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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    Improving the limits of detection in sensor systems
    Bent, J.F. van der - \ 2017
    Wageningen University. Promotor(en): C.J.M. van Rijn. - Wageningen : Wageningen University - ISBN 9789463430555 - 127
    sensors - data processing - nanotechnology - potentiometers - detection - sensors - gegevensverwerking - nanotechnologie - potentiometers - detectie

    Nowadays, sensors are designed to consume less power with decreased size, making them suitable for application in low-power wireless sensor networks (WSN) systems. The challenge is not to compromise on the sensor’s sensitivity and selectivity towards the target. This thesis studies various options to improve the limits of detection. Usually, sensors are limited in detection range and resolution; they are also restricted by cross sensitivity towards other target agents and other parameters. This cross sensitivity, towards humidity and temperature, for instance, reduces the sensor’s detection limit and, therefore, its usability. This work discusses three examples where the limit of detection has been investigated, localised and improved with nanotech-based sensors.

    The first example is a nanowire-based hydrogen sensor. The second example was based on a potentiometric-sensor principle, capable of sensing CO2. The third example is an Inter-Digitated Electrode (IDE) sensor, capable of selective sensing through the coating of an active layer.

    Dick de Ridder over de bioloog die steeds meer een datawetenschapper wordt
    Ridder, D. de - \ 2015
    Wageningen UR
    bio-informatica - gegevensverwerking - informatica - beroepen - moleculaire biologie - bioinformatics - data processing - informatics - occupations - molecular biology
    De biologie krijgt snel het karakter van een datawetenschap. Miljarden gegevens over genomen, genen, eiwitten en andere moleculen worden in grote bestanden bij elkaar gebracht en systematisch onderzocht. Dit moet leiden tot meer basiskennis en begrip van levende organismen waarvan gewassen en vee aan de basis staan van de voedselvoorziening van de wereldbevolking. Dat zegt prof.dr.ir. Dick de Ridder in zijn inaugurele rede bij de aanvaarding van het ambt van hoogleraar Bioinformatica aan Wageningen University op 30 april.
    Overview of topics and questions to be addressed by the FG Mainstreaming Precision Farming : starting paper for FG meeting held on 3 and 4 June 2014
    Kempenaar, C. - \ 2014
    Brussels : EIP-AGRI - 9
    precisielandbouw - akkerbouw - voedselketens - agro-industriële ketens - software-ontwikkeling - gegevensanalyse - gegevensverwerking - akkerbouw- en tuinbouwbedrijven - veehouderijbedrijven - precision agriculture - arable farming - food chains - agro-industrial chains - software engineering - data analysis - data processing - crop enterprises - livestock enterprises
    Precision farming is an innovation in agriculture allowing the right treatment of crops and livestock at the right time and smallest scale possible. It requires a seamless integration of different technologies and intelligence. Optimization of treatments at the lowest scale possible will improve yields and resource efficiency in agri-food chains, so reducing the agricultural footprint. More and more, precision farming will become the ‘licence to produce’ for farmers in the EU.
    Trendanalyse van contaminanten in diervoeders : mogelijkheden en problemen bij het gebruik van historische monitoringsgegens
    Adamse, P. ; Boer, W.J. de; Nijs, W.C.M. de - \ 2014
    Wageningen : RIKILT Wageningen UR (RIKILT report 2014.007) - 53
    besmetters - diervoeding - historische verslagen - tendensen - statistische analyse - gevalsanalyse - voedselveiligheid - voedingsnormen - gegevensverwerking - analytische methoden - contaminants - animal nutrition - historical records - trends - statistical analysis - case studies - food safety - feeding standards - data processing - analytical methods
    Voor het verkrijgen van inzicht in het basisniveau van een contaminant in een diervoeder kan gebruik worden gemaakt van monitoringsgegevens. Zowel de gegevens als de te gebruiken technieken moeten wel aan bepaalde voorwaarden voldoen. In een vorig rapport (Adamse, 2014) staat beschreven hoe met redelijk eenvoudige statistische basistools analyses kunnen worden uitgevoerd. In het huidige rapport staan meer complexe statistische analyses beschreven met daarbij de mogelijkheden en potentiele problemen.
    Trendanalyse van historische gegevens : handleiding voor het gebruik van monitoringsgegevens
    Adamse, P. - \ 2014
    Wageningen : RIKILT Wageningen UR (RIKILT report 2014.001) - 22
    tendensen - historische verslagen - monitoring - analytische methoden - statistische analyse - diervoeding - besmetters - voedselveiligheid - voedingsnormen - gegevensverwerking - voederveiligheid - trends - historical records - monitoring - analytical methods - statistical analysis - animal nutrition - contaminants - food safety - feeding standards - data processing - feed safety
    Het doel van dit rapport is om aan te geven welke technieken gebruikt kunnen worden om inzicht te krijgen in het achtergrondniveau van contaminanten in diervoeders en diervoederproducten. Beschreven is tevens met welke factoren rekening gehouden moet worden bij het gebruik van historische monitoringsgegevens. Deze gegevens zijn verzameld in het kader van monitoringsprogramma’s.
    Citizen science in hydrology and waterresources: opportunities for knowledge generation, ecosystem service management, and sustainable development
    Buytaert, W. ; Zulkafi, Z. ; Grainger, S. ; Acosta, L. ; Alemie, T.C. ; Bastiaensen, J. ; Bièvre, B. de; Bhusal, J. ; Clark, J. ; Dewulf, A.R.P.J. ; Foggin, M. ; Hannah, D.M. ; Hergarten, C. ; Isaeva, A. ; Karpouzoglou, T.D. ; Pandeya, B. ; Paudel, D. ; Sharma, K. ; Steenhuis, T.S. ; Tilahun, S. ; Hecken, G. van; Zhumanova, M. - \ 2014
    Frontiers in Earth Science 2 (2014). - ISSN 2296-6463 - 21
    klimaatverandering - gegevensverwerking - gegevensanalyse - burgers - publieke participatie - climatic change - data processing - data analysis - citizens - public participation
    The participation of the general public in the research design, data collection and interpretation process together with scientists is often referred to as citizen science. While citizen science itself has existed since the start of scientific practice, developments in sensing technology, data processing and visualization, and communication of ideas and results, are creating a wide range of new opportunities for public participation in scientific research. This paper reviews the state of citizen science in a hydrological context and explores the potential of citizen science to complement more traditional ways of scientific data collection and knowledge generation for hydrological sciences and water resources management. Although hydrological data collection often involves advanced technology, the advent of robust, cheap, and low-maintenance sensing equipment provides unprecedented opportunities for data collection in a citizen science context. These data have a significant potential to create new hydrological knowledge, especially in relation to the characterization of process heterogeneity, remote regions, and human impacts on the water cycle. However, the nature and quality of data collected in citizen science experiments is potentially very different from those of traditional monitoring networks. This poses challenges in terms of their processing, interpretation, and use, especially with regard to assimilation of traditional knowledge, the quantification of uncertainties, and their role in decision support. It also requires care in designing citizen science projects such that the generated data complement optimally other available knowledge. Lastly, using 4 case studies from remote mountain regions we reflect on the challenges and opportunities in the integration of hydrologically-oriented citizen science in water resources management, the role of scientific knowledge in the decision-making process, and the potential contestation to established community institutions posed by co-generation of new knowledge.
    Gezonde kas : van toekomstbeeld naar realiteit
    Zijlstra, C. - \ 2014
    Kas techniek 2014 (2014)september. - p. 10 - 13.
    glastuinbouw - kastechniek - automatisering - monitoring - detectie - sensors - methodologie - gegevensverwerking - cultuurmethoden - greenhouse horticulture - greenhouse technology - automation - monitoring - detection - sensors - methodology - data processing - cultural methods
    Het Gezonde Kas-systeem is een innovatief, integraal gewasbeschermingssysteem voor in de moderne kas. Het is een hulpmiddel dat telers tijdig attendeert op de aanwezigheid van ziekten en plagen, helpt bij het nemen van beslissingen en bij het toepassen van maatregelen. In deze editie van KAS Techniek word stilgestaan bij verschillende deelprojecten, in dit artikel een toelichting op het Gezonde Kas-project.
    Kansen voor verbinden en analyseren van datastromen in de schapenhouderij
    Holster, H.C. ; Antonis, A.F.G. ; Bergevoet, R.H.M. ; Vellema, P. ; Verkaik, J.C. ; Bokma-Bakker, M.H. - \ 2014
    Lelystad : Wageningen UR Livestock Research (Report / Wageningen UR Livestock Research 780) - 46
    schapenhouderij - schapen - nederland - publiek-private samenwerking - diergezondheid - dierenwelzijn - gegevensverwerking - gegevensanalyse - bedrijfsgegevens - professionaliteit - sheep farming - sheep - netherlands - public-private cooperation - animal health - animal welfare - data processing - data analysis - farm accountancy data - professionalism
    Een grote uitdaging is het professionaliseren van de schapenhouderij en het verbeteren van het economisch perspectief ervan, met behoud van het goede imago. Binnen de Publiek-Private Samenwerking Kleine Herkauwers-Schapen (PVE en EZ) is onderzoek uitgevoerd naar kansen voor van het verbinden van bestaande datastromen in de keten en het analyseren van data ter ondersteuning van de kwaliteitsslag die de sector wil maken.
    Sprectraaldata voor perceelsanalyse (140)
    Evert, F.K. van; Aarts, H. - \ 2013
    Wageningen : Plant Research International, Business Unit Agrosysteemkunde - 11
    akkerbouw - spectrale gegevens - precisielandbouw - geografische informatiesystemen - perceelsvorm (landbouwkundig) - gegevensverwerking - computer software - sensors - arable farming - spectral data - precision agriculture - geographical information systems - field shape - data processing - computer software - sensors
    Spectraaldata voor perceelsanalyse: In QMS akkerbouw, dat deels binnen PPL is ontwikkeld, kunnen de groei en andere parameters van een gewasperceel worden vergeleken met vergelijkbare percelen. QMS Akkerbouw ontvangt hiertoe beelden van Mijnakker waarop biomassa (toename per week, kg/ha; of cumulatief, kg/ha) staat afgebeeld met waarden op perceelsniveau. Deze informatie wordt aangevuld met aangevuld met specifieke perceelgegevens en andere metingen aan het gewas op het veld.
    Plantspecifieke data uit onkruidherkenning : PPL-138
    Nieuwenhuizen, A.T. ; Hemming, J. ; Verwijs, B.R. - \ 2013
    Wageningen : Plant Research International, Business Unit Agrosysteemkunde - 10
    akkerbouw - precisielandbouw - onkruiden - gewasbescherming - detectie - gegevensverwerking - plaatselijke toepassing - geografische informatiesystemen - onkruidwieders - arable farming - precision agriculture - weeds - plant protection - detection - data processing - topical application - geographical information systems - weeders
    Het ontwikkelen van cameragestuurde intrarijwieders is een van de voorbeelden van ontwikkelingen richting hightech precisielandbouw. Voor deze vorm van precisielandbouw wordt veel informatie verzameld die maar ten dele gebruikt wordt in het gewasmanagement en bedrijfsvoering van het akkerbouwbedrijf. Bij de ontwikkeling van een cameragestuurde intrarijwieder wordt de opgenomen informatie alleen verwerkt en gebruikt voor het op het juiste moment aansturen van schoffelelementen die in de rij werken. Met de recent ontwikkelde plantentelmachine worden, op dit moment, alleen suikerbietenplanten geteld. Bij beide machines bevatten de beelden ook informatie waarmee bijvoorbeeld de onkruiddruk, groeistadium en plantkleur van het cultuurgewas opgenomen kan worden. Wanneer de verkregen data aan GPS data wordt gekoppeld kan locatie specifieke data verzameld worden waardoor de data onder andere ook grafisch gepresenteerd kan worden.
    Automatisch onkruid bestrijden PPL-094 : doorontwikkelen algoritmes voor herkenning onkruid in uien, peen en spinazie
    Hemming, J. ; Barth, R. ; Nieuwenhuizen, A.T. - \ 2013
    Wageningen : Plant Research International, Business Unit Agrosysteemkunde - 21
    akkerbouw - groenteteelt - veldgewassen - uien - penen - spinazie - precisielandbouw - onkruidbestrijding - gewasbescherming - geografische informatiesystemen - gegevensverwerking - arable farming - vegetable growing - field crops - onions - carrots - spinach - precision agriculture - weed control - plant protection - geographical information systems - data processing
    Detectie van onkruiden in een volvelds gewas als spinazie heeft zeker kans van slagen. Op basis van het beschikbare beeldmateriaal zijn richtingen aangegeven hoe onkruid in volvelds gewassen herkend kan worden. Detectie van onkruiden in uien is mogelijk. Op basis van historisch beeldmateriaal op lage en hoge resolutie, aangevuld met een goede kasproef met beelden op hoge resolutie hebben aangetoond dat onkruid van geclusterde zaaiui kan worden onderscheiden. Voor detectie van onkruiden in peen gaat vrijwel hetzelfde op als beschreven bij de uien. Peen heeft namelijk ook een zeer sprieterig blad karakter. Belangrijk extra onderscheid is dat peen na de kieming twee verschillende karakteristieke vormen heeft.
    Netwerk Land en Water ‘Nieuwe wegen in de hydrologie’
    Breugem, A. ; Knotters, M. - \ 2013
    Stromingen : vakblad voor hydrologen 19 (2013)1. - ISSN 1382-6069 - p. 63 - 67.
    hydrologie - monitoring - neerslag - stedelijke gebieden - gegevensverwerking - overstromingen - hoogwaterbeheersing - watergebruik - conferenties - hydrology - monitoring - precipitation - urban areas - data processing - floods - flood control - water use - conferences
    Op woensdag 20 juni 2012 belegde het Netwerk Land en Water een studiemiddag over het thema ‘Nieuwe wegen in de hydrologie’. Dit thema is ingegeven vanuit de verwachting dat door klimaatverandering extreme neerslaggebeurtenissen frequenter zullen optreden, wat kan leiden tot grote wateroverlast. Om voor deze gebeurtenissen adequate oplossingen te vinden zijn nieuwe wegen in de hydrologie noodzakelijk, zowel in de wetenschap als in de aan het beleid gekoppelde praktijk. Op deze middag werden in drie lezingen enkele wetenschappelijke ontwikkelingen in de hydrologie voor het voetlicht gebracht: - Stedelijke neerslagmetingen, door Marie-Claire ten Veldhuis (TuD); - Extreme neerslag en afvoerprocessen in het stroomgebied van de Hupselse Beek, door Claudia Brauer (WUR); - Operationele monitoring van hydrologische processen op verschillende schalen, door Henk Pelgrum van eLEAF
    Bioinformatics assisted breeding, from QTL to candidate genes
    Chibon, P.Y. - \ 2013
    Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Richard Finkers. - S.l. : s.n. - ISBN 9789461737366 - 149
    plantenveredeling - bio-informatica - moleculaire veredeling - marker assisted breeding - loci voor kwantitatief kenmerk - genetische kartering - gegevensverwerking - ontologieën - plant breeding - bioinformatics - molecular breeding - marker assisted breeding - quantitative trait loci - genetic mapping - data processing - ontologies

    Over the last decade, the amount of data generated by a single run of a NGS sequencer outperforms days of work done with Sanger sequencing. Metabolomics, proteomics and transcriptomics technologies have also involved producing more and more information at an ever faster rate. In addition, the number of databases available to biologists and breeders is increasing every year. The challenge for them becomes two-fold, namely: to cope with the increased amount of data produced by these new technologies and to cope with the distribution of the information across the Web. An example of a study with a lot of ~omics data is described in Chapter 2, where more than 600 peaks have been measured using liquid chromatography mass-spectrometry (LCMS) in peel and flesh of a segregating F1apple population. In total, 669 mQTL were identified in this study. The amount of mQTL identified is vast and almost overwhelming. Extracting meaningful information from such an experiment requires appropriate data filtering and data visualization techniques. The visualization of the distribution of the mQTL on the genetic map led to the discovery of QTL hotspots on linkage group: 1, 8, 13 and 16. The mQTL hotspot on linkage group 16 was further investigated and mainly contained compounds involved in the phenylpropanoid pathway. The apple genome sequence and its annotation were used to gain insight in genes potentially regulating this QTL hotspot. This led to the identification of the structural gene leucoanthocyanidin reductase (LAR1) as well as seven genes encoding transcription factors as putative candidates regulating the phenylpropanoid pathway, and thus candidates for the biosynthesis of health beneficial compounds. However, this study also indicated bottlenecks in the availability of biologist-friendly tools to visualize large-scale QTL mapping results and smart ways to mine genes underlying QTL intervals.

    In this thesis, we provide bioinformatics solutions to allow exploration of regions of interest on the genome more efficiently. In Chapter 3, we describe MQ2, a tool to visualize results of large-scale QTL mapping experiments. It allows biologists and breeders to use their favorite QTL mapping tool such as MapQTL or R/qtl and visualize the distribution of these QTL among the genetic map used in the analysis with MQ2. MQ2provides the distribution of the QTL over the markers of the genetic map for a few hundreds traits. MQ2is accessible online via its web interface but can also be used locally via its command line interface. In Chapter 4, we describe Marker2sequence (M2S), a tool to filter out genes of interest from all the genes underlying a QTL. M2S returns the list of genes for a specific genome interval and provides a search function to filter out genes related to the provided keyword(s) by their annotation. Genome annotations often contain cross-references to resources such as the Gene Ontology (GO), or proteins of the UniProt database. Via these annotations, additional information can be gathered about each gene. By integrating information from different resources and offering a way to mine the list of genes present in a QTL interval, M2S provides a way to reduce a list of hundreds of genes to possibly tens or less of genes potentially related to the trait of interest. Using semantic web technologies M2S integrates multiple resources and has the flexibility to extend this integration to more resources as they become available to these technologies.

    Besides the importance of efficient bioinformatics tools to analyze and visualize data, the work in Chapter 2also revealed the importance of regulatory elements controlling key genes of pathways. The limitation of M2S is that it only considers genes within the interval. In genome annotations, transcription factors are not linked to the trait (keyword) and to the gene it controls, and these relationships will therefore not be considered. By integrating information about the gene regulatory network of the organism into Marker2sequence, it should be able to integrate in its list of genes, genes outside of the QTL interval but regulated by elements present within the QTL interval. In tomato, the genome annotation already lists a number of transcription factors, however, it does not provide any information about their target. In Chapter 5, we describe how we combined transcriptomics information with six genotypes from an Introgression Line (IL) population to find genes differentially expressed while being in a similar genomic background (i.e.: outside of any introgression segments) as the reference genotype (with no introgression). These genes may be differentially expressed as a result of a regulatory element present in an introgression. The promoter regions of these genes have been analyzed for DNA motifs, and putative transcription factor binding sites have been found.

    The approaches taken in M2S (Chaper 4) are focused on a specific region of the genome, namely the QTL interval. In Chapter 6, we generalized this approach to develop Annotex. Annotex provides a simple way to browse the cross-references existing between biological databases (ChEBI, Rhea, UniProt, GO) and genome annotations. The main concept of Annotex being, that from any type of data present in the databases, one can navigate the cross-references to retrieve the desired type of information.

    This thesis has resulted in the production of three tools that biologists and breeders can use to speed up their research and build new hypothesis on. This thesis also revealed the state of bioinformatics with regards to data integration. It also reveals the need for integration into annotations (for example, genome annotations, protein annotations, and pathway annotations) of more ontologies than just the Gene Ontology (GO) currently used. Multiple platforms are arising to build these new ontologies but the process of integrating them into existing resources remains to be done. It also confirms the state of the data in plants where multiples resources may contain overlapping. Finally, this thesis also shows what can be achieved when the data is made inter-operable which should be an incentive to the community to work together and build inter-operable, non-overlapping resources, creating a bioinformatics Web for plant research.

    Automatisch onkruid bestrijden in de gewasrij : rapport PPL Fase4C-II: doorontwikkelen van hardware en software
    Hemming, J. ; Nieuwenhuizen, A.T. ; Struik, L. - \ 2012
    Wageningen : Plant Research International, Business Unit Agrosysteemkunde - 13
    precisielandbouw - akkerbouw - gewasbescherming - onkruidbestrijding - computer hardware - software-ontwikkeling - teelt in rijen - geografische informatiesystemen - sensors - gegevensverwerking - precision agriculture - arable farming - plant protection - weed control - computer hardware - software engineering - alley cropping - geographical information systems - sensors - data processing
    Alle in deze fase geplande activiteiten zijn uitgevoerd volgens projectplan. Het user interface is aangepast voor gemakkelijk gebruik door de eindgebruiker en geheel in de huisstijl van Steketee. Er is overgestapt naar een ander type microcontroller met CAN bus interface waardoor de communicatie tussen high-level PC, sensoren en actuatoren sneller en robuuster verloopt. Op de machine is een remote service verbinding aangelegd zodat van afstand met de eindgebruiker kan worden meegekeken bij het oplossen van problemen en het maken van instellingen. De softwarealgoritmes voor plantdetectie zijn aangepast zodat beter om de gewasplanten heen geschoffeld kan worden. Een mechanische hoogteregeling van de machine is in hardware en software gerealiseerd en getest. Hierdoor kan de afstand van de camera’s t.o.v. van het gewas constant worden gehouden wat de beeldkwaliteit ten goede
    Gegevens delen via Linked Open Data ; case study over het delen van grondwatergegevens bij de bouw van de A2 tunnel in Maastricht
    Verhelst, E.C.H. ; Houtkamp, J.M. ; Randen, Y. van - \ 2012
    Wageningen : Alterra (Alterra-rapport 2306) - 32
    infrastructuur - wegen - tunnels - grondwaterstand - datacommunicatie - gegevensverwerking - zuid-limburg - infrastructure - roads - tunnels - groundwater level - data communication - data processing - zuid-limburg
    In dit rapport is een case study beschreven waarin wordt gekeken naar het delen van gegevens bij de bouw van een groot infrastructuur project (Maastricht A2). De manier van gegevensdelen die is uitgewerkt wordt Linked Open Data genoemd. Bij Linked Open Data zijn de brongegevens toegankelijk en aan elkaar verbonden met web links. Omdat de gegevens toegankelijk zijn via de bron kan elke partij zijn eigen overzichten maken en applicaties en visualisaties bouwen. De gekoppelde data vormen een wereldwijde netwerkstructuur waaraan makkelijk nieuwe gegevens kunnen worden toegevoegd. Zo wordt de samenhang tussen gegevens beter zichtbaar.
    On-line monitoring van transpiratie en fotosynthese: de praktijk
    Bontsema, J. ; Hemming, J. ; Janssen, H.J.J. ; Meinen, E. ; Rispens, S. ; Steenhuizen, J.W. ; Visser, P.H.B. de - \ 2011
    Wageningen : Wageningen UR Glastuinbouw (Rapporten GTB 1091) - 65
    gasuitwisseling - fotosynthese - transpiratie - glastuinbouw - kasgewassen - gewasmonitoring - on-line - gegevensverwerking - gas exchange - photosynthesis - transpiration - greenhouse horticulture - greenhouse crops - crop monitoring - on line - data processing
    WUR Glastuinbouw heeft monitoren ontwikkeld voor de on-line bepaling van de verdamping en fotosynthese. Deze monitoren zijn uitgetest bij diverse vruchtgroentetelers en slatelers. In het onderzoek is ook een nieuwe transpiratiemonitor ontwikkeld, op basis van een statische energie- en vochtbalans
    Towards transparent development of food frequency questionnaires : scientific basis of the Dutch FFQ-TOOL tm: a computer system to generate, apply and process FFQs
    Molag, M.L. - \ 2010
    Wageningen University. Promotor(en): Pieter van 't Veer; P.A. van den Brandt, co-promotor(en): Jeanne de Vries. - [S,l, : S.n. - ISBN 9789085855392 - 159
    dieetonderzoeken - vragenlijsten - voedingsfrequentie - gegevens verzamelen - gegevensverwerking - computer software - dietary surveys - questionnaires - feeding frequency - data collection - data processing - computer software
    Introduction
    A well-designed food frequency questionnaire (FFQ) aims to assess habitual intake
    of foods or nutrients of interest in the target population. Therefore, the food list of
    an FFQ has to be adapted to the prevailing dietary habits of the target population
    and updated when re-used some time after initial development. However, due to
    lack of expertise, time, or finances, FFQs are often re-used without adaptations. To
    simplify and standardize the development of new FFQs, we developed a computer
    system, the Dutch FFQ-TOOLTM, to generate, apply, and process FFQs. The aim of
    this thesis was to provide the scientific basis for development of this system.
    Methods
    We first characterized FFQ design by a systematic review of validation studies.
    For selecting food items in the system, we evaluated a simple procedure, called
    MOM2, which selected food items on the basis of explained variance in nutrient
    intake without taking covariance from other food items into account. To improve
    questions in FFQs, we conducted focus group discussions to investigate problems
    encountered by adults when filling out FFQs. Using the information from these
    studies; we developed a prototype of the system, which used the Dutch National
    Food Consumption Survey 1998 for the selection of food items. This prototype was
    used to generate an FFQ, which was subsequently validated against biomarkers and
    3-day food records.
    Results
    In the systematic review, we observed that FFQs with more items (>200 items)
    were better able to rank people according to their intake of most nutrients than
    shorter FFQs (<100 items). MOM2 appeared suitable to select food items that
    contributed importantly to variance in nutrient intake, leading to only a few
    more food items than regression analysis. Focus group discussions showed that
    36 out of 40 respondents were confused by examples that were meant to clarify
    questions and 31 out of 40 respondents had difficulties in identifying consumed
    foods, because categorization of foods was not logical to them. This information
    was used to develop standard questions and answering categories which were
    included in the Dutch FFQ-TOOLTM. The validation of a first FFQ generated by the
    system showed that validity coefficients between FFQ and true intake were 0.50
    for protein, 0.36 for potassium and 0.50 for PUFA, as assessed by the methods of
    triads applied to the FFQ, food records, and biomarkers of intake. These results
    are similar to those from validation studies of other FFQs.
    Conclusion
    We have developed a flexible data-based computer system that can generate FFQs
    using standardized procedures for multiple nutrients of interest, which is suitable
    to assess habitual food and nutrient intake of adults with sufficient validity.
    Precisielandbouw : van meten naar weten ; Interview met Jan Nammen Jukema
    Drenth, H.J. ; Jukema, J.N. - \ 2009
    Akker magazine 2009 (2009)8. - ISSN 1875-9688 - p. 20 - 21.
    akkerbouw - landbouwtechniek - precisielandbouw - globale plaatsbepalingssystemen - gegevensverwerking - arable farming - agricultural engineering - precision agriculture - global positioning systems - data processing
    Van recht rijden met een druk op de knop kijkt niemand meer op. De tweede stap in de precisielandbouw is het meten van variatie in het veld en daar gericht op inspelen. Dat is lastig. Pioniers proberen grip te krijgen op de brij aan meetgegevens.
    Web services for transcriptomics
    Neerincx, P. - \ 2009
    Wageningen University. Promotor(en): Jack Leunissen. - [S.l. : S.n. - ISBN 9789085854647 - 184
    bio-informatica - internet - moleculaire biologie - computers - datacommunicatie - gegevensverwerking - transcriptomics - computernetwerken - microarrays - genexpressieanalyse - datamining - bioinformatics - internet - molecular biology - computers - data communication - data processing - transcriptomics - computer networks - microarrays - genomics - data mining
    Transcriptomics is part of a family of disciplines focussing on high throughput molecular biology experiments. In the case of transcriptomics, scientists study the expression of genes resulting in transcripts. These transcripts can either perform a biological function themselves or function as messenger molecules containing a copy of the genetic code, which can be used by the ribosomes as templates to synthesise proteins. Over the past decade microarray technology has become the dominant technology for performing high throughput gene expression experiments.
    A microarray contains short sequences (oligos or probes), which are the reverse complement of fragments of the targets (transcripts or sequences derived thereof). When genes are expressed, their transcripts (or sequences derived thereof) can hybridise to these probes. Many thousand copies of a probe are immobilised in a small region on a support. These regions are called spots and a typical microarray contains thousands or sometimes even more than a million spots. When the transcripts (or sequences derived thereof) are fluorescently labelled and it is known which spots are located where on the support, a fluorescent signal in a certain region represents expression of a certain gene. For interpretation of microarray data it is essential to make sure the oligos are specific for their targets. Hence for proper probe design one needs to know all transcripts that may be expressed and how well they can hybridise with candidate oligos. Therefore oligo design requires:
    1. A complete reference genome assembly.
    2. Complete annotation of the genome to know which parts may be transcribed.
    3. Insight in the amount of natural variation in the genomes of different individuals.
    4. Knowledge on how experimental conditions influence the ability of probes to hybridise with certain transcripts.
    Unfortunately such complete information does not exist, but many microarrays were designed based on incomplete data nevertheless. This can lead to a variety of problems including cross-hybridisation (non-specific binding), erroneously annotated and therefore misleading probes, missing probes and orphan probes.
    Fortunately the amount of information on genes and their transcripts increases rapidly. Therefore, it is possible to improve the reliability of microarray data analysis by regular updates of the probe annotation using updated databases for genomes and their annotation. Several tools have been developed for this purpose, but these either used simplistic annotation strategies or did not support our species and/ or microarray platforms of interest. Therefore, we developed OligoRAP (Oligo Re- Annotation Pipeline), which is described in chapter 2. OligoRAP was designed to take advantage of amongst others annotation provided by Ensembl, which is the largest genome annotation effort in the world. Thereby OligoRAP supports most of the major animal model organisms including farm animals like chicken and cow. In addition to support for our species and array platforms of interest OligoRAP employs a new annotation strategy combining information from genome and transcript databases in a non-redundant way to get the most complete annotation possible.
    In chapter 3 we compared annotation generated with 3 oligo annotation pipelines including OligoRAP and investigated the effect on functional analysis of a microarray experiment involving chickens infected with Eimeria bacteria. As an example of functional analysis we investigated if up- or downregulated genes were enriched for Terms from the Gene Ontology (GO). We discovered that small differences in annotation strategy could lead to alarmingly large differences in enriched GO terms.
    Therefore it is important to know, which annotation strategy works best, but it was not possible to assess this due to the lack of a good reference or benchmark dataset. There are a few limited studies investigating the hybridisation potential of imperfect alignments of oligos with potential targets, but in general such data is scarce. In addition it is difficult to compare these studies due to differences in experimental setup including different hybridisation temperatures and different probe lengths. As result we cannot determine exact thresholds for the alignments of oligos with non-targets to prevent cross-hybridisation, but from these different studies we can get an idea of the range for the thresholds that would be required for optimal target specificity. Note that in these studies experimental conditions were first optimised for an optimal signal to noise ratio for hybridisation of oligos with targets. Then these conditions were used to determine the thresholds for alignments of oligos with non-targets to prevent cross-hybridisation.
    Chapter 4 describes a parameter sweep using OligoRAP to explore hybridisation potential thresholds from a different perspective. Given the mouse genome thresholds were determined for the largest amount of gene specific probes. Using those thresholds we then determined thresholds for optimal signal to noise ratios. Unfortunately the annotation-based thresholds we found did not fall within the range of experimentally determined thresholds; in fact they were not even close. Hence what was experimentally determined to be optimal for the technology was not in sync with what was determined to be optimal for the mouse genome. Further research will be required to determine whether microarray technology can be modified in such a way that it is better suited for gene expression experiments. The requirement of a priori information on possible targets and the lack of sufficient knowledge on how experimental conditions influence hybridisation potential can be considered the Achiles’ heels of microarray technology.
    Chapter 5 is a collection of 3 application notes describing other tools that can aid in analysis of transcriptomics data. Firstly, RShell, which is a plugin for the Taverna workbench allowing users to execute statistical computations remotely on R-servers. Secondly, MADMAX services, which provide quality control and normalisation of microarray data for AffyMetrix arrays. Finally, GeneIlluminator, which is a tool to disambiguate gene symbols allowing researchers to specifically retrieve literature for their genes of interest even if the gene symbols for those genes had many synonyms and homonyms.

    Web services

    High throughput experiments like those performed in transcriptomics usually require subsequent analysis with many different tools to make biological sense of the data. Installing all these tools on a single, local computer and making them compatible so users can build analysis pipelines can be very cumbersome. Therefore distributed analysis strategies have been explored extensively over the past decades. In a distributed system providers offer remote access to tools and data via the Internet allowing users to create pipelines from modules from all over the globe.
    Chapter 1 provides an overview of the evolution of web services, which represent the latest breed in technology for creating distributed systems. The major advantage of web services over older technology is that web services are programming language independent, Internet communication protocol independent and operating system independent. Therefore web services are very flexible and most of them are firewall-proof. Web services play a major role in the remaining chapters of this thesis: OligoRAP is a workflow entirely made from web services and the tools described in chapter 5 all provide remote programmatic access via web service interfaces. Although web services can be used to build relatively complex workflows like OligoRAP, a lack of mainly de facto standards and of user-friendly clients has limited the use of web services to bioinformaticians. A semantic web where biologists can easily link web services into complex workflows does n
    Mapping and monitoring heterogeneous landscapes: spatial, spectral and temporal unmixing of MERIS data
    Zurita Milla, R. - \ 2008
    Wageningen University. Promotor(en): Michael Schaepman, co-promotor(en): Jan Clevers. - [S.l.] : S.n. - ISBN 9789085049883 - 141
    remote sensing - cartografie - monitoring - landschap - gegevensverwerking - spectrale gegevens - variatie in de tijd - satellietbeelden - satellietkarteringen - geodata - remote sensing - mapping - monitoring - landscape - data processing - spectral data - temporal variation - satellite imagery - satellite surveys - geodata
    Our environment is continuously undergoing change. This change takes place at several spatial and temporal scales and it is largely driven by anthropogenic activities. In order to protect our environment and to ensure a sustainable use of natural resources, a wide variety of national and international initiatives have been established. In this context, Earth observation sensors can provide a substantial amount of information about the biotic and abiotic conditions of our planet. For instance, high spatial resolution sensors, like Landsat TM, deliver data that can be used to produce maps of canopy properties and of land cover types. However, the use of this kind of sensors is not feasible for obtaining full coverage of large areas. Furthermore, high spatial resolution sensors generally do not provide sufficient temporal resolution for monitoring vegetation development during the year. This is especially true for areas having severe cloud coverage throughout the year. In this respect, coarse spatial resolution sensors, which deliver nearly daily data, have a higher chance of encountering cloud free areas. This facilitates large scale monitoring studies but at the expense of a lower spatial resolution providing images with potentially many mixed pixels.
    Recent developments in imaging devices resulted into a new kind of sensor that works at a medium spatial resolution while providing high temporal and spectral resolutions. The MEdium Resolution Imaging Spectrometer (MERIS) aboard the European Space Agency’s ENVISAT platform belongs to this category. MERIS measures the solar radiation reflected from the Earth’s surface in 15 narrow spectral bands and it has a revisit time of 2-3 days. This unprecedented spectral and temporal resolution has resulted in several land, water and atmospheric products. In addition, two vegetation indices have been specifically designed to monitor vegetated canopies using this sensor: the MERIS Terrestrial Chlorophyll index (MTCI) and the MERIS Global Vegetation Index (MGVI). However, the spatial resolution provided by this sensor – 300 m in full resolution (FR mode) – is not sufficient to accurately map and monitor heterogeneous and fragmented landscapes. This is why the synergic use of high spatial resolution and MERIS data is investigated in this thesis. More precisely, the objective of this thesis is to develop a multi-sensor and multi-resolution data fusion approach that allows mapping and monitoring of heterogeneous and highly fragmented landscapes using MERIS data. The Netherlands is selected as study area because of its mixed landscapes where patches of arable land, natural vegetation, forests, and water bodies can be found next to each other. Besides this, The Netherlands also suffers from frequent cloud coverage, which severely hampers operational mapping and monitoring with both high spatial and high temporal resolution.
    Chapter 1 outlines the challenges of mapping and monitoring heterogeneous and fragmented landscapes using data from the current optical Earth observing missions, sketches the core concepts of data fusion and linear spectral (un)mixing and, after that, lists the research objectives of this PhD thesis.
    Chapter 2 presents the calibration scheme of the MERIS sensor and subsequently focuses on the smile effect and on the vicarious calibration corrections. The effects of these corrections on regional land cover mapping and vegetation status assessment are studied. Our analysis showed that MERIS delivers data with a very high radiometric quality. Nevertheless, some effects were observed when using MERIS data without the smile correction. Therefore, we recommend to systematically apply all the necessary corrections to generate stable long-term series of MERIS data.
    Chapter 3 introduces a data fusion technique that can be used to generate images with the spatial resolution provided by Landsat TM and the spectral resolution provided by MERIS. The method is based on the linear mixing model and requires the use of a high spatial resolution dataset (in this case, a Landsat TM image) to downscale the information collected by MERIS. Two parameters need to be optimized in this implementation of the unmixing-based data fusion approach: the number of classes used to classify the TM image and the size of the MERIS neighbourhood used to solve the unmixing equations. A quantitative data fusion quality analysis was used to assist with the identification of the best combination of these two parameters. The results of this analysis demonstrated that it is possible to downscale MERIS FR images to a Landsat-like spatial resolution (25 m).
    Chapter 4 elaborates in more detail on the potential of MERIS fused images for land cover mapping and vegetation status assessment in heterogeneous and fragmented landscapes. First, the fused images are used to produce land cover maps, which are validated using a high spatial resolution dataset. Then, the fused image with the highest overall classification accuracy is selected as the best fused image. Subsequently, this image is used to compute three vegetation indices: the normalized difference vegetation index (NDVI), which is an indicator of vegetation amount and its ‘greenness’, and the two vegetation indices specifically designed to monitor vegetation status using MERIS data (i.e. the MTCI and the MGVI). Classification results for the best fused image and for the TM image used to downscale MERIS are very similar and when comparing spectrally similar images (i.e. no SWIR bands in the TM image), the results of the best fused image outperform those of TM. With respect to the vegetation indices, a good correlation was found between the NDVI computed from TM and from the best fused image (in spite of their different spectral configuration). For the MTCI and the MGVI, the spatial patterns found when using MERIS fused images were consistent with those found in MERIS. The main advantage of using fused images is the possibility of monitoring individual agricultural fields and small vegetation patches. This is not possible when using the original MERIS FR images.
    Chapter 5 investigates the use of the unmixing-based data fusion approach to downscale time series of MERIS FR data. In this case, a high spatial resolution land use database is used to characterize the landscape composition. Because of this, only the size of the MERIS neighbourhood used for the unmixing needs to be optimized. In this chapter, the AMORGOS 3.0 software was used to ensure working with the best possible MERIS geo-location values. This allowed an automatic image co-registration and the calculation of the actual ground instantaneous field of view (GIFOV) of each MERIS pixel which, in turn, allows us to determine the real number of TM pixels covered by each MERIS pixel without having to re-project the datasets. Similar to chapter 2, a quantitative data fusion assessment was performed in order to test the validity of the proposed method and to identify the best neighbourhood size. After that, the series of fused images was used to compute the MTCI and the MGVI. Finally, MTCI and MGVI temporal profiles were extracted for the main land cover types present in the study area. Results indicate that the selected data fusion approach can be successfully used to downscale time series of MERIS FR data and, therefore, to monitor vegetation dynamics at high spatial, spectral and temporal resolutions.
    Chapter 6 contains the final conclusions and gives recommendations for further research. The overall conclusion is that the selected unmixing-based data fusion approach is able to downscale MERIS FR data to a Landsat-like resolution with little compromises on the spectral quality. This allows mapping and monitoring heterogeneous and fragmented landscapes that suffer from frequent cloud coverage. The results presented in this thesis should, therefore, encourage further research on multi-sensor and multi-resolution data fusion approaches as a means to bridge spatial, spectral and temporal scaling gaps in current and future Earth observation missions.





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