evaluated for performance using simulated independent test data with Cohen's Kappa and the area under the receiver operating characteristic curve. Results Positional uncertainty in species location led to a reduction in prediction accuracy for all SDMs, although the magnitude of the reduction varied between SDMs. In all cases the magnitude of this impact varied according to the degree of spatial autocorrelation in predictors and the levels of positional uncertainty. It was shown that when the range of spatial autocorrelation in the predictors was less than or equal to three times the standard deviation of the positional error, the models were less affected by error and, consequently, had smaller decreases in prediction accuracy. When the range of spatial autocorrelation in predictors was larger than three times the standard deviation of positional error, the prediction accuracy was low for all scenarios. Main conclusions The potential impact of positional uncertainty in species occurrences on the predictions of SDMs can be understood by comparing it with the spatial autocorrelation range in predictor variables.
    Exploring the diversity of urban and peri-urban agricultural systems in Sudano-Sahelian West Africa: An attempt towards a regional typology
    Dossa, L.C. ; Abdulkadir, A. ; Amadou, H. ; Sangare, S. ; Schlecht, E. - \ 2011
    Landscape and Urban Planning 102 (2011)3. - ISSN 0169-2046 - p. 197 - 206.
    principal-components-analysis - farming systems - milk-production - burkina-faso - management - opportunities - classification - potentials - algorithm - countries
    Developing appropriate and innovative technologies and policies to respond to the challenges that urban and peri-urban agriculture (UPA) faces in West Africa requires a better understanding of the existing production systems. Although there is an increasing recognition of the importance of UPA in the region, its extent, forms and related practices may vary across countries and cities because of different socio-economic conditions and urbanization patterns. A systematic classification of the regional UPA systems is lacking but is necessary to allow for meaningful comparisons between cities and avoid misleading generalizations. The purpose of this study was to develop a typology of UPA households across three selected West African cities. Survey data from 318 UPA households (Kano: 99, Bobo Dioulasso: 111, Sikasso: 108) were submitted to principal components analysis for categorical variables (CATPCA). Next, the Two-Step cluster method was used to classify the households using object scores obtained from the CATPCA. Diversification of farm activities, farm resource endowment and production orientation were the major discriminating variables. In each city, four distinct UPA systems were identified, of which three were common to Kano, Bobo Dioulasso and Sikasso: commercial gardening plus field crops and livestock (59%, 18%, and 37%), commercial livestock plus subsistence field cropping (14%, 41%, and 7%), and commercial gardening plus semi-commercial field cropping (14%, 28%, and 30%). The fourth group was different at each location and was characterized as follows: commercial gardening plus semi-commercial livestock in Kano (13%), commercial field cropping in Bobo Dioulasso (13%) and commercial gardening in Sikasso (26%).
    Doppenclassificatie fruitteelt : driftmetingen klassengroepen : veldmetingen 2008-2009
    Stallinga, H. ; Zande, J.C. van de; Wenneker, M. ; Michielsen, J.G.P. ; Velde, P. van; Joosten, N. - \ 2011
    Wageningen : Plant Research International (Rapport / Plant Research International 365) - 66
    boomgaarden - gewasbescherming - chemische bestrijding - spuitapparatuur - spuitstukken - classificatie - spuiten - drift - reductie - fruitteelt - spuitdoppen - orchards - plant protection - chemical control - spraying equipment - nozzles - classification - spraying - drift - reduction - fruit growing - fan nozzles
    Op basis van laboratorium metingen kunnen spuitdoppen geïdentificeerd worden waarvan de dop-drukcombinaties in te delen zijn in driftreductieklassen van 50, 75, 90 en 95%. In deze rapportage worden de resultaten van de veldmetingen beschreven die deze indeling onder veldomstandigheden aantonen. De metingen werden uitgevoerd bij PPO Fruit te Randwijk.
    Actualisering van de kennis van de zouttolerantie van landbouwgewassen, op basis van literatuuronderzoek, expertkennis en praktische ervaringen
    Bakel, P.J.T. van; Stuyt, L.C.P.M. - \ 2011
    Wageningen : Alterra (Alterra-rapport 2201) - 72
    gewassen - veldgewassen - zouttolerantie - classificatie - waterbehoefte - crops - field crops - salt tolerance - classification - water requirements
    De tekorten aan zoetwater voor een aanvullende watervoorziening van de landbouw in Nederland zullen door klimaat-verandering in ernst en omvang toenemen. Dit vraagt om anders omgaan met zoet water maar ook om actualisering van kennis van de zouttolerantie van landbouwgewassen in de open vollegrond. Deze actualisatie is aan de hand van literatuuronderzoek, expertkennis en praktische ervaring uitgevoerd. Daarbij is aangesloten op de in de buitenlandse literatuur gebruikelijke indeling van gewassen in vier zouttolerantieklassen, met bijbehorende schadefuncties. Voor het waterbeheer is de relatie tussen chlorideconcentraties in bodemwater en die in het beregeningswater c.q. het oppervlaktewater van belang. Deze relatie is sterk afhankelijk van de weersomstandigheden en bodemeigenschappen en is alleen met simulatiemodellen te operationaliseren. Voor een worst case situatie is een tabel opgesteld waarmee de zoutschade aan landbouwgewassen door het gebruik van zouthoudend beregeningswater kan worden bepaald. In de discussie wordt ingegaan op de vraag of de resultaten van in het buitenland uitgevoerde proeven mogen worden gebruikt. Een belangrijke conclusie is dat het omgaan met verzilt water door zowel agrariërs als waterbeheerders kan worden verbeterd. Dit rapport geeft hiervoor handreikingen.
    Constructing naive Bayesian classifiers for veterinary medicine: A case study in the clinical diagnosis of classical swine fever
    Geenen, P.L. ; Gaag, L.C. van der; Loeffen, W.L.A. ; Elbers, A.R. - \ 2011
    Research in Veterinary Science 91 (2011)1. - ISSN 0034-5288 - p. 64 - 70.
    network classifiers - classification - epidemiology - netherlands - selection - diseases - signs - sheep
    For diseases of which the clinical diagnosis is uncertain, naive Bayesian classifiers can be of assistance to the veterinary practitioner. These simple probabilistic models have proven to be very powerful for solving classification problems in a variety of domains, but are not yet widely applied within the veterinary domain. In this paper, naive Bayesian classifiers and methods for their construction are reviewed. We demonstrate how to construct full and selective classifiers from a data set and how to build such classifiers from information in the literature. As a case study, naive Bayesian classifiers to discriminate between classical swine fever (CSF)-infected and non-infected pig herds were constructed from data collected during the 1997/1998 CSF epidemic in the Netherlands. The resulting classifiers were studied in terms of their accuracy and compared with the optimally efficient diagnostic rule that was reported earlier by Elbers et al. (2002). The classifiers were found to have accuracies within the range of 67–70% and performed comparable to or even better than the diagnostic rule on the available data. In contrast with the diagnostic rule, the classifiers had the advantage of taking both the presence and the absence of particular clinical signs into account, which resulted in more discriminative power. These results indicate that naive Bayesian classifiers are promising tools for solving diagnostic problems in the veterinary field.
    Chemometric investigation of the volatile content of young South African wines
    Weldegergis, B.T. ; Villiers, A. de; Crouch, A.M. - \ 2011
    Food Chemistry 128 (2011)4. - ISSN 0308-8146 - p. 1100 - 1109.
    bar sorptive extraction - white wines - saccharomyces-cerevisiae - instrumental analysis - isoamyl acetate - gc-ms - fermentation - aroma - yeast - classification
    The content of major volatiles of 334 wines of six different cultivars (Sauvignon Blanc, Chardonnay, Pinotage, Shiraz, Cabernet Sauvignon and Merlot) and vintage 2005 was used to investigate the aroma content of young South African wines. Wines were sourced from six different regions and various producers. Thirty-nine volatile components partially responsible for the flavour of wine were quantified. In order to investigate possible correlation between volatile content and grape variety and/or geographical origin, analysis of variance, factor analysis (FA), principal component analysis (PCA) and linear discriminant analysis (LDA) were used. Significant differences in the levels of certain volatiles were observed as a function of region and cultivar, with the latter factor proving to be more influential. A few volatile compounds were identified as potential predictors of the white wine cultivars. Prediction for red wine cultivars was poor, with the exception of Pinotage wines, for which three compounds (isoamyl acetate, isoamyl alcohol and ethyl octanoate) were identified as accurate predictors. The reasons for the importance of these three volatile compounds in distinguishing young Pinotage wines are discussed, and possible reasons for the unique levels in wines of this cultivar are highlighted
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