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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    Sediment toxicity of the fungicide fludioxonil to benthic macroinvertebrates -evaluation of the tiered effect assessment procedure
    Brock, Theo C.M. ; Romão, João ; Yin, Xiao ; Osman, Rima ; Roessink, Ivo - \ 2020
    Ecotoxicology and Environmental Safety 195 (2020). - ISSN 0147-6513
    Fungicide exposure - Sediment ecotoxicology - Species sensitivity distributions - Standard test species - Weight of evidence approach

    28-Day sediment-spiked laboratory toxicity tests with eight benthic macroinvertebrates and the lipophilic fungicide fludioxonil were conducted to verify the proposed tiered sediment effect assessment procedure as recommended by the European Food Safety Authority (EFSA). The test species were the oligochaetes Lumbriculus variegatus and Tubifex tubifex, the insects Chironomus riparius and Caenis horaria, the crustaceans Hyalella azteca and Asellus aquaticus and the bivalves Corbicula fluminalis and Pisidium amnicum. Toxicity estimates were expressed in terms of total concentration of dry sediment as well as in pore water concentration. Field-collected sediment, also used in a previously performed sediment-spiked microcosm experiment, was used in tests with all species. L. variegatus and C. riparius had similar lowest 28d-L(E)C10 values when expressed in terms of total sediment concentration, but in terms of pore water concentration L. variegatus was more sensitive. Three of the six additional benthic test species (A. aquaticus, C. horaria, C. fluminalis) had 28d-EC10 values a factor of 2–6 lower than that of L. variegatus. Comparing different effect assessment tiers for sediment organisms, i.e. Tier-0 (Modified Equilibrium Partitioning approach), Tier-1 (Standard Test Species approach), Tier-2 (Species Sensitivity Distribution (SSD) approach) and Tier-3 (Model Ecosystem approach), it is concluded that the tiers based on sediment-spiked laboratory toxicity tests provide sufficient protection when compared with the Tier-3 Regulatory Acceptable Concentration (RAC). Differences between Tier-1 and Tier-2 RACs, however, appear to be relatively small and not always consistent, irrespective of expressing the RAC in terms of total sediment or pore water concentration. Derivation of RACs by means of the SSD approach may be a challenge, because it is difficult obtaining a sufficient number of valid chronic EC10 values with appropriate 95% confidence bands for sediment-dwelling macroinvertebrates. Therefore, this paper proposes a Tier-2 Weight-of-Evidence approach to be used in case an insufficient number of valid additional toxicity data is made available. Similar studies with pesticides that differ in fate properties and toxic mode-of-action are necessary for further validation of the tiered effect assessment approach for sediment organisms.

    Heritability estimates for 361 blood metabolites across 40 genome-wide association studies
    Hagenbeek, Fiona A. ; Pool, René ; Dongen, Jenny van; Draisma, Harmen H.M. ; Hottenga, Jouke Jan ; Willemsen, Gonneke ; Abdellaoui, Abdel ; Fedko, Iryna O. ; Braber, Anouk den; Visser, Pieter Jelle ; Geus, Eco J.C.N. de; Willems van Dijk, Ko ; Verhoeven, Aswin ; Suchiman, H.E. ; Beekman, Marian ; Slagboom, Eline P. ; Duijn, Cornelia M. van; Barkey Wolf, J.J.H. ; Cats, D. ; Amin, N. ; Beulens, J.W. ; Bom, J.A. van der; Bomer, N. ; Demirkan, A. ; Hilten, J.A. van; Meessen, J.M.T.A. ; Moed, M.H. ; Fu, J. ; Onderwater, G.L.J. ; Rutters, F. ; So-Osman, C. ; Flier, W.M. van der; Heijden, A.A.W.A. van der; Spek, A. van der; Asselbergs, F.W. ; Boersma, E. ; Elders, P.M. ; Geleijnse, J.M. ; Ikram, M.A. ; Kloppenburg, M. ; Meulenbelt, I. ; Mooijaart, S.P. ; Nelissen, R.G.H.H. ; Netea, M.G. ; Penninx, B.W.J.H. ; Stehouwer, C.D.A. ; Teunissen, C.E. ; Terwindt, G.M. ; Jukema, J.W. ; Reinders, M.J.T. - \ 2020
    Nature Communications 11 (2020)1. - ISSN 2041-1723

    Metabolomics examines the small molecules involved in cellular metabolism. Approximately 50% of total phenotypic differences in metabolite levels is due to genetic variance, but heritability estimates differ across metabolite classes. We perform a review of all genome-wide association and (exome-) sequencing studies published between November 2008 and October 2018, and identify >800 class-specific metabolite loci associated with metabolite levels. In a twin-family cohort (N = 5117), these metabolite loci are leveraged to simultaneously estimate total heritability (h2 total), and the proportion of heritability captured by known metabolite loci (h2 Metabolite-hits) for 309 lipids and 52 organic acids. Our study reveals significant differences in h2 Metabolite-hits among different classes of lipids and organic acids. Furthermore, phosphatidylcholines with a high degree of unsaturation have higher h2 Metabolite-hits estimates than phosphatidylcholines with low degrees of unsaturation. This study highlights the importance of common genetic variants for metabolite levels, and elucidates the genetic architecture of metabolite classes.

    Automated Testing of Simulation Software in the Aviation Industry : An Experience Report
    Garousi, Vahid ; Tasli, Seckin ; Sertel, Onur ; Tokgoz, Mustafa ; Herkiloglu, Kadir ; Arkin, Hikmet Ferda Ergunes ; Bilir, Osman - \ 2019
    IEEE Software 36 (2019)4. - ISSN 0740-7459 - p. 63 - 75.
    automated testing - aviation industry - simulation software - test automation

    An industry-academia collaboration developed a test automation framework for aviation simulation software. The technology has been successfully deployed in several test teams.

    Effect of dietary fiber (inulin) addition on phenolics and in vitro bioaccessibility of tomato sauce
    Tomas, Merve ; Beekwilder, Jules ; Hall, Robert D. ; Diez Simon, Carmen ; Sagdic, Osman ; Capanoglu, Esra - \ 2018
    Food Research International 106 (2018). - ISSN 0963-9969 - p. 129 - 135.
    Antioxidant - Bioavailability - Dietary fiber - Food matrix - In vitro gastrointestinal digestion - Tomato sauce
    The effect of the addition of inulin (5 and 10%) on the phenolic content and in vitro gastrointestinal digestion of tomato sauces has been investigated. Results have shown that the addition of inulin to tomato sauce significantly decreased the total phenolic content (57–68%), total flavonoid content (48–60%), and total antioxidant capacity (49–61%). Similarly, all assays of the sauce containing both 5% and 10% inulin, showed a slight decrease during in vitro gastrointestinal digestion of tomato sauces. Higher levels of inulin added to tomato sauce resulted in the greatest decrease in phenolic content, probably because of the interaction between inulin and phenolic compounds. To address the effects of inulin on the global metabolite profile of tomato sauce, an untargeted metabolomics approach was followed. Changes related to the presence of inulin suggest that inulin quenches a subset of unidentified compounds which are present in sauce but not in fruit, suggesting that inulin can contribute to the conservation of fruit properties in tomato sauce.
    Evolution and patterns of global health financing 1995-2014 : Development assistance for health, and government, prepaid private, and out-of-pocket health spending in 184 countries
    Dieleman, Joseph ; Campbell, Madeline ; Chapin, Abigail ; Eldrenkamp, Erika ; Fan, Victoria Y. ; Haakenstad, Annie ; Kates, Jennifer ; Liu, Yingying ; Matyasz, Taylor ; Micah, Angela ; Reynolds, Alex ; Sadat, Nafis ; Schneider, Matthew T. ; Sorensen, Reed ; Evans, Tim ; Evans, David ; Kurowski, Christoph ; Tandon, Ajay ; Abbas, Kaja M. ; Abera, Semaw Ferede ; Ahmad Kiadaliri, Aliasghar ; Ahmed, Kedir Yimam ; Ahmed, Muktar Beshir ; Alam, Khurshid ; Alizadeh-Navaei, Reza ; Alkerwi, A. ; Amini, Erfan ; Ammar, Walid ; Amrock, Stephen Marc ; Antonio, Carl Abelardo T. ; Atey, Tesfay Mehari ; Avila-Burgos, Leticia ; Awasthi, Ashish ; Barac, Aleksandra ; Bernal, Oscar Alberto ; Beyene, Addisu Shunu ; Beyene, Tariku Jibat ; Birungi, Charles ; Bizuayehu, Habtamu Mellie ; Breitborde, Nicholas J.K. ; Cahuana-Hurtado, Lucero ; Castro, Ruben Estanislao ; Catalá-López, Ferran ; Dalal, Koustuv ; Dandona, Lalit ; Dandona, Rakhi ; Jager, Pieter De; Dharmaratne, Samath D. ; Dubey, Manisha ; Sa Farinha, Carla Sofia E. ; Faro, Andre ; Feigl, Andrea B. ; Fischer, Florian ; Fitchett, Joseph Robert Anderson ; Foigt, Nataliya ; Giref, Ababi Zergaw ; Gupta, Rahul ; Hamidi, Samer ; Harb, Hilda L. ; Hay, Simon I. ; Hendrie, Delia ; Horino, Masako ; Jürisson, Mikk ; Jakovljevic, Mihajlo B. ; Javanbakht, Mehdi ; John, Denny ; Jonas, Jost B. ; Karimi, Seyed M. ; Khang, Young Ho ; Khubchandani, Jagdish ; Kim, Yun Jin ; Kinge, Jonas M. ; Krohn, Kristopher J. ; Kumar, G.A. ; Magdy Abd El Razek, Hassan ; Magdy Abd El Razek, Mohammed ; Majeed, Azeem ; Malekzadeh, Reza ; Masiye, Felix ; Meier, Toni ; Meretoja, Atte ; Miller, Ted R. ; Mirrakhimov, Erkin M. ; Mohammed, Shafiu ; Nangia, Vinay ; Olgiati, Stefano ; Osman, Abdalla Sidahmed ; Owolabi, Mayowa O. ; Patel, Tejas ; Paternina Caicedo, Angel J. ; Pereira, David M. ; Perelman, Julian ; Polinder, Suzanne ; Rafay, Anwar ; Rahimi-Movaghar, Vafa ; Rai, Rajesh Kumar ; Ram, Usha ; Ranabhat, Chhabi Lal ; Roba, Hirbo Shore ; Salama, Joseph ; Savic, Miloje ; Sepanlou, Sadaf G. ; Shrime, Mark G. ; Talongwa, Roberto Tchio ; Ao, Braden J. Te; Tediosi, Fabrizio ; Tesema, Azeb Gebresilassie ; Thomson, Alan J. ; Tobe-Gai, Ruoyan ; Topor-Madry, Roman ; Undurraga, Eduardo A. ; Vasankari, Tommi ; Violante, Francesco S. ; Werdecker, Andrea ; Wijeratne, Tissa ; Xu, Gelin ; Yonemoto, Naohiro ; Younis, Mustafa Z. ; Yu, Chuanhua ; Zaidi, Zoubida ; Sayed Zaki, Maysaa El; Murray, Christopher J.L. - \ 2017
    The Lancet 389 (2017)10083. - ISSN 0140-6736 - p. 1981 - 2004.
    Background: An adequate amount of prepaid resources for health is important to ensure access to health services and for the pursuit of universal health coverage. Previous studies on global health financing have described the relationship between economic development and health financing. In this study, we further explore global health financing trends and examine how the sources of funds used, types of services purchased, and development assistance for health disbursed change with economic development. We also identify countries that deviate from the trends. Methods: We estimated national health spending by type of care and by source, including development assistance for health, based on a diverse set of data including programme reports, budget data, national estimates, and 964 National Health Accounts. These data represent health spending for 184 countries from 1995 through 2014. We converted these data into a common inflation-adjusted and purchasing power-adjusted currency, and used non-linear regression methods to model the relationship between health financing, time, and economic development. Findings: Between 1995 and 2014, economic development was positively associated with total health spending and a shift away from a reliance on development assistance and out-of-pocket (OOP) towards government spending. The largest absolute increase in spending was in high-income countries, which increased to purchasing power-adjusted $5221 per capita based on an annual growth rate of 3.0%. The largest health spending growth rates were in upper-middle-income (5.9) and lower-middle-income groups (5.0), which both increased spending at more than 5% per year, and spent $914 and $267 per capita in 2014, respectively. Spending in low-income countries grew nearly as fast, at 4.6%, and health spending increased from $51 to $120 per capita. In 2014, 59.2% of all health spending was financed by the government, although in low-income and lower-middle-income countries, 29.1% and 58.0% of spending was OOP spending and 35.7% and 3.0% of spending was development assistance. Recent growth in development assistance for health has been tepid; between 2010 and 2016, it grew annually at 1.8%, and reached US$37.6 billion in 2016. Nonetheless, there is a great deal of variation revolving around these averages. 29 countries spend at least 50% more than expected per capita, based on their level of economic development alone, whereas 11 countries spend less than 50% their expected amount. Interpretation: Health spending remains disparate, with low-income and lower-middle-income countries increasing spending in absolute terms the least, and relying heavily on OOP spending and development assistance. Moreover, tremendous variation shows that neither time nor economic development guarantee adequate prepaid health resources, which are vital for the pursuit of universal health coverage.
    Industrial processing versus home processing of tomato sauce : Effects on phenolics, flavonoids and in vitro bioaccessibility of antioxidants
    Tomas, Merve ; Beekwilder, Jules ; Hall, Robert D. ; Sagdic, Osman ; Boyacioglu, Dilek ; Capanoglu, Esra - \ 2017
    Food Chemistry 220 (2017). - ISSN 0308-8146 - p. 51 - 58.
    Antioxidant - Bioavailability - In vitro gastrointestinal digestion - Processing - Tomato sauce

    The effect of industrial and home processing, in vitro gastrointestinal digestion, individual phenolic content, and antioxidant capacity of tomato into tomato sauce were investigated. Industrial processing of tomato fruit into sauce had an overall positive effect on the total antioxidant capacity (∼1.2-fold higher) compared to tomato fruit whereas home processing of tomato fruit into sauce led to a decrease in these values. Untargeted LC–QTOF-MS analysis revealed 31 compounds in tomato that changed upon processing, of which 18 could be putatively identified. Naringenin chalcone is only detectable in the fruit, while naringenin is strongly increased in the sauces. Rutin content increased by 36% in the industrial processed sauce whereas decreased by 26% in the home processed sauce when compared to fruit. According to the results of an in vitro gastrointestinal digestion model, industrial processing may lead to enhanced bioaccessibility of antioxidants.

    A robust supply chain planning framework for revenue management in the semiconductor industry
    Seitz, Alexander ; Ehm, Hans ; Akkerman, Renzo ; Osman, Sarah - \ 2016
    Journal of Revenue and Pricing Management 15 (2016)6. - ISSN 1476-6930 - p. 523 - 533.
    dynamic pricing - forecast accuracy - order management - semiconductor industry - supply chain contracts - supply chain planning

    High demand uncertainties, long production lead times, and short product life cycles cause high risks for supply chain planning in the semiconductor industry. These affect all industries producing goods containing semiconductors. We present a robust supply chain planning framework for revenue management that consists of stable and flexible solutions for demand steering and dynamic pricing, extending current industry practice in several aspects. We introduce the concept of availabilities and capabilities, as well as various planning processes and process enablers. Based on our framework, we also highlight directions for future research.

    Bacterial Rhizosphere Biodiversity from Several Pioneer Desert Sand Plants Near Jizan, Saudi Arabia
    Osman, Jorge R. ; Zelicourt, Axel de; Bisseling, A.H.J. ; Geurts, Rene ; Hirt, H. ; DuBow, Michael S. - \ 2016
    The Open Conference Proceedings Journal 7 (2016)1. - ISSN 2210-2892 - p. 70 - 79.
    Life in arid regions and, in particular, hot deserts is often limited due to their harsh environmental conditions, such as large temperature fluctuations and low amounts of water. These extreme environments can influence the microbial community present on the surface sands and any rhizosphere members surrounding desert plant roots. The Jizan desert area, located in Saudi Arabia, supports particular vegetation that grows in the large sandy flat terrain. We examined five different samples, four from the rhizosphere of pioneer plants plus a surface sand sample, and used pyrosequencing of PCR-amplified V1-V3 regions of 16S rDNA genes from total extracted DNA to reveal and compare the bacterial population diversity of the samples. The results showed a total of 3,530 OTUs in the five samples, calculated using ≥ 97% sequence similarity levels. The Chao1 estimation of the bacterial diversity fluctuated from 637 to 2,026 OTUs for a given sample. The most abundant members found in the samples belong to the Bacteroidetes, Firmicutes and Proteobacteria phyla. This work shows that the Jizan desert area of Saudi Arabia can contain a diverse bacterial community on the sand and surrounding the roots of pioneer desert plants. It also shows that desert sand microbiomes can vary depending on conditions, with broad implications for sandstone monument bacterial communities
    Adapting spring wheat breeding to the needs of the organic sector
    Osman, A.M. ; Almekinders, C.J.M. ; Struik, P.C. ; Lammerts van Bueren, E.T. - \ 2016
    NJAS Wageningen Journal of Life Sciences 76 (2016). - ISSN 1573-5214 - p. 55 - 63.
    Baking quality - Organic breeding - Spring wheat - Technology system - The Netherlands - Variety development

    Organic farmers and food processors need plant varieties that are adapted to their crop husbandry and processing practices. Such varieties are scarce as the mainstream breeding sector focuses on developing varieties for the conventional product chain that has different goals and practices. In this paper we study the case of the Dutch bread production chain to assess options that might enhance the availability of varieties suitable for the organic sector. The research involves an analysis of organic crop management and food processing practices and associated variety requirements. The research shows that several variety traits prioritized by the organic sector are not adequately addressed by conventional plant breeders: high baking quality, weed suppressiveness and tolerance to harrowing. Some of the interviewed conventional breeders are willing to consider technical adjustments to their breeding programmes. However, seed legislation and company economics limit the space to implement such modifications. We conclude that developing spring wheat varieties for the organic bread production chain requires breeders to prioritize selection for high baking quality genotypes that tolerate an organic weed management regime. This would require a concerted initiative of all actors in the organic bread production chain that includes establishing new socio-economic partnerships to overcome current economic and legal barriers

    Impact of improved operation and maintenance on cohesive sediment transport in Gezira Scheme, Sudan
    Osman, I.S.E. - \ 2015
    Wageningen University. Promotor(en): E. Schultz, co-promotor(en): A.K. Osman; F.X. Suryadi. - Leiden : CRC Press/Balkema - ISBN 9781138028807 - 183
    sediment - geologische sedimentatie - waterbeheer - irrigatiekanalen - irrigatie - irrigatiewater-toedieningsschema - sudan - sediment - geological sedimentation - water management - irrigation channels - irrigation - irrigation scheduling - sudan

    Efficient operation and maintenance of irrigation schemes are needed for improving the hydraulic performance of the canals, enhancing the crop yields and insuring sustainable production. There is a great need to enhance the researches and for a variety of tools such as water control and regulation equipment, decision support systems, as well as field surveys and valuation techniques. Water management becomes difficult when dealing with sediment transport in irrigation canals. Most of the studies simulate the sediment transport of relatively coarse grain sizes. The sediment problem in irrigation canals becomes more complicated when dealing with cohesive sediment transport. Therefore, more research is needed to enhance the understanding of the behaviour of cohesive sediment transport under a variety of operation conditions.

    This study has been carried out in the Gezira Scheme in Sudan. The scheme, which is one of the largest irrigation schemes in the world under a single management, is located in the arid and semi-arid region. The scheme is chosen as a case study since it can act as a model for similar irrigation schemes. The scheme has a total area of 880,000 ha and uses 35% of Sudan’s current allocation of Nile waters. This represents 6 – 7 billion m3 per year. The scheme is irrigated from the Blue Nile River, which is characterized by its high load of fine sediment. The scheme is facing severe sediment accumulation in its irrigation canals, which represents a challenge to those responsible for the operation and maintenance of the canals. Each year large investments are required to maintain and to upgrade the canal system to keep it in an acceptable condition.

    A large quantity of cohesive sediment enters the scheme every year. According to previous studies, about 60% of the sediment deposits in the irrigation canals. The sediment accumulation in the canals reduces the canal conveyance capacity, causes irrigation difficulties, creates inequity and inadequate water supply and increases the rate of aquatic weed growth. The sedimentation problems are not only seriously affecting the performance of the irrigation canals, but are also jeopardizing their sustainability, as well as affecting crop production. Two canals in the scheme have been selected to be studied in detail: Zananda Major Canal, which takes water from Gezira Main Canal at 57 km from the offtake at Sennar Dam, and Toman Minor Canal at 12.5 km from the offtake of Zananda Major Canal.

    The hypothesis of the study postulates that the operation and maintenance of an irrigation scheme has a major influence on the hydrodynamic behaviour of canals and hence on sediment movement and deposition. The aim of this study was to improve the operation and maintenance procedures for better sediment and water management. This can be achieved through better understanding of the sediment processes in the irrigation canals of the Gezira Scheme and to understand clearly the link between irrigation system operation and resulting system performance in terms of transport of cohesive sediment.

    Data collection and field measurements have been conducted during the flood season between June and October in 2011 and 2012. Sediment sampling and water level measurements have been conducted on a daily basis at selected locations. The manually recorded water levels include about 1080 readings per year. In addition about 1290 sediment samples were analysed for different locations during the study period. Cross-sectional surveys have been performed at the beginning and end of the flood season to address the spatial and temporal variation of the sediment deposition in the canals under study and to detect changes in the bed profile. The head regulator and outlet control structures were calibrated by using the measured stage-discharge relationships. More elaboration is given to the properties of cohesive sediment and identification of the dominant factors that cause deposition in irrigation canals. Sediment properties were tested such as grain size distribution, mechanical and physico-chemical properties of the sediment. The irrigation schedules, cropped area and sowing dates for different crops were reported. Other data such as canal design data, historical data of the sediment and flow for certain canals were reviewed.

    The analysis of the data indicates a variation of the water level along the canals under study. It should be noted that the operation control in Gezira Scheme is by using upstream control structures. The field data show that the flow release in the system is not regularly adjusted in a systematic way to meet the demand and maintain the required water level. Continuous change in gate setting results in instability of the water level. This situation became worse with more sediment deposition. The water level has been raised far above the design level and there is lapse in working levels especially at the major and minor canals. The rise is found to be about 1.6 and 1.2 m above the design level at the head of the major and minor canals under study. Furthermore, reduction in the water depth has been detected along the canals as result of bed rise and enlarging of canal sections due to improper desilting. The results demonstrate that the supply of water was extremely large during the flood season of 2011 compared to the actual crop water requirement, especially during the period of high sediment concentration. The delivery performance ratio indicated an oversupply at the major canal in 2011 during most of the time. The study also provides some valuable insight into the nature of sediment in Gezira Scheme.

    There is a limitation in the existing models that deal with fine sediment transport in irrigation canals. Most of the sediment transport models are developed for estuaries and rivers. Therefore there was a great need to develop a simple but effective numerical model that incorporates control structures to simulate the fine sediment transport in irrigation canals. Although there are similarities between rivers and irrigation canals, irrigation canals are different. The presence of a large number of flow control structures and the high influence of the side banks on the velocity distribution create some differences in both types of channels. Hence, it was important to develop a model dealing with fine sediment in irrigation canals, including different types of hydraulic structures.

    In line with this the one dimensional numerical model Fine SEDiment Transport (FSEDT) dealing with fine sediment transport in irrigation canals has been developed. The model has been used as a tool to study the mechanism of water and sediment flow under different operation and maintenance scenarios. The water surface profile has been predicted by using the predictor corrector method to solve the gradually varied flow equation. The prediction of sediment concentration is based on the solution of the one dimensional advection-diffusion equation. The bed material exchange was determined based on the Partheniades (1962) and Krone (1965) equations. The change in bed level was computed based on the sediment mass balance equation that was solved numerically by using the finite difference method. The model has been applied in the Gezira Scheme. On the basis of the field data the model has been calibrated and validated. The predicted bed profiles depict good agreement with the measured ones. The model is capable to predict the bed profile for any period of simulation. The model can predict the sediment concentration hydrograph at different points within a canal reach, in addition to the total volume of the sediment deposition in the reach. The output of the model can be presented in tabular or graphical form.

    The sediment transport in the irrigation canals has been simulated by adopting different scenarios. The interrelationship between water flow and sediment transport in the irrigation canals under changing flow conditions has been investigated. Two scenarios of operation were tested at the major canal under study. The model evaluated the indent system that has been applied in Gezira Scheme for many years in regard to sediment deposition. Another proposed scenario based on crop water requirement was also tested. In addition, operation under future changed conditions in case of reduction in the sediment concentration was tested. The different operation scenarios have been compared with the existing condition based on data collected during the flood season in 2011 in terms of sedimentation. Based on this, the following remarks are made:

    the effect of varying crest settings of the movable weirs has been investigated and less sediment deposition was found to occur when the crest level was set at its lowest position. The sediment transport in the canals is influenced by the operation of the hydraulic structures, especially upstream of movable weirs. The effect is extended to about 3 km upstream of the weir;

    for many years the indent system of water allocation was applied in the Gezira Scheme based on duty and cropped area. However, this system of operation has been absent during the last years. The slope of Zananda Major Canal became 13 cm/km and 18 cm/km for the first and second reaches respectivelycampaigns

    the reduction of the water delivery during the period of high concentration between 10 July and 10 August, based on the crop water requirement results in reduction in the sediment deposition by 51 and 55% for the first and second reaches respectively when compared to the situation in 2011;

    the reduction of the Blue Nile River sediment concentration by 50% as result of the construction of the Ethiopia Renaissance Dam and/or improvement in the land use has been simulated. The results of the simulation of the suspended sediment transport at the major canal indicate that the deposition will be 74 and 81% lower for the first and second reaches respectively when compared with the situation in 2011.

    At the minor canals, the night storage weirs were designed as cross structures. The idea behind the night storage system was to store water during the night by closing all field outlet pipes and the gates of the cross structures along the minor canal at 6:00 pm and releasing them at 6:00 am. Although this system has been vanished to keep pace with crop intensification and to cope with the deterioration of the water supply due to the poor maintenance of the canals, this scenario has also been simulated. The hydrodynamic flow in the canals during the filling time has been simulated by using the DUFLOW model since the model can be applied for unsteady flow. A spreadsheet has been designed to predict the deposition every hour based on the output of the DUFLOW model. The night storage system has been compared with the continuous system regarding the sediment transport in addition to other scenarios. It was found that:

    the continuous system reduces the amount of deposited sediment by 55% compared to the night storage system;

    about 29% of the sediment was reduced in 2011 when the system was operated based on crop water requirement;

    the deposition lightly increased with reduced capacity of the field outlet pipes. The

    The main findings and the contributions that are made by this study:

    the study comes up with a model dealing with cohesive sediment in irrigation canals for effective sediment and water management, which can be applied widely for similar irrigation schemes dealing with fine sediment;

    it is possible to improve the sediment and water management by improving the operation and maintenance. The high irrigation efficiency is tending to mitigate the inflow sediment load and as a consequence less deposition is expected;

    the study comes up with strategies of water management that can reduce the deposition in irrigation canals by operating the system continuously based on crop water requirement at the period of high sediment concentration with the field outlet pipes operating at their full capacity.

    The absence of proper maintenance activities and water management has a prominent role in increasing the deposition along the irrigation canals in Gezira Scheme. Improving the operation and maintenance is not the only way to mitigate the sedimentation in the irrigation canals. A great consideration needs to be given to improve the design since conditions based on the original design have been changed with time such as the operation system (night storage system, indent system), cropping intensity and geometry of the canals. In other words, rehabilitation of the system will not be one of the solutions to mitigate the accumulation of the deposition along the canals but the system itself needs remodelling. The developed model can be used to assess the new design and to evaluate the proposed management plans in terms of transport of cohesive sediment.

    Adapting Value for Cultivation and Use testing to stimulate the release of improved varieties for the organic sector. The case of spring wheat in The Netherlands
    Osman, A.M. ; Bonthuis, H. ; Brink, L. van den; Struik, P.C. ; Almekinders, C.J.M. ; Lammerts Van Bueren, E. - \ 2015
    Organic Agriculture 5 (2015)2. - ISSN 1879-4238 - p. 101 - 111.
    Value for Cultivation and Use (VCU), the mandatory variety testing system for agricultural crops in the European Union (EU), has been used as a policy instrument by favouring the release of variety types that enable socially desirable developments, such as reducing fungicide use. With this paper, we aim to assess whether VCU can be used to enhance the availability of varieties suitable to organic farming. Therefore, we analyse data of an organic spring wheat VCU project that was conducted between 2001 and 2004 at three locations in the Netherlands. Varieties selected through organic VCU were clearly more suitable for organic production than those registered through the conventional procedure. However, new varieties could not match the baking quality of the organic standard variety. We conclude that enhancing the number of suitable varieties for the organic sector requires adapting both conventional breeding programmes as well as the VCU system.
    Towards an improved variety assortment for the Dutch organic sector : case studies on onion and spring wheat
    Osman, A.M. - \ 2014
    Wageningen University. Promotor(en): Edith Lammerts van Bueren; Paul Struik, co-promotor(en): Conny Almekinders. - Wageningen : Wageningen University - ISBN 9789462570689 - 212
    allium cepa - uien - triticum aestivum - zomertarwe - biologische landbouw - rassen (planten) - cultivars - rassenproeven - rasreacties - classificatie van rassen - plantenveredeling - allium cepa - onions - triticum aestivum - spring wheat - organic farming - varieties - cultivars - variety trials - varietal reactions - variety classification - plant breeding

    Key words:

    organic farming; principles of organic agriculture; food production chain;

    plant breeding; genetic correlation; plant traits; farmers’ preferences;

    variety testing; Value for Cultivation and Use; EU seed legislation;

    onion; Allium cepa; spring wheat; Triticum aestivum; baking quality

    Variety choice is an important component of organic crop management. The organic sector pursues to produce healthy, nutritious food without using synthetic inputs and excessive amounts of natural resources. Access to varieties that are able to cope with weeds, diseases and pests, and thrive well under an organic fertility management regime, allows actors in the organic food production chain to achieve these aspirations. In this thesis I analyse how the current breeding, variety assessment and registration process should be changed to provide varieties that fulfil the needs of organic farmers, traders and processors. The research is based on the cases of two crops, onion (Allium cepa) and spring wheat (Triticum aestivum), that differ in key issues that influence the options for change: breeding and variety registration aspects; organic seed and crop production issues; destination of the harvest; and composition of and relations between actors in the production chain.

    Variety trials, in which we evaluated onion and spring wheat varieties for traits prioritized by organic stakeholders, revealed that the variety assortment displayed important weaknesses when grown and processed organically. In the case of onion, farmers needed varieties with improvements for resistances against main diseases, root system, storability and erect plant types in combination with high yield. For spring wheat, weed suppressiveness and baking quality were the key traits that required improvements.

    Interviews with conventional onion breeders showed that they focussed on yield and post-harvest traits (storability, bulb quality). In addition to these traits, breeding for the organic sector would require breeders to pay more attention to the selection of field traits like partial resistance against leaf diseases and a better root system. To improve key traits for organic growers, selection should take place in a growing environment without the fungicides and herbicides that are typically applied in conventional nurseries.

    Interviewing conventional wheat breeders made clear that selection for the organic market would conflict with achieving the high yield demanded by conventional growers. Breeders have achieved high yields by increasing the harvest index, which goes at the expense of baking quality through a relative decrease in protein content. Based on a literature review, we propose two alternative approaches to improve yield and protein content simultaneously: selection for increased total biomass or/and selection for protein quality. The first approach would deliver taller, leafier varieties that are also more competitive against weeds. Improving protein quality would require selection under low nitrogen input or organic growing conditions as protein composition is strongly influenced by soil nitrogen availability. Analysis of data of our own conventional and organic variety trials, together with datasets from other European countries showed that for other important traits (e.g., yield, disease resistance, plant length) selection for the organic sector could also be conducted in non-organically managed breeding nurseries, which typically refrain from fungicides and growth regulator applications, as genetic correlations for these traits were high (0.8 -1.0).

    Conducting variety trials in organic fields and evaluating these for traits prioritized by the stakeholders make results more relevant for the latter. In the specific case of Value for Cultivation and Use (VCU) testing, that is part of the official variety registration procedure of field crops in the EU, adapting the research protocol proved crucial to provide market access to varieties better adapted to organic production. The organic spring wheat VCU testing resulted in the inclusion of varieties in an organic section of the Dutch Recommended List of Varieties, showing that the statutory variety testing system is flexible to address new needs. However, procedures are costly and not in proportion to market size and in this way prohibit the release of varieties for organic and other small markets.

    Although specifically wheat breeders proved to be open to consider adaptations in their programme, the relatively small market prevents conventional private sector breeders from investing in selecting varieties specifically targeted at the organic sector. Therefore we elaborate options to set up a way of breeding that is in line with organic principles and overcomes this economic barrier.

    Capacity Development in Scenario Development in Integrated Water Resources Management in Bangladesh
    Terwisscha Van Scheltinga, C.T.H.M. ; Sabbir Khan, M. ; Kulsum Navera, U. ; Heun, J. ; Ludwig, F. ; Aalst, M. van; Baldasarre, G. - \ 2013
    In: Proceedings of the International Conference on Climate Change Impact and Adaptation (I3CIA) 14-16 November 2013, Gazipur, Bangladesh. - s.n. - p. 737 - 748.
    Research Agenda on Water Sector Related Climate Change Adaptation and Disaster Management
    Terwisscha Van Scheltinga, C.T.H.M. ; Showkat Osman, Md. ; Alauddin, M. ; Atiqul Islam, S.M. ; Moors, E.J. ; Ludwig, F. ; Reaz Uddin Khan, M. - \ 2013
    Perspectives to breed for improved baking quality wheat varieties adapted to organic growing conditions
    Osman, A.M. ; Struik, P.C. ; Lammerts Van Bueren, E. - \ 2012
    Journal of the Science of Food and Agriculture 92 (2012)2. - ISSN 0022-5142 - p. 207 - 215.
    triticum-aestivum l. - bread-making quality - weight glutenin subunits - nitrogen use efficiency - winter-wheat - protein-composition - spring wheat - breadmaking quality - functional-properties - genetic-improvement
    Northwestern European consumers like their bread to be voluminous and easy to chew. These attributes require a raw material that is rich in protein with, among other characteristics, a suitable ratio between gliadins and glutenins. Achieving this is a challenge for organic growers, because they lack cultivars that can realise high protein concentrations under the relatively low and variable availability of nitrogen during the grain-filling phase common in organic farming. Relatively low protein content in wheat grains thus needs to be compensated by a high proportion of high-quality protein. Organic farming therefore needs cultivars with genes encoding for optimal levels of glutenins and gliadins, a maximum ability for nitrogen uptake, a large storage capacity of nitrogen in the biomass, an adequate balance between vegetative and reproductive growth, a high nitrogen translocation efficiency for the vegetative parts into the grains during grain filling and an efficient conversion of nitrogen into high-quality proteins. In this perspective paper the options to breed and grow such varieties are discussed.
    Are specific testing protocols required for organic onion varieties? Analysis of onion variety testing under conventional and organic growing conditions
    Lammerts Van Bueren, E. ; Osman, A.M. ; Tiemens-Hulscher, M. ; Struik, P.C. ; Burgers, S.L.G.E. ; Broek, R.C.F.M. van den - \ 2012
    Euphytica 184 (2012)2. - ISSN 0014-2336 - p. 181 - 193.
    rassenproeven - uien - biologische landbouw - rasverschillen - proefopzet - variety trials - onions - organic farming - breed differences - experimental design - farming systems - performance
    Organic growers need information on variety performance under their growing conditions. A 4-year onion variety research project was carried out to investigate whether setting up a variety testing system combining conventional and organic variety trials is feasible and efficient rather than organizing separate variety trials under the two management systems. During 4 years commercial onion cultivars were tested at a certified organic and a non-organic location. Both systems were managed without chemical pest, disease and sprouting control, but differed in fertility management (organic manure in autumn versus synthetic fertilizer), soil cultivation and weed management (mechanical weeding versus application of herbicide). Management system significantly affected plant density, thickness of neck, and proportion of small and large bulbs. Variety × management system interactions were significant for bulb uniformity, earliness, proportion of large bulbs, dormancy and relative storage success but did not change the ranking of the varieties. We conclude that organic growers can profit from a more conscious variety choice when conventionally fertilised trials would refrain from using pesticides, fungicides, herbicides and sprout inhibitors. However, this would require an adaptation of the management protocol in such a way that trials might no longer represent conditions of conventional farmers. Furthermore, assessments of leaf erectness, disease resistance to downy mildew and leaf blight should be included in the protocols for organic use. We advocate better communication between breeders and growers on specific variety characteristics contributing to improving yield stability under low-input, organic growing conditions
    Fusarium head blight and deoxynivalenol contamination in wheat as affected by nitrogen fertilization
    Burgt, G.J.H.M. van der; Timmermans, B.G.H. ; Scholberg, J.M.S. ; Osman, A.M. - \ 2011
    NJAS Wageningen Journal of Life Sciences 58 (2011)3-4. - ISSN 1573-5214 - p. 123 - 129.
    small-grain cereals - winter-wheat - spring wheat - cropping systems - don content - mycotoxins - resistance - aggressiveness - cultivars - culmorum
    Many studies have evaluated the effects of nitrogen-fertilizer rates on Fusarium head blight (FHB) and mycotoxin contamination of wheat (Triticum aestivum) in both conventional and organic systems. Results are often conflicting while underlying mechanisms remain illusive. This study aimed to provide insights into these conflicting results. Spring wheat was grown at two sites in the Netherlands in 2006 and 2007 using compost-, slurry-, or farmyard manure-based organic fertilizing systems, each with five total-nitrogen rates. In 2006, overall Fusarium infection levels and deoxynivalenol (DON) contents of the grain were low, and the data suggested a positive, multivariate relation between DON content and grain-nitrogen content. Higher DON contents were also accompanied by more vegetative growth (straw biomass). In 2007, plant density of the crop was relatively low while overall FHB infection levels and DON contents were relatively high. In this year, no clear correlations between straw dry matter production or grain-nitrogen content and DON content were found, while weed infestation increased with higher nitrogen levels. Practical implications of the multivariate relations between N-rates, N-contents, DON, microclimate and the presence of weeds are discussed.
    Improving the operation and maintenance for better sediment and water management in Gezira Scheme, Sudan
    Osman, I.S. ; Schultz, B. ; Suryadi, F.X. ; Mohamed, Y. ; Osman, A.K. - \ 2011
    In: Proceedings of the ICID 21st International Congress on Irrigation and Drainage, Tehran, Iran, 15-23 October, 2011. - Tehran, Iran : ICID - p. 51 - 62.
    Diversity of different farmer and modern wheat varieties cultivated in contrasting organic farming conditions in Western Europe and implications for European seed and variety legislation
    Serpolay, E. ; Dawson, J.C. ; Chable, V. ; Lammerts Van Bueren, E. ; Osman, A.M. ; Pino, S. ; Goldringer, I. - \ 2011
    Organic Agriculture 1 (2011)3. - ISSN 1879-4238 - p. 127 - 145.
    rassenproeven - tarwe - triticum aestivum - biologische landbouw - landrassen - oude plantenrassen - rassen (planten) - west-europa - akkerbouw - variety trials - wheat - triticum aestivum - organic farming - landraces - old varieties - varieties - western europe - arable farming
    The importance of genetic diversity in cultivated varieties for organic and low-input agriculture has attracted increasing attention in recent years, with a need to identify relevant sources of diversity and strategies for incorporating diversity in plant breeding for organic systems. However, the regulatory system in many countries, particularly in the European Union, restricts the varieties available to farmers to those registered in an official catalogue, and most countries require varieties to go through official tests under conventional management, which has resulted in a lack of suitable varieties available to organic farmers. This study characterized a sample of wheat (Triticum aestivum L.) landraces, historic varieties and varietal mixtures currently of interest to organic farmers in a diverse range of organic conditions on farms in Italy, France and the Netherlands. These varieties were assessed for individual plant and spike characteristics and compared to modern registered wheat varieties grown under the same on-farm conditions. Significant differences in mean values were found among varieties for many plant and spike traits, as well as significant variety-by-environment interactions. There were often similar levels of intra-varietal variability between farmer and modern varieties, indicating that the strong selection for genetic homogeneity to meet regulatory criteria has little impact on the phenotypic variability of certain traits when assessed on-farm. Several farmer varieties had high values of traits related to productivity outside their region of origin, which underlines the need for experimentation with diverse types of varieties in order to find and develop appropriate varieties for organic systems
    Climate Change: Global Risks, Challenges and Decisions
    Richardson, K. ; Steffen, W. ; Liverman, D. ; Barker, T. ; Jotzo, F. ; Kammen, D.M. ; Leemans, R. ; Lenton, T.M. ; Munasinghe, M. ; Osman-Elasha, B. ; Schellnhuber, H.J. ; Stern, N. ; Vogel, C. ; Waever, O. - \ 2011
    Cambridge : Cambridge University Press - ISBN 9780521198363 - 524
    klimaatverandering - koolstofcyclus - beleid - mitigatie - risico - klimaat - biofysica - economie - ethiek - climatic change - carbon cycle - policy - mitigation - risk - climate - biophysics - economics - ethics
    Providing an up-to-date synthesis of knowledge relevant to the climate change issue, this book ranges from the basic science documenting the need for policy action to the technologies, economic instruments and political strategies that can be employed in response to climate change. Ethical and cultural issues constraining the societal response to climate change are also discussed. This book covers a very wide range of disciplines – core biophysical sciences involved with climate change (geosciences, atmospheric sciences, ocean sciences, ecology/biology) as well as economics, political science, health sciences, institutions and governance, sociology, ethics and philosophy, and engineering.
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