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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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 p.
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

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 p.
rivieren - kaderrichtlijn water - waterbeheer - classificatie - waterkwaliteit - aquatische ecologie - monitoring - rivers - water framework directive - water management - classification - water quality - aquatic ecology
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.
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.
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
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.
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 - taxonomy - classification - 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.

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 - 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
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.
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 - 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.

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 - 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.
IEA Bioenergy Task 42 Biorefinery
Jong, E. de; Langeveld, H. ; Ree, R. van - \ 2011
IEA Bioenergy
biobased economy - bioraffinage - biomassa cascadering - classificatie - coproductie - fabrieken - biorefinery - biomass cascading - classification - coproduction - factories
The objective of the brochure is to inform policy makers, non-governmental organisations (NGOs), researchers and entrepreneurs on the principle of biorefinery, its potential contribution to food and feed production, bioenergy and waste management, and its perspectives in the context of a growing demand for food, feed, energy and products from renewable resources. This brochure will begin with the definition of biorefineries developed by IEA Bioenergy Task 42. The heterogeneity and diversity of the biorefinery field require a uniform definition and a clear classification system. To illustrate the different biorefinery types, and their current technological status and/or development and deployment perspectives, examples from different countries will subsequently be presented. They will be linked to the classification system, in order to give a clear classified overview of both the current status and future perspectives of biorefineries worldwide. The brochure will wrap up with some general comments and a future outlook for the next triennium.
Nederland is groener dan kaarten laten zien : mogelijkheden om 'groen' beter te inventariseren en monitoren met de automatische classificatie van digitale luchtfoto's
Kramer, H. ; Oldengarm, J. ; Roupioz, L.F.S. - \ 2010
Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-werkdocument 216) - 50
openbaar groen - vegetatie - landschapselementen - luchtfotografie - monitoring - databanken - classificatie - utrecht - stedelijke gebieden - zuidelijk flevoland - platteland - noord-brabant - public green areas - vegetation - landscape elements - aerial photography - databases - classification - urban areas - rural areas
Het doel van dit project is een methode te ontwikkelen waarmee landsdekkend informatie over kleine groene landschapselementen in het landelijke gebied en over het groen in de stad c.q. bebouwd gebied verzameld wordt. Op basis van de beschikbare luchtfoto 2006 is voor Utrecht en Almere het groen in het stedelijk gebied verzameld. Voor het landelijk gebied is een deel van het Nationaal Landschap Het Groene Woud verwerkt.
Alien and invasive woody species in the dunes of the Wadden Sea Island of Vlieland: a remote sensing approach
Hantson, W. ; Kooistra, L. ; Slim, P.A. - \ 2010
Wageningen : Alterra (Alterra-report 2101) - 54
struiken - invasie - cartografie - remote sensing - classificatie - prunus serotina - rosa rugosa - natuurbescherming - nederland - nederlandse waddeneilanden - shrubs - invasion - mapping - classification - nature conservation - netherlands - dutch wadden islands
In this study we mapped (alien) invasive shrubs for management and conservation purposes. On the study site, the Wadden Sea Island of Vlieland, they are a serious treat for the quality of the grey dune habitat. We developed a remote sensing approach that delivers detailed and standardized maps of (alien) shrub cover. Three classification methods are used: maximum likelihood (ML) classification of aerial photographs, maximum likelihood classification aerial photographs combined with vegetation heights derived from LIDAR data (ML+), and object-based shrub classification.
Landelijk Grondgebruiksbestand Nederland versie 6 (LGN6) : vervaardiging, nauwkeurigheid en gebruik
Hazeu, G.W. ; Schuiling, C. ; Dorland, G.J. van; Oldengarm, J. ; Gijsbertse, H.A. - \ 2010
Wageningen : Alterra (Alterra-rapport 2012) - 132
landgebruik - classificatie - databanken - monitoring - remote sensing - luchtfotografie - nederland - landbouw - landgebruiksmonitoring - natuur - land use - classification - databases - aerial photography - netherlands - agriculture - land use monitoring - nature
De snelle veranderingen die zich in Nederland voordoen met betrekking tot het gebruik van ruimte en de conflicterende belangen van veel gebruikers van deze ruimte, zorgen voor een voortdurende behoefte aan actuele geografische bestanden. Eén van deze bestanden is het Landelijke Grondgebruiksbestand Nederland (LGN). Sinds 1986 wordt met een periodiciteit van 3-5 jaar het LGN-bestand geproduceerd. Het LGN6-bestand is een rasterbestand met een resolutie van 25*25 m. Het bestand geeft het Nederlandse landgebruik voor de jaren 2007/2008 weer. De thematiek en geometrie van Top10vector (versie 2006) vormt op hoofdklassen de basis voor LGN6. Daarnaast zijn satellietbeelden, luchtfoto’s en enkele bestanden, o.a. ‘Bestand BodemGebruik 2003’ en ‘Basiskaart Natuur 2007’ gebruikt voor de productie van LGN6. In het bestand worden 39 verschillende typen van landgebruik onderscheiden. De 39 landgebruiksklassen zijn geaggregeerd naar de monitoringsklassen agrarisch gebied, boomgaarden, kassen, bebouwd gebied, bos, water, infrastructuur en natuur. Veranderingen in landgebruik tussen LGN5 en LGN6 zijn voor deze klassen gemonitoord. In de betreffende periode 2004-2008 is 0.7% van het Nederlands land oppervlak in landgebruik veranderd.
Morphology captures function in phytoplankton : a large-scale analysis of phytoplankton communities in relation to their environment
Kruk, C. - \ 2010
Wageningen University. Promotor(en): Marten Scheffer, co-promotor(en): Edwin Peeters. - [S.l : S.n. - ISBN 9789085856177 - 117
fytoplankton - gemeenschapsecologie - biomassa - biomassa productie - milieufactoren - morfologie - classificatie - aquatische ecologie - modelleren - ecologische modellering - phytoplankton - community ecology - biomass - biomass production - environmental factors - morphology - classification - aquatic ecology - modeling - ecological modeling
Predicting phytoplankton community dynamics in detail seems an overwhelming task as there are so many species, and a myriad of combinations of potential conditioning factors. Furthermore, even with full knowledge of all aspects of species biology intrinsic chaos in communities may make detailed prediction fundamentally impossible. Aggregated estimators of phytoplankton communities may work to predict overall community responses to varying environmental conditions. However, phytoplankton species differ strongly in their effect on ecosystem functioning and ecosystem services. Therefore, it is important to consider community composition rather than just biomass. This thesis focuses on the question whether species might be clustered in groups that are reasonably homogeneous in a functional sense, and might be better predictable from environmental conditions than individual species. To answer this question we first explored the factors that affect richness and biomass at the species level and then evaluated how well trait-based groups of species capture function and may be predicted from environmental conditions. We used a large data base including more than 700 species from 200 lakes in different climate zones and continents.
A multi-scale object-bases approach to mapping coastal Natura 2000 habitat types using high spatial resolution airborne imagery and LIDAR data
Baptist, E. - \ 2009
Wageningen : Alterra (Alterra-rapport 1929) - 69 p.
habitats - kustgebieden - cartografie - remote sensing - classificatie - nederland - natura 2000 - nederlandse waddeneilanden - coastal areas - mapping - classification - netherlands - dutch wadden islands
This study was conducted to provide a method for a remote sensing-based inventory of the coastal Natura 2000 habitats. A multilevel object-based approach was used. The habitat types were classified with a hierarchical rule-based key derived from the EUNIS habitat classification system. Data used for this classification were high-resolution true color images, high-resolution false color images, and DTM- and LIDAR-derived vegetation heights. The model developed was tested in the dynamic coastal zone of the island of Ameland
Graph-based methods for large-scale protein classification and orthology inference
Kuzniar, A. - \ 2009
Wageningen University. Promotor(en): Jack Leunissen, co-promotor(en): Roeland van Ham; S. Pongor. - [S.l. : S.n. - ISBN 9789085855019 - 139
bio-informatica - eiwitten - classificatie - algoritmen - grafieken - evolutie - bioinformatics - proteins - classification - algorithms - graphs - evolution
The quest for understanding how proteins evolve and function has been a prominent and costly human endeavor. With advances in genomics and use of bioinformatics tools, the diversity of proteins in present day genomes can now be studied more efficiently than ever before. This thesis describes computational methods suitable for large-scale protein classification of many proteomes of diverse species. Specifically, we focus on methods that combine unsupervised learning (clustering) techniques with the knowledge of molecular phylogenetics, particularly that of orthology. In chapter 1 we introduce the biological context of protein structure, function and evolution, review the state-of-the-art sequence-based protein classification methods, and then describe methods used to validate the predictions. Finally, we present the outline and objectives of this thesis. Evolutionary (phylogenetic) concepts are instrumental in studying subjects as diverse as the diversity of genomes, cellular networks, protein structures and functions, and functional genome annotation. In particular, the detection of orthologous proteins (genes) across genomes provides reliable means to infer biological functions and processes from one organism to another. Chapter 2 evaluates the available computational tools, such as algorithms and databases, used to infer orthologous relationships between genes from fully sequenced genomes. We discuss the main caveats of large-scale orthology detection in general as well as the merits and pitfalls of each method in particular. We argue that establishing true orthologous relationships requires a phylogenetic approach which combines both trees and graphs (networks), reliable species phylogeny, genomic data for more than two species, and an insight into the processes of molecular evolution. Also proposed is a set of guidelines to aid researchers in selecting the correct tool. Moreover, this review motivates further research in developing reliable and scalable methods for functional and phylogenetic classification of large protein collections. Chapter 3 proposes a framework in which various protein knowledge-bases are combined into unique network of mappings (links), and hence allows comparisons to be made between expert curated and fully-automated protein classifications from a single entry point. We developed an integrated annotation
resource for protein orthology, ProGMap (Protein Group Mappings, http://www.bioinformatics.nl/progmap), to help researchers and database annotators who often need to assess the coherence of proposed annotations and/or group assignments, as well as users of high throughput methodologies (e.g., microarrays or proteomics) who deal with partially annotated genomic data. ProGMap is based on a non-redundant dataset of over 6.6 million protein sequences which is mapped to 240,000 protein group descriptions collected from UniProt, RefSeq, Ensembl, COG, KOG, OrthoMCL-DB, HomoloGene, TRIBES and PIRSF using a fast and fully automated sequence-based mapping approach. The ProGMap database is equipped with a web interface that enables queries to be made using synonymous sequence identifiers, gene symbols, protein functions, and amino acid or nucleotide sequences. It incorporates also services, namely BLAST similarity search and QuickMatch identity search, for finding sequences similar (or identical) to a query sequence, and tools for presenting the results in graphic form. Graphs (networks) have gained an increasing attention in contemporary biology because they have enabled complex biological systems and processes to be modeled and better understood. For example, protein similarity networks constructed of all-versus-all sequence comparisons are frequently used to delineate similarity groups, such as protein families or orthologous groups in comparative genomics studies. Chapter 4.1 presents a benchmark study of freely available graph software used for this purpose. Specifically, the computational complexity of the programs is investigated using both simulated and biological networks. We show that most available software is not suitable for large networks, such as those encountered in large-scale proteome analyzes, because of the high demands on computational resources. To address this, we developed a fast and memory-efficient graph software, netclust (http://www.bioinformatics.nl/netclust/), which can scale to large protein networks, such as those constructed of millions of proteins and sequence similarities, on a standard computer. An extended version of this program called Multi-netclust is presented in chapter 4.2. This tool that can find connected clusters of data presented by different network data sets. It uses user-defined threshold values to combine the data sets in such a way that clusters connected in all or in either of the networks can be retrieved efficiently. Automated protein sequence clustering is an important task in genome annotation projects and phylogenomic studies. During the past years, several protein clustering programs have been developed for delineating protein families or orthologous groups from large sequence collections. However, most of these programs have not been benchmarked systematically, in particular with respect to the trade-off between computational complexity and biological soundness. In chapter 5 we evaluate three best known algorithms on different protein similarity networks and validation (or 'gold' standard) data sets to find out which one can scale to hundreds of proteomes and still delineate high quality similarity groups at the minimum computational cost. For this, a reliable partition-based approach was used to assess the biological soundness of predicted groups using known protein functions, manually curated protein/domain families and orthologous groups available in expert-curated databases. Our benchmark results support the view that a simple and computationally cheap method such as netclust can perform similar to and in cases even better than more sophisticated, yet much more costly methods. Moreover, we introduce an efficient graph-based method that can delineate protein orthologs of hundreds of proteomes into hierarchical similarity groups de novo. The validity of this method is demonstrated on data obtained from 347 prokaryotic proteomes. The resulting hierarchical protein classification is not only in agreement with manually curated classifications but also provides an enriched framework in which the functional and evolutionary relationships between proteins can be studied at various levels of specificity. Finally, in chapter 6 we summarize the main findings and discuss the merits and shortcomings of the methods developed herein. We also propose directions for future research. The ever increasing flood of new sequence data makes it clear that we need improved tools to be able to handle and extract relevant (orthological) information from these protein data. This thesis summarizes these needs and how they can be addressed by the available tools, or be improved by the new tools that were developed in the course of this research.
Proceedings of the Vth international symposium on taxonomy of cultivated plants
Berg, R.G. van den; Groendijk-Wilders, N. ; Alexander, C. ; Hetterscheid, W.L.A. - \ 2008
Leuven : ISHS (Acta horticulturae no. 799) - ISBN 9789066055711 - 210
gewassen - planten - classificatie - biologische naamgeving - taxonomie - crops - plants - classification - biological nomenclature - taxonomy
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