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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    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.
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