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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    Mobile PEAR transcription factors integrate positional cues to prime cambial growth
    Miyashima, Shunsuke ; Roszak, Pawel ; Sevilem, Iris ; Toyokura, Koichi ; Blob, Bernhard ; Heo, Jung-Ok ; Mellor, Nathan ; Help-Rinta-Rahko, Hanna ; Otero, Sofia ; Smet, Wouter ; Boekschoten, Mark ; Hooiveld, Guido ; Hashimoto, Kayo ; Smetana, Ondřej ; Siligato, Riccardo ; Wallner, Eva Sophie ; Mähönen, Ari Pekka ; Kondo, Yuki ; Melnyk, Charles W. ; Greb, Thomas ; Nakajima, Keiji ; Sozzani, Rosangela ; Bishopp, Anthony ; Rybel, Bert de; Helariutta, Ykä - \ 2019
    Nature 565 (2019)7740. - ISSN 0028-0836 - p. 490 - 494.

    Apical growth in plants initiates upon seed germination, whereas radial growth is primed only during early ontogenesis in procambium cells and activated later by the vascular cambium1. Although it is not known how radial growth is organized and regulated in plants, this system resembles the developmental competence observed in some animal systems, in which pre-existing patterns of developmental potential are established early on2,3. Here we show that in Arabidopsis the initiation of radial growth occurs around early protophloem-sieve-element cell files of the root procambial tissue. In this domain, cytokinin signalling promotes the expression of a pair of mobile transcription factors—PHLOEM EARLY DOF 1 (PEAR1) and PHLOEM EARLY DOF 2 (PEAR2)—and their four homologues (DOF6, TMO6, OBP2 and HCA2), which we collectively name PEAR proteins. The PEAR proteins form a short-range concentration gradient that peaks at protophloem sieve elements, and activates gene expression that promotes radial growth. The expression and function of PEAR proteins are antagonized by the HD-ZIP III proteins, well-known polarity transcription factors4—the expression of which is concentrated in the more-internal domain of radially non-dividing procambial cells by the function of auxin, and mobile miR165 and miR166 microRNAs. The PEAR proteins locally promote transcription of their inhibitory HD-ZIP III genes, and thereby establish a negative-feedback loop that forms a robust boundary that demarks the zone of cell division. Taken together, our data establish that during root procambial development there exists a network in which a module that links PEAR and HD-ZIP III transcription factors integrates spatial information of the hormonal domains and miRNA gradients to provide adjacent zones of dividing and more-quiescent cells, which forms a foundation for further radial growth.

    Theoretical approaches to understanding root vascular patterning : A consensus between recent models
    Mellor, Nathan ; Adibi, Milad ; El-Showk, Sedeer ; Rybel, Bert De; King, John ; Mähönen, Ari Pekka ; Weijers, Dolf ; Bishopp, Anthony ; Etchells, Peter - \ 2017
    Journal of Experimental Botany 68 (2017)1. - ISSN 0022-0957 - p. 5 - 16.
    Auxin - Cytokinin - Mathematical modeling - Organ patterning - Systems biology - Vascular development

    The root vascular tissues provide an excellent system for studying organ patterning, as the specification of these tissues signals a transition from radial symmetry to bisymmetric patterns. The patterning process is controlled by the combined action of hormonal signaling/transport pathways, transcription factors, and miRNA that operate through a series of non-linear pathways to drive pattern formation collectively. With the discovery of multiple components and feedback loops controlling patterning, it has become increasingly difficult to understand how these interactions act in unison to determine pattern formation in multicellular tissues. Three independent mathematical models of root vascular patterning have been formulated in the last few years, providing an excellent example of how theoretical approaches can complement experimental studies to provide new insights into complex systems. In many aspects these models support each other; however, each study also provides its own novel findings and unique viewpoints. Here we reconcile these models by identifying the commonalities and exploring the differences between them by testing how transferable findings are between models. New simulations herein support the hypothesis that an asymmetry in auxin input can direct the formation of vascular pattern. We show that the xylem axis can act as a sole source of cytokinin and specify the correct pattern, but also that broader patterns of cytokinin production are also able to pattern the root. By comparing the three modeling approaches, we gain further insight into vascular patterning and identify several key areas for experimental investigation.

    Engineers at the Patient’s Bedside: : The Case of Silence in Inter-institutional Educational Innovation
    Verouden, Nick ; Sanden, M.C.A. van der; Aarts, M.N.C. - \ 2016
    In: The Silences of Science / Mellor, Felicity, Webster, Stephen, London : Routledge - ISBN 9781472459978 - p. 89 - 112.
    Innovation in science and technology is increasingly linked with interdisciplinarity. Encouraging this trend depends in part on cutting-edge educational programmes that revise, reinvent and redesign curricula as interdisciplinary vehicles, establishing and re-establishing relations between traditional fields and areas of expertise (Stone et al., 1999; Casey, 1994). Such programmes are valuable because they can overcome ‘silo’ mentalities and equip prospective students with the skills and knowledge necessary for understanding and solving complex societal problems (Stone et al.,1999; McFadden et al., 2010). Although these programmes are very promising, their development and

    implementation also brings challenges. The literature on curriculum development shows that many programmes have struggled to achieve true integration (McFadden et al., 2010; Stone et al., 1999). Dam-Mieras et al. (2008), in their study of an international master’s programme in sustainable development and management developed collaboratively by nine universities, observed that universities have their own experts and own programmes and that the ‘not invented here’ argument influences how details about new programme are discussed. Focussing on innovative online instruction courses, Xu and Morris (2007) found that the absence of group cohesiveness between faculty and project coordinators can hinder the collaborative course development process and affect the quality of the end product. Stone et al. (1999) emphasize that faculty members and administrators work at cross-purposes and view each other’s initiatives with suspicion. Given the importance that scientists, academic institutions and policy makers ascribe to innovation, along with their assumption that such innovation is a sure result of interdisciplinarity, it is essential to gain a better understanding of how curriculum development in academic education actually works. For this chapter, we consider how processes of connecting and inter-

    relating could add to our understanding of the problems and dilemmas that arise in developing and implementing such programmes. Scholars of innovation, in science and technology and beyond, have explained that innovation is not some abstract algorithm: it relies on interaction and collaboration between

    multiple actors with different expertises, visions, priorities and investment (Van Bommel et al., 2011; Leeuwis and Aarts, 2011; Akrich et al., 2002; Fonseca, 2002). This process of interacting is very difficult, however, and creates many tensions. This is revealed by studies that show the lurking problems of connecting previously unconnected people around new ideas and technologies. These studies show how innovation processes become defined by competition for scarce resources, protracted negotiations over priorities and interests, and dynamics of inclusion and exclusion (Leeuwis andAarts, 2011; Pretty, 1995; Van Bommel et al., 2011). Fonseca (2002) hence explains that innovation always creates a paradoxical situation, in which organizations, in their search to accelerate change and adapt to and find solutions for external challenges and demands, unavoidably create new and unpredictable interactional patterns. Given that interacting is a complicated matter in innovation processes, a

    key question within the management of innovation literature is how we can account for the way relevant actors connect, or fail to connect (Akrich et al., 2002). In this respect, verbal communication is often cited as an essential mechanism for effectively connecting important actors and social groups around innovative ideas, products, or technologies (Van Bommel et al., 2011). In turn, the markers of effective verbal communication as a frame for innovation are seen to be openness, dialogue, and the ability to cooperate and be reflective on one’s thoughts and actions (Stilgoe et al., 2013). Thorp and Goldstein (2010), writing about university innovation, describe conversations as the fertile ground from which innovation grows and urge us to make time and space for those conversations. Dialogue and openness are seen as indicators of the quality of interaction, and process transparency as a decisive component of academic innovation. By being open or transparent in discussing issues and problems, actors build confidence that negotiation is ‘real’ and not a cover-up for private backroom deals (de Bruijn and ten Heuvelhof, 2008). Although there is a wealth of research on communication for innovation,

    most scholarly work focuses on what is exchanged verbally, on how actors collate all the relevant evidence, put it on the table and discuss it openly. As of yet, silence is absent from these studies of communication for innovation. Building on recent organizational and strategy scholarship, in which silence is approached as an intricate concept with powerful functions and meanings in social interaction (Van Assche and Costaglioli, 2012; Carter et al., 2008; Henriksen and Dayton, 2006; Panteli and Fineman, 2005; Tucker and Edmondson, 2003; Jaworski, 2005; Morrison and Milliken, 2000), we suggest that silence merits much more attention in analyses of academic innovation. This chapter therefore explores the role of moments of silence during interactions within networks developing and implementing educational innovation. The structure of this chapter is as follows. We start by looking at the litera-

    ture on dynamic innovation networks and communication and complement these insights with scholarship on silence within organization studies. After briefly introducing our approach, we present the findings of a study of an inter-institutional and interdisciplinary joint bachelor’s programme that was

    implemented at the interface of health and technology. The purpose of the study was to better understand the significance of moments of silence in developing and implementing this programme. We end with the implications of our findings for steering in the context of interdisciplinary innovation.
    Implementation of non-local boundary layer schemes in the Regional Atmospheric Modeling System and its impact on simulated mesoscale circulations
    Gómez, I. ; Ronda, R.J. ; Caselles, V. ; Estrela, M.J. - \ 2016
    Atmospheric Research 180 (2016). - ISSN 0169-8095 - p. 24 - 41.
    Boundary layer - Mesoscale modelling - Non-local schemes - Numerical weather prediction/forecasting - PBL parameterization - RAMS model

    This paper proposes the implementation of different non-local Planetary Boundary Layer schemes within the Regional Atmospheric Modeling System (RAMS) model. The two selected PBL parameterizations are the Medium-Range Forecast (MRF) PBL and its updated version, known as the Yonsei University (YSU) PBL. YSU is a first-order scheme that uses non-local eddy diffusivity coefficients to compute turbulent fluxes. It is based on the MRF, and improves it with an explicit treatment of the entrainment. With the aim of evaluating the RAMS results for these PBL parameterizations, a series of numerical simulations have been performed and contrasted with the results obtained using the Mellor and Yamada (MY) scheme, also widely used, and the standard PBL scheme in the RAMS model. The numerical study carried out here is focused on mesoscale circulation events during the summer, as these meteorological situations dominate this season of the year in the Western Mediterranean coast. In addition, the sensitivity of these PBL parameterizations to the initial soil moisture content is also evaluated. The results show a warmer and moister PBL for the YSU scheme compared to both MRF and MY. The model presents as well a tendency to overestimate the observed temperature and to underestimate the observed humidity, considering all PBL schemes and a low initial soil moisture content. In addition, the bias between the model and the observations is significantly reduced moistening the initial soil moisture of the corresponding run. Thus, varying this parameter has a positive effect and improves the simulated results in relation to the observations. However, there is still a significant overestimation of the wind speed over flatter terrain, independently of the PBL scheme and the initial soil moisture used, even though a different degree of accuracy is reproduced by RAMS taking into account the different sensitivity tests.

    Exploring the Impact of Land Cover and Topography on Rainfall Maxima in the Netherlands
    Maat, H.W. ter; Moors, E.J. ; Hutjes, R.W.A. ; Holtslag, A.A.M. ; Dolman, A.J. - \ 2013
    Journal of Hydrometeorology 14 (2013)2. - ISSN 1525-755X - p. 524 - 542.
    landgebruik - bossen - neerslag - bodemwater - simulatie - modellen - veluwe - land use - forests - precipitation - soil water - simulation - models - veluwe - climate-change - convective boundary - soil-moisture - surface - model - evaporation - prediction - diffusion - exchange
    The relative contribution of topography and land use on precipitation is analyzed in this paper for a forested area in the Netherlands. This area has an average yearly precipitation sum that can be 75–100 mm higher than the rest of the country. To analyze this contribution, different configurations of land use and topography are fed into a mesoscale model. The authors use the Regional Atmospheric Modeling System (RAMS) coupled with a land surface scheme simulating water vapor, heat, and momentum fluxes [Soil–Water–Atmosphere Plant System–Carbon (SWAPS-C)]. The model simulations are executed for two periods that cover varying large-scale synoptic conditions of summer and winter periods. The output of the experiments leads to the conclusion that the precipitation maximum at the Veluwe is forced by topography and land use. The effect of the forested area on the processes that influence precipitation is smaller in summertime conditions when the precipitation has a convective character. In frontal conditions, the forest has a more pronounced effect on local precipitation through the convergence of moisture. The effect of topography on monthly domain-averaged precipitation around the Veluwe is a 17% increase in the winter and a 10% increase in the summer, which is quite remarkable for topography with a maximum elevation of just above 100 m and moderate steepness. From this study, it appears that the version of RAMS using Mellor–Yamada turbulence parameterization simulates precipitation better in wintertime, but the configuration with the medium-range forecast (MRF) turbulence parameterization improves the simulation of precipitation in convective circumstances.
    Evaluation of the COSMO-SC turbulence scheme in a shear-driven stable boundary layer
    Buzzi, M. ; Rotach, M.W. ; Raschendorfer, M. ; Holtslag, A.A.M. - \ 2011
    Meteorologische Zeitschrift 20 (2011)3. - ISSN 0941-2948 - p. 335 - 350.
    weather prediction model - 2nd-order closure models - low-level jet - intermittent turbulence - surface - flows - land - oscillations - coordinate - stability
    The performance of the COSMOsingle column turbulence scheme (a TKE scheme with a 1.5 order turbulence closure at the hierarchy level 2.5 following Mellor and Yamada) is investigated in the framework of the first GABLS intercomparison case. This is an idealized shear-driven stable boundary layer case with no advection. Overall the COSMO model performs reasonably well compared to the other participating models and the reference Large Eddy Simulations. However, the modification of some model parameters, together with the prescribed high vertical resolution, reveals a problem of numerical stability in the turbulence scheme: for the investigated shear-driven stable boundary layer the vertical diffusivities show unrealistic oscillations. This model deficiency, which has previously been described in literature, is explored in quite substantial detail and possible solutions are evaluated. It is found that under the given conditions the numerical description of the vertical wind gradients is crucial for the stability of the turbulence scheme. It is shown that for the determination of vertical gradients information from grid points beyond the immediately neighboring model levels must be incorporated – as it is common practice in the treatment of horizontal gradients – in order to obtain a numerically stable turbulence scheme. As a first approach vertical wind gradients are filtered using a 5-point filter prior to the evaluation of the stability functions. This approach yields to the overall best performance among all those tested and found in literature. The simulations additionally show that the use of a too high minimum diffusion coefficient (which is introduced in the model in order to avoid too low mixing) leads to losing important structures of the planetary boundary layer, such as the low level jet or a near-surface temperature inversion
    The 2006 outbreak of bluetongue in northern Europe. The entomological perspective
    Meiswinkel, R. ; Baldet, T. ; Deken, R. de; Takken, W. ; Delécolle, J.C. ; Mellor, P.S. - \ 2008
    Preventive Veterinary Medicine 87 (2008)1-2. - ISSN 0167-5877 - p. 55 - 63.
    culicoides biting midges - virus - vector - ceratopogonidae - diptera - identification - transmission - temperature - imicola - africa
    After bluetongue (BT) appeared in northern Europe in August 2006 entomological studies were implemented in all five affected Member States (MSs) to establish which species of Culicoides had acted as vectors. The findings can be summarised as follows: (i) C. imicola the principal southern European/African vector of BTV has not penetrated into northern Europe, (ii) three pools of C. obsoletus/C. scoticus and one of C. dewulfi assayed RT-PCR-positive to BTV-8, (iii) in support of these results it was found that both potential vectors had also high parity rates (approximately 40%) indicating increased longevity favouring BTV virogenesis and transmission, (iv) furthermore, C. obsoletus/C. scoticus and C. dewulfi occurred also widely and abundantly on sheep and cattle holdings across the entire affected region, (v) and during the latter part of the season showed strong endophily readily entering livestock buildings in significant numbers to bite the animals inside (endophagy), (vi) which demonstrates that housing at best offers only limited protection to livestock from Culicoides attacks, (vii) in contrast the potential vector C. pulicaris sensu stricto was restricted geographically, was captured rarely, had a low parity rate (10%) and was exophilic indicating it played no role in the outbreak of BT, (viii) the incrimination of C. dewulfi as a novel vector is significant because it breeds in cattle and horse dung this close association raising its vectorial potential, but (ix) problems with its taxonomy (and that of the Obsoletus and Pulicaris species complexes) illustrates the need for morphological and molecular techniques to become more fully integrated to ensure progress in the accurate identification of vector Culicoides, (x) midge densities (as adjudged by light traps) were generally low indicating northern European Culicoides to have a high vector potential and/or that significant numbers of midges are going undetected because they are biting (and transmitting BTV) during the day when light traps are not effective, and (xi) the sporadic capture of Culicoides in the winter of 2007 invites re-examination of the current definition of a vector-free period. The re-emergence of BT over a wide front in 2007 raises anew questions as to precisely how the virus overwinters and asks also that we scrutinise our monitoring systems in terms of their sensitivity and early warning capability.
    Sequence analysis of bluetongue virus serotype 8 from the Netherlands 2006 and comparison to other European strains
    Maan, S. ; Maan, N.S. ; Ross-Smith, N. ; Batten, C. ; Shaw, A.E. ; Anthony, S. ; Samual, A.R. ; Darpel, K.E. ; Veronesi, E. ; Oura, C.A.L. ; Singh, K.P. ; Nomikou, K. ; Potgieter, A. ; Attoui, H. ; Rooij, E.M.A. van; Rijn, P.A. van; Clercq, K. ; Vandenbussche, F. ; Zientara, S. ; Breard, E. ; Sailleau, C. ; Beer, M. ; Hoffmann, B. ; Mellor, P.S. ; Mertens, P.P.C. - \ 2008
    Virology 377 (2008)2. - ISSN 0042-6822 - p. 308 - 318.
    epizootic hemorrhagic-disease - complete nucleotide-sequence - republic-of-china - rt-pcr assay - phylogenetic analyses - mediterranean basin - genome segments - capsid protein - gene - vectors
    During 2006 the first outbreak of bluetongue ever recorded in northern Europe started in Belgium and the Netherlands, spreading to Luxemburg, Germany and north-east France. The virus overwintered (2006¿2007) reappearing during May¿June 2007 with greatly increased severity in affected areas, spreading further into Germany and France, reaching Denmark, Switzerland, the Czech Republic and the UK. Infected animals were also imported into Poland, Italy, Spain and the UK. An initial isolate from the Netherlands (NET2006/04) was identified as BTV-8 by RT-PCR assays targeting genome segment 2. The full genome of NET2006/04 was sequenced and compared to selected European isolates, South African vaccine strains and other BTV-8 strains, indicating that it originated in sub-Saharan Africa. Although NET2006/04 showed high levels of nucleotide identity with other `western¿ BTV strains, it represents a new introduction and was not derived from the BTV-8 vaccine, although its route of entry into Europe has not been established.
    Possible routes of introduction of bluetongue serotype 8 virus into the epicentre of the 2006 epidemic in north-western Europe
    Mintiens, K. ; Meroc, E. ; Mellor, P.S. ; Staubach, C. ; Gerbier, G. ; Elbers, A.R.W. ; Hendrickx, G. ; Clercq, K. - \ 2008
    Preventive Veterinary Medicine 87 (2008)1-2. - ISSN 0167-5877 - p. 131 - 144.
    epizootic hemorrhagic-disease - possible windborne spread - animal diseases - air streams - vectors - surveillance - africa - cattle - semen - east
    In August 2006, bluetongue (BT) was notified in The Netherlands on several animal holdings. This was the onset of a rapidly spreading BT-epidemic in north-western Europe (latitude >51°N) that affected cattle and sheep holdings in The Netherlands, Belgium, Germany, France and Luxembourg. The outbreaks were caused by bluetongue virus (BTV) serotype 8, which had not been identified in the European Union before. Bluetongue virus can be introduced into a free area by movement of infected ruminants, infected midges or by infected semen and embryos. In this study, information on animal movements or transfer of ruminant germ plasms (semen and embryos) into the Area of First Infection (AFI), which occurred before and during the onset of the epidemic, were investigated in order to establish the conditions for the introduction of this virus. All inbound transfers of domestic or wild ruminants, non-susceptible mammal species and ruminant germ plasms into the AFI during the high-risk period (HRP), registered by the Trade Control and Expert System (TRACES) of the EC, were obtained. Imports originating from countries with a known or suspected history of BTV-incidence of any serotype were identified. The list of countries with a reported history of BTV incidence was obtained from the OIE Handistatus II for the period from 1996 until 2004. No ruminants were imported from a Member State (MS) with a known history of BTV-8 or from any other country with a known or suspected history of BTV incidence of any serotype. Of all non-susceptible mammal species only 233 horses were transported directly into the AFI during the HRP. No importations of semen or embryos into the AFI were registered in TRACES during the period of interest. An obvious source for the introduction of BTV-8, such as import of infected ruminants, could not be identified and the exact origin and route of the introduction of BTV-8 thus far remains unknown. However, the absence of legal import of ruminants from outside the EU into the AFI and the absence of BTV-8 in southern Europe suggest that, the introduction of the BTV-8 infection into the north-western part of Europe took place via another route. Specifically, in relation to this, the potential for Culicoides to be imported along with or independently of the import of animals, plants or other `materials¿, and the effectiveness of measures to reduce such a possibility, merit further study.
    Epidemiological analysis of the 2006 blue tongue virus serotype 8 epidemic in north-western Europe. Distribution and dynamics of vector species
    Meiswinkel, R. ; Baldet, T. ; Deken, R. de; Takken, W. ; Delécolle, J.C. ; Mellor, Ph. - \ 2007
    Institute for Animal Health, UK : CIDC-Lelystad, the Netherlands, CIRAD, France, ITM, Belgium, WUR, the Netherlands, Université Louis Pasteur, France. - 88
    epidemiologie - bluetonguevirus - orbivirus - vectoren, ziekten - noord-europa - west-europa - noordwest-europa - epidemiology - bluetongue virus - orbivirus - disease vectors - northern europe - western europe - northwestern europe
    Effectivity of vaccination strategies to control CSF epidemics
    Backer, J.A. ; Hagenaars, T.H.J. ; Jong, M.C.M. de - \ 2007
    In: Proceedings of the SVEPM Annual Conference, 20 - 28 March, 2007, Helsinki/Espoo, Finland. - - p. 141 - 153.
    Stochastic simulation of a milk quality assurance programme for paratuberculosis: within-herd infection dynamics and economics
    Weber, M.F. ; Roermund, H.J.W. van; Velthuis, A.G.J. ; Koeijer, A.A. de; Jong, M.C.M. de; Nielen, M. - \ 2006
    In: Proceedings of the annual SVEPM meeting, March 29-31, 2006, Exeter University, Devon, UK. - Exeter : Society for veterinary epidemiology and preventive medicine - ISBN 9780948073748 - p. 25 - 38.
    Colony forming units or prevalence: how to use experimental data in prevalence simulation modelling
    Vosough Ahmadi, B. ; Velthuis, A.G.J. ; Hogeveen, H. ; Huirne, R.B.M. - \ 2006
    In: Proceedings of the annual SVEPM meeting, March 29-31, 2006, Exeter University, Devon, UK / Mellor, D.J., Russell, A.m., Exeter : Society for veterinary epidemiology and preventive medicine - ISBN 9780948073748 - p. 63 - 69.
    FMD control strategies
    Wood, James ; Green, Laura ; Klink, Ed van; Mellor, Dominic ; Newton, Richard - \ 2003
    Veterinary Record 152 (2003)20. - ISSN 0042-4900 - p. 634 - 634.
    New organic stabilizers for vinyl resins II
    Es, S. van; Frissen, A.E. ; Haveren, J. van; Kolk, J.C. van der; Harvey, H.B. ; Mellor, M. ; Huisman, H. - \ 2003
    Research disclosure (2003)465. - ISSN 0374-4353 - p. P30 - P32.
    Object georiënteerde analyse en design van real-time systemen. Toepassing van de Shlaer & Mellor methode bij het ontwikkelen van een boordcomputer.
    Bergeijk, J. van; Goense, D. ; Wigboldus, K. - \ 1995
    In: Engelbart et al. (eds.) Agro Informatica Reeks No. 9 - Proceedings VIAS symposium - p. 101 - 113.
    Identifying technological potentials.
    Penning de Vries, F.W.T. ; Wit, C.T. de - \ 1987
    In: Accelerating food production in Sub-Saharan Africa. Potential and practice in food technology development / Mellor, John W., Delgado, Christopher L., Blackie, Malcolm J., - p. 109 - 117.
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