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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    Narrow-wide-row planting pattern increases the radiation use efficiency and seed yield of intercrop species in relay-intercropping system
    Raza, Muhammad Ali ; Feng, Ling Yang ; Werf, Wopke van der; Cai, Gao Ren ; Khalid, Muhammad Hayder Bin ; Iqbal, Nasir ; Hassan, Muhammad Jawad ; Meraj, Tehseen Ahmad ; Naeem, Muhammd ; Khan, Imran ; Ur Rehman, Sana ; Ansar, Muhammad ; Ahmed, Mukhtar ; Yang, Feng ; Yang, Wenyu - \ 2019
    Food and Energy Security 8 (2019)3. - ISSN 2048-3694
    competition - intercropping - land equivalent ratio - radiation use efficiency

    Planting arrangements affect radiation use efficiency (RUE) and competitiveness of intercrop species in intercropping systems. Here, we reveal that narrow-wide-row planting arrangement in maize-soybean relay-intercropping system increases the dry matter and competitiveness of soybean, increased the RUE of maize and soybean, and compensates the yield loss of maize by substantially increasing the yield of soybean. In this field study, maize was planted with soybean in different planting arrangements (P1, 20:180, P2, 40:160; P3, 60:140, and P4, 80:120) of relay intercropping, all the relay-intercropping treatments were compared with sole crops of maize (SM) and soybean (SS). Results showed that P1 improved the total RUE 3.26 g/MJ (maize RUE + soybean RUE) of maize and soybean in relay-intercropping system. Compared to P4, treatment P1 increased the soybean competition ratio (CR) values (by 55%) but reduced the maize CR values (by 29%), which in turn significantly improved the yield of soybean by maintaining the maize yield. Generally, in P1, soybean produced 82% of SS yield, and maize produced 88% of SM yield, and it achieved the land equivalent ratio of 1.7. These results suggest that by maintaining the appropriate planting distances between maize and soybean we can improve the competitiveness and yield of intercrop species in relay-intercropping system.

    Ten key short-term sectoral benchmarks to limit warming to 1.5º C
    Kuramochi, Takeshi ; Hoehne, N.E. ; Schaeffer, M. ; Cantzler, Jasmin ; Hare, William ; Deng, Yvonne ; Sterl, Sebastian ; Hagemann, Markus ; Rocha, Marcia ; Yanguas-Parra, Paola Andrea ; Mir, Goher-Ur-Rehman ; Wong, Lindee ; El-Laboudy, Tarik ; Wouters, Karlien ; Deryng, Delphine ; Blok, Kornelis - \ 2018
    Climate Policy 18 (2018)3. - ISSN 1469-3062 - p. 287 - 305.
    Benchmarking - COP21 - mitigation scenarios - Paris Agreement - technological change - transition - UNFCCC - 1.5º C
    This article identifies and quantifies the 10 most important benchmarks for climate action to be taken by 2020–2025 to keep the window open for a 1.5°C-consistent GHG emission pathway. We conducted a comprehensive review of existing emissions scenarios, scanned all sectors and the respective necessary transitions, and distilled the most important short-term benchmarks for action in line with the long-term perspective of the required global low-carbon transition. Owing to the limited carbon budget, combined with the inertia of existing systems, global energy economic models find only limited pathways to stay on track for a 1.5°C world consistent with the long-term temperature goal of the Paris Agreement.
    An expanded evaluation of protein function prediction methods shows an improvement in accuracy
    Jiang, Yuxiang ; Oron, Tal Ronnen ; Clark, Wyatt T. ; Bankapur, Asma R. ; Andrea, Daniel D'; Lepore, Rosalba ; Funk, Christopher S. ; Kahanda, Indika ; Verspoor, Karin M. ; Ben-Hur, Asa ; Koo, Da Chen Emily ; Penfold-Brown, Duncan ; Shasha, Dennis ; Youngs, Noah ; Bonneau, Richard ; Lin, Alexandra ; Sahraeian, Sayed M.E. ; Martelli, Pier Luigi ; Profiti, Giuseppe ; Casadio, Rita ; Cao, Renzhi ; Zhong, Zhaolong ; Cheng, Jianlin ; Altenhoff, Adrian ; Skunca, Nives ; Dessimoz, Christophe ; Dogan, Tunca ; Hakala, Kai ; Kaewphan, Suwisa ; Mehryary, Farrokh ; Salakoski, Tapio ; Ginter, Filip ; Fang, Hai ; Smithers, Ben ; Oates, Matt ; Gough, Julian ; Törönen, Petri ; Koskinen, Patrik ; Holm, Liisa ; Chen, Ching Tai ; Hsu, Wen Lian ; Bryson, Kevin ; Cozzetto, Domenico ; Minneci, Federico ; Jones, David T. ; Chapman, Samuel ; BKC, Dukka ; Khan, Ishita K. ; Kihara, Daisuke ; Ofer, Dan ; Rappoport, Nadav ; Stern, Amos ; Cibrian-Uhalte, Elena ; Denny, Paul ; Foulger, Rebecca E. ; Hieta, Reija ; Legge, Duncan ; Lovering, Ruth C. ; Magrane, Michele ; Melidoni, Anna N. ; Mutowo-Meullenet, Prudence ; Pichler, Klemens ; Shypitsyna, Aleksandra ; Li, Biao ; Zakeri, Pooya ; ElShal, Sarah ; Tranchevent, Léon Charles ; Das, Sayoni ; Dawson, Natalie L. ; Lee, David ; Lees, Jonathan G. ; Sillitoe, Ian ; Bhat, Prajwal ; Nepusz, Tamás ; Romero, Alfonso E. ; Sasidharan, Rajkumar ; Yang, Haixuan ; Paccanaro, Alberto ; Gillis, Jesse ; Sedeño-Cortés, Adriana E. ; Pavlidis, Paul ; Feng, Shou ; Cejuela, Juan M. ; Goldberg, Tatyana ; Hamp, Tobias ; Richter, Lothar ; Salamov, Asaf ; Gabaldon, Toni ; Marcet-Houben, Marina ; Supek, Fran ; Gong, Qingtian ; Ning, Wei ; Zhou, Yuanpeng ; Tian, Weidong ; Falda, Marco ; Fontana, Paolo ; Lavezzo, Enrico ; Toppo, Stefano ; Ferrari, Carlo ; Giollo, Manuel ; Piovesan, Damiano ; Tosatto, Silvio C.E. ; Pozo, Angela del; Fernández, José M. ; Maietta, Paolo ; Valencia, Alfonso ; Tress, Michael L. ; Benso, Alfredo ; Carlo, Stefano Di; Politano, Gianfranco ; Savino, Alessandro ; Rehman, Hafeez Ur ; Re, Matteo ; Mesiti, Marco ; Valentini, Giorgio ; Bargsten, Joachim W. ; Dijk, Aalt-Jan van; Gemovic, Branislava ; Glisic, Sanja ; Perovic, Vladmir ; Veljkovic, Veljko ; Veljkovic, Nevena ; Almeida-e-Silva, Danillo C. ; Vencio, Ricardo Z.N. ; Sharan, Malvika ; Vogel, Jörg ; Kansakar, Lakesh ; Zhang, Shanshan ; Vucetic, Slobodan ; Wang, Zheng ; Sternberg, Michael J.E. ; Wass, Mark N. ; Huntley, Rachael P. ; Martin, Maria J. ; O'Donovan, Claire ; Robinson, Peter N. ; Moreau, Yves ; Tramontano, Anna ; Babbitt, Patricia C. ; Brenner, Steven E. ; Linial, Michal ; Orengo, Christine A. ; Rost, Burkhard ; Greene, Casey S. ; Mooney, Sean D. ; Friedberg, Iddo ; Radivojac, Predrag - \ 2016
    Genome Biology 17 (2016)1. - ISSN 1474-7596
    Disease gene prioritization - Protein function prediction

    Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.

    Water management in NWFP.
    Murray-Rust, D.H. ; Vander Velde, E.J. ; Habib-ur-Rehman, - \ 1997
    Wageningen : Wageningen Agricultural University - 367 p.
    Irrigation resources of NWFP.
    Murray-Rust, D.H. ; Vander Velde, E.J. ; Habib-ur-Rehman, - \ 1997
    In: Water management in NWFP / Murray-Rust, D.H., Peshawar/Wageningen : NWFP Agric. Univ. and Wageningen Agric. Univ. - p. 49 - 78.
    Report on chemical degradation of lactose induced by heating of milk.
    Zia-Ur-Rehman, - \ 1987
    Vakgr. Levensm. techn. Sectie Zuivel en Levensm. natk
    Determination of hydroxymethylfurfural in heated milk by high-performance liquid chromatography.
    Boekel, M.A.J.S. van; Zia-Ur-Rehman, - \ 1987
    Netherlands Milk and Dairy Journal 41 (1987). - ISSN 0028-209X - p. 297 - 306.
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